Starting phenix.real_space_refine on Thu May 15 17:13:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jrq_36602/05_2025/8jrq_36602.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jrq_36602/05_2025/8jrq_36602.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jrq_36602/05_2025/8jrq_36602.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jrq_36602/05_2025/8jrq_36602.map" model { file = "/net/cci-nas-00/data/ceres_data/8jrq_36602/05_2025/8jrq_36602.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jrq_36602/05_2025/8jrq_36602.cif" } resolution = 4.15 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= 0.035 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 76 5.16 5 C 8444 2.51 5 N 2248 2.21 5 O 2498 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13270 Number of models: 1 Model: "" Number of chains: 3 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: 5442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5442 Classifications: {'peptide': 676} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 27, 'TRANS': 648} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 60 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 241 SG CYS B 37 68.309 32.585 95.791 1.00112.82 S ATOM 522 SG CYS B 70 65.473 35.707 93.423 1.00109.09 S ATOM 864 SG CYS B 110 65.476 31.891 77.991 1.00 99.70 S ATOM 886 SG CYS B 113 63.164 30.431 80.490 1.00107.26 S ATOM 1148 SG CYS B 143 61.168 31.418 77.705 1.00129.08 S ATOM 1168 SG CYS B 146 62.382 34.471 79.323 1.00135.09 S Restraints were copied for chains: D, C Time building chain proxies: 11.52, per 1000 atoms: 0.87 Number of scatterers: 13270 At special positions: 0 Unit cell: (144.585, 106.029, 111.384, 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 76 16.00 O 2498 8.00 N 2248 7.00 C 8444 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.92 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 201 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 37 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 70 " 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 37 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 70 " 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 : 12 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3136 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 12 sheets defined 57.5% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'B' and resid 18 through 23 Processing helix chain 'B' and resid 45 through 55 removed outlier: 4.074A pdb=" N ALA B 53 " --> pdb=" O VAL B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 85 removed outlier: 3.528A pdb=" N PHE B 76 " --> pdb=" O LYS B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 99 removed outlier: 4.376A pdb=" N GLU B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN B 97 " --> pdb=" O THR B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 106 Processing helix chain 'B' and resid 120 through 128 removed outlier: 3.771A pdb=" N HIS B 125 " --> pdb=" O GLU B 121 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 148 removed outlier: 4.185A pdb=" N ARG B 148 " --> pdb=" O SER B 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 141 Processing helix chain 'A' and resid 148 through 156 removed outlier: 4.579A pdb=" N VAL A 156 " --> pdb=" O VAL A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 166 removed outlier: 3.857A pdb=" N VAL A 164 " --> pdb=" O ALA A 160 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER A 166 " --> pdb=" O ALA A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 243 removed outlier: 3.667A pdb=" N ILE A 239 " --> pdb=" O ASP A 235 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG A 240 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ARG A 241 " --> pdb=" O ASP A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 273 removed outlier: 3.723A pdb=" N ASN A 258 " --> pdb=" O THR A 254 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ALA A 259 " --> pdb=" O ALA A 255 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU A 260 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR A 262 " --> pdb=" O ASN A 258 " (cutoff:3.500A) Proline residue: A 265 - end of helix removed outlier: 4.243A pdb=" N ASP A 270 " --> pdb=" O ASN A 266 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU A 271 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 280 removed outlier: 3.918A pdb=" N ARG A 279 " --> pdb=" O ASN A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 292 removed outlier: 3.958A pdb=" N ILE A 288 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE A 289 " --> pdb=" O ASN A 285 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 Proline residue: A 299 - end of helix removed outlier: 3.543A pdb=" N LEU A 302 " --> pdb=" O PRO A 299 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU A 303 " --> pdb=" O GLU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 315 removed outlier: 4.381A pdb=" N LEU A 308 " --> pdb=" O MET A 304 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 328 Processing helix chain 'A' and resid 329 through 331 No H-bonds generated for 'chain 'A' and resid 329 through 331' Processing helix chain 'A' and resid 332 through 354 removed outlier: 3.733A pdb=" N PHE A 343 " --> pdb=" O MET A 339 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL A 351 " --> pdb=" O ILE A 347 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE A 352 " --> pdb=" O THR A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 386 removed outlier: 3.788A pdb=" N VAL A 369 " --> pdb=" O ASP A 365 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL A 383 " --> pdb=" O TYR A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 413 removed outlier: 3.528A pdb=" N GLN A 410 " --> pdb=" O GLU A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 433 Processing helix chain 'A' and resid 435 through 439 Processing helix chain 'A' and resid 445 through 449 Processing helix chain 'A' and resid 459 through 469 removed outlier: 3.884A pdb=" N ASP A 463 " --> pdb=" O GLU A 459 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N THR A 465 " --> pdb=" O ASP A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 484 Proline residue: A 481 - end of helix Processing helix chain 'A' and resid 488 through 514 removed outlier: 3.907A pdb=" N THR A 508 " --> pdb=" O GLU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 546 removed outlier: 4.041A pdb=" N VAL A 538 " --> pdb=" O ASP A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 553 removed outlier: 4.010A pdb=" N LEU A 551 " --> pdb=" O PRO A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 583 removed outlier: 3.996A pdb=" N PHE A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLN A 576 " --> pdb=" O LYS A 572 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 625 removed outlier: 3.655A pdb=" N LEU A 614 " --> pdb=" O GLY A 610 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE A 615 " --> pdb=" O GLN A 611 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY A 616 " --> pdb=" O PHE A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 643 removed outlier: 3.970A pdb=" N TYR A 638 " --> pdb=" O PRO A 634 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N MET A 642 " --> pdb=" O TYR A 638 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLY A 643 " --> pdb=" O ARG A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 655 removed outlier: 3.675A pdb=" N SER A 654 " --> pdb=" O ASP A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 667 removed outlier: 3.718A pdb=" N SER A 661 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LEU A 665 " --> pdb=" O SER A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 723 removed outlier: 4.634A pdb=" N ASP A 719 " --> pdb=" O ASN A 715 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE A 721 " --> pdb=" O TYR A 717 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU A 722 " --> pdb=" O SER A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 742 removed outlier: 4.251A 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: 3.850A pdb=" N GLU A 756 " --> pdb=" O PRO A 752 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU A 757 " --> pdb=" O GLU A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 773 removed outlier: 3.639A pdb=" N GLU A 772 " --> pdb=" O GLN A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 797 removed outlier: 4.352A pdb=" N ARG A 788 " --> pdb=" O SER A 784 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N PHE A 790 " --> pdb=" O LEU A 786 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TRP A 791 " --> pdb=" O ILE A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 810 removed outlier: 4.251A pdb=" N PHE A 808 " --> pdb=" O LEU A 804 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR A 809 " --> pdb=" O PHE A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 867 Processing helix chain 'D' and resid 18 through 23 Processing helix chain 'D' and resid 45 through 55 removed outlier: 4.074A pdb=" N ALA D 53 " --> pdb=" O VAL D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 85 removed outlier: 3.528A pdb=" N PHE D 76 " --> pdb=" O LYS D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 99 removed outlier: 4.376A pdb=" N GLU D 96 " --> pdb=" O GLY D 92 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 106 Processing helix chain 'D' and resid 120 through 128 removed outlier: 3.771A pdb=" N HIS D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU D 126 " --> pdb=" O LYS D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 148 removed outlier: 4.185A pdb=" N ARG D 148 " --> pdb=" O SER D 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 141 Processing helix chain 'C' and resid 148 through 156 removed outlier: 4.579A pdb=" N VAL C 156 " --> pdb=" O VAL C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 166 removed outlier: 3.857A pdb=" N VAL C 164 " --> pdb=" O ALA C 160 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER C 166 " --> pdb=" O ALA C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 243 removed outlier: 3.667A pdb=" N ILE C 239 " --> pdb=" O ASP C 235 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG C 240 " --> pdb=" O ILE C 236 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ARG C 241 " --> pdb=" O ASP C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 273 removed outlier: 3.723A pdb=" N ASN C 258 " --> pdb=" O THR C 254 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ALA C 259 " --> pdb=" O ALA C 255 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU C 260 " --> pdb=" O PHE C 256 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR C 262 " --> pdb=" O ASN C 258 " (cutoff:3.500A) Proline residue: C 265 - end of helix removed outlier: 4.243A pdb=" N ASP C 270 " --> pdb=" O ASN C 266 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU C 271 " --> pdb=" O VAL C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 280 removed outlier: 3.918A pdb=" N ARG C 279 " --> pdb=" O ASN C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 292 removed outlier: 3.958A pdb=" N ILE C 288 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE C 289 " --> pdb=" O ASN C 285 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 303 Proline residue: C 299 - end of helix removed outlier: 3.543A pdb=" N LEU C 302 " --> pdb=" O PRO C 299 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU C 303 " --> pdb=" O GLU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 315 removed outlier: 4.381A pdb=" N LEU C 308 " --> pdb=" O MET C 304 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE C 309 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 328 Processing helix chain 'C' and resid 329 through 331 No H-bonds generated for 'chain 'C' and resid 329 through 331' Processing helix chain 'C' and resid 332 through 354 removed outlier: 3.733A pdb=" N PHE C 343 " --> pdb=" O MET C 339 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL C 351 " --> pdb=" O ILE C 347 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE C 352 " --> pdb=" O THR C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 386 removed outlier: 3.788A pdb=" N VAL C 369 " --> pdb=" O ASP C 365 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET C 377 " --> pdb=" O LYS C 373 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL C 383 " --> pdb=" O TYR C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 413 removed outlier: 3.528A pdb=" N GLN C 410 " --> pdb=" O GLU C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 433 Processing helix chain 'C' and resid 435 through 439 Processing helix chain 'C' and resid 445 through 449 Processing helix chain 'C' and resid 459 through 469 removed outlier: 3.884A pdb=" N ASP C 463 " --> pdb=" O GLU C 459 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N THR C 465 " --> pdb=" O ASP C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 484 Proline residue: C 481 - end of helix Processing helix chain 'C' and resid 488 through 514 removed outlier: 3.907A pdb=" N THR C 508 " --> pdb=" O GLU C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 531 through 546 removed outlier: 4.041A pdb=" N VAL C 538 " --> pdb=" O ASP C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 553 removed outlier: 4.010A pdb=" N LEU C 551 " --> pdb=" O PRO C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 583 removed outlier: 3.996A pdb=" N PHE C 575 " --> pdb=" O SER C 571 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLN C 576 " --> pdb=" O LYS C 572 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU C 580 " --> pdb=" O GLN C 576 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU C 581 " --> pdb=" O LEU C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 625 removed outlier: 3.655A pdb=" N LEU C 614 " --> pdb=" O GLY C 610 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE C 615 " --> pdb=" O GLN C 611 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY C 616 " --> pdb=" O PHE C 612 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 643 removed outlier: 3.970A pdb=" N TYR C 638 " --> pdb=" O PRO C 634 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N MET C 642 " --> pdb=" O TYR C 638 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLY C 643 " --> pdb=" O ARG C 639 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 655 removed outlier: 3.675A pdb=" N SER C 654 " --> pdb=" O ASP C 650 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 667 removed outlier: 3.718A pdb=" N SER C 661 " --> pdb=" O VAL C 657 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LEU C 665 " --> pdb=" O SER C 661 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 723 removed outlier: 4.634A pdb=" N ASP C 719 " --> pdb=" O ASN C 715 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE C 721 " --> pdb=" O TYR C 717 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU C 722 " --> pdb=" O SER C 718 " (cutoff:3.500A) Processing helix chain 'C' and resid 726 through 742 removed outlier: 4.251A 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: 3.850A pdb=" N GLU C 756 " --> pdb=" O PRO C 752 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU C 757 " --> pdb=" O GLU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 767 through 773 removed outlier: 3.639A pdb=" N GLU C 772 " --> pdb=" O GLN C 768 " (cutoff:3.500A) Processing helix chain 'C' and resid 784 through 797 removed outlier: 4.352A pdb=" N ARG C 788 " --> pdb=" O SER C 784 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N PHE C 790 " --> pdb=" O LEU C 786 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TRP C 791 " --> pdb=" O ILE C 787 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 810 removed outlier: 4.251A pdb=" N PHE C 808 " --> pdb=" O LEU C 804 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR C 809 " --> pdb=" O PHE C 805 " (cutoff:3.500A) Processing helix chain 'C' and resid 858 through 867 Processing sheet with id=AA1, first strand: chain 'B' and resid 60 through 61 Processing sheet with id=AA2, first strand: chain 'B' and resid 86 through 88 removed outlier: 3.679A pdb=" N TYR B 88 " --> pdb=" O ASN B 134 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ARG B 109 " --> pdb=" O GLY B 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 523 through 527 removed outlier: 5.810A pdb=" N LEU A 523 " --> pdb=" O TYR A 556 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLU A 558 " --> pdb=" O LEU A 523 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N LEU A 525 " --> pdb=" O GLU A 558 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 590 through 593 removed outlier: 3.563A pdb=" N LEU A 598 " --> pdb=" O ASP A 593 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 681 through 685 Processing sheet with id=AA6, first strand: chain 'A' and resid 828 through 829 removed outlier: 6.724A pdb=" N ALA A 828 " --> pdb=" O LEU A 849 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 60 through 61 Processing sheet with id=AA8, first strand: chain 'D' and resid 86 through 88 removed outlier: 3.679A pdb=" N TYR D 88 " --> pdb=" O ASN D 134 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ARG D 109 " --> pdb=" O GLY D 141 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 523 through 527 removed outlier: 5.810A pdb=" N LEU C 523 " --> pdb=" O TYR C 556 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLU C 558 " --> pdb=" O LEU C 523 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N LEU C 525 " --> pdb=" O GLU C 558 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 590 through 593 removed outlier: 3.563A pdb=" N LEU C 598 " --> pdb=" O ASP C 593 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 681 through 685 Processing sheet with id=AB3, first strand: chain 'C' and resid 828 through 829 removed outlier: 6.724A pdb=" N ALA C 828 " --> pdb=" O LEU C 849 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 502 hydrogen bonds defined for protein. 1392 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: 3.53 Time building geometry restraints manager: 3.