Starting phenix.real_space_refine on Mon Dec 30 15:13:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jrq_36602/12_2024/8jrq_36602.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jrq_36602/12_2024/8jrq_36602.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jrq_36602/12_2024/8jrq_36602.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jrq_36602/12_2024/8jrq_36602.map" model { file = "/net/cci-nas-00/data/ceres_data/8jrq_36602/12_2024/8jrq_36602.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jrq_36602/12_2024/8jrq_36602.cif" } resolution = 4.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 92 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 76 5.16 5 C 8444 2.51 5 N 2248 2.21 5 O 2498 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 13270 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 1191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1191 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "A" Number of atoms: 5442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5442 Classifications: {'peptide': 676} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 27, 'TRANS': 648} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 60 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 241 SG CYS B 37 68.309 32.585 95.791 1.00112.82 S ATOM 522 SG CYS B 70 65.473 35.707 93.423 1.00109.09 S ATOM 864 SG CYS B 110 65.476 31.891 77.991 1.00 99.70 S ATOM 886 SG CYS B 113 63.164 30.431 80.490 1.00107.26 S ATOM 1148 SG CYS B 143 61.168 31.418 77.705 1.00129.08 S ATOM 1168 SG CYS B 146 62.382 34.471 79.323 1.00135.09 S Restraints were copied for chains: D, C Time building chain proxies: 11.78, per 1000 atoms: 0.89 Number of scatterers: 13270 At special positions: 0 Unit cell: (144.585, 106.029, 111.384, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 4 29.99 S 76 16.00 O 2498 8.00 N 2248 7.00 C 8444 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.07 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 201 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 37 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 70 " pdb=" ZN B 202 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 113 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 110 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 146 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 143 " pdb=" ZN D 201 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 37 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 70 " pdb=" ZN D 202 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 113 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 110 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 146 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 143 " Number of angles added : 12 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3136 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 12 sheets defined 57.5% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 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: 4.30 Time building geometry restraints manager: 3.53 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 36.670 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.910 ------------------------------------------------------------------------------- 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 : 0.007 0.065 13522 Z= 0.466 Angle : 1.091 11.295 18260 Z= 0.625 Chirality : 0.058 0.384 2014 Planarity : 0.007 0.073 2372 Dihedral : 16.229 87.399 5138 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 0.69 % Allowed : 12.26 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.43 (0.16), residues: 1610 helix: -3.55 (0.12), residues: 748 sheet: -3.93 (0.40), residues: 64 loop : -2.12 (0.19), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP D 139 HIS 0.005 0.002 HIS C 632 PHE 0.025 0.003 PHE C 633 TYR 0.029 0.003 TYR A 134 ARG 0.008 0.001 ARG C 836 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 557 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 CYS cc_start: 0.6979 (m) cc_final: 0.6684 (m) REVERT: B 79 LYS cc_start: 0.8271 (tppt) cc_final: 0.7222 (tppt) REVERT: B 108 ILE cc_start: 0.8087 (mt) cc_final: 0.7832 (tt) REVERT: B 124 ARG cc_start: 0.8225 (ttt-90) cc_final: 0.7854 (ttt-90) REVERT: B 128 LYS cc_start: 0.8083 (mttt) cc_final: 0.7797 (mttt) REVERT: B 132 PHE cc_start: 0.6844 (m-80) cc_final: 0.6009 (m-80) REVERT: A 130 GLU cc_start: 0.8522 (pt0) cc_final: 0.7837 (pp20) REVERT: A 237 ASP cc_start: 0.8054 (m-30) cc_final: 0.7437 (t70) REVERT: A 283 TYR cc_start: 0.7509 (t80) cc_final: 0.7177 (t80) REVERT: A 287 PHE cc_start: 0.7067 (m-80) cc_final: 0.6865 (m-80) REVERT: A 294 ARG cc_start: 0.8121 (mpt-90) cc_final: 0.7867 (mpt-90) REVERT: A 304 MET cc_start: 0.4377 (tpt) cc_final: 0.4147 (tpt) REVERT: A 315 LYS cc_start: 0.7698 (mmtm) cc_final: 0.7367 (mmtm) REVERT: A 332 ASN cc_start: 0.8061 (t0) cc_final: 0.7615 (t0) REVERT: A 337 ARG cc_start: 0.8089 (ttm170) cc_final: 0.7435 (ttp80) REVERT: A 341 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7738 (mt-10) REVERT: A 344 GLN cc_start: 0.8053 (tp-100) cc_final: 0.7701 (pp30) REVERT: A 349 TYR cc_start: 0.7651 (t80) cc_final: 0.7369 (t80) REVERT: A 361 LEU cc_start: 0.7317 (tp) cc_final: 0.6969 (tp) REVERT: A 403 GLU cc_start: 0.7064 (pm20) cc_final: 0.5932 (pm20) REVERT: A 406 GLU cc_start: 0.7412 (tp30) cc_final: 0.7014 (tp30) REVERT: A 407 LEU cc_start: 0.8852 (mt) cc_final: 0.8483 (mt) REVERT: A 410 GLN cc_start: 0.8609 (mm-40) cc_final: 0.7733 (mm-40) REVERT: A 447 GLU cc_start: 0.7781 (mp0) cc_final: 0.7392 (tp30) REVERT: A 449 PHE cc_start: 0.7345 (m-10) cc_final: 0.7105 (m-10) REVERT: A 450 ILE cc_start: 0.8188 (mt) cc_final: 0.7578 (mt) REVERT: A 458 LEU cc_start: 0.7940 (tp) cc_final: 0.7682 (tt) REVERT: A 463 ASP cc_start: 0.6874 (t0) cc_final: 0.6604 (t70) REVERT: A 477 PHE cc_start: 0.7731 (m-80) cc_final: 0.7200 (m-80) REVERT: A 478 MET cc_start: 0.7885 (mtp) cc_final: 0.6521 (mtp) REVERT: A 482 PHE cc_start: 0.7664 (p90) cc_final: 0.7431 (p90) REVERT: A 488 THR cc_start: 0.7105 (m) cc_final: 0.6713 (p) REVERT: A 493 LEU cc_start: 0.7548 (tp) cc_final: 0.6910 (tt) REVERT: A 501 MET cc_start: 0.7485 (mtt) cc_final: 0.6628 (mmt) REVERT: A 502 TYR cc_start: 0.6988 (m-10) cc_final: 0.6717 (m-10) REVERT: A 504 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7097 (mm-30) REVERT: A 505 ARG cc_start: 0.8066 (mtt90) cc_final: 0.7721 (mtt90) REVERT: A 507 ILE cc_start: 0.8339 (mt) cc_final: 0.7927 (mt) REVERT: A 520 ASN cc_start: 0.7089 (t0) cc_final: 0.6611 (m-40) REVERT: A 522 TYR cc_start: 0.8029 (m-80) cc_final: 0.7601 (m-80) REVERT: A 523 LEU cc_start: 0.8585 (tp) cc_final: 0.8136 (tp) REVERT: A 534 ASP cc_start: 0.7681 (m-30) cc_final: 0.7427 (m-30) REVERT: A 540 LEU cc_start: 0.8568 (mm) cc_final: 0.8358 (mm) REVERT: A 542 MET cc_start: 0.7949 (tpp) cc_final: 0.7586 (tpp) REVERT: A 553 LYS cc_start: 0.8720 (mtmt) cc_final: 0.7794 (ptmt) REVERT: A 554 GLN cc_start: 0.7655 (tt0) cc_final: 0.7012 (mm-40) REVERT: A 581 GLU cc_start: 0.7810 (tt0) cc_final: 0.7446 (tt0) REVERT: A 600 TRP cc_start: 0.8196 (t-100) cc_final: 0.7943 (t-100) REVERT: A 617 ILE cc_start: 0.8393 (mm) cc_final: 0.7935 (mm) REVERT: A 621 LEU cc_start: 0.8199 (mm) cc_final: 0.7802 (mp) REVERT: A 635 MET cc_start: 0.7797 (mpp) cc_final: 0.7118 (mpp) REVERT: A 638 TYR cc_start: 0.8037 (m-80) cc_final: 0.6507 (m-80) REVERT: A 658 LEU cc_start: 0.8505 (tp) cc_final: 0.8262 (mt) REVERT: A 660 GLN cc_start: 0.8122 (pp30) cc_final: 0.7863 (pp30) REVERT: A 661 SER cc_start: 0.8321 (m) cc_final: 0.8054 (p) REVERT: A 663 LYS cc_start: 0.7609 (ptmm) cc_final: 0.7053 (ttpp) REVERT: A 708 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8359 (pm20) REVERT: A 711 LYS cc_start: 0.9091 (mmtt) cc_final: 0.8566 (mmtm) REVERT: A 712 GLU cc_start: 0.8548 (tt0) cc_final: 0.8207 (tt0) REVERT: A 720 TYR cc_start: 0.6947 (t80) cc_final: 0.6406 (t80) REVERT: A 726 VAL cc_start: 0.8325 (OUTLIER) cc_final: 0.7987 (t) REVERT: A 727 GLU cc_start: 0.7874 (pt0) cc_final: 0.7416 (pm20) REVERT: A 729 GLN cc_start: 0.8185 (mp10) cc_final: 0.7749 (mp10) REVERT: A 730 PHE cc_start: 0.7459 (t80) cc_final: 0.7191 (t80) REVERT: A 734 ARG cc_start: 0.8484 (ttt-90) cc_final: 0.7725 (ttm-80) REVERT: A 743 GLU cc_start: 0.7143 (mm-30) cc_final: 0.6730 (mp0) REVERT: A 751 ARG cc_start: 0.7257 (mtm-85) cc_final: 0.6927 (mtp85) REVERT: A 753 GLU cc_start: 0.8120 (mp0) cc_final: 0.7788 (mp0) REVERT: A 756 GLU cc_start: 0.7458 (tp30) cc_final: 0.6630 (tp30) REVERT: A 787 ILE cc_start: 0.6650 (OUTLIER) cc_final: 0.6432 (mm) REVERT: A 788 ARG cc_start: 0.7961 (ptp90) cc_final: 0.7450 (ptp90) REVERT: A 789 GLU cc_start: 0.7729 (pt0) cc_final: 0.6933 (mt-10) REVERT: A 805 PHE cc_start: 0.8519 (t80) cc_final: 0.8287 (t80) REVERT: A 820 LEU cc_start: 0.7700 (mm) cc_final: 0.6969 (mm) REVERT: A 822 LYS cc_start: 0.8400 (mptt) cc_final: 0.8097 (mmtm) REVERT: A 862 LEU cc_start: 0.8459 (tt) cc_final: 0.8244 (mt) REVERT: D 21 GLN cc_start: 0.7491 (mt0) cc_final: 0.6866 (mt0) REVERT: D 79 LYS cc_start: 0.8298 (tppt) cc_final: 0.7226 (tppt) REVERT: D 124 ARG cc_start: 0.8168 (ttt-90) cc_final: 0.7843 (ttt-90) REVERT: D 132 PHE cc_start: 0.6801 (m-80) cc_final: 0.6119 (m-80) REVERT: C 129 THR cc_start: 0.8052 (m) cc_final: 0.7634 (p) REVERT: C 131 GLU cc_start: 0.8252 (mp0) cc_final: 0.7729 (mp0) REVERT: C 237 ASP cc_start: 0.7890 (m-30) cc_final: 0.7066 (t70) REVERT: C 241 ARG cc_start: 0.8455 (mtm-85) cc_final: 0.8221 (mtm-85) REVERT: C 283 TYR cc_start: 0.7716 (t80) cc_final: 0.7385 (t80) REVERT: C 287 PHE cc_start: 0.7291 (m-80) cc_final: 0.7070 (m-80) REVERT: C 294 ARG cc_start: 0.8112 (mpt-90) cc_final: 0.7878 (mpt-90) REVERT: C 321 GLN cc_start: 0.8246 (mt0) cc_final: 0.8018 (mm-40) REVERT: C 324 LEU cc_start: 0.8316 (tt) cc_final: 0.8090 (tp) REVERT: C 332 ASN cc_start: 0.7945 (t0) cc_final: 0.7383 (t0) REVERT: C 337 ARG cc_start: 0.8135 (ttm170) cc_final: 0.7497 (ttp80) REVERT: C 349 TYR cc_start: 0.7753 (t80) cc_final: 0.7409 (t80) REVERT: C 382 ASN cc_start: 0.8120 (m-40) cc_final: 0.7891 (m-40) REVERT: C 394 GLU cc_start: 0.6391 (mm-30) cc_final: 0.5398 (mm-30) REVERT: C 403 GLU cc_start: 0.7042 (pm20) cc_final: 0.6003 (pm20) REVERT: C 406 GLU cc_start: 0.7550 (tp30) cc_final: 0.6996 (tp30) REVERT: C 407 LEU cc_start: 0.8812 (mt) cc_final: 0.8473 (mt) REVERT: C 410 GLN cc_start: 0.8537 (mm-40) cc_final: 0.7671 (mm-40) REVERT: C 411 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7481 (mt-10) REVERT: C 447 GLU cc_start: 0.7611 (mp0) cc_final: 0.7128 (tp30) REVERT: C 477 PHE cc_start: 0.7637 (m-80) cc_final: 0.7286 (m-10) REVERT: C 478 MET cc_start: 0.7730 (mtp) cc_final: 0.6907 (mtp) REVERT: C 482 PHE cc_start: 0.7634 (p90) cc_final: 0.7378 (p90) REVERT: C 488 THR cc_start: 0.7213 (m) cc_final: 0.6893 (p) REVERT: C 493 LEU cc_start: 0.7773 (tp) cc_final: 0.7016 (tt) REVERT: C 499 ILE cc_start: 0.7700 (tp) cc_final: 0.7491 (tp) REVERT: C 501 MET cc_start: 0.7400 (mtt) cc_final: 0.7165 (mtt) REVERT: C 504 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7292 (mm-30) REVERT: C 505 ARG cc_start: 0.8059 (mtt90) cc_final: 0.7533 (mtt90) REVERT: C 507 ILE cc_start: 0.8387 (mt) cc_final: 0.7935 (mt) REVERT: C 520 ASN cc_start: 0.7360 (t0) cc_final: 0.7040 (m-40) REVERT: C 522 TYR cc_start: 0.8011 (m-80) cc_final: 0.7720 (m-80) REVERT: C 540 LEU cc_start: 0.8501 (mm) cc_final: 0.8282 (mm) REVERT: C 542 MET cc_start: 0.7984 (tpp) cc_final: 0.7447 (tpp) REVERT: C 546 GLU cc_start: 0.6875 (tt0) cc_final: 0.6317 (tt0) REVERT: C 553 LYS cc_start: 0.8735 (mtmt) cc_final: 0.8166 (ptmt) REVERT: C 555 LEU cc_start: 0.8730 (tp) cc_final: 0.8514 (tp) REVERT: C 589 MET cc_start: 0.6343 (mtp) cc_final: 0.6119 (mtp) REVERT: C 600 TRP cc_start: 0.8253 (t-100) cc_final: 0.7992 (t-100) REVERT: C 617 ILE cc_start: 0.8573 (mm) cc_final: 0.8143 (mm) REVERT: C 621 LEU cc_start: 0.8219 (mm) cc_final: 0.7838 (mt) REVERT: C 635 MET cc_start: 0.7695 (mpp) cc_final: 0.6950 (mpp) REVERT: C 638 TYR cc_start: 0.7934 (m-80) cc_final: 0.6373 (m-80) REVERT: C 651 LEU cc_start: 0.8202 (tp) cc_final: 0.7956 (mt) REVERT: C 658 LEU cc_start: 0.8745 (tp) cc_final: 0.8340 (tp) REVERT: C 661 SER cc_start: 0.8402 (m) cc_final: 0.8008 (p) REVERT: C 682 ILE cc_start: 0.6755 (pt) cc_final: 0.5788 (pt) REVERT: C 711 LYS cc_start: 0.9019 (mmtt) cc_final: 0.8515 (mmtm) REVERT: C 712 GLU cc_start: 0.8649 (tt0) cc_final: 0.8355 (tt0) REVERT: C 720 TYR cc_start: 0.7030 (t80) cc_final: 0.6378 (t80) REVERT: C 726 VAL cc_start: 0.8058 (OUTLIER) cc_final: 0.7672 (t) REVERT: C 729 GLN cc_start: 0.8186 (mp10) cc_final: 0.7879 (mp10) REVERT: C 730 PHE cc_start: 0.7485 (t80) cc_final: 0.7117 (t80) REVERT: C 739 MET cc_start: 0.7184 (ptm) cc_final: 0.6949 (ptm) REVERT: C 743 GLU cc_start: 0.7418 (mm-30) cc_final: 0.7125 (mm-30) REVERT: C 748 TYR cc_start: 0.7149 (t80) cc_final: 0.6854 (t80) REVERT: C 751 ARG cc_start: 0.7315 (mtm-85) cc_final: 0.7052 (mtp85) REVERT: C 753 GLU cc_start: 0.8164 (mp0) cc_final: 0.7905 (mp0) REVERT: C 756 GLU cc_start: 0.7376 (tp30) cc_final: 0.6486 (tp30) REVERT: C 757 LEU cc_start: 0.7371 (mm) cc_final: 0.7147 (mm) REVERT: C 763 ARG cc_start: 0.5179 (mmm160) cc_final: 0.4858 (tpp80) REVERT: C 787 ILE cc_start: 0.6891 (OUTLIER) cc_final: 0.6533 (mm) REVERT: C 788 ARG cc_start: 0.7999 (ptp90) cc_final: 0.7369 (ptp90) REVERT: C 789 GLU cc_start: 0.7881 (pt0) cc_final: 0.7175 (mt-10) REVERT: C 805 PHE cc_start: 0.8475 (t80) cc_final: 0.8244 (t80) REVERT: C 820 LEU cc_start: 0.7518 (mm) cc_final: 0.6792 (mm) REVERT: C 822 LYS cc_start: 0.8473 (mptt) cc_final: 0.8235 (mmtp) REVERT: C 855 LYS cc_start: 0.8803 (tttt) cc_final: 0.7586 (tmtt) outliers start: 10 outliers final: 4 residues processed: 565 average time/residue: 0.3462 time to fit residues: 265.0560 Evaluate side-chains 514 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 506 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 126 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 147 optimal weight: 0.5980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN B 134 ASN ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 ASN A 285 ASN ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 GLN D 65 ASN D 97 GLN D 134 ASN ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 ASN C 285 ASN C 455 ASN C 515 GLN ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 723 ASN C 738 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13522 Z= 0.258 Angle : 0.723 8.316 18260 Z= 0.387 Chirality : 0.045 0.227 2014 Planarity : 0.006 0.070 2372 Dihedral : 6.248 23.604 1806 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.21 % Allowed : 6.61 % Favored : 93.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.18), residues: 1610 helix: -2.09 (0.15), residues: 834 sheet: -3.18 (0.50), residues: 72 loop : -1.62 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 328 HIS 0.003 0.001 HIS A 655 PHE 0.039 0.002 PHE D 54 TYR 0.032 0.002 TYR C 127 ARG 0.012 0.001 ARG D 84 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 550 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 ILE cc_start: 0.8241 (tt) cc_final: 0.7981 (tt) REVERT: B 59 ILE cc_start: 0.7613 (mm) cc_final: 0.7398 (tp) REVERT: B 65 ASN cc_start: 0.7693 (m-40) cc_final: 0.7468 (m-40) REVERT: B 73 CYS cc_start: 0.7061 (m) cc_final: 0.6648 (m) REVERT: B 80 ILE cc_start: 0.8300 (mm) cc_final: 0.7941 (mm) REVERT: B 88 TYR cc_start: 0.7043 (p90) cc_final: 0.6716 (p90) REVERT: B 128 LYS cc_start: 0.8102 (mttt) cc_final: 0.7775 (mmtt) REVERT: B 132 PHE cc_start: 0.6647 (m-80) cc_final: 0.6069 (m-80) REVERT: B 134 ASN cc_start: 0.7104 (t0) cc_final: 0.6674 (t0) REVERT: A 130 GLU cc_start: 0.8569 (pt0) cc_final: 0.7581 (pm20) REVERT: A 138 GLU cc_start: 0.8152 (mp0) cc_final: 0.7615 (mp0) REVERT: A 237 ASP cc_start: 0.8328 (m-30) cc_final: 0.7298 (t0) REVERT: A 260 LEU cc_start: 0.9013 (mm) cc_final: 0.8727 (mm) REVERT: A 291 MET cc_start: 0.8257 (ttt) cc_final: 0.7761 (ttm) REVERT: A 304 MET cc_start: 0.4776 (tpt) cc_final: 0.4272 (tpt) REVERT: A 315 LYS cc_start: 0.7850 (mmtm) cc_final: 0.7388 (mmtm) REVERT: A 332 ASN cc_start: 0.7784 (t0) cc_final: 0.7285 (t0) REVERT: A 337 ARG cc_start: 0.8062 (ttm170) cc_final: 0.7732 (ttp80) REVERT: A 341 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7310 (mt-10) REVERT: A 343 PHE cc_start: 0.8828 (m-80) cc_final: 0.8590 (m-80) REVERT: A 344 GLN cc_start: 0.8299 (tp-100) cc_final: 0.7003 (tp-100) REVERT: A 348 THR cc_start: 0.7806 (m) cc_final: 0.7504 (m) REVERT: A 361 LEU cc_start: 0.7577 (tp) cc_final: 0.7287 (tp) REVERT: A 392 HIS cc_start: 0.7914 (m90) cc_final: 0.7432 (m-70) REVERT: A 407 LEU cc_start: 0.9013 (mt) cc_final: 0.8721 (mt) REVERT: A 409 LEU cc_start: 0.8522 (tp) cc_final: 0.8160 (pp) REVERT: A 410 GLN cc_start: 0.8496 (mm-40) cc_final: 0.8287 (mm110) REVERT: A 447 GLU cc_start: 0.7867 (mp0) cc_final: 0.7448 (tp30) REVERT: A 449 PHE cc_start: 0.7193 (m-10) cc_final: 0.6872 (m-10) REVERT: A 450 ILE cc_start: 0.8204 (mt) cc_final: 0.7440 (mt) REVERT: A 455 ASN cc_start: 0.7643 (m110) cc_final: 0.7413 (m110) REVERT: A 458 LEU cc_start: 0.8294 (tp) cc_final: 0.7703 (tt) REVERT: A 464 TYR cc_start: 0.7012 (t80) cc_final: 0.6464 (t80) REVERT: A 478 MET cc_start: 0.7870 (mtp) cc_final: 0.7071 (mtp) REVERT: A 499 ILE cc_start: 0.7877 (tp) cc_final: 0.7346 (tp) REVERT: A 501 MET cc_start: 0.7927 (mtt) cc_final: 0.6880 (ptp) REVERT: A 504 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7069 (mm-30) REVERT: A 507 ILE cc_start: 0.8403 (mt) cc_final: 0.7872 (mt) REVERT: A 523 LEU cc_start: 0.8349 (tp) cc_final: 0.7922 (tp) REVERT: A 535 ASP cc_start: 0.6471 (m-30) cc_final: 0.6260 (m-30) REVERT: A 545 MET cc_start: 0.7569 (mtm) cc_final: 0.7170 (mtm) REVERT: A 550 ASP cc_start: 0.7577 (p0) cc_final: 0.7218 (p0) REVERT: A 553 LYS cc_start: 0.8778 (mtmt) cc_final: 0.8514 (mtpp) REVERT: A 572 LYS cc_start: 0.8370 (tttp) cc_final: 0.7977 (ttmm) REVERT: A 573 GLU cc_start: 0.7734 (pp20) cc_final: 0.7332 (pp20) REVERT: A 576 GLN cc_start: 0.7634 (tp-100) cc_final: 0.6991 (tp-100) REVERT: A 577 LEU cc_start: 0.8718 (mt) cc_final: 0.8316 (mt) REVERT: A 593 ASP cc_start: 0.7572 (t0) cc_final: 0.7371 (t0) REVERT: A 613 THR cc_start: 0.8235 (m) cc_final: 0.8025 (m) REVERT: A 617 ILE cc_start: 0.8389 (mm) cc_final: 0.7981 (mm) REVERT: A 621 LEU cc_start: 0.7985 (mm) cc_final: 0.7543 (mp) REVERT: A 635 MET cc_start: 0.7713 (mpp) cc_final: 0.7091 (mpp) REVERT: A 641 LEU cc_start: 0.8374 (mt) cc_final: 0.7531 (pp) REVERT: A 651 LEU cc_start: 0.8416 (mt) cc_final: 0.8137 (mt) REVERT: A 658 LEU cc_start: 0.8358 (tp) cc_final: 0.7920 (tp) REVERT: A 660 GLN cc_start: 0.8167 (pp30) cc_final: 0.7812 (pp30) REVERT: A 661 SER cc_start: 0.8526 (m) cc_final: 0.8194 (p) REVERT: A 663 LYS cc_start: 0.7993 (ptmm) cc_final: 0.7483 (ttpp) REVERT: A 711 LYS cc_start: 0.9200 (mmtt) cc_final: 0.8883 (mmtm) REVERT: A 716 LEU cc_start: 0.8740 (mt) cc_final: 0.8449 (mt) REVERT: A 717 TYR cc_start: 0.8023 (t80) cc_final: 0.7744 (t80) REVERT: A 720 TYR cc_start: 0.7162 (t80) cc_final: 0.6710 (t80) REVERT: A 728 LYS cc_start: 0.8485 (ttpt) cc_final: 0.7805 (ptmm) REVERT: A 730 PHE cc_start: 0.7498 (t80) cc_final: 0.7131 (t80) REVERT: A 734 ARG cc_start: 0.8238 (ttt-90) cc_final: 0.7151 (tpt-90) REVERT: A 743 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7424 (mm-30) REVERT: A 751 ARG cc_start: 0.7453 (mtm-85) cc_final: 0.7242 (mmm160) REVERT: A 753 GLU cc_start: 0.8377 (mp0) cc_final: 0.8066 (mp0) REVERT: A 756 GLU cc_start: 0.7756 (tp30) cc_final: 0.7305 (tp30) REVERT: A 792 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8274 (mm-30) REVERT: A 805 PHE cc_start: 0.8470 (t80) cc_final: 0.8036 (t80) REVERT: A 806 LEU cc_start: 0.8359 (mt) cc_final: 0.7910 (mt) REVERT: A 822 LYS cc_start: 0.8524 (mptt) cc_final: 0.8164 (mmtm) REVERT: A 862 LEU cc_start: 0.8501 (tt) cc_final: 0.8233 (mt) REVERT: D 47 ARG cc_start: 0.7469 (mmm160) cc_final: 0.6504 (mmm160) REVERT: D 59 ILE cc_start: 0.7489 (mm) cc_final: 0.7278 (tp) REVERT: D 65 ASN cc_start: 0.7776 (m-40) cc_final: 0.7486 (m-40) REVERT: D 73 CYS cc_start: 0.6937 (m) cc_final: 0.6407 (m) REVERT: D 79 LYS cc_start: 0.8378 (tppt) cc_final: 0.7201 (tppt) REVERT: D 80 ILE cc_start: 0.8245 (mm) cc_final: 0.7894 (mm) REVERT: D 94 THR cc_start: 0.7274 (p) cc_final: 