Starting phenix.real_space_refine on Thu Jul 31 11:01:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jrq_36602/07_2025/8jrq_36602.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jrq_36602/07_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_36602/07_2025/8jrq_36602.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jrq_36602/07_2025/8jrq_36602.map" model { file = "/net/cci-nas-00/data/ceres_data/8jrq_36602/07_2025/8jrq_36602.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jrq_36602/07_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-5711/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: 11.72, per 1000 atoms: 0.88 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: 3.09 Conformation dependent library (CDL) restraints added in 1.6 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: 1.79 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: 3.97 Time building geometry restraints manager: 3.70 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: 0.07 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'A' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 37.510 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.610 ------------------------------------------------------------------------------- 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 : 1.804 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: 0.3151 time to fit residues: 241.0698 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 : 1.354 ------------------------------------------------------------------------------- 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 = 29)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.114695 restraints weight = 29734.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.119239 restraints weight = 18438.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.122618 restraints weight = 12813.226| |-----------------------------------------------------------------------------| 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 9.53316 ( 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 : 1.561 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: 0.8179 (tt) cc_final: 0.7770 (tt) REVERT: B 42 GLN cc_start: 0.8493 (mt0) cc_final: 0.8201 (mt0) REVERT: B 59 ILE cc_start: 0.7678 (mm) cc_final: 0.7256 (tp) REVERT: B 65 ASN cc_start: 0.8377 (m-40) cc_final: 0.8127 (m-40) REVERT: B 73 CYS cc_start: 0.7511 (m) cc_final: 0.7051 (m) REVERT: B 76 PHE cc_start: 0.8505 (t80) cc_final: 0.8096 (t80) REVERT: B 80 ILE cc_start: 0.8723 (mm) cc_final: 0.8381 (mm) REVERT: B 88 TYR cc_start: 0.7253 (p90) cc_final: 0.6918 (p90) REVERT: B 108 ILE cc_start: 0.8084 (mt) cc_final: 0.7678 (tt) REVERT: B 128 LYS cc_start: 0.8371 (mttt) cc_final: 0.8034 (mmtt) REVERT: B 132 PHE cc_start: 0.7572 (m-80) cc_final: 0.6755 (m-80) REVERT: A 130 GLU cc_start: 0.8538 (pt0) cc_final: 0.7738 (pm20) REVERT: A 138 GLU cc_start: 0.8333 (mp0) cc_final: 0.7809 (mp0) REVERT: A 237 ASP cc_start: 0.8389 (m-30) cc_final: 0.7370 (t0) REVERT: A 260 LEU cc_start: 0.9078 (mm) cc_final: 0.8819 (mm) REVERT: A 283 TYR cc_start: 0.7847 (t80) cc_final: 0.7595 (t80) REVERT: A 287 PHE cc_start: 0.7291 (m-80) cc_final: 0.7027 (m-80) REVERT: A 291 MET cc_start: 0.8494 (ttt) cc_final: 0.7982 (ttm) REVERT: A 294 ARG cc_start: 0.8521 (mpt-90) cc_final: 0.8272 (mpt-90) REVERT: A 304 MET cc_start: 0.5295 (tpt) cc_final: 0.4717 (tpt) REVERT: A 315 LYS cc_start: 0.7963 (mmtm) cc_final: 0.7446 (mmtm) REVERT: A 332 ASN cc_start: 0.7806 (t0) cc_final: 0.7302 (t0) REVERT: A 337 ARG cc_start: 0.8166 (ttm170) cc_final: 0.7729 (ttp80) REVERT: A 341 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7583 (mt-10) REVERT: A 343 PHE cc_start: 0.9008 (m-80) cc_final: 0.8752 (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: 0.7561 (tp) cc_final: 0.7295 (tp) REVERT: A 392 HIS cc_start: 0.8080 (m90) cc_final: 0.7513 (m-70) REVERT: A 406 GLU cc_start: 0.8288 (tp30) cc_final: 0.7798 (tt0) REVERT: A 407 LEU cc_start: 0.8870 (mt) cc_final: 0.8653 (mt) REVERT: A 409 LEU cc_start: 0.8637 (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: 0.8217 (mp0) cc_final: 0.7608 (tp30) REVERT: A 449 PHE cc_start: 0.7586 (m-10) cc_final: 0.6978 (m-10) REVERT: A 450 ILE cc_start: 0.7943 (mt) cc_final: 0.7334 (mt) REVERT: A 455 ASN cc_start: 0.7978 (m110) cc_final: 0.7720 (m110) REVERT: A 458 LEU cc_start: 0.8477 (tp) cc_final: 0.7965 (tt) REVERT: A 464 TYR cc_start: 0.7971 (t80) cc_final: 0.7340 (t80) REVERT: A 477 PHE cc_start: 0.8181 (m-80) cc_final: 0.7795 (m-80) REVERT: A 478 MET cc_start: 0.8108 (mtp) cc_final: 0.7342 (mtp) REVERT: A 482 PHE cc_start: 0.8044 (p90) cc_final: 0.7717 (p90) REVERT: A 495 TYR cc_start: 0.7499 (m-10) cc_final: 0.7289 (m-10) REVERT: A 499 ILE cc_start: 0.7958 (tp) cc_final: 0.7639 (tp) REVERT: A 501 MET cc_start: 0.8255 (mtt) cc_final: 0.7279 (ptp) REVERT: A 504 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7562 (mm-30) REVERT: A 507 ILE cc_start: 0.8612 (mt) cc_final: 0.8173 (mt) REVERT: A 523 LEU cc_start: 0.8593 (tp) cc_final: 0.8132 (tp) REVERT: A 535 ASP cc_start: 0.7246 (m-30) cc_final: 0.6851 (m-30) REVERT: A 545 MET cc_start: 0.7997 (mtm) cc_final: 0.7460 (mtm) REVERT: A 546 GLU cc_start: 0.7385 (tt0) cc_final: 0.7151 (tt0) REVERT: A 550 ASP cc_start: 0.7951 (p0) cc_final: 0.7649 (p0) REVERT: A 553 LYS cc_start: 0.8561 (mtmt) cc_final: 0.8324 (mtpp) REVERT: A 572 LYS cc_start: 0.8551 (tttp) cc_final: 0.8211 (ttmm) REVERT: A 573 GLU cc_start: 0.8104 (pp20) cc_final: 0.7664 (pp20) REVERT: A 576 GLN cc_start: 0.8403 (tp-100) cc_final: 0.7667 (tp-100) REVERT: A 577 LEU cc_start: 0.8909 (mt) cc_final: 0.8486 (mt) REVERT: A 593 ASP cc_start: 0.8340 (t0) cc_final: 0.7939 (t0) REVERT: A 617 ILE cc_start: 0.8448 (mm) cc_final: 0.8082 (mm) REVERT: A 621 LEU cc_start: 0.8137 (mm) cc_final: 0.7774 (mp) REVERT: A 635 MET cc_start: 0.8174 (mpp) cc_final: 0.7424 (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: 0.8187 (mt) REVERT: A 658 LEU cc_start: 0.8417 (tp) cc_final: 0.7978 (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: 0.8186 (ptmm) cc_final: 0.7829 (ttpp) REVERT: A 711 LYS cc_start: 0.9222 (mmtt) cc_final: 0.8900 (mmtm) REVERT: A 716 LEU cc_start: 0.8729 (mt) cc_final: 0.8482 (mt) REVERT: A 717 TYR cc_start: 0.8408 (t80) cc_final: 0.8016 (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: 0.7805 (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: 0.7864 (mm-30) REVERT: A 751 ARG cc_start: 0.7794 (mtm-85) cc_final: 0.7398 (mmm160) REVERT: A 753 GLU cc_start: 0.8747 (mp0) cc_final: 0.8377 (mp0) REVERT: A 756 GLU cc_start: 0.8007 (tp30) cc_final: 0.7414 (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: 0.8291 (t80) REVERT: A 806 LEU cc_start: 0.8263 (mt) cc_final: 0.7923 (mt) REVERT: A 820 LEU cc_start: 0.7718 (mm) cc_final: 0.7505 (mm) REVERT: A 822 LYS cc_start: 0.8564 (mptt) cc_final: 0.8179 (mmtm) REVERT: A 862 LEU cc_start: 0.8603 (tt) cc_final: 0.8325 (mt) REVERT: D 42 GLN cc_start: 0.8552 (mt0) cc_final: 0.8263 (mt0) REVERT: D 47 ARG cc_start: 0.7770 (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: 0.7477 (m) cc_final: 0.6925 (m) REVERT: D 76 PHE cc_start: 0.8535 (t80) cc_final: 0.8019 (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: 0.8350 (mm) REVERT: D 88 TYR cc_start: 0.7184 (p90) cc_final: 0.6871 (p90) REVERT: D 94 THR cc_start: 0.7357 (p) cc_final: 0.6971 (p) REVERT: D 132 PHE cc_start: 0.7505 (m-80) cc_final: 0.6805 (m-80) REVERT: D 134 ASN cc_start: 0.7595 (t0) cc_final: 0.7072 (t0) REVERT: C 130 GLU cc_start: 0.8413 (pt0) cc_final: 0.8098 (pt0) REVERT: C 237 ASP cc_start: 0.8033 (m-30) cc_final: 0.7607 (t0) REVERT: C 241 ARG cc_start: 0.8690 (mtm-85) cc_final: 0.8447 (mtm-85) REVERT: C 260 LEU cc_start: 0.8970 (mm) cc_final: 0.8711 (mm) REVERT: C 287 PHE cc_start: 0.7527 (m-80) cc_final: 0.7253 (m-80) REVERT: C 291 MET cc_start: 0.8664 (ttt) cc_final: 0.8234 (ttt) REVERT: C 315 LYS cc_start: 0.7980 (mtmm) cc_final: 0.7477 (mttp) REVERT: C 321 GLN cc_start: 0.8427 (mt0) cc_final: 0.8186 (mm-40) REVERT: C 332 ASN cc_start: 0.7657 (t0) cc_final: 0.7191 (t0) REVERT: C 337 ARG cc_start: 0.8249 (ttm170) cc_final: 0.7674 (ttp80) REVERT: C 338 ARG cc_start: 0.8241 (mtp85) cc_final: 0.7528 (mtp-110) REVERT: C 344 GLN cc_start: 0.8468 (tp-100) cc_final: 0.7390 (tp-100) REVERT: C 349 TYR cc_start: 0.7898 (t80) cc_final: 0.7691 (t80) REVERT: C 376 LYS cc_start: 0.8545 (ttmt) cc_final: 0.7631 (tttt) REVERT: C 380 TYR cc_start: 0.8734 (m-10) cc_final: 0.8061 (m-10) REVERT: C 382 ASN cc_start: 0.8522 (m-40) cc_final: 0.8196 (m110) REVERT: C 394 GLU cc_start: 0.6340 (mm-30) cc_final: 0.6020 (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: 0.8102 (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: 0.7269 (mt-10) REVERT: C 426 ASP cc_start: 0.8582 (t70) cc_final: 0.8342 (t0) REVERT: C 447 GLU cc_start: 0.8076 (mp0) cc_final: 0.7488 (tp30) REVERT: C 449 PHE cc_start: 0.7815 (m-10) cc_final: 0.7172 (m-10) REVERT: C 450 ILE cc_start: 0.7869 (mt) cc_final: 0.7167 (mt) REVERT: C 458 LEU cc_start: 0.8805 (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: 0.8039 (p90) cc_final: 0.7726 (p90) REVERT: C 491 LEU cc_start: 0.8608 (mt) cc_final: 0.8319 (mt) REVERT: C 493 LEU cc_start: 0.8045 (tp) cc_final: 0.7654 (tp) REVERT: C 495 TYR cc_start: 0.7687 (m-10) cc_final: 0.7256 (m-10) REVERT: C 497 ASN cc_start: 0.8043 (m-40) cc_final: 0.7825 (m-40) REVERT: C 499 ILE cc_start: 0.8074 (tp) cc_final: 0.7742 (tp) REVERT: C 501 MET cc_start: 0.8244 (mtt) cc_final: 0.7871 (mtt) REVERT: C 502 TYR cc_start: 0.7632 (m-10) cc_final: 0.7205 (m-10) REVERT: C 505 ARG cc_start: 0.8769 (mtt90) cc_final: 0.8258 (mtt90) REVERT: C 507 ILE cc_start: 0.8563 (mt) cc_final: 0.8325 (mt) REVERT: C 542 MET cc_start: 0.8282 (tpp) cc_final: 0.7563 (tpp) REVERT: C 545 MET cc_start: 0.7970 (mtm) cc_final: 0.7264 (mtm) REVERT: C 546 GLU cc_start: 0.7496 (tt0) cc_final: 0.6875 (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: 0.7305 (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: 0.8246 (tp) REVERT: C 589 MET cc_start: 0.7035 (mtp) cc_final: 0.6642 (mtp) REVERT: C 600 TRP cc_start: 0.8779 (t-100) cc_final: 0.8572 (t-100) REVERT: C 619 LEU cc_start: 0.8737 (tp) cc_final: 0.8447 (tp) REVERT: C 621 LEU cc_start: 0.8321 (mm) cc_final: 0.7983 (mm) REVERT: C 625 ASN cc_start: 0.8457 (m110) cc_final: 0.8142 (m-40) REVERT: C 626 ASN cc_start: 0.7969 (m-40) cc_final: 0.7754 (m110) REVERT: C 635 MET cc_start: 0.7957 (mpp) cc_final: 0.7269 (mpp) REVERT: C 641 LEU cc_start: 0.8515 (mt) cc_final: 0.7952 (pp) REVERT: C 648 PHE cc_start: 0.8760 (p90) cc_final: 0.8341 (p90) REVERT: C 658 LEU cc_start: 0.8563 (tp) cc_final: 0.8157 (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: 0.8184 (m-30) cc_final: 0.6579 (p0) REVERT: C 667 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8404 (pp20) REVERT: C 711 LYS cc_start: 0.9190 (mmtt) cc_final: 0.8694 (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: 0.7772 (t80) cc_final: 0.7194 (t80) REVERT: C 730 PHE cc_start: 0.8226 (t80) cc_final: 0.7856 (t80) REVERT: C 738 HIS cc_start: 0.8305 (t-90) cc_final: 0.7695 (t-90) REVERT: C 739 MET cc_start: 0.7802 (ptm) cc_final: 0.7580 (ptm) REVERT: C 743 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8049 (mm-30) REVERT: C 748 TYR cc_start: 0.7618 (t80) cc_final: 0.7085 (t80) REVERT: C 753 GLU cc_start: 0.8691 (mp0) cc_final: 0.8402 (mp0) REVERT: C 756 GLU cc_start: 0.7866 (tp30) cc_final: 0.7271 (tp30) REVERT: C 789 GLU cc_start: 0.8091 (pt0) cc_final: 0.7570 (mt-10) REVERT: C 791 TRP cc_start: 0.7887 (t60) cc_final: 0.7472 (t60) REVERT: C 855 LYS cc_start: 0.8865 (tttt) cc_final: 0.7811 (tppt) outliers start: 3 outliers final: 0 residues processed: 553 average time/residue: 0.3099 time to fit residues: 232.6991 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 : 1.372 ------------------------------------------------------------------------------- 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: 0.3980 chunk 138 optimal weight: 0.9980 chunk 155 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 chunk 150 optimal weight: 4.9990 chunk 157 optimal weight: 5.9990 chunk 85 optimal weight: 0.5980 chunk 145 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 625 ASN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.143955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.116402 restraints weight = 30377.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.121066 restraints weight = 18756.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.124558 restraints weight = 13003.372| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.3974 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= 0.148 Angle : 0.670 12.892 18272 Z= 0.337 Chirality : 0.044 0.168 2014 Planarity : 0.005 0.069 2372 Dihedral : 5.556 21.059 1806 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.07 % Allowed : 4.75 % Favored : 95.18 % 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: -2.32 (0.19), residues: 1610 helix: -1.41 (0.16), residues: 838 sheet: -3.18 (0.52), residues: 72 loop : -1.33 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 600 HIS 0.002 0.001 HIS C 655 PHE 0.027 0.002 PHE A 790 TYR 0.022 0.002 TYR A 717 ARG 0.011 0.000 ARG A 539 Details of bonding type rmsd hydrogen bonds : bond 0.04258 ( 502) hydrogen bonds : angle 5.43168 ( 1392) metal coordination : bond 0.00823 ( 12) metal coordination : angle 7.20946 ( 12) covalent geometry : bond 0.00302 (13522) covalent geometry : angle 0.64437 (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 534 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 533 time to evaluate : 1.448 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: B 42 GLN cc_start: 0.8420 (mt0) cc_final: 0.8154 (mt0) REVERT: B 59 ILE cc_start: 0.7652 (mm) cc_final: 0.7284 (tp) REVERT: B 65 ASN cc_start: 0.8386 (m-40) cc_final: 0.8132 (m-40) REVERT: B 73 CYS cc_start: 0.7472 (m) cc_final: 0.6847 (m) REVERT: B 77 TYR cc_start: 0.8337 (m-80) cc_final: 0.7623 (m-80) REVERT: B 82 GLU cc_start: 0.8576 (tt0) cc_final: 0.8057 (tt0) REVERT: B 88 TYR cc_start: 0.7062 (p90) cc_final: 0.6780 (p90) REVERT: B 94 THR cc_start: 0.7217 (p) cc_final: 0.6697 (p) REVERT: B 98 GLN cc_start: 0.8651 (mp10) cc_final: 0.8371 (mp10) REVERT: B 108 ILE cc_start: 0.8107 (mt) cc_final: 0.7748 (tt) REVERT: B 114 GLN cc_start: 0.7605 (mp10) cc_final: 0.7351 (mp10) REVERT: B 124 ARG cc_start: 0.8491 (ttt-90) cc_final: 0.8013 (ttt-90) REVERT: B 128 LYS cc_start: 0.8351 (mttt) cc_final: 0.8127 (mttt) REVERT: B 132 PHE cc_start: 0.7523 (m-80) cc_final: 0.6843 (m-80) REVERT: B 134 ASN cc_start: 0.7697 (t0) cc_final: 0.7101 (t0) REVERT: A 130 GLU cc_start: 0.8507 (pt0) cc_final: 0.7659 (pm20) REVERT: A 138 GLU cc_start: 0.8430 (mp0) cc_final: 0.8014 (mp0) REVERT: A 237 ASP cc_start: 0.8563 (m-30) cc_final: 0.7985 (t0) REVERT: A 241 ARG cc_start: 0.8712 (mtp-110) cc_final: 0.8436 (mtp-110) REVERT: A 287 PHE cc_start: 0.7296 (m-80) cc_final: 0.6992 (m-80) REVERT: A 291 MET cc_start: 0.8390 (ttt) cc_final: 0.8085 (ttt) REVERT: A 294 ARG cc_start: 0.8572 (mpt-90) cc_final: 0.8366 (mpt-90) REVERT: A 304 MET cc_start: 0.5164 (tpt) cc_final: 0.4325 (tpt) REVERT: A 315 LYS cc_start: 0.7970 (mmtm) cc_final: 0.7416 (mttm) REVERT: A 337 ARG cc_start: 0.8148 (ttm170) cc_final: 0.7265 (ttp80) REVERT: A 338 ARG cc_start: 0.7934 (mtp85) cc_final: 0.7558 (mmm-85) REVERT: A 341 GLU cc_start: 0.8355 (mt-10) cc_final: 0.6957 (mt-10) REVERT: A 344 GLN cc_start: 0.8421 (tp-100) cc_final: 0.7267 (tp-100) REVERT: A 345 GLN cc_start: 0.8457 (mt0) cc_final: 0.7617 (tp40) REVERT: A 346 LEU cc_start: 0.8800 (tp) cc_final: 0.8597 (tp) REVERT: A 350 LYS cc_start: 0.7757 (mmpt) cc_final: 0.7353 (tptt) REVERT: A 361 LEU cc_start: 0.7367 (tp) cc_final: 0.7127 (tp) REVERT: A 376 LYS cc_start: 0.8696 (tttt) cc_final: 0.8293 (tppt) REVERT: A 392 HIS cc_start: 0.8111 (m90) cc_final: 0.7581 (m-70) REVERT: A 406 GLU cc_start: 0.8428 (tp30) cc_final: 0.7799 (tp30) REVERT: A 407 LEU cc_start: 0.8847 (mt) cc_final: 0.8495 (pp) REVERT: A 410 GLN cc_start: 0.8987 (mm-40) cc_final: 0.8612 (mm-40) REVERT: A 437 LEU cc_start: 0.8259 (mm) cc_final: 0.7819 (tt) REVERT: A 447 GLU cc_start: 0.8152 (mp0) cc_final: 0.7620 (tp30) REVERT: A 449 PHE cc_start: 0.7447 (m-10) cc_final: 0.6981 (m-10) REVERT: A 450 ILE cc_start: 0.8058 (mt) cc_final: 0.7426 (mt) REVERT: A 455 ASN cc_start: 0.7965 (m-40) cc_final: 0.7751 (m110) REVERT: A 458 LEU cc_start: 0.8296 (tp) cc_final: 0.7977 (tt) REVERT: A 459 GLU cc_start: 0.7004 (mp0) cc_final: 0.6739 (mp0) REVERT: A 477 PHE cc_start: 0.8083 (m-80) cc_final: 0.7667 (m-80) REVERT: A 478 MET cc_start: 0.8133 (mtp) cc_final: 0.6884 (mtp) REVERT: A 489 LYS cc_start: 0.8488 (mtmm) cc_final: 0.8085 (ptpp) REVERT: A 499 ILE cc_start: 0.7872 (tp) cc_final: 0.7519 (tp) REVERT: A 502 TYR cc_start: 0.7543 (m-10) cc_final: 0.7241 (m-10) REVERT: A 504 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7634 (mm-30) REVERT: A 505 ARG cc_start: 0.8707 (mtt90) cc_final: 0.8280 (mtt90) REVERT: A 507 ILE cc_start: 0.8644 (mt) cc_final: 0.8166 (mp) REVERT: A 522 TYR cc_start: 0.8338 (m-80) cc_final: 0.7908 (m-80) REVERT: A 523 LEU cc_start: 0.8535 (tp) cc_final: 0.8257 (tp) REVERT: A 535 ASP cc_start: 0.7140 (m-30) cc_final: 0.6936 (t0) REVERT: A 539 ARG cc_start: 0.8165 (ttm110) cc_final: 0.6985 (ptm160) REVERT: A 542 MET cc_start: 0.8496 (ptt) cc_final: 0.8017 (tmm) REVERT: A 543 ILE cc_start: 0.8899 (mt) cc_final: 0.8338 (mt) REVERT: A 545 MET cc_start: 0.7925 (mtm) cc_final: 0.7357 (mtm) REVERT: A 550 ASP cc_start: 0.7940 (p0) cc_final: 0.7624 (p0) REVERT: A 553 LYS cc_start: 0.8569 (mtmt) cc_final: 0.8265 (mtpp) REVERT: A 554 GLN cc_start: 0.7813 (mm110) cc_final: 0.7308 (tp40) REVERT: A 573 GLU cc_start: 0.8091 (pp20) cc_final: 0.7683 (pp20) REVERT: A 576 GLN cc_start: 0.8415 (tp-100) cc_final: 0.7684 (tp-100) REVERT: A 577 LEU cc_start: 0.8927 (mt) cc_final: 0.8620 (mt) REVERT: A 587 ILE cc_start: 0.7888 (tp) cc_final: 0.7621 (tp) REVERT: A 589 MET cc_start: 0.6270 (mtt) cc_final: 0.4257 (mtt) REVERT: A 593 ASP cc_start: 0.8215 (t0) cc_final: 0.7819 (t0) REVERT: A 617 ILE cc_start: 0.8538 (mm) cc_final: 0.8080 (mm) REVERT: A 621 LEU cc_start: 0.8089 (mm) cc_final: 0.7614 (mp) REVERT: A 635 MET cc_start: 0.8256 (mpp) cc_final: 0.7407 (mpp) REVERT: A 641 LEU cc_start: 0.8490 (mt) cc_final: 0.8071 (mt) REVERT: A 642 MET cc_start: 0.8150 (mmp) cc_final: 0.7758 (mmp) REVERT: A 651 LEU cc_start: 0.8422 (mt) cc_final: 0.8202 (mt) REVERT: A 658 LEU cc_start: 0.8440 (tp) cc_final: 0.7832 (tp) REVERT: A 660 GLN cc_start: 0.8281 (pp30) cc_final: 0.7946 (pp30) REVERT: A 661 SER cc_start: 0.8504 (m) cc_final: 0.8157 (p) REVERT: A 663 LYS cc_start: 0.8234 (ptmm) cc_final: 0.7463 (ttpp) REVERT: A 682 ILE cc_start: 0.8349 (tp) cc_final: 0.8011 (tp) REVERT: A 707 ASN cc_start: 0.8257 (p0) cc_final: 0.8018 (m-40) REVERT: A 708 GLU cc_start: 0.8346 (pm20) cc_final: 0.8026 (pm20) REVERT: A 711 LYS cc_start: 0.9245 (mmtt) cc_final: 0.8759 (mmtm) REVERT: A 716 LEU cc_start: 0.8670 (mt) cc_final: 0.8411 (mt) REVERT: A 720 TYR cc_start: 0.7723 (t80) cc_final: 0.7010 (t80) REVERT: A 727 GLU cc_start: 0.7954 (pt0) cc_final: 0.7749 (pm20) REVERT: A 728 LYS cc_start: 0.8365 (ttpt) cc_final: 0.7768 (ptmm) REVERT: A 734 ARG cc_start: 0.8529 (ttt-90) cc_final: 0.8106 (ttt180) REVERT: A 743 GLU cc_start: 0.8401 (mm-30) cc_final: 0.7902 (mm-30) REVERT: A 748 TYR cc_start: 0.7377 (t80) cc_final: 0.6986 (t80) REVERT: A 753 GLU cc_start: 0.8677 (mp0) cc_final: 0.8307 (mp0) REVERT: A 756 GLU cc_start: 0.7267 (tp30) cc_final: 0.6935 (tp30) REVERT: A 792 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8236 (mm-30) REVERT: A 820 LEU cc_start: 0.7593 (mm) cc_final: 0.7378 (mm) REVERT: A 822 LYS cc_start: 0.8477 (mptt) cc_final: 0.8029 (mmtm) REVERT: A 862 LEU cc_start: 0.8600 (tt) cc_final: 0.8297 (mt) REVERT: D 22 LEU cc_start: 0.8196 (mm) cc_final: 0.7840 (mm) REVERT: D 42 GLN cc_start: 0.8460 (mt0) cc_final: 0.8217 (mt0) REVERT: D 47 ARG cc_start: 0.7807 (mmm160) cc_final: 0.7291 (mmm160) REVERT: D 65 ASN cc_start: 0.8497 (m-40) cc_final: 0.8062 (m-40) REVERT: D 73 CYS cc_start: 0.7500 (m) cc_final: 0.6874 (m) REVERT: D 82 GLU cc_start: 0.8524 (tt0) cc_final: 0.8286 (tt0) REVERT: D 88 TYR cc_start: 0.7180 (p90) cc_final: 0.6839 (p90) REVERT: D 132 PHE cc_start: 0.7611 (m-80) cc_final: 0.6753 (m-80) REVERT: D 134 ASN cc_start: 0.7742 (t0) cc_final: 0.7304 (t0) REVERT: D 138 ARG cc_start: 0.7884 (ptt-90) cc_final: 0.6714 (ptt-90) REVERT: C 130 GLU cc_start: 0.8433 (pt0) cc_final: 0.8100 (pt0) REVERT: C 138 GLU cc_start: 0.8482 (mp0) cc_final: 0.8041 (mp0) REVERT: C 237 ASP cc_start: 0.8098 (m-30) cc_final: 0.7817 (t0) REVERT: C 241 ARG cc_start: 0.8703 (mtm-85) cc_final: 0.8483 (mtm-85) REVERT: C 287 PHE cc_start: 0.7546 (m-80) cc_final: 0.7343 (m-80) REVERT: C 288 ILE cc_start: 0.8640 (tt) cc_final: 0.8109 (tt) REVERT: C 315 LYS cc_start: 0.7916 (mtmm) cc_final: 0.7353 (mttt) REVERT: C 321 GLN cc_start: 0.8398 (mt0) cc_final: 0.8113 (mm-40) REVERT: C 332 ASN cc_start: 0.7659 (t0) cc_final: 0.7176 (t0) REVERT: C 337 ARG cc_start: 0.8204 (ttm170) cc_final: 0.7844 (tmm-80) REVERT: C 349 TYR cc_start: 0.7894 (t80) cc_final: 0.7595 (t80) REVERT: C 361 LEU cc_start: 0.7192 (tp) cc_final: 0.6736 (tp) REVERT: C 376 LYS cc_start: 0.8595 (ttpt) cc_final: 0.7722 (tppt) REVERT: C 382 ASN cc_start: 0.8503 (m-40) cc_final: 0.8240 (m110) REVERT: C 392 HIS cc_start: 0.8171 (m170) cc_final: 0.7760 (m-70) REVERT: C 394 GLU cc_start: 0.6320 (mm-30) cc_final: 0.5821 (mm-30) REVERT: C 406 GLU cc_start: 0.8522 (tp30) cc_final: 0.7878 (mt-10) REVERT: C 407 LEU cc_start: 0.8781 (mt) cc_final: 0.8215 (pp) REVERT: C 408 THR cc_start: 0.8568 (m) cc_final: 0.8042 (m) REVERT: C 409 LEU cc_start: 0.8637 (tp) cc_final: 0.8109 (pp) REVERT: C 410 GLN cc_start: 0.8963 (mm-40) cc_final: 0.7917 (mm-40) REVERT: C 411 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7129 (mt-10) REVERT: C 447 GLU cc_start: 0.8084 (mp0) cc_final: 0.7544 (tp30) REVERT: C 449 PHE cc_start: 0.7695 (m-10) cc_final: 0.7164 (m-10) REVERT: C 459 GLU cc_start: 0.6715 (mp0) cc_final: 0.6359 (mp0) REVERT: C 478 MET cc_start: 0.7835 (mtp) cc_final: 0.7342 (mtp) REVERT: C 482 PHE cc_start: 0.8049 (p90) cc_final: 0.7169 (p90) REVERT: C 495 TYR cc_start: 0.7567 (m-10) cc_final: 0.7364 (m-10) REVERT: C 499 ILE cc_start: 0.8053 (tp) cc_final: 0.7671 (tp) REVERT: C 501 MET cc_start: 0.8221 (mtt) cc_final: 0.7830 (mtt) REVERT: C 502 TYR cc_start: 0.7633 (m-10) cc_final: 0.7180 (m-10) REVERT: C 505 ARG cc_start: 0.8747 (mtt90) cc_final: 0.8205 (mtt90) REVERT: C 507 ILE cc_start: 0.8589 (mt) cc_final: 0.8330 (mp) REVERT: C 522 TYR cc_start: 0.8145 (m-80) cc_final: 0.7684 (m-80) REVERT: C 533 ILE cc_start: 0.8568 (mp) cc_final: 0.8348 (mp) REVERT: C 540 LEU cc_start: 0.8770 (mm) cc_final: 0.8540 (mm) REVERT: C 542 MET cc_start: 0.8174 (tpp) cc_final: 0.7464 (tpp) REVERT: C 543 ILE cc_start: 0.8878 (mt) cc_final: 0.8629 (mt) REVERT: C 545 MET cc_start: 0.7901 (mtm) cc_final: 0.7170 (mtm) REVERT: C 551 LEU cc_start: 0.8886 (mp) cc_final: 0.8631 (mp) REVERT: C 553 LYS cc_start: 0.8429 (mtmt) cc_final: 0.8204 (mtpp) REVERT: C 555 LEU cc_start: 0.8498 (tp) cc_final: 0.8239 (tp) REVERT: C 572 LYS cc_start: 0.8450 (mmtt) cc_final: 0.8076 (ttmm) REVERT: C 573 GLU cc_start: 0.8009 (pm20) cc_final: 0.7702 (pm20) REVERT: C 576 GLN cc_start: 0.7601 (tm-30) cc_final: 0.7166 (tm-30) REVERT: C 577 LEU cc_start: 0.8660 (mt) cc_final: 0.8327 (mt) REVERT: C 587 ILE cc_start: 0.8412 (tp) cc_final: 0.8118 (tp) REVERT: C 589 MET cc_start: 0.6851 (mtp) cc_final: 0.6502 (mtp) REVERT: C 593 ASP cc_start: 0.7815 (t70) cc_final: 0.7550 (t70) REVERT: C 619 LEU cc_start: 0.8749 (tp) cc_final: 0.8479 (tp) REVERT: C 621 LEU cc_start: 0.8223 (mm) cc_final: 0.7812 (mm) REVERT: C 625 ASN cc_start: 0.8401 (m110) cc_final: 0.8058 (m110) REVERT: C 626 ASN cc_start: 0.7925 (m-40) cc_final: 0.7698 (m110) REVERT: C 630 ASP cc_start: 0.7260 (t70) cc_final: 0.7011 (t0) REVERT: C 635 MET cc_start: 0.8077 (mpp) cc_final: 0.7460 (mpp) REVERT: C 641 LEU cc_start: 0.8535 (mt) cc_final: 0.7959 (pp) REVERT: C 648 PHE cc_start: 0.8669 (p90) cc_final: 0.8319 (p90) REVERT: C 649 ARG cc_start: 0.8766 (ttm170) cc_final: 0.8470 (ttp-110) REVERT: C 658 LEU cc_start: 0.8568 (tp) cc_final: 0.8065 (tp) REVERT: C 661 SER cc_start: 0.8485 (m) cc_final: 0.8216 (p) REVERT: C 663 LYS cc_start: 0.8312 (ptmm) cc_final: 0.7189 (mmtt) REVERT: C 664 ASP cc_start: 0.8008 (m-30) cc_final: 0.6428 (p0) REVERT: C 668 TYR cc_start: 0.8239 (t80) cc_final: 0.7997 (t80) REVERT: C 711 LYS cc_start: 0.9213 (mmtt) cc_final: 0.8681 (mmtm) REVERT: C 712 GLU cc_start: 0.8715 (tt0) cc_final: 0.8105 (tt0) REVERT: C 717 TYR cc_start: 0.8551 (t80) cc_final: 0.8230 (t80) REVERT: C 719 ASP cc_start: 0.8284 (m-30) cc_final: 0.7955 (m-30) REVERT: C 720 TYR cc_start: 0.7810 (t80) cc_final: 0.7088 (t80) REVERT: C 727 GLU cc_start: 0.8022 (pm20) cc_final: 0.7821 (pm20) REVERT: C 730 PHE cc_start: 0.8168 (t80) cc_final: 0.7820 (t80) REVERT: C 738 HIS cc_start: 0.7898 (t-90) cc_final: 0.7645 (t-90) REVERT: C 739 MET cc_start: 0.7962 (ptp) cc_final: 0.7639 (ptp) REVERT: C 743 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8081 (mm-30) REVERT: C 748 TYR cc_start: 0.7413 (t80) cc_final: 0.6919 (t80) REVERT: C 751 ARG cc_start: 0.7895 (mtm-85) cc_final: 0.7633 (mmm-85) REVERT: C 753 GLU cc_start: 0.8673 (mp0) cc_final: 0.8367 (mp0) REVERT: C 789 GLU cc_start: 0.8147 (pt0) cc_final: 0.7753 (pm20) REVERT: C 791 TRP cc_start: 0.7816 (t60) cc_final: 0.7455 (t60) REVERT: C 805 PHE cc_start: 0.8638 (t80) cc_final: 0.8401 (t80) REVERT: C 855 LYS cc_start: 0.8790 (tttt) cc_final: 0.8253 (tppt) outliers start: 1 outliers final: 1 residues processed: 533 average time/residue: 0.3197 time to fit residues: 231.8971 Evaluate side-chains 509 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 508 time to evaluate : 1.517 ------------------------------------------------------------------------------- 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: 8.9990 chunk 142 optimal weight: 0.9980 chunk 154 optimal weight: 0.3980 chunk 57 optimal weight: 0.6980 chunk 118 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 158 optimal weight: 6.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 455 ASN C 723 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.143551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.115821 restraints weight = 30235.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.120499 restraints weight = 18613.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.123977 restraints weight = 12930.960| |-----------------------------------------------------------------------------| r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.4629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13534 Z= 0.126 Angle : 0.617 10.998 18272 Z= 0.313 Chirality : 0.042 0.154 2014 Planarity : 0.004 0.062 2372 Dihedral : 5.145 23.883 1806 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % 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: -1.72 (0.20), residues: 1610 helix: -0.82 (0.17), residues: 822 sheet: -2.96 (0.56), residues: 72 loop : -1.17 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP C 328 HIS 0.002 0.001 HIS B 31 PHE 0.029 0.001 PHE A 790 TYR 0.014 0.001 TYR A 717 ARG 0.008 0.000 ARG C 141 Details of bonding type rmsd hydrogen bonds : bond 0.03857 ( 502) hydrogen bonds : angle 5.15660 ( 1392) metal coordination : bond 0.00940 ( 12) metal coordination : angle 5.74328 ( 12) covalent geometry : bond 0.00258 (13522) covalent geometry : angle 0.59976 (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 539 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 539 time to evaluate : 1.536 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 42 GLN cc_start: 0.8368 (mt0) cc_final: 0.8064 (mt0) REVERT: B 49 VAL cc_start: 0.7210 (t) cc_final: 0.6888 (t) REVERT: B 65 ASN cc_start: 0.8387 (m-40) cc_final: 0.8136 (m-40) REVERT: B 73 CYS cc_start: 0.7342 (m) cc_final: 0.6818 (m) REVERT: B 77 TYR cc_start: 0.8338 (m-80) cc_final: 0.7638 (m-80) REVERT: B 82 GLU cc_start: 0.8689 (tt0) cc_final: 0.8199 (tt0) REVERT: B 88 TYR cc_start: 0.7111 (p90) cc_final: 0.6680 (p90) REVERT: B 108 ILE cc_start: 0.8145 (mt) cc_final: 0.7752 (tt) REVERT: B 114 GLN cc_start: 0.7872 (mp10) cc_final: 0.7603 (mp10) REVERT: B 132 PHE cc_start: 0.7557 (m-80) cc_final: 0.6860 (m-80) REVERT: B 134 ASN cc_start: 0.8023 (t0) cc_final: 0.7102 (t0) REVERT: A 130 GLU cc_start: 0.8486 (pt0) cc_final: 0.7727 (pm20) REVERT: A 237 ASP cc_start: 0.8506 (m-30) cc_final: 0.7864 (t0) REVERT: A 283 TYR cc_start: 0.7854 (t80) cc_final: 0.7473 (t80) REVERT: A 287 PHE cc_start: 0.7510 (m-80) cc_final: 0.7234 (m-80) REVERT: A 288 ILE cc_start: 0.8558 (tt) cc_final: 0.8332 (tt) REVERT: A 291 MET cc_start: 0.8447 (ttt) cc_final: 0.7970 (ptm) REVERT: A 294 ARG cc_start: 0.8587 (mpt-90) cc_final: 0.8368 (mpt-90) REVERT: A 297 HIS cc_start: 0.8072 (t70) cc_final: 0.7510 (t70) REVERT: A 304 MET cc_start: 0.5121 (tpt) cc_final: 0.4441 (tpt) REVERT: A 332 ASN cc_start: 0.7731 (t0) cc_final: 0.7157 (t0) REVERT: A 337 ARG cc_start: 0.8221 (ttm170) cc_final: 0.7384 (ttp80) REVERT: A 338 ARG cc_start: 0.8107 (mtp85) cc_final: 0.7454 (mmm-85) REVERT: A 341 GLU cc_start: 0.8429 (mt-10) cc_final: 0.7661 (mt-10) REVERT: A 344 GLN cc_start: 0.8400 (tp-100) cc_final: 0.7364 (tp-100) REVERT: A 347 ILE cc_start: 0.7438 (mt) cc_final: 0.7140 (mm) REVERT: A 350 LYS cc_start: 0.7647 (mmpt) cc_final: 0.7223 (tptt) REVERT: A 392 HIS cc_start: 0.8190 (m90) cc_final: 0.7719 (m90) REVERT: A 407 LEU cc_start: 0.8855 (mt) cc_final: 0.8488 (pp) REVERT: A 408 THR cc_start: 0.8576 (m) cc_final: 0.8347 (p) REVERT: A 410 GLN cc_start: 0.9043 (mm-40) cc_final: 0.8637 (mm-40) REVERT: A 437 LEU cc_start: 0.8259 (mm) cc_final: 0.7857 (tt) REVERT: A 447 GLU cc_start: 0.8178 (mp0) cc_final: 0.7633 (tp30) REVERT: A 449 PHE cc_start: 0.7420 (m-10) cc_final: 0.6895 (m-10) REVERT: A 450 ILE cc_start: 0.7966 (mt) cc_final: 0.7387 (mt) REVERT: A 455 ASN cc_start: 0.8037 (m-40) cc_final: 0.7800 (m110) REVERT: A 458 LEU cc_start: 0.8409 (tp) cc_final: 0.8036 (tt) REVERT: A 459 GLU cc_start: 0.7066 (mp0) cc_final: 0.6740 (mp0) REVERT: A 477 PHE cc_start: 0.8062 (m-80) cc_final: 0.7582 (m-80) REVERT: A 478 MET cc_start: 0.8081 (mtp) cc_final: 0.6806 (mtp) REVERT: A 482 PHE cc_start: 0.7904 (p90) cc_final: 0.7598 (p90) REVERT: A 491 LEU cc_start: 0.8393 (mt) cc_final: 0.8152 (mt) REVERT: A 499 ILE cc_start: 0.7880 (tp) cc_final: 0.7509 (tp) REVERT: A 501 MET cc_start: 0.8291 (mtt) cc_final: 0.7229 (mmt) REVERT: A 502 TYR cc_start: 0.7541 (m-10) cc_final: 0.7277 (m-10) REVERT: A 504 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7696 (mm-30) REVERT: A 505 ARG cc_start: 0.8742 (mtt90) cc_final: 0.8305 (mtt90) REVERT: A 507 ILE cc_start: 0.8656 (mt) cc_final: 0.8210 (mp) REVERT: A 515 GLN cc_start: 0.8235 (mm110) cc_final: 0.7595 (tm-30) REVERT: A 522 TYR cc_start: 0.8180 (m-80) cc_final: 0.7687 (m-80) REVERT: A 523 LEU cc_start: 0.8393 (tp) cc_final: 0.8114 (tp) REVERT: A 529 ARG cc_start: 0.8407 (mmm-85) cc_final: 0.8123 (mmm-85) REVERT: A 530 ASP cc_start: 0.8120 (p0) cc_final: 0.7870 (p0) REVERT: A 532 ILE cc_start: 0.8273 (pt) cc_final: 0.7621 (pt) REVERT: A 534 ASP cc_start: 0.8199 (m-30) cc_final: 0.7988 (m-30) REVERT: A 539 ARG cc_start: 0.8132 (ttm110) cc_final: 0.7665 (ptm160) REVERT: A 542 MET cc_start: 0.8497 (ptt) cc_final: 0.7941 (tmm) REVERT: A 543 ILE cc_start: 0.8968 (mt) cc_final: 0.8420 (mt) REVERT: A 545 MET cc_start: 0.7910 (mtm) cc_final: 0.7347 (mtm) REVERT: A 550 ASP cc_start: 0.7901 (p0) cc_final: 0.7486 (p0) REVERT: A 553 LYS cc_start: 0.8521 (mtmt) cc_final: 0.7789 (mtpp) REVERT: A 572 LYS cc_start: 0.8363 (mmtt) cc_final: 0.8152 (mmtt) REVERT: A 573 GLU cc_start: 0.8080 (pp20) cc_final: 0.7582 (pp20) REVERT: A 577 LEU cc_start: 0.8897 (mt) cc_final: 0.8452 (mt) REVERT: A 593 ASP cc_start: 0.8241 (t0) cc_final: 0.7826 (t70) REVERT: A 600 TRP cc_start: 0.8697 (t-100) cc_final: 0.8385 (t-100) REVERT: A 617 ILE cc_start: 0.8488 (mm) cc_final: 0.8116 (mm) REVERT: A 621 LEU cc_start: 0.8050 (mm) cc_final: 0.7714 (mp) REVERT: A 635 MET cc_start: 0.8274 (mpp) cc_final: 0.7458 (mpp) REVERT: A 641 LEU