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4358 1.34 - 1.46: 2828 1.46 - 1.58: 6220 1.58 - 1.70: 0 1.70 - 1.82: 116 Bond restraints: 13522 Sorted by residual: bond pdb=" N ARG A 763 " pdb=" CA ARG A 763 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.16e-02 7.43e+03 8.95e+00 bond pdb=" N ARG C 763 " pdb=" CA ARG C 763 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.16e-02 7.43e+03 8.95e+00 bond pdb=" N VAL C 362 " pdb=" CA VAL C 362 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.22e-02 6.72e+03 8.80e+00 bond pdb=" N VAL A 362 " pdb=" CA VAL A 362 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.22e-02 6.72e+03 8.80e+00 bond pdb=" N LEU A 361 " pdb=" CA LEU A 361 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.25e-02 6.40e+03 8.39e+00 ... (remaining 13517 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 17370 2.26 - 4.52: 782 4.52 - 6.78: 82 6.78 - 9.04: 20 9.04 - 11.30: 6 Bond angle restraints: 18260 Sorted by residual: angle pdb=" N VAL A 726 " pdb=" CA VAL A 726 " pdb=" C VAL A 726 " ideal model delta sigma weight residual 111.88 106.75 5.13 1.06e+00 8.90e-01 2.34e+01 angle pdb=" N VAL C 726 " pdb=" CA VAL C 726 " pdb=" C VAL C 726 " ideal model delta sigma weight residual 111.88 106.75 5.13 1.06e+00 8.90e-01 2.34e+01 angle pdb=" N ARG A 782 " pdb=" CA ARG A 782 " pdb=" C ARG A 782 " ideal model delta sigma weight residual 111.28 115.60 -4.32 1.09e+00 8.42e-01 1.57e+01 angle pdb=" N ARG C 782 " pdb=" CA ARG C 782 " pdb=" C ARG C 782 " ideal model delta sigma weight residual 111.28 115.60 -4.32 1.09e+00 8.42e-01 1.57e+01 angle pdb=" C THR A 798 " pdb=" N ASP A 799 " pdb=" CA ASP A 799 " ideal model delta sigma weight residual 120.38 125.59 -5.21 1.37e+00 5.33e-01 1.44e+01 ... (remaining 18255 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 7098 17.48 - 34.96: 956 34.96 - 52.44: 168 52.44 - 69.92: 36 69.92 - 87.40: 16 Dihedral angle restraints: 8274 sinusoidal: 3436 harmonic: 4838 Sorted by residual: dihedral pdb=" CA SER A 784 " pdb=" C SER A 784 " pdb=" N VAL A 785 " pdb=" CA VAL A 785 " ideal model delta harmonic sigma weight residual -180.00 -152.25 -27.75 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA SER C 784 " pdb=" C SER C 784 " pdb=" N VAL C 785 " pdb=" CA VAL C 785 " ideal model delta harmonic sigma weight residual -180.00 -152.25 -27.75 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA ALA A 238 " pdb=" C ALA A 238 " pdb=" N ILE A 239 " pdb=" CA ILE A 239 " ideal model delta harmonic sigma weight residual -180.00 -153.78 -26.22 0 5.00e+00 4.00e-02 2.75e+01 ... (remaining 8271 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1696 0.077 - 0.154: 290 0.154 - 0.230: 24 0.230 - 0.307: 2 0.307 - 0.384: 2 Chirality restraints: 2014 Sorted by residual: chirality pdb=" CB ILE C 401 " pdb=" CA ILE C 401 " pdb=" CG1 ILE C 401 " pdb=" CG2 ILE C 401 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" CB ILE A 401 " pdb=" CA ILE A 401 " pdb=" CG1 ILE A 401 " pdb=" CG2 ILE A 401 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" CB ILE C 793 " pdb=" CA ILE C 793 " pdb=" CG1 ILE C 793 " pdb=" CG2 ILE C 793 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 2011 not shown) Planarity restraints: 2372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 444 " 0.048 5.00e-02 4.00e+02 7.34e-02 8.63e+00 pdb=" N PRO C 445 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO C 445 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 445 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 444 " -0.048 5.00e-02 4.00e+02 7.34e-02 8.63e+00 pdb=" N PRO A 445 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 445 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 445 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 751 " 0.043 5.00e-02 4.00e+02 6.46e-02 6.68e+00 pdb=" N PRO C 752 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO C 752 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 752 " 0.035 5.00e-02 4.00e+02 ... (remaining 2369 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2108 2.75 - 3.29: 13268 3.29 - 3.82: 22940 3.82 - 4.36: 27721 4.36 - 4.90: 43955 Nonbonded interactions: 109992 Sorted by model distance: nonbonded pdb=" N CYS B 70 " pdb="ZN ZN B 201 " model vdw 2.210 2.310 nonbonded pdb=" N CYS D 70 " pdb="ZN ZN D 201 " model vdw 2.210 2.310 nonbonded pdb=" O SER C 476 " pdb=" OG1 THR C 479 " model vdw 2.259 3.040 nonbonded pdb=" O SER A 476 " pdb=" OG1 THR A 479 " model vdw 2.259 3.040 nonbonded pdb=" OD1 ASN C 485 " pdb=" OG1 THR C 488 " model vdw 2.260 3.040 ... (remaining 109987 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'A' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 35.020 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 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 : 0.008 0.220 13534 Z= 0.374 Angle : 1.142 15.786 18272 Z= 0.628 Chirality : 0.058 0.384 2014 Planarity : 0.007 0.073 2372 Dihedral : 16.229 87.399 5138 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 0.69 % Allowed : 12.26 % Favored : 87.05 % 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: -4.43 (0.16), residues: 1610 helix: -3.55 (0.12), residues: 748 sheet: -3.93 (0.40), residues: 64 loop : -2.12 (0.19), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP D 139 HIS 0.005 0.002 HIS C 632 PHE 0.025 0.003 PHE C 633 TYR 0.029 0.003 TYR A 134 ARG 0.008 0.001 ARG C 836 Details of bonding type rmsd hydrogen bonds : bond 0.28834 ( 502) hydrogen bonds : angle 10.29116 ( 1392) metal coordination : bond 0.13923 ( 12) metal coordination : angle 13.15132 ( 12) covalent geometry : bond 0.00724 (13522) covalent geometry : angle 1.09124 (18260) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 557 time to evaluate : 1.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 CYS cc_start: 0.6979 (m) cc_final: 0.6684 (m) REVERT: B 79 LYS cc_start: 0.8271 (tppt) cc_final: 0.7222 (tppt) REVERT: B 108 ILE cc_start: 0.8087 (mt) cc_final: 0.7832 (tt) REVERT: B 124 ARG cc_start: 0.8225 (ttt-90) cc_final: 0.7854 (ttt-90) REVERT: B 128 LYS cc_start: 0.8083 (mttt) cc_final: 0.7797 (mttt) REVERT: B 132 PHE cc_start: 0.6844 (m-80) cc_final: 0.6009 (m-80) REVERT: A 130 GLU cc_start: 0.8522 (pt0) cc_final: 0.7837 (pp20) REVERT: A 237 ASP cc_start: 0.8054 (m-30) cc_final: 0.7437 (t70) REVERT: A 283 TYR cc_start: 0.7509 (t80) cc_final: 0.7177 (t80) REVERT: A 287 PHE cc_start: 0.7067 (m-80) cc_final: 0.6865 (m-80) REVERT: A 294 ARG cc_start: 0.8121 (mpt-90) cc_final: 0.7867 (mpt-90) REVERT: A 304 MET cc_start: 0.4377 (tpt) cc_final: 0.4147 (tpt) REVERT: A 315 LYS cc_start: 0.7698 (mmtm) cc_final: 0.7367 (mmtm) REVERT: A 332 ASN cc_start: 0.8061 (t0) cc_final: 0.7615 (t0) REVERT: A 337 ARG cc_start: 0.8089 (ttm170) cc_final: 0.7435 (ttp80) REVERT: A 341 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7738 (mt-10) REVERT: A 344 GLN cc_start: 0.8053 (tp-100) cc_final: 0.7701 (pp30) REVERT: A 349 TYR cc_start: 0.7651 (t80) cc_final: 0.7369 (t80) REVERT: A 361 LEU cc_start: 0.7317 (tp) cc_final: 0.6969 (tp) REVERT: A 403 GLU cc_start: 0.7064 (pm20) cc_final: 0.5932 (pm20) REVERT: A 406 GLU cc_start: 0.7412 (tp30) cc_final: 0.7014 (tp30) REVERT: A 407 LEU cc_start: 0.8852 (mt) cc_final: 0.8483 (mt) REVERT: A 410 GLN cc_start: 0.8609 (mm-40) cc_final: 0.7733 (mm-40) REVERT: A 447 GLU cc_start: 0.7781 (mp0) cc_final: 0.7392 (tp30) REVERT: A 449 PHE cc_start: 0.7345 (m-10) cc_final: 0.7105 (m-10) REVERT: A 450 ILE cc_start: 0.8188 (mt) cc_final: 0.7578 (mt) REVERT: A 458 LEU cc_start: 0.7940 (tp) cc_final: 0.7682 (tt) REVERT: A 463 ASP cc_start: 0.6874 (t0) cc_final: 0.6604 (t70) REVERT: A 477 PHE cc_start: 0.7731 (m-80) cc_final: 0.7200 (m-80) REVERT: A 478 MET cc_start: 0.7885 (mtp) cc_final: 0.6521 (mtp) REVERT: A 482 PHE cc_start: 0.7664 (p90) cc_final: 0.7431 (p90) REVERT: A 488 THR cc_start: 0.7105 (m) cc_final: 0.6713 (p) REVERT: A 493 LEU cc_start: 0.7548 (tp) cc_final: 0.6910 (tt) REVERT: A 501 MET cc_start: 0.7485 (mtt) cc_final: 0.6628 (mmt) REVERT: A 502 TYR cc_start: 0.6988 (m-10) cc_final: 0.6717 (m-10) REVERT: A 504 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7097 (mm-30) REVERT: A 505 ARG cc_start: 0.8066 (mtt90) cc_final: 0.7721 (mtt90) REVERT: A 507 ILE cc_start: 0.8339 (mt) cc_final: 0.7927 (mt) REVERT: A 520 ASN cc_start: 0.7089 (t0) cc_final: 0.6611 (m-40) REVERT: A 522 TYR cc_start: 0.8029 (m-80) cc_final: 0.7601 (m-80) REVERT: A 523 LEU cc_start: 0.8585 (tp) cc_final: 0.8136 (tp) REVERT: A 534 ASP cc_start: 0.7681 (m-30) cc_final: 0.7427 (m-30) REVERT: A 540 LEU cc_start: 0.8568 (mm) cc_final: 0.8358 (mm) REVERT: A 542 MET cc_start: 0.7949 (tpp) cc_final: 0.7586 (tpp) REVERT: A 553 LYS cc_start: 0.8720 (mtmt) cc_final: 0.7794 (ptmt) REVERT: A 554 GLN cc_start: 0.7655 (tt0) cc_final: 0.7012 (mm-40) REVERT: A 581 GLU cc_start: 0.7810 (tt0) cc_final: 0.7446 (tt0) REVERT: A 600 TRP cc_start: 0.8196 (t-100) cc_final: 0.7943 (t-100) REVERT: A 617 ILE cc_start: 0.8393 (mm) cc_final: 0.7935 (mm) REVERT: A 621 LEU cc_start: 0.8199 (mm) cc_final: 0.7802 (mp) REVERT: A 635 MET cc_start: 0.7797 (mpp) cc_final: 0.7118 (mpp) REVERT: A 638 TYR cc_start: 0.8037 (m-80) cc_final: 0.6507 (m-80) REVERT: A 658 LEU cc_start: 0.8505 (tp) cc_final: 0.8262 (mt) REVERT: A 660 GLN cc_start: 0.8122 (pp30) cc_final: 0.7863 (pp30) REVERT: A 661 SER cc_start: 0.8321 (m) cc_final: 0.8054 (p) REVERT: A 663 LYS cc_start: 0.7609 (ptmm) cc_final: 0.7053 (ttpp) REVERT: A 708 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8359 (pm20) REVERT: A 711 LYS cc_start: 0.9091 (mmtt) cc_final: 0.8566 (mmtm) REVERT: A 712 GLU cc_start: 0.8548 (tt0) cc_final: 0.8207 (tt0) REVERT: A 720 TYR cc_start: 0.6947 (t80) cc_final: 0.6406 (t80) REVERT: A 726 VAL cc_start: 0.8325 (OUTLIER) cc_final: 0.7987 (t) REVERT: A 727 GLU cc_start: 0.7874 (pt0) cc_final: 0.7416 (pm20) REVERT: A 729 GLN cc_start: 0.8185 (mp10) cc_final: 0.7749 (mp10) REVERT: A 730 PHE cc_start: 0.7459 (t80) cc_final: 0.7191 (t80) REVERT: A 734 ARG cc_start: 0.8484 (ttt-90) cc_final: 0.7725 (ttm-80) REVERT: A 743 GLU cc_start: 0.7143 (mm-30) cc_final: 0.6730 (mp0) REVERT: A 751 ARG cc_start: 0.7257 (mtm-85) cc_final: 0.6927 (mtp85) REVERT: A 753 GLU cc_start: 0.8120 (mp0) cc_final: 0.7788 (mp0) REVERT: A 756 GLU cc_start: 0.7458 (tp30) cc_final: 0.6630 (tp30) REVERT: A 787 ILE cc_start: 0.6650 (OUTLIER) cc_final: 0.6432 (mm) REVERT: A 788 ARG cc_start: 0.7961 (ptp90) cc_final: 0.7450 (ptp90) REVERT: A 789 GLU cc_start: 0.7729 (pt0) cc_final: 0.6933 (mt-10) REVERT: A 805 PHE cc_start: 0.8519 (t80) cc_final: 0.8287 (t80) REVERT: A 820 LEU cc_start: 0.7700 (mm) cc_final: 0.6969 (mm) REVERT: A 822 LYS cc_start: 0.8400 (mptt) cc_final: 0.8097 (mmtm) REVERT: A 862 LEU cc_start: 0.8459 (tt) cc_final: 0.8244 (mt) REVERT: D 21 GLN cc_start: 0.7491 (mt0) cc_final: 0.6866 (mt0) REVERT: D 79 LYS cc_start: 0.8298 (tppt) cc_final: 0.7226 (tppt) REVERT: D 124 ARG cc_start: 0.8168 (ttt-90) cc_final: 0.7843 (ttt-90) REVERT: D 132 PHE cc_start: 0.6801 (m-80) cc_final: 0.6119 (m-80) REVERT: C 129 THR cc_start: 0.8052 (m) cc_final: 0.7634 (p) REVERT: C 131 GLU cc_start: 0.8252 (mp0) cc_final: 0.7729 (mp0) REVERT: C 237 ASP cc_start: 0.7890 (m-30) cc_final: 0.7066 (t70) REVERT: C 241 ARG cc_start: 0.8455 (mtm-85) cc_final: 0.8221 (mtm-85) REVERT: C 283 TYR cc_start: 0.7716 (t80) cc_final: 0.7385 (t80) REVERT: C 287 PHE cc_start: 0.7291 (m-80) cc_final: 0.7070 (m-80) REVERT: C 294 ARG cc_start: 0.8112 (mpt-90) cc_final: 0.7878 (mpt-90) REVERT: C 321 GLN cc_start: 0.8246 (mt0) cc_final: 0.8018 (mm-40) REVERT: C 324 LEU cc_start: 0.8316 (tt) cc_final: 0.8090 (tp) REVERT: C 332 ASN cc_start: 0.7945 (t0) cc_final: 0.7383 (t0) REVERT: C 337 ARG cc_start: 0.8135 (ttm170) cc_final: 0.7497 (ttp80) REVERT: C 349 TYR cc_start: 0.7753 (t80) cc_final: 0.7409 (t80) REVERT: C 382 ASN cc_start: 0.8120 (m-40) cc_final: 0.7891 (m-40) REVERT: C 394 GLU cc_start: 0.6391 (mm-30) cc_final: 0.5398 (mm-30) REVERT: C 403 GLU cc_start: 0.7042 (pm20) cc_final: 0.6003 (pm20) REVERT: C 406 GLU cc_start: 0.7550 (tp30) cc_final: 0.6996 (tp30) REVERT: C 407 LEU cc_start: 0.8812 (mt) cc_final: 0.8473 (mt) REVERT: C 410 GLN cc_start: 0.8537 (mm-40) cc_final: 0.7671 (mm-40) REVERT: C 411 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7481 (mt-10) REVERT: C 447 GLU cc_start: 0.7611 (mp0) cc_final: 0.7128 (tp30) REVERT: C 477 PHE cc_start: 0.7637 (m-80) cc_final: 0.7286 (m-10) REVERT: C 478 MET cc_start: 0.7730 (mtp) cc_final: 0.6907 (mtp) REVERT: C 482 PHE cc_start: 0.7634 (p90) cc_final: 0.7378 (p90) REVERT: C 488 THR cc_start: 0.7213 (m) cc_final: 0.6893 (p) REVERT: C 493 LEU cc_start: 0.7773 (tp) cc_final: 0.7016 (tt) REVERT: C 499 ILE cc_start: 0.7700 (tp) cc_final: 0.7491 (tp) REVERT: C 501 MET cc_start: 0.7400 (mtt) cc_final: 0.7165 (mtt) REVERT: C 504 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7292 (mm-30) REVERT: C 505 ARG cc_start: 0.8059 (mtt90) cc_final: 0.7533 (mtt90) REVERT: C 507 ILE cc_start: 0.8387 (mt) cc_final: 0.7935 (mt) REVERT: C 520 ASN cc_start: 0.7360 (t0) cc_final: 0.7040 (m-40) REVERT: C 522 TYR cc_start: 0.8011 (m-80) cc_final: 0.7720 (m-80) REVERT: C 540 LEU cc_start: 0.8501 (mm) cc_final: 0.8282 (mm) REVERT: C 542 MET cc_start: 0.7984 (tpp) cc_final: 0.7447 (tpp) REVERT: C 546 GLU cc_start: 0.6875 (tt0) cc_final: 0.6317 (tt0) REVERT: C 553 LYS cc_start: 0.8735 (mtmt) cc_final: 0.8166 (ptmt) REVERT: C 555 LEU cc_start: 0.8730 (tp) cc_final: 0.8514 (tp) REVERT: C 589 MET cc_start: 0.6343 (mtp) cc_final: 0.6119 (mtp) REVERT: C 600 TRP cc_start: 0.8253 (t-100) cc_final: 0.7992 (t-100) REVERT: C 617 ILE cc_start: 0.8573 (mm) cc_final: 0.8143 (mm) REVERT: C 621 LEU cc_start: 0.8219 (mm) cc_final: 0.7838 (mt) REVERT: C 635 MET cc_start: 0.7695 (mpp) cc_final: 0.6950 (mpp) REVERT: C 638 TYR cc_start: 0.7934 (m-80) cc_final: 0.6373 (m-80) REVERT: C 651 LEU cc_start: 0.8202 (tp) cc_final: 0.7956 (mt) REVERT: C 658 LEU cc_start: 0.8745 (tp) cc_final: 0.8340 (tp) REVERT: C 661 SER cc_start: 0.8402 (m) cc_final: 0.8008 (p) REVERT: C 682 ILE cc_start: 0.6755 (pt) cc_final: 0.5788 (pt) REVERT: C 711 LYS cc_start: 0.9019 (mmtt) cc_final: 0.8515 (mmtm) REVERT: C 712 GLU cc_start: 0.8649 (tt0) cc_final: 0.8355 (tt0) REVERT: C 720 TYR cc_start: 0.7030 (t80) cc_final: 0.6378 (t80) REVERT: C 726 VAL cc_start: 0.8058 (OUTLIER) cc_final: 0.7672 (t) REVERT: C 729 GLN cc_start: 0.8186 (mp10) cc_final: 0.7879 (mp10) REVERT: C 730 PHE cc_start: 0.7485 (t80) cc_final: 0.7117 (t80) REVERT: C 739 MET cc_start: 0.7184 (ptm) cc_final: 0.6949 (ptm) REVERT: C 743 GLU cc_start: 0.7418 (mm-30) cc_final: 0.7125 (mm-30) REVERT: C 748 TYR cc_start: 0.7149 (t80) cc_final: 0.6854 (t80) REVERT: C 751 ARG cc_start: 0.7315 (mtm-85) cc_final: 0.7052 (mtp85) REVERT: C 753 GLU cc_start: 0.8164 (mp0) cc_final: 0.7905 (mp0) REVERT: C 756 GLU cc_start: 0.7376 (tp30) cc_final: 0.6486 (tp30) REVERT: C 757 LEU cc_start: 0.7371 (mm) cc_final: 0.7147 (mm) REVERT: C 763 ARG cc_start: 0.5179 (mmm160) cc_final: 0.4858 (tpp80) REVERT: C 787 ILE cc_start: 0.6891 (OUTLIER) cc_final: 0.6533 (mm) REVERT: C 788 ARG cc_start: 0.7999 (ptp90) cc_final: 0.7369 (ptp90) REVERT: C 789 GLU cc_start: 0.7881 (pt0) cc_final: 0.7175 (mt-10) REVERT: C 805 PHE cc_start: 0.8475 (t80) cc_final: 0.8244 (t80) REVERT: C 820 LEU cc_start: 0.7518 (mm) cc_final: 0.6792 (mm) REVERT: C 822 LYS cc_start: 0.8473 (mptt) cc_final: 0.8235 (mmtp) REVERT: C 855 LYS cc_start: 0.8803 (tttt) cc_final: 0.7586 (tmtt) outliers start: 10 outliers final: 4 residues processed: 565 average time/residue: 0.3074 time to fit residues: 234.8128 Evaluate side-chains 514 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 506 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 126 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 147 optimal weight: 0.5980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN B 134 ASN ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 ASN A 285 ASN ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 GLN D 65 ASN D 97 GLN D 134 ASN ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 ASN C 285 ASN C 455 ASN C 515 GLN ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 723 ASN C 738 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.141646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.114694 restraints weight = 29734.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.119240 restraints weight = 18437.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.122617 restraints weight = 12813.123| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13534 Z= 0.205 Angle : 0.763 16.441 18272 Z= 0.389 Chirality : 0.045 0.227 2014 Planarity : 0.006 0.070 2372 Dihedral : 6.248 23.604 1806 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.21 % Allowed : 6.61 % Favored : 93.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.18), residues: 1610 helix: -2.09 (0.15), residues: 834 sheet: -3.18 (0.50), residues: 72 loop : -1.62 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 328 HIS 0.003 0.001 HIS A 655 PHE 0.039 0.002 PHE D 54 TYR 0.032 0.002 TYR C 127 ARG 0.012 0.001 ARG D 84 Details of bonding type rmsd hydrogen bonds : bond 0.05246 ( 502) hydrogen bonds : angle 6.10430 ( 1392) metal coordination : bond 0.01023 ( 12) metal coordination : angle 9.53315 ( 12) covalent geometry : bond 0.00396 (13522) covalent geometry : angle 0.72334 (18260) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 550 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 ILE cc_start: 0.8176 (tt) cc_final: 0.7766 (tt) REVERT: B 42 GLN cc_start: 0.8493 (mt0) cc_final: 0.8201 (mt0) REVERT: B 59 ILE cc_start: 0.7676 (mm) cc_final: 0.7254 (tp) REVERT: B 65 ASN cc_start: 0.8378 (m-40) cc_final: 0.8129 (m-40) REVERT: B 73 CYS cc_start: 0.7512 (m) cc_final: 0.7054 (m) REVERT: B 76 PHE cc_start: 0.8504 (t80) cc_final: 0.8094 (t80) REVERT: B 80 ILE cc_start: 0.8723 (mm) cc_final: 0.8381 (mm) REVERT: B 88 TYR cc_start: 0.7254 (p90) cc_final: 0.6918 (p90) REVERT: B 108 ILE cc_start: 0.8077 (mt) cc_final: 0.7673 (tt) REVERT: B 128 LYS cc_start: 0.8372 (mttt) cc_final: 0.8033 (mmtt) REVERT: B 132 PHE cc_start: 0.7573 (m-80) cc_final: 0.6756 (m-80) REVERT: A 130 GLU cc_start: 0.8538 (pt0) cc_final: 0.7738 (pm20) REVERT: A 138 GLU cc_start: 0.8334 (mp0) cc_final: 0.7810 (mp0) REVERT: A 237 ASP cc_start: 0.8388 (m-30) cc_final: 0.7369 (t0) REVERT: A 260 LEU cc_start: 0.9079 (mm) cc_final: 0.8819 (mm) REVERT: A 283 TYR cc_start: 0.7850 (t80) cc_final: 0.7596 (t80) REVERT: A 287 PHE cc_start: 0.7290 (m-80) cc_final: 0.7027 (m-80) REVERT: A 291 MET cc_start: 0.8494 (ttt) cc_final: 0.7981 (ttm) REVERT: A 294 ARG cc_start: 0.8520 (mpt-90) cc_final: 0.8271 (mpt-90) REVERT: A 304 MET cc_start: 0.5291 (tpt) cc_final: 0.4713 (tpt) REVERT: A 315 LYS cc_start: 0.7964 (mmtm) cc_final: 0.7447 (mmtm) REVERT: A 332 ASN cc_start: 0.7807 (t0) cc_final: 0.7303 (t0) REVERT: A 337 ARG cc_start: 0.8166 (ttm170) cc_final: 0.7729 (ttp80) REVERT: A 341 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7584 (mt-10) REVERT: A 343 PHE cc_start: 0.9008 (m-80) cc_final: 0.8751 (m-80) REVERT: A 344 GLN cc_start: 0.8491 (tp-100) cc_final: 0.7328 (tp-100) REVERT: A 348 THR cc_start: 0.7813 (m) cc_final: 0.7539 (m) REVERT: A 361 LEU cc_start: 0.7562 (tp) cc_final: 0.7296 (tp) REVERT: A 392 HIS cc_start: 0.8079 (m90) cc_final: 0.7512 (m-70) REVERT: A 406 GLU cc_start: 0.8288 (tp30) cc_final: 0.7799 (tt0) REVERT: A 407 LEU cc_start: 0.8870 (mt) cc_final: 0.8654 (mt) REVERT: A 409 LEU cc_start: 0.8636 (tp) cc_final: 0.8182 (pp) REVERT: A 410 GLN cc_start: 0.9009 (mm-40) cc_final: 0.8740 (mm110) REVERT: A 447 GLU cc_start: 0.8219 (mp0) cc_final: 0.7609 (tp30) REVERT: A 449 PHE cc_start: 0.7588 (m-10) cc_final: 0.6980 (m-10) REVERT: A 450 ILE cc_start: 0.7940 (mt) cc_final: 0.7332 (mt) REVERT: A 455 ASN cc_start: 0.7975 (m110) cc_final: 0.7717 (m110) REVERT: A 458 LEU cc_start: 0.8478 (tp) cc_final: 0.7965 (tt) REVERT: A 464 TYR cc_start: 0.7975 (t80) cc_final: 0.7342 (t80) REVERT: A 477 PHE cc_start: 0.8181 (m-80) cc_final: 0.7795 (m-80) REVERT: A 478 MET cc_start: 0.8109 (mtp) cc_final: 0.7343 (mtp) REVERT: A 482 PHE cc_start: 0.8044 (p90) cc_final: 0.7718 (p90) REVERT: A 495 TYR cc_start: 0.7484 (m-10) cc_final: 0.7274 (m-10) REVERT: A 499 ILE cc_start: 0.7958 (tp) cc_final: 0.7638 (tp) REVERT: A 501 MET cc_start: 0.8251 (mtt) cc_final: 0.7277 (ptp) REVERT: A 504 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7561 (mm-30) REVERT: A 507 ILE cc_start: 0.8613 (mt) cc_final: 0.8175 (mt) REVERT: A 523 LEU cc_start: 0.8593 (tp) cc_final: 0.8133 (tp) REVERT: A 535 ASP cc_start: 0.7250 (m-30) cc_final: 0.6857 (m-30) REVERT: A 545 MET cc_start: 0.8000 (mtm) cc_final: 0.7464 (mtm) REVERT: A 546 GLU cc_start: 0.7385 (tt0) cc_final: 0.7152 (tt0) REVERT: A 550 ASP cc_start: 0.7954 (p0) cc_final: 0.7651 (p0) REVERT: A 553 LYS cc_start: 0.8563 (mtmt) cc_final: 0.8325 (mtpp) REVERT: A 572 LYS cc_start: 0.8552 (tttp) cc_final: 0.8211 (ttmm) REVERT: A 573 GLU cc_start: 0.8112 (pp20) cc_final: 0.7673 (pp20) REVERT: A 576 GLN cc_start: 0.8405 (tp-100) cc_final: 0.7667 (tp-100) REVERT: A 577 LEU cc_start: 0.8910 (mt) cc_final: 0.8487 (mt) REVERT: A 593 ASP cc_start: 0.8341 (t0) cc_final: 0.7941 (t0) REVERT: A 617 ILE cc_start: 0.8449 (mm) cc_final: 0.8084 (mm) REVERT: A 621 LEU cc_start: 0.8139 (mm) cc_final: 0.7775 (mp) REVERT: A 635 MET cc_start: 0.8174 (mpp) cc_final: 0.7426 (mpp) REVERT: A 641 LEU cc_start: 0.8506 (mt) cc_final: 0.7685 (pp) REVERT: A 651 LEU cc_start: 0.8409 (mt) cc_final: 0.8188 (mt) REVERT: A 658 LEU cc_start: 0.8419 (tp) cc_final: 0.7979 (tp) REVERT: A 660 GLN cc_start: 0.8366 (pp30) cc_final: 0.8105 (pp30) REVERT: A 661 SER cc_start: 0.8451 (m) cc_final: 0.8214 (p) REVERT: A 663 LYS cc_start: 0.8187 (ptmm) cc_final: 0.7830 (ttpp) REVERT: A 711 LYS cc_start: 0.9222 (mmtt) cc_final: 0.8900 (mmtm) REVERT: A 716 LEU cc_start: 0.8730 (mt) cc_final: 0.8484 (mt) REVERT: A 717 TYR cc_start: 0.8409 (t80) cc_final: 0.8018 (t80) REVERT: A 720 TYR cc_start: 0.7685 (t80) cc_final: 0.7081 (t80) REVERT: A 727 GLU cc_start: 0.8076 (pt0) cc_final: 0.7839 (pm20) REVERT: A 728 LYS cc_start: 0.8610 (ttpt) cc_final: 0.8061 (ptmm) REVERT: A 730 PHE cc_start: 0.8204 (t80) cc_final: 