Starting phenix.real_space_refine on Sat Aug 23 16:43:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jrq_36602/08_2025/8jrq_36602.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jrq_36602/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8jrq_36602/08_2025/8jrq_36602.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jrq_36602/08_2025/8jrq_36602.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jrq_36602/08_2025/8jrq_36602.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jrq_36602/08_2025/8jrq_36602.map" } resolution = 4.15 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.035 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'TYR:plan': 2, 'GLU:plan': 3, 'PHE:plan': 3, 'ASP:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 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: 4.44, per 1000 atoms: 0.33 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: 1.01 Conformation dependent library (CDL) restraints added in 421.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.38 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: 1.61 Time building geometry restraints manager: 1.27 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: 0.03 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: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.790 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.420 ------------------------------------------------------------------------------- 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 : 13.15 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.008 0.001 ARG C 836 TYR 0.029 0.003 TYR A 134 PHE 0.025 0.003 PHE C 633 TRP 0.013 0.003 TRP D 139 HIS 0.005 0.002 HIS C 632 Details of bonding type rmsd covalent geometry : bond 0.00724 (13522) covalent geometry : angle 1.09124 (18260) hydrogen bonds : bond 0.28834 ( 502) hydrogen bonds : angle 10.29116 ( 1392) metal coordination : bond 0.13923 ( 12) metal coordination : angle 13.15132 ( 12) *********************** 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 : 0.497 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 73 CYS cc_start: 0.6979 (m) cc_final: 0.6684 (m) REVERT: B 79 LYS cc_start: 0.8271 (tppt) cc_final: 0.7225 (tppt) REVERT: B 108 ILE cc_start: 0.8087 (mt) cc_final: 0.7830 (tt) REVERT: B 124 ARG cc_start: 0.8225 (ttt-90) cc_final: 0.7857 (ttt-90) REVERT: B 128 LYS cc_start: 0.8083 (mttt) cc_final: 0.7790 (mttt) REVERT: B 132 PHE cc_start: 0.6844 (m-80) cc_final: 0.6007 (m-80) REVERT: A 130 GLU cc_start: 0.8522 (pt0) cc_final: 0.7836 (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: 0.7176 (t80) REVERT: A 287 PHE cc_start: 0.7067 (m-80) cc_final: 0.6864 (m-80) REVERT: A 294 ARG cc_start: 0.8121 (mpt-90) cc_final: 0.7874 (mpt-90) REVERT: A 304 MET cc_start: 0.4377 (tpt) cc_final: 0.4145 (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: 0.7607 (t0) REVERT: A 337 ARG cc_start: 0.8089 (ttm170) cc_final: 0.7838 (ttp80) REVERT: A 341 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7702 (mt-10) REVERT: A 344 GLN cc_start: 0.8053 (tp-100) cc_final: 0.7702 (pp30) REVERT: A 349 TYR cc_start: 0.7651 (t80) cc_final: 0.7368 (t80) REVERT: A 361 LEU cc_start: 0.7317 (tp) cc_final: 0.6971 (tp) REVERT: A 403 GLU cc_start: 0.7064 (pm20) cc_final: 0.5937 (pm20) REVERT: A 406 GLU cc_start: 0.7412 (tp30) cc_final: 0.7013 (tp30) REVERT: A 407 LEU cc_start: 0.8852 (mt) cc_final: 0.8486 (mt) REVERT: A 410 GLN cc_start: 0.8609 (mm-40) cc_final: 0.7731 (mm-40) REVERT: A 447 GLU cc_start: 0.7781 (mp0) cc_final: 0.7389 (tp30) REVERT: A 449 PHE cc_start: 0.7345 (m-10) cc_final: 0.7107 (m-10) REVERT: A 450 ILE cc_start: 0.8188 (mt) cc_final: 0.7579 (mt) REVERT: A 458 LEU cc_start: 0.7940 (tp) cc_final: 0.7680 (tt) REVERT: A 463 ASP cc_start: 0.6874 (t0) cc_final: 0.6600 (t70) REVERT: A 477 PHE cc_start: 0.7731 (m-80) cc_final: 0.7198 (m-80) REVERT: A 478 MET cc_start: 0.7885 (mtp) cc_final: 0.6525 (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: 0.6717 (p) REVERT: A 493 LEU cc_start: 0.7548 (tp) cc_final: 0.7117 (tt) REVERT: A 501 MET cc_start: 0.7485 (mtt) cc_final: 0.6621 (mmt) REVERT: A 502 TYR cc_start: 0.6988 (m-10) cc_final: 0.6719 (m-10) REVERT: A 504 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7106 (mm-30) REVERT: A 505 ARG cc_start: 0.8066 (mtt90) cc_final: 0.7726 (mtt90) REVERT: A 507 ILE cc_start: 0.8339 (mt) cc_final: 0.7925 (mt) REVERT: A 520 ASN cc_start: 0.7089 (t0) cc_final: 0.6609 (m-40) REVERT: A 522 TYR cc_start: 0.8029 (m-80) cc_final: 0.7599 (m-80) REVERT: A 523 LEU cc_start: 0.8585 (tp) cc_final: 0.8134 (tp) REVERT: A 534 ASP cc_start: 0.7681 (m-30) cc_final: 0.7425 (m-30) REVERT: A 540 LEU cc_start: 0.8568 (mm) cc_final: 0.8364 (mm) REVERT: A 542 MET cc_start: 0.7949 (tpp) cc_final: 0.7588 (tpp) REVERT: A 553 LYS cc_start: 0.8720 (mtmt) cc_final: 0.7795 (ptmt) REVERT: A 554 GLN cc_start: 0.7655 (tt0) cc_final: 0.7017 (mm-40) REVERT: A 581 GLU cc_start: 0.7810 (tt0) cc_final: 0.7450 (tt0) REVERT: A 600 TRP cc_start: 0.8196 (t-100) cc_final: 0.7942 (t-100) REVERT: A 617 ILE cc_start: 0.8393 (mm) cc_final: 0.7925 (mm) REVERT: A 621 LEU cc_start: 0.8199 (mm) cc_final: 0.7788 (mp) REVERT: A 635 MET cc_start: 0.7797 (mpp) cc_final: 0.7119 (mpp) REVERT: A 638 TYR cc_start: 0.8037 (m-80) cc_final: 0.6509 (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: 0.8052 (p) REVERT: A 663 LYS cc_start: 0.7609 (ptmm) cc_final: 0.7052 (ttpp) REVERT: A 708 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8358 (pm20) REVERT: A 711 LYS cc_start: 0.9091 (mmtt) cc_final: 0.8565 (mmtm) REVERT: A 712 GLU cc_start: 0.8548 (tt0) cc_final: 0.8206 (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: 0.7985 (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: 0.7748 (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: 0.7722 (ttm-80) REVERT: A 743 GLU cc_start: 0.7143 (mm-30) cc_final: 0.6749 (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: 0.6624 (tp30) REVERT: A 787 ILE cc_start: 0.6650 (OUTLIER) cc_final: 0.6434 (mm) REVERT: A 788 ARG cc_start: 0.7961 (ptp90) cc_final: 0.7448 (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: 0.8286 (t80) REVERT: A 820 LEU cc_start: 0.7700 (mm) cc_final: 0.6963 (mm) REVERT: A 822 LYS cc_start: 0.8400 (mptt) cc_final: 0.8098 (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: 0.6931 (mt0) REVERT: D 79 LYS cc_start: 0.8298 (tppt) cc_final: 0.7222 (tppt) REVERT: D 124 ARG cc_start: 0.8168 (ttt-90) cc_final: 0.7838 (ttt-90) REVERT: D 132 PHE cc_start: 0.6801 (m-80) cc_final: 0.6108 (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: 0.7728 (mp0) REVERT: C 237 ASP cc_start: 0.7890 (m-30) cc_final: 0.7067 (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: 0.7379 (t80) REVERT: C 287 PHE cc_start: 0.7291 (m-80) cc_final: 0.7074 (m-80) REVERT: C 294 ARG cc_start: 0.8112 (mpt-90) cc_final: 0.7882 (mpt-90) REVERT: C 321 GLN cc_start: 0.8246 (mt0) cc_final: 0.8030 (mm-40) REVERT: C 324 LEU cc_start: 0.8316 (tt) cc_final: 0.8093 (tp) REVERT: C 332 ASN cc_start: 0.7945 (t0) cc_final: 0.7387 (t0) REVERT: C 337 ARG cc_start: 0.8135 (ttm170) cc_final: 0.7547 (ttp80) REVERT: C 349 TYR cc_start: 0.7753 (t80) cc_final: 0.7407 (t80) REVERT: C 382 ASN cc_start: 0.8120 (m-40) cc_final: 0.7893 (m-40) REVERT: C 394 GLU cc_start: 0.6391 (mm-30) cc_final: 0.5404 (mm-30) REVERT: C 403 GLU cc_start: 0.7042 (pm20) cc_final: 0.5970 (pm20) REVERT: C 406 GLU cc_start: 0.7550 (tp30) cc_final: 0.6980 (tp30) REVERT: C 407 LEU cc_start: 0.8812 (mt) cc_final: 0.8462 (mt) REVERT: C 410 GLN cc_start: 0.8537 (mm-40) cc_final: 0.7666 (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: 0.7272 (m-10) REVERT: C 478 MET cc_start: 0.7730 (mtp) cc_final: 0.6910 (mtp) REVERT: C 482 PHE cc_start: 0.7634 (p90) cc_final: 0.7377 (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: 0.7025 (tt) REVERT: C 499 ILE cc_start: 0.7700 (tp) cc_final: 0.7486 (tp) REVERT: C 501 MET cc_start: 0.7400 (mtt) cc_final: 0.7174 (mtt) REVERT: C 504 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7283 (tp30) REVERT: C 505 ARG cc_start: 0.8059 (mtt90) cc_final: 0.7538 (mtt90) REVERT: C 507 ILE cc_start: 0.8387 (mt) cc_final: 0.7668 (mt) REVERT: C 520 ASN cc_start: 0.7360 (t0) cc_final: 0.7055 (m-40) REVERT: C 522 TYR cc_start: 0.8011 (m-80) cc_final: 0.7757 (m-80) REVERT: C 540 LEU cc_start: 0.8501 (mm) cc_final: 0.8277 (mm) REVERT: C 542 MET cc_start: 0.7984 (tpp) cc_final: 0.7450 (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: 0.8102 (ptmt) REVERT: C 555 LEU cc_start: 0.8730 (tp) cc_final: 0.8508 (tp) REVERT: C 589 MET cc_start: 0.6343 (mtp) cc_final: 0.6120 (mtp) REVERT: C 600 TRP cc_start: 0.8253 (t-100) cc_final: 0.7996 (t-100) REVERT: C 617 ILE cc_start: 0.8573 (mm) cc_final: 0.8152 (mm) REVERT: C 621 LEU cc_start: 0.8219 (mm) cc_final: 0.7840 (mt) REVERT: C 635 MET cc_start: 0.7695 (mpp) cc_final: 0.6955 (mpp) REVERT: C 638 TYR cc_start: 0.7934 (m-80) cc_final: 0.6377 (m-80) REVERT: C 651 LEU cc_start: 0.8202 (tp) cc_final: 0.7960 (mt) REVERT: C 658 LEU cc_start: 0.8745 (tp) cc_final: 0.8339 (tp) REVERT: C 661 SER cc_start: 0.8402 (m) cc_final: 0.8009 (p) REVERT: C 682 ILE cc_start: 0.6755 (pt) cc_final: 0.5787 (pt) REVERT: C 711 LYS cc_start: 0.9019 (mmtt) cc_final: 0.8514 (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: 0.6375 (t80) REVERT: C 726 VAL cc_start: 0.8058 (OUTLIER) cc_final: 0.7673 (t) REVERT: C 729 GLN cc_start: 0.8186 (mp10) cc_final: 0.7872 (mp10) REVERT: C 730 PHE cc_start: 0.7485 (t80) cc_final: 0.7125 (t80) REVERT: C 743 GLU cc_start: 0.7418 (mm-30) cc_final: 0.7012 (mp0) REVERT: C 748 TYR cc_start: 0.7149 (t80) cc_final: 0.6851 (t80) REVERT: C 751 ARG cc_start: 0.7315 (mtm-85) cc_final: 0.7055 (mtp85) REVERT: C 753 GLU cc_start: 0.8164 (mp0) cc_final: 0.7906 (mp0) REVERT: C 756 GLU cc_start: 0.7376 (tp30) cc_final: 0.6480 (tp30) REVERT: C 757 LEU cc_start: 0.7371 (mm) cc_final: 0.7143 (mm) REVERT: C 763 ARG cc_start: 0.5179 (mmm160) cc_final: 0.4854 (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: 0.7370 (ptp90) REVERT: C 789 GLU cc_start: 0.7881 (pt0) cc_final: 0.7176 (mt-10) REVERT: C 805 PHE cc_start: 0.8475 (t80) cc_final: 0.8246 (t80) REVERT: C 820 LEU cc_start: 0.7518 (mm) cc_final: 0.6791 (mm) REVERT: C 822 LYS cc_start: 0.8473 (mptt) cc_final: 0.8236 (mmtp) REVERT: C 855 LYS cc_start: 0.8803 (tttt) cc_final: 0.7583 (tmtt) outliers start: 10 outliers final: 4 residues processed: 565 average time/residue: 0.1286 time to fit residues: 98.8464 Evaluate side-chains 516 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 508 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN B 134 ASN ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 ASN A 285 ASN A 382 ASN A 455 ASN A 515 GLN D 65 ASN D 97 GLN ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.143278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.115674 restraints weight = 29978.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.120248 restraints weight = 18554.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.123621 restraints weight = 12962.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.126220 restraints weight = 9618.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.128201 restraints weight = 7507.519| |-----------------------------------------------------------------------------| r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.3119 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= 0.162 Angle : 0.715 14.209 18272 Z= 0.366 Chirality : 0.044 0.242 2014 Planarity : 0.006 0.068 2372 Dihedral : 6.033 20.935 1806 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.14 % Allowed : 6.61 % Favored : 93.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.09 (0.18), residues: 1610 helix: -2.03 (0.15), residues: 838 sheet: -3.15 (0.50), residues: 72 loop : -1.76 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 84 TYR 0.028 0.002 TYR C 127 PHE 0.032 0.002 PHE D 54 TRP 0.014 0.002 TRP A 328 HIS 0.003 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00329 (13522) covalent geometry : angle 0.68984 (18260) hydrogen bonds : bond 0.04917 ( 502) hydrogen bonds : angle 5.97242 ( 1392) metal coordination : bond 0.00982 ( 12) metal coordination : angle 7.34658 ( 12) *********************** 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 551 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 549 time to evaluate : 0.357 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 21 GLN cc_start: 0.7454 (mt0) cc_final: 0.6749 (mt0) REVERT: B 30 ILE cc_start: 0.8138 (tt) cc_final: 0.7760 (tt) REVERT: B 42 GLN cc_start: 0.8463 (mt0) cc_final: 0.8171 (mt0) REVERT: B 65 ASN cc_start: 0.8292 (m-40) cc_final: 0.8049 (m-40) REVERT: B 73 CYS cc_start: 0.7593 (m) cc_final: 0.7116 (m) REVERT: B 76 PHE cc_start: 0.8481 (t80) cc_final: 0.8099 (t80) REVERT: B 80 ILE cc_start: 0.8660 (mm) cc_final: 0.8338 (mm) REVERT: B 88 TYR cc_start: 0.7264 (p90) cc_final: 0.6722 (p90) REVERT: B 108 ILE cc_start: 0.8051 (mt) cc_final: 0.7701 (tt) REVERT: B 128 LYS cc_start: 0.8308 (mttt) cc_final: 0.7974 (mmtt) REVERT: B 132 PHE cc_start: 0.7493 (m-80) cc_final: 0.6584 (m-80) REVERT: A 130 GLU cc_start: 0.8548 (pt0) cc_final: 0.7666 (pm20) REVERT: A 138 GLU cc_start: 0.8388 (mp0) cc_final: 0.7912 (mp0) REVERT: A 237 ASP cc_start: 0.8335 (m-30) cc_final: 0.7287 (t0) REVERT: A 260 LEU cc_start: 0.9083 (mm) cc_final: 0.8812 (mm) REVERT: A 283 TYR cc_start: 0.7770 (t80) cc_final: 0.7501 (t80) REVERT: A 287 PHE cc_start: 0.7132 (m-80) cc_final: 0.6888 (m-80) REVERT: A 294 ARG cc_start: 0.8504 (mpt-90) cc_final: 0.8234 (mpt-90) REVERT: A 304 MET cc_start: 0.5169 (tpt) cc_final: 0.4553 (tpt) REVERT: A 326 ARG cc_start: 0.8028 (mtm110) cc_final: 0.7718 (mtm-85) REVERT: A 332 ASN cc_start: 0.7648 (t0) cc_final: 0.7150 (t0) REVERT: A 337 ARG cc_start: 0.8180 (ttm170) cc_final: 0.7775 (ttp80) REVERT: A 344 GLN cc_start: 0.8371 (tp-100) cc_final: 0.7183 (tp-100) REVERT: A 345 GLN cc_start: 0.8452 (mt0) cc_final: 0.7806 (tp40) REVERT: A 361 LEU cc_start: 0.7485 (tp) cc_final: 0.7210 (tp) REVERT: A 392 HIS cc_start: 0.8033 (m90) cc_final: 0.7432 (m-70) REVERT: A 395 GLU cc_start: 0.6887 (tm-30) cc_final: 0.6639 (tm-30) REVERT: A 406 GLU cc_start: 0.8239 (tp30) cc_final: 0.7215 (tp30) REVERT: A 407 LEU cc_start: 0.8826 (mt) cc_final: 0.8500 (pp) REVERT: A 409 LEU cc_start: 0.8608 (tp) cc_final: 0.8020 (pp) REVERT: A 447 GLU cc_start: 0.8182 (mp0) cc_final: 0.7528 (tp30) REVERT: A 449 PHE cc_start: 0.7568 (m-10) cc_final: 0.6951 (m-10) REVERT: A 450 ILE cc_start: 0.7905 (mt) cc_final: 0.7368 (mt) REVERT: A 458 LEU cc_start: 0.8403 (tp) cc_final: 0.7616 (tt) REVERT: A 464 TYR cc_start: 0.7879 (t80) cc_final: 0.7217 (t80) REVERT: A 477 PHE cc_start: 0.8182 (m-80) cc_final: 0.7770 (m-80) REVERT: A 478 MET cc_start: 0.8141 (mtp) cc_final: 0.6788 (mtp) REVERT: A 482 PHE cc_start: 0.8031 (p90) cc_final: 0.7697 (p90) REVERT: A 495 TYR cc_start: 0.7455 (m-10) cc_final: 0.7241 (m-10) REVERT: A 499 ILE cc_start: 0.7907 (tp) cc_final: 0.7626 (tp) REVERT: A 501 MET cc_start: 0.8219 (mtt) cc_final: 0.7325 (ptp) REVERT: A 504 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7527 (mm-30) REVERT: A 507 ILE cc_start: 0.8610 (mt) cc_final: 0.8171 (mt) REVERT: A 545 MET cc_start: 0.7900 (mtm) cc_final: 0.7362 (mtm) REVERT: A 550 ASP cc_start: 0.7957 (p0) cc_final: 0.7564 (p0) REVERT: A 553 LYS cc_start: 0.8521 (mtmt) cc_final: 0.8163 (tppt) REVERT: A 572 LYS cc_start: 0.8557 (tttp) cc_final: 0.8219 (ttmm) REVERT: A 573 GLU cc_start: 0.8125 (pp20) cc_final: 0.7673 (pp20) REVERT: A 576 GLN cc_start: 0.8367 (tp-100) cc_final: 0.7576 (tp-100) REVERT: A 577 LEU cc_start: 0.8866 (mt) cc_final: 0.8396 (mt) REVERT: A 593 ASP cc_start: 0.8294 (t0) cc_final: 0.7874 (t0) REVERT: A 600 TRP cc_start: 0.8660 (t-100) cc_final: 0.8452 (t-100) REVERT: A 617 ILE cc_start: 0.8484 (mm) cc_final: 0.8106 (mm) REVERT: A 621 LEU cc_start: 0.8109 (mm) cc_final: 0.7702 (mp) REVERT: A 635 MET cc_start: 0.8168 (mpp) cc_final: 0.7440 (mpp) REVERT: A 641 LEU cc_start: 0.8529 (mt) cc_final: 0.7698 (pp) REVERT: A 651 LEU cc_start: 0.8371 (mt) cc_final: 0.8146 (mt) REVERT: A 658 LEU cc_start: 0.8417 (tp) cc_final: 0.7989 (tp) REVERT: A 663 LYS cc_start: 0.8150 (ptmm) cc_final: 0.7521 (ttpp) REVERT: A 711 LYS cc_start: 0.9229 (mmtt) cc_final: 0.8903 (mmtm) REVERT: A 715 ASN cc_start: 0.8763 (m-40) cc_final: 0.8512 (m110) REVERT: A 716 LEU cc_start: 0.8699 (mt) cc_final: 0.8427 (mt) REVERT: A 717 TYR cc_start: 0.8337 (t80) cc_final: 0.7921 (t80) REVERT: A 720 TYR cc_start: 0.7667 (t80) cc_final: 0.7079 (t80) REVERT: A 727 GLU cc_start: 0.8001 (pt0) cc_final: 0.7767 (pm20) REVERT: A 728 LYS cc_start: 0.8546 (ttpt) cc_final: 0.7995 (ptmm) REVERT: A 730 PHE cc_start: 0.8239 (t80) cc_final: 0.7846 (t80) REVERT: A 734 ARG cc_start: 0.8525 (ttt-90) cc_final: 0.7441 (tpt-90) REVERT: A 738 HIS cc_start: 0.8241 (t70) cc_final: 0.7992 (t-170) REVERT: A 743 GLU cc_start: 0.8328 (mm-30) cc_final: 0.7771 (mm-30) REVERT: A 748 TYR cc_start: 0.7562 (t80) cc_final: 0.7139 (t80) REVERT: A 751 ARG cc_start: 0.7813 (mtm-85) cc_final: 0.7328 (mmm160) REVERT: A 753 GLU cc_start: 0.8611 (mp0) cc_final: 0.8282 (mp0) REVERT: A 756 GLU cc_start: 0.7829 (tp30) cc_final: 0.7202 (tp30) REVERT: A 792 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8285 (mm-30) REVERT: A 805 PHE cc_start: 0.8653 (t80) cc_final: 0.8221 (t80) REVERT: A 806 LEU cc_start: 0.8172 (mt) cc_final: 0.7849 (mt) REVERT: A 820 LEU cc_start: 0.7658 (mm) cc_final: 0.7393 (mm) REVERT: A 822 LYS cc_start: 0.8514 (mptt) cc_final: 0.8178 (mmtm) REVERT: A 862 LEU cc_start: 