0.6908 (p) REVERT: D 132 PHE cc_start: 0.6625 (m-80) cc_final: 0.6183 (m-80) REVERT: D 134 ASN cc_start: 0.6666 (t0) cc_final: 0.6175 (t0) REVERT: C 130 GLU cc_start: 0.8507 (pt0) cc_final: 0.8099 (pt0) REVERT: C 237 ASP cc_start: 0.7948 (m-30) cc_final: 0.7493 (t0) REVERT: C 241 ARG cc_start: 0.8492 (mtm-85) cc_final: 0.8254 (mtm-85) REVERT: C 260 LEU cc_start: 0.8850 (mm) cc_final: 0.8557 (mm) REVERT: C 287 PHE cc_start: 0.7002 (m-80) cc_final: 0.6787 (m-80) REVERT: C 291 MET cc_start: 0.8433 (ttt) cc_final: 0.8077 (ttt) REVERT: C 315 LYS cc_start: 0.7995 (mtmm) cc_final: 0.7484 (mttp) REVERT: C 332 ASN cc_start: 0.7603 (t0) cc_final: 0.7162 (t0) REVERT: C 337 ARG cc_start: 0.8125 (ttm170) cc_final: 0.7640 (ttp80) REVERT: C 338 ARG cc_start: 0.8007 (mtp85) cc_final: 0.7389 (mtp-110) REVERT: C 344 GLN cc_start: 0.8247 (tp-100) cc_final: 0.6995 (tp-100) REVERT: C 349 TYR cc_start: 0.7522 (t80) cc_final: 0.7283 (t80) REVERT: C 376 LYS cc_start: 0.8470 (ttmt) cc_final: 0.7310 (tttt) REVERT: C 380 TYR cc_start: 0.8223 (m-10) cc_final: 0.7728 (m-10) REVERT: C 394 GLU cc_start: 0.6547 (mm-30) cc_final: 0.6105 (mm-30) REVERT: C 407 LEU cc_start: 0.8962 (mt) cc_final: 0.8289 (pp) REVERT: C 409 LEU cc_start: 0.8533 (tp) cc_final: 0.8061 (pp) REVERT: C 411 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7287 (mt-10) REVERT: C 447 GLU cc_start: 0.7702 (mp0) cc_final: 0.7331 (tp30) REVERT: C 449 PHE cc_start: 0.7375 (m-10) cc_final: 0.7028 (m-10) REVERT: C 450 ILE cc_start: 0.8158 (mt) cc_final: 0.7264 (mt) REVERT: C 458 LEU cc_start: 0.8638 (tp) cc_final: 0.8248 (tt) REVERT: C 478 MET cc_start: 0.7661 (mtp) cc_final: 0.7098 (mtp) REVERT: C 493 LEU cc_start: 0.7470 (tp) cc_final: 0.6985 (tp) REVERT: C 499 ILE cc_start: 0.8018 (tp) cc_final: 0.7619 (tp) REVERT: C 501 MET cc_start: 0.7870 (mtt) cc_final: 0.7386 (mtt) REVERT: C 502 TYR cc_start: 0.7050 (m-10) cc_final: 0.6764 (m-10) REVERT: C 505 ARG cc_start: 0.8186 (mtt90) cc_final: 0.7669 (mtt90) REVERT: C 507 ILE cc_start: 0.8405 (mt) cc_final: 0.8098 (mt) REVERT: C 522 TYR cc_start: 0.7919 (m-80) cc_final: 0.7714 (m-80) REVERT: C 542 MET cc_start: 0.7670 (tpp) cc_final: 0.7109 (tpp) REVERT: C 545 MET cc_start: 0.7548 (mtm) cc_final: 0.6948 (mtm) REVERT: C 546 GLU cc_start: 0.6841 (tt0) cc_final: 0.6302 (tt0) REVERT: C 553 LYS cc_start: 0.8687 (mtmt) cc_final: 0.8478 (mtpp) REVERT: C 576 GLN cc_start: 0.7146 (tm-30) cc_final: 0.6550 (tm-30) REVERT: C 577 LEU cc_start: 0.8599 (mt) cc_final: 0.8202 (mt) REVERT: C 613 THR cc_start: 0.8367 (m) cc_final: 0.8148 (p) REVERT: C 619 LEU cc_start: 0.8571 (tp) cc_final: 0.8353 (tp) REVERT: C 621 LEU cc_start: 0.8091 (mm) cc_final: 0.7738 (mm) REVERT: C 625 ASN cc_start: 0.7996 (m110) cc_final: 0.7622 (m-40) REVERT: C 626 ASN cc_start: 0.7882 (m-40) cc_final: 0.7541 (m110) REVERT: C 635 MET cc_start: 0.7562 (mpp) cc_final: 0.7007 (mpp) REVERT: C 641 LEU cc_start: 0.8378 (mt) cc_final: 0.7840 (pp) REVERT: C 648 PHE cc_start: 0.8757 (p90) cc_final: 0.8355 (p90) REVERT: C 651 LEU cc_start: 0.8240 (tp) cc_final: 0.7979 (mt) REVERT: C 658 LEU cc_start: 0.8524 (tp) cc_final: 0.8081 (tp) REVERT: C 661 SER cc_start: 0.8503 (m) cc_final: 0.8231 (p) REVERT: C 663 LYS cc_start: 0.8118 (ptmm) cc_final: 0.6965 (mmtt) REVERT: C 664 ASP cc_start: 0.8002 (m-30) cc_final: 0.6372 (p0) REVERT: C 711 LYS cc_start: 0.9178 (mmtt) cc_final: 0.8657 (mmtm) REVERT: C 712 GLU cc_start: 0.8777 (tt0) cc_final: 0.8544 (tt0) REVERT: C 720 TYR cc_start: 0.7254 (t80) cc_final: 0.6774 (t80) REVERT: C 730 PHE cc_start: 0.7520 (t80) cc_final: 0.7254 (t80) REVERT: C 738 HIS cc_start: 0.7835 (t-90) cc_final: 0.6927 (t-90) REVERT: C 743 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7566 (mm-30) REVERT: C 748 TYR cc_start: 0.6907 (t80) cc_final: 0.6610 (t80) REVERT: C 753 GLU cc_start: 0.8346 (mp0) cc_final: 0.8095 (mp0) REVERT: C 756 GLU cc_start: 0.7628 (tp30) cc_final: 0.7202 (tp30) REVERT: C 789 GLU cc_start: 0.7994 (pt0) cc_final: 0.7529 (mt-10) REVERT: C 791 TRP cc_start: 0.7618 (t60) cc_final: 0.7168 (t60) REVERT: C 855 LYS cc_start: 0.8897 (tttt) cc_final: 0.7756 (tppt) outliers start: 3 outliers final: 0 residues processed: 553 average time/residue: 0.3264 time to fit residues: 245.5689 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 : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 81 optimal weight: 8.9990 chunk 45 optimal weight: 0.5980 chunk 122 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 40 optimal weight: 0.0570 chunk 147 optimal weight: 4.9990 chunk 159 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 chunk 146 optimal weight: 6.9990 chunk 50 optimal weight: 0.0970 chunk 118 optimal weight: 3.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- 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 A 455 ASN A 518 GLN A 626 ASN D 123 GLN ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 455 ASN C 723 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13522 Z= 0.192 Angle : 0.650 8.187 18260 Z= 0.339 Chirality : 0.044 0.173 2014 Planarity : 0.005 0.065 2372 Dihedral : 5.528 20.758 1806 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.14 % Allowed : 5.03 % Favored : 94.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.20), residues: 1610 helix: -1.35 (0.16), residues: 828 sheet: -3.18 (0.53), residues: 72 loop : -1.31 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP D 139 HIS 0.003 0.001 HIS C 655 PHE 0.023 0.002 PHE C 633 TYR 0.024 0.002 TYR A 717 ARG 0.011 0.001 ARG A 539 *********************** 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 536 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 534 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 CYS cc_start: 0.7080 (m) cc_final: 0.6782 (m) REVERT: B 77 TYR cc_start: 0.8020 (m-80) cc_final: 0.7486 (m-80) REVERT: B 82 GLU cc_start: 0.8134 (tt0) cc_final: 0.7806 (tt0) REVERT: B 88 TYR cc_start: 0.6891 (p90) cc_final: 0.6619 (p90) REVERT: B 94 THR cc_start: 0.7047 (p) cc_final: 0.6632 (m) REVERT: B 98 GLN cc_start: 0.8644 (mp10) cc_final: 0.8234 (mp10) REVERT: B 124 ARG cc_start: 0.8252 (ttt-90) cc_final: 0.7797 (ttt-90) REVERT: B 134 ASN cc_start: 0.7222 (t0) cc_final: 0.6619 (t0) REVERT: A 130 GLU cc_start: 0.8512 (pt0) cc_final: 0.7601 (pm20) REVERT: A 138 GLU cc_start: 0.8306 (mp0) cc_final: 0.7712 (mp0) REVERT: A 237 ASP cc_start: 0.8433 (m-30) cc_final: 0.7891 (t0) REVERT: A 241 ARG cc_start: 0.8505 (mtp-110) cc_final: 0.8257 (mtp-110) REVERT: A 291 MET cc_start: 0.8199 (ttt) cc_final: 0.7718 (ttm) REVERT: A 294 ARG cc_start: 0.8318 (mpt180) cc_final: 0.7960 (mpt180) REVERT: A 304 MET cc_start: 0.4653 (tpt) cc_final: 0.3828 (tpt) REVERT: A 337 ARG cc_start: 0.8058 (ttm170) cc_final: 0.7236 (ttp80) REVERT: A 338 ARG cc_start: 0.7857 (mtp85) cc_final: 0.7531 (mmm-85) REVERT: A 341 GLU cc_start: 0.8157 (mt-10) cc_final: 0.6715 (mt-10) REVERT: A 344 GLN cc_start: 0.8187 (tp-100) cc_final: 0.6983 (tp-100) REVERT: A 345 GLN cc_start: 0.8302 (mt0) cc_final: 0.7493 (tp40) REVERT: A 346 LEU cc_start: 0.8555 (tp) cc_final: 0.8353 (tp) REVERT: A 350 LYS cc_start: 0.7576 (mmpt) cc_final: 0.6939 (tptt) REVERT: A 361 LEU cc_start: 0.7301 (tp) cc_final: 0.7053 (tp) REVERT: A 392 HIS cc_start: 0.7937 (m90) cc_final: 0.7559 (m90) REVERT: A 406 GLU cc_start: 0.7517 (tt0) cc_final: 0.7136 (tt0) REVERT: A 407 LEU cc_start: 0.8916 (mt) cc_final: 0.8497 (pp) REVERT: A 447 GLU cc_start: 0.7891 (mp0) cc_final: 0.7491 (tp30) REVERT: A 450 ILE cc_start: 0.8235 (mt) cc_final: 0.7134 (mt) REVERT: A 458 LEU cc_start: 0.8437 (tp) cc_final: 0.8228 (tp) REVERT: A 468 LYS cc_start: 0.7202 (pttt) cc_final: 0.6978 (pttt) REVERT: A 478 MET cc_start: 0.7849 (mtp) cc_final: 0.6630 (mtp) REVERT: A 489 LYS cc_start: 0.8079 (mtmm) cc_final: 0.7752 (ptpp) REVERT: A 499 ILE cc_start: 0.7817 (tp) cc_final: 0.7454 (tp) REVERT: A 502 TYR cc_start: 0.6988 (m-10) cc_final: 0.6688 (m-10) REVERT: A 504 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7140 (mm-30) REVERT: A 505 ARG cc_start: 0.8164 (mtt90) cc_final: 0.7777 (mtt90) REVERT: A 507 ILE cc_start: 0.8417 (mt) cc_final: 0.7857 (mp) REVERT: A 522 TYR cc_start: 0.7916 (m-80) cc_final: 0.7450 (m-80) REVERT: A 523 LEU cc_start: 0.8094 (tp) cc_final: 0.7845 (tp) REVERT: A 532 ILE cc_start: 0.7999 (pt) cc_final: 0.7232 (pt) REVERT: A 539 ARG cc_start: 0.7632 (ttm110) cc_final: 0.6902 (ptm160) REVERT: A 542 MET cc_start: 0.8032 (ptt) cc_final: 0.7641 (tmm) REVERT: A 543 ILE cc_start: 0.8758 (mt) cc_final: 0.8079 (mt) REVERT: A 545 MET cc_start: 0.7580 (mtm) cc_final: 0.7096 (mtm) REVERT: A 550 ASP cc_start: 0.7548 (p0) cc_final: 0.7194 (p0) REVERT: A 553 LYS cc_start: 0.8715 (mtmt) cc_final: 0.8490 (mtpp) REVERT: A 554 GLN cc_start: 0.7454 (mm110) cc_final: 0.6917 (tp40) REVERT: A 573 GLU cc_start: 0.7630 (pp20) cc_final: 0.7294 (pp20) REVERT: A 576 GLN cc_start: 0.7625 (tp-100) cc_final: 0.7030 (tp-100) REVERT: A 577 LEU cc_start: 0.8674 (mt) cc_final: 0.8303 (mt) REVERT: A 589 MET cc_start: 0.5747 (mtt) cc_final: 0.3988 (mtt) REVERT: A 593 ASP cc_start: 0.7498 (t0) cc_final: 0.7269 (t70) REVERT: A 617 ILE cc_start: 0.8425 (mm) cc_final: 0.8008 (mm) REVERT: A 621 LEU cc_start: 0.7834 (mm) cc_final: 0.7391 (mt) REVERT: A 625 ASN cc_start: 0.8036 (m110) cc_final: 0.7773 (m110) REVERT: A 635 MET cc_start: 0.7795 (mpp) cc_final: 0.7113 (mpp) REVERT: A 641 LEU cc_start: 0.8356 (mt) cc_final: 0.7903 (mt) REVERT: A 642 MET cc_start: 0.7753 (mmp) cc_final: 0.7525 (mmp) REVERT: A 651 LEU cc_start: 0.8416 (mt) cc_final: 0.8173 (mt) REVERT: A 658 LEU cc_start: 0.8367 (tp) cc_final: 0.8094 (tp) REVERT: A 660 GLN cc_start: 0.8107 (pp30) cc_final: 0.7525 (pp30) REVERT: A 663 LYS cc_start: 0.8032 (ptmm) cc_final: 0.7144 (ttpp) REVERT: A 682 ILE cc_start: 0.8680 (tp) cc_final: 0.8425 (tp) REVERT: A 711 LYS cc_start: 0.9245 (mmtt) cc_final: 0.8752 (mmtm) REVERT: A 716 LEU cc_start: 0.8666 (mt) cc_final: 0.8358 (mt) REVERT: A 717 TYR cc_start: 0.8199 (t80) cc_final: 0.7866 (t80) REVERT: A 720 TYR cc_start: 0.7311 (t80) cc_final: 0.6682 (t80) REVERT: A 728 LYS cc_start: 0.8250 (ttpt) cc_final: 0.7443 (ptmm) REVERT: A 730 PHE cc_start: 0.7473 (t80) cc_final: 0.7149 (t80) REVERT: A 734 ARG cc_start: 0.8194 (ttt-90) cc_final: 0.7674 (ttt180) REVERT: A 743 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7502 (mm-30) REVERT: A 753 GLU cc_start: 0.8319 (mp0) cc_final: 0.8003 (mp0) REVERT: A 792 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8189 (mm-30) REVERT: A 822 LYS cc_start: 0.8441 (mptt) cc_final: 0.8196 (mmtm) REVERT: A 862 LEU cc_start: 0.8538 (tt) cc_final: 0.8238 (mt) REVERT: D 22 LEU cc_start: 0.8216 (mm) cc_final: 0.7926 (mm) REVERT: D 47 ARG cc_start: 0.7521 (mmm160) cc_final: 0.6985 (mmm160) REVERT: D 65 ASN cc_start: 0.7755 (m-40) cc_final: 0.7421 (m-40) REVERT: D 73 CYS cc_start: 0.6843 (m) cc_final: 0.6306 (m) REVERT: D 79 LYS cc_start: 0.8172 (tppp) cc_final: 0.7016 (tppp) REVERT: D 80 ILE cc_start: 0.8122 (mm) cc_final: 0.7876 (mm) REVERT: D 82 GLU cc_start: 0.8244 (tt0) cc_final: 0.7685 (tt0) REVERT: D 88 TYR cc_start: 0.6981 (p90) cc_final: 0.6666 (p90) REVERT: D 94 THR cc_start: 0.7238 (p) cc_final: 0.6633 (p) REVERT: D 132 PHE cc_start: 0.6715 (m-80) cc_final: 0.6223 (m-80) REVERT: D 134 ASN cc_start: 0.7069 (t0) cc_final: 0.6494 (t0) REVERT: C 130 GLU cc_start: 0.8465 (pt0) cc_final: 0.8078 (pt0) REVERT: C 237 ASP cc_start: 0.7908 (m-30) cc_final: 0.7642 (t0) REVERT: C 241 ARG cc_start: 0.8469 (mtm-85) cc_final: 0.8268 (mtm-85) REVERT: C 288 ILE cc_start: 0.8555 (tt) cc_final: 0.8071 (tt) REVERT: C 315 LYS cc_start: 0.7967 (mtmm) cc_final: 0.7291 (mttt) REVERT: C 332 ASN cc_start: 0.7655 (t0) cc_final: 0.7150 (t0) REVERT: C 337 ARG cc_start: 0.8022 (ttm170) cc_final: 0.7822 (tmm-80) REVERT: C 344 GLN cc_start: 0.8146 (tp-100) cc_final: 0.6947 (tp-100) REVERT: C 345 GLN cc_start: 0.8218 (mt0) cc_final: 0.7987 (mt0) REVERT: C 349 TYR cc_start: 0.7544 (t80) cc_final: 0.7253 (t80) REVERT: C 361 LEU cc_start: 0.7141 (tp) cc_final: 0.6668 (tp) REVERT: C 376 LYS cc_start: 0.8540 (ttpt) cc_final: 0.8199 (tttt) REVERT: C 392 HIS cc_start: 0.8018 (m170) cc_final: 0.7678 (m-70) REVERT: C 406 GLU cc_start: 0.7640 (tt0) cc_final: 0.6699 (tt0) REVERT: C 407 LEU cc_start: 0.8915 (mt) cc_final: 0.8251 (pp) REVERT: C 408 THR cc_start: 0.8377 (m) cc_final: 0.7848 (m) REVERT: C 410 GLN cc_start: 0.8337 (mm110) cc_final: 0.7391 (mm110) REVERT: C 411 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7183 (mt-10) REVERT: C 437 LEU cc_start: 0.8030 (mt) cc_final: 0.7764 (mt) REVERT: C 447 GLU cc_start: 0.7732 (mp0) cc_final: 0.7379 (tp30) REVERT: C 450 ILE cc_start: 0.8137 (mt) cc_final: 0.7437 (mt) REVERT: C 458 LEU cc_start: 0.8400 (tp) cc_final: 0.8036 (tt) REVERT: C 478 MET cc_start: 0.7551 (mtp) cc_final: 0.7062 (mtp) REVERT: C 499 ILE cc_start: 0.7960 (tp) cc_final: 0.7528 (tp) REVERT: C 501 MET cc_start: 0.7808 (mtt) cc_final: 0.7356 (mtt) REVERT: C 502 TYR cc_start: 0.7015 (m-10) cc_final: 0.6742 (m-10) REVERT: C 505 ARG cc_start: 0.8150 (mtt90) cc_final: 0.7612 (mtt90) REVERT: C 507 ILE cc_start: 0.8388 (mt) cc_final: 0.8038 (mp) REVERT: C 522 TYR cc_start: 0.7710 (m-80) cc_final: 0.7421 (m-80) REVERT: C 542 MET cc_start: 0.7698 (tpp) cc_final: 0.7089 (tpp) REVERT: C 543 ILE cc_start: 0.8718 (mt) cc_final: 0.8443 (mt) REVERT: C 545 MET cc_start: 0.7607 (mtm) cc_final: 0.7024 (mtm) REVERT: C 553 LYS cc_start: 0.8613 (mtmt) cc_final: 0.8299 (mtpt) REVERT: C 555 LEU cc_start: 0.8396 (tp) cc_final: 0.8120 (tp) REVERT: C 572 LYS cc_start: 0.8321 (mmtt) cc_final: 