0.7806 (t80) REVERT: A 734 ARG cc_start: 0.8538 (ttt-90) cc_final: 0.7454 (tpt-90) REVERT: A 743 GLU cc_start: 0.8431 (mm-30) cc_final: 0.7865 (mm-30) REVERT: A 751 ARG cc_start: 0.7795 (mtm-85) cc_final: 0.7399 (mmm160) REVERT: A 753 GLU cc_start: 0.8746 (mp0) cc_final: 0.8376 (mp0) REVERT: A 756 GLU cc_start: 0.8009 (tp30) cc_final: 0.7415 (tp30) REVERT: A 792 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8340 (mm-30) REVERT: A 805 PHE cc_start: 0.8702 (t80) cc_final: 0.8292 (t80) REVERT: A 806 LEU cc_start: 0.8258 (mt) cc_final: 0.7920 (mt) REVERT: A 820 LEU cc_start: 0.7716 (mm) cc_final: 0.7504 (mm) REVERT: A 822 LYS cc_start: 0.8564 (mptt) cc_final: 0.8178 (mmtm) REVERT: A 862 LEU cc_start: 0.8601 (tt) cc_final: 0.8324 (mt) REVERT: D 42 GLN cc_start: 0.8551 (mt0) cc_final: 0.8262 (mt0) REVERT: D 47 ARG cc_start: 0.7769 (mmm160) cc_final: 0.6930 (mmm160) REVERT: D 59 ILE cc_start: 0.7665 (mm) cc_final: 0.7174 (tp) REVERT: D 65 ASN cc_start: 0.8458 (m-40) cc_final: 0.8167 (m-40) REVERT: D 73 CYS cc_start: 0.7480 (m) cc_final: 0.6927 (m) REVERT: D 76 PHE cc_start: 0.8538 (t80) cc_final: 0.8020 (t80) REVERT: D 79 LYS cc_start: 0.8379 (tppt) cc_final: 0.7297 (tppt) REVERT: D 80 ILE cc_start: 0.8647 (mm) cc_final: 0.8349 (mm) REVERT: D 88 TYR cc_start: 0.7183 (p90) cc_final: 0.6869 (p90) REVERT: D 94 THR cc_start: 0.7357 (p) cc_final: 0.6971 (p) REVERT: D 132 PHE cc_start: 0.7506 (m-80) cc_final: 0.6806 (m-80) REVERT: D 134 ASN cc_start: 0.7596 (t0) cc_final: 0.7073 (t0) REVERT: C 130 GLU cc_start: 0.8412 (pt0) cc_final: 0.8098 (pt0) REVERT: C 237 ASP cc_start: 0.8033 (m-30) cc_final: 0.7606 (t0) REVERT: C 241 ARG cc_start: 0.8691 (mtm-85) cc_final: 0.8447 (mtm-85) REVERT: C 260 LEU cc_start: 0.8969 (mm) cc_final: 0.8710 (mm) REVERT: C 287 PHE cc_start: 0.7524 (m-80) cc_final: 0.7251 (m-80) REVERT: C 291 MET cc_start: 0.8664 (ttt) cc_final: 0.8234 (ttt) REVERT: C 315 LYS cc_start: 0.7979 (mtmm) cc_final: 0.7476 (mttp) REVERT: C 321 GLN cc_start: 0.8427 (mt0) cc_final: 0.8186 (mm-40) REVERT: C 332 ASN cc_start: 0.7659 (t0) cc_final: 0.7194 (t0) REVERT: C 337 ARG cc_start: 0.8250 (ttm170) cc_final: 0.7675 (ttp80) REVERT: C 338 ARG cc_start: 0.8240 (mtp85) cc_final: 0.7526 (mtp-110) REVERT: C 344 GLN cc_start: 0.8468 (tp-100) cc_final: 0.7391 (tp-100) REVERT: C 349 TYR cc_start: 0.7899 (t80) cc_final: 0.7693 (t80) REVERT: C 376 LYS cc_start: 0.8545 (ttmt) cc_final: 0.7633 (tttt) REVERT: C 380 TYR cc_start: 0.8739 (m-10) cc_final: 0.8065 (m-10) REVERT: C 382 ASN cc_start: 0.8525 (m-40) cc_final: 0.8198 (m110) REVERT: C 394 GLU cc_start: 0.6339 (mm-30) cc_final: 0.6017 (mm-30) REVERT: C 406 GLU cc_start: 0.8429 (tp30) cc_final: 0.8220 (tt0) REVERT: C 407 LEU cc_start: 0.8786 (mt) cc_final: 0.8313 (pp) REVERT: C 409 LEU cc_start: 0.8598 (tp) cc_final: 0.8101 (pp) REVERT: C 410 GLN cc_start: 0.8967 (mm-40) cc_final: 0.8723 (mm110) REVERT: C 411 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7268 (mt-10) REVERT: C 426 ASP cc_start: 0.8582 (t70) cc_final: 0.8341 (t0) REVERT: C 447 GLU cc_start: 0.8079 (mp0) cc_final: 0.7490 (tp30) REVERT: C 449 PHE cc_start: 0.7820 (m-10) cc_final: 0.7177 (m-10) REVERT: C 450 ILE cc_start: 0.7867 (mt) cc_final: 0.7165 (mt) REVERT: C 458 LEU cc_start: 0.8804 (tp) cc_final: 0.8528 (tt) REVERT: C 459 GLU cc_start: 0.6860 (mp0) cc_final: 0.6633 (mp0) REVERT: C 478 MET cc_start: 0.7870 (mtp) cc_final: 0.7372 (mtp) REVERT: C 482 PHE cc_start: 0.8041 (p90) cc_final: 0.7727 (p90) REVERT: C 491 LEU cc_start: 0.8609 (mt) cc_final: 0.8320 (mt) REVERT: C 493 LEU cc_start: 0.8036 (tp) cc_final: 0.7644 (tp) REVERT: C 495 TYR cc_start: 0.7672 (m-10) cc_final: 0.7243 (m-10) REVERT: C 497 ASN cc_start: 0.8039 (m-40) cc_final: 0.7821 (m-40) REVERT: C 499 ILE cc_start: 0.8075 (tp) cc_final: 0.7743 (tp) REVERT: C 501 MET cc_start: 0.8240 (mtt) cc_final: 0.7864 (mtt) REVERT: C 502 TYR cc_start: 0.7635 (m-10) cc_final: 0.7208 (m-10) REVERT: C 505 ARG cc_start: 0.8768 (mtt90) cc_final: 0.8256 (mtt90) REVERT: C 507 ILE cc_start: 0.8563 (mt) cc_final: 0.8326 (mt) REVERT: C 542 MET cc_start: 0.8281 (tpp) cc_final: 0.7562 (tpp) REVERT: C 545 MET cc_start: 0.7975 (mtm) cc_final: 0.7268 (mtm) REVERT: C 546 GLU cc_start: 0.7498 (tt0) cc_final: 0.6876 (tt0) REVERT: C 553 LYS cc_start: 0.8492 (mtmt) cc_final: 0.8215 (mtpp) REVERT: C 576 GLN cc_start: 0.7916 (tm-30) cc_final: 0.7304 (tm-30) REVERT: C 577 LEU cc_start: 0.8758 (mt) cc_final: 0.8388 (mt) REVERT: C 587 ILE cc_start: 0.8514 (tp) cc_final: 0.8245 (tp) REVERT: C 589 MET cc_start: 0.7042 (mtp) cc_final: 0.6648 (mtp) REVERT: C 600 TRP cc_start: 0.8778 (t-100) cc_final: 0.8572 (t-100) REVERT: C 619 LEU cc_start: 0.8738 (tp) cc_final: 0.8447 (tp) REVERT: C 621 LEU cc_start: 0.8322 (mm) cc_final: 0.7984 (mm) REVERT: C 625 ASN cc_start: 0.8454 (m110) cc_final: 0.8140 (m-40) REVERT: C 626 ASN cc_start: 0.7965 (m-40) cc_final: 0.7752 (m110) REVERT: C 635 MET cc_start: 0.7957 (mpp) cc_final: 0.7268 (mpp) REVERT: C 641 LEU cc_start: 0.8515 (mt) cc_final: 0.7953 (pp) REVERT: C 648 PHE cc_start: 0.8762 (p90) cc_final: 0.8342 (p90) REVERT: C 658 LEU cc_start: 0.8564 (tp) cc_final: 0.8158 (tp) REVERT: C 661 SER cc_start: 0.8448 (m) cc_final: 0.8213 (p) REVERT: C 663 LYS cc_start: 0.8315 (ptmm) cc_final: 0.7169 (mmtt) REVERT: C 664 ASP cc_start: 0.8185 (m-30) cc_final: 0.6581 (p0) REVERT: C 667 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8405 (pp20) REVERT: C 711 LYS cc_start: 0.9189 (mmtt) cc_final: 0.8693 (mmtm) REVERT: C 712 GLU cc_start: 0.8715 (tt0) cc_final: 0.8489 (tt0) REVERT: C 719 ASP cc_start: 0.8295 (m-30) cc_final: 0.8077 (m-30) REVERT: C 720 TYR cc_start: 0.7771 (t80) cc_final: 0.7194 (t80) REVERT: C 730 PHE cc_start: 0.8227 (t80) cc_final: 0.7856 (t80) REVERT: C 738 HIS cc_start: 0.8304 (t-90) cc_final: 0.7696 (t-90) REVERT: C 739 MET cc_start: 0.7801 (ptm) cc_final: 0.7579 (ptm) REVERT: C 743 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8047 (mm-30) REVERT: C 748 TYR cc_start: 0.7620 (t80) cc_final: 0.7087 (t80) REVERT: C 753 GLU cc_start: 0.8690 (mp0) cc_final: 0.8401 (mp0) REVERT: C 756 GLU cc_start: 0.7867 (tp30) cc_final: 0.7273 (tp30) REVERT: C 789 GLU cc_start: 0.8092 (pt0) cc_final: 0.7571 (mt-10) REVERT: C 791 TRP cc_start: 0.7889 (t60) cc_final: 0.7473 (t60) REVERT: C 855 LYS cc_start: 0.8865 (tttt) cc_final: 0.7812 (tppt) outliers start: 3 outliers final: 0 residues processed: 553 average time/residue: 0.3013 time to fit residues: 225.5218 Evaluate side-chains 520 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 520 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 7 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 138 optimal weight: 0.9980 chunk 155 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 132 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 chunk 150 optimal weight: 4.9990 chunk 157 optimal weight: 5.9990 chunk 85 optimal weight: 0.7980 chunk 145 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 97 GLN B 134 ASN ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 ASN A 518 GLN A 626 ASN D 123 GLN ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 455 ASN C 723 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.143363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.115711 restraints weight = 30379.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.120387 restraints weight = 18723.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.123886 restraints weight = 12941.491| |-----------------------------------------------------------------------------| r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13534 Z= 0.150 Angle : 0.672 12.589 18272 Z= 0.338 Chirality : 0.044 0.173 2014 Planarity : 0.005 0.072 2372 Dihedral : 5.534 21.269 1806 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.07 % Allowed : 4.96 % Favored : 94.97 % 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: -2.30 (0.19), residues: 1610 helix: -1.39 (0.16), residues: 838 sheet: -3.17 (0.52), residues: 72 loop : -1.33 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 600 HIS 0.002 0.001 HIS C 655 PHE 0.026 0.002 PHE A 790 TYR 0.024 0.002 TYR A 717 ARG 0.011 0.001 ARG A 539 Details of bonding type rmsd hydrogen bonds : bond 0.04245 ( 502) hydrogen bonds : angle 5.41151 ( 1392) metal coordination : bond 0.00739 ( 12) metal coordination : angle 7.22081 ( 12) covalent geometry : bond 0.00302 (13522) covalent geometry : angle 0.64622 (18260) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 534 time to evaluate : 1.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 GLN cc_start: 0.8423 (mt0) cc_final: 0.8159 (mt0) REVERT: B 59 ILE cc_start: 0.7654 (mm) cc_final: 0.7290 (tp) REVERT: B 65 ASN cc_start: 0.8395 (m-40) cc_final: 0.8140 (m-40) REVERT: B 73 CYS cc_start: 0.7494 (m) cc_final: 0.6851 (m) REVERT: B 77 TYR cc_start: 0.8346 (m-80) cc_final: 0.7636 (m-80) REVERT: B 82 GLU cc_start: 0.8635 (tt0) cc_final: 0.8134 (tt0) REVERT: B 88 TYR cc_start: 0.7050 (p90) cc_final: 0.6758 (p90) REVERT: B 108 ILE cc_start: 0.8133 (mt) cc_final: 0.7779 (tt) REVERT: B 114 GLN cc_start: 0.7702 (mp10) cc_final: 0.7427 (mp10) REVERT: B 124 ARG cc_start: 0.8499 (ttt-90) cc_final: 0.8041 (ttt-90) REVERT: B 128 LYS cc_start: 0.8365 (mttt) cc_final: 0.8155 (mttt) REVERT: B 132 PHE cc_start: 0.7528 (m-80) cc_final: 0.6850 (m-80) REVERT: B 134 ASN cc_start: 0.7714 (t0) cc_final: 0.7157 (t0) REVERT: A 130 GLU cc_start: 0.8509 (pt0) cc_final: 0.7728 (pm20) REVERT: A 138 GLU cc_start: 0.8421 (mp0) cc_final: 0.7996 (mp0) REVERT: A 237 ASP cc_start: 0.8580 (m-30) cc_final: 0.7997 (t0) REVERT: A 241 ARG cc_start: 0.8706 (mtp-110) cc_final: 0.8432 (mtp-110) REVERT: A 287 PHE cc_start: 0.7306 (m-80) cc_final: 0.6990 (m-80) REVERT: A 291 MET cc_start: 0.8404 (ttt) cc_final: 0.7871 (ttm) REVERT: A 294 ARG cc_start: 0.8577 (mpt-90) cc_final: 0.8358 (mpt-90) REVERT: A 304 MET cc_start: 0.5181 (tpt) cc_final: 0.4315 (tpt) REVERT: A 315 LYS cc_start: 0.7991 (mmtm) cc_final: 0.7425 (mttm) REVERT: A 337 ARG cc_start: 0.8151 (ttm170) cc_final: 0.7273 (ttp80) REVERT: A 338 ARG cc_start: 0.7948 (mtp85) cc_final: 0.7577 (mmm-85) REVERT: A 341 GLU cc_start: 0.8369 (mt-10) cc_final: 0.6969 (mt-10) REVERT: A 344 GLN cc_start: 0.8442 (tp-100) cc_final: 0.7294 (tp-100) REVERT: A 345 GLN cc_start: 0.8427 (mt0) cc_final: 0.7560 (tp40) REVERT: A 346 LEU cc_start: 0.8791 (tp) cc_final: 0.8517 (tp) REVERT: A 350 LYS cc_start: 0.7638 (mmpt) cc_final: 0.7159 (tptt) REVERT: A 361 LEU cc_start: 0.7358 (tp) cc_final: 0.7069 (tp) REVERT: A 376 LYS cc_start: 0.8674 (tttt) cc_final: 0.8320 (tppt) REVERT: A 392 HIS cc_start: 0.8130 (m90) cc_final: 0.7609 (m-70) REVERT: A 406 GLU cc_start: 0.8437 (tp30) cc_final: 0.7778 (tp30) REVERT: A 407 LEU cc_start: 0.8854 (mt) cc_final: 0.8499 (pp) REVERT: A 410 GLN cc_start: 0.8999 (mm-40) cc_final: 0.8618 (mm-40) REVERT: A 447 GLU cc_start: 0.8158 (mp0) cc_final: 0.7627 (tp30) REVERT: A 449 PHE cc_start: 0.7452 (m-10) cc_final: 0.6969 (m-10) REVERT: A 450 ILE cc_start: 0.8094 (mt) cc_final: 0.7442 (mt) REVERT: A 455 ASN cc_start: 0.8002 (m-40) cc_final: 0.7795 (m110) REVERT: A 458 LEU cc_start: 0.8305 (tp) cc_final: 0.8006 (tt) REVERT: A 459 GLU cc_start: 0.6987 (mp0) cc_final: 0.6700 (mp0) REVERT: A 477 PHE cc_start: 0.8094 (m-80) cc_final: 0.7679 (m-80) REVERT: A 478 MET cc_start: 0.8138 (mtp) cc_final: 0.7387 (mtp) REVERT: A 489 LYS cc_start: 0.8496 (mtmm) cc_final: 0.8091 (ptpp) REVERT: A 499 ILE cc_start: 0.7872 (tp) cc_final: 0.7533 (tp) REVERT: A 502 TYR cc_start: 0.7550 (m-10) cc_final: 0.7255 (m-10) REVERT: A 504 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7656 (mm-30) REVERT: A 505 ARG cc_start: 0.8719 (mtt90) cc_final: 0.8298 (mtt90) REVERT: A 507 ILE cc_start: 0.8651 (mt) cc_final: 0.8172 (mp) REVERT: A 522 TYR cc_start: 0.8343 (m-80) cc_final: 0.7862 (m-80) REVERT: A 523 LEU cc_start: 0.8490 (tp) cc_final: 0.8187 (tp) REVERT: A 534 ASP cc_start: 0.8192 (m-30) cc_final: 0.7991 (m-30) REVERT: A 539 ARG cc_start: 0.8149 (ttm110) cc_final: 0.7587 (ptm160) REVERT: A 542 MET cc_start: 0.8510 (ptt) cc_final: 0.8020 (tmm) REVERT: A 543 ILE cc_start: 0.8906 (mt) cc_final: 0.8338 (mt) REVERT: A 545 MET cc_start: 0.7933 (mtm) cc_final: 0.7370 (mtm) REVERT: A 550 ASP cc_start: 0.7950 (p0) cc_final: 0.7604 (p0) REVERT: A 553 LYS cc_start: 0.8561 (mtmt) cc_final: 0.8259 (mtpp) REVERT: A 554 GLN cc_start: 0.7953 (mm110) cc_final: 0.7513 (tp40) REVERT: A 573 GLU cc_start: 0.8092 (pp20) cc_final: 0.7683 (pp20) REVERT: A 576 GLN cc_start: 0.8413 (tp-100) cc_final: 0.7681 (tp-100) REVERT: A 577 LEU cc_start: 0.8935 (mt) cc_final: 0.8607 (mt) REVERT: A 587 ILE cc_start: 0.7832 (tp) cc_final: 0.7603 (tp) REVERT: A 589 MET cc_start: 0.6205 (mtt) cc_final: 0.4301 (mtt) REVERT: A 593 ASP cc_start: 0.8239 (t0) cc_final: 0.7836 (t0) REVERT: A 617 ILE cc_start: 0.8540 (mm) cc_final: 0.8181 (mm) REVERT: A 621 LEU cc_start: 0.8088 (mm) cc_final: 0.7729 (mp) REVERT: A 635 MET cc_start: 0.8282 (mpp) cc_final: 0.7443 (mpp) REVERT: A 641 LEU cc_start: 0.8510 (mt) cc_final: 0.7956 (mt) REVERT: A 642 MET cc_start: 0.8153 (mmp) cc_final: 0.7840 (mmp) REVERT: A 651 LEU cc_start: 0.8425 (mt) cc_final: 0.8213 (mt) REVERT: A 658 LEU cc_start: 0.8426 (tp) cc_final: 0.7840 (tp) REVERT: A 660 GLN cc_start: 0.8276 (pp30) cc_final: 0.7940 (pp30) REVERT: A 661 SER cc_start: 0.8511 (m) cc_final: 0.8166 (p) REVERT: A 663 LYS cc_start: 0.8234 (ptmm) cc_final: 0.7471 (ttpp) REVERT: A 682 ILE cc_start: 0.8355 (tp) cc_final: 0.8101 (tp) REVERT: A 707 ASN cc_start: 0.8262 (p0) cc_final: 0.8002 (m-40) REVERT: A 711 LYS cc_start: 0.9248 (mmtt) cc_final: 0.8758 (mmtm) REVERT: A 716 LEU cc_start: 0.8685 (mt) cc_final: 0.8427 (mt) REVERT: A 717 TYR cc_start: 0.8648 (t80) cc_final: 0.8271 (t80) REVERT: A 720 TYR cc_start: 0.7730 (t80) cc_final: 0.6986 (t80) REVERT: A 727 GLU cc_start: 0.8044 (pt0) cc_final: 0.7809 (pm20) REVERT: A 728 LYS cc_start: 0.8377 (ttpt) cc_final: 0.7754 (ptmm) REVERT: A 730 PHE cc_start: 0.8145 (t80) cc_final: 0.7772 (t80) REVERT: A 743 GLU cc_start: 0.8408 (mm-30) cc_final: 0.7936 (mm-30) REVERT: A 753 GLU cc_start: 0.8686 (mp0) cc_final: 0.8317 (mp0) REVERT: A 756 GLU cc_start: 0.7333 (tp30) cc_final: 0.6986 (tp30) REVERT: A 792 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8240 (mm-30) REVERT: A 822 LYS cc_start: 0.8465 (mptt) cc_final: 0.8261 (mmtt) REVERT: A 862 LEU cc_start: 0.8623 (tt) cc_final: 0.8318 (mt) REVERT: D 22 LEU cc_start: 0.8189 (mm) cc_final: 0.7832 (mm) REVERT: D 42 GLN cc_start: 0.8470 (mt0) cc_final: 0.8225 (mt0) REVERT: D 65 ASN cc_start: 0.8543 (m-40) cc_final: 0.8128 (m-40) REVERT: D 73 CYS cc_start: 0.7516 (m) cc_final: 0.6887 (m) REVERT: D 88 TYR cc_start: 0.7178 (p90) cc_final: 0.6834 (p90) REVERT: D 132 PHE cc_start: 0.7650 (m-80) cc_final: 0.6754 (m-80) REVERT: D 134 ASN cc_start: 0.7773 (t0) cc_final: 0.7332 (t0) REVERT: D 138 ARG cc_start: 0.7906 (ptt-90) cc_final: 0.6711 (ptt-90) REVERT: C 130 GLU cc_start: 0.8432 (pt0) cc_final: 0.8105 (pt0) REVERT: C 138 GLU cc_start: 0.8500 (mp0) cc_final: 0.8116 (mp0) REVERT: C 237 ASP cc_start: 0.8061 (m-30) cc_final: 0.7815 (t0) REVERT: C 241 ARG cc_start: 0.8709 (mtm-85) cc_final: 0.8486 (mtm-85) REVERT: C 287 PHE cc_start: 0.7569 (m-80) cc_final: 0.7270 (m-80) REVERT: C 288 ILE cc_start: 0.8637 (tt) cc_final: 0.8180 (tt) REVERT: C 291 MET cc_start: 0.8395 (ttt) cc_final: 0.7798 (ptm) REVERT: C 295 ASN cc_start: 0.8685 (m110) cc_final: 0.8406 (m110) REVERT: C 315 LYS cc_start: 0.7925 (mtmm) cc_final: 0.7383 (mttt) REVERT: C 321 GLN cc_start: 0.8412 (mt0) cc_final: 0.8114 (mm-40) REVERT: C 332 ASN cc_start: 0.7664 (t0) cc_final: 0.7206 (t0) REVERT: C 337 ARG cc_start: 0.8200 (ttm170) cc_final: 0.7845 (tmm-80) REVERT: C 349 TYR cc_start: 0.7891 (t80) cc_final: 0.7607 (t80) REVERT: C 361 LEU cc_start: 0.7270 (tp) cc_final: 0.6798 (tp) REVERT: C 376 LYS cc_start: 0.8605 (ttpt) cc_final: 0.7750 (tppt) REVERT: C 382 ASN cc_start: 0.8525 (m-40) cc_final: 0.8159 (m110) REVERT: C 392 HIS cc_start: 0.8210 (m170) cc_final: 0.7809 (m-70) REVERT: C 394 GLU cc_start: 0.6240 (mm-30) cc_final: 0.5726 (mm-30) REVERT: C 406 GLU cc_start: 0.8521 (tp30) cc_final: 0.7854 (mt-10) REVERT: C 407 LEU cc_start: 0.8782 (mt) cc_final: 0.8223 (pp) REVERT: C 408 THR cc_start: 0.8569 (m) cc_final: 0.8046 (m) REVERT: C 409 LEU cc_start: 0.8639 (tp) cc_final: 0.8110 (pp) REVERT: C 410 GLN cc_start: 0.8979 (mm-40) cc_final: 0.7953 (mm-40) REVERT: C 411 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7151 (mt-10) REVERT: C 447 GLU cc_start: 0.8091 (mp0) cc_final: 0.7553 (tp30) REVERT: C 459 GLU cc_start: 0.6739 (mp0) cc_final: 0.6288 (mp0) REVERT: C 478 MET cc_start: 0.7834 (mtp) cc_final: 0.7312 (mtp) REVERT: C 482 PHE cc_start: 0.8067 (p90) cc_final: 0.7175 (p90) REVERT: C 495 TYR cc_start: 0.7574 (m-10) cc_final: 0.7361 (m-10) REVERT: C 499 ILE cc_start: 0.8057 (tp) cc_final: 0.7676 (tp) REVERT: C 501 MET cc_start: 0.8223 (mtt) cc_final: 0.7842 (mtt) REVERT: C 502 TYR cc_start: 0.7636 (m-10) cc_final: 0.7186 (m-10) REVERT: C 505 ARG cc_start: 0.8743 (mtt90) cc_final: 0.8211 (mtt90) REVERT: C 507 ILE cc_start: 0.8590 (mt) cc_final: 0.8338 (mp) REVERT: C 522 TYR cc_start: 0.8156 (m-80) cc_final: 0.7677 (m-80) REVERT: C 533 ILE cc_start: 0.8579 (mp) cc_final: 0.8343 (mp) REVERT: C 540 LEU cc_start: 0.8773 (mm) cc_final: 0.8543 (mm) REVERT: C 542 MET cc_start: 0.8177 (tpp) cc_final: 0.7471 (tpp) REVERT: C 543 ILE cc_start: 0.8869 (mt) cc_final: 0.8627 (mt) REVERT: C 545 MET cc_start: 0.7907 (mtm) cc_final: 0.7176 (mtm) REVERT: C 551 LEU cc_start: 0.8895 (mp) cc_final: 0.8644 (mp) REVERT: C 553 LYS cc_start: 0.8423 (mtmt) cc_final: 0.8203 (mtpp) REVERT: C 555 LEU cc_start: 0.8555 (tp) cc_final: 0.8297 (tp) REVERT: C 572 LYS cc_start: 0.8455 (mmtt) cc_final: 0.8082 (ttmm) REVERT: C 573 GLU cc_start: 0.7984 (pm20) cc_final: 0.7689 (pm20) REVERT: C 576 GLN cc_start: 0.7609 (tm-30) cc_final: 0.7161 (tm-30) REVERT: C 577 LEU cc_start: 0.8663 (mt) cc_final: 0.8306 (mt) REVERT: C 587 ILE cc_start: 0.8378 (tp) cc_final: 0.8088 (tp) REVERT: C 589 MET cc_start: 0.6833 (mtp) cc_final: 0.6479 (mtp) REVERT: C 593 ASP cc_start: 0.7819 (t70) cc_final: 0.7554 (t70) REVERT: C 594 GLU cc_start: 0.8551 (mp0) cc_final: 0.8341 (mp0) REVERT: C 619 LEU cc_start: 0.8758 (tp) cc_final: 0.8492 (tp) REVERT: C 621 LEU cc_start: 0.8218 (mm) cc_final: 0.7810 (mm) REVERT: C 625 ASN cc_start: 0.8379 (m110) cc_final: 0.8043 (m-40) REVERT: C 626 ASN cc_start: 0.7948 (m-40) cc_final: 0.7692 (m110) REVERT: C 630 ASP cc_start: 0.7289 (t70) cc_final: 0.7044 (t0) REVERT: C 635 MET cc_start: 0.8088 (mpp) cc_final: 0.7395 (mpp) REVERT: C 641 LEU cc_start: 0.8533 (mt) cc_final: 0.7954 (pp) REVERT: C 648 PHE cc_start: 0.8686 (p90) cc_final: 0.8340 (p90) REVERT: C 649 ARG cc_start: 0.8802 (ttm170) cc_final: 0.8514 (ttp-110) REVERT: C 658 LEU cc_start: 0.8578 (tp) cc_final: 0.8077 (tp) REVERT: C 661 SER cc_start: 0.8497 (m) cc_final: 0.8221 (p) REVERT: C 663 LYS cc_start: 0.8312 (ptmm) cc_final: 0.7220 (mmtt) REVERT: C 664 ASP cc_start: 0.7983 (m-30) cc_final: 0.6376 (p0) REVERT: C 711 LYS cc_start: 0.9217 (mmtt) cc_final: 0.8690 (mmtm) REVERT: C 712 GLU cc_start: 0.8731 (tt0) cc_final: 0.8143 (tt0) REVERT: C 717 TYR cc_start: 0.8605 (t80) cc_final: 0.8315 (t80) REVERT: C 719 ASP cc_start: 0.8289 (m-30) cc_final: 0.7955 (m-30) REVERT: C 720 TYR cc_start: 0.7823 (t80) cc_final: 0.7054 (t80) REVERT: C 727 GLU cc_start: 0.8030 (pm20) cc_final: 0.7828 (pm20) REVERT: C 730 PHE cc_start: 0.8202 (t80) cc_final: 0.7848 (t80) REVERT: C 738 HIS cc_start: 0.7910 (t-90) cc_final: 0.7654 (t-90) REVERT: C 739 MET cc_start: 0.7963 (ptp) cc_final: 0.7635 (ptp) REVERT: C 743 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8100 (mm-30) REVERT: C 748 TYR cc_start: 0.7441 (t80) cc_final: 0.6971 (t80) REVERT: C 751 ARG cc_start: 0.7890 (mtm-85) cc_final: 0.7623 (mmm-85) REVERT: C 753 GLU cc_start: 0.8673 (mp0) cc_final: 0.8270 (mp0) REVERT: C 791 TRP cc_start: 0.7810 (t60) cc_final: 0.7470 (t60) REVERT: C 805 PHE cc_start: 0.8645 (t80) cc_final: 0.8365 (t80) REVERT: C 855 LYS cc_start: 0.8802 (tttt) cc_final: 0.8230 (tppt) outliers start: 1 outliers final: 1 residues processed: 534 average time/residue: 0.3194 time to fit residues: 231.5022 Evaluate side-chains 512 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 511 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 82 optimal weight: 0.3980 chunk 80 optimal weight: 3.9990 chunk 142 optimal weight: 0.9990 chunk 154 optimal weight: 10.0000 chunk 57 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 119 optimal weight: 0.5980 chunk 98 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 ASN A 576 GLN A 723 ASN ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 723 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.142714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.115149 restraints weight = 30220.