0.8526 (tt) cc_final: 0.8226 (mt) REVERT: D 42 GLN cc_start: 0.8489 (mt0) cc_final: 0.8222 (mt0) REVERT: D 47 ARG cc_start: 0.7727 (mmm160) cc_final: 0.6797 (mmm160) REVERT: D 59 ILE cc_start: 0.7643 (mm) cc_final: 0.7227 (mm) REVERT: D 65 ASN cc_start: 0.8394 (m-40) cc_final: 0.8101 (m-40) REVERT: D 73 CYS cc_start: 0.7423 (m) cc_final: 0.6853 (m) REVERT: D 79 LYS cc_start: 0.8352 (tppt) cc_final: 0.7307 (tppt) REVERT: D 80 ILE cc_start: 0.8602 (mm) cc_final: 0.8379 (mm) REVERT: D 88 TYR cc_start: 0.7178 (p90) cc_final: 0.6736 (p90) REVERT: D 94 THR cc_start: 0.7608 (p) cc_final: 0.7181 (p) REVERT: D 132 PHE cc_start: 0.7437 (m-80) cc_final: 0.6782 (m-80) REVERT: D 134 ASN cc_start: 0.7577 (t0) cc_final: 0.6770 (t0) REVERT: C 130 GLU cc_start: 0.8430 (pt0) cc_final: 0.8097 (pt0) REVERT: C 138 GLU cc_start: 0.8466 (mp0) cc_final: 0.7999 (mp0) REVERT: C 237 ASP cc_start: 0.7902 (m-30) cc_final: 0.7445 (t70) REVERT: C 241 ARG cc_start: 0.8729 (mtm-85) cc_final: 0.8474 (mtm-85) REVERT: C 260 LEU cc_start: 0.8962 (mm) cc_final: 0.8697 (mm) REVERT: C 270 ASP cc_start: 0.7425 (t0) cc_final: 0.7132 (t0) REVERT: C 283 TYR cc_start: 0.7972 (t80) cc_final: 0.7491 (t80) REVERT: C 291 MET cc_start: 0.8566 (ttt) cc_final: 0.7980 (ptm) REVERT: C 315 LYS cc_start: 0.7972 (mtmm) cc_final: 0.7472 (mttp) REVERT: C 321 GLN cc_start: 0.8482 (mt0) cc_final: 0.8265 (mm-40) REVERT: C 332 ASN cc_start: 0.7548 (t0) cc_final: 0.7120 (t0) REVERT: C 337 ARG cc_start: 0.8212 (ttm170) cc_final: 0.7675 (ttp80) REVERT: C 338 ARG cc_start: 0.8235 (mtp85) cc_final: 0.7607 (mtp-110) REVERT: C 344 GLN cc_start: 0.8342 (tp-100) cc_final: 0.7248 (tp-100) REVERT: C 349 TYR cc_start: 0.7831 (t80) cc_final: 0.7621 (t80) REVERT: C 376 LYS cc_start: 0.8495 (ttmt) cc_final: 0.7620 (tttt) REVERT: C 380 TYR cc_start: 0.8701 (m-10) cc_final: 0.8086 (m-10) REVERT: C 382 ASN cc_start: 0.8511 (m-40) cc_final: 0.8232 (m110) REVERT: C 392 HIS cc_start: 0.7980 (m170) cc_final: 0.7521 (m-70) REVERT: C 407 LEU cc_start: 0.8736 (mt) cc_final: 0.8197 (pp) REVERT: C 409 LEU cc_start: 0.8576 (tp) cc_final: 0.8071 (pp) REVERT: C 410 GLN cc_start: 0.8940 (mm-40) cc_final: 0.8687 (mm110) REVERT: C 411 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7207 (mt-10) REVERT: C 426 ASP cc_start: 0.8561 (t70) cc_final: 0.8227 (t0) REVERT: C 447 GLU cc_start: 0.8068 (mp0) cc_final: 0.7423 (tp30) REVERT: C 449 PHE cc_start: 0.7760 (m-10) cc_final: 0.7102 (m-10) REVERT: C 450 ILE cc_start: 0.7907 (mt) cc_final: 0.7446 (mt) REVERT: C 459 GLU cc_start: 0.6784 (mp0) cc_final: 0.6466 (mp0) REVERT: C 460 MET cc_start: 0.7299 (mpp) cc_final: 0.7094 (mpp) REVERT: C 478 MET cc_start: 0.7927 (mtp) cc_final: 0.7354 (mtp) REVERT: C 482 PHE cc_start: 0.7883 (p90) cc_final: 0.7555 (p90) REVERT: C 491 LEU cc_start: 0.8568 (mt) cc_final: 0.8283 (mt) REVERT: C 493 LEU cc_start: 0.8018 (tp) cc_final: 0.7642 (tp) REVERT: C 495 TYR cc_start: 0.7609 (m-10) cc_final: 0.7149 (m-10) REVERT: C 497 ASN cc_start: 0.7963 (m-40) cc_final: 0.7746 (m-40) REVERT: C 499 ILE cc_start: 0.8047 (tp) cc_final: 0.7701 (tp) REVERT: C 501 MET cc_start: 0.8236 (mtt) cc_final: 0.7840 (mtt) REVERT: C 502 TYR cc_start: 0.7561 (m-10) cc_final: 0.7139 (m-10) REVERT: C 504 GLU cc_start: 0.8427 (mm-30) cc_final: 0.7827 (mm-30) REVERT: C 505 ARG cc_start: 0.8796 (mtt90) cc_final: 0.8270 (mtt90) REVERT: C 507 ILE cc_start: 0.8578 (mt) cc_final: 0.8137 (mt) REVERT: C 540 LEU cc_start: 0.8690 (mm) cc_final: 0.8473 (mm) REVERT: C 542 MET cc_start: 0.8275 (tpp) cc_final: 0.7501 (tpp) REVERT: C 545 MET cc_start: 0.7982 (mtm) cc_final: 0.7362 (mtm) REVERT: C 546 GLU cc_start: 0.7395 (tt0) cc_final: 0.6746 (tt0) REVERT: C 553 LYS cc_start: 0.8504 (mtmt) cc_final: 0.8188 (mtpp) REVERT: C 576 GLN cc_start: 0.7860 (tm-30) cc_final: 0.7363 (tm-30) REVERT: C 577 LEU cc_start: 0.8703 (mt) cc_final: 0.8265 (mt) REVERT: C 587 ILE cc_start: 0.8487 (tp) cc_final: 0.8215 (tp) REVERT: C 589 MET cc_start: 0.7000 (mtp) cc_final: 0.6596 (mtp) REVERT: C 600 TRP cc_start: 0.8695 (t-100) cc_final: 0.8455 (t-100) REVERT: C 617 ILE cc_start: 0.8641 (mm) cc_final: 0.8421 (mm) REVERT: C 619 LEU cc_start: 0.8696 (tp) cc_final: 0.8385 (tp) REVERT: C 621 LEU cc_start: 0.8254 (mm) cc_final: 0.7890 (mm) REVERT: C 625 ASN cc_start: 0.8590 (m110) cc_final: 0.8237 (m110) REVERT: C 635 MET cc_start: 0.8018 (mpp) cc_final: 0.7182 (mpp) REVERT: C 641 LEU cc_start: 0.8526 (mt) cc_final: 0.7970 (pp) REVERT: C 648 PHE cc_start: 0.8744 (p90) cc_final: 0.8286 (p90) REVERT: C 658 LEU cc_start: 0.8547 (tp) cc_final: 0.8107 (tp) REVERT: C 661 SER cc_start: 0.8414 (m) cc_final: 0.8196 (p) REVERT: C 663 LYS cc_start: 0.8363 (ptmm) cc_final: 0.7276 (mmtt) REVERT: C 664 ASP cc_start: 0.8147 (m-30) cc_final: 0.6545 (p0) REVERT: C 667 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8383 (pp20) REVERT: C 711 LYS cc_start: 0.9199 (mmtt) cc_final: 0.8700 (mmtm) REVERT: C 712 GLU cc_start: 0.8693 (tt0) cc_final: 0.8340 (tt0) REVERT: C 716 LEU cc_start: 0.8765 (mt) cc_final: 0.8512 (mp) REVERT: C 719 ASP cc_start: 0.8287 (m-30) cc_final: 0.7988 (m-30) REVERT: C 720 TYR cc_start: 0.7762 (t80) cc_final: 0.7061 (t80) REVERT: C 727 GLU cc_start: 0.8108 (pt0) cc_final: 0.7882 (pm20) REVERT: C 730 PHE cc_start: 0.8227 (t80) cc_final: 0.7836 (t80) REVERT: C 738 HIS cc_start: 0.8186 (t-90) cc_final: 0.7677 (t-90) REVERT: C 743 GLU cc_start: 0.8434 (mm-30) cc_final: 0.7846 (mm-30) REVERT: C 748 TYR cc_start: 0.7573 (t80) cc_final: 0.6937 (t80) REVERT: C 753 GLU cc_start: 0.8600 (mp0) cc_final: 0.8322 (mp0) REVERT: C 754 GLU cc_start: 0.8373 (mt-10) cc_final: 0.8079 (mp0) REVERT: C 756 GLU cc_start: 0.7708 (tp30) cc_final: 0.6941 (tp30) REVERT: C 789 GLU cc_start: 0.8020 (pt0) cc_final: 0.7396 (mt-10) REVERT: C 791 TRP cc_start: 0.7895 (t60) cc_final: 0.7487 (t60) REVERT: C 855 LYS cc_start: 0.8891 (tttt) cc_final: 0.7878 (tppt) outliers start: 2 outliers final: 0 residues processed: 551 average time/residue: 0.1304 time to fit residues: 97.5405 Evaluate side-chains 509 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 509 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 109 optimal weight: 0.7980 chunk 141 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 73 optimal weight: 0.1980 chunk 158 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 97 GLN ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 ASN A 518 GLN A 625 ASN ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 455 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 = 0.4089 r_free = 0.4089 target = 0.140110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.112559 restraints weight = 30625.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.117164 restraints weight = 18935.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.120587 restraints weight = 13172.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.123123 restraints weight = 9764.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.125024 restraints weight = 7598.566| |-----------------------------------------------------------------------------| r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13534 Z= 0.200 Angle : 0.729 16.368 18272 Z= 0.365 Chirality : 0.045 0.184 2014 Planarity : 0.005 0.093 2372 Dihedral : 5.688 23.791 1806 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.34 % Allowed : 5.10 % Favored : 94.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.35 (0.19), residues: 1610 helix: -1.40 (0.16), residues: 836 sheet: -3.22 (0.51), residues: 72 loop : -1.39 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 539 TYR 0.025 0.002 TYR A 717 PHE 0.027 0.002 PHE C 633 TRP 0.013 0.002 TRP A 328 HIS 0.003 0.001 HIS A 531 Details of bonding type rmsd covalent geometry : bond 0.00382 (13522) covalent geometry : angle 0.68884 (18260) hydrogen bonds : bond 0.04620 ( 502) hydrogen bonds : angle 5.51731 ( 1392) metal coordination : bond 0.01014 ( 12) metal coordination : angle 9.28830 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 530 time to evaluate : 0.532 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 18 LYS cc_start: 0.7553 (mmtm) cc_final: 0.7010 (mmmm) REVERT: B 42 GLN cc_start: 0.8470 (mt0) cc_final: 0.8203 (mt0) REVERT: B 65 ASN cc_start: 0.8514 (m-40) cc_final: 0.8249 (m-40) REVERT: B 73 CYS cc_start: 0.7604 (m) cc_final: 0.6856 (m) REVERT: B 77 TYR cc_start: 0.8394 (m-80) cc_final: 0.7705 (m-80) REVERT: B 82 GLU cc_start: 0.8709 (tt0) cc_final: 0.8226 (tt0) REVERT: B 88 TYR cc_start: 0.7277 (p90) cc_final: 0.6834 (p90) REVERT: B 108 ILE cc_start: 0.8100 (mt) cc_final: 0.7698 (tt) REVERT: B 114 GLN cc_start: 0.7882 (mp10) cc_final: 0.7484 (mp10) REVERT: B 132 PHE cc_start: 0.7442 (m-80) cc_final: 0.6703 (m-80) REVERT: B 134 ASN cc_start: 0.7951 (t0) cc_final: 0.7227 (t0) REVERT: A 130 GLU cc_start: 0.8522 (pt0) cc_final: 0.7740 (pm20) REVERT: A 138 GLU cc_start: 0.8452 (mp0) cc_final: 0.7846 (mp0) REVERT: A 237 ASP cc_start: 0.8596 (m-30) cc_final: 0.8001 (t70) REVERT: A 287 PHE cc_start: 0.7183 (m-80) cc_final: 0.6906 (m-80) REVERT: A 291 MET cc_start: 0.8604 (ttt) cc_final: 0.8034 (ttp) REVERT: A 294 ARG cc_start: 0.8580 (mpt-90) cc_final: 0.8378 (mpt-90) REVERT: A 304 MET cc_start: 0.5135 (tpt) cc_final: 0.4251 (tpt) REVERT: A 337 ARG cc_start: 0.8088 (ttm170) cc_final: 0.7654 (ttp80) REVERT: A 338 ARG cc_start: 0.7870 (mtp85) cc_final: 0.7502 (mtp180) REVERT: A 344 GLN cc_start: 0.8388 (tp-100) cc_final: 0.7322 (tp-100) REVERT: A 361 LEU cc_start: 0.7438 (tp) cc_final: 0.7233 (tp) REVERT: A 376 LYS cc_start: 0.8715 (tttt) cc_final: 0.8217 (tppt) REVERT: A 392 HIS cc_start: 0.8200 (m90) cc_final: 0.7730 (m90) REVERT: A 406 GLU cc_start: 0.8216 (tp30) cc_final: 0.7032 (tp30) REVERT: A 407 LEU cc_start: 0.8893 (mt) cc_final: 0.8539 (pp) REVERT: A 409 LEU cc_start: 0.8626 (tp) cc_final: 0.8054 (pp) REVERT: A 410 GLN cc_start: 0.8963 (mm-40) cc_final: 0.8052 (mm-40) REVERT: A 447 GLU cc_start: 0.8163 (mp0) cc_final: 0.7586 (tp30) REVERT: A 449 PHE cc_start: 0.7427 (m-10) cc_final: 0.6854 (m-10) REVERT: A 450 ILE cc_start: 0.8019 (mt) cc_final: 0.7292 (mt) REVERT: A 455 ASN cc_start: 0.7931 (m-40) cc_final: 0.7721 (m-40) REVERT: A 458 LEU cc_start: 0.8314 (tp) cc_final: 0.8063 (tp) REVERT: A 463 ASP cc_start: 0.8229 (m-30) cc_final: 0.7923 (m-30) REVERT: A 464 TYR cc_start: 0.7820 (t80) cc_final: 0.7142 (t80) REVERT: A 477 PHE cc_start: 0.8167 (m-80) cc_final: 0.7834 (m-80) REVERT: A 478 MET cc_start: 0.8198 (mtp) cc_final: 0.7356 (mtp) REVERT: A 482 PHE cc_start: 0.8053 (p90) cc_final: 0.7630 (p90) REVERT: A 499 ILE cc_start: 0.7908 (tp) cc_final: 0.7600 (tp) REVERT: A 501 MET cc_start: 0.8310 (mtt) cc_final: 0.7710 (ptp) REVERT: A 504 GLU cc_start: 0.8335 (mm-30) cc_final: 0.7778 (mm-30) REVERT: A 505 ARG cc_start: 0.8750 (mtt90) cc_final: 0.8346 (mtt90) REVERT: A 507 ILE cc_start: 0.8674 (mt) cc_final: 0.8206 (mp) REVERT: A 522 TYR cc_start: 0.8278 (m-80) cc_final: 0.7815 (m-80) REVERT: A 534 ASP cc_start: 0.8078 (m-30) cc_final: 0.7832 (m-30) REVERT: A 535 ASP cc_start: 0.7760 (t0) cc_final: 0.7426 (t0) REVERT: A 539 ARG cc_start: 0.8239 (ttm110) cc_final: 0.7795 (ptm160) REVERT: A 542 MET cc_start: 0.8513 (ptt) cc_final: 0.8036 (tmm) REVERT: A 543 ILE cc_start: 0.8981 (mt) cc_final: 0.8306 (mt) REVERT: A 545 MET cc_start: 0.7858 (mtm) cc_final: 0.7235 (mtm) REVERT: A 550 ASP cc_start: 0.7960 (p0) cc_final: 0.7568 (p0) REVERT: A 553 LYS cc_start: 0.8540 (mtmt) cc_final: 0.8261 (mtpp) REVERT: A 573 GLU cc_start: 0.8116 (pp20) cc_final: 0.7683 (pp20) REVERT: A 576 GLN cc_start: 0.8496 (tp-100) cc_final: 0.7788 (tp-100) REVERT: A 577 LEU cc_start: 0.8944 (mt) cc_final: 0.8594 (mt) REVERT: A 587 ILE cc_start: 0.7920 (tp) cc_final: 0.7719 (tp) REVERT: A 589 MET cc_start: 0.6260 (mtt) cc_final: 0.4457 (mtt) REVERT: A 593 ASP cc_start: 0.8246 (t0) cc_final: 0.7858 (t0) REVERT: A 617 ILE cc_start: 0.8438 (mm) cc_final: 0.7985 (mm) REVERT: A 635 MET cc_start: 0.8309 (mpp) cc_final: 0.7539 (mpp) REVERT: A 640 LYS cc_start: 0.7733 (mtpp) cc_final: 0.7255 (ttmm) REVERT: A 641 LEU cc_start: 0.8592 (mt) cc_final: 0.8240 (mm) REVERT: A 642 MET cc_start: 0.8217 (mmp) cc_final: 0.7871 (mmp) REVERT: A 651 LEU cc_start: 0.8413 (mt) cc_final: 0.8128 (mt) REVERT: A 658 LEU cc_start: 0.8274 (tp) cc_final: 0.8019 (tp) REVERT: A 659 TYR cc_start: 0.8605 (t80) cc_final: 0.7972 (t80) REVERT: A 663 LYS cc_start: 0.7800 (ptmm) cc_final: 0.7528 (mmtm) REVERT: A 707 ASN cc_start: 0.8363 (p0) cc_final: 0.8057 (m-40) REVERT: A 711 LYS cc_start: 0.9273 (mmtt) cc_final: 0.8931 (mmtm) REVERT: A 716 LEU cc_start: 0.8739 (mt) cc_final: 0.8515 (mt) REVERT: A 720 TYR cc_start: 0.7818 (t80) cc_final: 0.7099 (t80) REVERT: A 723 ASN cc_start: 0.6884 (m-40) cc_final: 0.6216 (m-40) REVERT: A 727 GLU cc_start: 0.8108 (pt0) cc_final: 0.7824 (pm20) REVERT: A 730 PHE cc_start: 0.8219 (t80) cc_final: 0.7994 (t80) REVERT: A 734 ARG cc_start: 0.8603 (ttt-90) cc_final: 0.7737 (ttm-80) REVERT: A 743 GLU cc_start: 0.8472 (mm-30) cc_final: 0.7990 (mm-30) REVERT: A 753 GLU cc_start: 0.8735 (mp0) cc_final: 0.8406 (mp0) REVERT: A 756 GLU cc_start: 0.7403 (tp30) cc_final: 0.7057 (tp30) REVERT: A 792 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8275 (mm-30) REVERT: A 805 PHE cc_start: 0.8697 (t80) cc_final: 0.8290 (t80) REVERT: A 806 LEU cc_start: 0.8221 (mt) cc_final: 0.7892 (mt) REVERT: A 822 LYS cc_start: 0.8423 (mptt) cc_final: 0.8222 (mmtt) REVERT: A 862 LEU cc_start: 0.8607 (tt) cc_final: 0.8311 (mt) REVERT: D 22 LEU cc_start: 0.8164 (mm) cc_final: 0.7809 (mm) REVERT: D 42 GLN cc_start: 0.8485 (mt0) cc_final: 0.8242 (mt0) REVERT: D 65 ASN cc_start: 0.8567 (m-40) cc_final: 0.8265 (m-40) REVERT: D 73 CYS cc_start: 0.7391 (m) cc_final: 0.6743 (m) REVERT: D 88 TYR cc_start: 0.7265 (p90) cc_final: 0.6998 (p90) REVERT: D 114 GLN cc_start: 0.7894 (mp10) cc_final: 0.7402 (mp10) REVERT: D 124 ARG cc_start: 0.8746 (ttt-90) cc_final: 0.8330 (ttt-90) REVERT: D 132 PHE cc_start: 0.7495 (m-80) cc_final: 0.6770 (m-80) REVERT: D 134 ASN cc_start: 0.7812 (t0) cc_final: 0.7439 (t0) REVERT: D 138 ARG cc_start: 0.8100 (ptt-90) cc_final: 0.6919 (ptt-90) REVERT: D 139 TRP cc_start: 0.7331 (m100) cc_final: 0.7066 (m100) REVERT: C 130 GLU cc_start: 0.8451 (pt0) cc_final: 0.8117 (pt0) REVERT: C 138 GLU cc_start: 0.8508 (mp0) cc_final: 0.7945 (mp0) REVERT: C 141 ARG cc_start: 0.7494 (tmm-80) cc_final: 0.7206 (ttp80) REVERT: C 237 ASP cc_start: 0.8091 (m-30) cc_final: 0.7831 (t0) REVERT: C 241 ARG cc_start: 0.8779 (mtm-85) cc_final: 0.8525 (mtm-85) REVERT: C 270 ASP cc_start: 0.7452 (t0) cc_final: 0.7214 (t0) REVERT: C 287 PHE cc_start: 0.7383 (m-80) cc_final: 0.7126 (m-80) REVERT: C 288 ILE cc_start: 0.8764 (tt) cc_final: 0.8315 (tt) REVERT: C 291 MET cc_start: 0.8503 (ttt) cc_final: 0.7643 (ttt) REVERT: C 292 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8136 (mm-30) REVERT: C 294 ARG cc_start: 0.8544 (mpt-90) cc_final: 0.8330 (mpt-90) REVERT: C 321 GLN cc_start: 0.8393 (mt0) cc_final: 0.8097 (mm-40) REVERT: C 328 TRP cc_start: 0.7474 (m-10) cc_final: 0.7151 (m-10) REVERT: C 332 ASN cc_start: 0.7597 (t0) cc_final: 0.6871 (t0) REVERT: C 337 ARG cc_start: 0.8209 (ttm170) cc_final: 0.7865 (tmm-80) REVERT: C 349 TYR cc_start: 0.7924 (t80) cc_final: 0.7606 (t80) REVERT: C 361 LEU cc_start: 0.7317 (tp) cc_final: 0.6857 (tp) REVERT: C 376 LYS cc_start: 0.8605 (ttpt) cc_final: 0.7577 (tttt) REVERT: C 380 TYR cc_start: 0.8697 (m-10) cc_final: 0.7957 (m-10) REVERT: C 382 ASN cc_start: 0.8549 (m-40) cc_final: 0.8317 (m110) REVERT: C 392 HIS cc_start: 0.8355 (m170) cc_final: 0.7869 (m-70) REVERT: C 394 GLU cc_start: 0.5919 (mm-30) cc_final: 0.4222 (mm-30) REVERT: C 406 GLU cc_start: 0.8106 (tt0) cc_final: 0.7273 (tt0) REVERT: C 407 LEU cc_start: 0.8820 (mt) cc_final: 0.8432 (pp) REVERT: C 408 THR cc_start: 0.8565 (m) cc_final: 0.7971 (m) REVERT: C 409 LEU cc_start: 0.8693 (tp) cc_final: 0.8106 (pp) REVERT: C 410 GLN cc_start: 0.8997 (mm-40) cc_final: 0.7771 (mm-40) REVERT: C 411 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7254 (mt-10) REVERT: C 447 GLU cc_start: 0.8114 (mp0) cc_final: 0.7467 (tp30) REVERT: C 449 PHE cc_start: 0.7706 (m-10) cc_final: 0.7202 (m-10) REVERT: C 450 ILE cc_start: 0.8034 (mt) cc_final: 0.7661 (mt) REVERT: C 478 MET cc_start: 0.7884 (mtp) cc_final: 0.7512 (mtp) REVERT: C 482 PHE cc_start: 0.8085 (p90) cc_final: 0.7676 (p90) REVERT: C 495 TYR cc_start: 0.7696 (m-10) cc_final: 0.7450 (m-10) REVERT: C 497 ASN cc_start: 0.8015 (m-40) cc_final: 0.7786 (m-40) REVERT: C 499 ILE cc_start: 0.8118 (tp) cc_final: 0.7710 (tp) REVERT: C 501 MET cc_start: 0.8239 (mtt) cc_final: 0.7929 (mtt) REVERT: C 502 TYR cc_start: 0.7637 (m-10) cc_final: 0.6759 (m-10) REVERT: C 505 ARG cc_start: 0.8762 (mtt90) cc_final: 0.8248 (mtt90) REVERT: C 506 ARG cc_start: 0.8445 (mtt90) cc_final: 0.7832 (mtt-85) REVERT: C 507 ILE cc_start: 0.8644 (mt) cc_final: 0.8401 (mp) REVERT: C 522 TYR cc_start: 0.8231 (m-80) cc_final: 0.7706 (m-80) REVERT: C 530 ASP cc_start: 0.8020 (p0) cc_final: 0.7748 (p0) REVERT: C 533 ILE cc_start: 0.8636 (mp) cc_final: 0.8389 (mp) REVERT: C 542 MET cc_start: 0.8251 (tpp) cc_final: 0.7575 (tpp) REVERT: C 543 ILE cc_start: 0.8879 (mt) cc_final: 0.8617 (mt) REVERT: C 545 MET cc_start: 0.7955 (mtm) cc_final: 0.7319 (mtm) REVERT: C 551 LEU cc_start: 0.8886 (mp) cc_final: 0.8595 (mp) REVERT: C 553 LYS cc_start: 0.8444 (mtmt) cc_final: 0.8141 (mtpp) REVERT: C 555 LEU cc_start: 0.8582 (tp) cc_final: 0.8334 (tp) REVERT: C 576 GLN cc_start: 0.7853 (tm-30) cc_final: 0.7398 (tm-30) REVERT: C 577 LEU cc_start: 0.8724 (mt) cc_final: 0.8433 (mt) REVERT: C 587 ILE cc_start: 0.8417 (tp) cc_final: 