0.7892 (ttmm) REVERT: C 573 GLU cc_start: 0.7762 (pm20) cc_final: 0.7496 (pm20) REVERT: C 576 GLN cc_start: 0.6933 (tm-30) cc_final: 0.6431 (tm-30) REVERT: C 577 LEU cc_start: 0.8483 (mt) cc_final: 0.8100 (mt) REVERT: C 613 THR cc_start: 0.8380 (m) cc_final: 0.8161 (p) REVERT: C 617 ILE cc_start: 0.8592 (mm) cc_final: 0.8309 (mm) REVERT: C 621 LEU cc_start: 0.7926 (mm) cc_final: 0.7474 (mm) REVERT: C 625 ASN cc_start: 0.8027 (m110) cc_final: 0.7606 (m110) REVERT: C 626 ASN cc_start: 0.7877 (m-40) cc_final: 0.7512 (m110) REVERT: C 635 MET cc_start: 0.7717 (mpp) cc_final: 0.7230 (mpp) REVERT: C 641 LEU cc_start: 0.8365 (mt) cc_final: 0.7839 (pp) REVERT: C 649 ARG cc_start: 0.8643 (ttm170) cc_final: 0.8265 (ttp-110) REVERT: C 658 LEU cc_start: 0.8493 (tp) cc_final: 0.7938 (tp) REVERT: C 711 LYS cc_start: 0.9208 (mmtt) cc_final: 0.8673 (mmtm) REVERT: C 712 GLU cc_start: 0.8744 (tt0) cc_final: 0.8120 (tt0) REVERT: C 717 TYR cc_start: 0.8159 (t80) cc_final: 0.7923 (t80) REVERT: C 720 TYR cc_start: 0.7349 (t80) cc_final: 0.6762 (t80) REVERT: C 730 PHE cc_start: 0.7497 (t80) cc_final: 0.7269 (t80) REVERT: C 738 HIS cc_start: 0.7558 (t-90) cc_final: 0.7185 (t-90) REVERT: C 743 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7647 (mm-30) REVERT: C 748 TYR cc_start: 0.6819 (t80) cc_final: 0.6554 (t80) REVERT: C 753 GLU cc_start: 0.8309 (mp0) cc_final: 0.7971 (mp0) REVERT: C 754 GLU cc_start: 0.8282 (mt-10) cc_final: 0.8062 (mt-10) REVERT: C 789 GLU cc_start: 0.7978 (pt0) cc_final: 0.7714 (pm20) REVERT: C 791 TRP cc_start: 0.7561 (t60) cc_final: 0.7186 (t60) outliers start: 2 outliers final: 2 residues processed: 534 average time/residue: 0.3286 time to fit residues: 237.5623 Evaluate side-chains 511 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 509 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 145 optimal weight: 30.0000 chunk 110 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 147 optimal weight: 0.9990 chunk 156 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 140 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN A 625 ASN A 723 ASN ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 625 ASN C 723 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.4753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13522 Z= 0.210 Angle : 0.643 10.485 18260 Z= 0.336 Chirality : 0.043 0.161 2014 Planarity : 0.005 0.065 2372 Dihedral : 5.361 23.740 1806 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.20), residues: 1610 helix: -0.92 (0.17), residues: 812 sheet: -3.03 (0.54), residues: 72 loop : -1.22 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.004 TRP D 139 HIS 0.003 0.001 HIS A 655 PHE 0.031 0.002 PHE A 790 TYR 0.017 0.002 TYR A 495 ARG 0.007 0.001 ARG A 763 *********************** 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 532 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 532 time to evaluate : 1.606 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: B 65 ASN cc_start: 0.7714 (m-40) cc_final: 0.7463 (m-40) REVERT: B 73 CYS cc_start: 0.7016 (m) cc_final: 0.6430 (m) REVERT: B 77 TYR cc_start: 0.8080 (m-80) cc_final: 0.7561 (m-80) REVERT: B 82 GLU cc_start: 0.8244 (tt0) cc_final: 0.7982 (tt0) REVERT: B 88 TYR cc_start: 0.6847 (p90) cc_final: 0.6574 (p90) REVERT: B 114 GLN cc_start: 0.7010 (mp10) cc_final: 0.6506 (mp10) REVERT: B 134 ASN cc_start: 0.7430 (t0) cc_final: 0.6169 (t0) REVERT: A 130 GLU cc_start: 0.8538 (pt0) cc_final: 0.7652 (pm20) REVERT: A 237 ASP cc_start: 0.8419 (m-30) cc_final: 0.7840 (t0) REVERT: A 291 MET cc_start: 0.8182 (ttt) cc_final: 0.7872 (ptm) REVERT: A 297 HIS cc_start: 0.7877 (t70) cc_final: 0.7431 (t70) REVERT: A 304 MET cc_start: 0.4623 (tpt) cc_final: 0.3965 (tpt) REVERT: A 330 LYS cc_start: 0.8471 (mmtm) cc_final: 0.8244 (mmtt) REVERT: A 337 ARG cc_start: 0.8127 (ttm170) cc_final: 0.7370 (ttp80) REVERT: A 338 ARG cc_start: 0.7944 (mtp85) cc_final: 0.7366 (mmm-85) REVERT: A 341 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7575 (mt-10) REVERT: A 344 GLN cc_start: 0.8188 (tp-100) cc_final: 0.7070 (tp-100) REVERT: A 347 ILE cc_start: 0.7535 (mt) cc_final: 0.7133 (mm) REVERT: A 350 LYS cc_start: 0.7555 (mmpt) cc_final: 0.6996 (tptt) REVERT: A 377 MET cc_start: 0.8375 (mtt) cc_final: 0.8127 (mtp) REVERT: A 379 TYR cc_start: 0.7642 (t80) cc_final: 0.7214 (t80) REVERT: A 392 HIS cc_start: 0.8077 (m90) cc_final: 0.7660 (m90) REVERT: A 394 GLU cc_start: 0.6675 (mm-30) cc_final: 0.5626 (mm-30) REVERT: A 407 LEU cc_start: 0.8942 (mt) cc_final: 0.8451 (pp) REVERT: A 410 GLN cc_start: 0.8526 (mm110) cc_final: 0.8083 (mm-40) REVERT: A 437 LEU cc_start: 0.8285 (mm) cc_final: 0.7971 (tt) REVERT: A 447 GLU cc_start: 0.7914 (mp0) cc_final: 0.7562 (tp30) REVERT: A 450 ILE cc_start: 0.8188 (mt) cc_final: 0.7369 (mt) REVERT: A 458 LEU cc_start: 0.8469 (tp) cc_final: 0.8253 (tt) REVERT: A 478 MET cc_start: 0.7916 (mtp) cc_final: 0.7437 (ttm) REVERT: A 489 LYS cc_start: 0.8125 (mtmm) cc_final: 0.7767 (ptpp) REVERT: A 497 ASN cc_start: 0.7652 (m-40) cc_final: 0.7437 (m-40) REVERT: A 499 ILE cc_start: 0.7911 (tp) cc_final: 0.7599 (tp) REVERT: A 502 TYR cc_start: 0.6974 (m-10) cc_final: 0.6718 (m-10) REVERT: A 504 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7211 (mm-30) REVERT: A 505 ARG cc_start: 0.8181 (mtt90) cc_final: 0.7782 (mtt90) REVERT: A 507 ILE cc_start: 0.8467 (mt) cc_final: 0.7832 (mp) REVERT: A 522 TYR cc_start: 0.7862 (m-80) cc_final: 0.7316 (m-80) REVERT: A 530 ASP cc_start: 0.7710 (p0) cc_final: 0.7435 (p0) REVERT: A 533 ILE cc_start: 0.8331 (pt) cc_final: 0.7586 (mp) REVERT: A 542 MET cc_start: 0.8053 (ptt) cc_final: 0.7567 (tmm) REVERT: A 543 ILE cc_start: 0.8811 (mt) cc_final: 0.8170 (mt) REVERT: A 545 MET cc_start: 0.7613 (mtm) cc_final: 0.7146 (mtm) REVERT: A 550 ASP cc_start: 0.7509 (p0) cc_final: 0.7173 (p0) REVERT: A 551 LEU cc_start: 0.8949 (mp) cc_final: 0.8716 (mp) REVERT: A 553 LYS cc_start: 0.8744 (mtmt) cc_final: 0.8477 (mtpp) REVERT: A 560 GLU cc_start: 0.5680 (pm20) cc_final: 0.5472 (pm20) REVERT: A 572 LYS cc_start: 0.8324 (mmtt) cc_final: 0.7909 (tttp) REVERT: A 589 MET cc_start: 0.4911 (mtt) cc_final: 0.4611 (mtt) REVERT: A 593 ASP cc_start: 0.7500 (t0) cc_final: 0.7277 (t70) REVERT: A 600 TRP cc_start: 0.8448 (t-100) cc_final: 0.8190 (t-100) REVERT: A 611 GLN cc_start: 0.7648 (tm-30) cc_final: 0.6532 (tm-30) REVERT: A 617 ILE cc_start: 0.8371 (mm) cc_final: 0.7873 (mm) REVERT: A 621 LEU cc_start: 0.7930 (mm) cc_final: 0.7390 (mp) REVERT: A 635 MET cc_start: 0.7661 (mpp) cc_final: 0.7085 (mpp) REVERT: A 641 LEU cc_start: 0.8357 (mt) cc_final: 0.7938 (mm) REVERT: A 642 MET cc_start: 0.7767 (mmp) cc_final: 0.7495 (mmp) REVERT: A 651 LEU cc_start: 0.8439 (mt) cc_final: 0.8130 (mt) REVERT: A 658 LEU cc_start: 0.8246 (tp) cc_final: 0.7893 (tp) REVERT: A 660 GLN cc_start: 0.8017 (pp30) cc_final: 0.7431 (pp30) REVERT: A 661 SER cc_start: 0.8574 (m) cc_final: 0.7995 (m) REVERT: A 663 LYS cc_start: 0.8024 (ptmm) cc_final: 0.7355 (ttpp) REVERT: A 667 GLU cc_start: 0.8081 (pp20) cc_final: 0.7768 (pp20) REVERT: A 676 MET cc_start: 0.6868 (tmm) cc_final: 0.6637 (tmm) REVERT: A 682 ILE cc_start: 0.8697 (tp) cc_final: 0.8336 (tp) REVERT: A 711 LYS cc_start: 0.9256 (mmtt) cc_final: 0.8919 (mmtm) REVERT: A 712 GLU cc_start: 0.8750 (tt0) cc_final: 0.8266 (tt0) REVERT: A 715 ASN cc_start: 0.8549 (m110) cc_final: 0.8327 (m110) REVERT: A 716 LEU cc_start: 0.8714 (mt) cc_final: 0.8359 (mt) REVERT: A 720 TYR cc_start: 0.7354 (t80) cc_final: 0.6807 (t80) REVERT: A 728 LYS cc_start: 0.8270 (ttpt) cc_final: 0.7457 (ptmm) REVERT: A 734 ARG cc_start: 0.8190 (ttt-90) cc_final: 0.7212 (ttm-80) REVERT: A 743 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7469 (mp0) REVERT: A 750 PHE cc_start: 0.7580 (m-80) cc_final: 0.7142 (m-80) REVERT: A 753 GLU cc_start: 0.8406 (mp0) cc_final: 0.8067 (mp0) REVERT: A 756 GLU cc_start: 0.7561 (tp30) cc_final: 0.6978 (tp30) REVERT: A 788 ARG cc_start: 0.8599 (ptt180) cc_final: 0.8214 (ptt180) REVERT: A 792 GLU cc_start: 0.8546 (mm-30) cc_final: 0.7774 (mm-30) REVERT: A 805 PHE cc_start: 0.8370 (t80) cc_final: 0.8097 (t80) REVERT: A 806 LEU cc_start: 0.8379 (mt) cc_final: 0.7902 (mt) REVERT: A 822 LYS cc_start: 0.8478 (mptt) cc_final: 0.8269 (mmtm) REVERT: D 22 LEU cc_start: 0.8291 (mm) cc_final: 0.8059 (mm) REVERT: D 65 ASN cc_start: 0.7864 (m-40) cc_final: 0.7464 (m-40) REVERT: D 73 CYS cc_start: 0.6944 (m) cc_final: 0.6276 (m) REVERT: D 79 LYS cc_start: 0.8208 (tppp) cc_final: 0.7018 (tppp) REVERT: D 80 ILE cc_start: 0.8124 (mm) cc_final: 0.7864 (mm) REVERT: D 88 TYR cc_start: 0.6807 (p90) cc_final: 0.6534 (p90) REVERT: D 132 PHE cc_start: 0.6906 (m-80) cc_final: 0.6236 (m-80) REVERT: D 134 ASN cc_start: 0.7071 (t0) cc_final: 0.6116 (t0) REVERT: C 241 ARG cc_start: 0.8502 (mtm-85) cc_final: 0.8275 (mtm-85) REVERT: C 304 MET cc_start: 0.4998 (tpt) cc_final: 0.4750 (tpt) REVERT: C 315 LYS cc_start: 0.7934 (mtmm) cc_final: 0.7261 (ptpp) REVERT: C 332 ASN cc_start: 0.7514 (t0) cc_final: 0.6930 (t0) REVERT: C 337 ARG cc_start: 0.8077 (ttm170) cc_final: 0.7816 (tmm-80) REVERT: C 344 GLN cc_start: 0.8212 (tp-100) cc_final: 0.7101 (tp-100) REVERT: C 349 TYR cc_start: 0.7626 (t80) cc_final: 0.7289 (t80) REVERT: C 361 LEU cc_start: 0.7182 (tp) cc_final: 0.6705 (tp) REVERT: C 376 LYS cc_start: 0.8673 (ttpt) cc_final: 0.8301 (tttt) REVERT: C 382 ASN cc_start: 0.8142 (m110) cc_final: 0.7918 (t0) REVERT: C 392 HIS cc_start: 0.8254 (m170) cc_final: 0.7902 (m-70) REVERT: C 397 ASP cc_start: 0.7769 (t0) cc_final: 0.7386 (t0) REVERT: C 406 GLU cc_start: 0.7479 (tt0) cc_final: 0.6920 (tt0) REVERT: C 407 LEU cc_start: 0.8933 (mt) cc_final: 0.8201 (pp) REVERT: C 408 THR cc_start: 0.8355 (m) cc_final: 0.7671 (m) REVERT: C 409 LEU cc_start: 0.8624 (tp) cc_final: 0.8017 (pp) REVERT: C 410 GLN cc_start: 0.8439 (mm110) cc_final: 0.6362 (mm-40) REVERT: C 411 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7166 (mt-10) REVERT: C 447 GLU cc_start: 0.7752 (mp0) cc_final: 0.7436 (tp30) REVERT: C 449 PHE cc_start: 0.7305 (m-10) cc_final: 0.6902 (m-10) REVERT: C 450 ILE cc_start: 0.8286 (mt) cc_final: 0.7392 (mt) REVERT: C 458 LEU cc_start: 0.8493 (tp) cc_final: 0.8024 (tp) REVERT: C 478 MET cc_start: 0.7618 (mtp) cc_final: 0.7320 (mtp) REVERT: C 493 LEU cc_start: 0.7414 (tp) cc_final: 0.6926 (tp) REVERT: C 499 ILE cc_start: 0.8052 (tp) cc_final: 0.7480 (tp) REVERT: C 501 MET cc_start: 0.7802 (mtt) cc_final: 0.7337 (mtt) REVERT: C 502 TYR cc_start: 0.7033 (m-10) cc_final: 0.6797 (m-10) REVERT: C 505 ARG cc_start: 0.8162 (mtt90) cc_final: 0.7622 (mtt90) REVERT: C 507 ILE cc_start: 0.8426 (mt) cc_final: 0.8099 (mp) REVERT: C 522 TYR cc_start: 0.7757 (m-80) cc_final: 0.7464 (m-80) REVERT: C 530 ASP cc_start: 0.7631 (p0) cc_final: 0.7362 (p0) REVERT: C 539 ARG cc_start: 0.8111 (ttm-80) cc_final: 0.7768 (ttm-80) REVERT: C 542 MET cc_start: 0.7640 (tpp) cc_final: 0.7066 (tpp) REVERT: C 545 MET cc_start: 0.7593 (mtm) cc_final: 0.7022 (mtm) REVERT: C 553 LYS cc_start: 0.8627 (mtmt) cc_final: 0.8365 (mtpp) REVERT: C 555 LEU cc_start: 0.8425 (tp) cc_final: 0.8022 (tp) REVERT: C 573 GLU cc_start: 0.7756 (pm20) cc_final: 0.7453 (pp20) REVERT: C 576 GLN cc_start: 0.7256 (tm-30) cc_final: 0.6756 (tm-30) REVERT: C 577 LEU cc_start: 0.8576 (mt) cc_final: 0.7768 (mt) REVERT: C 613 THR cc_start: 0.8402 (m) cc_final: 0.8175 (p) REVERT: C 617 ILE cc_start: 0.8538 (mm) cc_final: 0.8281 (mm) REVERT: C 619 LEU cc_start: 0.8685 (tp) cc_final: 0.8467 (tp) REVERT: C 621 LEU cc_start: 0.8029 (mm) cc_final: 0.7553 (mm) REVERT: C 625 ASN cc_start: 0.8036 (m-40) cc_final: 0.7646 (m110) REVERT: C 626 ASN cc_start: 0.7970 (m-40) cc_final: 0.7658 (m110) REVERT: C 635 MET cc_start: 0.7745 (mpp) cc_final: 0.7150 (mpp) REVERT: C 641 LEU cc_start: 0.8403 (mt) cc_final: 0.8026 (mm) REVERT: C 642 MET cc_start: 0.7870 (mmp) cc_final: 0.7560 (mmp) REVERT: C 651 LEU cc_start: 0.8380 (mt) cc_final: 0.8089 (mp) REVERT: C 658 LEU cc_start: 0.8277 (tp) cc_final: 0.8034 (tp) REVERT: C 659 TYR cc_start: 0.8697 (t80) cc_final: 0.8492 (t80) REVERT: C 663 LYS cc_start: 0.8115 (ttpp) cc_final: 0.7869 (ttpp) REVERT: C 711 LYS cc_start: 0.9213 (mmtt) cc_final: 0.8685 (mmtm) REVERT: C 712 GLU cc_start: 0.8788 (tt0) cc_final: 0.8195 (tt0) REVERT: C 717 TYR cc_start: 0.8515 (t80) cc_final: 0.8221 (t80) REVERT: C 720 TYR cc_start: 0.7383 (t80) cc_final: 0.6859 (t80) REVERT: C 724 LYS cc_start: 0.7973 (ptpp) cc_final: 0.7600 (pttm) REVERT: C 734 ARG cc_start: 0.8534 (ttt-90) cc_final: 0.8183 (ttm170) REVERT: C 738 HIS cc_start: 0.7684 (t-90) cc_final: 0.7259 (t70) REVERT: C 743 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7732 (mm-30) REVERT: C 748 TYR cc_start: 0.6883 (t80) cc_final: 0.6494 (t80) REVERT: C 750 PHE cc_start: 0.7863 (m-10) cc_final: 0.7590 (m-10) REVERT: C 751 ARG cc_start: 0.6601 (mmm-85) cc_final: 0.6340 (mmm-85) REVERT: C 788 ARG cc_start: 0.8557 (ptt180) cc_final: 0.7975 (ptt180) REVERT: C 791 TRP cc_start: 0.7552 (t60) cc_final: 0.7266 (t60) REVERT: C 792 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7960 (mm-30) REVERT: C 807 GLN cc_start: 0.8486 (tt0) cc_final: 0.7739 (tt0) REVERT: C 822 LYS cc_start: 0.8577 (mmtt) cc_final: 0.8233 (mmtm) REVERT: C 855 LYS cc_start: 0.8851 (tttt) cc_final: 0.8035 (tppt) outliers start: 0 outliers final: 0 residues processed: 532 average time/residue: 0.3460 time to fit residues: 245.7002 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 : 2.