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.119823 restraints weight = 18557.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.123283 restraints weight = 12842.633| |-----------------------------------------------------------------------------| r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.4645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13534 Z= 0.137 Angle : 0.626 10.832 18272 Z= 0.316 Chirality : 0.042 0.150 2014 Planarity : 0.004 0.065 2372 Dihedral : 5.218 24.541 1806 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % 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: -1.74 (0.20), residues: 1610 helix: -0.83 (0.17), residues: 818 sheet: -2.97 (0.55), residues: 72 loop : -1.18 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP A 328 HIS 0.003 0.001 HIS A 655 PHE 0.029 0.002 PHE A 790 TYR 0.015 0.002 TYR A 717 ARG 0.008 0.000 ARG C 539 Details of bonding type rmsd hydrogen bonds : bond 0.03899 ( 502) hydrogen bonds : angle 5.18055 ( 1392) metal coordination : bond 0.01318 ( 12) metal coordination : angle 6.02234 ( 12) covalent geometry : bond 0.00270 (13522) covalent geometry : angle 0.60663 (18260) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 534 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 GLN cc_start: 0.8379 (mt0) cc_final: 0.8093 (mt0) REVERT: B 49 VAL cc_start: 0.7183 (t) cc_final: 0.6874 (t) REVERT: B 65 ASN cc_start: 0.8407 (m-40) cc_final: 0.8143 (m-40) REVERT: B 73 CYS cc_start: 0.7299 (m) cc_final: 0.6739 (m) REVERT: B 77 TYR cc_start: 0.8339 (m-80) cc_final: 0.7632 (m-80) REVERT: B 82 GLU cc_start: 0.8668 (tt0) cc_final: 0.8176 (tt0) REVERT: B 88 TYR cc_start: 0.7073 (p90) cc_final: 0.6669 (p90) REVERT: B 108 ILE cc_start: 0.8166 (mt) cc_final: 0.7794 (tt) REVERT: B 132 PHE cc_start: 0.7562 (m-80) cc_final: 0.6878 (m-80) REVERT: B 134 ASN cc_start: 0.7985 (t0) cc_final: 0.7005 (t0) REVERT: A 130 GLU cc_start: 0.8498 (pt0) cc_final: 0.7727 (pm20) REVERT: A 237 ASP cc_start: 0.8501 (m-30) cc_final: 0.7861 (t0) REVERT: A 283 TYR cc_start: 0.7829 (t80) cc_final: 0.7448 (t80) REVERT: A 287 PHE cc_start: 0.7433 (m-80) cc_final: 0.7139 (m-80) REVERT: A 291 MET cc_start: 0.8354 (ttt) cc_final: 0.7926 (ptm) REVERT: A 294 ARG cc_start: 0.8532 (mpt-90) cc_final: 0.8329 (mpt-90) REVERT: A 297 HIS cc_start: 0.7984 (t70) cc_final: 0.7685 (t70) REVERT: A 304 MET cc_start: 0.5126 (tpt) cc_final: 0.4439 (tpt) REVERT: A 330 LYS cc_start: 0.8500 (mmtm) cc_final: 0.8273 (mmtt) REVERT: A 337 ARG cc_start: 0.8209 (ttm170) cc_final: 0.7389 (ttp80) REVERT: A 338 ARG cc_start: 0.8082 (mtp85) cc_final: 0.7510 (mmm-85) REVERT: A 341 GLU cc_start: 0.8411 (mt-10) cc_final: 0.7812 (mt-10) REVERT: A 344 GLN cc_start: 0.8397 (tp-100) cc_final: 0.7360 (tp-100) REVERT: A 347 ILE cc_start: 0.7484 (mt) cc_final: 0.7185 (mm) REVERT: A 350 LYS cc_start: 0.7628 (mmpt) cc_final: 0.7208 (tptt) REVERT: A 392 HIS cc_start: 0.8187 (m90) cc_final: 0.7718 (m90) REVERT: A 407 LEU cc_start: 0.8853 (mt) cc_final: 0.8504 (pp) REVERT: A 408 THR cc_start: 0.8579 (m) cc_final: 0.8354 (p) REVERT: A 410 GLN cc_start: 0.9035 (mm-40) cc_final: 0.8604 (mm-40) REVERT: A 437 LEU cc_start: 0.8266 (mm) cc_final: 0.7866 (tt) REVERT: A 447 GLU cc_start: 0.8153 (mp0) cc_final: 0.7655 (tp30) REVERT: A 449 PHE cc_start: 0.7404 (m-10) cc_final: 0.6902 (m-10) REVERT: A 450 ILE cc_start: 0.7980 (mt) cc_final: 0.7198 (mt) REVERT: A 455 ASN cc_start: 0.8035 (m-40) cc_final: 0.7811 (m110) REVERT: A 458 LEU cc_start: 0.8402 (tp) cc_final: 0.8018 (tt) REVERT: A 459 GLU cc_start: 0.7021 (mp0) cc_final: 0.6705 (mp0) REVERT: A 477 PHE cc_start: 0.8068 (m-80) cc_final: 0.7616 (m-80) REVERT: A 478 MET cc_start: 0.8127 (mtp) cc_final: 0.7376 (mtp) REVERT: A 482 PHE cc_start: 0.7941 (p90) cc_final: 0.7659 (p90) REVERT: A 491 LEU cc_start: 0.8395 (mt) cc_final: 0.8163 (mt) REVERT: A 499 ILE cc_start: 0.7889 (tp) cc_final: 0.7516 (tp) REVERT: A 501 MET cc_start: 0.8271 (mtt) cc_final: 0.7183 (mmt) REVERT: A 502 TYR cc_start: 0.7548 (m-10) cc_final: 0.7292 (m-10) REVERT: A 504 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7718 (mm-30) REVERT: A 505 ARG cc_start: 0.8723 (mtt90) cc_final: 0.8294 (mtt90) REVERT: A 507 ILE cc_start: 0.8660 (mt) cc_final: 0.8173 (mp) REVERT: A 515 GLN cc_start: 0.8242 (mm110) cc_final: 0.7640 (tm-30) REVERT: A 522 TYR cc_start: 0.8198 (m-80) cc_final: 0.7685 (m-80) REVERT: A 523 LEU cc_start: 0.8440 (tp) cc_final: 0.8172 (tp) REVERT: A 530 ASP cc_start: 0.8099 (p0) cc_final: 0.7853 (p0) REVERT: A 532 ILE cc_start: 0.8446 (pt) cc_final: 0.7619 (pt) REVERT: A 542 MET cc_start: 0.8487 (ptt) cc_final: 0.7952 (tmm) REVERT: A 543 ILE cc_start: 0.8942 (mt) cc_final: 0.8387 (mt) REVERT: A 545 MET cc_start: 0.7921 (mtm) cc_final: 0.7301 (mtm) REVERT: A 550 ASP cc_start: 0.7902 (p0) cc_final: 0.7517 (p0) REVERT: A 553 LYS cc_start: 0.8532 (mtmt) cc_final: 0.7767 (mtpp) REVERT: A 560 GLU cc_start: 0.6428 (pm20) cc_final: 0.6146 (pm20) REVERT: A 572 LYS cc_start: 0.8382 (mmtt) cc_final: 0.8177 (mmtt) REVERT: A 573 GLU cc_start: 0.8074 (pp20) cc_final: 0.7566 (pp20) REVERT: A 577 LEU cc_start: 0.8899 (mt) cc_final: 0.8442 (mt) REVERT: A 593 ASP cc_start: 0.8179 (t0) cc_final: 0.7818 (t70) REVERT: A 600 TRP cc_start: 0.8728 (t-100) cc_final: 0.8440 (t-100) REVERT: A 617 ILE cc_start: 0.8498 (mm) cc_final: 0.8043 (mm) REVERT: A 621 LEU cc_start: 0.8056 (mm) cc_final: 0.7619 (mp) REVERT: A 635 MET cc_start: 0.8228 (mpp) cc_final: 0.7422 (mpp) REVERT: A 641 LEU cc_start: 0.8506 (mt) cc_final: 0.8102 (mm) REVERT: A 642 MET cc_start: 0.8130 (mmp) cc_final: 0.7790 (mmp) REVERT: A 648 PHE cc_start: 0.8642 (p90) cc_final: 0.8417 (p90) REVERT: A 651 LEU cc_start: 0.8464 (mt) cc_final: 0.8178 (mt) REVERT: A 658 LEU cc_start: 0.8314 (tp) cc_final: 0.7990 (tp) REVERT: A 660 GLN cc_start: 0.8240 (pp30) cc_final: 0.7757 (pp30) REVERT: A 663 LYS cc_start: 0.8133 (ptmm) cc_final: 0.7603 (ttpp) REVERT: A 667 GLU cc_start: 0.8176 (pp20) cc_final: 0.7855 (pp20) REVERT: A 682 ILE cc_start: 0.8395 (tp) cc_final: 0.8027 (tp) REVERT: A 711 LYS cc_start: 0.9261 (mmtt) cc_final: 0.8795 (mmtm) REVERT: A 712 GLU cc_start: 0.8608 (tt0) cc_final: 0.8050 (tt0) REVERT: A 716 LEU cc_start: 0.8714 (mt) cc_final: 0.8377 (mt) REVERT: A 719 ASP cc_start: 0.8193 (m-30) cc_final: 0.7921 (m-30) REVERT: A 720 TYR cc_start: 0.7767 (t80) cc_final: 0.7112 (t80) REVERT: A 728 LYS cc_start: 0.8311 (ttpt) cc_final: 0.7710 (ptmm) REVERT: A 734 ARG cc_start: 0.8447 (ttt-90) cc_final: 0.7459 (ttm-80) REVERT: A 743 GLU cc_start: 0.8354 (mm-30) cc_final: 0.7700 (mp0) REVERT: A 750 PHE cc_start: 0.8255 (m-80) cc_final: 0.8019 (m-80) REVERT: A 753 GLU cc_start: 0.8650 (mp0) cc_final: 0.8271 (mp0) REVERT: A 756 GLU cc_start: 0.7248 (tp30) cc_final: 0.6975 (tp30) REVERT: A 788 ARG cc_start: 0.8608 (ptt180) cc_final: 0.8220 (ptt180) REVERT: A 792 GLU cc_start: 0.8583 (mm-30) cc_final: 0.7817 (mm-30) REVERT: A 822 LYS cc_start: 0.8491 (mptt) cc_final: 0.8199 (mmtm) REVERT: D 22 LEU cc_start: 0.8222 (mm) cc_final: 0.7925 (mm) REVERT: D 42 GLN cc_start: 0.8416 (mt0) cc_final: 0.8178 (mt0) REVERT: D 65 ASN cc_start: 0.8491 (m-40) cc_final: 0.8045 (m-40) REVERT: D 73 CYS cc_start: 0.7490 (m) cc_final: 0.6893 (m) REVERT: D 79 LYS cc_start: 0.8442 (tppp) cc_final: 0.7054 (tppp) REVERT: D 82 GLU cc_start: 0.8614 (tt0) cc_final: 0.7774 (tt0) REVERT: D 88 TYR cc_start: 0.7066 (p90) cc_final: 0.6660 (p90) REVERT: D 114 GLN cc_start: 0.7803 (mp10) cc_final: 0.7590 (mp10) REVERT: D 132 PHE cc_start: 0.7761 (m-80) cc_final: 0.6778 (m-80) REVERT: D 134 ASN cc_start: 0.7854 (t0) cc_final: 0.7035 (t0) REVERT: D 138 ARG cc_start: 0.7822 (ptt-90) cc_final: 0.6978 (ptt-90) REVERT: D 139 TRP cc_start: 0.7120 (m100) cc_final: 0.6871 (m100) REVERT: C 138 GLU cc_start: 0.8577 (mp0) cc_final: 0.8365 (mm-30) REVERT: C 237 ASP cc_start: 0.7964 (m-30) cc_final: 0.7763 (t0) REVERT: C 241 ARG cc_start: 0.8690 (mtm-85) cc_final: 0.8458 (mtm-85) REVERT: C 270 ASP cc_start: 0.7493 (m-30) cc_final: 0.7168 (t70) REVERT: C 283 TYR cc_start: 0.8339 (t80) cc_final: 0.7907 (t80) REVERT: C 287 PHE cc_start: 0.7562 (m-80) cc_final: 0.7317 (m-80) REVERT: C 288 ILE cc_start: 0.8590 (tt) cc_final: 0.8359 (tt) REVERT: C 291 MET cc_start: 0.8343 (ttt) cc_final: 0.7763 (ttt) REVERT: C 292 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7916 (mm-30) REVERT: C 315 LYS cc_start: 0.7994 (mtmm) cc_final: 0.7534 (ptpp) REVERT: C 321 GLN cc_start: 0.8400 (mt0) cc_final: 0.8152 (mm-40) REVERT: C 326 ARG cc_start: 0.8237 (mtm180) cc_final: 0.7946 (mtm110) REVERT: C 330 LYS cc_start: 0.8704 (mmmt) cc_final: 0.8280 (mmtm) REVERT: C 332 ASN cc_start: 0.7615 (t0) cc_final: 0.7041 (t0) REVERT: C 337 ARG cc_start: 0.8173 (ttm170) cc_final: 0.7731 (tmm-80) REVERT: C 349 TYR cc_start: 0.7984 (t80) cc_final: 0.7674 (t80) REVERT: C 361 LEU cc_start: 0.7129 (tp) cc_final: 0.6648 (tp) REVERT: C 373 LYS cc_start: 0.8051 (ttmt) cc_final: 0.7791 (mtpp) REVERT: C 380 TYR cc_start: 0.8741 (m-10) cc_final: 0.8226 (m-10) REVERT: C 382 ASN cc_start: 0.8500 (m-40) cc_final: 0.8164 (m110) REVERT: C 392 HIS cc_start: 0.8326 (m170) cc_final: 0.7876 (m-70) REVERT: C 394 GLU cc_start: 0.6160 (mm-30) cc_final: 0.5726 (mm-30) REVERT: C 403 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7642 (tm-30) REVERT: C 406 GLU cc_start: 0.8487 (tp30) cc_final: 0.7818 (mt-10) REVERT: C 407 LEU cc_start: 0.8831 (mt) cc_final: 0.8274 (pp) REVERT: C 408 THR cc_start: 0.8562 (m) cc_final: 0.8011 (m) REVERT: C 409 LEU cc_start: 0.8731 (tp) cc_final: 0.8125 (pp) REVERT: C 410 GLN cc_start: 0.8995 (mm-40) cc_final: 0.7696 (mm-40) REVERT: C 411 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7106 (mt-10) REVERT: C 420 LYS cc_start: 0.8016 (pttm) cc_final: 0.7729 (ptmm) REVERT: C 441 LYS cc_start: 0.9097 (tttm) cc_final: 0.8856 (tptp) REVERT: C 447 GLU cc_start: 0.8083 (mp0) cc_final: 0.7494 (tp30) REVERT: C 450 ILE cc_start: 0.8024 (mt) cc_final: 0.7679 (mt) REVERT: C 478 MET cc_start: 0.7852 (mtp) cc_final: 0.7531 (mtp) REVERT: C 482 PHE cc_start: 0.7963 (p90) cc_final: 0.7524 (p90) REVERT: C 493 LEU cc_start: 0.7924 (tp) cc_final: 0.7589 (tp) REVERT: C 495 TYR cc_start: 0.7493 (m-10) cc_final: 0.7268 (m-10) REVERT: C 499 ILE cc_start: 0.8093 (tp) cc_final: 0.7639 (tp) REVERT: C 501 MET cc_start: 0.8223 (mtt) cc_final: 0.7807 (mtt) REVERT: C 502 TYR cc_start: 0.7625 (m-10) cc_final: 0.7196 (m-10) REVERT: C 505 ARG cc_start: 0.8708 (mtt90) cc_final: 0.8181 (mtt90) REVERT: C 507 ILE cc_start: 0.8573 (mt) cc_final: 0.8317 (mp) REVERT: C 522 TYR cc_start: 0.8121 (m-80) cc_final: 0.7578 (m-80) REVERT: C 530 ASP cc_start: 0.8032 (p0) cc_final: 0.7824 (p0) REVERT: C 539 ARG cc_start: 0.8444 (ttm-80) cc_final: 0.8206 (ttm-80) REVERT: C 540 LEU cc_start: 0.8909 (mm) cc_final: 0.8692 (mm) REVERT: C 542 MET cc_start: 0.8147 (tpp) cc_final: 0.7410 (tpp) REVERT: C 545 MET cc_start: 0.7843 (mtm) cc_final: 0.7170 (mtm) REVERT: C 551 LEU cc_start: 0.8850 (mp) cc_final: 0.8580 (mp) REVERT: C 553 LYS cc_start: 0.8444 (mtmt) cc_final: 0.8144 (mtpp) REVERT: C 555 LEU cc_start: 0.8545 (tp) cc_final: 0.8198 (tp) REVERT: C 576 GLN cc_start: 0.7819 (tm-30) cc_final: 0.7367 (tm-30) REVERT: C 577 LEU cc_start: 0.8756 (mt) cc_final: 0.8376 (mt) REVERT: C 587 ILE cc_start: 0.8248 (tp) cc_final: 0.7931 (tp) REVERT: C 589 MET cc_start: 0.6750 (mtp) cc_final: 0.6374 (mtp) REVERT: C 593 ASP cc_start: 0.7889 (t70) cc_final: 0.7620 (t70) REVERT: C 594 GLU cc_start: 0.8645 (mp0) cc_final: 0.8442 (mp0) REVERT: C 617 ILE cc_start: 0.8643 (mm) cc_final: 0.8403 (mm) REVERT: C 619 LEU cc_start: 0.8775 (tp) cc_final: 0.8505 (tp) REVERT: C 621 LEU cc_start: 0.8211 (mm) cc_final: 0.7757 (mm) REVERT: C 625 ASN cc_start: 0.8532 (m110) cc_final: 0.8141 (m110) REVERT: C 626 ASN cc_start: 0.8009 (m-40) cc_final: 0.7705 (m110) REVERT: C 630 ASP cc_start: 0.7262 (t70) cc_final: 0.7007 (t0) REVERT: C 635 MET cc_start: 0.8099 (mpp) cc_final: 0.7433 (mpp) REVERT: C 641 LEU cc_start: 0.8540 (mt) cc_final: 0.8128 (mm) REVERT: C 642 MET cc_start: 0.8113 (mmp) cc_final: 0.7787 (mmp) REVERT: C 649 ARG cc_start: 0.8757 (ttm170) cc_final: 0.8464 (mtp85) REVERT: C 658 LEU cc_start: 0.8472 (tp) cc_final: 0.8191 (tp) REVERT: C 659 TYR cc_start: 0.8660 (t80) cc_final: 0.8011 (t80) REVERT: C 663 LYS cc_start: 0.8230 (ptmm) cc_final: 0.7443 (mmtm) REVERT: C 667 GLU cc_start: 0.7985 (pp20) cc_final: 0.7713 (pp20) REVERT: C 711 LYS cc_start: 0.9270 (mmtt) cc_final: 0.8754 (mmtm) REVERT: C 712 GLU cc_start: 0.8709 (tt0) cc_final: 0.8197 (tt0) REVERT: C 717 TYR cc_start: 0.8869 (t80) cc_final: 0.8650 (t80) REVERT: C 719 ASP cc_start: 0.8252 (m-30) cc_final: 0.7892 (p0) REVERT: C 720 TYR cc_start: 0.7830 (t80) cc_final: 0.7196 (t80) REVERT: C 724 LYS cc_start: 0.8184 (ptpp) cc_final: 0.7690 (mtmm) REVERT: C 727 GLU cc_start: 0.8010 (pm20) cc_final: 0.7759 (pm20) REVERT: C 730 PHE cc_start: 0.8192 (t80) cc_final: 0.7910 (t80) REVERT: C 734 ARG cc_start: 0.8764 (ttt-90) cc_final: 0.8458 (ttm170) REVERT: C 739 MET cc_start: 0.7938 (ptp) cc_final: 0.7592 (ptp) REVERT: C 743 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8096 (mm-30) REVERT: C 748 TYR cc_start: 0.7409 (t80) cc_final: 0.6913 (t80) REVERT: C 754 GLU cc_start: 0.8541 (mt-10) cc_final: 0.7934 (mp0) REVERT: C 788 ARG cc_start: 0.8576 (ptt180) cc_final: 0.7993 (ptt180) REVERT: C 791 TRP cc_start: 0.7776 (t60) cc_final: 0.7508 (t60) REVERT: C 792 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7983 (mm-30) REVERT: C 805 PHE cc_start: 0.8594 (t80) cc_final: 0.8336 (t80) REVERT: C 822 LYS cc_start: 0.8530 (mmtt) cc_final: 0.8239 (mmtm) REVERT: C 855 LYS cc_start: 0.8907 (tttt) cc_final: 0.8163 (tppt) outliers start: 0 outliers final: 0 residues processed: 534 average time/residue: 0.3277 time to fit residues: 234.0245 Evaluate side-chains 515 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 515 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 152 optimal weight: 0.9990 chunk 1 optimal weight: 0.0970 chunk 115 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 153 optimal weight: 8.9990 chunk 83 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 130 optimal weight: 0.4980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 114 GLN ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 ASN ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 ASN ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 ASN ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 363 ASN C 723 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.143577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.115831 restraints weight = 29893.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.120475 restraints weight = 18498.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.123892 restraints weight = 12853.857| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.5017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13534 Z= 0.125 Angle : 0.613 12.017 18272 Z= 0.309 Chirality : 0.043 0.170 2014 Planarity : 0.004 0.062 2372 Dihedral : 5.004 19.664 1806 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.07 % Allowed : 1.79 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.20), residues: 1610 helix: -0.47 (0.18), residues: 802 sheet: -2.69 (0.58), residues: 72 loop : -1.04 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.004 TRP A 328 HIS 0.004 0.001 HIS A 655 PHE 0.023 0.001 PHE A 790 TYR 0.019 0.001 TYR A 494 ARG 0.009 0.000 ARG B 84 Details of bonding type rmsd hydrogen bonds : bond 0.03685 ( 502) hydrogen bonds : angle 5.06749 ( 1392) metal coordination : bond 0.00513 ( 12) metal coordination : angle 4.43707 ( 12) covalent geometry : bond 0.00256 (13522) covalent geometry : angle 0.60278 (18260) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 526 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 LEU cc_start: 0.8167 (mm) cc_final: 0.7822 (mm) REVERT: B 42 GLN cc_start: 0.8146 (mt0) cc_final: 0.7923 (mt0) REVERT: B 65 ASN cc_start: 0.8297 (m-40) cc_final: 0.7907 (m-40) REVERT: B 73 CYS cc_start: 0.6568 (m) cc_final: 0.6220 (m) REVERT: B 77 TYR cc_start: 0.8183 (m-80) cc_final: 0.7720 (m-80) REVERT: B 82 GLU cc_start: 0.8720 (tt0) cc_final: 0.8301 (tt0) REVERT: B 88 TYR cc_start: 0.7036 (p90) cc_final: 0.6782 (p90) REVERT: B 108 ILE cc_start: 0.8135 (mt) cc_final: 0.7713 (tt) REVERT: B 114 GLN cc_start: 0.7730 (mp10) cc_final: 0.7497 (mp10) REVERT: B 124 ARG cc_start: 0.8657 (ttt-90) cc_final: 0.8384 (ttt-90) REVERT: B 132 PHE cc_start: 0.7744 (m-80) cc_final: 0.6978 (m-80) REVERT: A 130 GLU cc_start: 0.8464 (pt0) cc_final: 0.7641 (pm20) REVERT: A 138 GLU cc_start: 0.8475 (mp0) cc_final: 0.7943 (mp0) REVERT: A 237 ASP cc_start: 0.8530 (m-30) cc_final: 0.7911 (t0) REVERT: A 283 TYR cc_start: 0.7736 (t80) cc_final: 0.7505 (t80) REVERT: A 287 PHE cc_start: 0.7419 (m-80) cc_final: 0.7122 (m-80) REVERT: A 288 ILE cc_start: 0.8613 (tt) cc_final: 0.8394 (tt) REVERT: A 291 MET cc_start: 0.8468 (ttt) cc_final: 0.7950 (ptm) REVERT: A 294 ARG cc_start: 0.8554 (mpt-90) cc_final: 0.8350 (mpt-90) REVERT: A 304 MET cc_start: 0.5100 (tpt) cc_final: 0.4344 (tpt) REVERT: A 332 ASN cc_start: 0.7676 (t0) cc_final: 0.7280 (t0) REVERT: A 337 ARG cc_start: 0.8247 (ttm170) cc_final: 0.7325 (ttp80) REVERT: A 338 ARG cc_start: 0.8079 (mtp85) cc_final: 0.7711 (mmm-85) REVERT: A 341 GLU cc_start: 0.8455 (mt-10) cc_final: 0.7923 (mt-10) REVERT: A 344 GLN cc_start: 0.8461 (tp-100) cc_final: 0.7487 (tp-100) REVERT: A 345 GLN cc_start: 0.8282 (mt0) cc_final: 0.7974 (mt0) REVERT: A 350 LYS cc_start: 0.7635 (mmpt) cc_final: 0.7259 (tptt) REVERT: A 392 HIS cc_start: 0.8218 (m90) cc_final: 0.7712 (m90) REVERT: A 407 LEU cc_start: 0.8891 (mt) cc_final: 0.8387 (pp) REVERT: A 411 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7211 (mt-10) REVERT: A 437 LEU cc_start: 0.8270 (mm) cc_final: 0.7869 (tt) REVERT: A 447 GLU cc_start: 0.8112 (mp0) cc_final: 0.7632 (tp30) REVERT: A 449 PHE cc_start: 0.7308 (m-10) cc_final: 0.6739 (m-10) REVERT: A 450 ILE cc_start: 0.8022 (mt) cc_final: 0.7258 (mt) REVERT: A 458 LEU cc_start: 0.8381 (tp) cc_final: 0.8098 (tt) REVERT: A 459 GLU cc_start: 0.7105 (mp0) cc_final: 0.6774 (mp0) REVERT: A 477 PHE cc_start: 0.8032 (m-80) cc_final: 0.7689 (m-80) REVERT: A 478 MET cc_start: 0.8095 (mtp) cc_final: 0.7331 (mtp) REVERT: A 482 PHE cc_start: 0.7976 (p90) cc_final: 0.7670 (p90) REVERT: A 499 ILE cc_start: 0.7895 (tp) cc_final: 0.7587 (tp) REVERT: A 502 TYR cc_start: 0.7518 (m-10) cc_final: 0.7260 (m-10) REVERT: A 504 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7478 (mm-30) REVERT: A 505 ARG cc_start: 0.8769 (mtt90) cc_final: 0.8170 (mtt90) REVERT: A 507 ILE cc_start: 0.8639 (mt) cc_final: 0.8217 (mt) REVERT: A 515 GLN cc_start: 0.8199 (mm110) cc_final: 0.7762 (tm-30) REVERT: A 522 TYR cc_start: 0.8209 (m-80) cc_final: 0.7673 (m-80) REVERT: A 523 LEU cc_start: 0.8416 (tp) cc_final: 0.8156 (tp) REVERT: A 530 ASP cc_start: 0.7984 (p0) cc_final: 0.7703 (p0) REVERT: A 533 ILE cc_start: 0.8317 (pt) cc_final: 0.7713 (mp) REVERT: A 539 ARG cc_start: 0.8514 (ttm-80) cc_final: 0.7944 (ptm160) REVERT: A 540 LEU cc_start: 0.8979 (mm) cc_final: 0.8666 (mm) REVERT: A 542 MET cc_start: 0.8389 (ptt) cc_final: 0.7770 (tmm) REVERT: A 545 MET cc_start: 0.7823 (mtm) cc_final: 0.7194 (mtm) REVERT: A 550 ASP cc_start: 0.7869 (p0) cc_final: 0.7485 (p0) REVERT: A 553 LYS cc_start: 0.8489 (mtmt) cc_final: 0.8161 (mtpp) REVERT: A 572 LYS cc_start: 0.8364 (mmtt) cc_final: 0.8134 (mmtt) REVERT: A 573 GLU cc_start: 0.8084 (pp20) cc_final: 0.7613 (pp20) REVERT: A 576 GLN cc_start: 0.8447 (tp40) cc_final: 0.7782 (tp40) REVERT: A 577 LEU cc_start: 0.8839 (mt) cc_final: 0.8634 (mt) REVERT: A 593 ASP cc_start: 0.8222 (t0) cc_final: 0.7835 (t70) REVERT: A 600 TRP cc_start: 0.8718 (t-100) cc_final: 0.8460 (t-100) REVERT: A 603 PRO cc_start: 0.7250 (Cg_endo) cc_final: 0.6880 (Cg_exo) REVERT: A 617 ILE cc_start: 0.8487 (mm) cc_final: 0.8106 (mm) REVERT: A 630 ASP cc_start: 0.7396 (t0) cc_final: 0.7170 (t0) REVERT: A 635 MET cc_start: 0.8249 (mpp) cc_final: 0.7484 (mpp) REVERT: A 641 LEU cc_start: 0.8495 (mt) cc_final: 0.8191 (mt) REVERT: A 642 MET cc_start: 0.8166 (mmp) cc_final: 0.7796 (mmp) REVERT: A 651 LEU cc_start: 0.8456 (mt) cc_final: 0.8176 (mt) REVERT: A 658 LEU cc_start: 0.8274 (tp) cc_final: 0.7927 (tp) REVERT: A 663 LYS cc_start: 0.8243 (ptmm) cc_final: 0.7712 (ttpp) REVERT: A 667 GLU cc_start: 0.8206 (pp20) cc_final: 0.7904 (pp20) REVERT: A 682 ILE cc_start: 0.8337 (tp) cc_final: 0.7983 (tp) REVERT: A 711 LYS cc_start: 0.9289 (mmtt) cc_final: 0.8838 (mmtm) REVERT: A 712 GLU cc_start: 0.8604 (tt0) cc_final: 0.8067 (tt0) REVERT: A 716 LEU cc_start: 0.8700 (mt) cc_final: 0.8385 (mt) REVERT: A 717 TYR cc_start: 0.8882 (t80) cc_final: 0.8377 (t80) REVERT: A 719 ASP cc_start: 0.8195 (m-30) cc_final: 0.7888 (m-30) REVERT: A 720 TYR cc_start: 0.7853 (t80) cc_final: 0.7243 (t80) REVERT: A 727 GLU cc_start: 0.7939 (pm20) cc_final: 0.7633 (pm20) REVERT: A 734 ARG cc_start: 0.8455 (ttt-90) cc_final: 0.7517 (ttm-80) REVERT: A 738 HIS cc_start: 0.8185 (t70) cc_final: 0.7900 (t-170) REVERT: A 743 GLU cc_start: 0.8385 (mm-30) cc_final: 0.7716 (mp0) REVERT: A 750 PHE cc_start: 0.8273 (m-80) cc_final: 0.8050 (m-80) REVERT: A 753 GLU cc_start: 0.8622 (mp0) cc_final: 0.8257 (mp0) REVERT: A 788 ARG cc_start: 0.8608 (ptt180) cc_final: 0.7968 (ptt180) REVERT: A 792 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8126 (mm-30) REVERT: A 805 PHE cc_start: 0.8703 (t80) cc_final: 0.8427 (t80) REVERT: A 806 LEU cc_start: 0.8192 (mt) cc_final: 0.7874 (mt) REVERT: A 822 LYS cc_start: 0.8486 (mptt) cc_final: 0.8159 (mmtm) REVERT: D 22 LEU cc_start: 0.8205 (mm) cc_final: 0.7815 (mm) REVERT: D 42 GLN cc_start: 0.8417 (mt0) cc_final: 0.8186 (mt0) REVERT: D 65 ASN cc_start: 0.8381 (m-40) cc_final: 0.7942 (m-40) REVERT: D 73 CYS cc_start: 0.6895 (m) cc_final: 0.6518 (m) REVERT: D 79 LYS cc_start: 0.8480 (tppp) cc_final: 0.7064 (tppp) REVERT: D 80 ILE cc_start: 0.8580 (mm) cc_final: 0.8365 (mm) REVERT: D 82 GLU cc_start: 0.8681 (tt0) cc_final: 0.7816 (tt0) REVERT: D 114 GLN cc_start: 0.7965 (mp10) cc_final: 0.7593 (mp10) REVERT: D 132 PHE cc_start: 0.7796 (m-80) cc_final: 0.6803 (m-80) REVERT: D 134 ASN cc_start: 0.7913 (t0) cc_final: 0.7139 (t0) REVERT: D 138 ARG cc_start: 0.7934 (ptt-90) cc_final: 0.7250 (ptt-90) REVERT: C 130 GLU cc_start: 0.8386 (pt0) cc_final: 0.7691 (pm20) REVERT: C 138 GLU cc_start: 0.8605 (mp0) cc_final: 0.8181 (mp0) REVERT: C 241 ARG cc_start: 0.8705 (mtm-85) cc_final: 0.8457 (mtm-85) REVERT: C 287 PHE cc_start: 0.7678 (m-80) cc_final: 0.7416 (m-80) REVERT: C 291 MET cc_start: 0.8473 (ttt) cc_final: 0.7638 (ttt) REVERT: C 292 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7982 (mm-30) REVERT: C 304 MET cc_start: 0.5472 (tpt) cc_final: 0.5170 (tpt) REVERT: C 315 LYS cc_start: 0.7959 (mtmm) cc_final: 0.7463 (ptpp) REVERT: C 321 GLN cc_start: 0.8420 (mt0) cc_final: 0.8143 (mm-40) REVERT: C 326 ARG cc_start: 0.8215 (mtm180) cc_final: 0.7873 (mtm110) REVERT: C 330 LYS cc_start: 0.8714 (mmmt) cc_final: 0.8286 (mmtm) REVERT: C 332 ASN cc_start: 0.7630 (t0) cc_final: 0.7192 (t0) REVERT: C 337 ARG cc_start: 0.8204 (ttm170) cc_final: 0.7716 (tmm-80) REVERT: C 349 TYR cc_start: 0.7958 (t80) cc_final: 0.7751 (t80) REVERT: C 373 LYS cc_start: 0.8070 (ttmt) cc_final: 0.7833 (mtpp) REVERT: C 382 ASN cc_start: 0.8464 (m-40) cc_final: 0.8165 (m110) REVERT: C 392 HIS cc_start: 0.8348 (m170) cc_final: 0.7950 (m-70) REVERT: C 397 ASP cc_start: 0.7863 (t0) cc_final: 0.7252 (t0) REVERT: C 398 GLU cc_start: 0.8147 (pp20) cc_final: 0.7830 (pm20) REVERT: C 403 GLU cc_start: 0.8004 (tm-30) cc_final: 0.7711 (tm-30) REVERT: C 406 GLU cc_start: 0.8521 (tp30) cc_final: 0.7701 (mt-10) REVERT: C 407 LEU cc_start: 0.8787 (mt) cc_final: 0.8273 (pp) REVERT: C 410 GLN cc_start: 0.9043 (mm-40) cc_final: 0.8159 (mm110) REVERT: C 411 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7048 (mt-10) REVERT: C 420 LYS cc_start: 0.7965 (pttm) cc_final: 0.7701 (ptmm) REVERT: C 447 GLU cc_start: 0.8083 (mp0) cc_final: 0.7492 (tp30) REVERT: C 450 ILE cc_start: 0.8020 (mt) cc_final: 0.7727 (mt) REVERT: C 458 LEU cc_start: 0.8551 (tp) cc_final: 0.8205 (tp) REVERT: C 478 MET cc_start: 0.8067 (mtp) cc_final: 0.7459 (mtp) REVERT: C 482 PHE cc_start: 0.8021 (p90) cc_final: 0.7668 (p90) REVERT: C 495 TYR cc_start: 0.7591 (m-10) cc_final: 0.7374 (m-10) REVERT: C 499 ILE cc_start: 0.8067 (tp) cc_final: 0.7630 (tp) REVERT: C 501 MET cc_start: 0.8206 (mtt) cc_final: 0.7837 (mtt) REVERT: C 502 TYR cc_start: 0.7633 (m-10) cc_final: 0.7212 (m-10) REVERT: C 505 ARG cc_start: 0.8764 (mtt90) cc_final: 0.8213 (mtt90) REVERT: C 507 ILE cc_start: 0.8550 (mt) cc_final: 0.8301 (mp) REVERT: C 522 TYR cc_start: 0.8075 (m-80) cc_final: 0.7464 (m-80) REVERT: C 530 ASP cc_start: 0.7972 (p0) cc_final: 0.7729 (p0) REVERT: C 539 ARG cc_start: 0.8482 (ttm-80) cc_final: 0.7974 (ttm-80) REVERT: C 540 LEU cc_start: 0.8951 (mm) cc_final: 0.8732 (mm) REVERT: C 542 MET cc_start: 0.8162 (tpp) cc_final: 0.7451 (tpp) REVERT: C 543 ILE cc_start: 0.8872 (mt) cc_final: 0.8655 (mt) REVERT: C 545 MET cc_start: 0.7879 (mtm) cc_final: 0.7204 (mtm) REVERT: C 551 LEU cc_start: 0.8842 (mp) cc_final: 0.8553 (mp) REVERT: C 553 LYS cc_start: 0.8430 (mtmt) cc_final: 0.8135 (mtpp) REVERT: C 555 LEU cc_start: 0.8569 (tp) cc_final: 0.8220 (tp) REVERT: C 573 GLU cc_start: 0.8048 (pm20) cc_final: 0.7742 (pp20) REVERT: C 576 GLN cc_start: 0.7865 (tm-30) cc_final: 0.7398 (tm-30) REVERT: C 577 LEU cc_start: 0.8684 (mt) cc_final: 0.8120 (mt) REVERT: C 587 ILE cc_start: 0.8135 (tp) cc_final: 0.7801 (tp) REVERT: C 589 MET cc_start: 0.6680 (mtp) cc_final: 0.6269 (mtp) REVERT: C 593 ASP cc_start: 0.7933 (t70) cc_final: 0.7663 (t70) REVERT: C 594 GLU cc_start: 0.8641 (mp0) cc_final: 0.8439 (mp0) REVERT: C 617 ILE cc_start: 0.8613 (mm) cc_final: 0.8343 (mm) REVERT: C 619 LEU cc_start: 0.8828 (tp) cc_final: 0.8572 (tp) REVERT: C 621 LEU cc_start: 0.8207 (mm) cc_final: 0.7744 (mm) REVERT: C 625 ASN cc_start: 0.8556 (m110) cc_final: 0.8187 (m110) REVERT: C 626 ASN cc_start: 0.8032 (m110) cc_final: 0.7729 (m110) REVERT: C 630 ASP cc_start: 0.7312 (t70) cc_final: 0.7037 (t0) REVERT: C 635 MET cc_start: 0.8136 (mpp) cc_final: 0.7482 (mpp) REVERT: C 641 LEU cc_start: 0.8522 (mt) cc_final: 0.8218 (mm) REVERT: C 642 MET cc_start: 0.8115 (mmp) cc_final: 0.7742 (mmp) REVERT: C 649 ARG cc_start: 0.8807 (ttm170) cc_final: 0.8527 (mtp85) REVERT: C 651 LEU cc_start: 0.8338 (mp) cc_final: 0.8119 (mm) REVERT: C 658 LEU cc_start: 0.8478 (tp) cc_final: 0.8119 (tt) REVERT: C 661 SER cc_start: 0.8588 (m) cc_final: 0.8344 (p) REVERT: C 663 LYS cc_start: 0.8152 (ptmm) cc_final: 0.7646 (ttpp) REVERT: C 667 GLU cc_start: 0.8000 (pp20) cc_final: 0.7707 (pp20) REVERT: C 692 MET cc_start: 0.7310 (ttm) cc_final: 0.7104 (ttm) REVERT: C 711 LYS cc_start: 0.9280 (mmtt) cc_final: 0.8776 (mmtm) REVERT: C 712 GLU cc_start: 0.8671 (tt0) cc_final: 0.8145 (tt0) REVERT: C 717 TYR cc_start: 0.8907 (t80) cc_final: 0.8649 (t80) REVERT: C 719 ASP cc_start: 0.8288 (m-30) cc_final: 0.7818 (p0) REVERT: C 720 TYR cc_start: 0.7865 (t80) cc_final: 0.7335 (t80) REVERT: C 724 LYS cc_start: 0.8141 (ptpp) cc_final: 0.7606 (mtmm) REVERT: C 727 GLU cc_start: 0.8084 (pm20) cc_final: 0.7835 (pm20) REVERT: C 734 ARG cc_start: 0.8771 (ttt-90) cc_final: 0.8424 (ttm170) REVERT: C 739 MET cc_start: 0.7865 (ptp) cc_final: 0.7526 (ptp) REVERT: C 743 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8155 (mm-30) REVERT: C 747 LYS cc_start: 0.9092 (mtmt) cc_final: 0.8883 (mmmt) REVERT: C 748 TYR cc_start: 0.7391 (t80) cc_final: 0.6857 (t80) REVERT: C 788 ARG cc_start: 0.8530 (ptt180) cc_final: 0.7591 (ptt180) REVERT: C 789 GLU cc_start: 0.8032 (pt0) cc_final: 0.7800 (mt-10) REVERT: C 822 LYS cc_start: 0.8541 (mmtt) cc_final: 0.8188 (mmtm) REVERT: C 855 LYS cc_start: 0.8882 (tttt) cc_final: 0.7867 (tptt) outliers start: 1 outliers final: 0 residues processed: 527 average time/residue: 0.3275 time to fit residues: 231.9556 Evaluate side-chains 507 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 507 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 62 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 126 optimal weight: 0.5980 chunk 151 optimal weight: 0.0030 chunk 95 optimal weight: 0.6980 chunk 141 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 118 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 ASN ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 ASN ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 723 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.142899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.115083 restraints weight = 30059.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.119728 restraints weight = 18485.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.123138 restraints weight = 12823.295| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.5401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13534 Z= 0.120 Angle : 0.606 9.768 18272 Z= 0.305 Chirality : 0.043 0.211 2014 Planarity : 0.004 0.040 2372 Dihedral : 4.860 19.849 1806 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.20), residues: 1610 helix: -0.34 (0.18), residues: 810 sheet: -2.53 (0.58), residues: 72 loop : -1.08 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 TRP A 328 HIS 0.005 0.001 HIS C 738 PHE 0.016 0.001 PHE A 790 TYR 0.019 0.001 TYR A 464 ARG 0.008 0.000 ARG B 84 Details of bonding type rmsd hydrogen bonds : bond 0.03540 ( 502) hydrogen bonds : angle 4.94377 ( 1392) metal coordination : bond 0.00413 ( 12) metal coordination : angle 3.87213 ( 12) covalent geometry : bond 0.00249 (13522) covalent geometry : angle 0.59786 (18260) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 522 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 LEU cc_start: 0.8192 (mm) cc_final: 0.7851 (mm) REVERT: B 65 ASN cc_start: 0.8309 (m-40) cc_final: 0.7953 (m-40) REVERT: B 73 CYS cc_start: 0.6095 (m) cc_final: 0.5780 (m) REVERT: B 77 TYR cc_start: 0.8126 (m-80) cc_final: 0.7640 (m-80) REVERT: B 82 GLU cc_start: 0.8726 (tt0) cc_final: 0.8344 (tt0) REVERT: B 88 TYR cc_start: 0.6804 (p90) cc_final: 0.6419 (p90) REVERT: B 108 ILE cc_start: 0.8176 (mt) cc_final: 0.7795 (tt) REVERT: B 114 GLN cc_start: 0.7840 (mp10) cc_final: 0.7499 (mp10) REVERT: B 124 ARG cc_start: 0.8685 (ttt-90) cc_final: 0.8405 (ttt-90) REVERT: B 132 PHE cc_start: 0.7777 (m-80) cc_final: 0.6929 (m-80) REVERT: B 136 ARG cc_start: 0.8090 (mmm160) cc_final: 0.7290 (mmm160) REVERT: B 139 TRP cc_start: 0.6969 (m100) cc_final: 0.6586 (m100) REVERT: A 130 GLU cc_start: 0.8430 (pt0) cc_final: 0.7572 (pm20) REVERT: A 237 ASP cc_start: 0.8533 (m-30) cc_final: 0.7934 (t0) REVERT: A 283 TYR cc_start: 0.7657 (t80) cc_final: 0.7455 (t80) REVERT: A 287 PHE cc_start: 0.7385 (m-80) cc_final: 0.7028 (m-80) REVERT: A 291 MET cc_start: 0.8492 (ttt) cc_final: 0.8192 (ttt) REVERT: A 294 ARG cc_start: 0.8521 (mpt-90) cc_final: 0.8303 (mpt-90) REVERT: A 304 MET cc_start: 0.4872 (tpt) cc_final: 0.4111 (tpt) REVERT: A 315 LYS cc_start: 0.8108 (mmtm) cc_final: 0.7532 (mttm) REVERT: A 330 LYS cc_start: 0.8522 (mmtm) cc_final: 0.8305 (mptt) REVERT: A 332 ASN cc_start: 0.7572 (t0) cc_final: 0.7026 (t0) REVERT: A 337 ARG cc_start: 0.8234 (ttm170) cc_final: 0.7166 (ttp80) REVERT: A 338 ARG cc_start: 0.8145 (mtp85) cc_final: 0.7810 (mmm-85) REVERT: A 341 GLU cc_start: 0.8415 (mt-10) cc_final: 0.7804 (mt-10) REVERT: A 344 GLN cc_start: 0.8509 (tp-100) cc_final: 0.7521 (tp-100) REVERT: A 347 ILE cc_start: 0.7517 (mt) cc_final: 0.7257 (mm) REVERT: A 350 LYS cc_start: 0.7613 (mmpt) cc_final: 0.7274 (tptt) REVERT: A 392 HIS cc_start: 0.8138 (m90) cc_final: 0.7684 (m90) REVERT: A 407 LEU cc_start: 0.8909 (mt) cc_final: 0.8488 (pp) REVERT: A 408 THR cc_start: 0.8677 (m) cc_final: 0.8150 (p) REVERT: A 410 GLN cc_start: 0.8911 (mm-40) cc_final: 0.8138 (mm-40) REVERT: A 411 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7272 (mt-10) REVERT: A 424 ARG cc_start: 0.7785 (mmm-85) cc_final: 0.7078 (tpp80) REVERT: A 437 LEU cc_start: 0.8272 (mm) cc_final: 0.7871 (tt) REVERT: A 446 PHE cc_start: 0.7556 (m-80) cc_final: 0.7299 (m-80) REVERT: A 447 GLU cc_start: 0.8079 (mp0) cc_final: 0.7648 (tp30) REVERT: A 449 PHE cc_start: 0.7307 (m-10) cc_final: 0.6767 (m-10) REVERT: A 450 ILE cc_start: 0.8110 (mt) cc_final: 0.7177 (mt) REVERT: A 455 ASN cc_start: 0.7962 (m-40) cc_final: 0.7722 (m-40) REVERT: A 458 LEU cc_start: 0.8434 (tp) cc_final: 0.7970 (tt) REVERT: A 459 GLU cc_start: 0.7100 (mp0) cc_final: 0.6751 (mp0) REVERT: A 477 PHE cc_start: 0.8007 (m-80) cc_final: 0.7515 (m-80) REVERT: A 478 MET cc_start: 0.8120 (mtp) cc_final: 0.7369 (mtp) REVERT: A 482 PHE cc_start: 0.7988 (p90) cc_final: 0.7568 (p90) REVERT: A 497 ASN cc_start: 0.8006 (m-40) cc_final: 0.7683 (m-40) REVERT: A 499 ILE cc_start: 0.7835 (tp) cc_final: 0.7587 (tp) REVERT: A 501 MET cc_start: 0.7641 (mtt) cc_final: 0.7214 (mmt) REVERT: A 502 TYR cc_start: 0.7588 (m-10) cc_final: 0.7292 (m-10) REVERT: A 504 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7563 (mm-30) REVERT: A 505 ARG cc_start: 0.8748 (mtt90) cc_final: 0.8199 (mtt90) REVERT: A 507 ILE cc_start: 0.8686 (mt) cc_final: 0.8252 (mt) REVERT: A 515 GLN cc_start: 0.8215 (mm110) cc_final: 0.7770 (tm-30) REVERT: A 522 TYR cc_start: 0.8211 (m-80) cc_final: 0.7657 (m-80) REVERT: A 530 ASP cc_start: 0.8101 (p0) cc_final: 0.7892 (p0) REVERT: A 533 ILE cc_start: 0.8454 (pt) cc_final: 0.8134 (mp) REVERT: A 539 ARG cc_start: 0.8535 (ttm-80) cc_final: 0.7941 (ptm-80) REVERT: A 540 LEU cc_start: 0.9058 (mm) cc_final: 0.8722 (mm) REVERT: A 542 MET cc_start: 0.8414 (ptt) cc_final: 0.7695 (tmm) REVERT: A 545 MET cc_start: 0.7733 (mtm) cc_final: 0.7172 (mtm) REVERT: A 550 ASP cc_start: 0.7855 (p0) cc_final: 0.7483 (p0) REVERT: A 553 LYS cc_start: 0.8406 (mtmt) cc_final: 0.8111 (mtpp) REVERT: A 555 LEU cc_start: 0.8511 (tp) cc_final: 0.8260 (tp) REVERT: A 572 LYS cc_start: 0.8273 (mmtt) cc_final: 0.7767 (mmtt) REVERT: A 573 GLU cc_start: 0.8047 (pp20) cc_final: 0.7840 (pp20) REVERT: A 576 GLN cc_start: 0.8374 (tp40) cc_final: 0.7651 (tp40) REVERT: A 593 ASP cc_start: 0.8210 (t0) cc_final: 0.7761 (t70) REVERT: A 600 TRP cc_start: 0.8750 (t-100) cc_final: 0.8505 (t-100) REVERT: A 603 PRO cc_start: 0.7312 (Cg_endo) cc_final: 0.6950 (Cg_exo) REVERT: A 619 LEU cc_start: 0.8857 (tp) cc_final: 0.8539 (tp) REVERT: A 625 ASN cc_start: 0.7746 (p0) cc_final: 0.7491 (p0) REVERT: A 630 ASP cc_start: 0.7343 (t0) cc_final: 0.7100 (t0) REVERT: A 635 MET cc_start: 0.8234 (mpp) cc_final: 0.7358 (mpp) REVERT: A 641 LEU cc_start: 0.8517 (mt) cc_final: 0.8150 (mt) REVERT: A 642 MET cc_start: 0.8172 (mmp) cc_final: 0.7800 (mmp) REVERT: A 648 PHE cc_start: 0.8658 (p90) cc_final: 0.8120 (p90) REVERT: A 651 LEU cc_start: 0.8457 (mt) cc_final: 0.8123 (mt) REVERT: A 660 GLN cc_start: 0.8184 (pp30) cc_final: 0.7704 (pp30) REVERT: A 663 LYS cc_start: 0.8199 (ptmm) cc_final: 0.7602 (mptt) REVERT: A 667 GLU cc_start: 0.8193 (pp20) cc_final: 0.7888 (pp20) REVERT: A 682 ILE cc_start: 0.8272 (tp) cc_final: 0.7906 (tp) REVERT: A 711 LYS cc_start: 0.9290 (mmtt) cc_final: 0.8910 (mmtm) REVERT: A 712 GLU cc_start: 0.8596 (tt0) cc_final: 0.8116 (tt0) REVERT: A 715 ASN cc_start: 0.8688 (m110) cc_final: 0.8473 (m-40) REVERT: A 716 LEU cc_start: 0.8738 (mt) cc_final: 0.8473 (mp) REVERT: A 717 TYR cc_start: 0.8854 (t80) cc_final: 0.7999 (t80) REVERT: A 720 TYR cc_start: 0.7831 (t80) cc_final: 0.7302 (t80) REVERT: A 727 GLU cc_start: 0.7911 (pm20) cc_final: 0.7571 (pm20) REVERT: A 728 LYS cc_start: 0.8367 (ttpt) cc_final: 0.7608 (tmtt) REVERT: A 734 ARG cc_start: 0.8429 (ttt-90) cc_final: 0.7550 (ttm-80) REVERT: A 738 HIS cc_start: 0.8163 (t70) cc_final: 0.7868 (t-170) REVERT: A 739 MET cc_start: 0.8127 (ptm) cc_final: 0.7923 (ptm) REVERT: A 743 GLU cc_start: 0.8395 (mm-30) cc_final: 0.7776 (mp0) REVERT: A 753 GLU cc_start: 0.8621 (mp0) cc_final: 0.8279 (mp0) REVERT: A 756 GLU cc_start: 0.7139 (tp30) cc_final: 0.6921 (tp30) REVERT: A 788 ARG cc_start: 0.8538 (ptt180) cc_final: 0.8033 (ptt180) REVERT: A 792 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8097 (mm-30) REVERT: A 822 LYS cc_start: 0.8424 (mptt) cc_final: 0.8109 (mmtm) REVERT: D 22 LEU cc_start: 0.8335 (mm) cc_final: 0.7979 (mm) REVERT: D 65 ASN cc_start: 0.8371 (m-40) cc_final: 0.7978 (m-40) REVERT: D 73 CYS cc_start: 0.6650 (m) cc_final: 0.6306 (m) REVERT: D 79 LYS cc_start: 0.8418 (tppp) cc_final: 0.7080 (tppp) REVERT: D 82 GLU cc_start: 0.8610 (tt0) cc_final: 0.7788 (tt0) REVERT: D 114 GLN cc_start: 0.7978 (mp10) cc_final: 0.7594 (mp10) REVERT: D 128 LYS cc_start: 0.8588 (mttt) cc_final: 0.8305 (mttt) REVERT: D 132 PHE cc_start: 0.7706 (m-80) cc_final: 0.6947 (m-80) REVERT: D 134 ASN cc_start: 0.7792 (t0) cc_final: 0.7381 (t0) REVERT: D 138 ARG cc_start: 0.7994 (ptt-90) cc_final: 0.7102 (ptt-90) REVERT: C 130 GLU cc_start: 0.8329 (pt0) cc_final: 0.7636 (pm20) REVERT: C 138 GLU cc_start: 0.8635 (mp0) cc_final: 0.8280 (mp0) REVERT: C 287 PHE cc_start: 0.7649 (m-80) cc_final: 0.7398 (m-80) REVERT: C 294 ARG cc_start: 0.8584 (mpt-90) cc_final: 0.8380 (mpt-90) REVERT: C 326 ARG cc_start: 0.8172 (mtm180) cc_final: 0.7883 (mtm-85) REVERT: C 328 TRP cc_start: 0.7126 (m100) cc_final: 0.6425 (m100) REVERT: C 330 LYS cc_start: 0.8720 (mmmt) cc_final: 0.8288 (mptt) REVERT: C 332 ASN cc_start: 0.7655 (t0) cc_final: 0.7197 (t0) REVERT: C 337 ARG cc_start: 0.8195 (ttm170) cc_final: 0.7714 (tmm-80) REVERT: C 339 MET cc_start: 0.7297 (mtp) cc_final: 0.7068 (ttt) REVERT: C 373 LYS cc_start: 0.8092 (ttmt) cc_final: 0.7872 (mtpp) REVERT: C 382 ASN cc_start: 0.8495 (m-40) cc_final: 0.8183 (m110) REVERT: C 392 HIS cc_start: 0.8281 (m170) cc_final: 0.7929 (m-70) REVERT: C 397 ASP cc_start: 0.7916 (t0) cc_final: 0.7375 (t0) REVERT: C 398 GLU cc_start: 0.8246 (pp20) cc_final: 0.7972 (pm20) REVERT: C 403 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7478 (pp20) REVERT: C 406 GLU cc_start: 0.8480 (tp30) cc_final: 0.7260 (tp30) REVERT: C 408 THR cc_start: 0.8634 (m) cc_final: 0.8342 (p) REVERT: C 410 GLN cc_start: 0.9041 (mm-40) cc_final: 0.7422 (mm110) REVERT: C 411 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7266 (mt-10) REVERT: C 420 LYS cc_start: 0.7929 (pttm) cc_final: 0.7682 (ptmm) REVERT: C 447 GLU cc_start: 0.8043 (mp0) cc_final: 0.7417 (tp30) REVERT: C 450 ILE cc_start: 0.8087 (mt) cc_final: 0.7710 (mt) REVERT: C 478 MET cc_start: 0.8034 (mtp) cc_final: 0.7429 (mtp) REVERT: C 482 PHE cc_start: 0.8003 (p90) cc_final: 0.7741 (p90) REVERT: C 493 LEU cc_start: 0.8005 (tp) cc_final: 0.7699 (tp) REVERT: C 501 MET cc_start: 0.8206 (mtt) cc_final: 0.7606 (mtt) REVERT: C 502 TYR cc_start: 0.7628 (m-10) cc_final: 0.7380 (m-10) REVERT: C 505 ARG cc_start: 0.8738 (mtt90) cc_final: 0.8225 (mtt90) REVERT: C 507 ILE cc_start: 0.8517 (mt) cc_final: 0.8316 (mt) REVERT: C 522 TYR cc_start: 0.8044 (m-80) cc_final: 0.7427 (m-80) REVERT: C 530 ASP cc_start: 0.7922 (p0) cc_final: 0.7618 (p0) REVERT: C 539 ARG cc_start: 0.8532 (ttm-80) cc_final: 0.8094 (ttm-80) REVERT: C 540 LEU cc_start: 0.9000 (mm) cc_final: 0.8783 (mm) REVERT: C 542 MET cc_start: 0.8149 (tpp) cc_final: 0.7433 (tpp) REVERT: C 543 ILE cc_start: 0.8868 (mt) cc_final: 0.8643 (mt) REVERT: C 545 MET cc_start: 0.7818 (mtm) cc_final: 0.7146 (mtm) REVERT: C 551 LEU cc_start: 0.8836 (mp) cc_final: 0.8539 (mp) REVERT: C 553 LYS cc_start: 0.8382 (mtmt) cc_final: 0.8031 (mtpp) REVERT: C 554 GLN cc_start: 0.8038 (tt0) cc_final: 0.6504 (tt0) REVERT: C 555 LEU cc_start: 