0.8135 (tp) REVERT: C 589 MET cc_start: 0.6803 (mtp) cc_final: 0.6406 (mtp) REVERT: C 593 ASP cc_start: 0.7877 (t70) cc_final: 0.7601 (t70) REVERT: C 619 LEU cc_start: 0.8835 (tp) cc_final: 0.8562 (tp) REVERT: C 621 LEU cc_start: 0.8174 (mm) cc_final: 0.7743 (mm) REVERT: C 625 ASN cc_start: 0.8450 (m110) cc_final: 0.8135 (m-40) REVERT: C 626 ASN cc_start: 0.7937 (m110) cc_final: 0.7701 (m110) REVERT: C 635 MET cc_start: 0.8170 (mpp) cc_final: 0.7457 (mpp) REVERT: C 640 LYS cc_start: 0.7798 (mtpp) cc_final: 0.7278 (ttmm) REVERT: C 641 LEU cc_start: 0.8564 (mt) cc_final: 0.7986 (pp) REVERT: C 648 PHE cc_start: 0.8750 (p90) cc_final: 0.8442 (p90) REVERT: C 658 LEU cc_start: 0.8549 (tp) cc_final: 0.8092 (tp) REVERT: C 661 SER cc_start: 0.8510 (m) cc_final: 0.8229 (p) REVERT: C 663 LYS cc_start: 0.8363 (ptmm) cc_final: 0.7254 (mmtt) REVERT: C 664 ASP cc_start: 0.8062 (m-30) cc_final: 0.6470 (p0) REVERT: C 668 TYR cc_start: 0.8293 (t80) cc_final: 0.8052 (t80) REVERT: C 682 ILE cc_start: 0.8060 (tp) cc_final: 0.7734 (tp) REVERT: C 711 LYS cc_start: 0.9243 (mmtt) cc_final: 0.8726 (mmtm) REVERT: C 712 GLU cc_start: 0.8741 (tt0) cc_final: 0.8172 (tt0) REVERT: C 717 TYR cc_start: 0.8677 (t80) cc_final: 0.8264 (t80) REVERT: C 719 ASP cc_start: 0.8239 (m-30) cc_final: 0.7936 (m-30) REVERT: C 720 TYR cc_start: 0.7877 (t80) cc_final: 0.7222 (t80) REVERT: C 723 ASN cc_start: 0.6720 (m-40) cc_final: 0.6518 (m110) REVERT: C 735 ARG cc_start: 0.8240 (ttm-80) cc_final: 0.7920 (ttm-80) REVERT: C 738 HIS cc_start: 0.8159 (t-90) cc_final: 0.7870 (t-90) REVERT: C 743 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8171 (mm-30) REVERT: C 748 TYR cc_start: 0.7523 (t80) cc_final: 0.6934 (t80) REVERT: C 751 ARG cc_start: 0.7190 (mmm-85) cc_final: 0.6885 (mmm-85) REVERT: C 753 GLU cc_start: 0.8679 (mp0) cc_final: 0.8451 (mp0) REVERT: C 789 GLU cc_start: 0.8133 (pt0) cc_final: 0.7758 (pm20) REVERT: C 791 TRP cc_start: 0.7844 (t60) cc_final: 0.7475 (t60) REVERT: C 805 PHE cc_start: 0.8660 (t80) cc_final: 0.8366 (t80) REVERT: C 855 LYS cc_start: 0.8809 (tttt) cc_final: 0.8278 (tppt) outliers start: 5 outliers final: 2 residues processed: 533 average time/residue: 0.1297 time to fit residues: 93.9764 Evaluate side-chains 505 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 503 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 57 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 148 optimal weight: 5.9990 chunk 157 optimal weight: 0.9980 chunk 16 optimal weight: 0.0370 chunk 30 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 146 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- 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 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 123 GLN ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 625 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.142715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.114739 restraints weight = 29712.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.119336 restraints weight = 18348.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.122868 restraints weight = 12741.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.125454 restraints weight = 9382.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.127399 restraints weight = 7283.738| |-----------------------------------------------------------------------------| r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.4769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13534 Z= 0.133 Angle : 0.630 10.408 18272 Z= 0.319 Chirality : 0.042 0.147 2014 Planarity : 0.004 0.066 2372 Dihedral : 5.228 21.461 1806 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.62 (0.20), residues: 1610 helix: -0.75 (0.17), residues: 808 sheet: -2.92 (0.55), residues: 72 loop : -1.10 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 84 TYR 0.017 0.001 TYR C 717 PHE 0.031 0.001 PHE A 790 TRP 0.024 0.003 TRP B 139 HIS 0.004 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00272 (13522) covalent geometry : angle 0.61292 (18260) hydrogen bonds : bond 0.03937 ( 502) hydrogen bonds : angle 5.13150 ( 1392) metal coordination : bond 0.00755 ( 12) metal coordination : angle 5.73809 ( 12) *********************** 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 538 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 538 time to evaluate : 0.319 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: 0.7273 (mmtm) cc_final: 0.6952 (mmmm) REVERT: B 42 GLN cc_start: 0.8374 (mt0) cc_final: 0.8094 (mt0) REVERT: B 49 VAL cc_start: 0.7065 (t) cc_final: 0.6763 (t) REVERT: B 65 ASN cc_start: 0.8433 (m-40) cc_final: 0.8043 (m-40) REVERT: B 73 CYS cc_start: 0.7242 (m) cc_final: 0.6563 (m) REVERT: B 77 TYR cc_start: 0.8359 (m-80) cc_final: 0.7683 (m-80) REVERT: B 82 GLU cc_start: 0.8651 (tt0) cc_final: 0.8162 (tt0) REVERT: B 88 TYR cc_start: 0.7189 (p90) cc_final: 0.6856 (p90) REVERT: B 108 ILE cc_start: 0.8091 (mt) cc_final: 0.7693 (tt) REVERT: B 114 GLN cc_start: 0.7803 (mp10) cc_final: 0.7594 (mp10) REVERT: B 132 PHE cc_start: 0.7525 (m-80) cc_final: 0.6899 (m-80) REVERT: B 134 ASN cc_start: 0.7956 (t0) cc_final: 0.7727 (t0) REVERT: A 130 GLU cc_start: 0.8521 (pt0) cc_final: 0.7690 (pm20) REVERT: A 237 ASP cc_start: 0.8462 (m-30) cc_final: 0.7827 (t0) REVERT: A 283 TYR cc_start: 0.7824 (t80) cc_final: 0.7428 (t80) REVERT: A 287 PHE cc_start: 0.7229 (m-80) cc_final: 0.7005 (m-80) REVERT: A 291 MET cc_start: 0.8489 (ttt) cc_final: 0.7943 (ttp) REVERT: A 294 ARG cc_start: 0.8497 (mpt-90) cc_final: 0.8294 (mpt-90) REVERT: A 297 HIS cc_start: 0.7903 (t70) cc_final: 0.7616 (t70) REVERT: A 304 MET cc_start: 0.4926 (tpt) cc_final: 0.4230 (tpt) REVERT: A 332 ASN cc_start: 0.7632 (t0) cc_final: 0.7023 (t0) REVERT: A 337 ARG cc_start: 0.8103 (ttm170) cc_final: 0.7576 (ttp80) REVERT: A 344 GLN cc_start: 0.8392 (tp-100) cc_final: 0.7315 (tp-100) REVERT: A 347 ILE cc_start: 0.7466 (mt) cc_final: 0.7138 (mm) REVERT: A 350 LYS cc_start: 0.7602 (mttm) cc_final: 0.7244 (mttt) REVERT: A 392 HIS cc_start: 0.8264 (m90) cc_final: 0.7783 (m90) REVERT: A 395 GLU cc_start: 0.6500 (tm-30) cc_final: 0.6298 (tm-30) REVERT: A 403 GLU cc_start: 0.7253 (pm20) cc_final: 0.6428 (pm20) REVERT: A 406 GLU cc_start: 0.8448 (tp30) cc_final: 0.7670 (tp30) REVERT: A 408 THR cc_start: 0.8583 (m) cc_final: 0.8162 (p) REVERT: A 410 GLN cc_start: 0.9019 (mm-40) cc_final: 0.8628 (mm-40) REVERT: A 424 ARG cc_start: 0.7644 (mmm-85) cc_final: 0.7408 (tpt-90) REVERT: A 447 GLU cc_start: 0.8140 (mp0) cc_final: 0.7562 (tp30) REVERT: A 449 PHE cc_start: 0.7321 (m-10) cc_final: 0.6767 (m-10) REVERT: A 450 ILE cc_start: 0.8008 (mt) cc_final: 0.7328 (mt) REVERT: A 458 LEU cc_start: 0.8378 (tp) cc_final: 0.8000 (tt) REVERT: A 459 GLU cc_start: 0.7018 (mp0) cc_final: 0.6722 (mp0) REVERT: A 477 PHE cc_start: 0.8021 (m-80) cc_final: 0.7607 (m-80) REVERT: A 478 MET cc_start: 0.8127 (mtp) cc_final: 0.7344 (mtp) REVERT: A 482 PHE cc_start: 0.7969 (p90) cc_final: 0.7651 (p90) REVERT: A 491 LEU cc_start: 0.8351 (mt) cc_final: 0.8125 (mt) REVERT: A 497 ASN cc_start: 0.8073 (m-40) cc_final: 0.7756 (m-40) REVERT: A 499 ILE cc_start: 0.7906 (tp) cc_final: 0.7564 (tp) REVERT: A 502 TYR cc_start: 0.7486 (m-10) cc_final: 0.7241 (m-10) REVERT: A 504 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7672 (mm-30) REVERT: A 505 ARG cc_start: 0.8788 (mtt90) cc_final: 0.8313 (mtt90) REVERT: A 507 ILE cc_start: 0.8721 (mt) cc_final: 0.8237 (mp) REVERT: A 522 TYR cc_start: 0.8159 (m-80) cc_final: 0.7646 (m-80) REVERT: A 532 ILE cc_start: 0.8420 (pt) cc_final: 0.7661 (pt) REVERT: A 534 ASP cc_start: 0.8044 (m-30) cc_final: 0.7825 (m-30) REVERT: A 535 ASP cc_start: 0.7633 (t0) cc_final: 0.7358 (t0) REVERT: A 540 LEU cc_start: 0.8830 (mm) cc_final: 0.8548 (mm) REVERT: A 542 MET cc_start: 0.8424 (ptt) cc_final: 0.7812 (tmm) REVERT: A 545 MET cc_start: 0.7795 (mtm) cc_final: 0.7126 (mtm) REVERT: A 550 ASP cc_start: 0.7841 (p0) cc_final: 0.7482 (p0) REVERT: A 553 LYS cc_start: 0.8517 (mtmt) cc_final: 0.8284 (mtpp) REVERT: A 554 GLN cc_start: 0.8200 (tp40) cc_final: 0.7962 (mm-40) REVERT: A 577 LEU cc_start: 0.8875 (mt) cc_final: 0.8610 (mt) REVERT: A 579 VAL cc_start: 0.8539 (m) cc_final: 0.8243 (p) REVERT: A 581 GLU cc_start: 0.8369 (tt0) cc_final: 0.8163 (pt0) REVERT: A 593 ASP cc_start: 0.8142 (t0) cc_final: 0.7781 (t70) REVERT: A 603 PRO cc_start: 0.7226 (Cg_endo) cc_final: 0.6896 (Cg_exo) REVERT: A 621 LEU cc_start: 0.8245 (mt) cc_final: 0.8030 (mt) REVERT: A 635 MET cc_start: 0.8156 (mpp) cc_final: 0.7453 (mpp) REVERT: A 641 LEU cc_start: 0.8599 (mt) cc_final: 0.8205 (mm) REVERT: A 642 MET cc_start: 0.8064 (mmp) cc_final: 0.7741 (mmp) REVERT: A 649 ARG cc_start: 0.8779 (ttm170) cc_final: 0.8578 (ttm170) REVERT: A 651 LEU cc_start: 0.8440 (mt) cc_final: 0.8168 (mt) REVERT: A 658 LEU cc_start: 0.8286 (tp) cc_final: 0.8018 (tp) REVERT: A 660 GLN cc_start: 0.8622 (mm-40) cc_final: 0.8382 (mm-40) REVERT: A 667 GLU cc_start: 0.8337 (pp20) cc_final: 0.8095 (pp20) REVERT: A 676 MET cc_start: 0.6869 (tmm) cc_final: 0.6586 (tmm) REVERT: A 682 ILE cc_start: 0.8402 (tp) cc_final: 0.8042 (tp) REVERT: A 707 ASN cc_start: 0.8183 (p0) cc_final: 0.7965 (m-40) REVERT: A 711 LYS cc_start: 0.9282 (mmtt) cc_final: 0.8834 (mmtm) REVERT: A 712 GLU cc_start: 0.8659 (tt0) cc_final: 0.8097 (tt0) REVERT: A 716 LEU cc_start: 0.8763 (mt) cc_final: 0.8488 (mp) REVERT: A 717 TYR cc_start: 0.8785 (t80) cc_final: 0.8272 (t80) REVERT: A 720 TYR cc_start: 0.7740 (t80) cc_final: 0.7061 (t80) REVERT: A 728 LYS cc_start: 0.8305 (ttpt) cc_final: 0.7721 (ptmm) REVERT: A 730 PHE cc_start: 0.8227 (t80) cc_final: 0.7920 (t80) REVERT: A 734 ARG cc_start: 0.8549 (ttt-90) cc_final: 0.7512 (ttm-80) REVERT: A 743 GLU cc_start: 0.8434 (mm-30) cc_final: 0.7760 (mp0) REVERT: A 750 PHE cc_start: 0.8179 (m-80) cc_final: 0.7948 (m-80) REVERT: A 753 GLU cc_start: 0.8645 (mp0) cc_final: 0.8272 (mp0) REVERT: A 792 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8288 (mm-30) REVERT: A 822 LYS cc_start: 0.8531 (mptt) cc_final: 0.8208 (mmtm) REVERT: D 22 LEU cc_start: 0.8149 (mm) cc_final: 0.7832 (mm) REVERT: D 42 GLN cc_start: 0.8418 (mt0) cc_final: 0.8183 (mt0) REVERT: D 65 ASN cc_start: 0.8504 (m-40) cc_final: 0.8117 (m-40) REVERT: D 73 CYS cc_start: 0.7426 (m) cc_final: 0.6854 (m) REVERT: D 79 LYS cc_start: 0.8421 (tppp) cc_final: 0.7031 (tppp) REVERT: D 82 GLU cc_start: 0.8733 (tt0) cc_final: 0.7853 (tt0) REVERT: D 88 TYR cc_start: 0.7068 (p90) cc_final: 0.6854 (p90) REVERT: D 94 THR cc_start: 0.7995 (m) cc_final: 0.7118 (m) REVERT: D 98 GLN cc_start: 0.8725 (mp10) cc_final: 0.8229 (mp10) REVERT: D 114 GLN cc_start: 0.7831 (mp10) cc_final: 0.7629 (mp10) REVERT: D 124 ARG cc_start: 0.8655 (ttt-90) cc_final: 0.8275 (ttt-90) REVERT: D 132 PHE cc_start: 0.7596 (m-80) cc_final: 0.7017 (m-80) REVERT: D 134 ASN cc_start: 0.7760 (t0) cc_final: 0.6924 (t0) REVERT: D 138 ARG cc_start: 0.7998 (ptt-90) cc_final: 0.7317 (ptt-90) REVERT: C 130 GLU cc_start: 0.8435 (pt0) cc_final: 0.7746 (pm20) REVERT: C 237 ASP cc_start: 0.7902 (m-30) cc_final: 0.7686 (t0) REVERT: C 241 ARG cc_start: 0.8698 (mtm-85) cc_final: 0.8443 (mtm-85) REVERT: C 283 TYR cc_start: 0.7962 (t80) cc_final: 0.7262 (t80) REVERT: C 288 ILE cc_start: 0.8782 (tt) cc_final: 0.7147 (tt) REVERT: C 291 MET cc_start: 0.8523 (ttt) cc_final: 0.8044 (ptt) REVERT: C 292 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7785 (mm-30) REVERT: C 304 MET cc_start: 0.5352 (tpt) cc_final: 0.4997 (tpt) REVERT: C 321 GLN cc_start: 0.8366 (mt0) cc_final: 0.8115 (mm-40) REVERT: C 326 ARG cc_start: 0.8132 (mtm-85) cc_final: 0.7909 (mtm-85) REVERT: C 330 LYS cc_start: 0.8695 (mmmt) cc_final: 0.8295 (mmtm) REVERT: C 332 ASN cc_start: 0.7433 (t0) cc_final: 0.7088 (t0) REVERT: C 337 ARG cc_start: 0.8194 (ttm170) cc_final: 0.7739 (tmm-80) REVERT: C 344 GLN cc_start: 0.8367 (tp-100) cc_final: 0.7381 (tp-100) REVERT: C 349 TYR cc_start: 0.7933 (t80) cc_final: 0.7645 (t80) REVERT: C 361 LEU cc_start: 0.7127 (tp) cc_final: 0.6644 (tp) REVERT: C 376 LYS cc_start: 0.8542 (ttpt) cc_final: 0.7785 (tppt) REVERT: C 382 ASN cc_start: 0.8458 (m-40) cc_final: 0.8129 (m110) REVERT: C 392 HIS cc_start: 0.8395 (m170) cc_final: 0.7994 (m-70) REVERT: C 397 ASP cc_start: 0.7610 (t70) cc_final: 0.7329 (t0) REVERT: C 398 GLU cc_start: 0.8024 (pp20) cc_final: 0.7695 (pp20) REVERT: C 406 GLU cc_start: 0.7856 (tt0) cc_final: 0.7524 (tt0) REVERT: C 407 LEU cc_start: 0.8825 (mt) cc_final: 0.8387 (pp) REVERT: C 408 THR cc_start: 0.8500 (m) cc_final: 0.7916 (m) REVERT: C 410 GLN cc_start: 0.9049 (mm-40) cc_final: 0.8116 (mm110) REVERT: C 411 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7279 (mt-10) REVERT: C 446 PHE cc_start: 0.7717 (m-80) cc_final: 0.7508 (m-80) REVERT: C 447 GLU cc_start: 0.8052 (mp0) cc_final: 0.7499 (tp30) REVERT: C 450 ILE cc_start: 0.8053 (mt) cc_final: 0.7463 (mt) REVERT: C 458 LEU cc_start: 0.8615 (tp) cc_final: 0.8363 (tp) REVERT: C 477 PHE cc_start: 0.7907 (m-80) cc_final: 0.7353 (m-80) REVERT: C 478 MET cc_start: 0.8074 (mtp) cc_final: 0.7444 (mtp) REVERT: C 482 PHE cc_start: 0.7950 (p90) cc_final: 0.7309 (p90) REVERT: C 493 LEU cc_start: 0.7884 (tp) cc_final: 0.7609 (tp) REVERT: C 495 TYR cc_start: 0.7597 (m-10) cc_final: 0.7386 (m-10) REVERT: C 497 ASN cc_start: 0.7887 (m-40) cc_final: 0.7572 (m-40) REVERT: C 499 ILE cc_start: 0.8093 (tp) cc_final: 0.7633 (tp) REVERT: C 501 MET cc_start: 0.8212 (mtt) cc_final: 0.7849 (mtt) REVERT: C 502 TYR cc_start: 0.7563 (m-10) cc_final: 0.7130 (m-10) REVERT: C 505 ARG cc_start: 0.8740 (mtt90) cc_final: 0.8195 (mtt90) REVERT: C 507 ILE cc_start: 0.8634 (mt) cc_final: 0.8360 (mp) REVERT: C 522 TYR cc_start: 0.8099 (m-80) cc_final: 0.7534 (m-80) REVERT: C 532 ILE cc_start: 0.8333 (pt) cc_final: 0.7910 (mm) REVERT: C 533 ILE cc_start: 0.8596 (mp) cc_final: 0.8162 (mp) REVERT: C 542 MET cc_start: 0.8182 (tpp) cc_final: 0.7481 (tpp) REVERT: C 545 MET cc_start: 0.7810 (mtm) cc_final: 0.7149 (mtm) REVERT: C 551 LEU cc_start: 0.8854 (mp) cc_final: 0.8547 (mp) REVERT: C 553 LYS cc_start: 0.8421 (mtmt) cc_final: 0.8116 (mtpp) REVERT: C 555 LEU cc_start: 0.8501 (tp) cc_final: 0.8092 (tp) REVERT: C 572 LYS cc_start: 0.8447 (mmtt) cc_final: 0.8123 (ttmm) REVERT: C 576 GLN cc_start: 0.7689 (tm-30) cc_final: 0.7199 (tm-30) REVERT: C 577 LEU cc_start: 0.8730 (mt) cc_final: 0.8354 (mt) REVERT: C 587 ILE cc_start: 0.8314 (tp) cc_final: 0.8027 (tp) REVERT: C 589 MET cc_start: 0.6647 (mtp) cc_final: 0.6276 (mtp) REVERT: C 593 ASP cc_start: 0.7856 (t70) cc_final: 0.7579 (t70) REVERT: C 617 ILE cc_start: 0.8585 (mm) cc_final: 0.8305 (mm) REVERT: C 619 LEU cc_start: 0.8796 (tp) cc_final: 0.8514 (tp) REVERT: C 621 LEU cc_start: 0.8176 (mm) cc_final: 0.7709 (mm) REVERT: C 625 ASN cc_start: 0.8450 (m-40) cc_final: 0.8083 (m110) REVERT: C 626 ASN cc_start: 0.7901 (m110) cc_final: 0.7646 (m110) REVERT: C 635 MET cc_start: 0.8107 (mpp) cc_final: 0.7369 (mpp) REVERT: C 640 LYS cc_start: 0.7863 (mtpp) cc_final: 0.7370 (mtpp) REVERT: C 641 LEU cc_start: 0.8597 (mt) cc_final: 0.8037 (pp) REVERT: C 658 LEU cc_start: 0.8494 (tp) cc_final: 0.8157 (tt) REVERT: C 659 TYR cc_start: 0.8713 (t80) cc_final: 0.8336 (t80) REVERT: C 663 LYS cc_start: 0.8228 (ptmm) cc_final: 0.7592 (mmtt) REVERT: C 667 GLU cc_start: 0.7951 (pp20) cc_final: 0.7672 (pp20) REVERT: C 682 ILE cc_start: 0.8124 (tp) cc_final: 0.7757 (tp) REVERT: C 711 LYS cc_start: 0.9286 (mmtt) cc_final: 0.8892 (mmtm) REVERT: C 712 GLU cc_start: 0.8647 (tt0) cc_final: 0.8054 (tt0) REVERT: C 717 TYR cc_start: 0.8893 (t80) cc_final: 0.8531 (t80) REVERT: C 720 TYR cc_start: 0.7868 (t80) cc_final: 0.7152 (t80) REVERT: C 724 LYS cc_start: 0.8241 (ptpp) cc_final: 0.7948 (pttp) REVERT: C 727 GLU cc_start: 0.8012 (pm20) cc_final: 0.7761 (pm20) REVERT: C 730 PHE cc_start: 0.8167 (t80) cc_final: 0.7558 (t80) REVERT: C 735 ARG cc_start: 0.8283 (ttm-80) cc_final: 0.8041 (ttm-80) REVERT: C 738 HIS cc_start: 0.8048 (t-90) cc_final: 0.7740 (t70) REVERT: C 743 GLU cc_start: 0.8421 (mm-30) cc_final: 0.7936 (mm-30) REVERT: C 748 TYR cc_start: 0.7465 (t80) cc_final: 0.6900 (t80) REVERT: C 753 GLU cc_start: 0.8639 (mp0) cc_final: 0.8351 (mp0) REVERT: C 754 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8042 (mt-10) REVERT: C 788 ARG cc_start: 0.8550 (ptt180) cc_final: 0.7828 (ttp-110) REVERT: C 791 TRP cc_start: 0.7660 (t60) cc_final: 0.7341 (t60) REVERT: C 801 GLN cc_start: 0.8316 (mp10) cc_final: 0.8056 (mp10) REVERT: C 805 PHE cc_start: 0.8560 (t80) cc_final: 0.8308 (t80) REVERT: C 807 GLN cc_start: 0.8555 (tt0) cc_final: 0.7830 (tt0) REVERT: C 822 LYS cc_start: 0.8578 (mmtt) cc_final: 0.8261 (mmtm) REVERT: C 855 LYS cc_start: 0.8849 (tttt) cc_final: 0.8177 (tptp) outliers start: 0 outliers final: 0 residues processed: 538 average time/residue: 0.1268 time to fit residues: 93.0601 Evaluate side-chains 509 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 509 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 71 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 137 optimal weight: 6.9990 chunk 150 optimal weight: 0.3980 chunk 153 optimal weight: 0.9980 chunk 104 optimal weight: 7.9990 chunk 84 optimal weight: 0.1980 chunk 27 optimal weight: 0.7980 chunk 154 optimal weight: 2.9990 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 ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 ASN ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 ASN ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4121 r_free = 0.4121 target = 0.142407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.114330 restraints weight = 29598.