cc_start: 0.8530 (mt) cc_final: 0.8216 (mt) REVERT: A 642 MET cc_start: 0.8150 (mmp) cc_final: 0.7776 (mmp) REVERT: A 651 LEU cc_start: 0.8437 (mt) cc_final: 0.8158 (mt) REVERT: A 658 LEU cc_start: 0.8319 (tp) cc_final: 0.8011 (tp) REVERT: A 660 GLN cc_start: 0.8242 (pp30) cc_final: 0.7765 (pp30) REVERT: A 663 LYS cc_start: 0.8142 (ptmm) cc_final: 0.7613 (ttpp) REVERT: A 667 GLU cc_start: 0.8251 (pp20) cc_final: 0.7971 (pp20) REVERT: A 676 MET cc_start: 0.6899 (tmm) cc_final: 0.6633 (tmm) REVERT: A 682 ILE cc_start: 0.8311 (tp) cc_final: 0.7799 (tp) REVERT: A 711 LYS cc_start: 0.9258 (mmtt) cc_final: 0.8795 (mmtm) REVERT: A 712 GLU cc_start: 0.8585 (tt0) cc_final: 0.8028 (tt0) REVERT: A 716 LEU cc_start: 0.8704 (mt) cc_final: 0.8371 (mt) REVERT: A 717 TYR cc_start: 0.8771 (t80) cc_final: 0.8155 (t80) REVERT: A 719 ASP cc_start: 0.8162 (m-30) cc_final: 0.7887 (m-30) REVERT: A 720 TYR cc_start: 0.7764 (t80) cc_final: 0.7087 (t80) REVERT: A 728 LYS cc_start: 0.8292 (ttpt) cc_final: 0.7700 (ptmm) REVERT: A 730 PHE cc_start: 0.8124 (t80) cc_final: 0.7891 (t80) REVERT: A 734 ARG cc_start: 0.8454 (ttt-90) cc_final: 0.7858 (ttp80) REVERT: A 738 HIS cc_start: 0.8163 (t70) cc_final: 0.7878 (t-170) REVERT: A 743 GLU cc_start: 0.8386 (mm-30) cc_final: 0.7724 (mp0) REVERT: A 748 TYR cc_start: 0.7346 (t80) cc_final: 0.6905 (t80) REVERT: A 750 PHE cc_start: 0.8282 (m-80) cc_final: 0.8056 (m-80) REVERT: A 753 GLU cc_start: 0.8673 (mp0) cc_final: 0.8294 (mp0) REVERT: A 756 GLU cc_start: 0.7227 (tp30) cc_final: 0.6968 (tp30) REVERT: A 788 ARG cc_start: 0.8606 (ptt180) cc_final: 0.8260 (ptt180) REVERT: A 792 GLU cc_start: 0.8591 (mm-30) cc_final: 0.7928 (mm-30) REVERT: A 820 LEU cc_start: 0.7801 (mm) cc_final: 0.7508 (mm) REVERT: A 822 LYS cc_start: 0.8488 (mptt) cc_final: 0.8116 (mmtm) REVERT: D 22 LEU cc_start: 0.8186 (mm) cc_final: 0.7883 (mm) REVERT: D 42 GLN cc_start: 0.8424 (mt0) cc_final: 0.8184 (mt0) REVERT: D 65 ASN cc_start: 0.8504 (m-40) cc_final: 0.8073 (m-40) REVERT: D 73 CYS cc_start: 0.7524 (m) cc_final: 0.6903 (m) REVERT: D 79 LYS cc_start: 0.8404 (tppp) cc_final: 0.7184 (tppp) REVERT: D 82 GLU cc_start: 0.8640 (tt0) cc_final: 0.8140 (tt0) REVERT: D 88 TYR cc_start: 0.7025 (p90) cc_final: 0.6782 (p90) REVERT: D 114 GLN cc_start: 0.7832 (mp10) cc_final: 0.7604 (mp10) REVERT: D 132 PHE cc_start: 0.7766 (m-80) cc_final: 0.6887 (m-80) REVERT: D 134 ASN cc_start: 0.7860 (t0) cc_final: 0.7605 (t0) REVERT: D 138 ARG cc_start: 0.7914 (ptt-90) cc_final: 0.6789 (ptt-90) REVERT: C 130 GLU cc_start: 0.8332 (pt0) cc_final: 0.7643 (pm20) REVERT: C 138 GLU cc_start: 0.8511 (mp0) cc_final: 0.8181 (mp0) REVERT: C 241 ARG cc_start: 0.8736 (mtm-85) cc_final: 0.8505 (mtm-85) REVERT: C 283 TYR cc_start: 0.8366 (t80) cc_final: 0.7482 (t80) REVERT: C 287 PHE cc_start: 0.7844 (m-80) cc_final: 0.7635 (m-80) REVERT: C 304 MET cc_start: 0.5458 (tpt) cc_final: 0.5160 (tpt) REVERT: C 315 LYS cc_start: 0.7969 (mtmm) cc_final: 0.7511 (ptpp) REVERT: C 321 GLN cc_start: 0.8422 (mt0) cc_final: 0.8152 (mm-40) REVERT: C 326 ARG cc_start: 0.8245 (mtm180) cc_final: 0.7857 (mtm110) REVERT: C 330 LYS cc_start: 0.8722 (mmmt) cc_final: 0.8288 (mptt) REVERT: C 332 ASN cc_start: 0.7563 (t0) cc_final: 0.7197 (t0) REVERT: C 337 ARG cc_start: 0.8207 (ttm170) cc_final: 0.7754 (tmm-80) REVERT: C 344 GLN cc_start: 0.8427 (tp-100) cc_final: 0.7451 (tp-100) REVERT: C 349 TYR cc_start: 0.7986 (t80) cc_final: 0.7710 (t80) REVERT: C 361 LEU cc_start: 0.7159 (tp) cc_final: 0.6681 (tp) REVERT: C 373 LYS cc_start: 0.8046 (ttmt) cc_final: 0.7827 (mtpp) REVERT: C 376 LYS cc_start: 0.8580 (ttpt) cc_final: 0.7520 (tttt) REVERT: C 380 TYR cc_start: 0.8750 (m-10) cc_final: 0.8008 (m-10) REVERT: C 382 ASN cc_start: 0.8487 (m-40) cc_final: 0.8256 (m110) REVERT: C 392 HIS cc_start: 0.8313 (m170) cc_final: 0.7852 (m-70) REVERT: C 394 GLU cc_start: 0.6156 (mm-30) cc_final: 0.5792 (mm-30) REVERT: C 397 ASP cc_start: 0.7841 (t0) cc_final: 0.7405 (t0) REVERT: C 403 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7629 (tm-30) REVERT: C 406 GLU cc_start: 0.8527 (tp30) cc_final: 0.7832 (mt-10) REVERT: C 407 LEU cc_start: 0.8819 (mt) cc_final: 0.8278 (pp) REVERT: C 408 THR cc_start: 0.8570 (m) cc_final: 0.8042 (m) REVERT: C 409 LEU cc_start: 0.8741 (tp) cc_final: 0.8131 (pp) REVERT: C 410 GLN cc_start: 0.9053 (mm-40) cc_final: 0.7955 (mm-40) REVERT: C 411 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7142 (mt-10) REVERT: C 420 LYS cc_start: 0.8182 (pttm) cc_final: 0.7860 (ptmm) REVERT: C 426 ASP cc_start: 0.8595 (t0) cc_final: 0.8319 (t70) REVERT: C 441 LYS cc_start: 0.9092 (tttm) cc_final: 0.8832 (tptp) REVERT: C 447 GLU cc_start: 0.8120 (mp0) cc_final: 0.7486 (tp30) REVERT: C 449 PHE cc_start: 0.7689 (m-10) cc_final: 0.7123 (m-10) REVERT: C 450 ILE cc_start: 0.7997 (mt) cc_final: 0.7309 (mt) REVERT: C 455 ASN cc_start: 0.7848 (m110) cc_final: 0.7639 (m-40) REVERT: C 478 MET cc_start: 0.7841 (mtp) cc_final: 0.7580 (mtp) REVERT: C 482 PHE cc_start: 0.7990 (p90) cc_final: 0.7518 (p90) REVERT: C 493 LEU cc_start: 0.8017 (tp) cc_final: 0.7671 (tp) REVERT: C 495 TYR cc_start: 0.7502 (m-10) cc_final: 0.7246 (m-10) REVERT: C 499 ILE cc_start: 0.8074 (tp) cc_final: 0.7638 (tp) REVERT: C 501 MET cc_start: 0.8220 (mtt) cc_final: 0.7810 (mtt) REVERT: C 502 TYR cc_start: 0.7623 (m-10) cc_final: 0.7200 (m-10) REVERT: C 505 ARG cc_start: 0.8726 (mtt90) cc_final: 0.8180 (mtt90) REVERT: C 507 ILE cc_start: 0.8550 (mt) cc_final: 0.8276 (mp) REVERT: C 522 TYR cc_start: 0.8100 (m-80) cc_final: 0.7579 (m-80) REVERT: C 530 ASP cc_start: 0.8017 (p0) cc_final: 0.7141 (p0) REVERT: C 539 ARG cc_start: 0.8493 (ttm-80) cc_final: 0.8035 (ttm-80) REVERT: C 540 LEU cc_start: 0.8936 (mm) cc_final: 0.8722 (mm) REVERT: C 542 MET cc_start: 0.8109 (tpp) cc_final: 0.7332 (tpp) REVERT: C 545 MET cc_start: 0.7908 (mtm) cc_final: 0.7196 (mtm) REVERT: C 551 LEU cc_start: 0.8843 (mp) cc_final: 0.8577 (mp) REVERT: C 553 LYS cc_start: 0.8424 (mtmt) cc_final: 0.8129 (mtpp) REVERT: C 555 LEU cc_start: 0.8558 (tp) cc_final: 0.8221 (tp) REVERT: C 572 LYS cc_start: 0.8338 (mmtt) cc_final: 0.7712 (mmtt) REVERT: C 576 GLN cc_start: 0.7850 (tm-30) cc_final: 0.7365 (tm-30) REVERT: C 577 LEU cc_start: 0.8789 (mt) cc_final: 0.8396 (mt) REVERT: C 587 ILE cc_start: 0.8236 (tp) cc_final: 0.7926 (tp) REVERT: C 589 MET cc_start: 0.6820 (mtp) cc_final: 0.6474 (mtp) REVERT: C 593 ASP cc_start: 0.7884 (t70) cc_final: 0.7603 (t70) REVERT: C 594 GLU cc_start: 0.8652 (mp0) cc_final: 0.8450 (mp0) REVERT: C 617 ILE cc_start: 0.8626 (mm) cc_final: 0.8381 (mm) REVERT: C 619 LEU cc_start: 0.8764 (tp) cc_final: 0.8493 (tp) REVERT: C 621 LEU cc_start: 0.8211 (mm) cc_final: 0.7751 (mm) REVERT: C 625 ASN cc_start: 0.8556 (m110) cc_final: 0.8187 (m110) REVERT: C 626 ASN cc_start: 0.8009 (m-40) cc_final: 0.7705 (m110) REVERT: C 630 ASP cc_start: 0.7277 (t70) cc_final: 0.6986 (t0) REVERT: C 635 MET cc_start: 0.8135 (mpp) cc_final: 0.7464 (mpp) REVERT: C 641 LEU cc_start: 0.8548 (mt) cc_final: 0.8158 (mm) REVERT: C 642 MET cc_start: 0.8125 (mmp) cc_final: 0.7812 (mmp) REVERT: C 649 ARG cc_start: 0.8777 (ttm170) cc_final: 0.8493 (mtp85) REVERT: C 658 LEU cc_start: 0.8473 (tp) cc_final: 0.8194 (tp) REVERT: C 659 TYR cc_start: 0.8650 (t80) cc_final: 0.8027 (t80) REVERT: C 663 LYS cc_start: 0.8226 (ptmm) cc_final: 0.7482 (mmtm) REVERT: C 667 GLU cc_start: 0.7994 (pp20) cc_final: 0.7710 (pp20) REVERT: C 711 LYS cc_start: 0.9269 (mmtt) cc_final: 0.8760 (mmtm) REVERT: C 712 GLU cc_start: 0.8668 (tt0) cc_final: 0.8217 (tt0) REVERT: C 716 LEU cc_start: 0.8785 (mt) cc_final: 0.8042 (pp) REVERT: C 717 TYR cc_start: 0.8839 (t80) cc_final: 0.8389 (t80) REVERT: C 719 ASP cc_start: 0.8266 (m-30) cc_final: 0.7376 (p0) REVERT: C 720 TYR cc_start: 0.7844 (t80) cc_final: 0.7190 (t80) REVERT: C 724 LYS cc_start: 0.8196 (ptpp) cc_final: 0.7169 (ptpp) REVERT: C 727 GLU cc_start: 0.8032 (pm20) cc_final: 0.7783 (pm20) REVERT: C 730 PHE cc_start: 0.8228 (t80) cc_final: 0.7926 (t80) REVERT: C 734 ARG cc_start: 0.8761 (ttt-90) cc_final: 0.8516 (ttm170) REVERT: C 738 HIS cc_start: 0.8055 (t-90) cc_final: 0.7851 (t-170) REVERT: C 739 MET cc_start: 0.7909 (ptp) cc_final: 0.7559 (ptp) REVERT: C 743 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8086 (mm-30) REVERT: C 747 LYS cc_start: 0.9011 (mtmt) cc_final: 0.8783 (mmmt) REVERT: C 748 TYR cc_start: 0.7430 (t80) cc_final: 0.6910 (t80) REVERT: C 754 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8165 (mp0) REVERT: C 788 ARG cc_start: 0.8560 (ptt180) cc_final: 0.7605 (ptt180) REVERT: C 789 GLU cc_start: 0.8162 (pt0) cc_final: 0.7809 (mt-10) REVERT: C 805 PHE cc_start: 0.8622 (t80) cc_final: 0.8364 (t80) REVERT: C 822 LYS cc_start: 0.8556 (mmtt) cc_final: 0.8266 (mmtm) REVERT: C 855 LYS cc_start: 0.8865 (tttt) cc_final: 0.7870 (tptt) outliers start: 0 outliers final: 0 residues processed: 539 average time/residue: 0.3679 time to fit residues: 268.0268 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 : 2.489 ------------------------------------------------------------------------------- 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: 4.9990 chunk 1 optimal weight: 0.0070 chunk 115 optimal weight: 0.9980 chunk 52 optimal weight: 0.0020 chunk 88 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 153 optimal weight: 0.9990 chunk 83 optimal weight: 0.1980 chunk 75 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 130 optimal weight: 4.9990 overall best weight: 0.4406 ------------------------------------------------------------------------------- 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 723 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.145281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.117784 restraints weight = 29582.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.122495 restraints weight = 18261.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.125963 restraints weight = 12626.319| |-----------------------------------------------------------------------------| r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.5035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13534 Z= 0.115 Angle : 0.600 12.815 18272 Z= 0.304 Chirality : 0.042 0.196 2014 Planarity : 0.004 0.057 2372 Dihedral : 4.938 22.397 1806 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.07 % Allowed : 1.86 % Favored : 98.07 % 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: -1.26 (0.20), residues: 1610 helix: -0.37 (0.18), residues: 790 sheet: -2.69 (0.58), residues: 72 loop : -1.04 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.004 TRP C 328 HIS 0.004 0.001 HIS A 655 PHE 0.022 0.001 PHE A 790 TYR 0.020 0.001 TYR A 494 ARG 0.007 0.000 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.03620 ( 502) hydrogen bonds : angle 5.05384 ( 1392) metal coordination : bond 0.00427 ( 12) metal coordination : angle 3.80858 ( 12) covalent geometry : bond 0.00242 (13522) covalent geometry : angle 0.59248 (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 526 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 525 time to evaluate : 1.856 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 22 LEU cc_start: 0.8102 (mm) cc_final: 0.7745 (mm) REVERT: B 65 ASN cc_start: 0.8175 (m-40) cc_final: 0.7786 (m-40) REVERT: B 73 CYS cc_start: 0.6582 (m) cc_final: 0.6283 (m) REVERT: B 77 TYR cc_start: 0.8198 (m-80) cc_final: 0.7697 (m-80) REVERT: B 82 GLU cc_start: 0.8698 (tt0) cc_final: 0.8284 (tt0) REVERT: B 88 TYR cc_start: 0.7126 (p90) cc_final: 0.6862 (p90) REVERT: B 108 ILE cc_start: 0.8142 (mt) cc_final: 0.7773 (tt) REVERT: B 114 GLN cc_start: 0.7921 (mp-120) cc_final: 0.7583 (mp10) REVERT: B 132 PHE cc_start: 0.7567 (m-80) cc_final: 0.6929 (m-80) REVERT: A 130 GLU cc_start: 0.8443 (pt0) cc_final: 0.7588 (pm20) REVERT: A 138 GLU cc_start: 0.8422 (mp0) cc_final: 0.7835 (mp0) REVERT: A 237 ASP cc_start: 0.8451 (m-30) cc_final: 0.7815 (t0) REVERT: A 287 PHE cc_start: 0.7482 (m-80) cc_final: 0.7251 (m-80) REVERT: A 288 ILE cc_start: 0.8596 (tt) cc_final: 0.8366 (tt) REVERT: A 291 MET cc_start: 0.8339 (ttt) cc_final: 0.7839 (ptm) REVERT: A 304 MET cc_start: 0.5023 (tpt) cc_final: 0.4262 (tpt) REVERT: A 330 LYS cc_start: 0.8529 (mptt) cc_final: 0.8283 (mmtt) REVERT: A 332 ASN cc_start: 0.7695 (t0) cc_final: 0.7267 (t0) REVERT: A 337 ARG cc_start: 0.8250 (ttm170) cc_final: 0.7604 (ttp80) REVERT: A 341 GLU cc_start: 0.8400 (mt-10) cc_final: 0.7942 (mt-10) REVERT: A 344 GLN cc_start: 0.8437 (tp-100) cc_final: 0.7386 (tp-100) REVERT: A 350 LYS cc_start: 0.7621 (mmpt) cc_final: 0.7240 (tptt) REVERT: A 376 LYS cc_start: 0.8684 (tttt) cc_final: 0.8475 (tttt) REVERT: A 392 HIS cc_start: 0.8186 (m90) cc_final: 0.7676 (m90) REVERT: A 406 GLU cc_start: 0.8444 (tp30) cc_final: 0.7790 (tp30) REVERT: A 407 LEU cc_start: 0.8890 (mt) cc_final: 0.8513 (pp) REVERT: A 408 THR cc_start: 0.8605 (m) cc_final: 0.8322 (p) REVERT: A 437 LEU cc_start: 0.8218 (mm) cc_final: 0.7832 (tt) REVERT: A 446 PHE cc_start: 0.7562 (m-80) cc_final: 0.7275 (m-80) REVERT: A 447 GLU cc_start: 0.8095 (mp0) cc_final: 0.7622 (tp30) REVERT: A 449 PHE cc_start: 0.7326 (m-10) cc_final: 0.6780 (m-10) REVERT: A 450 ILE cc_start: 0.7997 (mt) cc_final: 0.7273 (mt) REVERT: A 458 LEU cc_start: 0.8348 (tp) cc_final: 0.7951 (tt) REVERT: A 459 GLU cc_start: 0.6987 (mp0) cc_final: 0.6659 (mp0) REVERT: A 477 PHE cc_start: 0.7978 (m-80) cc_final: 0.7640 (m-80) REVERT: A 478 MET cc_start: 0.8093 (mtp) cc_final: 0.6715 (mtp) REVERT: A 482 PHE cc_start: 0.7968 (p90) cc_final: 0.7655 (p90) REVERT: A 499 ILE cc_start: 0.7912 (tp) cc_final: 0.7557 (tp) REVERT: A 501 MET cc_start: 0.8156 (mtt) cc_final: 0.7293 (mmm) REVERT: A 502 TYR cc_start: 0.7530 (m-10) cc_final: 0.7289 (m-10) REVERT: A 504 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7539 (mm-30) REVERT: A 505 ARG cc_start: 0.8795 (mtt90) cc_final: 0.8203 (mtt90) REVERT: A 507 ILE cc_start: 0.8629 (mt) cc_final: 0.8216 (mt) REVERT: A 515 GLN cc_start: 0.8249 (mm110) cc_final: 0.7636 (tm-30) REVERT: A 522 TYR cc_start: 0.8143 (m-80) cc_final: 0.7759 (m-80) REVERT: A 523 LEU cc_start: 0.8369 (tp) cc_final: 0.8158 (tp) REVERT: A 530 ASP cc_start: 0.8027 (p0) cc_final: 0.7521 (p0) REVERT: A 533 ILE cc_start: 0.8246 (pt) cc_final: 0.7602 (mp) REVERT: A 542 MET cc_start: 0.8432 (ptt) cc_final: 0.7794 (tmm) REVERT: A 545 MET cc_start: 0.7821 (mtm) cc_final: 0.7187 (mtm) REVERT: A 550 ASP cc_start: 0.7891 (p0) cc_final: 0.7461 (p0) REVERT: A 553 LYS cc_start: 0.8481 (mtmt) cc_final: 0.7582 (mtpp) REVERT: A 554 GLN cc_start: 0.7958 (tp40) cc_final: 0.7526 (tp40) REVERT: A 572 LYS cc_start: 0.8376 (mmtt) cc_final: 0.8134 (mmtt) REVERT: A 573 GLU cc_start: 0.8039 (pp20) cc_final: 0.7608 (pp20) REVERT: A 576 GLN cc_start: 0.8405 (tp40) cc_final: 0.7725 (tp40) REVERT: A 577 LEU cc_start: 0.8835 (mt) cc_final: 0.8593 (mt) REVERT: A 593 ASP cc_start: 0.8258 (t0) cc_final: 0.7808 (t70) REVERT: A 600 TRP cc_start: 0.8654 (t-100) cc_final: 0.8364 (t-100) REVERT: A 603 PRO cc_start: 0.7299 (Cg_endo) cc_final: 0.6937 (Cg_exo) REVERT: A 621 LEU cc_start: 0.8022 (mm) cc_final: 0.7609 (mt) REVERT: A 635 MET cc_start: 0.8242 (mpp) cc_final: 0.7421 (mpp) REVERT: A 641 LEU cc_start: 0.8512 (mt) cc_final: 0.8209 (mt) REVERT: A 642 MET cc_start: 0.8129 (mmp) cc_final: 0.7746 (mmp) REVERT: A 651 LEU cc_start: 0.8423 (mt) cc_final: 0.8136 (mt) REVERT: A 658 LEU cc_start: 0.8297 (tp) cc_final: 0.7953 (tp) REVERT: A 663 LYS cc_start: 0.8220 (ptmm) cc_final: 0.7468 (mmtt) REVERT: A 667 GLU cc_start: 0.8194 (pp20) cc_final: 0.7906 (pp20) REVERT: A 682 ILE cc_start: 0.8298 (tp) cc_final: 0.8019 (tp) REVERT: A 711 LYS cc_start: 0.9301 (mmtt) cc_final: 0.8857 (mmtm) REVERT: A 712 GLU cc_start: 0.8627 (tt0) cc_final: 0.8070 (tt0) REVERT: A 716 LEU cc_start: 0.8694 (mt) cc_final: 0.8361 (mt) REVERT: A 717 TYR cc_start: 0.8858 (t80) cc_final: 0.8250 (t80) REVERT: A 719 ASP cc_start: 0.8171 (m-30) cc_final: 0.7863 (m-30) REVERT: A 720 TYR cc_start: 0.7812 (t80) cc_final: 0.7200 (t80) REVERT: A 727 GLU cc_start: 0.7935 (pm20) cc_final: 0.7615 (pm20) REVERT: A 734 ARG cc_start: 0.8436 (ttt-90) cc_final: 0.7962 (ttp80) REVERT: A 738 HIS cc_start: 0.8067 (t70) cc_final: 0.7770 (t-170) REVERT: A 743 GLU cc_start: 0.8340 (mm-30) cc_final: 0.7682 (mp0) REVERT: A 748 TYR cc_start: 0.7333 (t80) cc_final: 0.6872 (t80) REVERT: A 753 GLU cc_start: 0.8602 (mp0) cc_final: 0.8253 (mp0) REVERT: A 756 GLU cc_start: 0.7080 (tp30) cc_final: 0.6833 (tp30) REVERT: A 788 ARG cc_start: 0.8577 (ptt180) cc_final: 0.7931 (ptt180) REVERT: A 792 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8098 (mm-30) REVERT: A 820 LEU cc_start: 0.7759 (mm) cc_final: 0.7408 (mm) REVERT: A 822 LYS cc_start: 0.8459 (mptt) cc_final: 0.8085 (mmtm) REVERT: D 22 LEU cc_start: 0.8177 (mm) cc_final: 0.7846 (mm) REVERT: D 42 GLN cc_start: 0.8350 (mt0) cc_final: 0.8117 (mt0) REVERT: D 65 ASN cc_start: 0.8372 (m-40) cc_final: 0.7971 (m-40) REVERT: D 73 CYS cc_start: 0.6918 (m) cc_final: 0.6465 (m) REVERT: D 79 LYS cc_start: 0.8447 (tppp) cc_final: 0.7223 (tppp) REVERT: D 94 THR cc_start: 0.7658 (p) cc_final: 0.7403 (p) REVERT: D 114 GLN cc_start: 0.7974 (mp10) cc_final: 0.7574 (mp10) REVERT: D 132 PHE cc_start: 0.7783 (m-80) cc_final: 0.6897 (m-80) REVERT: D 138 ARG cc_start: 0.7841 (ptt-90) cc_final: 0.6981 (ptt-90) REVERT: C 130 GLU cc_start: 0.8366 (pt0) cc_final: 0.7637 (pm20) REVERT: C 138 GLU cc_start: 0.8581 (mp0) cc_final: 0.8121 (mp0) REVERT: C 283 TYR cc_start: 0.8028 (t80) cc_final: 0.7532 (t80) REVERT: C 288 ILE cc_start: 0.8512 (tt) cc_final: 0.8051 (tt) REVERT: C 292 GLU cc_start: 0.8335 (mm-30) cc_final: 0.7966 (mm-30) REVERT: C 304 MET cc_start: 0.5388 (tpt) cc_final: 0.5090 (tpt) REVERT: C 315 LYS cc_start: 0.7951 (mtmm) cc_final: 0.7534 (ptpp) REVERT: C 321 GLN cc_start: 0.8376 (mt0) cc_final: 0.8152 (mm-40) REVERT: C 326 ARG cc_start: 0.8213 (mtm180) cc_final: 0.7856 (mtm110) REVERT: C 330 LYS cc_start: 0.8729 (mmmt) cc_final: 0.8305 (mmtm) REVERT: C 332 ASN cc_start: 0.7528 (t0) cc_final: 0.7188 (t0) REVERT: C 337 ARG cc_start: 0.8274 (ttm170) cc_final: 0.7747 (tmm-80) REVERT: C 338 ARG cc_start: 0.8054 (mtp85) cc_final: 0.7838 (mmm-85) REVERT: C 344 GLN cc_start: 0.8439 (tp-100) cc_final: 0.7483 (tp-100) REVERT: C 349 TYR cc_start: 0.7933 (t80) cc_final: 0.7721 (t80) REVERT: C 373 LYS cc_start: 0.7961 (ttmt) cc_final: 0.7758 (mtpp) REVERT: C 380 TYR cc_start: 0.8714 (m-10) cc_final: 0.8139 (m-10) REVERT: C 382 ASN cc_start: 0.8493 (m-40) cc_final: 0.8206 (m110) REVERT: C 392 HIS cc_start: 0.8317 (m170) cc_final: 0.7956 (m-70) REVERT: C 397 ASP cc_start: 0.7807 (t0) cc_final: 0.7239 (t0) REVERT: C 398 GLU cc_start: 0.8125 (pp20) cc_final: 0.7832 (pm20) REVERT: C 403 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7737 (tm-30) REVERT: C 407 LEU cc_start: 0.8826 (mt) cc_final: 0.8313 (pp) REVERT: C 410 GLN cc_start: 0.9059 (mm-40) cc_final: 0.7923 (mm110) REVERT: C 411 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7077 (mt-10) REVERT: C 441 LYS cc_start: 0.9042 (tttm) cc_final: 0.8833 (tptp) REVERT: C 447 GLU cc_start: 0.8134 (mp0) cc_final: 0.7473 (tp30) REVERT: C 450 ILE cc_start: 0.8023 (mt) cc_final: 0.7499 (mt) REVERT: C 458 LEU cc_start: 0.8474 (tp) cc_final: 0.8221 (tp) REVERT: C 459 GLU cc_start: 0.7357 (mp0) cc_final: 0.6839 (mp0) REVERT: C 478 MET cc_start: 0.8051 (mtp) cc_final: 0.7474 (mtp) REVERT: C 482 PHE cc_start: 0.7980 (p90) cc_final: 0.7606 (p90) REVERT: C 493 LEU cc_start: 0.8025 (tp) cc_final: 0.7665 (tp) REVERT: C 495 TYR cc_start: 0.7551 (m-10) cc_final: 0.7312 (m-10) REVERT: C 499 ILE cc_start: 0.8059 (tp) cc_final: 0.7706 (tp) REVERT: C 501 MET cc_start: 0.8195 (mtt) cc_final: 0.7748 (mtt) REVERT: C 502 TYR cc_start: 0.7626 (m-10) cc_final: 0.7365 (m-10) REVERT: C 505 ARG cc_start: 0.8818 (mtt90) cc_final: 0.8241 (mtt90) REVERT: C 507 ILE cc_start: 0.8526 (mt) cc_final: 0.8250 (mp) REVERT: C 522 TYR cc_start: 0.8062 (m-80) cc_final: 0.7476 (m-80) REVERT: C 530 ASP cc_start: 0.7966 (p0) cc_final: 0.7023 (p0) REVERT: C 531 HIS cc_start: 0.7615 (m90) cc_final: 0.7245 (m90) REVERT: C 533 ILE cc_start: 0.8369 (mp) cc_final: 0.8064 (mp) REVERT: C 539 ARG cc_start: 0.8485 (ttm-80) cc_final: 0.8037 (ttm-80) REVERT: C 542 MET cc_start: 0.8081 (tpp) cc_final: 0.7394 (tpp) REVERT: C 543 ILE cc_start: 0.8881 (mt) cc_final: 0.8660 (mt) REVERT: C 545 MET cc_start: 0.7833 (mtm) cc_final: 0.7151 (mtm) REVERT: C 551 LEU cc_start: 0.8844 (mp) cc_final: 0.8568 (mp) REVERT: C 553 LYS cc_start: 0.8438 (mtmt) cc_final: 0.8151 (mtpp) REVERT: C 555 LEU cc_start: 0.8605 (tp) cc_final: 0.8244 (tp) REVERT: C 572 LYS cc_start: 0.8310 (mmtt) cc_final: 0.7729 (mmtt) REVERT: C 573 GLU cc_start: 0.7947 (pm20) cc_final: 0.7670 (pp20) REVERT: C 576 GLN cc_start: 0.7795 (tm-30) cc_final: 0.7288 (tm-30) REVERT: C 577 LEU cc_start: 0.8675 (mt) cc_final: 0.8091 (mt) REVERT: C 581 GLU cc_start: 0.8148 (pp20) cc_final: 0.7716 (pp20) REVERT: C 587 ILE cc_start: 0.8162 (tp) cc_final: 0.7833 (tp) REVERT: C 589 MET cc_start: 0.6608 (mtp) cc_final: 0.6202 (mtp) REVERT: C 593 ASP cc_start: 0.7918 (t70) cc_final: 0.7709 (t0) REVERT: C 617 ILE cc_start: 0.8602 (mm) cc_final: 0.8309 (mm) REVERT: C 619 LEU cc_start: 0.8813 (tp) cc_final: 0.8545 (tp) REVERT: C 621 LEU cc_start: 0.8188 (mm) cc_final: 0.7748 (mm) REVERT: C 625 ASN cc_start: 0.8564 (m110) cc_final: 0.8242 (m110) REVERT: C 626 ASN cc_start: 0.8047 (m-40) cc_final: 0.7729 (m110) REVERT: C 630 ASP cc_start: 0.7273 (t70) cc_final: 0.6945 (t0) REVERT: C 635 MET cc_start: 0.8112 (mpp) cc_final: 0.7487 (mpp) REVERT: C 641 LEU cc_start: 0.8538 (mt) cc_final: 0.8231 (mm) REVERT: C 642 MET cc_start: 0.8072 (mmp) cc_final: 0.7721 (mmp) REVERT: C 649 ARG cc_start: 0.8789 (ttm170) cc_final: 0.8561 (mtp85) REVERT: C 658 LEU cc_start: 0.8441 (tp) cc_final: 0.8094 (tt) REVERT: C 660 GLN cc_start: 0.8581 (mm-40) cc_final: 0.8122 (mm-40) REVERT: C 661 SER cc_start: 0.8574 (m) cc_final: 0.8307 (p) REVERT: C 663 LYS cc_start: 0.8026 (ptmm) cc_final: 0.7627 (ttpp) REVERT: C 667 GLU cc_start: 0.7954 (pp20) cc_final: 0.7647 (pp20) REVERT: C 692 MET cc_start: 0.7091 (ttm) cc_final: 0.6872 (ttm) REVERT: C 711 LYS cc_start: 0.9285 (mmtt) cc_final: 0.8779 (mmtm) REVERT: C 712 GLU cc_start: 0.8701 (tt0) cc_final: 0.8169 (tt0) REVERT: C 717 TYR cc_start: 0.8857 (t80) cc_final: 0.8459 (t80) REVERT: C 720 TYR cc_start: 0.7831 (t80) cc_final: 0.7287 (t80) REVERT: C 724 LYS cc_start: 0.8151 (ptpp) cc_final: 0.7807 (pttm) REVERT: C 727 GLU cc_start: 0.8071 (pm20) cc_final: 0.7834 (pm20) REVERT: C 734 ARG cc_start: 0.8738 (ttt-90) cc_final: 0.8282 (ttm170) REVERT: C 738 HIS cc_start: 0.8017 (t-90) cc_final: 0.7784 (t-170) REVERT: C 739 MET cc_start: 0.7852 (ptp) cc_final: 0.7520 (ptp) REVERT: C 743 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8094 (mm-30) REVERT: C 747 LYS cc_start: 0.9020 (mtmt) cc_final: 0.8809 (mmmt) REVERT: C 748 TYR cc_start: 0.7356 (t80) cc_final: 0.6837 (t80) REVERT: C 750 PHE cc_start: 0.8574 (m-10) cc_final: 0.8368 (m-10) REVERT: C 754 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8201 (mp0) REVERT: C 780 TYR cc_start: 0.6100 (t80) cc_final: 0.5761 (t80) REVERT: C 788 ARG cc_start: 0.8505 (ptt180) cc_final: 0.8129 (ptt180) REVERT: C 805 PHE cc_start: 0.8554 (t80) cc_final: 0.8336 (t80) REVERT: C 822 LYS cc_start: 0.8480 (mmtt) cc_final: 0.8125 (mmtm) outliers start: 1 outliers final: 0 residues processed: 526 average time/residue: 0.4247 time to fit residues: 304.0050 Evaluate side-chains 511 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 511 time to evaluate : 2.243 ------------------------------------------------------------------------------- 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: 0.9990 chunk 109 optimal weight: 0.1980 chunk 126 optimal weight: 0.6980 chunk 151 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 118 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 114 GLN B 134 ASN ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 ASN 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 = 0.4141 r_free = 0.4141 target = 0.144357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.116533 restraints weight = 29822.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.121214 restraints weight = 18279.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.124724 restraints weight = 12659.350| |-----------------------------------------------------------------------------| r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.5350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13534 Z= 0.116 Angle : 0.597 9.698 18272 Z= 0.300 Chirality : 0.042 0.198 2014 Planarity : 0.004 0.039 2372 Dihedral : 4.826 20.316 1806 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % 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: -1.19 (0.21), residues: 1610 helix: -0.26 (0.18), residues: 814 sheet: -2.45 (0.60), residues: 72 loop : -1.11 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A 328 HIS 0.004 0.001 HIS C 655 PHE 0.021 0.001 PHE C 790 TYR 0.019 0.001 TYR A 464 ARG 0.006 0.000 ARG C 141 Details of bonding type rmsd hydrogen bonds : bond 0.03449 ( 502) hydrogen bonds : angle 4.97897 ( 1392) metal coordination : bond 0.00376 ( 12) metal coordination : angle 3.42412 ( 12) covalent geometry : bond 0.00244 (13522) covalent geometry : angle 0.59025 (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 514 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 514 time to evaluate : 1.781 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: 0.7580 (mmtm) cc_final: 0.7093 (mmmm) REVERT: B 22 LEU cc_start: 0.8152 (mm) cc_final: 0.7813 (mm) REVERT: B 65 ASN cc_start: 0.8286 (m-40) cc_final: 0.7927 (m-40) REVERT: B 73 CYS cc_start: 0.6119 (m) cc_final: 0.5848 (m) REVERT: B 77 TYR cc_start: 0.8169 (m-80) cc_final: 0.7683 (m-80) REVERT: B 82 GLU cc_start: 0.8725 (tt0) cc_final: 0.8315 (tt0) REVERT: B 88 TYR cc_start: 0.6832 (p90) cc_final: 0.6322 (p90) REVERT: B 108 ILE cc_start: 0.8141 (mt) cc_final: 0.7734 (tt) REVERT: B 114 GLN cc_start: 0.7697 (mp10) cc_final: 0.7464 (mp10) REVERT: B 124 ARG cc_start: 0.8686 (ttt-90) cc_final: 0.8409 (ttt-90) REVERT: B 132 PHE cc_start: 0.7577 (m-80) cc_final: 0.6850 (m-80) REVERT: B 134 ASN cc_start: 0.7629 (t0) cc_final: 0.6567 (t0) REVERT: B 139 TRP cc_start: 0.7163 (m100) cc_final: 0.6667 (m100) REVERT: A 130 GLU cc_start: 0.8433 (pt0) cc_final: 0.7554 (pm20) REVERT: A 237 ASP cc_start: 0.8447 (m-30) cc_final: 0.7845 (t0) REVERT: A 283 TYR cc_start: 0.7674 (t80) cc_final: 0.7244 (t80) REVERT: A 287 PHE cc_start: 0.7325 (m-80) cc_final: 0.6866 (m-80) REVERT: A 291 MET cc_start: 0.8450 (ttt) cc_final: 0.7995 (ttt) REVERT: A 294 ARG cc_start: 0.8496 (mpt-90) cc_final: 0.8290 (mpt-90) REVERT: A 304 MET cc_start: 0.4898 (tpt) cc_final: 0.4144 (tpt) REVERT: A 315 LYS cc_start: 0.8090 (mmtm) cc_final: 0.7468 (mttm) REVERT: A 326 ARG cc_start: 0.7966 (mtm110) cc_final: 0.7655 (mtm-85) REVERT: A 332 ASN cc_start: 0.7566 (t0) cc_final: 0.7000 (t0) REVERT: A 337 ARG cc_start: 0.8210 (ttm170) cc_final: 0.7281 (ttp80) REVERT: A 338 ARG cc_start: 0.8108 (mtp85) cc_final: 0.7723 (mmm-85) REVERT: A 339 MET cc_start: 0.6728 (mtm) cc_final: 0.6464 (mtm) REVERT: A 341 GLU cc_start: 0.8393 (mt-10) cc_final: 0.7956 (mt-10) REVERT: A 344 GLN cc_start: 0.8506 (tp-100) cc_final: 0.7513 (tp-100) REVERT: A 347 ILE cc_start: 0.7464 (mt) cc_final: 0.7190 (mm) REVERT: A 350 LYS cc_start: 0.7614 (mmpt) cc_final: 0.7257 (tptt) REVERT: A 392 HIS cc_start: 0.8108 (m90) cc_final: 0.7643 (m90) REVERT: A 406 GLU cc_start: 0.8424 (tp30) cc_final: 0.7895 (tp30) REVERT: A 407 LEU cc_start: 0.8890 (mt) cc_final: 0.8396 (pp) REVERT: A 408 THR cc_start: 0.8641 (m) cc_final: 0.8100 (p) REVERT: A 411 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7282 (mt-10) REVERT: A 424 ARG cc_start: 0.7849 (mmm-85) cc_final: 0.7443 (tpt-90) REVERT: A 437 LEU cc_start: 0.8278 (mm) cc_final: 0.7862 (tt) REVERT: A 446 PHE cc_start: 0.7599 (m-80) cc_final: 0.7370 (m-80) REVERT: A 447 GLU cc_start: 0.8085 (mp0) cc_final: 0.7632 (tp30) REVERT: A 449 PHE cc_start: 0.7252 (m-10) cc_final: 0.6696 (m-10) REVERT: A 450 ILE cc_start: 0.7981 (mt) cc_final: 0.7107 (mt) REVERT: A 455 ASN cc_start: 0.7895 (m-40) cc_final: 0.7630 (m-40) REVERT: A 458 LEU cc_start: 0.8419 (tp) cc_final: 0.7979 (tt) REVERT: A 459 GLU cc_start: 0.6999 (mp0) cc_final: 0.6672 (mp0) REVERT: A 477 PHE cc_start: 0.8000 (m-80) cc_final: 0.7551 (m-80) REVERT: A 478 MET cc_start: 0.8083 (mtp) cc_final: 0.7575 (ttm) REVERT: A 482 PHE cc_start: 0.7911 (p90) cc_final: 0.7617 (p90) REVERT: A 488 THR cc_start: 0.7712 (m) cc_final: 0.7440 (p) REVERT: A 489 LYS cc_start: 0.8270 (mtmm) cc_final: 0.8036 (ptpp) REVERT: A 499 ILE cc_start: 0.7833 (tp) cc_final: 0.7593 (tp) REVERT: A 502 TYR cc_start: 0.7538 (m-10) cc_final: 0.7298 (m-10) REVERT: A 504 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7561 (mm-30) REVERT: A 505 ARG cc_start: 0.8801 (mtt90) cc_final: 0.8187 (mtt90) REVERT: A 507 ILE cc_start: 0.8674 (mt) cc_final: 0.8296 (mt) REVERT: A 522 TYR cc_start: 0.8151 (m-80) cc_final: 0.7727 (m-80) REVERT: A 530 ASP cc_start: 0.8155 (p0) cc_final: 0.7898 (p0) REVERT: A 533 ILE cc_start: 0.8351 (pt) cc_final: 0.7932 (mp) REVERT: A 539 ARG cc_start: 0.8501 (ttm-80) cc_final: 0.8027 (ptm160) REVERT: A 540 LEU cc_start: 0.9030 (mm) cc_final: 0.8741 (mm) REVERT: A 542 MET cc_start: 0.8400 (ptt) cc_final: 0.7728 (tmm) REVERT: A 545 MET cc_start: 0.7750 (mtm) cc_final: 0.7178 (mtm) REVERT: A 550 ASP cc_start: 0.7838 (p0) cc_final: 0.7461 (p0) REVERT: A 553 LYS cc_start: 0.8461 (mtmt) cc_final: 0.8219 (mtpp) REVERT: A 573 GLU cc_start: 0.8049 (pp20) cc_final: 0.7583 (pp20) REVERT: A 576 GLN cc_start: 0.8338 (tp40) cc_final: 0.7692 (tp40) REVERT: A 577 LEU cc_start: 0.8874 (mt) cc_final: 0.8547 (mt) REVERT: A 587 ILE cc_start: 0.7939 (tp) cc_final: 0.7710 (tp) REVERT: A 593 ASP cc_start: 0.8186 (t0) cc_final: 0.7728 (t70) REVERT: A 600 TRP cc_start: 0.8687 (t-100) cc_final: 0.8396 (t-100) REVERT: A 603 PRO cc_start: 0.7329 (Cg_endo) cc_final: 0.6998 (Cg_exo) REVERT: A 621 LEU cc_start: 0.8019 (mm) cc_final: 0.7561 (mt) REVERT: A 635 MET cc_start: 0.8235 (mpp) cc_final: 0.7451 (mpp) REVERT: A 641 LEU cc_start: 0.8536 (mt) cc_final: 0.8201 (mt) REVERT: A 642 MET cc_start: 0.8155 (mmp) cc_final: 0.7780 (mmp) REVERT: A 648 PHE cc_start: 0.8597 (p90) cc_final: 0.8150 (p90) REVERT: A 651 LEU cc_start: 0.8434 (mt) cc_final: 0.8143 (mt) REVERT: A 660 GLN cc_start: 0.8182 (pp30) cc_final: 0.7732 (pp30) REVERT: A 663 LYS cc_start: 0.8180 (ptmm) cc_final: 0.7556 (mptt) REVERT: A 667 GLU cc_start: 0.8147 (pp20) cc_final: 0.7872 (pp20) REVERT: A 682 ILE cc_start: 0.8318 (tp) cc_final: 0.7957 (tp) REVERT: A 710 ARG cc_start: 0.8728 (ttp-170) cc_final: 0.8448 (ptp-170) REVERT: A 711 LYS cc_start: 0.9310 (mmtt) cc_final: 0.8774 (mmtm) REVERT: A 712 GLU cc_start: 0.8613 (tt0) cc_final: 0.8072 (tt0) REVERT: A 716 LEU cc_start: 0.8712 (mt) cc_final: 0.8407 (mp) REVERT: A 717 TYR cc_start: 0.8902 (t80) cc_final: 0.8039 (t80) REVERT: A 719 ASP cc_start: 0.8181 (m-30) cc_final: 0.7841 (m-30) REVERT: A 720 TYR cc_start: 0.7837 (t80) cc_final: 0.7295 (t80) REVERT: A 727 GLU cc_start: 0.7901 (pm20) cc_final: 0.7540 (pm20) REVERT: A 728 LYS cc_start: 0.8368 (ttpt) cc_final: 0.7620 (tmtt) REVERT: A 734 ARG cc_start: 0.8407 (ttt-90) cc_final: 0.7675 (ttm-80) REVERT: A 738 HIS cc_start: 0.8036 (t70) cc_final: 0.7737 (t-170) REVERT: A 743 GLU cc_start: 0.8363 (mm-30) cc_final: 0.7862 (mp0) REVERT: A 750 PHE cc_start: 0.8326 (m-80) cc_final: 0.8083 (m-10) REVERT: A 753 GLU cc_start: 0.8607 (mp0) cc_final: 0.8225 (mp0) REVERT: A 788 ARG cc_start: 0.8520 (ptt180) cc_final: 0.8043 (ptt180) REVERT: A 792 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8096 (mm-30) REVERT: A 822 LYS cc_start: 0.8402 (mptt) cc_final: 0.8042 (mmtm) REVERT: D 22 LEU cc_start: 0.8145 (mm) cc_final: 0.7819 (mm) REVERT: D 65 ASN cc_start: 0.8352 (m-40) cc_final: 0.7958 (m-40) REVERT: D 73 CYS cc_start: 0.6780 (m) cc_final: 0.6250 (m) REVERT: D 79 LYS cc_start: 0.8430 (tppp) cc_final: 0.7143 (tppp) REVERT: D 80 ILE cc_start: 0.8574 (mm) cc_final: 0.8354 (mm) REVERT: D 82 GLU cc_start: 0.8660 (tt0) cc_final: 0.7936 (tt0) REVERT: D 84 ARG cc_start: 0.7231 (mtp180) cc_final: 0.6958 (mtp180) REVERT: D 94 THR cc_start: 0.7609 (p) cc_final: 0.7063 (p) REVERT: D 98 GLN cc_start: 0.8424 (mp10) cc_final: 0.8121 (mp10) REVERT: D 114 GLN cc_start: 0.7959 (mp10) cc_final: 0.7503 (mp10) REVERT: D 128 LYS cc_start: 0.8622 (mttt) cc_final: 0.8328 (mttt) REVERT: D 132 PHE cc_start: 0.7844 (m-80) cc_final: 0.6942 (m-80) REVERT: D 138 ARG cc_start: 0.7785 (ptt-90) cc_final: 0.6495 (ptt-90) REVERT: C 130 GLU cc_start: 0.8348 (pt0) cc_final: 0.7627 (pm20) REVERT: C 138 GLU cc_start: 0.8636 (mp0) cc_final: 0.8240 (mp0) REVERT: C 246 LEU cc_start: 0.8189 (tp) cc_final: 0.7984 (tp) REVERT: C 270 ASP cc_start: 0.7245 (t70) cc_final: 0.7040 (t70) REVERT: C 283 TYR cc_start: 0.7917 (t80) cc_final: 0.7608 (t80) REVERT: C 288 ILE cc_start: 0.8565 (tt) cc_final: 0.7798 (tt) REVERT: C 292 GLU cc_start: 0.8352 (mm-30) cc_final: 0.7691 (mm-30) REVERT: C 294 ARG cc_start: 0.8468 (mpt-90) cc_final: 0.8149 (mmm160) REVERT: C 326 ARG cc_start: 0.8179 (mtm180) cc_final: 0.7884 (mtm-85) REVERT: C 330 LYS cc_start: 0.8740 (mmmt) cc_final: 0.8322 (mmtm) REVERT: C 332 ASN cc_start: 0.7533 (t0) cc_final: 0.7178 (t0) REVERT: C 337 ARG cc_start: 0.8241 (ttm170) cc_final: 0.7828 (tmm-80) REVERT: C 338 ARG cc_start: 0.8105 (mtp85) cc_final: 0.7844 (mmt90) REVERT: C 341 GLU cc_start: 0.8204 (pp20) cc_final: 0.7696 (pp20) REVERT: C 344 GLN cc_start: 0.8488 (tp-100) cc_final: 0.7614 (tp-100) REVERT: C 349 TYR cc_start: 0.7959 (t80) cc_final: 0.7725 (t80) REVERT: C 373 LYS cc_start: 0.8049 (ttmt) cc_final: 0.7833 (mtpp) REVERT: C 380 TYR cc_start: 0.8549 (m-10) cc_final: 0.8205 (m-10) REVERT: C 382 ASN cc_start: 0.8510 (m-40) cc_final: 0.8194 (m110) REVERT: C 392 HIS cc_start: 0.8304 (m170) cc_final: 0.7946 (m-70) REVERT: C 397 ASP cc_start: 0.7898 (t0) cc_final: 0.7453 (t0) REVERT: C 398 GLU cc_start: 0.8138 (pp20) cc_final: 0.7848 (pm20) REVERT: C 403 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7704 (pp20) REVERT: C 406 GLU cc_start: 0.8612 (tp30) cc_final: 0.7350 (tp30) REVERT: C 407 LEU cc_start: 0.8857 (mt) cc_final: 0.8339 (pp) REVERT: C 408 THR cc_start: 0.8580 (m) cc_final: 0.8109 (p) REVERT: C 409 LEU cc_start: 0.8712 (tp) cc_final: 0.7986 (pp) REVERT: C 410 GLN cc_start: 0.9052 (mm-40) cc_final: 0.7240 (mm-40) REVERT: C 411 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7053 (mt-10) REVERT: C 441 LYS cc_start: 0.9062 (tttm) cc_final: 0.8799 (tptp) REVERT: C 447 GLU cc_start: 0.8097 (mp0) cc_final: 0.7497 (tp30) REVERT: C 450 ILE cc_start: 0.8079 (mt) cc_final: 0.7490 (mt) REVERT: C 459 GLU cc_start: 0.7367 (mp0) cc_final: 0.7017 (mp0) REVERT: C 478 MET cc_start: 0.8045 (mtp) cc_final: 0.7451 (mtp) REVERT: C 482 PHE cc_start: 0.7961 (p90) cc_final: 0.7664 (p90) REVERT: C 495 TYR cc_start: 0.7609 (m-10) cc_final: 0.7381 (m-10) REVERT: C 499 ILE cc_start: 0.8069 (tp) cc_final: 0.7728 (tp) REVERT: C 501 MET cc_start: 0.8188 (mtt) cc_final: 0.7544 (mtt) REVERT: C 502 TYR cc_start: 0.7644 (m-10) cc_final: 0.7381 (m-10) REVERT: C 505 ARG cc_start: 0.8750 (mtt90) cc_final: 0.8216 (mtt90) REVERT: C 522 TYR cc_start: 0.8024 (m-80) cc_final: 0.7422 (m-80) REVERT: C 530 ASP cc_start: 0.7984 (p0) cc_final: 0.7670 (p0) REVERT: C 539 ARG cc_start: 0.8490 (ttm-80) cc_final: 0.8097 (ttm-80) REVERT: C 542 MET cc_start: 0.8087 (tpp) cc_final: 0.7372 (tpp) REVERT: C 543 ILE cc_start: 0.8826 (mt) cc_final: 0.8570 (mt) REVERT: C 545 MET cc_start: 0.7787 (mtm) cc_final: 0.7105 (mtm) REVERT: C 551 LEU cc_start: 0.8825 (mp) cc_final: 0.8558 (mp) REVERT: C 553 LYS cc_start: 0.8310 (mtmt) cc_final: 0.7971 (mtpp) REVERT: C 554 GLN cc_start: 0.8053 (tt0) cc_final: 0.6452 (tt0) REVERT: C 555 LEU cc_start: 0.8612 (tp) cc_final: 0.8290 (tp) REVERT: C 572 LYS cc_start: 0.8316 (mmtt) cc_final: 0.7816 (mmtt) REVERT: C 573 GLU cc_start: 0.8054 (pm20) cc_final: 0.7626 (pm20) REVERT: C 576 GLN cc_start: 0.7766 (tm-30) cc_final: 0.7269 (tm-30) REVERT: C 577 LEU cc_start: 0.8613 (mt) cc_final: 0.8038 (mt) REVERT: C 587 ILE cc_start: 0.8094 (tp) cc_final: 0.7753 (tp) REVERT: C 589 MET cc_start: 0.6540 (mtp) cc_final: 0.6111 (mtp) REVERT: C 593 ASP cc_start: 0.7976 (t70) cc_final: 0.7745 (t0) REVERT: C 617 ILE cc_start: 0.8564 (mm) cc_final: 0.8303 (mm) REVERT: C 619 LEU cc_start: 0.8817 (tp) cc_final: 0.8553 (tp) REVERT: C 621 LEU cc_start: 0.8199 (mm) cc_final: 0.7741 (mm) REVERT: C 625 ASN cc_start: 0.8531 (m110) cc_final: 0.8154 (m110) REVERT: C 626 ASN cc_start: 0.8080 (m110) cc_final: 0.7776 (m110) REVERT: C 635 MET cc_start: 0.8114 (mpp) cc_final: 0.7466 (mpp) REVERT: C 641 LEU cc_start: 0.8542 (mt) cc_final: 0.8154 (mm) REVERT: C 642 MET cc_start: 0.8129 (mmp) cc_final: 0.7826 (mmp) REVERT: C 658 LEU cc_start: 0.8456 (tp) cc_final: 0.8144 (tt) REVERT: C 660 GLN cc_start: 0.8644 (mm-40) cc_final: 0.8051 (mm-40) REVERT: C 661 SER cc_start: 0.8711 (m) cc_final: 0.8456 (p) REVERT: C 663 LYS cc_start: 0.8120 (ptmm) cc_final: 0.7652 (ttpp) REVERT: C 667 GLU cc_start: 0.7969 (pp20) cc_final: 0.7662 (pp20) REVERT: C 707 ASN cc_start: 0.8319 (p0) cc_final: 0.8095 (p0) REVERT: C 708 GLU cc_start: 0.8563 (pm20) cc_final: 0.8350 (pm20) REVERT: C 712 GLU cc_start: 0.8723 (tt0) cc_final: 0.8166 (tt0) REVERT: C 717 TYR cc_start: 0.8895 (t80) cc_final: 0.8588 (t80) REVERT: C 719 ASP cc_start: 0.8313 (m-30) cc_final: 0.7722 (p0) REVERT: C 720 TYR cc_start: 0.7845 (t80) cc_final: 0.7270 (t80) REVERT: C 727 GLU cc_start: 0.8068 (pm20) cc_final: 0.7794 (pm20) REVERT: C 738 HIS cc_start: 0.8060 (t-90) cc_final: 0.7796 (t-170) REVERT: C 739 MET cc_start: 0.7874 (ptp) cc_final: 0.7547 (ptp) REVERT: C 743 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8111 (mm-30) REVERT: C 748 TYR cc_start: 0.7357 (t80) cc_final: 0.6769 (t80) REVERT: C 788 ARG cc_start: 0.8431 (ptt180) cc_final: 0.7909 (ttp80) REVERT: C 822 LYS cc_start: 0.8437 (mmtt) cc_final: 0.8059 (mmtm) outliers start: 0 outliers final: 0 residues processed: 514 average time/residue: 0.4045 time to fit residues: 280.5785 Evaluate side-chains 493 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 493 time to evaluate : 1.424 ------------------------------------------------------------------------------- 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: 3.9990 chunk 13 optimal weight: 0.2980 chunk 10 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 101 optimal weight: 0.0170 chunk 7 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 overall best weight: 0.8020 ------------------------------------------------------------------------------- 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 626 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 = 0.4127 r_free = 0.4127 target = 0.143315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.115549 restraints weight = 29590.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.120224 restraints weight = 18075.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.123707 restraints weight = 12514.750| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.5579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13534 Z= 0.134 Angle : 0.629 9.430 18272 Z= 0.316 Chirality : 0.044 0.180 2014 Planarity : 0.004 0.079 2372 Dihedral : 4.815 19.014 1806 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.07 % Allowed : 0.90 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.21), residues: 1610 helix: -0.21 (0.18), residues: 810 sheet: -2.40 (0.59), residues: 72 loop : -1.03 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP C 328 HIS 0.006 0.001 HIS A 655 PHE 0.015 0.001 PHE A 790 TYR 0.021 0.001 TYR C 659 ARG 0.006 0.000 ARG C 141 Details of bonding type rmsd hydrogen bonds : bond 0.03657 ( 502) hydrogen bonds : angle 5.04665 ( 1392) metal coordination : bond 0.00475 ( 12) metal coordination : angle 4.10435 ( 12) covalent geometry : bond 0.00275 (13522) covalent geometry : angle 0.62005 (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 515 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 514 time to evaluate : 1.402 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: B 22 LEU cc_start: 0.8239 (mm) cc_final: 0.7914 (mm) REVERT: B 65 ASN cc_start: 0.8405 (m-40) cc_final: 0.8049 (m-40) REVERT: B 73 CYS cc_start: 0.5887 (m) cc_final: 0.5536 (m) REVERT: B 77 TYR cc_start: 0.8174 (m-80) cc_final: 0.7702 (m-80) REVERT: B 82 GLU cc_start: 0.8756 (tt0) cc_final: 0.8384 (tt0) REVERT: B 88 TYR cc_start: 0.6988 (p90) cc_final: 0.6612 (p90) REVERT: B 108 ILE cc_start: 0.8124 (mt) cc_final: 0.7697 (tt) REVERT: B 114 GLN cc_start: 0.7861 (mp10) cc_final: 0.7609 (mp10) REVERT: B 124 ARG cc_start: 0.8730 (ttt-90) cc_final: 0.8464 (ttt-90) REVERT: B 132 PHE cc_start: 0.7735 (m-80) cc_final: 0.6981 (m-80) REVERT: B 134 ASN cc_start: 0.8105 (t0) cc_final: 0.7055 (t0) REVERT: B 136 ARG cc_start: 0.8130 (mmm160) cc_final: 0.7260 (mmm160) REVERT: B 139 TRP cc_start: 0.7293 (m100) cc_final: 0.6809 (m100) REVERT: A 130 GLU cc_start: 0.8420 (pt0) cc_final: 0.7558 (pm20) REVERT: A 237 ASP cc_start: 0.8409 (m-30) cc_final: 0.7800 (t0) REVERT: A 283 TYR cc_start: 0.7692 (t80) cc_final: 0.7248 (t80) REVERT: A 287 PHE cc_start: 0.7404 (m-80) cc_final: 0.6941 (m-80) REVERT: A 294 ARG cc_start: 0.8503 (mpt-90) cc_final: 0.8293 (mpt-90) REVERT: A 304 MET cc_start: 0.4754 (tpt) cc_final: 0.4019 (tpt) REVERT: A 315 LYS cc_start: 0.8180 (mmtm) cc_final: 0.7578 (mttm) REVERT: A 332 ASN cc_start: 0.7638 (t0) cc_final: 0.7068 (t0) REVERT: A 337 ARG cc_start: 0.8257 (ttm170) cc_final: 0.7435 (ttp80) REVERT: A 338 ARG cc_start: 0.8073 (mtp85) cc_final: 0.7678 (mmm160) REVERT: A 341 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8051 (mt-10) REVERT: A 344 GLN cc_start: 0.8570 (tp-100) cc_final: 0.7592 (tp-100) REVERT: A 347 ILE cc_start: 0.7575 (mt) cc_final: 0.7302 (mm) REVERT: A 350 LYS cc_start: 0.7564 (mmpt) cc_final: 0.7309 (tptt) REVERT: A 392 HIS cc_start: 0.8181 (m90) cc_final: 0.7703 (m90) REVERT: A 406 GLU cc_start: 0.8437 (tp30) cc_final: 0.7941 (tp30) REVERT: A 407 LEU cc_start: 0.8891 (mt) cc_final: 0.8429 (pp) REVERT: A 408 THR cc_start: 0.8669 (m) cc_final: 0.8043 (p) REVERT: A 411 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7226 (mt-10) REVERT: A 424 ARG cc_start: 0.7886 (mmm-85) cc_final: 0.6893 (tpp80) REVERT: A 437 LEU cc_start: 0.8294 (mm) cc_final: 0.7900 (tt) REVERT: A 446 PHE cc_start: 0.7645 (m-80) cc_final: 0.7406 (m-80) REVERT: A 447 GLU cc_start: 0.8105 (mp0) cc_final: 0.7647 (tp30) REVERT: A 449 PHE cc_start: 0.7238 (m-10) cc_final: 0.6682 (m-10) REVERT: A 450 ILE cc_start: 0.8029 (mt) cc_final: 0.7096 (mt) REVERT: A 455 ASN cc_start: 0.7913 (m-40) cc_final: 0.7675 (m-40) REVERT: A 458 LEU cc_start: 0.8434 (tp) cc_final: 0.7954 (tt) REVERT: A 459 GLU cc_start: 0.7068 (mp0) cc_final: 0.6739 (mp0) REVERT: A 477 PHE cc_start: 0.8043 (m-80) cc_final: 0.7570 (m-80) REVERT: A 478 MET cc_start: 0.8110 (mtp) cc_final: 0.7358 (mtp) REVERT: A 482 PHE cc_start: 0.7948 (p90) cc_final: 0.7532 (p90) REVERT: A 489 LYS cc_start: 0.8270 (mtmm) cc_final: 0.7974 (ptpp) REVERT: A 497 ASN cc_start: 0.7972 (m-40) cc_final: 0.7717 (m-40) REVERT: A 499 ILE cc_start: 0.7944 (tp) cc_final: 0.7676 (tp) REVERT: A 502 TYR cc_start: 0.7584 (m-10) cc_final: 0.7302 (m-10) REVERT: A 504 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7578 (mm-30) REVERT: A 505 ARG cc_start: 0.8808 (mtt90) cc_final: 0.8258 (mtt90) REVERT: A 507 ILE cc_start: 0.8675 (mt) cc_final: 0.8222 (mt) REVERT: A 530 ASP cc_start: 0.8093 (p0) cc_final: 0.7891 (p0) REVERT: A 533 ILE cc_start: 0.8385 (pt) cc_final: 0.7945 (mp) REVERT: A 539 ARG cc_start: 0.8543 (ttm-80) cc_final: 0.7962 (ptm-80) REVERT: A 540 LEU cc_start: 0.9063 (mm) cc_final: 0.8780 (mm) REVERT: A 542 MET cc_start: 0.8372 (ptt) cc_final: 0.7678 (tmm) REVERT: A 545 MET cc_start: 0.7726 (mtm) cc_final: 0.7144 (mtm) REVERT: A 550 ASP cc_start: 0.7833 (p0) cc_final: 0.7423 (p0) REVERT: A 553 LYS cc_start: 0.8458 (mtmt) cc_final: 0.8213 (mtpp) REVERT: A 555 LEU cc_start: 0.8512 (tp) cc_final: 0.8250 (tp) REVERT: A 572 LYS cc_start: 0.8239 (mmtt) cc_final: 0.7916 (tptt) REVERT: A 573 GLU cc_start: 0.8024 (pp20) cc_final: 0.7552 (pp20) REVERT: A 576 GLN cc_start: 0.8493 (tp40) cc_final: 0.8169 (tp40) REVERT: A 577 LEU cc_start: 0.8875 (mt) cc_final: 0.8558 (mt) REVERT: A 593 ASP cc_start: 0.8188 (t0) cc_final: 0.7750 (t70) REVERT: A 600 TRP cc_start: 0.8760 (t-100) cc_final: 0.8522 (t-100) REVERT: A 603 PRO cc_start: 0.7558 (Cg_endo) cc_final: 0.7230 (Cg_exo) REVERT: A 617 ILE cc_start: 0.8424 (mm) cc_final: 0.8177 (mm) REVERT: A 619 LEU cc_start: 0.8854 (tp) cc_final: 0.8510 (tp) REVERT: A 621 LEU cc_start: 0.8116 (mm) cc_final: 0.7621 (mt) REVERT: A 625 ASN cc_start: 0.8409 (m110) cc_final: 0.8161 (m110) REVERT: A 635 MET cc_start: 0.8288 (mpp) cc_final: 0.7424 (mpp) REVERT: A 641 LEU cc_start: 0.8528 (mt) cc_final: 0.8239 (mt) REVERT: A 642 MET cc_start: 0.8174 (mmp) cc_final: 0.7825 (mmp) REVERT: A 651 LEU cc_start: 0.8365 (mt) cc_final: 0.8040 (mt) REVERT: A 660 GLN cc_start: 0.8228 (pp30) cc_final: 0.7616 (pp30) REVERT: A 663 LYS cc_start: 0.8210 (ptmm) cc_final: 0.7601 (mptt) REVERT: A 667 GLU cc_start: 0.8164 (pp20) cc_final: 0.7899 (pp20) REVERT: A 682 ILE cc_start: 0.8263 (tp) cc_final: 0.7888 (tp) REVERT: A 711 LYS cc_start: 0.9302 (mmtt) cc_final: 0.8845 (mmtm) REVERT: A 712 GLU cc_start: 0.8688 (tt0) cc_final: 0.8181 (tt0) REVERT: A 716 LEU cc_start: 0.8762 (mt) cc_final: 0.8522 (mp) REVERT: A 717 TYR cc_start: 0.8839 (t80) cc_final: 0.8047 (t80) REVERT: A 720 TYR cc_start: 0.7830 (t80) cc_final: 0.7304 (t80) REVERT: A 727 GLU cc_start: 0.7900 (pm20) cc_final: 0.7533 (pm20) REVERT: A 728 LYS cc_start: 0.8379 (ttpt) cc_final: 0.7653 (tmtt) REVERT: A 734 ARG cc_start: 0.8498 (ttt-90) cc_final: 0.8271 (ttt90) REVERT: A 738 HIS cc_start: 0.8105 (t70) cc_final: 0.7813 (t-170) REVERT: A 743 GLU cc_start: 0.8419 (mm-30) cc_final: 0.7783 (mp0) REVERT: A 750 PHE cc_start: 0.8300 (m-80) cc_final: 0.8079 (m-10) REVERT: A 753 GLU cc_start: 0.8690 (mp0) cc_final: 0.8368 (mp0) REVERT: A 756 GLU cc_start: 0.7047 (tp30) cc_final: 0.6834 (tp30) REVERT: A 788 ARG cc_start: 0.8513 (ptt180) cc_final: 0.8044 (ptt180) REVERT: A 792 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8111 (mm-30) REVERT: A 822 LYS cc_start: 0.8394 (mptt) cc_final: 0.8032 (mmtm) REVERT: D 22 LEU cc_start: 0.8115 (mm) cc_final: 0.7623 (mm) REVERT: D 65 ASN cc_start: 0.8403 (m-40) cc_final: 0.8005 (m-40) REVERT: D 73 CYS cc_start: 0.6888 (m) cc_final: 0.6471 (m) REVERT: D 79 LYS cc_start: 0.8489 (tppp) cc_final: 0.7167 (tppp) REVERT: D 80 ILE cc_start: 0.8622 (mm) cc_final: 0.8406 (mm) REVERT: D 82 GLU cc_start: 0.8675 (tt0) cc_final: 0.7865 (tt0) REVERT: D 94 THR cc_start: 0.7589 (p) cc_final: 0.6998 (p) REVERT: D 98 GLN cc_start: 0.8488 (mp10) cc_final: 0.8124 (mp10) REVERT: D 114 GLN cc_start: 0.8038 (mp10) cc_final: 0.7703 (mp10) REVERT: D 128 LYS cc_start: 0.8677 (mttt) cc_final: 0.8397 (mttt) REVERT: D 132 PHE cc_start: 0.7882 (m-80) cc_final: 0.6991 (m-80) REVERT: D 138 ARG cc_start: 0.7945 (ptt-90) cc_final: 0.7172 (ptt-90) REVERT: C 130 GLU cc_start: 0.8364 (pt0) cc_final: 0.7644 (pm20) REVERT: C 138 GLU cc_start: 0.8665 (mp0) cc_final: 0.8409 (mm-30) REVERT: C 260 LEU cc_start: 0.8890 (mm) cc_final: 0.8541 (pp) REVERT: C 270 ASP cc_start: 0.7255 (t70) cc_final: 0.7000 (t0) REVERT: C 283 TYR cc_start: 0.7959 (t80) cc_final: 0.7553 (t80) REVERT: C 287 PHE cc_start: 0.7763 (m-80) cc_final: 0.7526 (m-80) REVERT: C 294 ARG cc_start: 0.8521 (mpt-90) cc_final: 0.8159 (mmm160) REVERT: C 315 LYS cc_start: 0.8179 (mtmm) cc_final: 0.7366 (ptpp) REVERT: C 321 GLN cc_start: 0.8539 (mp-120) cc_final: 0.7790 (mp10) REVERT: C 326 ARG cc_start: 0.8066 (mtm180) cc_final: 0.7840 (mtt180) REVERT: C 330 LYS cc_start: 0.8739 (mmmt) cc_final: 0.8319 (mmtm) REVERT: C 332 ASN cc_start: 0.7576 (t0) cc_final: 0.7083 (t0) REVERT: C 337 ARG cc_start: 0.8293 (ttm170) cc_final: 0.7824 (tmm-80) REVERT: C 338 ARG cc_start: 0.8149 (mtp85) cc_final: 0.7613 (mmm160) REVERT: C 341 GLU cc_start: 0.8236 (pp20) cc_final: 0.7266 (pp20) REVERT: C 344 GLN cc_start: 0.8532 (tp-100) cc_final: 0.7663 (tp-100) REVERT: C 345 GLN cc_start: 0.8177 (mt0) cc_final: 0.7491 (tp40) REVERT: C 349 TYR cc_start: 0.7957 (t80) cc_final: 0.7704 (t80) REVERT: C 376 LYS cc_start: 0.8634 (ttpt) cc_final: 0.7426 (ttpt) REVERT: C 380 TYR cc_start: 0.8562 (m-10) cc_final: 0.8091 (m-10) REVERT: C 382 ASN cc_start: 0.8508 (m-40) cc_final: 0.8208 (m110) REVERT: C 394 GLU cc_start: 0.5921 (mm-30) cc_final: 0.5454 (mm-30) REVERT: C 397 ASP cc_start: 0.7892 (t0) cc_final: 0.7631 (t0) REVERT: C 407 LEU cc_start: 0.8866 (mt) cc_final: 0.8636 (mt) REVERT: C 410 GLN cc_start: 0.9065 (mm-40) cc_final: 0.7899 (mm-40) REVERT: C 411 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7442 (mt-10) REVERT: C 441 LYS cc_start: 0.9122 (tttm) cc_final: 0.8801 (tptp) REVERT: C 447 GLU cc_start: 0.8121 (mp0) cc_final: 0.7466 (tp30) REVERT: C 450 ILE cc_start: 0.7977 (mt) cc_final: 0.7132 (mt) REVERT: C 459 GLU cc_start: 0.7438 (mp0) cc_final: 0.7081 (mp0) REVERT: C 478 MET cc_start: 0.8056 (mtp) cc_final: 0.7514 (mtp) REVERT: C 482 PHE cc_start: 0.7972 (p90) cc_final: 0.7563 (p90) REVERT: C 491 LEU cc_start: 0.8541 (mt) cc_final: 0.8336 (mt) REVERT: C 493 LEU cc_start: 0.8056 (tp) cc_final: 0.7750 (tp) REVERT: C 495 TYR cc_start: 0.7680 (m-10) cc_final: 0.7435 (m-10) REVERT: C 499 ILE cc_start: 0.7986 (tp) cc_final: 0.7746 (tp) REVERT: C 501 MET cc_start: 0.8149 (mtt) cc_final: 0.7815 (mtt) REVERT: C 502 TYR cc_start: 0.7680 (m-10) cc_final: 0.7427 (m-10) REVERT: C 505 ARG cc_start: 0.8770 (mtt90) cc_final: 0.8294 (mtt90) REVERT: C 507 ILE cc_start: 0.8461 (mt) cc_final: 0.8257 (mt) REVERT: C 522 TYR cc_start: 0.8062 (m-80) cc_final: 0.7430 (m-80) REVERT: C 539 ARG cc_start: 0.8543 (ttm-80) cc_final: 0.8154 (ttm-80) REVERT: C 542 MET cc_start: 0.8087 (tpp) cc_final: 0.7330 (tpp) REVERT: C 545 MET cc_start: 0.7860 (mtm) cc_final: 0.7165 (mtm) REVERT: C 553 LYS cc_start: 0.8288 (mtmt) cc_final: 0.8034 (mtpp) REVERT: C 555 LEU cc_start: 0.8590 (tp) cc_final: 0.8237 (tp) REVERT: C 576 GLN cc_start: 0.7698 (tm-30) cc_final: 0.7252 (tm-30) REVERT: C 577 LEU cc_start: 0.8639 (mt) cc_final: 0.7982 (mt) REVERT: C 581 GLU cc_start: 0.8218 (pp20) cc_final: 0.7881 (pp20) REVERT: C 587 ILE cc_start: 0.8071 (tp) cc_final: 0.7762 (tp) REVERT: C 589 MET cc_start: 0.6441 (mtp) cc_final: 0.6034 (mtp) REVERT: C 593 ASP cc_start: 0.7994 (t70) cc_final: 0.7790 (t70) REVERT: C 603 PRO cc_start: 0.7620 (Cg_endo) cc_final: 0.7372 (Cg_exo) REVERT: C 617 ILE cc_start: 0.8591 (mm) cc_final: 0.8351 (mm) REVERT: C 619 LEU cc_start: 0.8823 (tp) cc_final: 0.8554 (tp) REVERT: C 621 LEU cc_start: 0.8210 (mm) cc_final: 0.7791 (mm) REVERT: C 625 ASN cc_start: 0.8564 (m110) cc_final: 0.8214 (m110) REVERT: C 626 ASN cc_start: 0.8117 (m110) cc_final: 0.7789 (m110) REVERT: C 635 MET cc_start: 0.8142 (mpp) cc_final: 0.7420 (mpp) REVERT: C 641 LEU cc_start: 0.8583 (mt) cc_final: 0.8161 (mm) REVERT: C 642 MET cc_start: 0.8156 (mmp) cc_final: 0.7864 (mmp) REVERT: C 658 LEU cc_start: 0.8541 (tp) cc_final: 0.8208 (tt) REVERT: C 660 GLN cc_start: 0.8636 (mm-40) cc_final: 0.8400 (mm-40) REVERT: C 661 SER cc_start: 0.8787 (m) cc_final: 0.8574 (p) REVERT: C 667 GLU cc_start: 0.7956 (pp20) cc_final: 0.7620 (pp20) REVERT: C 692 MET cc_start: 0.7275 (ttm) cc_final: 0.7074 (ttm) REVERT: C 693 MET cc_start: 0.6405 (tpt) cc_final: 0.6004 (tpt) REVERT: C 712 GLU cc_start: 0.8680 (tt0) cc_final: 0.8239 (tt0) REVERT: C 716 LEU cc_start: 0.8726 (mt) cc_final: 0.8106 (pp) REVERT: C 717 TYR cc_start: 0.8917 (t80) cc_final: 0.8334 (t80) REVERT: C 720 TYR cc_start: 0.7866 (t80) cc_final: 0.7279 (t80) REVERT: C 727 GLU cc_start: 0.8062 (pm20) cc_final: 0.7779 (pm20) REVERT: C 730 PHE cc_start: 0.8165 (t80) cc_final: 0.7879 (t80) REVERT: C 738 HIS cc_start: 0.8097 (t-90) cc_final: 0.7808 (t-90) REVERT: C 739 MET cc_start: 0.7886 (ptp) cc_final: 0.7554 (ptp) REVERT: C 743 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8145 (mm-30) REVERT: C 748 TYR cc_start: 0.7484 (t80) cc_final: 0.6867 (t80) REVERT: C 754 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8067 (mt-10) REVERT: C 756 GLU cc_start: 0.7068 (tp30) cc_final: 0.6277 (tp30) REVERT: C 788 ARG cc_start: 0.8425 (ptt180) cc_final: 0.7869 (ttp80) REVERT: C 805 PHE cc_start: 0.8566 (t80) cc_final: 0.8175 (t80) REVERT: C 806 LEU cc_start: 0.8213 (mt) cc_final: 0.7743 (mt) REVERT: C 822 LYS cc_start: 0.8476 (mmtt) cc_final: 0.8093 (mmtm) outliers start: 1 outliers final: 0 residues processed: 514 average time/residue: 0.3541 time to fit residues: 244.6863 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 : 1.834 ------------------------------------------------------------------------------- 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: 0.6980 chunk 76 optimal weight: 3.9990 chunk 153 optimal weight: 0.9980 chunk 119 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 611 GLN ** 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 = 0.4103 r_free = 0.4103 target = 0.141345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.113564 restraints weight = 29727.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.118239 restraints weight = 18200.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.121662 restraints weight = 12590.703| |-----------------------------------------------------------------------------| r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.5779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13534 Z= 0.140 Angle : 0.638 9.325 18272 Z= 0.323 Chirality : 0.044 0.208 2014 Planarity : 0.004 0.074 2372 Dihedral : 4.819 19.830 1806 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % 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: -1.05 (0.21), residues: 1610 helix: -0.18 (0.18), residues: 818 sheet: -2.48 (0.61), residues: 68 loop : -1.00 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP C 328 HIS 0.006 0.001 HIS D 85 PHE 0.028 0.002 PHE C 730 TYR 0.016 0.001 TYR A 464 ARG 0.013 0.001 ARG C 168 Details of bonding type rmsd hydrogen bonds : bond 0.03654 ( 502) hydrogen bonds : angle 5.06983 ( 1392) metal coordination : bond 0.00525 ( 12) metal coordination : angle 4.40324 ( 12) covalent geometry : bond 0.00284 (13522) covalent geometry : angle 0.62815 (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 515 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 515 time to evaluate : 1.937 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 22 LEU cc_start: 0.8263 (mm) cc_final: 0.7930 (mm) REVERT: B 59 ILE cc_start: 0.7690 (mm) cc_final: 0.7314 (mm) REVERT: B 65 ASN cc_start: 0.8448 (m-40) cc_final: 0.8055 (m-40) REVERT: B 73 CYS cc_start: 0.5937 (m) cc_final: 0.5537 (m) REVERT: B 74 LEU cc_start: 0.8655 (mm) cc_final: 0.8406 (mm) REVERT: B 77 TYR cc_start: 0.8183 (m-80) cc_final: 0.7668 (m-80) REVERT: B 82 GLU cc_start: 0.8771 (tt0) cc_final: 0.8364 (tt0) REVERT: B 108 ILE cc_start: 0.8129 (mt) cc_final: 0.7668 (tt) REVERT: B 114 GLN cc_start: 0.7968 (mp10) cc_final: 0.7757 (mp10) REVERT: B 124 ARG cc_start: 0.8775 (ttt-90) cc_final: 0.8517 (ttt-90) REVERT: B 128 LYS cc_start: 0.8785 (mttt) cc_final: 0.8465 (mttt) REVERT: B 132 PHE cc_start: 0.7764 (m-80) cc_final: 0.7111 (m-80) REVERT: B 136 ARG cc_start: 0.8175 (mmm160) cc_final: 0.7275 (mmm160) REVERT: A 130 GLU cc_start: 0.8426 (pt0) cc_final: 0.7550 (pm20) REVERT: A 237 ASP cc_start: 0.8506 (m-30) cc_final: 0.7910 (t0) REVERT: A 283 TYR cc_start: 0.7747 (t80) cc_final: 0.7277 (t80) REVERT: A 287 PHE cc_start: 0.7507 (m-80) cc_final: 0.7263 (m-80) REVERT: A 288 ILE cc_start: 0.8710 (tt) cc_final: 0.8380 (tt) REVERT: A 291 MET cc_start: 0.8466 (ttt) cc_final: 0.7914 (ptm) REVERT: A 292 GLU cc_start: 0.8315 (mm-30) cc_final: 0.8018 (mm-30) REVERT: A 294 ARG cc_start: 0.8580 (mpt-90) cc_final: 0.8346 (mpt-90) REVERT: A 304 MET cc_start: 0.4826 (tpt) cc_final: 0.4103 (tpt) REVERT: A 328 TRP cc_start: 0.7131 (m100) cc_final: 0.6887 (m100) REVERT: A 337 ARG cc_start: 0.8251 (ttm170) cc_final: 0.7443 (ttp80) REVERT: A 338 ARG cc_start: 0.8092 (mtp85) cc_final: 0.7501 (mmm160) REVERT: A 341 GLU cc_start: 0.8591 (mt-10) cc_final: 0.7397 (mt-10) REVERT: A 347 ILE cc_start: 0.7609 (mt) cc_final: 0.7358 (mm) REVERT: A 350 LYS cc_start: 0.7606 (mmpt) cc_final: 0.7267 (tptt) REVERT: A 376 LYS cc_start: 0.8660 (tttt) cc_final: 0.8379 (tttt) REVERT: A 392 HIS cc_start: 0.8244 (m90) cc_final: 0.7809 (m90) REVERT: A 406 GLU cc_start: 0.8477 (tp30) cc_final: 0.7845 (tp30) REVERT: A 410 GLN cc_start: 0.9024 (mm-40) cc_final: 0.8770 (mm110) REVERT: A 411 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7986 (tm-30) REVERT: A 424 ARG cc_start: 0.7889 (mmm-85) cc_final: 0.7128 (tpp80) REVERT: A 437 LEU cc_start: 0.8325 (mm) cc_final: 0.7952 (tt) REVERT: A 447 GLU cc_start: 0.8127 (mp0) cc_final: 0.7683 (tp30) REVERT: A 449 PHE cc_start: 0.7227 (m-10) cc_final: 0.6655 (m-10) REVERT: A 450 ILE cc_start: 0.8012 (mt) cc_final: 0.7369 (mt) REVERT: A 455 ASN cc_start: 0.7979 (m-40) cc_final: 0.7774 (m-40) REVERT: A 458 LEU cc_start: 0.8410 (tp) cc_final: 0.7970 (tt) REVERT: A 459 GLU cc_start: 0.7139 (mp0) cc_final: 0.6789 (mp0) REVERT: A 477 PHE cc_start: 0.8010 (m-80) cc_final: 0.7525 (m-80) REVERT: A 478 MET cc_start: 0.8105 (mtp) cc_final: 0.7369 (mtp) REVERT: A 482 PHE cc_start: 0.7984 (p90) cc_final: 0.7554 (p90) REVERT: A 499 ILE cc_start: 0.7848 (tp) cc_final: 0.7533 (tp) REVERT: A 501 MET cc_start: 0.8100 (mtt) cc_final: 0.7608 (mmm) REVERT: A 502 TYR cc_start: 0.7705 (m-10) cc_final: 0.7409 (m-10) REVERT: A 504 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7619 (mm-30) REVERT: A 505 ARG cc_start: 0.8824 (mtt90) cc_final: 0.8411 (mtt90) REVERT: A 507 ILE cc_start: 0.8674 (mt) cc_final: 0.8353 (mt) REVERT: A 522 TYR cc_start: 0.8129 (m-80) cc_final: 0.7857 (m-80) REVERT: A 530 ASP cc_start: 0.8055 (p0) cc_final: 0.7854 (p0) REVERT: A 533 ILE cc_start: 0.8383 (pt) cc_final: 0.7967 (mp) REVERT: A 535 ASP cc_start: 0.7614 (t0) cc_final: 0.7321 (t0) REVERT: A 539 ARG cc_start: 0.8587 (ttm-80) cc_final: 0.7730 (ptm-80) REVERT: A 540 LEU cc_start: 0.9092 (mm) cc_final: 0.8794 (mm) REVERT: A 542 MET cc_start: 0.8349 (ptt) cc_final: 0.7495 (ptt) REVERT: A 545 MET cc_start: 0.7751 (mtm) cc_final: 0.7292 (mtm) REVERT: A 550 ASP cc_start: 0.7850 (p0) cc_final: 0.7459 (p0) REVERT: A 553 LYS cc_start: 0.8479 (mtmt) cc_final: 0.7614 (mtpp) REVERT: A 572 LYS cc_start: 0.8250 (mmtt) cc_final: 0.7978 (tptt) REVERT: A 573 GLU cc_start: 0.8063 (pp20) cc_final: 0.7756 (pp20) REVERT: A 576 GLN cc_start: 0.8512 (tp40) cc_final: 0.8211 (tp40) REVERT: A 593 ASP cc_start: 0.8244 (t0) cc_final: 0.7808 (t70) REVERT: A 600 TRP cc_start: 0.8816 (t-100) cc_final: 0.8562 (t-100) REVERT: A 603 PRO cc_start: 0.7463 (Cg_endo) cc_final: 0.7176 (Cg_exo) REVERT: A 617 ILE cc_start: 0.8411 (mm) cc_final: 0.8135 (mm) REVERT: A 621 LEU cc_start: 0.8086 (mm) cc_final: 0.7649 (mp) REVERT: A 625 ASN cc_start: 0.8436 (m110) cc_final: 0.8106 (m110) REVERT: A 635 MET cc_start: 0.8299 (mpp) cc_final: 0.7573 (mpp) REVERT: A 641 LEU cc_start: 0.8529 (mt) cc_final: 0.8241 (mt) REVERT: A 642 MET cc_start: 0.8214 (mmp) cc_final: 0.7848 (mmp) REVERT: A 649 ARG cc_start: 0.8644 (ptm160) cc_final: 0.8438 (ptm160) REVERT: A 651 LEU cc_start: 0.8383 (mt) cc_final: 0.8061 (mt) REVERT: A 660 GLN cc_start: 0.8233 (pp30) cc_final: 0.7647 (pp30) REVERT: A 663 LYS cc_start: 0.8298 (ptmm) cc_final: 0.7724 (mptt) REVERT: A 667 GLU cc_start: 0.8206 (pp20) cc_final: 0.7891 (pp20) REVERT: A 682 ILE cc_start: 0.8201 (tp) cc_final: 0.7926 (tp) REVERT: A 711 LYS cc_start: 0.9275 (mmtt) cc_final: 0.8844 (mmtm) REVERT: A 712 GLU cc_start: 0.8649 (tt0) cc_final: 0.8100 (tt0) REVERT: A 716 LEU cc_start: 0.8727 (mt) cc_final: 0.8502 (mp) REVERT: A 717 TYR cc_start: 0.8916 (t80) cc_final: 0.8444 (t80) REVERT: A 728 LYS cc_start: 0.8410 (ttpt) cc_final: 0.7601 (tmtt) REVERT: A 738 HIS cc_start: 0.8166 (t70) cc_final: 0.7876 (t-170) REVERT: A 743 GLU cc_start: 0.8423 (mm-30) cc_final: 0.7785 (mp0) REVERT: A 753 GLU cc_start: 0.8672 (mp0) cc_final: 0.8357 (mp0) REVERT: A 754 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8249 (mp0) REVERT: A 756 GLU cc_start: 0.6960 (tp30) cc_final: 0.6380 (tp30) REVERT: A 788 ARG cc_start: 0.8517 (ptt180) cc_final: 0.8039 (ptt180) REVERT: A 792 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8120 (mm-30) REVERT: A 797 PHE cc_start: 0.7001 (m-80) cc_final: 0.6591 (m-80) REVERT: A 822 LYS cc_start: 0.8285 (mptt) cc_final: 0.8080 (mmtt) REVERT: D 22 LEU cc_start: 0.8085 (mm) cc_final: 0.7706 (mm) REVERT: D 65 ASN cc_start: 0.8461 (m-40) cc_final: 0.8077 (m-40) REVERT: D 73 CYS cc_start: 0.6259 (m) cc_final: 0.5940 (m) REVERT: D 82 GLU cc_start: 0.8668 (tt0) cc_final: 0.8178 (tt0) REVERT: D 84 ARG cc_start: 0.7228 (mtp-110) cc_final: 0.5688 (mtp-110) REVERT: D 114 GLN cc_start: 0.8121 (mp10) cc_final: 0.7753 (mp10) REVERT: D 128 LYS cc_start: 0.8708 (mttt) cc_final: 0.8427 (mttt) REVERT: D 138 ARG cc_start: 0.8036 (ptt-90) cc_final: 0.7289 (ptt-90) REVERT: C 130 GLU cc_start: 0.8323 (pt0) cc_final: 0.7620 (pm20) REVERT: C 138 GLU cc_start: 0.8660 (mp0) cc_final: 0.8354 (mm-30) REVERT: C 270 ASP cc_start: 0.7274 (t70) cc_final: 0.7017 (t0) REVERT: C 283 TYR cc_start: 0.7984 (t80) cc_final: 0.7501 (t80) REVERT: C 294 ARG cc_start: 0.8549 (mpt-90) cc_final: 0.8192 (mmm160) REVERT: C 304 MET cc_start: 0.5114 (tpt) cc_final: 0.4772 (tpt) REVERT: C 315 LYS cc_start: 0.8127 (mtmm) cc_final: 0.7350 (ptpp) REVERT: C 326 ARG cc_start: 0.8109 (mtm180) cc_final: 0.7846 (mtt180) REVERT: C 332 ASN cc_start: 0.7725 (t0) cc_final: 0.7245 (t0) REVERT: C 337 ARG cc_start: 0.8344 (ttm170) cc_final: 0.7890 (tmm-80) REVERT: C 338 ARG cc_start: 0.8086 (mtp85) cc_final: 0.7434 (mmm160) REVERT: C 341 GLU cc_start: 0.8211 (pp20) cc_final: 0.7633 (pp20) REVERT: C 344 GLN cc_start: 0.8531 (tp-100) cc_final: 0.7706 (tp-100) REVERT: C 349 TYR cc_start: 0.7993 (t80) cc_final: 0.7786 (t80) REVERT: C 376 LYS cc_start: 0.8700 (ttpt) cc_final: 0.7564 (ttpt) REVERT: C 380 TYR cc_start: 0.8582 (m-10) cc_final: 0.8172 (m-10) REVERT: C 382 ASN cc_start: 0.8552 (m-40) cc_final: 0.8244 (m110) REVERT: C 397 ASP cc_start: 0.7693 (t0) cc_final: 0.7433 (t0) REVERT: C 406 GLU cc_start: 0.8560 (tp30) cc_final: 0.7879 (mt-10) REVERT: C 407 LEU cc_start: 0.8811 (mt) cc_final: 0.8546 (mt) REVERT: C 410 GLN cc_start: 0.9058 (mm-40) cc_final: 0.8208 (mm-40) REVERT: C 411 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7388 (mt-10) REVERT: C 429 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8241 (mt-10) REVERT: C 441 LYS cc_start: 0.9094 (tttm) cc_final: 0.8764 (tptt) REVERT: C 447 GLU cc_start: 0.8142 (mp0) cc_final: 0.7479 (tp30) REVERT: C 450 ILE cc_start: 0.7999 (mt) cc_final: 0.6978 (mt) REVERT: C 459 GLU cc_start: 0.7440 (mp0) cc_final: 0.6897 (mp0) REVERT: C 478 MET cc_start: 0.8142 (mtp) cc_final: 0.7614 (mtp) REVERT: C 482 PHE cc_start: 0.8040 (p90) cc_final: 0.7592 (p90) REVERT: C 491 LEU cc_start: 0.8548 (mt) cc_final: 0.8332 (mt) REVERT: C 493 LEU cc_start: 0.8095 (tp) cc_final: 0.7791 (tp) REVERT: C 495 TYR cc_start: 0.7704 (m-10) cc_final: 0.7440 (m-10) REVERT: C 499 ILE cc_start: 0.7994 (tp) cc_final: 0.7730 (tp) REVERT: C 501 MET cc_start: 0.8222 (mtt) cc_final: 0.7782 (mtt) REVERT: C 502 TYR cc_start: 0.7693 (m-10) cc_final: 0.6973 (m-10) REVERT: C 505 ARG cc_start: 0.8795 (mtt90) cc_final: 0.8326 (mtt90) REVERT: C 506 ARG cc_start: 0.8400 (mtt90) cc_final: 0.7735 (mtt-85) REVERT: C 522 TYR cc_start: 0.8062 (m-80) cc_final: 0.7374 (m-80) REVERT: C 530 ASP cc_start: 0.7975 (p0) cc_final: 0.7674 (p0) REVERT: C 539 ARG cc_start: 0.8577 (ttm-80) cc_final: 0.8181 (ttm-80) REVERT: C 541 GLU cc_start: 0.8153 (tt0) cc_final: 0.7240 (tt0) REVERT: C 542 MET cc_start: 0.8143 (tpp) cc_final: 0.7423 (tpp) REVERT: C 545 MET cc_start: 0.7920 (mtm) cc_final: 0.7251 (mtm) REVERT: C 550 ASP cc_start: 0.7745 (p0) cc_final: 0.7455 (p0) REVERT: C 553 LYS cc_start: 0.8248 (mtmt) cc_final: 0.8007 (mtpp) REVERT: C 555 LEU cc_start: 0.8595 (tp) cc_final: 0.8265 (tp) REVERT: C 576 GLN cc_start: 0.8215 (tm-30) cc_final: 0.7824 (tm-30) REVERT: C 577 LEU cc_start: 0.8776 (mt) cc_final: 0.8362 (pp) REVERT: C 587 ILE cc_start: 0.8022 (tp) cc_final: 0.7730 (tp) REVERT: C 589 MET cc_start: 0.6383 (mtp) cc_final: 0.6008 (mtp) REVERT: C 593 ASP cc_start: 0.8032 (t70) cc_final: 0.7567 (t70) REVERT: C 594 GLU cc_start: 0.8655 (mp0) cc_final: 0.8437 (mp0) REVERT: C 603 PRO cc_start: 0.7534 (Cg_endo) cc_final: 0.7288 (Cg_exo) REVERT: C 617 ILE cc_start: 0.8616 (mm) cc_final: 0.8393 (mm) REVERT: C 619 LEU cc_start: 0.8833 (tp) cc_final: 0.8578 (tp) REVERT: C 621 LEU cc_start: 0.8220 (mm) cc_final: 0.7814 (mm) REVERT: C 625 ASN cc_start: 0.8628 (m110) cc_final: 0.8230 (m110) REVERT: C 626 ASN cc_start: 0.8128 (m110) cc_final: 0.7809 (m110) REVERT: C 635 MET cc_start: 0.8126 (mpp) cc_final: 0.7400 (mpp) REVERT: C 642 MET cc_start: 0.8183 (mmp) cc_final: 0.7884 (mmp) REVERT: C 658 LEU cc_start: 0.8535 (tp) cc_final: 0.8225 (tt) REVERT: C 667 GLU cc_start: 0.7956 (pp20) cc_final: 0.7602 (pp20) REVERT: C 692 MET cc_start: 0.7575 (ttm) cc_final: 0.7351 (ttm) REVERT: C 707 ASN cc_start: 0.8370 (p0) cc_final: 0.7956 (m-40) REVERT: C 712 GLU cc_start: 0.8690 (tt0) cc_final: 0.8277 (tt0) REVERT: C 713 PHE cc_start: 0.8569 (t80) cc_final: 0.7733 (t80) REVERT: C 716 LEU cc_start: 0.8744 (mt) cc_final: 0.8137 (pp) REVERT: C 717 TYR cc_start: 0.8963 (t80) cc_final: 0.8444 (t80) REVERT: C 720 TYR cc_start: 0.7892 (t80) cc_final: 0.7341 (t80) REVERT: C 727 GLU cc_start: 0.8085 (pm20) cc_final: 0.7799 (pm20) REVERT: C 738 HIS cc_start: 0.8117 (t-90) cc_final: 0.7849 (t-170) REVERT: C 739 MET cc_start: 0.7871 (ptp) cc_final: 0.7537 (ptp) REVERT: C 743 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8244 (mm-30) REVERT: C 747 LYS cc_start: 0.9097 (mtpp) cc_final: 0.8823 (mmmm) REVERT: C 748 TYR cc_start: 0.7550 (t80) cc_final: 0.6976 (t80) REVERT: C 754 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8055 (mt-10) REVERT: C 756 GLU cc_start: 0.7143 (tp30) cc_final: 0.6352 (tp30) REVERT: C 788 ARG cc_start: 0.8542 (ptt180) cc_final: 0.7687 (ptt180) REVERT: C 797 PHE cc_start: 0.6504 (m-80) cc_final: 0.6139 (m-80) REVERT: C 805 PHE cc_start: 0.8554 (t80) cc_final: 0.8178 (t80) REVERT: C 806 LEU cc_start: 0.8242 (mt) cc_final: 0.7782 (mt) REVERT: C 822 LYS cc_start: 0.8445 (mmtt) cc_final: 0.8048 (mmtm) REVERT: C 835 GLU cc_start: 0.7672 (pm20) cc_final: 0.7470 (pm20) REVERT: C 855 LYS cc_start: 0.9011 (tttt) cc_final: 0.8158 (tptt) outliers start: 0 outliers final: 0 residues processed: 515 average time/residue: 0.3577 time to fit residues: 249.9543 Evaluate side-chains 495 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 495 time to evaluate : 1.559 ------------------------------------------------------------------------------- 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: 10.0000 chunk 125 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 8 optimal weight: 0.3980 chunk 139 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 ASN ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 455 ASN ** C 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 715 ASN C 723 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.140210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.113072 restraints weight = 29198.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.117684 restraints weight = 17880.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.121084 restraints weight = 12327.310| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.5956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13534 Z= 0.156 Angle : 0.656 9.818 18272 Z= 0.331 Chirality : 0.045 0.234 2014 Planarity : 0.005 0.118 2372 Dihedral : 4.872 19.734 1806 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % 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: -1.04 (0.21), residues: 1610 helix: -0.24 (0.18), residues: 818 sheet: -1.93 (0.65), residues: 64 loop : -0.99 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP D 139 HIS 0.006 0.001 HIS C 655 PHE 0.034 0.002 PHE C 730 TYR 0.020 0.002 TYR A 494 ARG 0.012 0.001 ARG B 84 Details of bonding type rmsd hydrogen bonds : bond 0.03835 ( 502) hydrogen bonds : angle 5.17115 ( 1392) metal coordination : bond 0.00635 ( 12) metal coordination : angle 4.84174 ( 12) covalent geometry : bond 0.00310 (13522) covalent geometry : angle 0.64457 (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 513 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 513 time to evaluate : 1.485 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: 0.7759 (mmtm) cc_final: 0.7352 (mmmm) REVERT: B 22 LEU cc_start: 0.8369 (mm) cc_final: 0.8007 (mm) REVERT: B 59 ILE cc_start: 0.7681 (mm) cc_final: 0.7477 (mm) REVERT: B 65 ASN cc_start: 0.8464 (m-40) cc_final: 0.8068 (m-40) REVERT: B 73 CYS cc_start: 0.5926 (m) cc_final: 0.5524 (m) REVERT: B 74 LEU cc_start: 0.8615 (mm) cc_final: 0.8352 (mm) REVERT: B 77 TYR cc_start: 0.8204 (m-80) cc_final: 0.7695 (m-80) REVERT: B 82 GLU cc_start: 0.8784 (tt0) cc_final: 0.8380 (tt0) REVERT: B 88 TYR cc_start: 0.7036 (p90) cc_final: 0.6641 (p90) REVERT: B 108 ILE cc_start: 0.8189 (mt) cc_final: 0.7659 (tt) REVERT: B 114 GLN cc_start: 0.8088 (mp10) cc_final: 0.7855 (mp10) REVERT: B 124 ARG cc_start: 0.8769 (ttt-90) cc_final: 0.8363 (ttt-90) REVERT: B 128 LYS cc_start: 0.8797 (mttt) cc_final: 0.8450 (mttt) REVERT: B 132 PHE cc_start: 0.7754 (m-80) cc_final: 0.7116 (m-80) REVERT: B 134 ASN cc_start: 0.7836 (t0) cc_final: 0.7617 (t0) REVERT: B 136 ARG cc_start: 0.8145 (mmm160) cc_final: 0.7324 (tpp80) REVERT: A 130 GLU cc_start: 0.8444 (pt0) cc_final: 0.7588 (pm20) REVERT: A 237 ASP cc_start: 0.8514 (m-30) cc_final: 0.7942 (t0) REVERT: A 251 LYS cc_start: 0.8521 (mttp) cc_final: 0.8233 (mtmm) REVERT: A 283 TYR cc_start: 0.7770 (t80) cc_final: 0.7569 (t80) REVERT: A 287 PHE cc_start: 0.7406 (m-80) cc_final: 0.7147 (m-80) REVERT: A 291 MET cc_start: 0.8436 (ttt) cc_final: 0.7930 (ttp) REVERT: A 292 GLU cc_start: 0.8263 (mm-30) cc_final: 0.8037 (mm-30) REVERT: A 294 ARG cc_start: 0.8559 (mpt-90) cc_final: 0.8332 (mpt-90) REVERT: A 304 MET cc_start: 0.4860 (tpt) cc_final: 0.4165 (tpt) REVERT: A 315 LYS cc_start: 0.8192 (mmtm) cc_final: 0.7549 (mmtm) REVERT: A 332 ASN cc_start: 0.7707 (t0) cc_final: 0.7275 (t0) REVERT: A 337 ARG cc_start: 0.8295 (ttm170) cc_final: 0.7451 (ttp80) REVERT: A 338 ARG cc_start: 0.8076 (mtp85) cc_final: 0.7688 (mmm160) REVERT: A 341 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8087 (mt-10) REVERT: A 347 ILE cc_start: 0.7787 (mt) cc_final: 0.7471 (mm) REVERT: A 350 LYS cc_start: 0.7711 (mmpt) cc_final: 0.7321 (tptt) REVERT: A 373 LYS cc_start: 0.8121 (mtpt) cc_final: 0.7783 (mtpp) REVERT: A 376 LYS cc_start: 0.8662 (tttt) cc_final: 0.8371 (tttt) REVERT: A 392 HIS cc_start: 0.8399 (m90) cc_final: 0.7902 (m90) REVERT: A 406 GLU cc_start: 0.8210 (tp30) cc_final: 0.6313 (tp30) REVERT: A 410 GLN cc_start: 0.9034 (mm-40) cc_final: 0.7639 (mm110) REVERT: A 420 LYS cc_start: 0.7960 (pttp) cc_final: 0.7668 (ptmm) REVERT: A 424 ARG cc_start: 0.8027 (mmm-85) cc_final: 0.6990 (tpp80) REVERT: A 437 LEU cc_start: 0.8388 (mm) cc_final: 0.8017 (tt) REVERT: A 446 PHE cc_start: 0.7723 (m-80) cc_final: 0.7456 (m-80) REVERT: A 447 GLU cc_start: 0.8162 (mp0) cc_final: 0.7635 (tp30) REVERT: A 449 PHE cc_start: 0.7207 (m-10) cc_final: 0.6708 (m-80) REVERT: A 450 ILE cc_start: 0.7993 (mt) cc_final: 0.7456 (mt) REVERT: A 458 LEU cc_start: 0.8436 (tp) cc_final: 0.8003 (tt) REVERT: A 459 GLU cc_start: 0.7218 (mp0) cc_final: 0.6884 (mp0) REVERT: A 477 PHE cc_start: 0.7891 (m-80) cc_final: 0.7452 (m-80) REVERT: A 478 MET cc_start: 0.8096 (mtp) cc_final: 0.7660 (ttm) REVERT: A 482 PHE cc_start: 0.8005 (p90) cc_final: 0.7616 (p90) REVERT: A 499 ILE cc_start: 0.7919 (tp) cc_final: 0.7587 (tp) REVERT: A 501 MET cc_start: 0.8101 (mtt) cc_final: 0.7594 (mmm) REVERT: A 502 TYR cc_start: 0.7686 (m-10) cc_final: 0.7406 (m-10) REVERT: A 504 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7593 (mm-30) REVERT: A 505 ARG cc_start: 0.8810 (mtt90) cc_final: 0.8411 (mtt90) REVERT: A 507 ILE cc_start: 0.8678 (mt) cc_final: 0.8352 (mt) REVERT: A 530 ASP cc_start: 0.7947 (p0) cc_final: 0.7632 (p0) REVERT: A 533 ILE cc_start: 0.8402 (pt) cc_final: 0.7989 (mp) REVERT: A 535 ASP cc_start: 0.7633 (t0) cc_final: 0.7306 (t0) REVERT: A 539 ARG cc_start: 0.8597 (ttm-80) cc_final: 0.7734 (ptm-80) REVERT: A 540 LEU cc_start: 0.9122 (mm) cc_final: 0.8820 (mm) REVERT: A 542 MET cc_start: 0.8385 (ptt) cc_final: 0.7538 (ptt) REVERT: A 545 MET cc_start: 0.7743 (mtm) cc_final: 0.7284 (mtm) REVERT: A 550 ASP cc_start: 0.7824 (p0) cc_final: 0.7472 (p0) REVERT: A 553 LYS cc_start: 0.8421 (mtmt) cc_final: 0.7598 (mtpp) REVERT: A 572 LYS cc_start: 0.8297 (mmtt) cc_final: 0.7777 (tptt) REVERT: A 573 GLU cc_start: 0.8079 (pp20) cc_final: 0.7748 (pp20) REVERT: A 576 GLN cc_start: 0.8508 (tp40) cc_final: 0.8119 (tp40) REVERT: A 582 ILE cc_start: 0.8476 (mm) cc_final: 0.8272 (mm) REVERT: A 593 ASP cc_start: 0.8230 (t0) cc_final: 0.7791 (t70) REVERT: A 600 TRP cc_start: 0.8838 (t-100) cc_final: 0.8563 (t-100) REVERT: A 603 PRO cc_start: 0.7556 (Cg_endo) cc_final: 0.7260 (Cg_exo) REVERT: A 617 ILE cc_start: 0.8433 (mm) cc_final: 0.8227 (mm) REVERT: A 619 LEU cc_start: 0.8873 (tp) cc_final: 0.8541 (tp) REVERT: A 621 LEU cc_start: 0.8097 (mm) cc_final: 0.7710 (mp) REVERT: A 625 ASN cc_start: 0.8399 (m110) cc_final: 0.8075 (m110) REVERT: A 635 MET cc_start: 0.8311 (mpp) cc_final: 0.7590 (mpp) REVERT: A 641 LEU cc_start: 0.8611 (mt) cc_final: 0.8200 (mt) REVERT: A 642 MET cc_start: 0.8173 (mmp) cc_final: 0.7859 (mmp) REVERT: A 651 LEU cc_start: 0.8371 (mt) cc_final: 0.8093 (mt) REVERT: A 660 GLN cc_start: 0.8207 (pp30) cc_final: 0.7732 (pp30) REVERT: A 663 LYS cc_start: 0.8322 (ptmm) cc_final: 0.7869 (ttpp) REVERT: A 665 LEU cc_start: 0.8553 (mp) cc_final: 0.8352 (mp) REVERT: A 667 GLU cc_start: 0.8156 (pp20) cc_final: 0.7807 (pp20) REVERT: A 668 TYR cc_start: 0.7713 (t80) cc_final: 0.7076 (t80) REVERT: A 682 ILE cc_start: 0.8213 (tp) cc_final: 0.7981 (tp) REVERT: A 711 LYS cc_start: 0.9263 (mmtt) cc_final: 0.8848 (mmtt) REVERT: A 712 GLU cc_start: 0.8700 (tt0) cc_final: 0.8379 (tt0) REVERT: A 716 LEU cc_start: 0.8770 (mt) cc_final: 0.8352 (tp) REVERT: A 717 TYR cc_start: 0.8979 (t80) cc_final: 0.8558 (t80) REVERT: A 719 ASP cc_start: 0.8204 (m-30) cc_final: 0.7893 (m-30) REVERT: A 727 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7757 (mm-30) REVERT: A 738 HIS cc_start: 0.8151 (t70) cc_final: 0.7859 (t-170) REVERT: A 739 MET cc_start: 0.8061 (ptm) cc_final: 0.7858 (ptm) REVERT: A 743 GLU cc_start: 0.8461 (mm-30) cc_final: 0.7902 (mp0) REVERT: A 747 LYS cc_start: 0.9081 (mtpt) cc_final: 0.8778 (mtpt) REVERT: A 754 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8196 (mp0) REVERT: A 756 GLU cc_start: 0.7136 (tp30) cc_final: 0.6586 (tp30) REVERT: A 763 ARG cc_start: 0.7284 (ttm-80) cc_final: 0.7005 (tpp-160) REVERT: A 788 ARG cc_start: 0.8498 (ptt180) cc_final: 0.8090 (ptt180) REVERT: A 792 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8144 (mm-30) REVERT: A 822 LYS cc_start: 0.8265 (mptt) cc_final: 0.7941 (mmtm) REVERT: D 22 LEU cc_start: 0.8135 (mm) cc_final: 0.7758 (mm) REVERT: D 65 ASN cc_start: 0.8491 (m-40) cc_final: 0.8138 (t0) REVERT: D 73 CYS cc_start: 0.6426 (m) cc_final: 0.6017 (m) REVERT: D 82 GLU cc_start: 0.8677 (tt0) cc_final: 0.8210 (tt0) REVERT: D 84 ARG cc_start: 0.7236 (mtp-110) cc_final: 0.5277 (mtp-110) REVERT: D 98 GLN cc_start: 0.8526 (mp10) cc_final: 0.8277 (mp10) REVERT: D 114 GLN cc_start: 0.8216 (mp10) cc_final: 0.7852 (mp10) REVERT: D 128 LYS cc_start: 0.8724 (mttt) cc_final: 0.8412 (mttt) REVERT: D 132 PHE cc_start: 0.8017 (m-80) cc_final: 0.7134 (m-80) REVERT: D 138 ARG cc_start: 0.8012 (ptt-90) cc_final: 0.7187 (ptt-90) REVERT: C 130 GLU cc_start: 0.8356 (pt0) cc_final: 0.7620 (pm20) REVERT: C 138 GLU cc_start: 0.8639 (mp0) cc_final: 0.8318 (mm-30) REVERT: C 246 LEU cc_start: 0.8335 (tp) cc_final: 0.8131 (tp) REVERT: C 270 ASP cc_start: 0.7300 (t70) cc_final: 0.7026 (t70) REVERT: C 283 TYR cc_start: 0.8053 (t80) cc_final: 0.7666 (t80) REVERT: C 315 LYS cc_start: 0.8178 (mtmm) cc_final: 0.7437 (ptpp) REVERT: C 330 LYS cc_start: 0.8809 (mmmt) cc_final: 0.8350 (mmtm) REVERT: C 332 ASN cc_start: 0.7821 (t0) cc_final: 0.7281 (t0) REVERT: C 337 ARG cc_start: 0.8279 (ttm170) cc_final: 0.7852 (tmm-80) REVERT: C 338 ARG cc_start: 0.8009 (mtp85) cc_final: 0.7673 (mtp180) REVERT: C 341 GLU cc_start: 0.8084 (pp20) cc_final: 0.7781 (pp20) REVERT: C 376 LYS cc_start: 0.8730 (ttpt) cc_final: 0.8404 (ttpt) REVERT: C 382 ASN cc_start: 0.8587 (m-40) cc_final: 0.8255 (m110) REVERT: C 397 ASP cc_start: 0.7654 (t0) cc_final: 0.7215 (t0) REVERT: C 406 GLU cc_start: 0.8615 (tp30) cc_final: 0.7864 (mt-10) REVERT: C 410 GLN cc_start: 0.9026 (mm-40) cc_final: 0.8159 (mm-40) REVERT: C 447 GLU cc_start: 0.8163 (mp0) cc_final: 0.7483 (tp30) REVERT: C 450 ILE cc_start: 0.8041 (mt) cc_final: 0.7180 (mt) REVERT: C 459 GLU cc_start: 0.7401 (mp0) cc_final: 0.7021 (mp0) REVERT: C 478 MET cc_start: 0.8268 (mtp) cc_final: 0.7857 (mtp) REVERT: C 482 PHE cc_start: 0.8070 (p90) cc_final: 0.7673 (p90) REVERT: C 491 LEU cc_start: 0.8531 (mt) cc_final: 0.8303 (mt) REVERT: C 495 TYR cc_start: 0.7714 (m-10) cc_final: 0.7459 (m-10) REVERT: C 499 ILE cc_start: 0.8011 (tp) cc_final: 0.7787 (tp) REVERT: C 501 MET cc_start: 0.8228 (mtt) cc_final: 0.7863 (mtt) REVERT: C 502 TYR cc_start: 0.7721 (m-10) cc_final: 0.7446 (m-10) REVERT: C 505 ARG cc_start: 0.8805 (mtt90) cc_final: 0.8349 (mtt90) REVERT: C 522 TYR cc_start: 0.8069 (m-80) cc_final: 0.7377 (m-80) REVERT: C 530 ASP cc_start: 0.8028 (p0) cc_final: 0.7712 (p0) REVERT: C 539 ARG cc_start: 0.8589 (ttm-80) cc_final: 0.7977 (ptm160) REVERT: C 540 LEU cc_start: 0.9048 (mm) cc_final: 0.8757 (mm) REVERT: C 541 GLU cc_start: 0.8229 (tt0) cc_final: 0.7353 (tt0) REVERT: C 542 MET cc_start: 0.8249 (tpp) cc_final: 0.7492 (tpp) REVERT: C 545 MET cc_start: 0.7933 (mtm) cc_final: 0.7269 (mtm) REVERT: C 550 ASP cc_start: 0.7686 (p0) cc_final: 0.7395 (p0) REVERT: C 555 LEU cc_start: 0.8608 (tp) cc_final: 0.8260 (tp) REVERT: C 576 GLN cc_start: 0.8194 (tm-30) cc_final: 0.7665 (tm-30) REVERT: C 577 LEU cc_start: 0.8777 (mt) cc_final: 0.8132 (mt) REVERT: C 587 ILE cc_start: 0.8060 (tp) cc_final: 0.7779 (tp) REVERT: C 589 MET cc_start: 0.6347 (mtp) cc_final: 0.5979 (mtp) REVERT: C 593 ASP cc_start: 0.8081 (t70) cc_final: 0.7631 (t0) REVERT: C 603 PRO cc_start: 0.7546 (Cg_endo) cc_final: 0.7334 (Cg_exo) REVERT: C 617 ILE cc_start: 0.8616 (mm) cc_final: 0.8403 (mm) REVERT: C 621 LEU cc_start: 0.8183 (mm) cc_final: 0.7749 (mm) REVERT: C 625 ASN cc_start: 0.8719 (m110) cc_final: 0.8369 (m110) REVERT: C 626 ASN cc_start: 0.8125 (m110) cc_final: 0.7818 (m110) REVERT: C 635 MET cc_start: 0.8112 (mpp) cc_final: 0.7381 (mpp) REVERT: C 640 LYS cc_start: 0.8196 (tttt) cc_final: 0.7974 (tttt) REVERT: C 642 MET cc_start: 0.8149 (mmp) cc_final: 0.7874 (mmp) REVERT: C 649 ARG cc_start: 0.8784 (ttm170) cc_final: 0.8433 (mtm180) REVERT: C 660 GLN cc_start: 0.8653 (mm-40) cc_final: 0.8365 (mm-40) REVERT: C 667 GLU cc_start: 0.7995 (pp20) cc_final: 0.7660 (pp20) REVERT: C 681 GLN cc_start: 0.7229 (tm-30) cc_final: 0.6517 (tm-30) REVERT: C 707 ASN cc_start: 0.8357 (p0) cc_final: 0.7945 (m-40) REVERT: C 712 GLU cc_start: 0.8749 (tt0) cc_final: 0.8351 (tt0) REVERT: C 716 LEU cc_start: 0.8771 (mt) cc_final: 0.8162 (pp) REVERT: C 717 TYR cc_start: 0.9007 (t80) cc_final: 0.8527 (t80) REVERT: C 720 TYR cc_start: 0.7901 (t80) cc_final: 0.7374 (t80) REVERT: C 727 GLU cc_start: 0.8078 (pm20) cc_final: 0.7802 (pm20) REVERT: C 730 PHE cc_start: 0.8045 (t80) cc_final: 0.7562 (t80) REVERT: C 738 HIS cc_start: 0.8114 (t-90) cc_final: 0.7796 (t70) REVERT: C 739 MET cc_start: 0.7780 (ptp) cc_final: 0.7475 (ptp) REVERT: C 743 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8262 (mm-30) REVERT: C 748 TYR cc_start: 0.7614 (t80) cc_final: 0.6952 (t80) REVERT: C 754 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8087 (mt-10) REVERT: C 756 GLU cc_start: 0.7419 (tp30) cc_final: 0.6660 (tp30) REVERT: C 788 ARG cc_start: 0.8564 (ptt180) cc_final: 0.7734 (ptt180) REVERT: C 805 PHE cc_start: 0.8550 (t80) cc_final: 0.8152 (t80) REVERT: C 806 LEU cc_start: 0.8285 (mt) cc_final: 0.7850 (mt) REVERT: C 822 LYS cc_start: 0.8407 (mmtt) cc_final: 0.8074 (mmtm) REVERT: C 855 LYS cc_start: 0.9006 (tttt) cc_final: 0.8184 (tptt) outliers start: 0 outliers final: 0 residues processed: 513 average time/residue: 0.3281 time to fit residues: 226.0353 Evaluate side-chains 493 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 493 time to evaluate : 1.391 ------------------------------------------------------------------------------- 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: 1.9990 chunk 60 optimal weight: 0.5980 chunk 147 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 62 optimal weight: 0.1980 chunk 85 optimal weight: 0.9980 chunk 121 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 21 optimal weight: 0.0060 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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 ** D 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 HIS C 410 GLN C 455 ASN C 681 GLN C 723 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.142608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.114953 restraints weight = 29553.