0.8632 (tp) cc_final: 0.8288 (tp) REVERT: C 576 GLN cc_start: 0.7789 (tm-30) cc_final: 0.7325 (tm-30) REVERT: C 577 LEU cc_start: 0.8656 (mt) cc_final: 0.8046 (mt) REVERT: C 581 GLU cc_start: 0.8169 (pp20) cc_final: 0.7697 (pp20) REVERT: C 587 ILE cc_start: 0.8071 (tp) cc_final: 0.7747 (tp) REVERT: C 589 MET cc_start: 0.6499 (mtp) cc_final: 0.6090 (mtp) REVERT: C 617 ILE cc_start: 0.8586 (mm) cc_final: 0.8312 (mm) REVERT: C 619 LEU cc_start: 0.8814 (tp) cc_final: 0.8562 (tp) REVERT: C 621 LEU cc_start: 0.8190 (mm) cc_final: 0.7741 (mm) REVERT: C 625 ASN cc_start: 0.8598 (m110) cc_final: 0.8235 (m110) REVERT: C 626 ASN cc_start: 0.8130 (m110) cc_final: 0.7710 (m110) REVERT: C 630 ASP cc_start: 0.7277 (t70) cc_final: 0.6970 (t0) REVERT: C 635 MET cc_start: 0.8081 (mpp) cc_final: 0.7320 (mpp) REVERT: C 641 LEU cc_start: 0.8511 (mt) cc_final: 0.8221 (mm) REVERT: C 642 MET cc_start: 0.8115 (mmp) cc_final: 0.7861 (mmp) REVERT: C 649 ARG cc_start: 0.8780 (ttm170) cc_final: 0.8459 (mtp85) REVERT: C 658 LEU cc_start: 0.8522 (tp) cc_final: 0.8190 (tt) REVERT: C 661 SER cc_start: 0.8762 (m) cc_final: 0.8522 (p) REVERT: C 663 LYS cc_start: 0.8184 (ptmm) cc_final: 0.7644 (ttpp) REVERT: C 667 GLU cc_start: 0.7985 (pp20) cc_final: 0.7665 (pp20) REVERT: C 692 MET cc_start: 0.7309 (ttm) cc_final: 0.7102 (ttm) REVERT: C 712 GLU cc_start: 0.8663 (tt0) cc_final: 0.8111 (tt0) REVERT: C 717 TYR cc_start: 0.8947 (t80) cc_final: 0.8648 (t80) REVERT: C 719 ASP cc_start: 0.8338 (m-30) cc_final: 0.7709 (p0) REVERT: C 720 TYR cc_start: 0.7879 (t80) cc_final: 0.7277 (t80) REVERT: C 724 LYS cc_start: 0.8080 (ptpp) cc_final: 0.7489 (mtmm) REVERT: C 727 GLU cc_start: 0.8078 (pm20) cc_final: 0.7791 (pm20) REVERT: C 734 ARG cc_start: 0.8700 (ttt-90) cc_final: 0.8243 (ttm170) REVERT: C 738 HIS cc_start: 0.8205 (t-170) cc_final: 0.7975 (t-170) REVERT: C 739 MET cc_start: 0.7882 (ptp) cc_final: 0.7536 (ptp) REVERT: C 743 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8108 (mm-30) REVERT: C 747 LYS cc_start: 0.9053 (mtpt) cc_final: 0.8475 (mmmm) REVERT: C 748 TYR cc_start: 0.7400 (t80) cc_final: 0.6840 (t80) REVERT: C 754 GLU cc_start: 0.8520 (mt-10) cc_final: 0.7972 (mp0) REVERT: C 788 ARG cc_start: 0.8401 (ptt180) cc_final: 0.8008 (ptt180) REVERT: C 805 PHE cc_start: 0.8598 (t80) cc_final: 0.8177 (t80) REVERT: C 806 LEU cc_start: 0.8217 (mt) cc_final: 0.7711 (mt) REVERT: C 822 LYS cc_start: 0.8483 (mmtt) cc_final: 0.8138 (mmtm) outliers start: 0 outliers final: 0 residues processed: 522 average time/residue: 0.3197 time to fit residues: 222.8315 Evaluate side-chains 498 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 498 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 82 optimal weight: 0.0870 chunk 101 optimal weight: 0.0060 chunk 7 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 123 optimal weight: 0.2980 overall best weight: 0.3974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 ASN ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 723 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.142346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.113939 restraints weight = 29957.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.118645 restraints weight = 18542.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.122066 restraints weight = 12827.947| |-----------------------------------------------------------------------------| r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.5680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13534 Z= 0.114 Angle : 0.607 9.842 18272 Z= 0.304 Chirality : 0.043 0.179 2014 Planarity : 0.004 0.075 2372 Dihedral : 4.799 17.708 1806 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % 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: -1.08 (0.21), residues: 1610 helix: -0.20 (0.19), residues: 792 sheet: -2.31 (0.59), residues: 72 loop : -1.01 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP A 328 HIS 0.007 0.001 HIS A 655 PHE 0.025 0.001 PHE C 790 TYR 0.019 0.001 TYR A 494 ARG 0.008 0.000 ARG C 168 Details of bonding type rmsd hydrogen bonds : bond 0.03516 ( 502) hydrogen bonds : angle 4.91050 ( 1392) metal coordination : bond 0.00362 ( 12) metal coordination : angle 3.03740 ( 12) covalent geometry : bond 0.00244 (13522) covalent geometry : angle 0.60190 (18260) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 510 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 18 LYS cc_start: 0.7677 (mmtm) cc_final: 0.7177 (mmmm) REVERT: B 22 LEU cc_start: 0.8230 (mm) cc_final: 0.7891 (mm) REVERT: B 65 ASN cc_start: 0.8277 (m-40) cc_final: 0.7933 (m-40) REVERT: B 73 CYS cc_start: 0.5746 (m) cc_final: 0.5398 (m) REVERT: B 77 TYR cc_start: 0.8110 (m-80) cc_final: 0.7645 (m-80) REVERT: B 82 GLU cc_start: 0.8737 (tt0) cc_final: 0.8346 (tt0) REVERT: B 88 TYR cc_start: 0.6973 (p90) cc_final: 0.6525 (p90) REVERT: B 108 ILE cc_start: 0.8229 (mt) cc_final: 0.7838 (tt) REVERT: B 114 GLN cc_start: 0.7930 (mp10) cc_final: 0.7653 (mp10) REVERT: B 124 ARG cc_start: 0.8632 (ttt-90) cc_final: 0.8346 (ttt-90) REVERT: B 132 PHE cc_start: 0.7733 (m-80) cc_final: 0.6910 (m-80) REVERT: A 130 GLU cc_start: 0.8399 (pt0) cc_final: 0.7545 (pm20) REVERT: A 138 GLU cc_start: 0.8503 (mp0) cc_final: 0.8246 (mp0) REVERT: A 237 ASP cc_start: 0.8449 (m-30) cc_final: 0.7852 (t0) REVERT: A 240 ARG cc_start: 0.8427 (mtt180) cc_final: 0.7761 (mtt180) REVERT: A 283 TYR cc_start: 0.7598 (t80) cc_final: 0.7220 (t80) REVERT: A 287 PHE cc_start: 0.7339 (m-80) cc_final: 0.6959 (m-80) REVERT: A 288 ILE cc_start: 0.8731 (tt) cc_final: 0.8436 (tt) REVERT: A 291 MET cc_start: 0.8396 (ttt) cc_final: 0.7603 (ttt) REVERT: A 294 ARG cc_start: 0.8467 (mpt-90) cc_final: 0.8258 (mpt-90) REVERT: A 304 MET cc_start: 0.4840 (tpt) cc_final: 0.4145 (tpt) REVERT: A 330 LYS cc_start: 0.8476 (mmtm) cc_final: 0.8276 (mmtm) REVERT: A 332 ASN cc_start: 0.7530 (t0) cc_final: 0.7143 (t0) REVERT: A 337 ARG cc_start: 0.8189 (ttm170) cc_final: 0.7090 (ttp80) REVERT: A 338 ARG cc_start: 0.8134 (mtp85) cc_final: 0.7788 (mmm-85) REVERT: A 341 GLU cc_start: 0.8412 (mt-10) cc_final: 0.7675 (mt-10) REVERT: A 344 GLN cc_start: 0.8516 (tp-100) cc_final: 0.7558 (tp-100) REVERT: A 350 LYS cc_start: 0.7508 (mmpt) cc_final: 0.7275 (tptt) REVERT: A 376 LYS cc_start: 0.8632 (tttt) cc_final: 0.8402 (tttt) REVERT: A 392 HIS cc_start: 0.8147 (m90) cc_final: 0.7698 (m90) REVERT: A 407 LEU cc_start: 0.8912 (mt) cc_final: 0.8444 (pp) REVERT: A 408 THR cc_start: 0.8656 (m) cc_final: 0.8068 (p) REVERT: A 411 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7114 (mt-10) REVERT: A 424 ARG cc_start: 0.7766 (mmm-85) cc_final: 0.7278 (tpt-90) REVERT: A 437 LEU cc_start: 0.8298 (mm) cc_final: 0.7927 (tt) REVERT: A 446 PHE cc_start: 0.7612 (m-80) cc_final: 0.7340 (m-80) REVERT: A 447 GLU cc_start: 0.8095 (mp0) cc_final: 0.7621 (tp30) REVERT: A 449 PHE cc_start: 0.7246 (m-10) cc_final: 0.6669 (m-10) REVERT: A 450 ILE cc_start: 0.8012 (mt) cc_final: 0.7142 (mt) REVERT: A 458 LEU cc_start: 0.8355 (tp) cc_final: 0.7894 (tt) REVERT: A 459 GLU cc_start: 0.7100 (mp0) cc_final: 0.6787 (mp0) REVERT: A 477 PHE cc_start: 0.7967 (m-80) cc_final: 0.7455 (m-80) REVERT: A 478 MET cc_start: 0.8124 (mtp) cc_final: 0.6911 (ttm) REVERT: A 482 PHE cc_start: 0.7931 (p90) cc_final: 0.7522 (p90) REVERT: A 497 ASN cc_start: 0.7903 (m-40) cc_final: 0.7596 (m-40) REVERT: A 499 ILE cc_start: 0.7800 (tp) cc_final: 0.7493 (tp) REVERT: A 501 MET cc_start: 0.7733 (mtt) cc_final: 0.7264 (mmt) REVERT: A 504 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7509 (mm-30) REVERT: A 505 ARG cc_start: 0.8781 (mtt90) cc_final: 0.8182 (mtt90) REVERT: A 507 ILE cc_start: 0.8673 (mt) cc_final: 0.8232 (mt) REVERT: A 522 TYR cc_start: 0.8206 (m-80) cc_final: 0.7595 (m-80) REVERT: A 530 ASP cc_start: 0.8116 (p0) cc_final: 0.7899 (p0) REVERT: A 533 ILE cc_start: 0.8447 (pt) cc_final: 0.8121 (mp) REVERT: A 539 ARG cc_start: 0.8521 (ttm-80) cc_final: 0.7985 (ptm-80) REVERT: A 540 LEU cc_start: 0.9086 (mm) cc_final: 0.8846 (mm) REVERT: A 542 MET cc_start: 0.8321 (ptt) cc_final: 0.7652 (tmm) REVERT: A 543 ILE cc_start: 0.8916 (mt) cc_final: 0.8431 (mt) REVERT: A 545 MET cc_start: 0.7736 (mtm) cc_final: 0.7172 (mtm) REVERT: A 550 ASP cc_start: 0.7859 (p0) cc_final: 0.7432 (p0) REVERT: A 553 LYS cc_start: 0.8463 (mtmt) cc_final: 0.8127 (mtpp) REVERT: A 573 GLU cc_start: 0.8019 (pp20) cc_final: 0.7781 (pp20) REVERT: A 576 GLN cc_start: 0.8420 (tp40) cc_final: 0.7959 (tp40) REVERT: A 593 ASP cc_start: 0.8196 (t0) cc_final: 0.7767 (t70) REVERT: A 600 TRP cc_start: 0.8692 (t-100) cc_final: 0.8446 (t-100) REVERT: A 603 PRO cc_start: 0.7479 (Cg_endo) cc_final: 0.7117 (Cg_exo) REVERT: A 625 ASN cc_start: 0.7686 (p0) cc_final: 0.7392 (p0) REVERT: A 630 ASP cc_start: 0.7384 (t0) cc_final: 0.7146 (t0) REVERT: A 635 MET cc_start: 0.8229 (mpp) cc_final: 0.7409 (mpp) REVERT: A 641 LEU cc_start: 0.8552 (mt) cc_final: 0.8207 (mt) REVERT: A 642 MET cc_start: 0.8189 (mmp) cc_final: 0.7862 (mmp) REVERT: A 651 LEU cc_start: 0.8386 (mt) cc_final: 0.8057 (mt) REVERT: A 660 GLN cc_start: 0.8241 (pp30) cc_final: 0.7662 (pp30) REVERT: A 663 LYS cc_start: 0.8245 (ptmm) cc_final: 0.7661 (mptt) REVERT: A 667 GLU cc_start: 0.8194 (pp20) cc_final: 0.7880 (pp20) REVERT: A 682 ILE cc_start: 0.8233 (tp) cc_final: 0.7862 (tp) REVERT: A 711 LYS cc_start: 0.9289 (mmtt) cc_final: 0.8879 (mmtm) REVERT: A 712 GLU cc_start: 0.8606 (tt0) cc_final: 0.8111 (tt0) REVERT: A 716 LEU cc_start: 0.8749 (mt) cc_final: 0.8514 (mp) REVERT: A 717 TYR cc_start: 0.8860 (t80) cc_final: 0.8085 (t80) REVERT: A 720 TYR cc_start: 0.7819 (t80) cc_final: 0.7287 (t80) REVERT: A 727 GLU cc_start: 0.7902 (pm20) cc_final: 0.7567 (pm20) REVERT: A 728 LYS cc_start: 0.8337 (ttpt) cc_final: 0.7606 (tmtt) REVERT: A 734 ARG cc_start: 0.8428 (ttt-90) cc_final: 0.8124 (ttp80) REVERT: A 738 HIS cc_start: 0.8093 (t70) cc_final: 0.7795 (t-170) REVERT: A 743 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7800 (mp0) REVERT: A 748 TYR cc_start: 0.7392 (t80) cc_final: 0.6803 (t80) REVERT: A 753 GLU cc_start: 0.8581 (mp0) cc_final: 0.8243 (mp0) REVERT: A 788 ARG cc_start: 0.8496 (ptt180) cc_final: 0.7986 (ptt180) REVERT: A 792 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8092 (mm-30) REVERT: A 822 LYS cc_start: 0.8393 (mptt) cc_final: 0.8035 (mmtm) REVERT: D 22 LEU cc_start: 0.8311 (mm) cc_final: 0.7950 (mm) REVERT: D 65 ASN cc_start: 0.8347 (m-40) cc_final: 0.7957 (m-40) REVERT: D 73 CYS cc_start: 0.6570 (m) cc_final: 0.6186 (m) REVERT: D 79 LYS cc_start: 0.8409 (tppp) cc_final: 0.7949 (tppp) REVERT: D 80 ILE cc_start: 0.8597 (mm) cc_final: 0.8388 (mm) REVERT: D 82 GLU cc_start: 0.8616 (tt0) cc_final: 0.8132 (tt0) REVERT: D 114 GLN cc_start: 0.8056 (mp10) cc_final: 0.7690 (mp10) REVERT: D 128 LYS cc_start: 0.8646 (mttt) cc_final: 0.8385 (mttt) REVERT: D 132 PHE cc_start: 0.7772 (m-80) cc_final: 0.6961 (m-80) REVERT: D 138 ARG cc_start: 0.7887 (ptt-90) cc_final: 0.6945 (ptt-90) REVERT: C 130 GLU cc_start: 0.8325 (pt0) cc_final: 0.7572 (pm20) REVERT: C 138 GLU cc_start: 0.8653 (mp0) cc_final: 0.8410 (mm-30) REVERT: C 283 TYR cc_start: 0.8211 (t80) cc_final: 0.7312 (t80) REVERT: C 287 PHE cc_start: 0.7724 (m-80) cc_final: 0.7473 (m-80) REVERT: C 315 LYS cc_start: 0.8058 (mtmm) cc_final: 0.7251 (ptpp) REVERT: C 321 GLN cc_start: 0.8636 (mm-40) cc_final: 0.8052 (mp-120) REVERT: C 326 ARG cc_start: 0.8046 (mtm180) cc_final: 0.7738 (mtt180) REVERT: C 328 TRP cc_start: 0.6920 (m100) cc_final: 0.6369 (m100) REVERT: C 330 LYS cc_start: 0.8710 (mmmt) cc_final: 0.8265 (mptt) REVERT: C 332 ASN cc_start: 0.7645 (t0) cc_final: 0.7191 (t0) REVERT: C 337 ARG cc_start: 0.8204 (ttm170) cc_final: 0.7759 (tmm-80) REVERT: C 339 MET cc_start: 0.7355 (mtp) cc_final: 0.7034 (ttt) REVERT: C 344 GLN cc_start: 0.8474 (tp-100) cc_final: 0.7618 (tp-100) REVERT: C 376 LYS cc_start: 0.8588 (ttpt) cc_final: 0.8150 (tttt) REVERT: C 382 ASN cc_start: 0.8413 (m-40) cc_final: 0.8114 (m110) REVERT: C 397 ASP cc_start: 0.7878 (t0) cc_final: 0.7368 (t0) REVERT: C 398 GLU cc_start: 0.8249 (pp20) cc_final: 0.7976 (pm20) REVERT: C 403 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7524 (pp20) REVERT: C 406 GLU cc_start: 0.8594 (tp30) cc_final: 0.7040 (tp30) REVERT: C 408 THR cc_start: 0.8595 (m) cc_final: 0.8325 (p) REVERT: C 410 GLN cc_start: 0.9022 (mm-40) cc_final: 0.7396 (mm110) REVERT: C 411 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7359 (mt-10) REVERT: C 420 LYS cc_start: 0.7932 (pttm) cc_final: 0.7666 (ptmm) REVERT: C 458 LEU cc_start: 0.8562 (tp) cc_final: 0.8202 (tt) REVERT: C 477 PHE cc_start: 0.7798 (m-80) cc_final: 0.7224 (m-80) REVERT: C 478 MET cc_start: 0.8120 (mtp) cc_final: 0.7454 (mtp) REVERT: C 482 PHE cc_start: 0.7993 (p90) cc_final: 0.7658 (p90) REVERT: C 499 ILE cc_start: 0.7914 (tp) cc_final: 0.7682 (tp) REVERT: C 501 MET cc_start: 0.8173 (mtt) cc_final: 0.7694 (mtt) REVERT: C 502 TYR cc_start: 0.7646 (m-10) cc_final: 0.7417 (m-10) REVERT: C 505 ARG cc_start: 0.8750 (mtt90) cc_final: 0.8163 (mtt90) REVERT: C 507 ILE cc_start: 0.8578 (mt) cc_final: 0.8255 (mt) REVERT: C 522 TYR cc_start: 0.7999 (m-80) cc_final: 0.7327 (m-80) REVERT: C 530 ASP cc_start: 0.7934 (p0) cc_final: 0.7684 (p0) REVERT: C 539 ARG cc_start: 0.8526 (ttm-80) cc_final: 0.8113 (ttm-80) REVERT: C 542 MET cc_start: 0.8080 (tpp) cc_final: 0.7333 (tpp) REVERT: C 545 MET cc_start: 0.7900 (mtm) cc_final: 0.7212 (mtm) REVERT: C 550 ASP cc_start: 0.7780 (p0) cc_final: 0.7408 (p0) REVERT: C 553 LYS cc_start: 0.8444 (mtmt) cc_final: 0.8000 (mtpp) REVERT: C 554 GLN cc_start: 0.8018 (tt0) cc_final: 0.6579 (tt0) REVERT: C 555 LEU cc_start: 0.8603 (tp) cc_final: 0.8192 (tp) REVERT: C 576 GLN cc_start: 0.7724 (tm-30) cc_final: 0.7281 (tm-30) REVERT: C 577 LEU cc_start: 0.8573 (mt) cc_final: 0.7926 (mt) REVERT: C 581 GLU cc_start: 0.8168 (pp20) cc_final: 0.7730 (pp20) REVERT: C 587 ILE cc_start: 0.8001 (tp) cc_final: 0.7671 (tp) REVERT: C 589 MET cc_start: 0.6403 (mtp) cc_final: 0.6007 (mtp) REVERT: C 603 PRO cc_start: 0.7556 (Cg_endo) cc_final: 0.7307 (Cg_exo) REVERT: C 617 ILE cc_start: 0.8556 (mm) cc_final: 0.8321 (mm) REVERT: C 626 ASN cc_start: 0.8045 (m110) cc_final: 0.7688 (m110) REVERT: C 630 ASP cc_start: 0.7296 (t70) cc_final: 0.7044 (t0) REVERT: C 635 MET cc_start: 0.8070 (mpp) cc_final: 0.7420 (mpp) REVERT: C 641 LEU cc_start: 0.8538 (mt) cc_final: 0.8170 (mm) REVERT: C 642 MET cc_start: 0.8182 (mmp) cc_final: 0.7919 (mmp) REVERT: C 658 LEU cc_start: 0.8480 (tp) cc_final: 0.8151 (tt) REVERT: C 661 SER cc_start: 0.8796 (m) cc_final: 0.8596 (p) REVERT: C 663 LYS cc_start: 0.8112 (ptmm) cc_final: 0.7631 (ttpp) REVERT: C 667 GLU cc_start: 0.7975 (pp20) cc_final: 0.7645 (pp20) REVERT: C 692 MET cc_start: 0.7170 (ttm) cc_final: 0.6961 (ttm) REVERT: C 712 GLU cc_start: 0.8640 (tt0) cc_final: 0.8198 (tt0) REVERT: C 716 LEU cc_start: 0.8687 (mt) cc_final: 0.8098 (pp) REVERT: C 717 TYR cc_start: 0.8923 (t80) cc_final: 0.8418 (t80) REVERT: C 719 ASP cc_start: 0.8344 (m-30) cc_final: 0.8047 (m-30) REVERT: C 720 TYR cc_start: 0.7902 (t80) cc_final: 0.7376 (t80) REVERT: C 727 GLU cc_start: 0.8051 (pm20) cc_final: 0.7754 (pm20) REVERT: C 730 PHE cc_start: 0.8149 (t80) cc_final: 0.7881 (t80) REVERT: C 738 HIS cc_start: 0.8253 (t-170) cc_final: 0.8001 (t-170) REVERT: C 739 MET cc_start: 0.7879 (ptp) cc_final: 0.7524 (ptp) REVERT: C 743 GLU cc_start: 0.8439 (mm-30) cc_final: 0.7992 (mm-30) REVERT: C 747 LYS cc_start: 0.9046 (mtpt) cc_final: 0.8482 (mmmm) REVERT: C 748 TYR cc_start: 0.7393 (t80) cc_final: 0.6839 (t80) REVERT: C 788 ARG cc_start: 0.8453 (ptt180) cc_final: 0.7588 (ttp-110) REVERT: C 805 PHE cc_start: 0.8540 (t80) cc_final: 0.8160 (t80) REVERT: C 806 LEU cc_start: 0.8223 (mt) cc_final: 0.7750 (mt) REVERT: C 822 LYS cc_start: 0.8438 (mmtt) cc_final: 0.8105 (mmtm) outliers start: 0 outliers final: 0 residues processed: 510 average time/residue: 0.3087 time to fit residues: 211.5992 Evaluate side-chains 491 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 491 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 112 optimal weight: 0.0270 chunk 76 optimal weight: 4.9990 chunk 153 optimal weight: 0.9980 chunk 119 optimal weight: 0.5980 chunk 155 optimal weight: 8.9990 chunk 84 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 16 optimal weight: 0.0670 chunk 139 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 ASN ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 723 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.141751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.113594 restraints weight = 29813.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.118249 restraints weight = 18487.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.121638 restraints weight = 12839.763| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.5918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13534 Z= 0.114 Angle : 0.598 9.329 18272 Z= 0.302 Chirality : 0.043 0.197 2014 Planarity : 0.004 0.065 2372 Dihedral : 4.711 18.300 1806 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % 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: -0.98 (0.21), residues: 1610 helix: -0.13 (0.19), residues: 794 sheet: -2.39 (0.61), residues: 68 loop : -0.94 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.004 TRP B 139 HIS 0.006 0.001 HIS A 655 PHE 0.025 0.001 PHE C 730 TYR 0.030 0.001 TYR C 301 ARG 0.007 0.000 ARG B 84 Details of bonding type rmsd hydrogen bonds : bond 0.03434 ( 502) hydrogen bonds : angle 4.85652 ( 1392) metal coordination : bond 0.00343 ( 12) metal coordination : angle 2.93437 ( 12) covalent geometry : bond 0.00242 (13522) covalent geometry : angle 0.59344 (18260) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 509 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 18 LYS cc_start: 0.7567 (mmtm) cc_final: 0.7161 (mmmm) REVERT: B 22 LEU cc_start: 0.8172 (mm) cc_final: 0.7821 (mm) REVERT: B 65 ASN cc_start: 0.8281 (m-40) cc_final: 0.7937 (m-40) REVERT: B 73 CYS cc_start: 0.5968 (m) cc_final: 0.5573 (m) REVERT: B 77 TYR cc_start: 0.8143 (m-80) cc_final: 0.7697 (m-80) REVERT: B 82 GLU cc_start: 0.8743 (tt0) cc_final: 0.8367 (tt0) REVERT: B 88 TYR cc_start: 0.7070 (p90) cc_final: 0.6842 (p90) REVERT: B 108 ILE cc_start: 0.8189 (mt) cc_final: 0.7795 (tt) REVERT: B 114 GLN cc_start: 0.7961 (mp10) cc_final: 0.7650 (mp10) REVERT: B 124 ARG cc_start: 0.8655 (ttt-90) cc_final: 0.8374 (ttt-90) REVERT: B 132 PHE cc_start: 0.7725 (m-80) cc_final: 0.7108 (m-80) REVERT: B 136 ARG cc_start: 0.8115 (mmm160) cc_final: 0.7407 (mmm160) REVERT: A 130 GLU cc_start: 0.8405 (pt0) cc_final: 0.7575 (pm20) REVERT: A 138 GLU cc_start: 0.8497 (mp0) cc_final: 0.8235 (mp0) REVERT: A 237 ASP cc_start: 0.8408 (m-30) cc_final: 0.7816 (t0) REVERT: A 260 LEU cc_start: 0.9069 (mm) cc_final: 0.8803 (pp) REVERT: A 287 PHE cc_start: 0.7314 (m-80) cc_final: 0.7098 (m-80) REVERT: A 291 MET cc_start: 0.8135 (ttt) cc_final: 0.7894 (ttt) REVERT: A 304 MET cc_start: 0.4848 (tpt) cc_final: 0.4192 (tpt) REVERT: A 332 ASN cc_start: 0.7439 (t0) cc_final: 0.6878 (t0) REVERT: A 337 ARG cc_start: 0.8183 (ttm170) cc_final: 0.7048 (ttp80) REVERT: A 338 ARG cc_start: 0.8072 (mtp85) cc_final: 0.7735 (mmm-85) REVERT: A 341 GLU cc_start: 0.8470 (mt-10) cc_final: 0.7722 (mt-10) REVERT: A 344 GLN cc_start: 0.8532 (tp-100) cc_final: 0.7544 (tp-100) REVERT: A 347 ILE cc_start: 0.7534 (mt) cc_final: 0.7270 (mt) REVERT: A 350 LYS cc_start: 0.7517 (mmpt) cc_final: 0.7213 (tptt) REVERT: A 376 LYS cc_start: 0.8618 (tttt) cc_final: 0.8363 (tttt) REVERT: A 392 HIS cc_start: 0.8217 (m90) cc_final: 0.7759 (m90) REVERT: A 394 GLU cc_start: 0.6162 (mm-30) cc_final: 0.5090 (mm-30) REVERT: A 403 GLU cc_start: 0.7558 (pm20) cc_final: 0.7317 (pm20) REVERT: A 407 LEU cc_start: 0.8881 (mt) cc_final: 0.8423 (pp) REVERT: A 408 THR cc_start: 0.8674 (m) cc_final: 0.8098 (p) REVERT: A 410 GLN cc_start: 0.8903 (mm-40) cc_final: 0.8109 (mm-40) REVERT: A 411 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7109 (mt-10) REVERT: A 424 ARG cc_start: 0.7735 (mmm-85) cc_final: 0.6910 (tpp80) REVERT: A 437 LEU cc_start: 0.8330 (mm) cc_final: 0.7987 (tt) REVERT: A 447 GLU cc_start: 0.8075 (mp0) cc_final: 0.7634 (tp30) REVERT: A 449 PHE cc_start: 0.7195 (m-10) cc_final: 0.6606 (m-10) REVERT: A 450 ILE cc_start: 0.8069 (mt) cc_final: 0.7177 (mt) REVERT: A 455 ASN cc_start: 0.8033 (m-40) cc_final: 0.7724 (m-40) REVERT: A 458 LEU cc_start: 0.8356 (tp) cc_final: 0.7801 (tt) REVERT: A 459 GLU cc_start: 0.7085 (mp0) cc_final: 0.6789 (mp0) REVERT: A 477 PHE cc_start: 0.7931 (m-80) cc_final: 0.7477 (m-80) REVERT: A 478 MET cc_start: 0.8123 (mtp) cc_final: 0.7631 (ttm) REVERT: A 482 PHE cc_start: 0.7939 (p90) cc_final: 0.7579 (p90) REVERT: A 497 ASN cc_start: 0.7850 (m-40) cc_final: 0.7583 (m-40) REVERT: A 499 ILE cc_start: 0.7806 (tp) cc_final: 0.7501 (tp) REVERT: A 501 MET cc_start: 0.7482 (mtt) cc_final: 0.7236 (mmt) REVERT: A 504 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7471 (mm-30) REVERT: A 505 ARG cc_start: 0.8777 (mtt90) cc_final: 0.8174 (mtt90) REVERT: A 507 ILE cc_start: 0.8711 (mt) cc_final: 0.8249 (mt) REVERT: A 530 ASP cc_start: 0.8082 (p0) cc_final: 0.7781 (p0) REVERT: A 533 ILE cc_start: 0.8438 (pt) cc_final: 0.8087 (mp) REVERT: A 535 ASP cc_start: 0.7297 (t0) cc_final: 0.6991 (t0) REVERT: A 539 ARG cc_start: 0.8413 (ttm-80) cc_final: 0.7764 (ptm-80) REVERT: A 540 LEU cc_start: 0.9139 (mm) cc_final: 0.8916 (mm) REVERT: A 542 MET cc_start: 0.8295 (ptt) cc_final: 0.7457 (ptt) REVERT: A 545 MET cc_start: 0.7718 (mtm) cc_final: 0.7255 (mtm) REVERT: A 550 ASP cc_start: 0.7842 (p0) cc_final: 0.7400 (p0) REVERT: A 553 LYS cc_start: 0.8396 (mtmt) cc_final: 0.7988 (mtpp) REVERT: A 572 LYS cc_start: 0.8022 (mmtt) cc_final: 0.7526 (tptt) REVERT: A 573 GLU cc_start: 0.7909 (pp20) cc_final: 0.7655 (pp20) REVERT: A 576 GLN cc_start: 0.8325 (tp40) cc_final: 0.7876 (tp40) REVERT: A 593 ASP cc_start: 0.8176 (t0) cc_final: 0.7737 (t70) REVERT: A 600 TRP cc_start: 0.8703 (t-100) cc_final: 0.8477 (t-100) REVERT: A 603 PRO cc_start: 0.7486 (Cg_endo) cc_final: 0.7141 (Cg_exo) REVERT: A 611 GLN cc_start: 0.7924 (tm-30) cc_final: 0.7467 (tm-30) REVERT: A 617 ILE cc_start: 0.8434 (mm) cc_final: 0.8181 (mm) REVERT: A 619 LEU cc_start: 0.8813 (tp) cc_final: 0.8507 (tp) REVERT: A 621 LEU cc_start: 0.8117 (mt) cc_final: 0.7911 (mt) REVERT: A 635 MET cc_start: 0.7985 (mpp) cc_final: 0.7249 (mpp) REVERT: A 640 LYS cc_start: 0.7677 (mtpp) cc_final: 0.7129 (ttmm) REVERT: A 641 LEU cc_start: 0.8545 (mt) cc_final: 0.8298 (mt) REVERT: A 642 MET cc_start: 0.8141 (mmp) cc_final: 0.7841 (mmp) REVERT: A 648 PHE cc_start: 0.8696 (p90) cc_final: 0.8211 (p90) REVERT: A 651 LEU cc_start: 0.8367 (mt) cc_final: 0.8045 (mt) REVERT: A 660 GLN cc_start: 0.8165 (pp30) cc_final: 0.7554 (pp30) REVERT: A 663 LYS cc_start: 0.8294 (ptmm) cc_final: 0.7690 (mmtm) REVERT: A 667 GLU cc_start: 0.8204 (pp20) cc_final: 0.7878 (pp20) REVERT: A 682 ILE cc_start: 0.8210 (tp) cc_final: 0.7922 (tp) REVERT: A 711 LYS cc_start: 0.9299 (mmtt) cc_final: 0.8944 (mmtm) REVERT: A 712 GLU cc_start: 0.8630 (tt0) cc_final: 0.8145 (tt0) REVERT: A 716 LEU cc_start: 0.8753 (mt) cc_final: 0.8534 (mp) REVERT: A 717 TYR cc_start: 0.8908 (t80) cc_final: 0.8289 (t80) REVERT: A 720 TYR cc_start: 0.7795 (t80) cc_final: 0.7271 (t80) REVERT: A 723 ASN cc_start: 0.7009 (m-40) cc_final: 0.6608 (m110) REVERT: A 727 GLU cc_start: 0.7864 (pm20) cc_final: 0.7514 (pm20) REVERT: A 728 LYS cc_start: 0.8347 (ttpt) cc_final: 0.7589 (tmtt) REVERT: A 730 PHE cc_start: 0.8119 (t80) cc_final: 0.7744 (t80) REVERT: A 734 ARG cc_start: 0.8503 (ttt-90) cc_final: 0.8118 (ttp80) REVERT: A 738 HIS cc_start: 0.8120 (t70) cc_final: 0.7854 (t-170) REVERT: A 743 GLU cc_start: 0.8322 (mm-30) cc_final: 0.7804 (mp0) REVERT: A 753 GLU cc_start: 0.8604 (mp0) cc_final: 0.8246 (mp0) REVERT: A 754 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8362 (mp0) REVERT: A 756 GLU cc_start: 0.7635 (tp30) cc_final: 0.7110 (tp30) REVERT: A 788 ARG cc_start: 0.8453 (ptt180) cc_final: 0.7978 (ptt180) REVERT: A 792 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8107 (mm-30) REVERT: A 797 PHE cc_start: 0.6843 (m-80) cc_final: 0.6479 (m-80) REVERT: A 822 LYS cc_start: 0.8366 (mptt) cc_final: 0.7999 (mmtm) REVERT: D 21 GLN cc_start: 0.8084 (mt0) cc_final: 0.7837 (mp10) REVERT: D 22 LEU cc_start: 0.8335 (mm) cc_final: 0.7964 (mm) REVERT: D 65 ASN cc_start: 0.8325 (m-40) cc_final: 0.7933 (m-40) REVERT: D 73 CYS cc_start: 0.6442 (m) cc_final: 0.6131 (m) REVERT: D 82 GLU cc_start: 0.8693 (tt0) cc_final: 0.8283 (tt0) REVERT: D 84 ARG cc_start: 0.7744 (mtt180) cc_final: 0.6723 (ttt180) REVERT: D 114 GLN cc_start: 0.8021 (mp10) cc_final: 0.7575 (mp10) REVERT: D 128 LYS cc_start: 0.8674 (mttt) cc_final: 0.8397 (mttt) REVERT: D 132 PHE cc_start: 0.7871 (m-80) cc_final: 0.7134 (m-80) REVERT: D 138 ARG cc_start: 0.7860 (ptt-90) cc_final: 0.6689 (ptt-90) REVERT: C 130 GLU cc_start: 0.8337 (pt0) cc_final: 0.7630 (pm20) REVERT: C 138 GLU cc_start: 0.8676 (mp0) cc_final: 0.8379 (mm-30) REVERT: C 246 LEU cc_start: 0.8258 (tp) cc_final: 0.8056 (tp) REVERT: C 283 TYR cc_start: 0.7917 (t80) cc_final: 0.7344 (t80) REVERT: C 287 PHE cc_start: 0.7727 (m-80) cc_final: 0.7497 (m-80) REVERT: C 304 MET cc_start: 0.4927 (tpt) cc_final: 0.4586 (tpt) REVERT: C 321 GLN cc_start: 0.8521 (mm-40) cc_final: 0.8145 (mm110) REVERT: C 328 TRP cc_start: 0.6901 (m100) cc_final: 0.6415 (m100) REVERT: C 332 ASN cc_start: 0.7659 (t0) cc_final: 0.7136 (t0) REVERT: C 334 ASP cc_start: 0.7768 (p0) cc_final: 0.7538 (p0) REVERT: C 337 ARG cc_start: 0.8239 (ttm170) cc_final: 0.7866 (tmm-80) REVERT: C 339 MET cc_start: 0.7366 (mtp) cc_final: 0.6996 (ttt) REVERT: C 344 GLN cc_start: 0.8474 (tp-100) cc_final: 0.7643 (tp-100) REVERT: C 373 LYS cc_start: 0.7874 (mtpp) cc_final: 0.7648 (mtpp) REVERT: C 376 LYS cc_start: 0.8552 (ttpt) cc_final: 0.8067 (tttt) REVERT: C 377 MET cc_start: 0.8419 (mtt) cc_final: 0.7781 (mtt) REVERT: C 382 ASN cc_start: 0.8402 (m-40) cc_final: 0.8098 (m110) REVERT: C 397 ASP cc_start: 0.7658 (t0) cc_final: 0.7059 (t0) REVERT: C 398 GLU cc_start: 0.8294 (pp20) cc_final: 0.7914 (pm20) REVERT: C 403 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7754 (tm-30) REVERT: C 406 GLU cc_start: 0.8613 (tp30) cc_final: 0.7928 (mt-10) REVERT: C 407 LEU cc_start: 0.8857 (mt) cc_final: 0.8522 (mt) REVERT: C 408 THR cc_start: 0.8607 (m) cc_final: 0.8298 (p) REVERT: C 409 LEU cc_start: 0.8731 (tp) cc_final: 0.8094 (pp) REVERT: C 410 GLN cc_start: 0.9038 (mm-40) cc_final: 0.7936 (mm-40) REVERT: C 411 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7397 (mt-10) REVERT: C 429 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8288 (mt-10) REVERT: C 477 PHE cc_start: 0.7725 (m-80) cc_final: 0.7212 (m-80) REVERT: C 478 MET cc_start: 0.8113 (mtp) cc_final: 0.7501 (mtp) REVERT: C 482 PHE cc_start: 0.7981 (p90) cc_final: 0.7689 (p90) REVERT: C 491 LEU cc_start: 0.8507 (mt) cc_final: 0.8156 (mt) REVERT: C 495 TYR cc_start: 0.7629 (m-10) cc_final: 0.7359 (m-10) REVERT: C 499 ILE cc_start: 0.7978 (tp) cc_final: 0.7669 (tp) REVERT: C 501 MET cc_start: 0.8108 (mtt) cc_final: 0.7835 (mtt) REVERT: C 502 TYR cc_start: 0.7670 (m-10) cc_final: 0.7432 (m-10) REVERT: C 505 ARG cc_start: 0.8801 (mtt90) cc_final: 0.8231 (mtt90) REVERT: C 507 ILE cc_start: 0.8513 (mt) cc_final: 0.8280 (mt) REVERT: C 520 ASN cc_start: 0.7555 (t0) cc_final: 0.7254 (p0) REVERT: C 522 TYR cc_start: 0.7990 (m-80) cc_final: 0.7339 (m-80) REVERT: C 530 ASP cc_start: 0.7883 (p0) cc_final: 0.7631 (p0) REVERT: C 539 ARG cc_start: 0.8513 (ttm-80) cc_final: 0.7974 (ptm160) REVERT: C 540 LEU cc_start: 0.9034 (mm) cc_final: 0.8759 (mm) REVERT: C 542 MET cc_start: 0.8064 (tpp) cc_final: 0.7330 (tpp) REVERT: C 545 MET cc_start: 0.7928 (mtm) cc_final: 0.7256 (mtm) REVERT: C 550 ASP cc_start: 0.7914 (p0) cc_final: 0.7537 (p0) REVERT: C 553 LYS cc_start: 0.8537 (mtmt) cc_final: 0.7823 (mtpp) REVERT: C 555 LEU cc_start: 0.8651 (tp) cc_final: 0.8300 (tp) REVERT: C 576 GLN cc_start: 0.8045 (tm-30) cc_final: 0.7607 (tm-30) REVERT: C 577 LEU cc_start: 0.8696 (mt) cc_final: 0.8295 (pp) REVERT: C 581 GLU cc_start: 0.8105 (pp20) cc_final: 0.7700 (pp20) REVERT: C 587 ILE cc_start: 0.8004 (tp) cc_final: 0.7688 (tp) REVERT: C 589 MET cc_start: 0.6417 (mtp) cc_final: 0.6037 (mtp) REVERT: C 603 PRO cc_start: 0.7594 (Cg_endo) cc_final: 0.7357 (Cg_exo) REVERT: C 617 ILE cc_start: 0.8612 (mm) cc_final: 0.8406 (mm) REVERT: C 619 LEU cc_start: 0.8850 (tp) cc_final: 0.8588 (tp) REVERT: C 621 LEU cc_start: 0.8188 (mm) cc_final: 0.7755 (mm) REVERT: C 625 ASN cc_start: 0.8496 (m110) cc_final: 0.8191 (m110) REVERT: C 626 ASN cc_start: 0.8058 (m110) cc_final: 0.7692 (m110) REVERT: C 635 MET cc_start: 0.8078 (mpp) cc_final: 0.7304 (mpp) REVERT: C 642 MET cc_start: 0.8138 (mmp) cc_final: 0.7901 (mmp) REVERT: C 649 ARG cc_start: 0.8704 (ttm170) cc_final: 0.8427 (mtm180) REVERT: C 658 LEU cc_start: 0.8493 (tp) cc_final: 0.8193 (tt) REVERT: C 663 LYS cc_start: 0.8184 (ptmm) cc_final: 0.7654 (ttpp) REVERT: C 667 GLU cc_start: 0.7964 (pp20) cc_final: 0.7645 (pp20) REVERT: C 707 ASN cc_start: 0.8267 (p0) cc_final: 0.7961 (m-40) REVERT: C 712 GLU cc_start: 0.8690 (tt0) cc_final: 0.8220 (tt0) REVERT: C 716 LEU cc_start: 0.8713 (mt) cc_final: 0.8146 (pp) REVERT: C 717 TYR cc_start: 0.8946 (t80) cc_final: 0.8514 (t80) REVERT: C 719 ASP cc_start: 0.8266 (m-30) cc_final: 0.7993 (m-30) REVERT: C 720 TYR cc_start: 0.7880 (t80) cc_final: 0.7362 (t80) REVERT: C 730 PHE cc_start: 0.8010 (t80) cc_final: 0.7602 (t80) REVERT: C 734 ARG cc_start: 0.8681 (ttt-90) cc_final: 0.8266 (ttm170) REVERT: C 738 HIS cc_start: 0.8299 (t-170) cc_final: 0.8048 (t-170) REVERT: C 739 MET cc_start: 0.7845 (ptp) cc_final: 0.7535 (ptp) REVERT: C 743 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8009 (mm-30) REVERT: C 747 LYS cc_start: 0.9075 (mtpt) cc_final: 0.8609 (mmtt) REVERT: C 748 TYR cc_start: 0.7423 (t80) cc_final: 0.6912 (t80) REVERT: C 754 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8182 (mt-10) REVERT: C 756 GLU cc_start: 0.7100 (tp30) cc_final: 0.6315 (tp30) REVERT: C 788 ARG cc_start: 0.8457 (ptt180) cc_final: 0.7991 (ptt180) REVERT: C 805 PHE cc_start: 0.8525 (t80) cc_final: 0.8096 (t80) REVERT: C 806 LEU cc_start: 0.8228 (mt) cc_final: 0.7732 (mt) REVERT: C 822 LYS cc_start: 0.8399 (mmtt) cc_final: 0.8046 (mmtm) REVERT: C 835 GLU cc_start: 0.7657 (pm20) cc_final: 0.7433 (pm20) outliers start: 0 outliers final: 0 residues processed: 509 average time/residue: 0.3423 time to fit residues: 235.9696 Evaluate side-chains 486 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 486 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 130 optimal weight: 3.9990 chunk 113 optimal weight: 0.1980 chunk 125 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 116 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 ASN A 554 GLN ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 723 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.138901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.111510 restraints weight = 29493.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.115987 restraints weight = 18242.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.119342 restraints weight = 12703.859| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.6075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13534 Z= 0.167 Angle : 0.661 8.965 18272 Z= 0.332 Chirality : 0.045 0.302 2014 Planarity : 0.005 0.125 2372 Dihedral : 4.909 20.767 1806 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % 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: -1.08 (0.21), residues: 1610 helix: -0.26 (0.18), residues: 812 sheet: -2.26 (0.62), residues: 68 loop : -0.96 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A 328 HIS 0.005 0.001 HIS C 655 PHE 0.036 0.002 PHE C 730 TYR 0.028 0.002 TYR C 301 ARG 0.009 0.001 ARG B 84 Details of bonding type rmsd hydrogen bonds : bond 0.03746 ( 502) hydrogen bonds : angle 5.02710 ( 1392) metal coordination : bond 0.00657 ( 12) metal coordination : angle 5.12474 ( 12) covalent geometry : bond 0.00332 (13522) covalent geometry : angle 0.64836 (18260) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 517 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 18 LYS cc_start: 0.7780 (mmtm) cc_final: 0.7357 (mmmm) REVERT: B 22 LEU cc_start: 0.8357 (mm) cc_final: 0.7998 (mm) REVERT: B 65 ASN cc_start: 0.8464 (m-40) cc_final: 0.8060 (m-40) REVERT: B 73 CYS cc_start: 0.6001 (m) cc_final: 0.5558 (m) REVERT: B 74 LEU cc_start: 0.8656 (mm) cc_final: 0.8387 (mm) REVERT: B 77 TYR cc_start: 0.8172 (m-80) cc_final: 0.7688 (m-80) REVERT: B 82 GLU cc_start: 0.8769 (tt0) cc_final: 0.8295 (tt0) REVERT: B 108 ILE cc_start: 0.8139 (mt) cc_final: 0.7763 (tt) REVERT: B 114 GLN cc_start: 0.8101 (mp10) cc_final: 0.7838 (mp10) REVERT: B 124 ARG cc_start: 0.8688 (ttt-90) cc_final: 0.8268 (ttt-90) REVERT: B 128 LYS cc_start: 0.8819 (mttt) cc_final: 0.8512 (mttt) REVERT: B 132 PHE cc_start: 0.7724 (m-80) cc_final: 0.7111 (m-80) REVERT: B 134 ASN cc_start: 0.7910 (t0) cc_final: 0.7579 (t0) REVERT: B 136 ARG cc_start: 0.8175 (mmm160) cc_final: 0.7337 (mmm160) REVERT: A 130 GLU cc_start: 0.8444 (pt0) cc_final: 0.7591 (pm20) REVERT: A 237 ASP cc_start: 0.8529 (m-30) cc_final: 0.7935 (t0) REVERT: A 283 TYR cc_start: 0.7643 (t80) cc_final: 0.7432 (t80) REVERT: A 287 PHE cc_start: 0.7319 (m-80) cc_final: 0.6991 (m-80) REVERT: A 294 ARG cc_start: 0.8563 (mpt-90) cc_final: 0.8339 (mpt-90) REVERT: A 304 MET cc_start: 0.4595 (tpt) cc_final: 0.4095 (tpt) REVERT: A 332 ASN cc_start: 0.7533 (t0) cc_final: 0.7099 (t0) REVERT: A 337 ARG cc_start: 0.8264 (ttm170) cc_final: 0.7326 (ttp80) REVERT: A 338 ARG cc_start: 0.8088 (mtp85) cc_final: 0.7782 (mmm-85) REVERT: A 341 GLU cc_start: 0.8490 (mt-10) cc_final: 0.7775 (mt-10) REVERT: A 343 PHE cc_start: 0.8614 (m-80) cc_final: 0.8392 (m-80) REVERT: A 347 ILE cc_start: 0.7725 (mt) cc_final: 0.7494 (mt) REVERT: A 350 LYS cc_start: 0.7737 (mmpt) cc_final: 0.7279 (tptt) REVERT: A 392 HIS cc_start: 0.8344 (m90) cc_final: 0.7880 (m90) REVERT: A 395 GLU cc_start: 0.6569 (tm-30) cc_final: 0.6331 (tm-30) REVERT: A 411 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7988 (tm-30) REVERT: A 424 ARG cc_start: 0.7866 (mmm-85) cc_final: 0.7565 (tpp-160) REVERT: A 437 LEU cc_start: 0.8375 (mm) cc_final: 0.8165 (tt) REVERT: A 447 GLU cc_start: 0.8141 (mp0) cc_final: 0.7668 (tp30) REVERT: A 449 PHE cc_start: 0.7175 (m-10) cc_final: 0.6625 (m-10) REVERT: A 450 ILE cc_start: 0.8033 (mt) cc_final: 0.7449 (mt) REVERT: A 458 LEU cc_start: 0.8401 (tp) cc_final: 0.8014 (tt) REVERT: A 459 GLU cc_start: 0.7188 (mp0) cc_final: 0.6872 (mp0) REVERT: A 477 PHE cc_start: 0.7895 (m-80) cc_final: 0.7468 (m-80) REVERT: A 478 MET cc_start: 0.8097 (mtp) cc_final: 0.7636 (ttm) REVERT: A 482 PHE cc_start: 0.8002 (p90) cc_final: 0.7631 (p90) REVERT: A 497 ASN cc_start: 0.7944 (m-40) cc_final: 0.7573 (m-40) REVERT: A 499 ILE cc_start: 0.7856 (tp) cc_final: 0.7543 (tp) REVERT: A 501 MET cc_start: 0.7412 (mtt) cc_final: 0.7196 (mmp) REVERT: A 504 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7512 (mm-30) REVERT: A 505 ARG cc_start: 0.8791 (mtt90) cc_final: 0.8231 (mtt90) REVERT: A 507 ILE cc_start: 0.8737 (mt) cc_final: 0.8352 (mt) REVERT: A 522 TYR cc_start: 0.8187 (m-80) cc_final: 0.7426 (m-80) REVERT: A 530 ASP cc_start: 0.8019 (p0) cc_final: 0.7732 (p0) REVERT: A 533 ILE cc_start: 0.8551 (pt) cc_final: 0.8068 (mp) REVERT: A 539 ARG cc_start: 0.8522 (ttm-80) cc_final: 0.7888 (ptm160) REVERT: A 540 LEU cc_start: 0.9143 (mm) cc_final: 0.8861 (mm) REVERT: A 542 MET cc_start: 0.8399 (ptt) cc_final: 0.7714 (ptt) REVERT: A 545 MET cc_start: 0.7726 (mtm) cc_final: 0.7287 (mtm) REVERT: A 550 ASP cc_start: 0.7853 (p0) cc_final: 0.7427 (p0) REVERT: A 553 LYS cc_start: 0.8318 (mtmt) cc_final: 0.8057 (mtpp) REVERT: A 573 GLU cc_start: 0.7949 (pp20) cc_final: 0.7698 (pp20) REVERT: A 576 GLN cc_start: 0.8446 (tp40) cc_final: 0.7859 (tp40) REVERT: A 593 ASP cc_start: 0.8140 (t0) cc_final: 0.7723 (t70) REVERT: A 600 TRP cc_start: 0.8820 (t-100) cc_final: 0.8558 (t-100) REVERT: A 603 PRO cc_start: 0.7512 (Cg_endo) cc_final: 0.7228 (Cg_exo) REVERT: A 617 ILE cc_start: 0.8428 (mm) cc_final: 0.8200 (mm) REVERT: A 619 LEU cc_start: 0.8822 (tp) cc_final: 0.8516 (tp) REVERT: A 621 LEU cc_start: 0.8179 (mt) cc_final: 0.7955 (mt) REVERT: A 635 MET cc_start: 0.8033 (mpp) cc_final: 0.7311 (mpp) REVERT: A 641 LEU cc_start: 0.8564 (mt) cc_final: 0.8259 (mt) REVERT: A 642 MET cc_start: 0.8183 (mmp) cc_final: 0.7832 (mmp) REVERT: A 648 PHE cc_start: 0.8717 (p90) cc_final: 0.8210 (p90) REVERT: A 651 LEU cc_start: 0.8390 (mt) cc_final: 0.8073 (mt) REVERT: A 660 GLN cc_start: 0.8146 (pp30) cc_final: 0.7479 (pp30) REVERT: A 663 LYS cc_start: 0.8324 (ptmm) cc_final: 0.7688 (mptt) REVERT: A 667 GLU cc_start: 0.8219 (pp20) cc_final: 0.7890 (pp20) REVERT: A 682 ILE cc_start: 0.8261 (tp) cc_final: 0.8035 (tp) REVERT: A 711 LYS cc_start: 0.9282 (mmtt) cc_final: 0.8840 (mmtm) REVERT: A 712 GLU cc_start: 0.8694 (tt0) cc_final: 0.8381 (tt0) REVERT: A 716 LEU cc_start: 0.8827 (mt) cc_final: 0.8406 (tp) REVERT: A 717 TYR cc_start: 0.8903 (t80) cc_final: 0.8493 (t80) REVERT: A 728 LYS cc_start: 0.8353 (ttpt) cc_final: 0.7444 (tmtt) REVERT: A 734 ARG cc_start: 0.8578 (ttt-90) cc_final: 0.8376 (ttt90) REVERT: A 738 HIS cc_start: 0.8180 (t70) cc_final: 0.7664 (t-170) REVERT: A 743 GLU cc_start: 0.8437 (mm-30) cc_final: 0.7829 (mp0) REVERT: A 753 GLU cc_start: 0.8630 (mp0) cc_final: 0.8315 (mp0) REVERT: A 754 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8499 (mt-10) REVERT: A 756 GLU cc_start: 0.7700 (tp30) cc_final: 0.7216 (tp30) REVERT: A 763 ARG cc_start: 0.6973 (ttm-80) cc_final: 0.6692 (ttm-80) REVERT: A 788 ARG cc_start: 0.8474 (ptt180) cc_final: 0.7972 (ptt180) REVERT: A 792 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8145 (mm-30) REVERT: A 797 PHE cc_start: 0.6956 (m-80) cc_final: 0.6531 (m-80) REVERT: A 822 LYS cc_start: 0.8299 (mptt) cc_final: 0.7870 (mmtm) REVERT: D 22 LEU cc_start: 0.8534 (mm) cc_final: 0.8166 (mm) REVERT: D 47 ARG cc_start: 0.7832 (mmm160) cc_final: 0.7225 (mmm160) REVERT: D 65 ASN cc_start: 0.8491 (m-40) cc_final: 0.8070 (m-40) REVERT: D 73 CYS cc_start: 0.6639 (m) cc_final: 0.6229 (m) REVERT: D 77 TYR cc_start: 0.8194 (m-80) cc_final: 0.7761 (m-80) REVERT: D 82 GLU cc_start: 0.8686 (tt0) cc_final: 0.8203 (tt0) REVERT: D 84 ARG cc_start: 0.7850 (mtt180) cc_final: 0.7113 (ttt180) REVERT: D 108 ILE cc_start: 0.8144 (mt) cc_final: 0.7938 (mt) REVERT: D 114 GLN cc_start: 0.8152 (mp10) cc_final: 0.7817 (mp10) REVERT: D 128 LYS cc_start: 0.8705 (mttt) cc_final: 0.8408 (mttt) REVERT: D 132 PHE cc_start: 0.7945 (m-80) cc_final: 0.7145 (m-80) REVERT: D 138 ARG cc_start: 0.7957 (ptt-90) cc_final: 0.7171 (ptt-90) REVERT: C 130 GLU cc_start: 0.8347 (pt0) cc_final: 0.7631 (pm20) REVERT: C 138 GLU cc_start: 0.8646 (mp0) cc_final: 0.8259 (mm-30) REVERT: C 246 LEU cc_start: 0.8278 (tp) cc_final: 0.8065 (tp) REVERT: C 270 ASP cc_start: 0.7237 (t70) cc_final: 0.6959 (t0) REVERT: C 283 TYR cc_start: 0.7855 (t80) cc_final: 0.7478 (t80) REVERT: C 287 PHE cc_start: 0.7737 (m-80) cc_final: 0.7455 (m-80) REVERT: C 304 MET cc_start: 0.5091 (tpt) cc_final: 0.4742 (tpt) REVERT: C 330 LYS cc_start: 0.8762 (mmmt) cc_final: 0.8343 (mmtm) REVERT: C 332 ASN cc_start: 0.7675 (t0) cc_final: 0.7180 (t0) REVERT: C 337 ARG cc_start: 0.8214 (ttm170) cc_final: 0.7884 (tmm-80) REVERT: C 376 LYS cc_start: 0.8631 (ttpt) cc_final: 0.8187 (tttt) REVERT: C 382 ASN cc_start: 0.8528 (m-40) cc_final: 0.8124 (t0) REVERT: C 397 ASP cc_start: 0.7580 (t0) cc_final: 0.7206 (t0) REVERT: C 398 GLU cc_start: 0.8225 (pp20) cc_final: 0.7960 (pm20) REVERT: C 403 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7692 (tm-30) REVERT: C 406 GLU cc_start: 0.8612 (tp30) cc_final: 0.7759 (mt-10) REVERT: C 410 GLN cc_start: 0.9014 (mm-40) cc_final: 0.8096 (mm-40) REVERT: C 477 PHE cc_start: 0.7766 (m-80) cc_final: 0.7185 (m-80) REVERT: C 478 MET cc_start: 0.8187 (mtp) cc_final: 0.7712 (mtp) REVERT: C 482 PHE cc_start: 0.8079 (p90) cc_final: 0.7853 (p90) REVERT: C 491 LEU cc_start: 0.8538 (mt) cc_final: 0.8200 (mt) REVERT: C 495 TYR cc_start: 0.7711 (m-10) cc_final: 0.7453 (m-10) REVERT: C 499 ILE cc_start: 0.8029 (tp) cc_final: 0.7739 (tp) REVERT: C 501 MET cc_start: 0.8098 (mtt) cc_final: 0.7794 (mtt) REVERT: C 502 TYR cc_start: 0.7678 (m-10) cc_final: 0.7476 (m-10) REVERT: C 505 ARG cc_start: 0.8765 (mtt90) cc_final: 0.8246 (mtt90) REVERT: C 507 ILE cc_start: 0.8510 (mt) cc_final: 0.8276 (mt) REVERT: C 520 ASN cc_start: 0.7597 (t0) cc_final: 0.7206 (p0) REVERT: C 522 TYR cc_start: 0.8064 (m-80) cc_final: 0.7399 (m-80) REVERT: C 531 HIS cc_start: 0.7683 (m90) cc_final: 0.7479 (m90) REVERT: C 539 ARG cc_start: 0.8571 (ttm-80) cc_final: 0.8014 (ptm160) REVERT: C 540 LEU cc_start: 0.9064 (mm) cc_final: 0.8781 (mm) REVERT: C 541 GLU cc_start: 0.8176 (tt0) cc_final: 0.7247 (tt0) REVERT: C 542 MET cc_start: 0.8160 (tpp) cc_final: 0.7441 (tpp) REVERT: C 543 ILE cc_start: 0.8777 (mt) cc_final: 0.8535 (mt) REVERT: C 545 MET cc_start: 0.7912 (mtm) cc_final: 0.7226 (mtm) REVERT: C 553 LYS cc_start: 0.8529 (mtmt) cc_final: 0.7692 (mtpp) REVERT: C 555 LEU cc_start: 0.8632 (tp) cc_final: 0.8279 (tp) REVERT: C 573 GLU cc_start: 0.8108 (pm20) cc_final: 0.7643 (pp20) REVERT: C 576 GLN cc_start: 0.8144 (tm-30) cc_final: 0.7596 (tm-30) REVERT: C 577 LEU cc_start: 0.8746 (mt) cc_final: 0.8097 (mt) REVERT: C 581 GLU cc_start: 0.8163 (pp20) cc_final: 0.7842 (pp20) REVERT: C 587 ILE cc_start: 0.8106 (tp) cc_final: 0.7834 (tp) REVERT: C 589 MET cc_start: 0.6334 (mtp) cc_final: 0.6032 (mtp) REVERT: C 617 ILE cc_start: 0.8621 (mm) cc_final: 0.8369 (mm) REVERT: C 619 LEU cc_start: 0.8873 (tp) cc_final: 0.8599 (tp) REVERT: C 621 LEU cc_start: 0.8178 (mm) cc_final: 0.7678 (mm) REVERT: C 625 ASN cc_start: 0.8606 (m110) cc_final: 0.8348 (m110) REVERT: C 630 ASP cc_start: 0.7408 (t70) cc_final: 0.7177 (t0) REVERT: C 635 MET cc_start: 0.8092 (mpp) cc_final: 0.7378 (mpp) REVERT: C 642 MET cc_start: 0.8167 (mmp) cc_final: 0.7873 (mmp) REVERT: C 649 ARG cc_start: 0.8722 (ttm170) cc_final: 0.8410 (mtm180) REVERT: C 651 LEU cc_start: 0.8517 (mt) cc_final: 0.8258 (mt) REVERT: C 659 TYR cc_start: 0.8828 (t80) cc_final: 0.8607 (t80) REVERT: C 660 GLN cc_start: 0.8518 (mm-40) cc_final: 0.7972 (mm-40) REVERT: C 663 LYS cc_start: 0.8321 (ptmm) cc_final: 0.7881 (ttpp) REVERT: C 667 GLU cc_start: 0.8010 (pp20) cc_final: 0.7654 (pp20) REVERT: C 682 ILE cc_start: 0.7881 (tp) cc_final: 0.7675 (tp) REVERT: C 712 GLU cc_start: 0.8751 (tt0) cc_final: 0.8355 (tt0) REVERT: C 716 LEU cc_start: 0.8791 (mt) cc_final: 0.8229 (pp) REVERT: C 717 TYR cc_start: 0.9005 (t80) cc_final: 0.8600 (t80) REVERT: C 719 ASP cc_start: 0.8307 (m-30) cc_final: 0.8062 (m-30) REVERT: C 720 TYR cc_start: 0.8038 (t80) cc_final: 0.7435 (t80) REVERT: C 730 PHE cc_start: 0.8066 (t80) cc_final: 0.7733 (t80) REVERT: C 738 HIS cc_start: 0.8306 (t-170) cc_final: 0.7970 (t-90) REVERT: C 743 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8074 (mm-30) REVERT: C 747 LYS cc_start: 0.9126 (mtpt) cc_final: 0.8541 (mmmm) REVERT: C 748 TYR cc_start: 0.7482 (t80) cc_final: 0.6799 (t80) REVERT: C 756 GLU cc_start: 0.7329 (tp30) cc_final: 0.6567 (tp30) REVERT: C 763 ARG cc_start: 0.7393 (tpp-160) cc_final: 0.7120 (tpp-160) REVERT: C 788 ARG cc_start: 0.8391 (ptt180) cc_final: 0.7623 (ptt180) REVERT: C 801 GLN cc_start: 0.8275 (mp10) cc_final: 0.8021 (mp10) REVERT: C 805 PHE cc_start: 0.8561 (t80) cc_final: 0.8231 (t80) REVERT: C 806 LEU cc_start: 0.8272 (mt) cc_final: 0.7930 (mt) REVERT: C 822 LYS cc_start: 0.8354 (mmtt) cc_final: 0.7995 (mmtm) REVERT: C 855 LYS cc_start: 0.8991 (tttt) cc_final: 0.8527 (tptt) outliers start: 0 outliers final: 0 residues processed: 517 average time/residue: 0.3213 time to fit residues: 221.6413 Evaluate side-chains 498 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 498 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 117 optimal weight: 0.9990 chunk 150 optimal weight: 0.7980 chunk 60 optimal weight: 0.0980 chunk 147 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 121 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 21 optimal weight: 0.0050 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 554 GLN A 715 ASN A 723 ASN ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 723 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.142365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.115033 restraints weight = 29662.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.119779 restraints weight = 18112.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.123196 restraints weight = 12401.808| |-----------------------------------------------------------------------------| r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.6329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13534 Z= 0.120 Angle : 0.640 10.126 18272 Z= 0.321 Chirality : 0.044 0.207 2014 Planarity : 0.005 0.082 2372 Dihedral : 4.764 19.483 1806 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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: -1.09 (0.21), residues: 1610 helix: -0.26 (0.18), residues: 822 sheet: -2.12 (0.63), residues: 68 loop : -1.01 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP D 139 HIS 0.007 0.001 HIS C 655 PHE 0.028 0.001 PHE C 730 TYR 0.025 0.001 TYR C 301 ARG 0.007 0.000 ARG B 84 Details of bonding type rmsd hydrogen bonds : bond 0.03563 ( 502) hydrogen bonds : angle 5.04971 ( 1392) metal coordination : bond 0.00384 ( 12) metal coordination : angle 3.18423 ( 12) covalent geometry : bond 0.00256 (13522) covalent geometry : angle 0.63514 (18260) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 515 time to evaluate : 1.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 18 LYS cc_start: 0.7675 (mmtm) cc_final: 0.7263 (mmmm) REVERT: B 22 LEU cc_start: 0.8300 (mm) cc_final: 0.7924 (mm) REVERT: B 59 ILE cc_start: 0.7632 (mm) cc_final: 0.7251 (mm) REVERT: B 65 ASN cc_start: 0.8354 (m-40) cc_final: 0.7964 (m-40) REVERT: B 73 CYS cc_start: 0.5841 (m) cc_final: 0.5488 (m) REVERT: B 77 TYR cc_start: 0.8138 (m-80) cc_final: 0.7666 (m-80) REVERT: B 82 GLU cc_start: 0.8712 (tt0) cc_final: 0.8302 (tt0) REVERT: B 108 ILE cc_start: 0.8126 (mt) cc_final: 0.7715 (tt) REVERT: B 114 GLN cc_start: 0.8095 (mp10) cc_final: 0.7789 (mp10) REVERT: B 124 ARG cc_start: 0.8737 (ttt-90) cc_final: 0.8308 (ttt-90) REVERT: B 128 LYS cc_start: 0.8811 (mttt) cc_final: 0.8463 (mttt) REVERT: B 132 PHE cc_start: 0.7735 (m-80) cc_final: 0.7129 (m-80) REVERT: B 136 ARG cc_start: 0.8107 (mmm160) cc_final: 0.7336 (mmm160) REVERT: A 130 GLU cc_start: 0.8435 (pt0) cc_final: 0.7536 (pm20) REVERT: A 237 ASP cc_start: 0.8407 (m-30) cc_final: 0.7788 (t0) REVERT: A 260 LEU cc_start: 0.9022 (mm) cc_final: 0.8759 (pp) REVERT: A 283 TYR cc_start: 0.7674 (t80) cc_final: 0.7280 (t80) REVERT: A 287 PHE cc_start: 0.7430 (m-80) cc_final: 0.7100 (m-80) REVERT: A 288 ILE cc_start: 0.8682 (tt) cc_final: 0.8250 (tt) REVERT: A 291 MET cc_start: 0.8306 (ttt) cc_final: 0.7893 (ptt) REVERT: A 292 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7775 (mm-30) REVERT: A 294 ARG cc_start: 0.8512 (mpt-90) cc_final: 0.8292 (mpt-90) REVERT: A 304 MET cc_start: 0.4598 (tpt) cc_final: 0.4077 (tpt) REVERT: A 332 ASN cc_start: 0.7526 (t0) cc_final: 0.6927 (t0) REVERT: A 337 ARG cc_start: 0.8301 (ttm170) cc_final: 0.7228 (ttp80) REVERT: A 338 ARG cc_start: 0.8123 (mtp85) cc_final: 0.7288 (mmm-85) REVERT: A 341 GLU cc_start: 0.8543 (mt-10) cc_final: 0.7174 (mt-10) REVERT: A 343 PHE cc_start: 0.8603 (m-80) cc_final: 0.8228 (m-80) REVERT: A 350 LYS cc_start: 0.7539 (mmpt) cc_final: 0.7313 (mmtt) REVERT: A 392 HIS cc_start: 0.8304 (m90) cc_final: 0.7827 (m90) REVERT: A 395 GLU cc_start: 0.6442 (tm-30) cc_final: 0.6234 (tm-30) REVERT: A 404 SER cc_start: 0.8800 (p) cc_final: 0.8545 (p) REVERT: A 406 GLU cc_start: 0.8248 (tp30) cc_final: 0.7817 (mt-10) REVERT: A 410 GLN cc_start: 0.8678 (mm110) cc_final: 0.8345 (mm-40) REVERT: A 411 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7893 (tm-30) REVERT: A 424 ARG cc_start: 0.7817 (mmm-85) cc_final: 0.7374 (tpt-90) REVERT: A 447 GLU cc_start: 0.8143 (mp0) cc_final: 0.7741 (tp30) REVERT: A 449 PHE cc_start: 0.7169 (m-10) cc_final: 0.6600 (m-80) REVERT: A 450 ILE cc_start: 0.7954 (mt) cc_final: 0.7438 (mt) REVERT: A 455 ASN cc_start: 0.8013 (m-40) cc_final: 0.7788 (m-40) REVERT: A 458 LEU cc_start: 0.8374 (tp) cc_final: 0.7996 (tt) REVERT: A 459 GLU cc_start: 0.7120 (mp0) cc_final: 0.6796 (mp0) REVERT: A 467 PHE cc_start: 0.8550 (t80) cc_final: 0.7306 (t80) REVERT: A 477 PHE cc_start: 0.7800 (m-80) cc_final: 0.7412 (m-80) REVERT: A 478 MET cc_start: 0.8132 (mtp) cc_final: 0.7008 (ttm) REVERT: A 482 PHE cc_start: 0.7919 (p90) cc_final: 0.7576 (p90) REVERT: A 497 ASN cc_start: 0.7749 (m-40) cc_final: 0.7334 (m-40) REVERT: A 499 ILE cc_start: 0.7724 (tp) cc_final: 0.7403 (tp) REVERT: A 501 MET cc_start: 0.7375 (mtt) cc_final: 0.7055 (mmp) REVERT: A 504 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7597 (mm-30) REVERT: A 505 ARG cc_start: 0.8775 (mtt90) cc_final: 0.8201 (mtt90) REVERT: A 507 ILE cc_start: 0.8710 (mt) cc_final: 0.8283 (mt) REVERT: A 522 TYR cc_start: 0.8180 (m-80) cc_final: 0.7387 (m-80) REVERT: A 532 ILE cc_start: 0.8667 (pt) cc_final: 0.8156 (mm) REVERT: A 533 ILE cc_start: 0.8442 (pt) cc_final: 0.8130 (mp) REVERT: A 539 ARG cc_start: 0.8423 (ttm-80) cc_final: 0.7842 (ptm160) REVERT: A 542 MET cc_start: 0.8395 (ptt) cc_final: 0.7624 (ptt) REVERT: A 545 MET cc_start: 0.7700 (mtm) cc_final: 0.7211 (mtm) REVERT: A 550 ASP cc_start: 0.7841 (p0) cc_final: 0.7413 (p0) REVERT: A 572 LYS cc_start: 0.7923 (mmtt) cc_final: 0.7654 (tptt) REVERT: A 573 GLU cc_start: 0.7872 (pp20) cc_final: 0.7622 (pp20) REVERT: A 576 GLN cc_start: 0.8470 (tp40) cc_final: 0.7947 (tp40) REVERT: A 581 GLU cc_start: 0.8431 (pp20) cc_final: 0.8117 (pp20) REVERT: A 593 ASP cc_start: 0.8144 (t0) cc_final: 0.7754 (t70) REVERT: A 600 TRP cc_start: 0.8757 (t-100) cc_final: 0.8532 (t-100) REVERT: A 603 PRO cc_start: 0.7572 (Cg_endo) cc_final: 0.7293 (Cg_exo) REVERT: A 619 LEU cc_start: 0.8834 (tp) cc_final: 0.8098 (tp) REVERT: A 625 ASN cc_start: 0.7807 (p0) cc_final: 0.7569 (p0) REVERT: A 635 MET cc_start: 0.8059 (mpp) cc_final: 0.7347 (mpp) REVERT: A 641 LEU cc_start: 0.8552 (mt) cc_final: 0.8280 (mm) REVERT: A 642 MET cc_start: 0.8116 (mmp) cc_final: 0.7832 (mmp) REVERT: A 651 LEU cc_start: 0.8332 (mt) cc_final: 0.8022 (mt) REVERT: A 660 GLN cc_start: 0.8184 (pp30) cc_final: 0.7558 (pp30) REVERT: A 663 LYS cc_start: 0.8287 (ptmm) cc_final: 0.7685 (mptt) REVERT: A 667 GLU cc_start: 0.8185 (pp20) cc_final: 0.7844 (pp20) REVERT: A 668 TYR cc_start: 0.7265 (t80) cc_final: 0.6501 (t80) REVERT: A 711 LYS cc_start: 0.9296 (mmtt) cc_final: 0.8801 (mmtm) REVERT: A 712 GLU cc_start: 0.8622 (tt0) cc_final: 0.8320 (tt0) REVERT: A 716 LEU cc_start: 0.8774 (mt) cc_final: 0.8256 (tt) REVERT: A 717 TYR cc_start: 0.8900 (t80) cc_final: 0.8532 (t80) REVERT: A 719 ASP cc_start: 0.8148 (m-30) cc_final: 0.7841 (m-30) REVERT: A 727 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7764 (mm-30) REVERT: A 737 PHE cc_start: 0.8090 (t80) cc_final: 0.7603 (t80) REVERT: A 738 HIS cc_start: 0.8105 (t70) cc_final: 0.7546 (t-170) REVERT: A 743 GLU cc_start: 0.8374 (mm-30) cc_final: 0.7928 (mm-30) REVERT: A 747 LYS cc_start: 0.9013 (mtmt) cc_final: 0.8630 (mmmt) REVERT: A 748 TYR cc_start: 0.7364 (t80) cc_final: 0.6854 (t80) REVERT: A 753 GLU cc_start: 0.8565 (mp0) cc_final: 0.8227 (mp0) REVERT: A 754 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8423 (mt-10) REVERT: A 756 GLU cc_start: 0.7594 (tp30) cc_final: 0.7203 (tp30) REVERT: A 788 ARG cc_start: 0.8423 (ptt180) cc_final: 0.7931 (ptt180) REVERT: A 792 GLU cc_start: 0.8403 (mm-30) cc_final: 0.8060 (mm-30) REVERT: A 797 PHE cc_start: 0.6667 (m-80) cc_final: 0.6336 (m-80) REVERT: A 822 LYS cc_start: 0.8235 (mptt) cc_final: 0.7912 (mmtm) REVERT: D 18 LYS cc_start: 0.7579 (mmtm) cc_final: 0.7288 (mmmm) REVERT: D 22 LEU cc_start: 0.8427 (mm) cc_final: 0.8079 (mm) REVERT: D 47 ARG cc_start: 0.7767 (mmm160) cc_final: 0.7144 (mmm160) REVERT: D 65 ASN cc_start: 0.8293 (m-40) cc_final: 0.7876 (m-40) REVERT: D 73 CYS cc_start: 0.6301 (m) cc_final: 0.6063 (m) REVERT: D 82 GLU cc_start: 0.8519 (tt0) cc_final: 0.8063 (tt0) REVERT: D 84 ARG cc_start: 0.7822 (mtt180) cc_final: 0.7084 (ttt180) REVERT: D 98 GLN cc_start: 0.8573 (mp10) cc_final: 0.8308 (mp10) REVERT: D 114 GLN cc_start: 0.8105 (mp10) cc_final: 0.7707 (mp10) REVERT: D 128 LYS cc_start: 0.8698 (mttt) cc_final: 0.8332 (mttt) REVERT: D 132 PHE cc_start: 0.7813 (m-80) cc_final: 0.7161 (m-80) REVERT: D 138 ARG cc_start: 0.7845 (ptt-90) cc_final: 0.6752 (ptt-90) REVERT: C 130 GLU cc_start: 0.8351 (pt0) cc_final: 0.7565 (pm20) REVERT: C 138 GLU cc_start: 0.8425 (mp0) cc_final: 0.7798 (mp0) REVERT: C 246 LEU cc_start: 0.8274 (tp) cc_final: 0.8037 (tp) REVERT: C 270 ASP cc_start: 0.7370 (t70) cc_final: 0.7124 (t0) REVERT: C 283 TYR cc_start: 0.7820 (t80) cc_final: 0.7410 (t80) REVERT: C 287 PHE cc_start: 0.7686 (m-80) cc_final: 0.7410 (m-80) REVERT: C 304 MET cc_start: 0.5004 (tpt) cc_final: 0.4634 (tpt) REVERT: C 321 GLN cc_start: 0.8524 (mm-40) cc_final: 0.8098 (mm110) REVERT: C 326 ARG cc_start: 0.8119 (mtm180) cc_final: 0.7719 (mtt180) REVERT: C 328 TRP cc_start: 0.6845 (m100) cc_final: 0.6130 (m100) REVERT: C 332 ASN cc_start: 0.7768 (t0) cc_final: 0.7329 (t0) REVERT: C 337 ARG cc_start: 0.8271 (ttm170) cc_final: 0.7824 (tmm-80) REVERT: C 338 ARG cc_start: 0.7652 (mmm-85) cc_final: 0.7137 (mmm-85) REVERT: C 339 MET cc_start: 0.7347 (mtp) cc_final: 0.6921 (ttt) REVERT: C 345 GLN cc_start: 0.8226 (mt0) cc_final: 0.7350 (tp40) REVERT: C 373 LYS cc_start: 0.8052 (mtpt) cc_final: 0.7815 (mtpt) REVERT: C 377 MET cc_start: 0.8333 (mtt) cc_final: 0.7771 (mtt) REVERT: C 382 ASN cc_start: 0.8458 (m-40) cc_final: 0.8116 (t0) REVERT: C 397 ASP cc_start: 0.7445 (t0) cc_final: 0.7143 (t0) REVERT: C 398 GLU cc_start: 0.8185 (pp20) cc_final: 0.7881 (pm20) REVERT: C 403 GLU cc_start: 0.8122 (tm-30) cc_final: 0.7673 (tm-30) REVERT: C 406 GLU cc_start: 0.8614 (tp30) cc_final: 0.7925 (mt-10) REVERT: C 407 LEU cc_start: 0.8976 (mt) cc_final: 0.8643 (pp) REVERT: C 408 THR cc_start: 0.8731 (m) cc_final: 0.8419 (p) REVERT: C 410 GLN cc_start: 0.9030 (mm-40) cc_final: 0.8193 (mm-40) REVERT: C 447 GLU cc_start: 0.7680 (pm20) cc_final: 0.7454 (tp30) REVERT: C 450 ILE cc_start: 0.8023 (mt) cc_final: 0.6297 (mt) REVERT: C 477 PHE cc_start: 0.7906 (m-80) cc_final: 0.7316 (m-80) REVERT: C 478 MET cc_start: 0.8092 (mtp) cc_final: 0.7402 (mtp) REVERT: C 482 PHE cc_start: 0.7994 (p90) cc_final: 0.7736 (p90) REVERT: C 491 LEU cc_start: 0.8506 (mt) cc_final: 0.8147 (mt) REVERT: C 493 LEU cc_start: 0.8039 (tp) cc_final: 0.7682 (tp) REVERT: C 495 TYR cc_start: 0.7648 (m-10) cc_final: 0.7373 (m-10) REVERT: C 499 ILE cc_start: 0.7970 (tp) cc_final: 0.7641 (tp) REVERT: C 501 MET cc_start: 0.8094 (mtt) cc_final: 0.7577 (mtt) REVERT: C 502 TYR cc_start: 0.7695 (m-10) cc_final: 0.7342 (m-10) REVERT: C 505 ARG cc_start: 0.8804 (mtt90) cc_final: 0.8244 (mtt90) REVERT: C 507 ILE cc_start: 0.8427 (mt) cc_final: 0.8201 (mt) REVERT: C 520 ASN cc_start: 0.7537 (t0) cc_final: 0.7319 (p0) REVERT: C 522 TYR cc_start: 0.8033 (m-80) cc_final: 0.7434 (m-80) REVERT: C 523 LEU cc_start: 0.8449 (tp) cc_final: 0.8136 (tp) REVERT: C 530 ASP cc_start: 0.7984 (p0) cc_final: 0.7647 (p0) REVERT: C 539 ARG cc_start: 0.8480 (ttm-80) cc_final: 0.8089 (ttm-80) REVERT: C 542 MET cc_start: 0.8090 (tpp) cc_final: 0.7405 (tpp) REVERT: C 543 ILE cc_start: 0.8788 (mt) cc_final: 0.8565 (mt) REVERT: C 545 MET cc_start: 0.7915 (mtm) cc_final: 0.7258 (mtm) REVERT: C 553 LYS cc_start: 0.8505 (mtmt) cc_final: 0.7846 (mmmt) REVERT: C 554 GLN cc_start: 0.7988 (tt0) cc_final: 0.6678 (tt0) REVERT: C 555 LEU cc_start: 0.8624 (tp) cc_final: 0.8331 (tp) REVERT: C 576 GLN cc_start: 0.8015 (tm-30) cc_final: 0.7638 (tm-30) REVERT: C 577 LEU cc_start: 0.8788 (mt) cc_final: 0.8427 (pp) REVERT: C 581 GLU cc_start: 0.8156 (pp20) cc_final: 0.7784 (pp20) REVERT: C 587 ILE cc_start: 0.7961 (tp) cc_final: 0.7747 (tp) REVERT: C 589 MET cc_start: 0.6389 (mtp) cc_final: 0.6009 (mtp) REVERT: C 617 ILE cc_start: 0.8587 (mm) cc_final: 0.8309 (mm) REVERT: C 619 LEU cc_start: 0.8896 (tp) cc_final: 0.8634 (tp) REVERT: C 621 LEU cc_start: 0.8150 (mm) cc_final: 0.7677 (mm) REVERT: C 625 ASN cc_start: 0.8569 (m110) cc_final: 0.8213 (m110) REVERT: C 635 MET cc_start: 0.8136 (mpp) cc_final: 0.7384 (mpp) REVERT: C 642 MET cc_start: 0.8112 (mmp) cc_final: 0.7787 (mmp) REVERT: C 651 LEU cc_start: 0.8485 (mt) cc_final: 0.8095 (mm) REVERT: C 660 GLN cc_start: 0.8459 (mm-40) cc_final: 0.8043 (mm-40) REVERT: C 667 GLU cc_start: 0.7985 (pp20) cc_final: 0.7653 (pp20) REVERT: C 676 MET cc_start: 0.7628 (mmp) cc_final: 0.7276 (mmp) REVERT: C 707 ASN cc_start: 0.8242 (p0) cc_final: 0.7688 (m-40) REVERT: C 712 GLU cc_start: 0.8756 (tt0) cc_final: 0.8451 (tt0) REVERT: C 715 ASN cc_start: 0.8785 (m-40) cc_final: 0.8570 (m110) REVERT: C 716 LEU cc_start: 0.8770 (mt) cc_final: 0.8247 (pp) REVERT: C 717 TYR cc_start: 0.8984 (t80) cc_final: 0.8600 (t80) REVERT: C 719 ASP cc_start: 0.8308 (m-30) cc_final: 0.8067 (m-30) REVERT: C 720 TYR cc_start: 0.7998 (t80) cc_final: 0.7392 (t80) REVERT: C 730 PHE cc_start: 0.8141 (t80) cc_final: 0.7759 (t80) REVERT: C 738 HIS cc_start: 0.8223 (t-170) cc_final: 0.7841 (t-170) REVERT: C 739 MET cc_start: 0.8060 (ptp) cc_final: 0.7348 (ptp) REVERT: C 743 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8016 (mm-30) REVERT: C 747 LYS cc_start: 0.9041 (mtpt) cc_final: 0.8499 (ttmm) REVERT: C 748 TYR cc_start: 0.7398 (t80) cc_final: 0.6842 (t80) REVERT: C 756 GLU cc_start: 0.7263 (tp30) cc_final: 0.6491 (tp30) REVERT: C 788 ARG cc_start: 0.8360 (ptt180) cc_final: 0.7612 (ptt180) REVERT: C 797 PHE cc_start: 0.6367 (m-80) cc_final: 0.5969 (m-80) REVERT: C 805 PHE cc_start: 0.8448 (t80) cc_final: 0.8143 (t80) REVERT: C 806 LEU cc_start: 0.8304 (mt) cc_final: 0.7947 (mt) REVERT: C 822 LYS cc_start: 0.8421 (mmtt) cc_final: 0.7966 (mmtm) REVERT: C 835 GLU cc_start: 0.7663 (pm20) cc_final: 0.7445 (pm20) REVERT: C 855 LYS cc_start: 0.9017 (tttt) cc_final: 0.8595 (tptt) outliers start: 0 outliers final: 0 residues processed: 515 average time/residue: 0.3215 time to fit residues: 221.9623 Evaluate side-chains 494 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 494 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 29 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 chunk 99 optimal weight: 8.9990 chunk 21 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 109 optimal weight: 0.0970 chunk 43 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 56 optimal weight: 0.3980 chunk 35 optimal weight: 0.8980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 554 GLN A 684 GLN A 723 ASN ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 HIS C 723 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.142677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.115554 restraints weight = 29392.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.120270 restraints weight = 17803.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.123735 restraints weight = 12163.305| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.6492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13534 Z= 0.123 Angle : 0.650 11.246 18272 Z= 0.324 Chirality : 0.045 0.299 2014 Planarity : 0.004 0.073 2372 Dihedral : 4.741 20.992 1806 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: -0.97 (0.21), residues: 1610 helix: -0.16 (0.19), residues: 800 sheet: -1.96 (0.64), residues: 68 loop : -0.96 (0.23), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRP B 139 HIS 0.010 0.001 HIS C 297 PHE 0.027 0.002 PHE C 730 TYR 0.020 0.001 TYR A 134 ARG 0.008 0.000 ARG A 326 Details of bonding type rmsd hydrogen bonds : bond 0.03469 ( 502) hydrogen bonds : angle 5.03215 ( 1392) metal coordination : bond 0.00377 ( 12) metal coordination : angle 3.05601 ( 12) covalent geometry : bond 0.00264 (13522) covalent geometry : angle 0.64544 (18260) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5190.79 seconds wall clock time: 91 minutes 13.21 seconds (5473.21 seconds total)