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.118930 restraints weight = 18246.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.122378 restraints weight = 12680.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.124991 restraints weight = 9432.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.126936 restraints weight = 7349.159| |-----------------------------------------------------------------------------| r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.5168 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= 0.126 Angle : 0.614 8.011 18272 Z= 0.310 Chirality : 0.043 0.146 2014 Planarity : 0.004 0.062 2372 Dihedral : 5.061 18.546 1806 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.07 % Allowed : 2.07 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.36 (0.20), residues: 1610 helix: -0.51 (0.18), residues: 786 sheet: -2.61 (0.59), residues: 72 loop : -1.02 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 141 TYR 0.018 0.001 TYR A 494 PHE 0.025 0.001 PHE C 790 TRP 0.040 0.004 TRP A 328 HIS 0.004 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00263 (13522) covalent geometry : angle 0.60311 (18260) hydrogen bonds : bond 0.03744 ( 502) hydrogen bonds : angle 5.07136 ( 1392) metal coordination : bond 0.00475 ( 12) metal coordination : angle 4.46103 ( 12) *********************** 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 535 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 534 time to evaluate : 0.528 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: 0.8167 (mm) cc_final: 0.7739 (mm) REVERT: B 42 GLN cc_start: 0.8118 (mt0) cc_final: 0.7905 (mt0) REVERT: B 59 ILE cc_start: 0.7625 (mm) cc_final: 0.7206 (mm) REVERT: B 65 ASN cc_start: 0.8335 (m-40) cc_final: 0.7976 (m-40) REVERT: B 73 CYS cc_start: 0.6859 (m) cc_final: 0.6422 (m) REVERT: B 77 TYR cc_start: 0.8191 (m-80) cc_final: 0.7635 (m-80) REVERT: B 82 GLU cc_start: 0.8695 (tt0) cc_final: 0.8284 (tt0) REVERT: B 88 TYR cc_start: 0.7116 (p90) cc_final: 0.6857 (p90) REVERT: B 108 ILE cc_start: 0.8099 (mt) cc_final: 0.7706 (tt) REVERT: B 114 GLN cc_start: 0.8010 (mp-120) cc_final: 0.7705 (mp10) REVERT: B 132 PHE cc_start: 0.7686 (m-80) cc_final: 0.7027 (m-80) REVERT: B 134 ASN cc_start: 0.7973 (t0) cc_final: 0.7711 (t0) REVERT: A 130 GLU cc_start: 0.8484 (pt0) cc_final: 0.7576 (pm20) REVERT: A 138 GLU cc_start: 0.8448 (mp0) cc_final: 0.7885 (mp0) REVERT: A 237 ASP cc_start: 0.8444 (m-30) cc_final: 0.7818 (t0) REVERT: A 283 TYR cc_start: 0.7664 (t80) cc_final: 0.7450 (t80) REVERT: A 287 PHE cc_start: 0.7237 (m-80) cc_final: 0.7034 (m-80) REVERT: A 291 MET cc_start: 0.8513 (ttt) cc_final: 0.7959 (ttp) REVERT: A 304 MET cc_start: 0.5025 (tpt) cc_final: 0.4321 (tpt) REVERT: A 332 ASN cc_start: 0.7623 (t0) cc_final: 0.7190 (t0) REVERT: A 337 ARG cc_start: 0.8114 (ttm170) cc_final: 0.7554 (ttp80) REVERT: A 338 ARG cc_start: 0.7943 (mtp85) cc_final: 0.7654 (mmm-85) REVERT: A 344 GLN cc_start: 0.8368 (tp-100) cc_final: 0.7281 (tp-100) REVERT: A 347 ILE cc_start: 0.7467 (mt) cc_final: 0.7165 (mm) REVERT: A 350 LYS cc_start: 0.7529 (mttm) cc_final: 0.7181 (tttp) REVERT: A 392 HIS cc_start: 0.8229 (m90) cc_final: 0.7761 (m90) REVERT: A 406 GLU cc_start: 0.8376 (tp30) cc_final: 0.8085 (mt-10) REVERT: A 424 ARG cc_start: 0.7794 (mmm-85) cc_final: 0.6877 (tpp80) REVERT: A 426 ASP cc_start: 0.8474 (t70) cc_final: 0.8260 (t0) REVERT: A 447 GLU cc_start: 0.8104 (mp0) cc_final: 0.7610 (tp30) REVERT: A 449 PHE cc_start: 0.7223 (m-10) cc_final: 0.6684 (m-10) REVERT: A 450 ILE cc_start: 0.8042 (mt) cc_final: 0.7202 (mt) REVERT: A 455 ASN cc_start: 0.7919 (m-40) cc_final: 0.7718 (m-40) REVERT: A 458 LEU cc_start: 0.8358 (tp) cc_final: 0.7961 (tt) REVERT: A 459 GLU cc_start: 0.7070 (mp0) cc_final: 0.6752 (mp0) REVERT: A 477 PHE cc_start: 0.8011 (m-80) cc_final: 0.7598 (m-80) REVERT: A 478 MET cc_start: 0.8127 (mtp) cc_final: 0.6805 (mtp) REVERT: A 482 PHE cc_start: 0.7997 (p90) cc_final: 0.7559 (p90) REVERT: A 499 ILE cc_start: 0.7937 (tp) cc_final: 0.7598 (tp) REVERT: A 501 MET cc_start: 0.8211 (mtt) cc_final: 0.7646 (mmm) REVERT: A 502 TYR cc_start: 0.7481 (m-10) cc_final: 0.7243 (m-10) REVERT: A 504 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7439 (mm-30) REVERT: A 505 ARG cc_start: 0.8790 (mtt90) cc_final: 0.8269 (mtt90) REVERT: A 507 ILE cc_start: 0.8698 (mt) cc_final: 0.8265 (mt) REVERT: A 522 TYR cc_start: 0.8180 (m-80) cc_final: 0.7726 (m-80) REVERT: A 532 ILE cc_start: 0.8585 (pt) cc_final: 0.7765 (pt) REVERT: A 535 ASP cc_start: 0.7493 (t0) cc_final: 0.7174 (t0) REVERT: A 539 ARG cc_start: 0.8384 (ptm160) cc_final: 0.7684 (ptm-80) REVERT: A 540 LEU cc_start: 0.8897 (mm) cc_final: 0.8671 (mm) REVERT: A 542 MET cc_start: 0.8253 (ptt) cc_final: 0.7684 (tmm) REVERT: A 545 MET cc_start: 0.7709 (mtm) cc_final: 0.7054 (mtm) REVERT: A 550 ASP cc_start: 0.7833 (p0) cc_final: 0.7462 (p0) REVERT: A 553 LYS cc_start: 0.8492 (mtmt) cc_final: 0.7874 (mtpp) REVERT: A 577 LEU cc_start: 0.8891 (mt) cc_final: 0.8594 (mt) REVERT: A 581 GLU cc_start: 0.8400 (tt0) cc_final: 0.8167 (pt0) REVERT: A 593 ASP cc_start: 0.8181 (t0) cc_final: 0.7828 (t70) REVERT: A 603 PRO cc_start: 0.7221 (Cg_endo) cc_final: 0.6901 (Cg_exo) REVERT: A 621 LEU cc_start: 0.8223 (mt) cc_final: 0.8017 (mt) REVERT: A 635 MET cc_start: 0.8083 (mpp) cc_final: 0.7351 (mpp) REVERT: A 641 LEU cc_start: 0.8625 (mt) cc_final: 0.8306 (mm) REVERT: A 642 MET cc_start: 0.8051 (mmp) cc_final: 0.7720 (mmp) REVERT: A 649 ARG cc_start: 0.8719 (ttm170) cc_final: 0.8404 (ttm170) REVERT: A 651 LEU cc_start: 0.8440 (mt) cc_final: 0.8132 (mt) REVERT: A 658 LEU cc_start: 0.8265 (tp) cc_final: 0.7972 (tp) REVERT: A 663 LYS cc_start: 0.8067 (ptmm) cc_final: 0.7611 (mmtm) REVERT: A 667 GLU cc_start: 0.8342 (pp20) cc_final: 0.8086 (pp20) REVERT: A 682 ILE cc_start: 0.8311 (tp) cc_final: 0.7902 (tp) REVERT: A 711 LYS cc_start: 0.9306 (mmtt) cc_final: 0.8977 (mmtm) REVERT: A 712 GLU cc_start: 0.8654 (tt0) cc_final: 0.8186 (tt0) REVERT: A 715 ASN cc_start: 0.8693 (m110) cc_final: 0.8472 (m110) REVERT: A 716 LEU cc_start: 0.8744 (mt) cc_final: 0.8490 (mp) REVERT: A 717 TYR cc_start: 0.8902 (t80) cc_final: 0.8278 (t80) REVERT: A 720 TYR cc_start: 0.7798 (t80) cc_final: 0.7232 (t80) REVERT: A 727 GLU cc_start: 0.7961 (pm20) cc_final: 0.7627 (pm20) REVERT: A 730 PHE cc_start: 0.8177 (t80) cc_final: 0.7902 (t80) REVERT: A 734 ARG cc_start: 0.8568 (ttt-90) cc_final: 0.8284 (ttt90) REVERT: A 738 HIS cc_start: 0.8222 (t70) cc_final: 0.7956 (t-170) REVERT: A 743 GLU cc_start: 0.8445 (mm-30) cc_final: 0.7767 (mp0) REVERT: A 748 TYR cc_start: 0.7294 (t80) cc_final: 0.6789 (t80) REVERT: A 753 GLU cc_start: 0.8640 (mp0) cc_final: 0.8292 (mp0) REVERT: A 756 GLU cc_start: 0.7186 (tp30) cc_final: 0.6858 (tp30) REVERT: A 792 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8166 (mm-30) REVERT: A 822 LYS cc_start: 0.8487 (mptt) cc_final: 0.8198 (mmtm) REVERT: D 22 LEU cc_start: 0.8121 (mm) cc_final: 0.7746 (mm) REVERT: D 42 GLN cc_start: 0.8409 (mt0) cc_final: 0.8172 (mt0) REVERT: D 65 ASN cc_start: 0.8388 (m-40) cc_final: 0.8002 (m-40) REVERT: D 73 CYS cc_start: 0.6867 (m) cc_final: 0.6476 (m) REVERT: D 79 LYS cc_start: 0.8332 (tppp) cc_final: 0.6959 (tppp) REVERT: D 82 GLU cc_start: 0.8720 (tt0) cc_final: 0.7865 (tt0) REVERT: D 88 TYR cc_start: 0.7015 (p90) cc_final: 0.6779 (p90) REVERT: D 94 THR cc_start: 0.7994 (m) cc_final: 0.7357 (p) REVERT: D 98 GLN cc_start: 0.8758 (mp10) cc_final: 0.8373 (mp10) REVERT: D 114 GLN cc_start: 0.7891 (mp10) cc_final: 0.7580 (mp10) REVERT: D 124 ARG cc_start: 0.8684 (ttt-90) cc_final: 0.8479 (ttt-90) REVERT: D 132 PHE cc_start: 0.7652 (m-80) cc_final: 0.6949 (m-80) REVERT: D 138 ARG cc_start: 0.8025 (ptt-90) cc_final: 0.7163 (ptt-90) REVERT: C 130 GLU cc_start: 0.8399 (pt0) cc_final: 0.7635 (pm20) REVERT: C 138 GLU cc_start: 0.8544 (mp0) cc_final: 0.8088 (mp0) REVERT: C 241 ARG cc_start: 0.8702 (mtm-85) cc_final: 0.8431 (mtm-85) REVERT: C 283 TYR cc_start: 0.7956 (t80) cc_final: 0.7469 (t80) REVERT: C 291 MET cc_start: 0.8515 (ttt) cc_final: 0.8216 (ptt) REVERT: C 304 MET cc_start: 0.5376 (tpt) cc_final: 0.5000 (tpt) REVERT: C 315 LYS cc_start: 0.8008 (mtmm) cc_final: 0.7505 (mtmm) REVERT: C 321 GLN cc_start: 0.8383 (mt0) cc_final: 0.8147 (mm-40) REVERT: C 330 LYS cc_start: 0.8684 (mmmt) cc_final: 0.8278 (mmtm) REVERT: C 332 ASN cc_start: 0.7432 (t0) cc_final: 0.7071 (t0) REVERT: C 337 ARG cc_start: 0.8224 (ttm170) cc_final: 0.7958 (tmm-80) REVERT: C 344 GLN cc_start: 0.8453 (tp-100) cc_final: 0.7524 (tp-100) REVERT: C 349 TYR cc_start: 0.7919 (t80) cc_final: 0.7617 (t80) REVERT: C 376 LYS cc_start: 0.8532 (ttpt) cc_final: 0.7817 (tppt) REVERT: C 382 ASN cc_start: 0.8449 (m-40) cc_final: 0.8142 (m110) REVERT: C 392 HIS cc_start: 0.8393 (m170) cc_final: 0.7992 (m-70) REVERT: C 407 LEU cc_start: 0.8827 (mt) cc_final: 0.8252 (pp) REVERT: C 408 THR cc_start: 0.8504 (m) cc_final: 0.7877 (m) REVERT: C 410 GLN cc_start: 0.9081 (mm-40) cc_final: 0.8183 (mm110) REVERT: C 411 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7239 (mt-10) REVERT: C 441 LYS cc_start: 0.9105 (tttm) cc_final: 0.8879 (tptp) REVERT: C 478 MET cc_start: 0.8085 (mtp) cc_final: 0.7441 (mtp) REVERT: C 482 PHE cc_start: 0.7953 (p90) cc_final: 0.7273 (p90) REVERT: C 495 TYR cc_start: 0.7610 (m-10) cc_final: 0.7399 (m-10) REVERT: C 499 ILE cc_start: 0.8082 (tp) cc_final: 0.7685 (tp) REVERT: C 501 MET cc_start: 0.8185 (mtt) cc_final: 0.7793 (mtt) REVERT: C 502 TYR cc_start: 0.7589 (m-10) cc_final: 0.6812 (m-10) REVERT: C 505 ARG cc_start: 0.8755 (mtt90) cc_final: 0.8203 (mtt90) REVERT: C 506 ARG cc_start: 0.8402 (mtt90) cc_final: 0.7754 (mtt-85) REVERT: C 522 TYR cc_start: 0.8068 (m-80) cc_final: 0.7415 (m-80) REVERT: C 532 ILE cc_start: 0.8368 (pt) cc_final: 0.7906 (mm) REVERT: C 541 GLU cc_start: 0.8108 (tt0) cc_final: 0.7139 (tt0) REVERT: C 542 MET cc_start: 0.8165 (tpp) cc_final: 0.7460 (tpp) REVERT: C 543 ILE cc_start: 0.8851 (mt) cc_final: 0.8610 (mt) REVERT: C 545 MET cc_start: 0.7807 (mtm) cc_final: 0.7260 (mtm) REVERT: C 551 LEU cc_start: 0.8845 (mp) cc_final: 0.8541 (mp) REVERT: C 553 LYS cc_start: 0.8479 (mtmt) cc_final: 0.8164 (mtpp) REVERT: C 555 LEU cc_start: 0.8487 (tp) cc_final: 0.8099 (tp) REVERT: C 576 GLN cc_start: 0.7703 (tm-30) cc_final: 0.7209 (tm-30) REVERT: C 577 LEU cc_start: 0.8694 (mt) cc_final: 0.8229 (mt) REVERT: C 581 GLU cc_start: 0.8152 (pp20) cc_final: 0.7838 (pp20) REVERT: C 587 ILE cc_start: 0.8263 (tp) cc_final: 0.7948 (tp) REVERT: C 589 MET cc_start: 0.6548 (mtp) cc_final: 0.6166 (mtp) REVERT: C 593 ASP cc_start: 0.7944 (t70) cc_final: 0.7700 (t0) REVERT: C 617 ILE cc_start: 0.8601 (mm) cc_final: 0.8307 (mm) REVERT: C 621 LEU cc_start: 0.8181 (mm) cc_final: 0.7686 (mm) REVERT: C 625 ASN cc_start: 0.8437 (m-40) cc_final: 0.8105 (m-40) REVERT: C 635 MET cc_start: 0.8130 (mpp) cc_final: 0.7422 (mpp) REVERT: C 640 LYS cc_start: 0.7829 (mtpp) cc_final: 0.7403 (mtpp) REVERT: C 641 LEU cc_start: 0.8584 (mt) cc_final: 0.8167 (mm) REVERT: C 642 MET cc_start: 0.8123 (mmp) cc_final: 0.7787 (mmp) REVERT: C 649 ARG cc_start: 0.8794 (ttm170) cc_final: 0.8511 (ttp-110) REVERT: C 651 LEU cc_start: 0.8363 (mp) cc_final: 0.8128 (mm) REVERT: C 663 LYS cc_start: 0.8195 (ptmm) cc_final: 0.7668 (ttpp) REVERT: C 667 GLU cc_start: 0.7963 (pp20) cc_final: 0.7662 (pp20) REVERT: C 692 MET cc_start: 0.7129 (ttm) cc_final: 0.6918 (ttm) REVERT: C 711 LYS cc_start: 0.9296 (mmtt) cc_final: 0.8814 (mmtm) REVERT: C 712 GLU cc_start: 0.8713 (tt0) cc_final: 0.8152 (tt0) REVERT: C 715 ASN cc_start: 0.8758 (m110) cc_final: 0.8266 (m-40) REVERT: C 717 TYR cc_start: 0.8876 (t80) cc_final: 0.8541 (t80) REVERT: C 719 ASP cc_start: 0.8314 (m-30) cc_final: 0.7671 (p0) REVERT: C 720 TYR cc_start: 0.7832 (t80) cc_final: 0.7122 (t80) REVERT: C 724 LYS cc_start: 0.8121 (ptpp) cc_final: 0.6778 (pttp) REVERT: C 730 PHE cc_start: 0.8147 (t80) cc_final: 0.7526 (t80) REVERT: C 735 ARG cc_start: 0.8225 (ttm-80) cc_final: 0.7877 (ttm-80) REVERT: C 738 HIS cc_start: 0.8008 (t-90) cc_final: 0.7710 (t70) REVERT: C 743 GLU cc_start: 0.8432 (mm-30) cc_final: 0.7950 (mm-30) REVERT: C 748 TYR cc_start: 0.7409 (t80) cc_final: 0.6851 (t80) REVERT: C 750 PHE cc_start: 0.8346 (m-10) cc_final: 0.8106 (m-10) REVERT: C 753 GLU cc_start: 0.8539 (mp0) cc_final: 0.8324 (mp0) REVERT: C 754 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8026 (mt-10) REVERT: C 788 ARG cc_start: 0.8562 (ptt180) cc_final: 0.7981 (ttp80) REVERT: C 822 LYS cc_start: 0.8512 (mmtt) cc_final: 0.8173 (mmtm) outliers start: 1 outliers final: 0 residues processed: 534 average time/residue: 0.1360 time to fit residues: 97.8363 Evaluate side-chains 508 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 508 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 3 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 150 optimal weight: 0.8980 chunk 147 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 139 optimal weight: 0.0470 chunk 27 optimal weight: 2.9990 chunk 112 optimal weight: 0.2980 chunk 144 optimal weight: 6.9990 chunk 16 optimal weight: 0.0370 overall best weight: 0.4156 ------------------------------------------------------------------------------- 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 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 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 = 0.4131 r_free = 0.4131 target = 0.143652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.116694 restraints weight = 29361.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.121248 restraints weight = 17893.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.124615 restraints weight = 12316.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.127178 restraints weight = 9086.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.129124 restraints weight = 7020.820| |-----------------------------------------------------------------------------| r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.5495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13534 Z= 0.115 Angle : 0.610 8.021 18272 Z= 0.306 Chirality : 0.043 0.195 2014 Planarity : 0.004 0.041 2372 Dihedral : 4.907 19.722 1806 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.21), residues: 1610 helix: -0.37 (0.18), residues: 798 sheet: -2.48 (0.60), residues: 72 loop : -0.92 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 46 TYR 0.020 0.001 TYR A 464 PHE 0.019 0.001 PHE A 750 TRP 0.029 0.003 TRP A 328 HIS 0.004 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00248 (13522) covalent geometry : angle 0.60461 (18260) hydrogen bonds : bond 0.03645 ( 502) hydrogen bonds : angle 5.01685 ( 1392) metal coordination : bond 0.00324 ( 12) metal coordination : angle 3.21750 ( 12) *********************** 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 524 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 524 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.7563 (mmtm) cc_final: 0.7137 (mmmm) REVERT: B 22 LEU cc_start: 0.8182 (mm) cc_final: 0.7913 (mm) REVERT: B 65 ASN cc_start: 0.8164 (m-40) cc_final: 0.7820 (m-40) REVERT: B 73 CYS cc_start: 0.6325 (m) cc_final: 0.5961 (m) REVERT: B 77 TYR cc_start: 0.8115 (m-80) cc_final: 0.7653 (m-80) REVERT: B 82 GLU cc_start: 0.8724 (tt0) cc_final: 0.8307 (tt0) REVERT: B 108 ILE cc_start: 0.8067 (mt) cc_final: 0.7660 (tt) REVERT: B 124 ARG cc_start: 0.8729 (ttt-90) cc_final: 0.8436 (ttt-90) REVERT: B 132 PHE cc_start: 0.7633 (m-80) cc_final: 0.6974 (m-80) REVERT: B 134 ASN cc_start: 0.7941 (t0) cc_final: 0.7656 (t0) REVERT: B 136 ARG cc_start: 0.8073 (mmm160) cc_final: 0.7248 (mmm160) REVERT: A 130 GLU cc_start: 0.8437 (pt0) cc_final: 0.7528 (pm20) REVERT: A 237 ASP cc_start: 0.8371 (m-30) cc_final: 0.7759 (t0) REVERT: A 260 LEU cc_start: 0.9056 (mm) cc_final: 0.8705 (pp) REVERT: A 291 MET cc_start: 0.8489 (ttt) cc_final: 0.8040 (ttp) REVERT: A 294 ARG cc_start: 0.8477 (mpt-90) cc_final: 0.8270 (mpt-90) REVERT: A 304 MET cc_start: 0.4997 (tpt) cc_final: 0.4292 (tpt) REVERT: A 306 LEU cc_start: 0.6697 (tp) cc_final: 0.6284 (tt) REVERT: A 332 ASN cc_start: 0.7665 (t0) cc_final: 0.7048 (t0) REVERT: A 337 ARG cc_start: 0.8140 (ttm170) cc_final: 0.7564 (ttp80) REVERT: A 344 GLN cc_start: 0.8373 (tp-100) cc_final: 0.7241 (tp-100) REVERT: A 392 HIS cc_start: 0.8210 (m90) cc_final: 0.7792 (m90) REVERT: A 403 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7435 (pp20) REVERT: A 406 GLU cc_start: 0.8250 (tp30) cc_final: 0.7743 (tp30) REVERT: A 446 PHE cc_start: 0.7581 (m-80) cc_final: 0.7304 (m-80) REVERT: A 447 GLU cc_start: 0.8097 (mp0) cc_final: 0.7648 (tp30) REVERT: A 449 PHE cc_start: 0.7178 (m-10) cc_final: 0.6655 (m-80) REVERT: A 450 ILE cc_start: 0.7996 (mt) cc_final: 0.7019 (mt) REVERT: A 455 ASN cc_start: 0.7861 (m-40) cc_final: 0.7578 (m-40) REVERT: A 458 LEU cc_start: 0.8279 (tp) cc_final: 0.7799 (tt) REVERT: A 459 GLU cc_start: 0.6973 (mp0) cc_final: 0.6633 (mp0) REVERT: A 477 PHE cc_start: 0.7994 (m-80) cc_final: 0.7524 (m-80) REVERT: A 478 MET cc_start: 0.8103 (mtp) cc_final: 0.6832 (ttm) REVERT: A 482 PHE cc_start: 0.7945 (p90) cc_final: 0.7538 (p90) REVERT: A 488 THR cc_start: 0.7755 (m) cc_final: 0.7445 (p) REVERT: A 489 LYS cc_start: 0.8248 (mtmm) cc_final: 0.8017 (ptpp) REVERT: A 499 ILE cc_start: 0.7840 (tp) cc_final: 0.7584 (tp) REVERT: A 501 MET cc_start: 0.8237 (mtt) cc_final: 0.7503 (mmt) REVERT: A 502 TYR cc_start: 0.7476 (m-10) cc_final: 0.7257 (m-10) REVERT: A 504 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7531 (mm-30) REVERT: A 505 ARG cc_start: 0.8804 (mtt90) cc_final: 0.8201 (mtt90) REVERT: A 507 ILE cc_start: 