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.119597 restraints weight = 18046.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.123050 restraints weight = 12455.656| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.6245 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= 0.121 Angle : 0.649 11.714 18272 Z= 0.323 Chirality : 0.045 0.285 2014 Planarity : 0.005 0.085 2372 Dihedral : 4.784 23.893 1806 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % 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: -0.96 (0.21), residues: 1610 helix: -0.17 (0.18), residues: 802 sheet: -1.78 (0.66), residues: 64 loop : -0.94 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP C 328 HIS 0.011 0.001 HIS C 297 PHE 0.033 0.002 PHE A 590 TYR 0.018 0.001 TYR A 134 ARG 0.019 0.001 ARG B 84 Details of bonding type rmsd hydrogen bonds : bond 0.03564 ( 502) hydrogen bonds : angle 5.11213 ( 1392) metal coordination : bond 0.00363 ( 12) metal coordination : angle 3.16490 ( 12) covalent geometry : bond 0.00261 (13522) covalent geometry : angle 0.64459 (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 501 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 501 time to evaluate : 1.380 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: B 18 LYS cc_start: 0.7670 (mmtm) cc_final: 0.7282 (mmmm) REVERT: B 22 LEU cc_start: 0.8271 (mm) cc_final: 0.7916 (mm) REVERT: B 62 ARG cc_start: 0.7550 (mmt-90) cc_final: 0.7217 (mmt-90) REVERT: B 65 ASN cc_start: 0.8272 (m-40) cc_final: 0.7907 (m-40) REVERT: B 73 CYS cc_start: 0.5899 (m) cc_final: 0.5516 (m) REVERT: B 77 TYR cc_start: 0.8148 (m-80) cc_final: 0.7737 (m-80) REVERT: B 82 GLU cc_start: 0.8742 (tt0) cc_final: 0.8355 (tt0) REVERT: B 88 TYR cc_start: 0.7172 (p90) cc_final: 0.6789 (p90) REVERT: B 108 ILE cc_start: 0.8144 (mt) cc_final: 0.7629 (tt) REVERT: B 114 GLN cc_start: 0.8050 (mp10) cc_final: 0.7769 (mp10) REVERT: B 124 ARG cc_start: 0.8752 (ttt-90) cc_final: 0.8310 (ttt-90) REVERT: B 128 LYS cc_start: 0.8793 (mttt) cc_final: 0.8443 (mttt) REVERT: B 132 PHE cc_start: 0.7729 (m-80) cc_final: 0.7109 (m-80) REVERT: B 136 ARG cc_start: 0.8136 (mmm160) cc_final: 0.7169 (mmm160) REVERT: A 130 GLU cc_start: 0.8437 (pt0) cc_final: 0.7547 (pm20) REVERT: A 237 ASP cc_start: 0.8468 (m-30) cc_final: 0.7860 (t0) REVERT: A 251 LYS cc_start: 0.8532 (mttp) cc_final: 0.8248 (mtmm) REVERT: A 260 LEU cc_start: 0.9048 (mm) cc_final: 0.8772 (pp) REVERT: A 288 ILE cc_start: 0.8698 (tt) cc_final: 0.8408 (tt) REVERT: A 291 MET cc_start: 0.8442 (ttt) cc_final: 0.7934 (ptm) REVERT: A 292 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7916 (mm-30) REVERT: A 294 ARG cc_start: 0.8556 (mpt-90) cc_final: 0.8309 (mpt-90) REVERT: A 304 MET cc_start: 0.4850 (tpt) cc_final: 0.4253 (tpt) REVERT: A 315 LYS cc_start: 0.8159 (mmtm) cc_final: 0.7520 (mmtm) REVERT: A 328 TRP cc_start: 0.7032 (m100) cc_final: 0.6752 (m100) REVERT: A 332 ASN cc_start: 0.7672 (t0) cc_final: 0.7065 (t0) REVERT: A 337 ARG cc_start: 0.8280 (ttm170) cc_final: 0.7216 (ttp80) REVERT: A 338 ARG cc_start: 0.8065 (mtp85) cc_final: 0.7757 (mmm-85) REVERT: A 341 GLU cc_start: 0.8617 (mt-10) cc_final: 0.7915 (mt-10) REVERT: A 347 ILE cc_start: 0.7743 (mt) cc_final: 0.7530 (mt) REVERT: A 350 LYS cc_start: 0.7798 (mmpt) cc_final: 0.7295 (tptt) REVERT: A 373 LYS cc_start: 0.8033 (mtpt) cc_final: 0.7684 (mtpp) REVERT: A 376 LYS cc_start: 0.8626 (tttt) cc_final: 0.8337 (tttt) REVERT: A 392 HIS cc_start: 0.8344 (m90) cc_final: 0.7848 (m90) REVERT: A 406 GLU cc_start: 0.8110 (tp30) cc_final: 0.7747 (tp30) REVERT: A 420 LYS cc_start: 0.7900 (pttp) cc_final: 0.7266 (ptmm) REVERT: A 437 LEU cc_start: 0.8324 (mm) cc_final: 0.7905 (tt) REVERT: A 446 PHE cc_start: 0.7639 (m-80) cc_final: 0.7415 (m-80) REVERT: A 447 GLU cc_start: 0.8170 (mp0) cc_final: 0.7716 (tp30) REVERT: A 449 PHE cc_start: 0.7166 (m-10) cc_final: 0.6631 (m-80) REVERT: A 450 ILE cc_start: 0.7978 (mt) cc_final: 0.7246 (mt) REVERT: A 458 LEU cc_start: 0.8378 (tp) cc_final: 0.7937 (tt) REVERT: A 459 GLU cc_start: 0.7218 (mp0) cc_final: 0.6865 (mp0) REVERT: A 477 PHE cc_start: 0.7803 (m-80) cc_final: 0.7379 (m-80) REVERT: A 478 MET cc_start: 0.8099 (mtp) cc_final: 0.7756 (ttm) REVERT: A 482 PHE cc_start: 0.7882 (p90) cc_final: 0.7545 (p90) REVERT: A 497 ASN cc_start: 0.7858 (m-40) cc_final: 0.7570 (m-40) REVERT: A 499 ILE cc_start: 0.7911 (tp) cc_final: 0.7629 (tp) REVERT: A 502 TYR cc_start: 0.7650 (m-10) cc_final: 0.7402 (m-10) REVERT: A 504 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7506 (mm-30) REVERT: A 505 ARG cc_start: 0.8797 (mtt90) cc_final: 0.8431 (mtt90) REVERT: A 507 ILE cc_start: 0.8679 (mt) cc_final: 0.8310 (mt) REVERT: A 520 ASN cc_start: 0.7536 (t0) cc_final: 0.7044 (p0) REVERT: A 530 ASP cc_start: 0.8086 (p0) cc_final: 0.7798 (p0) REVERT: A 533 ILE cc_start: 0.8348 (pt) cc_final: 0.7944 (mp) REVERT: A 535 ASP cc_start: 0.7564 (t0) cc_final: 0.7231 (t0) REVERT: A 539 ARG cc_start: 0.8431 (ttm-80) cc_final: 0.7667 (ptm-80) REVERT: A 540 LEU cc_start: 0.9199 (mm) cc_final: 0.8871 (mm) REVERT: A 542 MET cc_start: 0.8291 (ptt) cc_final: 0.7490 (ptt) REVERT: A 545 MET cc_start: 0.7715 (mtm) cc_final: 0.7228 (mtm) REVERT: A 550 ASP cc_start: 0.7885 (p0) cc_final: 0.7631 (p0) REVERT: A 553 LYS cc_start: 0.8454 (mtmt) cc_final: 0.8129 (mtpp) REVERT: A 573 GLU cc_start: 0.8017 (pp20) cc_final: 0.7683 (pp20) REVERT: A 576 GLN cc_start: 0.8498 (tp40) cc_final: 0.8122 (tp40) REVERT: A 593 ASP cc_start: 0.8229 (t0) cc_final: 0.7822 (t70) REVERT: A 600 TRP cc_start: 0.8749 (t-100) cc_final: 0.8482 (t-100) REVERT: A 603 PRO cc_start: 0.7578 (Cg_endo) cc_final: 0.7263 (Cg_exo) REVERT: A 619 LEU cc_start: 0.8864 (tp) cc_final: 0.8542 (tp) REVERT: A 635 MET cc_start: 0.8284 (mpp) cc_final: 0.7546 (mpp) REVERT: A 641 LEU cc_start: 0.8644 (mt) cc_final: 0.8186 (mt) REVERT: A 642 MET cc_start: 0.8132 (mmp) cc_final: 0.7912 (mmp) REVERT: A 651 LEU cc_start: 0.8364 (mt) cc_final: 0.8066 (mt) REVERT: A 660 GLN cc_start: 0.8211 (pp30) cc_final: 0.7776 (pp30) REVERT: A 663 LYS cc_start: 0.8276 (ptmm) cc_final: 0.7839 (ttpp) REVERT: A 665 LEU cc_start: 0.8569 (mp) cc_final: 0.8320 (mp) REVERT: A 667 GLU cc_start: 0.8144 (pp20) cc_final: 0.7777 (pp20) REVERT: A 668 TYR cc_start: 0.7919 (t80) cc_final: 0.7125 (t80) REVERT: A 712 GLU cc_start: 0.8661 (tt0) cc_final: 0.8373 (tt0) REVERT: A 716 LEU cc_start: 0.8743 (mt) cc_final: 0.8378 (tp) REVERT: A 717 TYR cc_start: 0.8949 (t80) cc_final: 0.8581 (t80) REVERT: A 719 ASP cc_start: 0.8185 (m-30) cc_final: 0.7880 (m-30) REVERT: A 727 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7755 (mm-30) REVERT: A 738 HIS cc_start: 0.8143 (t70) cc_final: 0.7574 (t-170) REVERT: A 743 GLU cc_start: 0.8415 (mm-30) cc_final: 0.7760 (mp0) REVERT: A 747 LYS cc_start: 0.9037 (mtpt) cc_final: 0.8531 (mmtt) REVERT: A 753 GLU cc_start: 0.8701 (mp0) cc_final: 0.8353 (mp0) REVERT: A 754 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8190 (mp0) REVERT: A 756 GLU cc_start: 0.7043 (tp30) cc_final: 0.6534 (tp30) REVERT: A 763 ARG cc_start: 0.7165 (ttm-80) cc_final: 0.6794 (ttm-80) REVERT: A 788 ARG cc_start: 0.8462 (ptt180) cc_final: 0.8058 (ptt180) REVERT: A 792 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8114 (mm-30) REVERT: A 797 PHE cc_start: 0.6830 (m-80) cc_final: 0.6498 (m-80) REVERT: A 822 LYS cc_start: 0.8232 (mptt) cc_final: 0.7913 (mmtm) REVERT: D 22 LEU cc_start: 0.8089 (mm) cc_final: 0.7709 (mm) REVERT: D 47 ARG cc_start: 0.7763 (mmm160) cc_final: 0.7185 (mmm160) REVERT: D 65 ASN cc_start: 0.8334 (m-40) cc_final: 0.8098 (t0) REVERT: D 73 CYS cc_start: 0.6188 (m) cc_final: 0.5851 (m) REVERT: D 82 GLU cc_start: 0.8633 (tt0) cc_final: 0.8145 (tt0) REVERT: D 114 GLN cc_start: 0.8203 (mp10) cc_final: 0.7795 (mp10) REVERT: D 128 LYS cc_start: 0.8713 (mttt) cc_final: 0.8345 (mttt) REVERT: D 132 PHE cc_start: 0.7953 (m-80) cc_final: 0.7160 (m-80) REVERT: D 138 ARG cc_start: 0.7940 (ptt-90) cc_final: 0.6822 (ptt-90) REVERT: C 130 GLU cc_start: 0.8362 (pt0) cc_final: 0.7595 (pm20) REVERT: C 138 GLU cc_start: 0.8520 (mp0) cc_final: 0.7911 (mp0) REVERT: C 246 LEU cc_start: 0.8351 (tp) cc_final: 0.8119 (tp) REVERT: C 270 ASP cc_start: 0.7433 (t70) cc_final: 0.7182 (t70) REVERT: C 283 TYR cc_start: 0.7941 (t80) cc_final: 0.7484 (t80) REVERT: C 294 ARG cc_start: 0.8598 (mpt-90) cc_final: 0.8392 (mpt-90) REVERT: C 315 LYS cc_start: 0.8096 (mtmm) cc_final: 0.7344 (ptpp) REVERT: C 326 ARG cc_start: 0.8120 (mtm180) cc_final: 0.7872 (mtm-85) REVERT: C 330 LYS cc_start: 0.8789 (mmmt) cc_final: 0.8326 (mmtm) REVERT: C 332 ASN cc_start: 0.7814 (t0) cc_final: 0.7366 (t0) REVERT: C 337 ARG cc_start: 0.8342 (ttm170) cc_final: 0.7873 (tmm-80) REVERT: C 338 ARG cc_start: 0.8051 (mtp85) cc_final: 0.7469 (mmm160) REVERT: C 341 GLU cc_start: 0.8092 (pp20) cc_final: 0.6759 (pp20) REVERT: C 345 GLN cc_start: 0.8196 (mt0) cc_final: 0.7220 (tp40) REVERT: C 349 TYR cc_start: 0.7981 (t80) cc_final: 0.7754 (t80) REVERT: C 376 LYS cc_start: 0.8678 (ttpt) cc_final: 0.8349 (ttpt) REVERT: C 382 ASN cc_start: 0.8554 (m-40) cc_final: 0.8234 (m110) REVERT: C 397 ASP cc_start: 0.7421 (t0) cc_final: 0.7181 (t0) REVERT: C 403 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7696 (pp20) REVERT: C 407 LEU cc_start: 0.8971 (mt) cc_final: 0.8707 (mt) REVERT: C 410 GLN cc_start: 0.9023 (mm110) cc_final: 0.8239 (mm-40) REVERT: C 429 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8265 (mt-10) REVERT: C 447 GLU cc_start: 0.8152 (mp0) cc_final: 0.7469 (tp30) REVERT: C 450 ILE cc_start: 0.8031 (mt) cc_final: 0.7236 (mt) REVERT: C 478 MET cc_start: 0.8149 (mtp) cc_final: 0.7684 (mtp) REVERT: C 482 PHE cc_start: 0.8035 (p90) cc_final: 0.7721 (p90) REVERT: C 491 LEU cc_start: 0.8507 (mt) cc_final: 0.8267 (mt) REVERT: C 495 TYR cc_start: 0.7619 (m-10) cc_final: 0.7341 (m-10) REVERT: C 499 ILE cc_start: 0.7967 (tp) cc_final: 0.7668 (tp) REVERT: C 501 MET cc_start: 0.8166 (mtt) cc_final: 0.7856 (mtt) REVERT: C 502 TYR cc_start: 0.7715 (m-10) cc_final: 0.7428 (m-10) REVERT: C 505 ARG cc_start: 0.8817 (mtt90) cc_final: 0.8247 (mtt90) REVERT: C 520 ASN cc_start: 0.7761 (t0) cc_final: 0.7497 (p0) REVERT: C 522 TYR cc_start: 0.8136 (m-80) cc_final: 0.7349 (m-80) REVERT: C 530 ASP cc_start: 0.8044 (p0) cc_final: 0.7733 (p0) REVERT: C 539 ARG cc_start: 0.8525 (ttm-80) cc_final: 0.7981 (ptm160) REVERT: C 540 LEU cc_start: 0.9071 (mm) cc_final: 0.8792 (mm) REVERT: C 542 MET cc_start: 0.8211 (tpp) cc_final: 0.7450 (tpp) REVERT: C 545 MET cc_start: 0.7885 (mtm) cc_final: 0.7186 (mtm) REVERT: C 550 ASP cc_start: 0.7778 (p0) cc_final: 0.7331 (p0) REVERT: C 553 LYS cc_start: 0.8383 (mtpp) cc_final: 0.7813 (tppp) REVERT: C 555 LEU cc_start: 0.8596 (tp) cc_final: 0.8280 (tp) REVERT: C 576 GLN cc_start: 0.8113 (tm-30) cc_final: 0.7745 (tm-30) REVERT: C 577 LEU cc_start: 0.8772 (mt) cc_final: 0.8393 (pp) REVERT: C 587 ILE cc_start: 0.8007 (tp) cc_final: 0.7736 (tp) REVERT: C 589 MET cc_start: 0.6446 (mtp) cc_final: 0.6091 (mtp) REVERT: C 593 ASP cc_start: 0.8007 (t70) cc_final: 0.7651 (t70) REVERT: C 603 PRO cc_start: 0.7552 (Cg_endo) cc_final: 0.7328 (Cg_exo) REVERT: C 617 ILE cc_start: 0.8593 (mm) cc_final: 0.8333 (mm) REVERT: C 619 LEU cc_start: 0.8849 (tp) cc_final: 0.8568 (tp) REVERT: C 621 LEU cc_start: 0.8159 (mm) cc_final: 0.7708 (mm) REVERT: C 625 ASN cc_start: 0.8588 (m110) cc_final: 0.8234 (m110) REVERT: C 626 ASN cc_start: 0.8092 (m110) cc_final: 0.7750 (m110) REVERT: C 635 MET cc_start: 0.8091 (mpp) cc_final: 0.7375 (mpp) REVERT: C 640 LYS cc_start: 0.8162 (tttt) cc_final: 0.7868 (tttt) REVERT: C 649 ARG cc_start: 0.8780 (ttm170) cc_final: 0.8511 (ttp-110) REVERT: C 659 TYR cc_start: 0.8790 (t80) cc_final: 0.8558 (t80) REVERT: C 660 GLN cc_start: 0.8646 (mm-40) cc_final: 0.8071 (mm-40) REVERT: C 663 LYS cc_start: 0.8242 (ptmm) cc_final: 0.7888 (ttpp) REVERT: C 667 GLU cc_start: 0.7988 (pp20) cc_final: 0.7645 (pp20) REVERT: C 681 GLN cc_start: 0.6807 (tm130) cc_final: 0.6400 (tm-30) REVERT: C 707 ASN cc_start: 0.8293 (p0) cc_final: 0.7853 (m-40) REVERT: C 712 GLU cc_start: 0.8744 (tt0) cc_final: 0.8409 (tt0) REVERT: C 716 LEU cc_start: 0.8762 (mt) cc_final: 0.8199 (pp) REVERT: C 717 TYR cc_start: 0.9018 (t80) cc_final: 0.8515 (t80) REVERT: C 719 ASP cc_start: 0.8297 (m-30) cc_final: 0.8051 (m-30) REVERT: C 720 TYR cc_start: 0.7940 (t80) cc_final: 0.7350 (t80) REVERT: C 730 PHE cc_start: 0.8059 (t80) cc_final: 0.7555 (t80) REVERT: C 738 HIS cc_start: 0.8114 (t-90) cc_final: 0.7825 (t70) REVERT: C 739 MET cc_start: 0.7796 (ptp) cc_final: 0.7540 (ptp) REVERT: C 743 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8157 (mm-30) REVERT: C 747 LYS cc_start: 0.9089 (mtpt) cc_final: 0.8711 (mmmm) REVERT: C 748 TYR cc_start: 0.7533 (t80) cc_final: 0.6932 (t80) REVERT: C 754 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8105 (mt-10) REVERT: C 756 GLU cc_start: 0.7256 (tp30) cc_final: 0.6568 (tp30) REVERT: C 763 ARG cc_start: 0.7652 (tpp80) cc_final: 0.7393 (tpp80) REVERT: C 788 ARG cc_start: 0.8584 (ptt180) cc_final: 0.7776 (ptt180) REVERT: C 820 LEU cc_start: 0.7800 (mm) cc_final: 0.7324 (mm) REVERT: C 822 LYS cc_start: 0.8438 (mmtt) cc_final: 0.8093 (mmtm) REVERT: C 835 GLU cc_start: 0.7679 (pm20) cc_final: 0.7459 (pm20) REVERT: C 855 LYS cc_start: 0.9054 (tttt) cc_final: 0.8258 (tptt) outliers start: 0 outliers final: 0 residues processed: 501 average time/residue: 0.3275 time to fit residues: 220.0993 Evaluate side-chains 478 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 478 time to evaluate : 1.474 ------------------------------------------------------------------------------- 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: 0.8980 chunk 49 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 684 GLN A 723 ASN D 27 GLN ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 455 ASN ** C 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 723 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.141371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.114488 restraints weight = 29215.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.119005 restraints weight = 17780.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.122375 restraints weight = 12268.675| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.6388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13534 Z= 0.143 Angle : 0.664 9.401 18272 Z= 0.334 Chirality : 0.045 0.200 2014 Planarity : 0.005 0.096 2372 Dihedral : 4.796 21.018 1806 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.21), residues: 1610 helix: -0.28 (0.18), residues: 802 sheet: -1.60 (0.66), residues: 64 loop : -0.94 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP C 328 HIS 0.007 0.001 HIS C 655 PHE 0.029 0.002 PHE C 730 TYR 0.036 0.002 TYR A 301 ARG 0.023 0.001 ARG D 84 Details of bonding type rmsd hydrogen bonds : bond 0.03750 ( 502) hydrogen bonds : angle 5.24481 ( 1392) metal coordination : bond 0.00546 ( 12) metal coordination : angle 4.01993 ( 12) covalent geometry : bond 0.00301 (13522) covalent geometry : angle 0.65591 (18260) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5667.17 seconds wall clock time: 101 minutes 59.41 seconds (6119.41 seconds total)