0.8678 (mt) cc_final: 0.8301 (mt) REVERT: A 522 TYR cc_start: 0.8136 (m-80) cc_final: 0.7592 (m-80) REVERT: A 529 ARG cc_start: 0.8289 (mmm-85) cc_final: 0.7964 (mtt180) REVERT: A 534 ASP cc_start: 0.8012 (m-30) cc_final: 0.7812 (m-30) REVERT: A 535 ASP cc_start: 0.7589 (t0) cc_final: 0.7263 (t0) REVERT: A 539 ARG cc_start: 0.8209 (ptm160) cc_final: 0.7505 (ptm-80) REVERT: A 542 MET cc_start: 0.8266 (ptt) cc_final: 0.7799 (tmm) REVERT: A 545 MET cc_start: 0.7576 (mtm) cc_final: 0.7189 (mtm) REVERT: A 550 ASP cc_start: 0.7823 (p0) cc_final: 0.7423 (p0) REVERT: A 553 LYS cc_start: 0.8417 (mtmt) cc_final: 0.7683 (mtpp) REVERT: A 572 LYS cc_start: 0.7999 (mmtt) cc_final: 0.7707 (tptt) REVERT: A 576 GLN cc_start: 0.8327 (tp40) cc_final: 0.7581 (tp40) REVERT: A 577 LEU cc_start: 0.8874 (mt) cc_final: 0.8601 (mt) REVERT: A 579 VAL cc_start: 0.8561 (m) cc_final: 0.8281 (p) REVERT: A 593 ASP cc_start: 0.8173 (t0) cc_final: 0.7717 (t70) REVERT: A 600 TRP cc_start: 0.8706 (t-100) cc_final: 0.8392 (t-100) REVERT: A 603 PRO cc_start: 0.7312 (Cg_endo) cc_final: 0.6958 (Cg_exo) REVERT: A 617 ILE cc_start: 0.8411 (mm) cc_final: 0.8174 (mm) REVERT: A 619 LEU cc_start: 0.8842 (tp) cc_final: 0.8495 (tp) REVERT: A 621 LEU cc_start: 0.8214 (mt) cc_final: 0.8009 (mt) REVERT: A 635 MET cc_start: 0.8191 (mpp) cc_final: 0.7590 (mpp) REVERT: A 641 LEU cc_start: 0.8586 (mt) cc_final: 0.8292 (mm) REVERT: A 642 MET cc_start: 0.8096 (mmp) cc_final: 0.7746 (mmp) REVERT: A 648 PHE cc_start: 0.8682 (p90) cc_final: 0.8243 (p90) REVERT: A 651 LEU cc_start: 0.8424 (mt) cc_final: 0.8169 (mt) REVERT: A 663 LYS cc_start: 0.8006 (ptmm) cc_final: 0.7561 (mmtm) REVERT: A 667 GLU cc_start: 0.8325 (pp20) cc_final: 0.8049 (pp20) REVERT: A 682 ILE cc_start: 0.8315 (tp) cc_final: 0.7942 (tp) REVERT: A 711 LYS cc_start: 0.9308 (mmtt) cc_final: 0.8977 (mmtm) REVERT: A 712 GLU cc_start: 0.8687 (tt0) cc_final: 0.8199 (tt0) REVERT: A 715 ASN cc_start: 0.8743 (m110) cc_final: 0.8517 (m110) REVERT: A 716 LEU cc_start: 0.8737 (mt) cc_final: 0.8479 (mp) REVERT: A 717 TYR cc_start: 0.8918 (t80) cc_final: 0.8286 (t80) REVERT: A 720 TYR cc_start: 0.7822 (t80) cc_final: 0.7255 (t80) REVERT: A 727 GLU cc_start: 0.7934 (pm20) cc_final: 0.7591 (pm20) REVERT: A 728 LYS cc_start: 0.8359 (ttpt) cc_final: 0.7604 (tmtt) REVERT: A 734 ARG cc_start: 0.8509 (ttt-90) cc_final: 0.8228 (ttt180) REVERT: A 738 HIS cc_start: 0.8136 (t70) cc_final: 0.7861 (t-170) REVERT: A 743 GLU cc_start: 0.8400 (mm-30) cc_final: 0.7779 (mp0) REVERT: A 748 TYR cc_start: 0.7294 (t80) cc_final: 0.6791 (t80) REVERT: A 750 PHE cc_start: 0.8071 (m-80) cc_final: 0.7824 (m-10) REVERT: A 753 GLU cc_start: 0.8626 (mp0) cc_final: 0.8261 (mp0) REVERT: A 792 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8105 (mm-30) REVERT: A 822 LYS cc_start: 0.8462 (mptt) cc_final: 0.8121 (mmtm) REVERT: D 18 LYS cc_start: 0.7448 (mmtm) cc_final: 0.7041 (mmmt) REVERT: D 22 LEU cc_start: 0.8216 (mm) cc_final: 0.7872 (mm) REVERT: D 65 ASN cc_start: 0.8343 (m-40) cc_final: 0.7946 (m-40) REVERT: D 73 CYS cc_start: 0.6473 (m) cc_final: 0.6070 (m) REVERT: D 79 LYS cc_start: 0.8301 (tppp) cc_final: 0.7007 (tppp) REVERT: D 82 GLU cc_start: 0.8636 (tt0) cc_final: 0.7904 (tt0) REVERT: D 88 TYR cc_start: 0.6831 (p90) cc_final: 0.6444 (p90) REVERT: D 94 THR cc_start: 0.7919 (m) cc_final: 0.7392 (p) REVERT: D 98 GLN cc_start: 0.8676 (mp10) cc_final: 0.8413 (mp10) REVERT: D 114 GLN cc_start: 0.7865 (mp10) cc_final: 0.7518 (mp10) REVERT: D 124 ARG cc_start: 0.8793 (ttt-90) cc_final: 0.8455 (ttt-90) REVERT: D 132 PHE cc_start: 0.7669 (m-80) cc_final: 0.6852 (m-80) REVERT: D 134 ASN cc_start: 0.7412 (t0) cc_final: 0.6503 (t0) REVERT: D 138 ARG cc_start: 0.7900 (ptt-90) cc_final: 0.6779 (ptt-90) REVERT: D 139 TRP cc_start: 0.7017 (m100) cc_final: 0.6775 (m100) REVERT: C 130 GLU cc_start: 0.8394 (pt0) cc_final: 0.7615 (pm20) REVERT: C 138 GLU cc_start: 0.8595 (mp0) cc_final: 0.8194 (mp0) REVERT: C 270 ASP cc_start: 0.7226 (t70) cc_final: 0.7022 (t0) REVERT: C 283 TYR cc_start: 0.7836 (t80) cc_final: 0.7494 (t80) REVERT: C 288 ILE cc_start: 0.8734 (tt) cc_final: 0.7384 (tt) REVERT: C 291 MET cc_start: 0.8542 (ttt) cc_final: 0.7860 (ptt) REVERT: C 292 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8005 (mm-30) REVERT: C 304 MET cc_start: 0.5048 (tpt) cc_final: 0.4643 (tpt) REVERT: C 315 LYS cc_start: 0.7923 (mtmm) cc_final: 0.7491 (mtmm) REVERT: C 332 ASN cc_start: 0.7407 (t0) cc_final: 0.7043 (t0) REVERT: C 337 ARG cc_start: 0.8234 (ttm170) cc_final: 0.7812 (tmm-80) REVERT: C 339 MET cc_start: 0.7225 (mtm) cc_final: 0.7023 (mtm) REVERT: C 344 GLN cc_start: 0.8488 (tp-100) cc_final: 0.7565 (tp-100) REVERT: C 347 ILE cc_start: 0.7431 (mt) cc_final: 0.7105 (mm) REVERT: C 349 TYR cc_start: 0.7894 (t80) cc_final: 0.7597 (t80) REVERT: C 376 LYS cc_start: 0.8455 (ttpt) cc_final: 0.7300 (tttt) REVERT: C 380 TYR cc_start: 0.8489 (m-10) cc_final: 0.8082 (m-10) REVERT: C 382 ASN cc_start: 0.8414 (m-40) cc_final: 0.8143 (m110) REVERT: C 392 HIS cc_start: 0.8379 (m170) cc_final: 0.8002 (m-70) REVERT: C 407 LEU cc_start: 0.8811 (mt) cc_final: 0.8290 (pp) REVERT: C 408 THR cc_start: 0.8545 (m) cc_final: 0.7995 (p) REVERT: C 409 LEU cc_start: 0.8709 (tp) cc_final: 0.8089 (pp) REVERT: C 410 GLN cc_start: 0.9057 (mm-40) cc_final: 0.7871 (mm110) REVERT: C 411 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7202 (mt-10) REVERT: C 441 LYS cc_start: 0.9106 (tttm) cc_final: 0.8838 (tptp) REVERT: C 450 ILE cc_start: 0.8043 (mt) cc_final: 0.6691 (mt) REVERT: C 478 MET cc_start: 0.8107 (mtp) cc_final: 0.7451 (mtp) REVERT: C 482 PHE cc_start: 0.7926 (p90) cc_final: 0.7511 (p90) REVERT: C 491 LEU cc_start: 0.8524 (mt) cc_final: 0.8279 (mt) REVERT: C 495 TYR cc_start: 0.7621 (m-10) cc_final: 0.7370 (m-10) REVERT: C 497 ASN cc_start: 0.7799 (m110) cc_final: 0.7588 (m-40) REVERT: C 499 ILE cc_start: 0.8017 (tp) cc_final: 0.7665 (tp) REVERT: C 501 MET cc_start: 0.8196 (mtt) cc_final: 0.7848 (mtt) REVERT: C 502 TYR cc_start: 0.7596 (m-10) cc_final: 0.7330 (m-10) REVERT: C 505 ARG cc_start: 0.8770 (mtt90) cc_final: 0.8195 (mtt90) REVERT: C 522 TYR cc_start: 0.8037 (m-80) cc_final: 0.7368 (m-80) REVERT: C 532 ILE cc_start: 0.8426 (pt) cc_final: 0.7938 (mm) REVERT: C 542 MET cc_start: 0.8164 (tpp) cc_final: 0.7406 (tpp) REVERT: C 545 MET cc_start: 0.7726 (mtm) cc_final: 0.7134 (mtm) REVERT: C 553 LYS cc_start: 0.8486 (mtmt) cc_final: 0.8150 (mtpp) REVERT: C 555 LEU cc_start: 0.8518 (tp) cc_final: 0.8106 (tp) REVERT: C 576 GLN cc_start: 0.7751 (tm-30) cc_final: 0.7270 (tm-30) REVERT: C 577 LEU cc_start: 0.8606 (mt) cc_final: 0.7994 (mt) REVERT: C 581 GLU cc_start: 0.8159 (pp20) cc_final: 0.7774 (pp20) REVERT: C 587 ILE cc_start: 0.8153 (tp) cc_final: 0.7834 (tp) REVERT: C 589 MET cc_start: 0.6522 (mtp) cc_final: 0.6089 (mtp) REVERT: C 593 ASP cc_start: 0.7948 (t70) cc_final: 0.7705 (t0) REVERT: C 617 ILE cc_start: 0.8579 (mm) cc_final: 0.8287 (mm) REVERT: C 619 LEU cc_start: 0.8885 (tp) cc_final: 0.8588 (tp) REVERT: C 621 LEU cc_start: 0.8153 (mm) cc_final: 0.7675 (mm) REVERT: C 625 ASN cc_start: 0.8460 (m-40) cc_final: 0.8130 (m110) REVERT: C 626 ASN cc_start: 0.7955 (m110) cc_final: 0.7729 (m110) REVERT: C 635 MET cc_start: 0.8168 (mpp) cc_final: 0.7410 (mpp) REVERT: C 640 LYS cc_start: 0.7861 (mtpp) cc_final: 0.7598 (mtpp) REVERT: C 641 LEU cc_start: 0.8612 (mt) cc_final: 0.8221 (mm) REVERT: C 642 MET cc_start: 0.8076 (mmp) cc_final: 0.7809 (mmp) REVERT: C 649 ARG cc_start: 0.8771 (ttm170) cc_final: 0.8432 (ttm170) REVERT: C 651 LEU cc_start: 0.8416 (mp) cc_final: 0.8203 (mt) REVERT: C 663 LYS cc_start: 0.8194 (ptmm) cc_final: 0.7712 (ttpp) REVERT: C 667 GLU cc_start: 0.7972 (pp20) cc_final: 0.7642 (pp20) REVERT: C 707 ASN cc_start: 0.8337 (p0) cc_final: 0.8122 (p0) REVERT: C 711 LYS cc_start: 0.9292 (mmtt) cc_final: 0.8887 (mmtm) REVERT: C 712 GLU cc_start: 0.8669 (tt0) cc_final: 0.8161 (tt0) REVERT: C 715 ASN cc_start: 0.8765 (m110) cc_final: 0.8336 (m110) REVERT: C 717 TYR cc_start: 0.8836 (t80) cc_final: 0.8377 (t80) REVERT: C 719 ASP cc_start: 0.8313 (m-30) cc_final: 0.7968 (m-30) REVERT: C 720 TYR cc_start: 0.7958 (t80) cc_final: 0.7249 (t80) REVERT: C 730 PHE cc_start: 0.8114 (t80) cc_final: 0.7744 (t80) REVERT: C 731 LYS cc_start: 0.7866 (pptt) cc_final: 0.7628 (pptt) REVERT: C 738 HIS cc_start: 0.8000 (t-90) cc_final: 0.7446 (t70) REVERT: C 743 GLU cc_start: 0.8430 (mm-30) cc_final: 0.7986 (mm-30) REVERT: C 747 LYS cc_start: 0.9108 (mtpp) cc_final: 0.8761 (mmmm) REVERT: C 748 TYR cc_start: 0.7376 (t80) cc_final: 0.6797 (t80) REVERT: C 753 GLU cc_start: 0.8582 (mp0) cc_final: 0.8291 (mp0) REVERT: C 788 ARG cc_start: 0.8435 (ptt180) cc_final: 0.7823 (tmm-80) REVERT: C 805 PHE cc_start: 0.8511 (t80) cc_final: 0.8263 (t80) REVERT: C 822 LYS cc_start: 0.8492 (mmtt) cc_final: 0.8118 (mmtm) outliers start: 0 outliers final: 0 residues processed: 524 average time/residue: 0.1382 time to fit residues: 97.5548 Evaluate side-chains 508 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 508 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 116 optimal weight: 3.9990 chunk 148 optimal weight: 0.8980 chunk 72 optimal weight: 0.4980 chunk 152 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 chunk 19 optimal weight: 0.0670 chunk 56 optimal weight: 0.6980 chunk 142 optimal weight: 0.4980 chunk 15 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 ASN ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4130 r_free = 0.4130 target = 0.144025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.117171 restraints weight = 29564.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.121790 restraints weight = 18008.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.125194 restraints weight = 12357.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.127707 restraints weight = 9078.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.129498 restraints weight = 7031.205| |-----------------------------------------------------------------------------| r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.5753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13534 Z= 0.115 Angle : 0.601 8.900 18272 Z= 0.301 Chirality : 0.043 0.173 2014 Planarity : 0.004 0.071 2372 Dihedral : 4.754 17.830 1806 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.21), residues: 1610 helix: -0.30 (0.18), residues: 808 sheet: -2.59 (0.61), residues: 68 loop : -0.97 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 141 TYR 0.027 0.001 TYR C 301 PHE 0.015 0.001 PHE A 750 TRP 0.018 0.003 TRP A 328 HIS 0.005 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00242 (13522) covalent geometry : angle 0.59510 (18260) hydrogen bonds : bond 0.03549 ( 502) hydrogen bonds : angle 4.97955 ( 1392) metal coordination : bond 0.00317 ( 12) metal coordination : angle 3.22254 ( 12) *********************** 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 524 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 524 time to evaluate : 0.467 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: B 18 LYS cc_start: 0.7532 (mmtm) cc_final: 0.7102 (mmmm) REVERT: B 22 LEU cc_start: 0.8046 (mm) cc_final: 0.7741 (mm) REVERT: B 65 ASN cc_start: 0.8209 (m-40) cc_final: 0.7868 (m-40) REVERT: B 73 CYS cc_start: 0.6554 (m) cc_final: 0.6080 (m) REVERT: B 77 TYR cc_start: 0.8114 (m-80) cc_final: 0.7638 (m-80) REVERT: B 82 GLU cc_start: 0.8721 (tt0) cc_final: 0.8317 (tt0) REVERT: B 84 ARG cc_start: 0.6672 (mtm110) cc_final: 0.6013 (mtm110) REVERT: B 88 TYR cc_start: 0.7304 (p90) cc_final: 0.6579 (p90) REVERT: B 108 ILE cc_start: 0.8068 (mt) cc_final: 0.7660 (tt) REVERT: B 114 GLN cc_start: 0.7940 (mp10) cc_final: 0.7624 (mp10) REVERT: B 124 ARG cc_start: 0.8751 (ttt-90) cc_final: 0.8457 (ttt-90) REVERT: B 132 PHE cc_start: 0.7555 (m-80) cc_final: 0.6910 (m-80) REVERT: B 134 ASN cc_start: 0.7927 (t0) cc_final: 0.7065 (t0) REVERT: B 136 ARG cc_start: 0.8038 (mmm160) cc_final: 0.7323 (mmm160) REVERT: B 139 TRP cc_start: 0.7088 (m100) cc_final: 0.6514 (m100) REVERT: A 130 GLU cc_start: 0.8426 (pt0) cc_final: 0.7509 (pm20) REVERT: A 138 GLU cc_start: 0.8486 (mp0) cc_final: 0.8257 (mp0) REVERT: A 237 ASP cc_start: 0.8310 (m-30) cc_final: 0.7734 (t0) REVERT: A 260 LEU cc_start: 0.9030 (mm) cc_final: 0.8687 (pp) REVERT: A 287 PHE cc_start: 0.7195 (m-80) cc_final: 0.5961 (m-80) REVERT: A 291 MET cc_start: 0.8494 (ttt) cc_final: 0.7933 (ttp) REVERT: A 294 ARG cc_start: 0.8446 (mpt-90) cc_final: 0.8228 (mpt-90) REVERT: A 304 MET cc_start: 0.5015 (tpt) cc_final: 0.4320 (tpt) REVERT: A 306 LEU cc_start: 0.6770 (tp) cc_final: 0.6122 (tt) REVERT: A 328 TRP cc_start: 0.6905 (m100) cc_final: 0.5859 (m100) REVERT: A 330 LYS cc_start: 0.8480 (mptt) cc_final: 0.8183 (mmtt) REVERT: A 337 ARG cc_start: 0.8148 (ttm170) cc_final: 0.7571 (ttp80) REVERT: A 338 ARG cc_start: 0.7940 (mtp180) cc_final: 0.7656 (mmm-85) REVERT: A 344 GLN cc_start: 0.8376 (tp-100) cc_final: 0.7268 (tp-100) REVERT: A 392 HIS cc_start: 0.8360 (m90) cc_final: 0.7914 (m90) REVERT: A 403 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7919 (tm-30) REVERT: A 406 GLU cc_start: 0.8099 (tp30) cc_final: 0.7834 (mt-10) REVERT: A 424 ARG cc_start: 0.7886 (tpp-160) cc_final: 0.7524 (tpp80) REVERT: A 446 PHE cc_start: 0.7637 (m-80) cc_final: 0.7367 (m-80) REVERT: A 447 GLU cc_start: 0.8091 (mp0) cc_final: 0.7672 (tp30) REVERT: A 449 PHE cc_start: 0.7116 (m-10) cc_final: 0.6568 (m-80) REVERT: A 450 ILE cc_start: 0.7976 (mt) cc_final: 0.6990 (mt) REVERT: A 455 ASN cc_start: 0.7853 (m-40) cc_final: 0.7562 (m-40) REVERT: A 458 LEU cc_start: 0.8353 (tp) cc_final: 0.7831 (tt) REVERT: A 459 GLU cc_start: 0.6976 (mp0) cc_final: 0.6640 (mp0) REVERT: A 477 PHE cc_start: 0.7944 (m-80) cc_final: 0.7477 (m-80) REVERT: A 478 MET cc_start: 0.8076 (mtp) cc_final: 0.7428 (ttm) REVERT: A 482 PHE cc_start: 0.7880 (p90) cc_final: 0.7503 (p90) REVERT: A 488 THR cc_start: 0.7736 (m) cc_final: 0.7460 (p) REVERT: A 497 ASN cc_start: 0.7950 (m-40) cc_final: 0.7621 (m-40) REVERT: A 499 ILE cc_start: 0.7893 (tp) cc_final: 0.7632 (tp) REVERT: A 502 TYR cc_start: 0.7536 (m-10) cc_final: 0.7279 (m-10) REVERT: A 504 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7544 (mm-30) REVERT: A 505 ARG cc_start: 0.8805 (mtt90) cc_final: 0.8215 (mtt90) REVERT: A 507 ILE cc_start: 0.8708 (mt) cc_final: 0.8317 (mt) REVERT: A 520 ASN cc_start: 0.7495 (t0) cc_final: 0.6964 (p0) REVERT: A 522 TYR cc_start: 0.8133 (m-80) cc_final: 0.7679 (m-80) REVERT: A 532 ILE cc_start: 0.8597 (pt) cc_final: 0.7880 (pt) REVERT: A 535 ASP cc_start: 0.7597 (t0) cc_final: 0.7244 (t0) REVERT: A 539 ARG cc_start: 0.8135 (ptm160) cc_final: 0.7532 (ptm-80) REVERT: A 542 MET cc_start: 0.8264 (ptt) cc_final: 0.7783 (tmm) REVERT: A 545 MET cc_start: 0.7601 (mtm) cc_final: 0.7204 (mtm) REVERT: A 550 ASP cc_start: 0.7797 (p0) cc_final: 0.7411 (p0) REVERT: A 553 LYS cc_start: 0.8449 (mtmt) cc_final: 0.8072 (mtpp) REVERT: A 555 LEU cc_start: 0.8580 (tp) cc_final: 0.8377 (tp) REVERT: A 572 LYS cc_start: 0.8024 (mmtt) cc_final: 0.7700 (tptt) REVERT: A 576 GLN cc_start: 0.8315 (tp40) cc_final: 0.7595 (tp40) REVERT: A 577 LEU cc_start: 0.8848 (mt) cc_final: 0.8469 (mt) REVERT: A 579 VAL cc_start: 0.8563 (m) cc_final: 0.8275 (p) REVERT: A 581 GLU cc_start: 0.8451 (tt0) cc_final: 0.8166 (pt0) REVERT: A 593 ASP cc_start: 0.8172 (t0) cc_final: 0.7725 (t70) REVERT: A 600 TRP cc_start: 0.8704 (t-100) cc_final: 0.8366 (t-100) REVERT: A 603 PRO cc_start: 0.7329 (Cg_endo) cc_final: 0.6991 (Cg_exo) REVERT: A 617 ILE cc_start: 0.8431 (mm) cc_final: 0.8204 (mm) REVERT: A 621 LEU cc_start: 0.8232 (mt) cc_final: 0.8009 (mt) REVERT: A 635 MET cc_start: 0.8225 (mpp) cc_final: 0.7619 (mpp) REVERT: A 641 LEU cc_start: 0.8569 (mt) cc_final: 0.8227 (mm) REVERT: A 642 MET cc_start: 0.8081 (mmp) cc_final: 0.7659 (mmp) REVERT: A 648 PHE cc_start: 0.8654 (p90) cc_final: 0.8166 (p90) REVERT: A 651 LEU cc_start: 0.8437 (mt) cc_final: 0.8183 (mt) REVERT: A 663 LYS cc_start: 0.8073 (ptmm) cc_final: 0.7631 (mmtt) REVERT: A 667 GLU cc_start: 0.8288 (pp20) cc_final: 0.8041 (pp20) REVERT: A 682 ILE cc_start: 0.8289 (tp) cc_final: 0.7898 (tp) REVERT: A 711 LYS cc_start: 0.9300 (mmtt) cc_final: 0.8970 (mptt) REVERT: A 712 GLU cc_start: 0.8726 (tt0) cc_final: 0.8258 (tt0) REVERT: A 715 ASN cc_start: 0.8746 (m110) cc_final: 0.8386 (m110) REVERT: A 716 LEU cc_start: 0.8763 (mt) cc_final: 0.8506 (mp) REVERT: A 717 TYR cc_start: 0.8972 (t80) cc_final: 0.8228 (t80) REVERT: A 719 ASP cc_start: 0.8180 (m-30) cc_final: 0.7853 (m-30) REVERT: A 720 TYR cc_start: 0.7802 (t80) cc_final: 0.7260 (t80) REVERT: A 727 GLU cc_start: 0.7884 (pm20) cc_final: 0.7513 (pm20) REVERT: A 730 PHE cc_start: 0.8129 (t80) cc_final: 0.7848 (t80) REVERT: A 734 ARG cc_start: 0.8508 (ttt-90) cc_final: 0.8067 (ttp80) REVERT: A 738 HIS cc_start: 0.8113 (t70) cc_final: 0.7869 (t-170) REVERT: A 743 GLU cc_start: 0.8343 (mm-30) cc_final: 0.7834 (mp0) REVERT: A 753 GLU cc_start: 0.8654 (mp0) cc_final: 0.8312 (mp0) REVERT: A 788 ARG cc_start: 0.8639 (ttm170) cc_final: 0.7936 (ttm170) REVERT: A 792 GLU cc_start: 0.8501 (mm-30) cc_final: 0.7987 (mm-30) REVERT: A 822 LYS cc_start: 0.8447 (mptt) cc_final: 0.8068 (mmtm) REVERT: D 18 LYS cc_start: 0.7464 (mmtm) cc_final: 0.6874 (mmmt) REVERT: D 22 LEU cc_start: 0.8268 (mm) cc_final: 0.7908 (mm) REVERT: D 65 ASN cc_start: 0.8345 (m-40) cc_final: 0.7946 (m-40) REVERT: D 73 CYS cc_start: 0.6725 (m) cc_final: 0.6253 (m) REVERT: D 79 LYS cc_start: 0.8337 (tppp) cc_final: 0.7082 (tppp) REVERT: D 80 ILE cc_start: 0.8569 (mm) cc_final: 0.8270 (mm) REVERT: D 82 GLU cc_start: 0.8701 (tt0) cc_final: 0.7983 (tt0) REVERT: D 88 TYR cc_start: 0.6971 (p90) cc_final: 0.6549 (p90) REVERT: D 98 GLN cc_start: 0.8684 (mp10) cc_final: 0.8232 (mp10) REVERT: D 114 GLN cc_start: 0.7864 (mp10) cc_final: 0.7548 (mp10) REVERT: D 124 ARG cc_start: 0.8855 (ttt-90) cc_final: 0.8446 (ttt-90) REVERT: D 128 LYS cc_start: 0.8519 (mttt) cc_final: 0.8279 (mttt) REVERT: D 132 PHE cc_start: 0.7697 (m-80) cc_final: 0.6882 (m-80) REVERT: D 134 ASN cc_start: 0.7825 (t0) cc_final: 0.6703 (t0) REVERT: D 138 ARG cc_start: 0.8000 (ptt-90) cc_final: 0.6939 (ptt-90) REVERT: D 139 TRP cc_start: 0.7061 (m100) cc_final: 0.6690 (m100) REVERT: C 130 GLU cc_start: 0.8365 (pt0) cc_final: 0.7597 (pm20) REVERT: C 138 GLU cc_start: 0.8639 (mp0) cc_final: 0.8396 (mm-30) REVERT: C 260 LEU cc_start: 0.8834 (mm) cc_final: 0.8495 (pp) REVERT: C 283 TYR cc_start: 0.7836 (t80) cc_final: 0.7617 (t80) REVERT: C 288 ILE cc_start: 0.8802 (tt) cc_final: 0.7987 (tt) REVERT: C 291 MET cc_start: 0.8530 (ttt) cc_final: 0.7959 (ptt) REVERT: C 292 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7852 (mm-30) REVERT: C 304 MET cc_start: 0.5017 (tpt) cc_final: 0.4614 (tpt) REVERT: C 328 TRP cc_start: 0.7253 (m100) cc_final: 0.6692 (m100) REVERT: C 332 ASN cc_start: 0.7479 (t0) cc_final: 0.7111 (t0) REVERT: C 337 ARG cc_start: 0.8266 (ttm170) cc_final: 0.7883 (tmm-80) REVERT: C 339 MET cc_start: 0.7164 (mtm) cc_final: 0.6529 (mtp) REVERT: C 344 GLN cc_start: 0.8502 (tp-100) cc_final: 0.7590 (tp-100) REVERT: C 349 TYR cc_start: 0.7896 (t80) cc_final: 0.7615 (t80) REVERT: C 376 LYS cc_start: 0.8456 (ttpt) cc_final: 0.8046 (tttt) REVERT: C 382 ASN cc_start: 0.8411 (m-40) cc_final: 0.8105 (t0) REVERT: C 392 HIS cc_start: 0.8385 (m170) cc_final: 0.8034 (m-70) REVERT: C 403 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7841 (tm-30) REVERT: C 407 LEU cc_start: 0.8840 (mt) cc_final: 0.8320 (pp) REVERT: C 408 THR cc_start: 0.8613 (m) cc_final: 0.8035 (p) REVERT: C 409 LEU cc_start: 0.8775 (tp) cc_final: 0.8121 (pp) REVERT: C 410 GLN cc_start: 0.9074 (mm-40) cc_final: 0.7936 (mm-40) REVERT: C 411 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7197 (mt-10) REVERT: C 419 ASN cc_start: 0.8320 (p0) cc_final: 0.8050 (m-40) REVERT: C 429 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8359 (mt-10) REVERT: C 441 LYS cc_start: 0.9097 (tttm) cc_final: 0.8845 (tptp) REVERT: C 447 GLU cc_start: 0.7906 (tp30) cc_final: 0.7057 (tp30) REVERT: C 450 ILE cc_start: 0.8082 (mt) cc_final: 0.7331 (mt) REVERT: C 478 MET cc_start: 0.8088 (mtp) cc_final: 0.7482 (mtp) REVERT: C 482 PHE cc_start: 0.7945 (p90) cc_final: 0.7529 (p90) REVERT: C 491 LEU cc_start: 0.8521 (mt) cc_final: 0.8252 (mt) REVERT: C 495 TYR cc_start: 0.7648 (m-10) cc_final: 0.7375 (m-10) REVERT: C 499 ILE cc_start: 0.7928 (tp) cc_final: 0.7692 (tp) REVERT: C 501 MET cc_start: 0.8124 (mtt) cc_final: 0.7805 (mtt) REVERT: C 502 TYR cc_start: 0.7650 (m-10) cc_final: 0.7384 (m-10) REVERT: C 505 ARG cc_start: 0.8799 (mtt90) cc_final: 0.8241 (mtt90) REVERT: C 507 ILE cc_start: 0.8669 (mt) cc_final: 0.8344 (mt) REVERT: C 522 TYR cc_start: 0.8017 (m-80) cc_final: 0.7339 (m-80) REVERT: C 532 ILE cc_start: 0.8451 (pt) cc_final: 0.7952 (mm) REVERT: C 542 MET cc_start: 0.8161 (tpp) cc_final: 0.7496 (tpp) REVERT: C 543 ILE cc_start: 0.8845 (mt) cc_final: 0.8580 (mt) REVERT: C 545 MET cc_start: 0.7721 (mtm) cc_final: 0.7277 (mtm) REVERT: C 553 LYS cc_start: 0.8419 (mtmt) cc_final: 0.8056 (mtpp) REVERT: C 555 LEU cc_start: 0.8524 (tp) cc_final: 0.8117 (tp) REVERT: C 576 GLN cc_start: 0.7968 (tm-30) cc_final: 0.7585 (tm-30) REVERT: C 577 LEU cc_start: 0.8761 (mt) cc_final: 0.8415 (pp) REVERT: C 581 GLU cc_start: 0.8142 (pp20) cc_final: 0.7755 (pp20) REVERT: C 587 ILE cc_start: 0.8095 (tp) cc_final: 0.7779 (tp) REVERT: C 589 MET cc_start: 0.6422 (mtp) cc_final: 0.6018 (mtp) REVERT: C 593 ASP cc_start: 0.7938 (t70) cc_final: 0.7717 (t0) REVERT: C 617 ILE cc_start: 0.8574 (mm) cc_final: 0.8252 (mm) REVERT: C 619 LEU cc_start: 0.8883 (tp) cc_final: 0.8580 (tp) REVERT: C 621 LEU cc_start: 0.8123 (mm) cc_final: 0.7583 (mm) REVERT: C 625 ASN cc_start: 0.8460 (m-40) cc_final: 0.8122 (m110) REVERT: C 635 MET cc_start: 0.8175 (mpp) cc_final: 0.7417 (mpp) REVERT: C 641 LEU cc_start: 0.8605 (mt) cc_final: 0.8230 (mm) REVERT: C 642 MET cc_start: 0.8104 (mmp) cc_final: 0.7796 (mmp) REVERT: C 649 ARG cc_start: 0.8756 (ttm170) cc_final: 0.8442 (mtp85) REVERT: C 651 LEU cc_start: 0.8414 (mp) cc_final: 0.8185 (mt) REVERT: C 663 LYS cc_start: 0.8212 (ptmm) cc_final: 0.7675 (ttpp) REVERT: C 667 GLU cc_start: 0.7976 (pp20) cc_final: 0.7631 (pp20) REVERT: C 711 LYS cc_start: 0.9297 (mmtt) cc_final: 0.8893 (mmtm) REVERT: C 712 GLU cc_start: 0.8638 (tt0) cc_final: 0.8236 (tt0) REVERT: C 715 ASN cc_start: 0.8689 (m110) cc_final: 0.8346 (m110) REVERT: C 716 LEU cc_start: 0.8683 (mt) cc_final: 0.8114 (pp) REVERT: C 717 TYR cc_start: 0.8802 (t80) cc_final: 0.8285 (t80) REVERT: C 719 ASP cc_start: 0.8393 (m-30) cc_final: 0.8073 (m-30) REVERT: C 720 TYR cc_start: 0.7947 (t80) cc_final: 0.7255 (t80) REVERT: C 727 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7861 (mm-30) REVERT: C 730 PHE cc_start: 0.8165 (t80) cc_final: 0.7804 (t80) REVERT: C 731 LYS cc_start: 0.7883 (pptt) cc_final: 0.7577 (pptt) REVERT: C 734 ARG cc_start: 0.8623 (ttt-90) cc_final: 0.8222 (ttm-80) REVERT: C 738 HIS cc_start: 0.7992 (t-90) cc_final: 0.7788 (t70) REVERT: C 743 GLU cc_start: 0.8425 (mm-30) cc_final: 0.7988 (mm-30) REVERT: C 747 LYS cc_start: 0.9072 (mtpp) cc_final: 0.8741 (mmmm) REVERT: C 748 TYR cc_start: 0.7429 (t80) cc_final: 0.6843 (t80) REVERT: C 751 ARG cc_start: 0.7917 (ptp-110) cc_final: 0.7516 (mmm-85) REVERT: C 753 GLU cc_start: 0.8548 (mp0) cc_final: 0.8327 (mp0) REVERT: C 763 ARG cc_start: 0.7279 (tpp80) cc_final: 0.6967 (tpp-160) REVERT: C 788 ARG cc_start: 0.8428 (ptt180) cc_final: 0.7496 (ptt180) REVERT: C 805 PHE cc_start: 0.8520 (t80) cc_final: 0.8139 (t80) REVERT: C 806 LEU cc_start: 0.8167 (mt) cc_final: 0.7676 (mt) REVERT: C 822 LYS cc_start: 0.8458 (mmtt) cc_final: 0.8156 (mmtm) REVERT: C 855 LYS cc_start: 0.8743 (tttt) cc_final: 0.8229 (tptt) outliers start: 0 outliers final: 0 residues processed: 524 average time/residue: 0.1494 time to fit residues: 104.6711 Evaluate side-chains 509 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 509 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 0.9990 chunk 135 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 108 optimal weight: 0.5980 chunk 109 optimal weight: 0.4980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 A 723 ASN ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4107 r_free = 0.4107 target = 0.141715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.114966 restraints weight = 29537.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.119548 restraints weight = 17985.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.122886 restraints weight = 12363.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.125365 restraints weight = 9084.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.127189 restraints weight = 7027.653| |-----------------------------------------------------------------------------| r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.5973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13534 Z= 0.131 Angle : 0.625 9.028 18272 Z= 0.314 Chirality : 0.043 0.160 2014 Planarity : 0.004 0.068 2372 Dihedral : 4.779 18.104 1806 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.13 (0.21), residues: 1610 helix: -0.30 (0.18), residues: 822 sheet: -2.34 (0.63), residues: 68 loop : -0.99 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 84 TYR 0.020 0.001 TYR C 301 PHE 0.018 0.001 PHE C 730 TRP 0.025 0.003 TRP B 139 HIS 0.005 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00271 (13522) covalent geometry : angle 0.61764 (18260) hydrogen bonds : bond 0.03626 ( 502) hydrogen bonds : angle 4.96724 ( 1392) metal coordination : bond 0.00440 ( 12) metal coordination : angle 3.86007 ( 12) *********************** 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 518 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 518 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 18 LYS cc_start: 0.7723 (mmtm) cc_final: 0.7142 (mmmm) REVERT: B 22 LEU cc_start: 0.8115 (mm) cc_final: 0.7635 (mm) REVERT: B 52 PHE cc_start: 0.6705 (t80) cc_final: 0.6227 (t80) REVERT: B 59 ILE cc_start: 0.7633 (mm) cc_final: 0.7302 (mm) REVERT: B 65 ASN cc_start: 0.8290 (m-40) cc_final: 0.7924 (m-40) REVERT: B 73 CYS cc_start: 0.6631 (m) cc_final: 0.6241 (m) REVERT: B 77 TYR cc_start: 0.8161 (m-80) cc_final: 0.7669 (m-80) REVERT: B 82 GLU cc_start: 0.8715 (tt0) cc_final: 0.8340 (tt0) REVERT: B 84 ARG cc_start: 0.6633 (mtm110) cc_final: 0.5926 (mtm110) REVERT: B 88 TYR cc_start: 0.7398 (p90) cc_final: 0.6499 (p90) REVERT: B 98 GLN cc_start: 0.8800 (mp10) cc_final: 0.8570 (mp10) REVERT: B 108 ILE cc_start: 0.8066 (mt) cc_final: 0.7671 (tt) REVERT: B 114 GLN cc_start: 0.8014 (mp10) cc_final: 0.7686 (mp10) REVERT: B 124 ARG cc_start: 0.8741 (ttt-90) cc_final: 0.8468 (ttt-90) REVERT: B 128 LYS cc_start: 0.8732 (mttt) cc_final: 0.8427 (mttt) REVERT: B 132 PHE cc_start: 0.7694 (m-80) cc_final: 0.6996 (m-80) REVERT: B 136 ARG cc_start: 0.8057 (mmm160) cc_final: 0.7313 (mmm160) REVERT: B 139 TRP cc_start: 0.7021 (m100) cc_final: 0.6810 (m100) REVERT: A 130 GLU cc_start: 0.8457 (pt0) cc_final: 0.7539 (pm20) REVERT: A 237 ASP cc_start: 0.8384 (m-30) cc_final: 0.7786 (t0) REVERT: A 291 MET cc_start: 0.8482 (ttt) cc_final: 0.8032 (mmp) REVERT: A 294 ARG cc_start: 0.8484 (mpt-90) cc_final: 0.8282 (mpt-90) REVERT: A 304 MET cc_start: 0.5007 (tpt) cc_final: 0.4367 (tpt) REVERT: A 313 MET cc_start: 0.7527 (mmp) cc_final: 0.6943 (mmm) REVERT: A 315 LYS cc_start: 0.8026 (mmtm) cc_final: 0.7526 (mttt) REVERT: A 326 ARG cc_start: 0.7954 (mtm110) cc_final: 0.7688 (mtm-85) REVERT: A 328 TRP cc_start: 0.6961 (m100) cc_final: 0.6653 (m100) REVERT: A 330 LYS cc_start: 0.8500 (mptt) cc_final: 0.8225 (mmtt) REVERT: A 337 ARG cc_start: 0.8193 (ttm170) cc_final: 0.7609 (ttp80) REVERT: A 338 ARG cc_start: 0.7926 (mtp180) cc_final: 0.7540 (mmm-85) REVERT: A 344 GLN cc_start: 0.8455 (tp-100) cc_final: 0.7382 (tp-100) REVERT: A 345 GLN cc_start: 0.8046 (mt0) cc_final: 0.7778 (mt0) REVERT: A 347 ILE cc_start: 0.7594 (mt) cc_final: 0.7124 (tp) REVERT: A 392 HIS cc_start: 0.8365 (m90) cc_final: 0.7891 (m90) REVERT: A 403 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7952 (tm-30) REVERT: A 406 GLU cc_start: 0.8142 (tp30) cc_final: 0.7866 (mt-10) REVERT: A 424 ARG cc_start: 0.8000 (tpp-160) cc_final: 0.7474 (tpt-90) REVERT: A 447 GLU cc_start: 0.8113 (mp0) cc_final: 0.7633 (tp30) REVERT: A 449 PHE cc_start: 0.7054 (m-10) cc_final: 0.6479 (m-80) REVERT: A 450 ILE cc_start: 0.8015 (mt) cc_final: 0.6970 (mt) REVERT: A 455 ASN cc_start: 0.7879 (m-40) cc_final: 0.7610 (m-40) REVERT: A 458 LEU cc_start: 0.8340 (tp) cc_final: 0.7755 (tt) REVERT: A 459 GLU cc_start: 0.7013 (mp0) cc_final: 0.6696 (mp0) REVERT: A 477 PHE cc_start: 0.7879 (m-80) cc_final: 0.7437 (m-80) REVERT: A 478 MET cc_start: 0.8099 (mtp) cc_final: 0.7448 (ttm) REVERT: A 482 PHE cc_start: 0.7896 (p90) cc_final: 0.7567 (p90) REVERT: A 499 ILE cc_start: 0.7869 (tp) cc_final: 0.7584 (tp) REVERT: A 501 MET cc_start: 0.8140 (mtt) cc_final: 0.7496 (mmm) REVERT: A 502 TYR cc_start: 0.7593 (m-10) cc_final: 0.7352 (m-10) REVERT: A 504 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7552 (mm-30) REVERT: A 505 ARG cc_start: 0.8831 (mtt90) cc_final: 0.8374 (mtt90) REVERT: A 507 ILE cc_start: 0.8705 (mt) cc_final: 0.8306 (mt) REVERT: A 520 ASN cc_start: 0.7523 (t0) cc_final: 0.7022 (p0) REVERT: A 522 TYR cc_start: 0.8128 (m-80) cc_final: 0.7739 (m-80) REVERT: A 535 ASP cc_start: 0.7607 (t0) cc_final: 0.7212 (t0) REVERT: A 539 ARG cc_start: 0.8103 (ptm160) cc_final: 0.7500 (ptm-80) REVERT: A 542 MET cc_start: 0.8236 (ptt) cc_final: 0.7739 (tmm) REVERT: A 545 MET cc_start: 0.7533 (mtm) cc_final: 0.7187 (mtm) REVERT: A 550 ASP cc_start: 0.7760 (p0) cc_final: 0.7416 (p0) REVERT: A 553 LYS cc_start: 0.8486 (mtmt) cc_final: 0.7777 (mtpp) REVERT: A 572 LYS cc_start: 0.7978 (mmtt) cc_final: 0.7721 (tptt) REVERT: A 576 GLN cc_start: 0.8552 (tp40) cc_final: 0.7980 (tp40) REVERT: A 581 GLU cc_start: 0.8441 (tt0) cc_final: 0.7714 (tt0) REVERT: A 593 ASP cc_start: 0.8152 (t0) cc_final: 0.7750 (t70) REVERT: A 600 TRP cc_start: 0.8750 (t-100) cc_final: 0.8391 (t-100) REVERT: A 603 PRO cc_start: 0.7448 (Cg_endo) cc_final: 0.7095 (Cg_exo) REVERT: A 617 ILE cc_start: 0.8434 (mm) cc_final: 0.8190 (mm) REVERT: A 619 LEU cc_start: 0.8841 (tp) cc_final: 0.8493 (tp) REVERT: A 621 LEU cc_start: 0.8212 (mt) cc_final: 0.8010 (mt) REVERT: A 635 MET cc_start: 0.8284 (mpp) cc_final: 0.7651 (mpp) REVERT: A 641 LEU cc_start: 0.8621 (mt) cc_final: 0.8222 (mm) REVERT: A 642 MET cc_start: 0.8050 (mmp) cc_final: 0.7652 (mmp) REVERT: A 649 ARG cc_start: 0.8747 (ptm160) cc_final: 0.8532 (ptm160) REVERT: A 651 LEU cc_start: 0.8481 (mt) cc_final: 0.8207 (mt) REVERT: A 663 LYS cc_start: 0.8151 (ptmm) cc_final: 0.7674 (mmtm) REVERT: A 667 GLU cc_start: 0.8242 (pp20) cc_final: 0.7945 (pp20) REVERT: A 682 ILE cc_start: 0.8285 (tp) cc_final: 0.7963 (tp) REVERT: A 712 GLU cc_start: 0.8731 (tt0) cc_final: 0.8362 (tt0) REVERT: A 715 ASN cc_start: 0.8814 (m110) cc_final: 0.8460 (m110) REVERT: A 716 LEU cc_start: 0.8810 (mt) cc_final: 0.8577 (mp) REVERT: A 717 TYR cc_start: 0.9000 (t80) cc_final: 0.8514 (t80) REVERT: A 719 ASP cc_start: 0.8189 (m-30) cc_final: 0.7833 (m-30) REVERT: A 727 GLU cc_start: 0.7896 (pm20) cc_final: 0.7556 (pm20) REVERT: A 728 LYS cc_start: 0.8348 (ttpt) cc_final: 0.7567 (tmtt) REVERT: A 734 ARG cc_start: 0.8535 (ttt-90) cc_final: 0.7986 (ttp80) REVERT: A 738 HIS cc_start: 0.8152 (t70) cc_final: 0.7904 (t-170) REVERT: A 739 MET cc_start: 0.7942 (ptm) cc_final: 0.7725 (ptm) REVERT: A 754 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8280 (mp0) REVERT: A 756 GLU cc_start: 0.7052 (tp30) cc_final: 0.6555 (tp30) REVERT: A 788 ARG cc_start: 0.8671 (ttm170) cc_final: 0.7945 (ttm170) REVERT: A 792 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8029 (mm-30) REVERT: A 797 PHE cc_start: 0.6849 (m-80) cc_final: 0.6443 (m-80) REVERT: A 822 LYS cc_start: 0.8314 (mptt) cc_final: 0.8098 (mmtt) REVERT: D 22 LEU cc_start: 0.8285 (mm) cc_final: 0.7925 (mm) REVERT: D 65 ASN cc_start: 0.8357 (m-40) cc_final: 0.7968 (m-40) REVERT: D 73 CYS cc_start: 0.6673 (m) cc_final: 0.6349 (m) REVERT: D 79 LYS cc_start: 0.8388 (tppp) cc_final: 0.7944 (tppp) REVERT: D 82 GLU cc_start: 0.8683 (tt0) cc_final: 0.8235 (tt0) REVERT: D 84 ARG cc_start: 0.7653 (mtt180) cc_final: 0.7324 (ttt180) REVERT: D 88 TYR cc_start: 0.6957 (p90) cc_final: 0.6533 (p90) REVERT: D 94 THR cc_start: 0.7962 (m) cc_final: 0.7403 (m) REVERT: D 98 GLN cc_start: 0.8671 (mp10) cc_final: 0.8267 (mp10) REVERT: D 114 GLN cc_start: 0.7913 (mp10) cc_final: 0.7631 (mp10) REVERT: D 124 ARG cc_start: 0.8872 (ttt-90) cc_final: 0.8533 (ttt-90) REVERT: D 132 PHE cc_start: 0.7764 (m-80) cc_final: 0.6957 (m-80) REVERT: D 134 ASN cc_start: 0.7841 (t0) cc_final: 0.6631 (t0) REVERT: D 138 ARG cc_start: 0.8065 (ptt-90) cc_final: 0.6955 (ptt-90) REVERT: D 139 TRP cc_start: 0.7086 (m100) cc_final: 0.6718 (m100) REVERT: C 130 GLU cc_start: 0.8370 (pt0) cc_final: 0.7603 (pm20) REVERT: C 138 GLU cc_start: 0.8593 (mp0) cc_final: 0.8187 (tp30) REVERT: C 246 LEU cc_start: 0.8291 (tp) cc_final: 0.8082 (tp) REVERT: C 260 LEU cc_start: 0.8829 (mm) cc_final: 0.8496 (pp) REVERT: C 288 ILE cc_start: 0.8830 (tt) cc_final: 0.8585 (tt) REVERT: C 291 MET cc_start: 0.8535 (ttt) cc_final: 0.7626 (ttt) REVERT: C 304 MET cc_start: 0.5000 (tpt) cc_final: 0.4600 (tpt) REVERT: C 315 LYS cc_start: 0.8173 (mtmm) cc_final: 0.7472 (mtmm) REVERT: C 326 ARG cc_start: 0.7984 (mtm-85) cc_final: 0.7720 (mtm110) REVERT: C 330 LYS cc_start: 0.8749 (mmmt) cc_final: 0.8406 (mptt) REVERT: C 332 ASN cc_start: 0.7562 (t0) cc_final: 0.7111 (t0) REVERT: C 337 ARG cc_start: 0.8277 (ttm170) cc_final: 0.7845 (ttp80) REVERT: C 338 ARG cc_start: 0.7710 (tpp80) cc_final: 0.6742 (tpp80) REVERT: C 344 GLN cc_start: 0.8507 (tp-100) cc_final: 0.7660 (tp-100) REVERT: C 349 TYR cc_start: 0.7944 (t80) cc_final: 0.7690 (t80) REVERT: C 376 LYS cc_start: 0.8572 (ttpt) cc_final: 0.8179 (ttpt) REVERT: C 382 ASN cc_start: 0.8477 (m-40) cc_final: 0.8128 (t0) REVERT: C 392 HIS cc_start: 0.8481 (m170) cc_final: 0.8114 (m-70) REVERT: C 403 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7954 (tm-30) REVERT: C 407 LEU cc_start: 0.8795 (mt) cc_final: 0.8277 (pp) REVERT: C 409 LEU cc_start: 0.8742 (tp) cc_final: 0.8197 (pp) REVERT: C 410 GLN cc_start: 0.9081 (mm-40) cc_final: 0.7965 (mm-40) REVERT: C 411 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7027 (mt-10) REVERT: C 429 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8378 (mt-10) REVERT: C 441 LYS cc_start: 0.9092 (tttm) cc_final: 0.8886 (tptp) REVERT: C 447 GLU cc_start: 0.7920 (tp30) cc_final: 0.7101 (tp30) REVERT: C 450 ILE cc_start: 0.8083 (mt) cc_final: 0.7310 (mt) REVERT: C 478 MET cc_start: 0.8111 (mtp) cc_final: 0.7537 (mtp) REVERT: C 482 PHE cc_start: 0.7981 (p90) cc_final: 0.7609 (p90) REVERT: C 491 LEU cc_start: 0.8555 (mt) cc_final: 0.8332 (mt) REVERT: C 495 TYR cc_start: 0.7688 (m-10) cc_final: 0.7423 (m-10) REVERT: C 499 ILE cc_start: 0.7997 (tp) cc_final: 0.7697 (tp) REVERT: C 501 MET cc_start: 0.8114 (mtt) cc_final: 0.7817 (mtt) REVERT: C 505 ARG cc_start: 0.8780 (mtt90) cc_final: 0.8220 (mtt90) REVERT: C 507 ILE cc_start: 0.8589 (mt) cc_final: 0.8346 (mt) REVERT: C 522 TYR cc_start: 0.8063 (m-80) cc_final: 0.7304 (m-80) REVERT: C 539 ARG cc_start: 0.8514 (tpp-160) cc_final: 0.7939 (ttt180) REVERT: C 541 GLU cc_start: 0.8047 (tt0) cc_final: 0.6656 (tm-30) REVERT: C 542 MET cc_start: 0.8064 (tpp) cc_final: 0.7390 (tpp) REVERT: C 550 ASP cc_start: 0.8073 (p0) cc_final: 0.7611 (p0) REVERT: C 553 LYS cc_start: 0.8548 (mtmt) cc_final: 0.8166 (mtpp) REVERT: C 555 LEU cc_start: 0.8525 (tp) cc_final: 0.8081 (tp) REVERT: C 576 GLN cc_start: 0.8019 (tm-30) cc_final: 0.7644 (tm-30) REVERT: C 577 LEU cc_start: 0.8771 (mt) cc_final: 0.8407 (pp) REVERT: C 581 GLU cc_start: 0.8172 (pp20) cc_final: 0.7760 (pp20) REVERT: C 587 ILE cc_start: 0.8083 (tp) cc_final: 0.7824 (tp) REVERT: C 589 MET cc_start: 0.6394 (mtp) cc_final: 0.5964 (mtp) REVERT: C 593 ASP cc_start: 0.7985 (t70) cc_final: 0.7732 (t0) REVERT: C 617 ILE cc_start: 0.8565 (mm) cc_final: 0.8253 (mm) REVERT: C 619 LEU cc_start: 0.8903 (tp) cc_final: 0.8616 (tp) REVERT: C 621 LEU cc_start: 0.8073 (mm) cc_final: 0.7504 (mm) REVERT: C 625 ASN cc_start: 0.8523 (m-40) cc_final: 0.8205 (m110) REVERT: C 635 MET cc_start: 0.8119 (mpp) cc_final: 0.7469 (mpp) REVERT: C 649 ARG cc_start: 0.8770 (ttm170) cc_final: 0.8349 (mtm180) REVERT: C 651 LEU cc_start: 0.8409 (mp) cc_final: 0.7976 (tp) REVERT: C 660 GLN cc_start: 0.8404 (mm-40) cc_final: 0.7943 (mm-40) REVERT: C 663 LYS cc_start: 0.8251 (ptmm) cc_final: 0.7790 (ttpp) REVERT: C 667 GLU cc_start: 0.8000 (pp20) cc_final: 0.7636 (pp20) REVERT: C 707 ASN cc_start: 0.8161 (p0) cc_final: 0.7723 (p0) REVERT: C 712 GLU cc_start: 0.8723 (tt0) cc_final: 0.8330 (tt0) REVERT: C 715 ASN cc_start: 0.8819 (m110) cc_final: 0.8481 (m110) REVERT: C 716 LEU cc_start: 0.8702 (mt) cc_final: 0.8119 (pp) REVERT: C 717 TYR cc_start: 0.8897 (t80) cc_final: 0.8345 (t80) REVERT: C 719 ASP cc_start: 0.8288 (m-30) cc_final: 0.7944 (m-30) REVERT: C 720 TYR cc_start: 0.7950 (t80) cc_final: 0.7274 (t80) REVERT: C 730 PHE cc_start: 0.8223 (t80) cc_final: 0.7858 (t80) REVERT: C 731 LYS cc_start: 0.7939 (pptt) cc_final: 0.7605 (pptt) REVERT: C 734 ARG cc_start: 0.8655 (ttt-90) cc_final: 0.8289 (ttm170) REVERT: C 738 HIS cc_start: 0.8034 (t-90) cc_final: 0.7813 (t70) REVERT: C 739 MET cc_start: 0.8039 (ptm) cc_final: 0.7811 (ptm) REVERT: C 743 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8022 (mm-30) REVERT: C 747 LYS cc_start: 0.9097 (mtpp) cc_final: 0.8755 (mmmm) REVERT: C 748 TYR cc_start: 0.7440 (t80) cc_final: 0.6895 (t80) REVERT: C 756 GLU cc_start: 0.7320 (tp30) cc_final: 0.6654 (tp30) REVERT: C 788 ARG cc_start: 0.8379 (ptt180) cc_final: 0.7443 (ptt180) REVERT: C 805 PHE cc_start: 0.8495 (t80) cc_final: 0.8119 (t80) REVERT: C 806 LEU cc_start: 0.8232 (mt) cc_final: 0.7718 (mt) REVERT: C 822 LYS cc_start: 0.8443 (mmtt) cc_final: 0.8124 (mmtm) REVERT: C 855 LYS cc_start: 0.8805 (tttt) cc_final: 0.8277 (tptt) outliers start: 0 outliers final: 0 residues processed: 518 average time/residue: 0.1466 time to fit residues: 102.1120 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 : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 132 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 127 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 141 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 HIS ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 ASN ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4108 r_free = 0.4108 target = 0.141445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.114970 restraints weight = 29841.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.119459 restraints weight = 18136.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.122765 restraints weight = 12454.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.125211 restraints weight = 9167.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.127057 restraints weight = 7106.257| |-----------------------------------------------------------------------------| r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.6156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13534 Z= 0.141 Angle : 0.644 9.433 18272 Z= 0.321 Chirality : 0.045 0.256 2014 Planarity : 0.004 0.042 2372 Dihedral : 4.751 18.519 1806 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.13 (0.21), residues: 1610 helix: -0.38 (0.18), residues: 828 sheet: -1.80 (0.66), residues: 64 loop : -0.95 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 17 TYR 0.020 0.001 TYR C 301 PHE 0.024 0.002 PHE C 730 TRP 0.036 0.003 TRP C 328 HIS 0.007 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00290 (13522) covalent geometry : angle 0.63646 (18260) hydrogen bonds : bond 0.03668 ( 502) hydrogen bonds : angle 5.07046 ( 1392) metal coordination : bond 0.00509 ( 12) metal coordination : angle 3.96968 ( 12) *********************** 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 521 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 521 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 18 LYS cc_start: 0.7665 (mmtm) cc_final: 0.7159 (mmmm) REVERT: B 22 LEU cc_start: 0.8221 (mm) cc_final: 0.7733 (mm) REVERT: B 52 PHE cc_start: 0.6764 (t80) cc_final: 0.6257 (t80) REVERT: B 59 ILE cc_start: 0.7638 (mm) cc_final: 0.7266 (mm) REVERT: B 65 ASN cc_start: 0.8320 (m-40) cc_final: 0.7949 (m-40) REVERT: B 69 VAL cc_start: 0.7789 (m) cc_final: 0.7149 (t) REVERT: B 73 CYS cc_start: 0.6457 (m) cc_final: 0.6150 (m) REVERT: B 77 TYR cc_start: 0.8165 (m-80) cc_final: 0.7647 (m-80) REVERT: B 79 LYS cc_start: 0.8469 (tppp) cc_final: 0.7183 (tppp) REVERT: B 82 GLU cc_start: 0.8733 (tt0) cc_final: 0.8011 (tt0) REVERT: B 84 ARG cc_start: 0.6647 (mtm110) cc_final: 0.5892 (mtm110) REVERT: B 88 TYR cc_start: 0.7361 (p90) cc_final: 0.6494 (p90) REVERT: B 108 ILE cc_start: 0.8094 (mt) cc_final: 0.7672 (tt) REVERT: B 114 GLN cc_start: 0.8132 (mp10) cc_final: 0.7797 (mp10) REVERT: B 124 ARG cc_start: 0.8771 (ttt-90) cc_final: 0.8355 (ttt-90) REVERT: B 128 LYS cc_start: 0.8772 (mttt) cc_final: 0.8443 (mttt) REVERT: B 132 PHE cc_start: 0.7691 (m-80) cc_final: 0.6997 (m-80) REVERT: B 139 TRP cc_start: 0.7095 (m100) cc_final: 0.6783 (m100) REVERT: A 130 GLU cc_start: 0.8461 (pt0) cc_final: 0.7542 (pm20) REVERT: A 237 ASP cc_start: 0.8339 (m-30) cc_final: 0.7725 (t0) REVERT: A 260 LEU cc_start: 0.9038 (mm) cc_final: 0.8716 (pp) REVERT: A 287 PHE cc_start: 0.6629 (m-80) cc_final: 0.6320 (m-80) REVERT: A 291 MET cc_start: 0.8478 (ttt) cc_final: 0.7675 (tmm) REVERT: A 294 ARG cc_start: 0.8495 (mpt-90) cc_final: 0.8285 (mpt-90) REVERT: A 304 MET cc_start: 0.4615 (tpt) cc_final: 0.3987 (tpt) REVERT: A 313 MET cc_start: 0.7970 (mmp) cc_final: 0.7469 (mmm) REVERT: A 315 LYS cc_start: 0.7844 (mmtm) cc_final: 0.7366 (mttt) REVERT: A 326 ARG cc_start: 0.7909 (mtm110) cc_final: 0.7582 (mtm-85) REVERT: A 330 LYS cc_start: 0.8505 (mptt) cc_final: 0.8212 (mmtt) REVERT: A 337 ARG cc_start: 0.8235 (ttm170) cc_final: 0.7606 (ttp80) REVERT: A 338 ARG cc_start: 0.7928 (mtp180) cc_final: 0.7587 (mmm-85) REVERT: A 341 GLU cc_start: 0.8071 (pp20) cc_final: 0.7815 (pp20) REVERT: A 377 MET cc_start: 0.8528 (mtt) cc_final: 0.8325 (mtp) REVERT: A 392 HIS cc_start: 0.8388 (m90) cc_final: 0.7906 (m90) REVERT: A 395 GLU cc_start: 0.6326 (tm-30) cc_final: 0.6067 (tm-30) REVERT: A 403 GLU cc_start: 0.8275 (tm-30) cc_final: 0.7908 (tm-30) REVERT: A 406 GLU cc_start: 0.8125 (tp30) cc_final: 0.7861 (mt-10) REVERT: A 424 ARG cc_start: 0.7964 (tpp-160) cc_final: 0.7640 (tpp80) REVERT: A 447 GLU cc_start: 0.8161 (mp0) cc_final: 0.7680 (tp30) REVERT: A 449 PHE cc_start: 0.7072 (m-10) cc_final: 0.6555 (m-80) REVERT: A 450 ILE cc_start: 0.8031 (mt) cc_final: 0.7251 (mt) REVERT: A 455 ASN cc_start: 0.7936 (m-40) cc_final: 0.7723 (m-40) REVERT: A 458 LEU cc_start: 0.8357 (tp) cc_final: 0.7870 (tt) REVERT: A 459 GLU cc_start: 0.6999 (mp0) cc_final: 0.6694 (mp0) REVERT: A 477 PHE cc_start: 0.7862 (m-80) cc_final: 0.7441 (m-80) REVERT: A 478 MET cc_start: 0.8148 (mtp) cc_final: 0.7486 (ttm) REVERT: A 482 PHE cc_start: 0.7849 (p90) cc_final: 0.7572 (p90) REVERT: A 499 ILE cc_start: 0.7943 (tp) cc_final: 0.7652 (tp) REVERT: A 501 MET cc_start: 0.8069 (mtt) cc_final: 0.7459 (mmm) REVERT: A 502 TYR cc_start: 0.7595 (m-10) cc_final: 0.7322 (m-10) REVERT: A 504 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7516 (mm-30) REVERT: A 505 ARG cc_start: 0.8811 (mtt90) cc_final: 0.8418 (mtt90) REVERT: A 507 ILE cc_start: 0.8691 (mt) cc_final: 0.8294 (mt) REVERT: A 520 ASN cc_start: 0.7517 (t0) cc_final: 0.7026 (p0) REVERT: A 522 TYR cc_start: 0.8073 (m-80) cc_final: 0.7771 (m-80) REVERT: A 535 ASP cc_start: 0.7657 (t0) cc_final: 0.7319 (t0) REVERT: A 539 ARG cc_start: 0.8106 (ptm160) cc_final: 0.7287 (ptm-80) REVERT: A 542 MET cc_start: 0.8242 (ptt) cc_final: 0.7502 (ptt) REVERT: A 545 MET cc_start: 0.7561 (mtm) cc_final: 0.7216 (mtm) REVERT: A 550 ASP cc_start: 0.7754 (p0) cc_final: 0.7403 (p0) REVERT: A 553 LYS cc_start: 0.8438 (mtmt) cc_final: 0.7759 (mtpp) REVERT: A 572 LYS cc_start: 0.8012 (mmtt) cc_final: 0.7737 (tptt) REVERT: A 576 GLN cc_start: 0.8527 (tp40) cc_final: 0.7902 (tp40) REVERT: A 581 GLU cc_start: 0.8431 (tt0) cc_final: 0.7737 (tt0) REVERT: A 593 ASP cc_start: 0.8145 (t0) cc_final: 0.7746 (t70) REVERT: A 600 TRP cc_start: 0.8788 (t-100) cc_final: 0.8444 (t-100) REVERT: A 603 PRO cc_start: 0.7429 (Cg_endo) cc_final: 0.7086 (Cg_exo) REVERT: A 617 ILE cc_start: 0.8441 (mm) cc_final: 0.8210 (mm) REVERT: A 619 LEU cc_start: 0.8868 (tp) cc_final: 0.8520 (tp) REVERT: A 621 LEU cc_start: 0.8197 (mt) cc_final: 0.7963 (mt) REVERT: A 635 MET cc_start: 0.8292 (mpp) cc_final: 0.7665 (mpp) REVERT: A 641 LEU cc_start: 0.8599 (mt) cc_final: 0.7823 (mm) REVERT: A 648 PHE cc_start: 0.8745 (p90) cc_final: 0.8207 (p90) REVERT: A 651 LEU cc_start: 0.8426 (mt) cc_final: 0.8166 (mt) REVERT: A 660 GLN cc_start: 0.8560 (mm-40) cc_final: 0.7950 (mm-40) REVERT: A 663 LYS cc_start: 0.8190 (ptmm) cc_final: 0.7727 (mptt) REVERT: A 667 GLU cc_start: 0.8237 (pp20) cc_final: 0.7899 (pp20) REVERT: A 682 ILE cc_start: 0.8299 (tp) cc_final: 0.8039 (tp) REVERT: A 711 LYS cc_start: 0.9288 (mmtt) cc_final: 0.8867 (mmtm) REVERT: A 712 GLU cc_start: 0.8770 (tt0) cc_final: 0.8530 (tt0) REVERT: A 715 ASN cc_start: 0.8903 (m110) cc_final: 0.8538 (m110) REVERT: A 716 LEU cc_start: 0.8805 (mt) cc_final: 0.8358 (tp) REVERT: A 717 TYR cc_start: 0.9000 (t80) cc_final: 0.8563 (t80) REVERT: A 719 ASP cc_start: 0.8129 (m-30) cc_final: 0.7818 (m-30) REVERT: A 734 ARG cc_start: 0.8531 (ttt-90) cc_final: 0.7329 (tpt-90) REVERT: A 738 HIS cc_start: 0.8198 (t70) cc_final: 0.7693 (t-170) REVERT: A 747 LYS cc_start: 0.9042 (mtpt) cc_final: 0.8549 (mmtt) REVERT: A 753 GLU cc_start: 0.8668 (mp0) cc_final: 0.8339 (mp0) REVERT: A 754 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8571 (mt-10) REVERT: A 756 GLU cc_start: 0.7137 (tp30) cc_final: 0.6670 (tp30) REVERT: A 788 ARG cc_start: 0.8632 (ttm170) cc_final: 0.7910 (ttm170) REVERT: A 792 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8014 (mm-30) REVERT: A 797 PHE cc_start: 0.6876 (m-80) cc_final: 0.6503 (m-80) REVERT: A 822 LYS cc_start: 0.8279 (mptt) cc_final: 0.8075 (mmtt) REVERT: D 22 LEU cc_start: 0.8417 (mm) cc_final: 0.8038 (mm) REVERT: D 65 ASN cc_start: 0.8354 (m-40) cc_final: 0.7945 (m-40) REVERT: D 73 CYS cc_start: 0.6244 (m) cc_final: 0.5956 (m) REVERT: D 77 TYR cc_start: 0.8208 (m-80) cc_final: 0.7824 (m-80) REVERT: D 79 LYS cc_start: 0.8412 (tppp) cc_final: 0.7949 (tppp) REVERT: D 82 GLU cc_start: 0.8660 (tt0) cc_final: 0.8197 (tt0) REVERT: D 88 TYR cc_start: 0.7069 (p90) cc_final: 0.6619 (p90) REVERT: D 94 THR cc_start: 0.7967 (m) cc_final: 0.7400 (m) REVERT: D 98 GLN cc_start: 0.8677 (mp10) cc_final: 0.8248 (mp10) REVERT: D 108 ILE cc_start: 0.8016 (mt) cc_final: 0.7549 (tt) REVERT: D 114 GLN cc_start: 0.7995 (mp10) cc_final: 0.7721 (mp10) REVERT: D 124 ARG cc_start: 0.8921 (ttt-90) cc_final: 0.8625 (ttt-90) REVERT: D 132 PHE cc_start: 0.7830 (m-80) cc_final: 0.7085 (m-80) REVERT: D 134 ASN cc_start: 0.7882 (t0) cc_final: 0.6661 (t0) REVERT: D 136 ARG cc_start: 0.8313 (mmm160) cc_final: 0.7053 (mmm160) REVERT: D 138 ARG cc_start: 0.8073 (ptt-90) cc_final: 0.7332 (ptt-90) REVERT: D 139 TRP cc_start: 0.7113 (m100) cc_final: 0.6767 (m100) REVERT: C 130 GLU cc_start: 0.8378 (pt0) cc_final: 0.7594 (pm20) REVERT: C 138 GLU cc_start: 0.8581 (mp0) cc_final: 0.8305 (mm-30) REVERT: C 246 LEU cc_start: 0.8326 (tp) cc_final: 0.8115 (tp) REVERT: C 270 ASP cc_start: 0.7471 (t70) cc_final: 0.7159 (t0) REVERT: C 283 TYR cc_start: 0.7969 (t80) cc_final: 0.7697 (t80) REVERT: C 288 ILE cc_start: 0.8693 (tt) cc_final: 0.8161 (tt) REVERT: C 304 MET cc_start: 0.5079 (tpt) cc_final: 0.4655 (tpt) REVERT: C 315 LYS cc_start: 0.8129 (mtmm) cc_final: 0.7485 (mtmm) REVERT: C 330 LYS cc_start: 0.8754 (mmmt) cc_final: 0.8343 (mppt) REVERT: C 332 ASN cc_start: 0.7558 (t0) cc_final: 0.7181 (t0) REVERT: C 337 ARG cc_start: 0.8283 (ttm170) cc_final: 0.7853 (ttp80) REVERT: C 338 ARG cc_start: 0.7652 (tpp80) cc_final: 0.6549 (tpp80) REVERT: C 344 GLN cc_start: 0.8524 (tp-100) cc_final: 0.7592 (tp-100) REVERT: C 349 TYR cc_start: 0.7931 (t80) cc_final: 0.7715 (t80) REVERT: C 382 ASN cc_start: 0.8520 (m-40) cc_final: 0.8224 (t0) REVERT: C 406 GLU cc_start: 0.7439 (pt0) cc_final: 0.7184 (pt0) REVERT: C 410 GLN cc_start: 0.9022 (mm-40) cc_final: 0.8125 (mm-40) REVERT: C 411 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7990 (tm-30) REVERT: C 429 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8384 (mt-10) REVERT: C 441 LYS cc_start: 0.9089 (tttm) cc_final: 0.8837 (tptp) REVERT: C 447 GLU cc_start: 0.7904 (tp30) cc_final: 0.7162 (tp30) REVERT: C 450 ILE cc_start: 0.8109 (mt) cc_final: 0.7292 (mt) REVERT: C 478 MET cc_start: 0.8068 (mtp) cc_final: 0.7528 (mtp) REVERT: C 482 PHE cc_start: 0.8020 (p90) cc_final: 0.7680 (p90) REVERT: C 491 LEU cc_start: 0.8560 (mt) cc_final: 0.8307 (mt) REVERT: C 493 LEU cc_start: 0.7999 (tp) cc_final: 0.7713 (tp) REVERT: C 495 TYR cc_start: 0.7719 (m-10) cc_final: 0.7459 (m-10) REVERT: C 497 ASN cc_start: 0.7711 (m110) cc_final: 0.7488 (m-40) REVERT: C 499 ILE cc_start: 0.7971 (tp) cc_final: 0.7455 (tp) REVERT: C 501 MET cc_start: 0.8108 (mtt) cc_final: 0.7787 (mtt) REVERT: C 502 TYR cc_start: 0.7503 (m-10) cc_final: 0.6982 (m-80) REVERT: C 505 ARG cc_start: 0.8805 (mtt90) cc_final: 0.8275 (mtt90) REVERT: C 507 ILE cc_start: 0.8595 (mt) cc_final: 0.8361 (mt) REVERT: C 522 TYR cc_start: 0.8061 (m-80) cc_final: 0.7398 (m-80) REVERT: C 532 ILE cc_start: 0.8535 (pt) cc_final: 0.8045 (mm) REVERT: C 539 ARG cc_start: 0.8506 (tpp-160) cc_final: 0.8120 (tpp80) REVERT: C 542 MET cc_start: 0.8101 (tpp) cc_final: 0.7434 (tpp) REVERT: C 543 ILE cc_start: 0.8904 (mt) cc_final: 0.8664 (mt) REVERT: C 545 MET cc_start: 0.7627 (mtm) cc_final: 0.7232 (mtm) REVERT: C 550 ASP cc_start: 0.7792 (p0) cc_final: 0.6672 (p0) REVERT: C 553 LYS cc_start: 0.8544 (mtmt) cc_final: 0.8132 (mtmt) REVERT: C 555 LEU cc_start: 0.8524 (tp) cc_final: 0.8053 (tp) REVERT: C 576 GLN cc_start: 0.8036 (tm-30) cc_final: 0.7633 (tm-30) REVERT: C 577 LEU cc_start: 0.8800 (mt) cc_final: 0.8383 (pp) REVERT: C 581 GLU cc_start: 0.8169 (pp20) cc_final: 0.7774 (pp20) REVERT: C 587 ILE cc_start: 0.8061 (tp) cc_final: 0.7832 (tp) REVERT: C 589 MET cc_start: 0.6389 (mtp) cc_final: 0.5962 (mtp) REVERT: C 593 ASP cc_start: 0.8023 (t70) cc_final: 0.7739 (t0) REVERT: C 617 ILE cc_start: 0.8568 (mm) cc_final: 0.8259 (mm) REVERT: C 619 LEU cc_start: 0.8910 (tp) cc_final: 0.8216 (tp) REVERT: C 621 LEU cc_start: 0.8058 (mm) cc_final: 0.7464 (mm) REVERT: C 625 ASN cc_start: 0.8488 (m-40) cc_final: 0.8134 (m110) REVERT: C 626 ASN cc_start: 0.7998 (m110) cc_final: 0.7791 (m110) REVERT: C 635 MET cc_start: 0.8231 (mpp) cc_final: 0.7478 (mpp) REVERT: C 649 ARG cc_start: 0.8751 (ttm170) cc_final: 0.8317 (ttm170) REVERT: C 651 LEU cc_start: 0.8431 (mp) cc_final: 0.8000 (tp) REVERT: C 660 GLN cc_start: 0.8386 (mm-40) cc_final: 0.7924 (mm-40) REVERT: C 663 LYS cc_start: 0.8288 (ptmm) cc_final: 0.7825 (ttpp) REVERT: C 667 GLU cc_start: 0.8002 (pp20) cc_final: 0.7651 (pp20) REVERT: C 707 ASN cc_start: 0.8149 (p0) cc_final: 0.7709 (p0) REVERT: C 708 GLU cc_start: 0.8192 (pm20) cc_final: 0.7981 (pm20) REVERT: C 712 GLU cc_start: 0.8741 (tt0) cc_final: 0.8381 (tt0) REVERT: C 713 PHE cc_start: 0.8664 (t80) cc_final: 0.7828 (t80) REVERT: C 715 ASN cc_start: 0.8835 (m110) cc_final: 0.8499 (m110) REVERT: C 716 LEU cc_start: 0.8730 (mt) cc_final: 0.8176 (pp) REVERT: C 717 TYR cc_start: 0.8934 (t80) cc_final: 0.8425 (t80) REVERT: C 719 ASP cc_start: 0.8297 (m-30) cc_final: 0.8041 (m-30) REVERT: C 720 TYR cc_start: 0.7949 (t80) cc_final: 0.7290 (t80) REVERT: C 728 LYS cc_start: 0.7867 (ttmt) cc_final: 0.7232 (ttmt) REVERT: C 730 PHE cc_start: 0.8328 (t80) cc_final: 0.7924 (t80) REVERT: C 737 PHE cc_start: 0.8050 (t80) cc_final: 0.7494 (t80) REVERT: C 738 HIS cc_start: 0.8093 (t-90) cc_final: 0.7572 (t70) REVERT: C 743 GLU cc_start: 0.8395 (mm-30) cc_final: 0.7989 (mm-30) REVERT: C 748 TYR cc_start: 0.7422 (t80) cc_final: 0.6824 (t80) REVERT: C 753 GLU cc_start: 0.8633 (mm-30) cc_final: 0.8240 (mp0) REVERT: C 756 GLU cc_start: 0.7387 (tp30) cc_final: 0.6708 (tp30) REVERT: C 788 ARG cc_start: 0.8368 (ptt180) cc_final: 0.7600 (ptt180) REVERT: C 805 PHE cc_start: 0.8465 (t80) cc_final: 0.8060 (t80) REVERT: C 806 LEU cc_start: 0.8247 (mt) cc_final: 0.7755 (mt) REVERT: C 822 LYS cc_start: 0.8497 (mmtt) cc_final: 0.8128 (mmtm) REVERT: C 835 GLU cc_start: 0.7638 (pm20) cc_final: 0.7430 (pm20) REVERT: C 855 LYS cc_start: 0.8806 (tttt) cc_final: 0.8374 (tptt) outliers start: 0 outliers final: 0 residues processed: 521 average time/residue: 0.1337 time to fit residues: 94.2232 Evaluate side-chains 499 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 499 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 48 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 133 optimal weight: 0.0020 chunk 149 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 chunk 152 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 139 optimal weight: 3.9990 overall best weight: 0.7590 ------------------------------------------------------------------------------- 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 363 ASN ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 ASN ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 HIS C 723 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.142088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.115240 restraints weight = 29571.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.119789 restraints weight = 17962.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.123141 restraints weight = 12355.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.125600 restraints weight = 9074.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.127475 restraints weight = 7011.259| |-----------------------------------------------------------------------------| r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 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 0.040 13534 Z= 0.133 Angle : 0.643 9.183 18272 Z= 0.323 Chirality : 0.045 0.250 2014 Planarity : 0.005 0.093 2372 Dihedral : 4.731 18.605 1806 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.07 % Allowed : 0.48 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.21), residues: 1610 helix: -0.32 (0.18), residues: 826 sheet: -1.69 (0.66), residues: 64 loop : -0.91 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 84 TYR 0.039 0.001 TYR C 301 PHE 0.024 0.002 PHE C 574 TRP 0.035 0.003 TRP C 328 HIS 0.010 0.001 HIS C 297 Details of bonding type rmsd covalent geometry : bond 0.00278 (13522) covalent geometry : angle 0.63712 (18260) hydrogen bonds : bond 0.03663 ( 502) hydrogen bonds : angle 5.03440 ( 1392) metal coordination : bond 0.00470 ( 12) metal coordination : angle 3.55145 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 514 time to evaluate : 0.333 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: 0.7727 (mmtm) cc_final: 0.7191 (mmmm) REVERT: B 22 LEU cc_start: 0.8252 (mm) cc_final: 0.7754 (mm) REVERT: B 52 PHE cc_start: 0.6773 (t80) cc_final: 0.6330 (t80) REVERT: B 59 ILE cc_start: 0.7663 (mm) cc_final: 0.7273 (mm) REVERT: B 65 ASN cc_start: 0.8273 (m-40) cc_final: 0.7919 (m-40) REVERT: B 73 CYS cc_start: 0.6467 (m) cc_final: 0.6148 (m) REVERT: B 77 TYR cc_start: 0.8169 (m-80) cc_final: 0.7621 (m-80) REVERT: B 79 LYS cc_start: 0.8482 (tppp) cc_final: 0.7138 (tppp) REVERT: B 80 ILE cc_start: 0.8498 (mm) cc_final: 0.8295 (mm) REVERT: B 82 GLU cc_start: 0.8753 (tt0) cc_final: 0.8041 (tt0) REVERT: B 84 ARG cc_start: 0.6651 (mtm110) cc_final: 0.5819 (mtm110) REVERT: B 108 ILE cc_start: 0.8084 (mt) cc_final: 0.7608 (tt) REVERT: B 114 GLN cc_start: 0.8138 (mp10) cc_final: 0.7808 (mp10) REVERT: B 124 ARG cc_start: 0.8782 (ttt-90) cc_final: 0.8333 (ttt-90) REVERT: B 128 LYS cc_start: 0.8801 (mttt) cc_final: 0.8467 (mttt) REVERT: B 132 PHE cc_start: 0.7746 (m-80) cc_final: 0.7060 (m-80) REVERT: B 136 ARG cc_start: 0.8074 (mmm160) cc_final: 0.7384 (mmm160) REVERT: B 139 TRP cc_start: 0.7116 (m100) cc_final: 0.6713 (m100) REVERT: A 130 GLU cc_start: 0.8457 (pt0) cc_final: 0.7527 (pm20) REVERT: A 237 ASP cc_start: 0.8334 (m-30) cc_final: 0.7736 (t0) REVERT: A 251 LYS cc_start: 0.8518 (mttp) cc_final: 0.8234 (mtmm) REVERT: A 260 LEU cc_start: 0.9021 (mm) cc_final: 0.8708 (pp) REVERT: A 287 PHE cc_start: 0.6596 (m-80) cc_final: 0.6311 (m-80) REVERT: A 291 MET cc_start: 0.8467 (ttt) cc_final: 0.7732 (tmm) REVERT: A 304 MET cc_start: 0.4603 (tpt) cc_final: 0.4052 (tpt) REVERT: A 313 MET cc_start: 0.7935 (mmp) cc_final: 0.7458 (mmm) REVERT: A 315 LYS cc_start: 0.7857 (mmtm) cc_final: 0.7201 (mmtm) REVERT: A 326 ARG cc_start: 0.7925 (mtm110) cc_final: 0.7297 (mtm-85) REVERT: A 330 LYS cc_start: 0.8520 (mptt) cc_final: 0.7942 (mmtt) REVERT: A 332 ASN cc_start: 0.7651 (t0) cc_final: 0.7253 (t0) REVERT: A 337 ARG cc_start: 0.8239 (ttm170) cc_final: 0.7597 (ttp80) REVERT: A 338 ARG cc_start: 0.7936 (mtp180) cc_final: 0.7342 (mmm-85) REVERT: A 341 GLU cc_start: 0.8142 (pp20) cc_final: 0.7642 (pp20) REVERT: A 373 LYS cc_start: 0.7936 (mtpt) cc_final: 0.7655 (mtpp) REVERT: A 392 HIS cc_start: 0.8367 (m90) cc_final: 0.7875 (m90) REVERT: A 395 GLU cc_start: 0.6308 (tm-30) cc_final: 0.6023 (tm-30) REVERT: A 397 ASP cc_start: 0.7365 (t0) cc_final: 0.7152 (t0) REVERT: A 403 GLU cc_start: 0.8298 (tm-30) cc_final: 0.7905 (tm-30) REVERT: A 406 GLU cc_start: 0.8110 (tp30) cc_final: 0.7785 (mt-10) REVERT: A 420 LYS cc_start: 0.7789 (pttp) cc_final: 0.7251 (ptmm) REVERT: A 447 GLU cc_start: 0.8183 (mp0) cc_final: 0.7684 (tp30) REVERT: A 449 PHE cc_start: 0.7051 (m-10) cc_final: 0.6524 (m-80) REVERT: A 450 ILE cc_start: 0.8011 (mt) cc_final: 0.7197 (mt) REVERT: A 455 ASN cc_start: 0.7910 (m-40) cc_final: 0.7687 (m-40) REVERT: A 458 LEU cc_start: 0.8365 (tp) cc_final: 0.7983 (tt) REVERT: A 459 GLU cc_start: 0.7050 (mp0) cc_final: 0.6719 (mp0) REVERT: A 478 MET cc_start: 0.8126 (mtp) cc_final: 0.7349 (mtp) REVERT: A 482 PHE cc_start: 0.7856 (p90) cc_final: 0.7621 (p90) REVERT: A 499 ILE cc_start: 0.7962 (tp) cc_final: 0.7676 (tp) REVERT: A 501 MET cc_start: 0.8066 (mtt) cc_final: 0.7392 (mmm) REVERT: A 502 TYR cc_start: 0.7609 (m-10) cc_final: 0.7386 (m-10) REVERT: A 504 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7624 (mm-30) REVERT: A 505 ARG cc_start: 0.8805 (mtt90) cc_final: 0.8414 (mtt90) REVERT: A 507 ILE cc_start: 0.8692 (mt) cc_final: 0.8384 (mt) REVERT: A 520 ASN cc_start: 0.7512 (t0) cc_final: 0.7045 (p0) REVERT: A 522 TYR cc_start: 0.8061 (m-80) cc_final: 0.7782 (m-80) REVERT: A 535 ASP cc_start: 0.7650 (t0) cc_final: 0.7219 (t0) REVERT: A 539 ARG cc_start: 0.8093 (ptm160) cc_final: 0.7231 (ptm-80) REVERT: A 542 MET cc_start: 0.8232 (ptt) cc_final: 0.7546 (ptt) REVERT: A 545 MET cc_start: 0.7508 (mtm) cc_final: 0.7181 (mtm) REVERT: A 550 ASP cc_start: 0.7727 (p0) cc_final: 0.7412 (p0) REVERT: A 553 LYS cc_start: 0.8395 (mtmt) cc_final: 0.7425 (mtpp) REVERT: A 572 LYS cc_start: 0.8024 (mmtt) cc_final: 0.7556 (tptt) REVERT: A 576 GLN cc_start: 0.8486 (tp40) cc_final: 0.7887 (tp40) REVERT: A 581 GLU cc_start: 0.8429 (tt0) cc_final: 0.7734 (tt0) REVERT: A 593 ASP cc_start: 0.8137 (t0) cc_final: 0.7751 (t70) REVERT: A 600 TRP cc_start: 0.8786 (t-100) cc_final: 0.8444 (t-100) REVERT: A 603 PRO cc_start: 0.7532 (Cg_endo) cc_final: 0.7213 (Cg_exo) REVERT: A 611 GLN cc_start: 0.7841 (tm-30) cc_final: 0.7611 (tm-30) REVERT: A 617 ILE cc_start: 0.8465 (mm) cc_final: 0.8237 (mm) REVERT: A 619 LEU cc_start: 0.8863 (tp) cc_final: 0.8523 (tp) REVERT: A 635 MET cc_start: 0.8284 (mpp) cc_final: 0.7594 (mpp) REVERT: A 641 LEU cc_start: 0.8590 (mt) cc_final: 0.7849 (mm) REVERT: A 648 PHE cc_start: 0.8780 (p90) cc_final: 0.8304 (p90) REVERT: A 651 LEU cc_start: 0.8395 (mt) cc_final: 0.8091 (mt) REVERT: A 660 GLN cc_start: 0.8555 (mm-40) cc_final: 0.7950 (mm-40) REVERT: A 663 LYS cc_start: 0.8192 (ptmm) cc_final: 0.7748 (mmtm) REVERT: A 667 GLU cc_start: 0.8205 (pp20) cc_final: 0.7920 (pp20) REVERT: A 682 ILE cc_start: 0.8291 (tp) cc_final: 0.8066 (tp) REVERT: A 712 GLU cc_start: 0.8705 (tt0) cc_final: 0.8486 (tt0) REVERT: A 715 ASN cc_start: 0.8922 (m110) cc_final: 0.8561 (m110) REVERT: A 716 LEU cc_start: 0.8821 (mt) cc_final: 0.8290 (tt) REVERT: A 717 TYR cc_start: 0.9044 (t80) cc_final: 0.8595 (t80) REVERT: A 719 ASP cc_start: 0.8148 (m-30) cc_final: 0.7853 (m-30) REVERT: A 727 GLU cc_start: 0.8169 (pt0) cc_final: 0.7884 (pm20) REVERT: A 734 ARG cc_start: 0.8535 (ttt-90) cc_final: 0.7688 (tpt-90) REVERT: A 738 HIS cc_start: 0.8189 (t70) cc_final: 0.7505 (t70) REVERT: A 739 MET cc_start: 0.7862 (ptm) cc_final: 0.7642 (ptm) REVERT: A 743 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8026 (mm-30) REVERT: A 747 LYS cc_start: 0.9045 (mtpt) cc_final: 0.8554 (mmtt) REVERT: A 753 GLU cc_start: 0.8660 (mp0) cc_final: 0.8318 (mp0) REVERT: A 754 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8572 (mt-10) REVERT: A 756 GLU cc_start: 0.7190 (tp30) cc_final: 0.6746 (tp30) REVERT: A 788 ARG cc_start: 0.8657 (ttm170) cc_final: 0.8044 (ttm170) REVERT: A 792 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8078 (mm-30) REVERT: A 797 PHE cc_start: 0.6834 (m-80) cc_final: 0.6489 (m-80) REVERT: A 822 LYS cc_start: 0.8260 (mptt) cc_final: 0.7945 (mmtm) REVERT: D 22 LEU cc_start: 0.8441 (mm) cc_final: 0.8060 (mm) REVERT: D 73 CYS cc_start: 0.6396 (m) cc_final: 0.5924 (m) REVERT: D 79 LYS cc_start: 0.8353 (tppp) cc_final: 0.7872 (tppp) REVERT: D 82 GLU cc_start: 0.8687 (tt0) cc_final: 0.8185 (tt0) REVERT: D 94 THR cc_start: 0.7995 (m) cc_final: 0.7451 (m) REVERT: D 98 GLN cc_start: 0.8649 (mp10) cc_final: 0.8235 (mp10) REVERT: D 108 ILE cc_start: 0.8012 (mt) cc_final: 0.7539 (tt) REVERT: D 114 GLN cc_start: 0.7984 (mp10) cc_final: 0.7707 (mp10) REVERT: D 124 ARG cc_start: 0.8956 (ttt-90) cc_final: 0.8355 (ttt-90) REVERT: D 128 LYS cc_start: 0.8616 (mttt) cc_final: 0.8366 (mttt) REVERT: D 132 PHE cc_start: 0.7811 (m-80) cc_final: 0.6925 (m-80) REVERT: D 134 ASN cc_start: 0.7883 (t0) cc_final: 0.6762 (t0) REVERT: D 136 ARG cc_start: 0.8330 (mmm160) cc_final: 0.7056 (mmm160) REVERT: D 138 ARG cc_start: 0.8076 (ptt-90) cc_final: 0.7315 (ptt-90) REVERT: D 139 TRP cc_start: 0.7105 (m100) cc_final: 0.6697 (m100) REVERT: C 130 GLU cc_start: 0.8407 (pt0) cc_final: 0.7621 (pm20) REVERT: C 246 LEU cc_start: 0.8330 (tp) cc_final: 0.8118 (tp) REVERT: C 270 ASP cc_start: 0.7477 (t70) cc_final: 0.7227 (t0) REVERT: C 283 TYR cc_start: 0.7911 (t80) cc_final: 0.7654 (t80) REVERT: C 288 ILE cc_start: 0.8677 (tt) cc_final: 0.8459 (tt) REVERT: C 292 GLU cc_start: 0.8280 (mm-30) cc_final: 0.8043 (mm-30) REVERT: C 304 MET cc_start: 0.5040 (tpt) cc_final: 0.4606 (tpt) REVERT: C 315 LYS cc_start: 0.8102 (mtmm) cc_final: 0.7448 (mtmm) REVERT: C 330 LYS cc_start: 0.8797 (mmmt) cc_final: 0.8402 (mmtm) REVERT: C 332 ASN cc_start: 0.7447 (t0) cc_final: 0.7087 (t0) REVERT: C 337 ARG cc_start: 0.8327 (ttm170) cc_final: 0.8020 (tmm160) REVERT: C 338 ARG cc_start: 0.7717 (tpp80) cc_final: 0.6528 (tpp80) REVERT: C 347 ILE cc_start: 0.7725 (mt) cc_final: 0.7489 (mt) REVERT: C 349 TYR cc_start: 0.7887 (t80) cc_final: 0.7661 (t80) REVERT: C 382 ASN cc_start: 0.8494 (m-40) cc_final: 0.8239 (t0) REVERT: C 397 ASP cc_start: 0.7625 (t70) cc_final: 0.7287 (t0) REVERT: C 403 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7541 (pp20) REVERT: C 406 GLU cc_start: 0.7265 (pt0) cc_final: 0.6311 (pt0) REVERT: C 410 GLN cc_start: 0.9046 (mm-40) cc_final: 0.8141 (mm110) REVERT: C 429 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8385 (mt-10) REVERT: C 441 LYS cc_start: 0.9067 (tttm) cc_final: 0.8833 (tptp) REVERT: C 447 GLU cc_start: 0.7903 (tp30) cc_final: 0.7133 (tp30) REVERT: C 450 ILE cc_start: 0.8113 (mt) cc_final: 0.7670 (mt) REVERT: C 464 TYR cc_start: 0.7677 (t80) cc_final: 0.7339 (t80) REVERT: C 478 MET cc_start: 0.8094 (mtp) cc_final: 0.7744 (mtp) REVERT: C 482 PHE cc_start: 0.7989 (p90) cc_final: 0.7681 (p90) REVERT: C 491 LEU cc_start: 0.8416 (mt) cc_final: 0.8194 (mt) REVERT: C 493 LEU cc_start: 0.7996 (tp) cc_final: 0.7718 (tp) REVERT: C 495 TYR cc_start: 0.7703 (m-10) cc_final: 0.7336 (m-10) REVERT: C 497 ASN cc_start: 0.7714 (m110) cc_final: 0.7469 (m-40) REVERT: C 499 ILE cc_start: 0.7972 (tp) cc_final: 0.7528 (tp) REVERT: C 501 MET cc_start: 0.8091 (mtt) cc_final: 0.7777 (mtt) REVERT: C 502 TYR cc_start: 0.7510 (m-10) cc_final: 0.6986 (m-10) REVERT: C 505 ARG cc_start: 0.8800 (mtt90) cc_final: 0.8273 (mtt90) REVERT: C 522 TYR cc_start: 0.8214 (m-80) cc_final: 0.7412 (m-80) REVERT: C 532 ILE cc_start: 0.8500 (pt) cc_final: 0.8012 (mm) REVERT: C 539 ARG cc_start: 0.8472 (tpp-160) cc_final: 0.8060 (tpp80) REVERT: C 542 MET cc_start: 0.8065 (tpp) cc_final: 0.7396 (tpp) REVERT: C 543 ILE cc_start: 0.8892 (mt) cc_final: 0.8666 (mt) REVERT: C 545 MET cc_start: 0.7661 (mtm) cc_final: 0.7275 (mtm) REVERT: C 550 ASP cc_start: 0.8009 (p0) cc_final: 0.7682 (p0) REVERT: C 553 LYS cc_start: 0.8475 (mtmt) cc_final: 0.7924 (mmmt) REVERT: C 555 LEU cc_start: 0.8531 (tp) cc_final: 0.8084 (tp) REVERT: C 572 LYS cc_start: 0.8495 (tptt) cc_final: 0.8219 (tptp) REVERT: C 573 GLU cc_start: 0.8217 (pm20) cc_final: 0.7978 (pm20) REVERT: C 576 GLN cc_start: 0.8010 (tm-30) cc_final: 0.7623 (tm-30) REVERT: C 577 LEU cc_start: 0.8791 (mt) cc_final: 0.8376 (pp) REVERT: C 581 GLU cc_start: 0.8121 (pp20) cc_final: 0.7766 (pp20) REVERT: C 587 ILE cc_start: 0.8026 (tp) cc_final: 0.7777 (tp) REVERT: C 589 MET cc_start: 0.6322 (mtp) cc_final: 0.5888 (mtp) REVERT: C 593 ASP cc_start: 0.7969 (t70) cc_final: 0.7720 (t0) REVERT: C 617 ILE cc_start: 0.8568 (mm) cc_final: 0.8239 (mm) REVERT: C 619 LEU cc_start: 0.8912 (tp) cc_final: 0.8629 (tp) REVERT: C 621 LEU cc_start: 0.8070 (mm) cc_final: 0.7478 (mm) REVERT: C 625 ASN cc_start: 0.8516 (m-40) cc_final: 0.8193 (m110) REVERT: C 626 ASN cc_start: 0.7987 (m110) cc_final: 0.7540 (m110) REVERT: C 635 MET cc_start: 0.8232 (mpp) cc_final: 0.7477 (mpp) REVERT: C 649 ARG cc_start: 0.8751 (ttm170) cc_final: 0.8446 (ttp-110) REVERT: C 651 LEU cc_start: 0.8431 (mp) cc_final: 0.8062 (tp) REVERT: C 660 GLN cc_start: 0.8367 (mm-40) cc_final: 0.7999 (mm-40) REVERT: C 663 LYS cc_start: 0.8297 (ptmm) cc_final: 0.7875 (ttpp) REVERT: C 667 GLU cc_start: 0.8019 (pp20) cc_final: 0.7666 (pp20) REVERT: C 676 MET cc_start: 0.7600 (mmp) cc_final: 0.7300 (mmp) REVERT: C 707 ASN cc_start: 0.8115 (p0) cc_final: 0.7688 (p0) REVERT: C 708 GLU cc_start: 0.8166 (pm20) cc_final: 0.7956 (pm20) REVERT: C 712 GLU cc_start: 0.8747 (tt0) cc_final: 0.8482 (tt0) REVERT: C 715 ASN cc_start: 0.8834 (m110) cc_final: 0.8496 (m110) REVERT: C 716 LEU cc_start: 0.8761 (mt) cc_final: 0.8249 (pp) REVERT: C 717 TYR cc_start: 0.8939 (t80) cc_final: 0.8492 (t80) REVERT: C 719 ASP cc_start: 0.8274 (m-30) cc_final: 0.8004 (m-30) REVERT: C 720 TYR cc_start: 0.7932 (t80) cc_final: 0.7267 (t80) REVERT: C 728 LYS cc_start: 0.7888 (ttmt) cc_final: 0.7245 (ttmt) REVERT: C 730 PHE cc_start: 0.8288 (t80) cc_final: 0.7912 (t80) REVERT: C 738 HIS cc_start: 0.8103 (t-90) cc_final: 0.7795 (t-170) REVERT: C 743 GLU cc_start: 0.8375 (mm-30) cc_final: 0.8015 (mm-30) REVERT: C 747 LYS cc_start: 0.9097 (mtpt) cc_final: 0.8716 (mmmm) REVERT: C 748 TYR cc_start: 0.7473 (t80) cc_final: 0.6859 (t80) REVERT: C 750 PHE cc_start: 0.8496 (m-10) cc_final: 0.7971 (m-80) REVERT: C 753 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8244 (mp0) REVERT: C 756 GLU cc_start: 0.7302 (tp30) cc_final: 0.6699 (tp30) REVERT: C 757 LEU cc_start: 0.8010 (mm) cc_final: 0.7806 (mm) REVERT: C 788 ARG cc_start: 0.8352 (ptt180) cc_final: 0.7588 (ptt180) REVERT: C 797 PHE cc_start: 0.5969 (m-80) cc_final: 0.5722 (m-80) REVERT: C 805 PHE cc_start: 0.8466 (t80) cc_final: 0.8049 (t80) REVERT: C 806 LEU cc_start: 0.8264 (mt) cc_final: 0.7788 (mt) REVERT: C 822 LYS cc_start: 0.8434 (mmtt) cc_final: 0.7974 (mmtm) REVERT: C 855 LYS cc_start: 0.8803 (tttt) cc_final: 0.8372 (tptt) outliers start: 1 outliers final: 0 residues processed: 515 average time/residue: 0.1268 time to fit residues: 88.3140 Evaluate side-chains 497 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 497 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 129 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 5 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 142 optimal weight: 0.0870 chunk 1 optimal weight: 0.0670 chunk 80 optimal weight: 5.9990 overall best weight: 0.4096 ------------------------------------------------------------------------------- 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 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 723 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.143426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.116476 restraints weight = 29564.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.121106 restraints weight = 17837.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.124514 restraints weight = 12217.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.127035 restraints weight = 8959.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.128690 restraints weight = 6902.716| |-----------------------------------------------------------------------------| r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.6565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13534 Z= 0.117 Angle : 0.637 9.742 18272 Z= 0.319 Chirality : 0.045 0.287 2014 Planarity : 0.005 0.118 2372 Dihedral : 4.644 18.220 1806 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.21), residues: 1610 helix: -0.23 (0.19), residues: 826 sheet: -1.65 (0.67), residues: 64 loop : -0.84 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 294 TYR 0.035 0.001 TYR C 301 PHE 0.022 0.001 PHE C 730 TRP 0.028 0.003 TRP C 328 HIS 0.007 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00251 (13522) covalent geometry : angle 0.63425 (18260) hydrogen bonds : bond 0.03585 ( 502) hydrogen bonds : angle 4.98099 ( 1392) metal coordination : bond 0.00333 ( 12) metal coordination : angle 2.39772 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2464.41 seconds wall clock time: 43 minutes 14.02 seconds (2594.02 seconds total)