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 130 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 64 optimal weight: 30.0000 chunk 133 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 140 optimal weight: 4.9990 chunk 39 optimal weight: 0.2980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 ASN A 625 ASN A 626 ASN A 723 ASN D 27 GLN ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 363 ASN ** C 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 455 ASN C 723 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.5274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13522 Z= 0.259 Angle : 0.681 10.345 18260 Z= 0.357 Chirality : 0.045 0.230 2014 Planarity : 0.005 0.070 2372 Dihedral : 5.385 22.272 1806 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.20), residues: 1610 helix: -0.82 (0.17), residues: 820 sheet: -2.69 (0.55), residues: 92 loop : -1.07 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.005 TRP C 328 HIS 0.004 0.001 HIS D 85 PHE 0.026 0.002 PHE A 790 TYR 0.019 0.002 TYR D 83 ARG 0.010 0.001 ARG B 84 *********************** 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 521 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 521 time to evaluate : 2.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 18 LYS cc_start: 0.7861 (mmtm) cc_final: 0.7259 (mmmm) REVERT: B 22 LEU cc_start: 0.8280 (mm) cc_final: 0.7959 (mm) REVERT: B 65 ASN cc_start: 0.8025 (m-40) cc_final: 0.7633 (m-40) REVERT: B 73 CYS cc_start: 0.7081 (m) cc_final: 0.6565 (m) REVERT: B 77 TYR cc_start: 0.8112 (m-80) cc_final: 0.7518 (m-80) REVERT: B 79 LYS cc_start: 0.8306 (tppp) cc_final: 0.7020 (tppp) REVERT: B 82 GLU cc_start: 0.8322 (tt0) cc_final: 0.7761 (tt0) REVERT: B 88 TYR cc_start: 0.6883 (p90) cc_final: 0.6627 (p90) REVERT: B 114 GLN cc_start: 0.7148 (mp10) cc_final: 0.6937 (mp10) REVERT: B 124 ARG cc_start: 0.8487 (ttt-90) cc_final: 0.7999 (ttt-90) REVERT: B 128 LYS cc_start: 0.8515 (mttt) cc_final: 0.8298 (mttt) REVERT: B 134 ASN cc_start: 0.7437 (t0) cc_final: 0.7007 (t0) REVERT: B 136 ARG cc_start: 0.7586 (mmm160) cc_final: 0.7261 (mmm160) REVERT: A 130 GLU cc_start: 0.8552 (pt0) cc_final: 0.7692 (pm20) REVERT: A 237 ASP cc_start: 0.8494 (m-30) cc_final: 0.7922 (t0) REVERT: A 287 PHE cc_start: 0.6882 (m-80) cc_final: 0.6596 (m-80) REVERT: A 291 MET cc_start: 0.8282 (ttt) cc_final: 0.8033 (ttp) REVERT: A 304 MET cc_start: 0.4721 (tpt) cc_final: 0.4089 (tpt) REVERT: A 330 LYS cc_start: 0.8448 (mmtm) cc_final: 0.8204 (mmtt) REVERT: A 332 ASN cc_start: 0.7779 (t0) cc_final: 0.7407 (t0) REVERT: A 337 ARG cc_start: 0.8190 (ttm170) cc_final: 0.7403 (ttp80) REVERT: A 338 ARG cc_start: 0.7880 (mtp85) cc_final: 0.7581 (mmm-85) REVERT: A 341 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7750 (mt-10) REVERT: A 344 GLN cc_start: 0.8313 (tp-100) cc_final: 0.7226 (tp-100) REVERT: A 345 GLN cc_start: 0.8231 (mt0) cc_final: 0.7969 (mt0) REVERT: A 347 ILE cc_start: 0.7641 (mt) cc_final: 0.7402 (mt) REVERT: A 350 LYS cc_start: 0.7618 (mmpt) cc_final: 0.7052 (tptt) REVERT: A 379 TYR cc_start: 0.7693 (t80) cc_final: 0.7309 (t80) REVERT: A 392 HIS cc_start: 0.8136 (m90) cc_final: 0.7761 (m90) REVERT: A 394 GLU cc_start: 0.6895 (mm-30) cc_final: 0.6512 (mm-30) REVERT: A 407 LEU cc_start: 0.8935 (mt) cc_final: 0.8707 (pp) REVERT: A 409 LEU cc_start: 0.8574 (tp) cc_final: 0.8235 (pp) REVERT: A 420 LYS cc_start: 0.7781 (pttp) cc_final: 0.7474 (pttp) REVERT: A 426 ASP cc_start: 0.8551 (t0) cc_final: 0.8251 (t0) REVERT: A 437 LEU cc_start: 0.8317 (mm) cc_final: 0.8003 (tt) REVERT: A 446 PHE cc_start: 0.7494 (m-80) cc_final: 0.7209 (m-80) REVERT: A 447 GLU cc_start: 0.7816 (mp0) cc_final: 0.7527 (tp30) REVERT: A 450 ILE cc_start: 0.8347 (mt) cc_final: 0.7143 (mt) REVERT: A 458 LEU cc_start: 0.8482 (tp) cc_final: 0.8251 (tt) REVERT: A 478 MET cc_start: 0.8019 (mtp) cc_final: 0.7578 (ttm) REVERT: A 482 PHE cc_start: 0.8051 (p90) cc_final: 0.7811 (p90) REVERT: A 499 ILE cc_start: 0.8074 (tp) cc_final: 0.7711 (tp) REVERT: A 502 TYR cc_start: 0.6996 (m-10) cc_final: 0.6787 (m-10) REVERT: A 504 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7040 (mm-30) REVERT: A 505 ARG cc_start: 0.8181 (mtt90) cc_final: 0.7689 (mtt90) REVERT: A 507 ILE cc_start: 0.8463 (mt) cc_final: 0.7786 (mt) REVERT: A 515 GLN cc_start: 0.7920 (mm110) cc_final: 0.7673 (tm-30) REVERT: A 522 TYR cc_start: 0.7927 (m-80) cc_final: 0.7124 (m-80) REVERT: A 530 ASP cc_start: 0.7751 (p0) cc_final: 0.7483 (p0) REVERT: A 533 ILE cc_start: 0.8508 (pt) cc_final: 0.7975 (mp) REVERT: A 538 VAL cc_start: 0.8497 (m) cc_final: 0.8088 (m) REVERT: A 539 ARG cc_start: 0.8147 (ttm-80) cc_final: 0.7664 (ptm160) REVERT: A 540 LEU cc_start: 0.8760 (mm) cc_final: 0.8503 (mm) REVERT: A 542 MET cc_start: 0.8110 (ptt) cc_final: 0.7252 (ptt) REVERT: A 545 MET cc_start: 0.7627 (mtm) cc_final: 0.7087 (mtm) REVERT: A 550 ASP cc_start: 0.7490 (p0) cc_final: 0.7200 (p0) REVERT: A 551 LEU cc_start: 0.8821 (mp) cc_final: 0.8582 (mp) REVERT: A 552 LYS cc_start: 0.8739 (mmtm) cc_final: 0.8460 (mmtt) REVERT: A 572 LYS cc_start: 0.8278 (mmtt) cc_final: 0.8048 (mmtt) REVERT: A 576 GLN cc_start: 0.7880 (tp40) cc_final: 0.7207 (tp40) REVERT: A 593 ASP cc_start: 0.7546 (t0) cc_final: 0.7308 (t0) REVERT: A 603 PRO cc_start: 0.7405 (Cg_endo) cc_final: 0.7185 (Cg_exo) REVERT: A 611 GLN cc_start: 0.7509 (tm-30) cc_final: 0.6459 (tm-30) REVERT: A 621 LEU cc_start: 0.7923 (mm) cc_final: 0.7464 (mp) REVERT: A 635 MET cc_start: 0.7645 (mpp) cc_final: 0.7024 (mpp) REVERT: A 641 LEU cc_start: 0.8340 (mt) cc_final: 0.8100 (mm) REVERT: A 642 MET cc_start: 0.7828 (mmp) cc_final: 0.7519 (mmp) REVERT: A 651 LEU cc_start: 0.8435 (mt) cc_final: 0.8092 (mt) REVERT: A 658 LEU cc_start: 0.8292 (tp) cc_final: 0.7927 (tp) REVERT: A 663 LYS cc_start: 0.8149 (ptmm) cc_final: 0.7535 (ttpp) REVERT: A 667 GLU cc_start: 0.8137 (pp20) cc_final: 0.7877 (pp20) REVERT: A 682 ILE cc_start: 0.8621 (tp) cc_final: 0.8154 (tp) REVERT: A 711 LYS cc_start: 0.9261 (mmtt) cc_final: 0.8937 (mmtm) REVERT: A 712 GLU cc_start: 0.8852 (tt0) cc_final: 0.8412 (tt0) REVERT: A 715 ASN cc_start: 0.8614 (m110) cc_final: 0.8392 (m110) REVERT: A 716 LEU cc_start: 0.8761 (mt) cc_final: 0.8466 (mp) REVERT: A 717 TYR cc_start: 0.8486 (t80) cc_final: 0.8071 (t80) REVERT: A 720 TYR cc_start: 0.7345 (t80) cc_final: 0.6887 (t80) REVERT: A 728 LYS cc_start: 0.8348 (ttpt) cc_final: 0.7438 (ptmm) REVERT: A 734 ARG cc_start: 0.8286 (ttt-90) cc_final: 0.7969 (ttt90) REVERT: A 739 MET cc_start: 0.7398 (ptm) cc_final: 0.7161 (ptm) REVERT: A 753 GLU cc_start: 0.8418 (mp0) cc_final: 0.8113 (mp0) REVERT: A 756 GLU cc_start: 0.7580 (tp30) cc_final: 0.7071 (tp30) REVERT: A 788 ARG cc_start: 0.8584 (ptt180) cc_final: 0.7942 (ptt180) REVERT: A 792 GLU cc_start: 0.8453 (mm-30) cc_final: 0.8097 (mm-30) REVERT: D 22 LEU cc_start: 0.8462 (mm) cc_final: 0.8157 (mm) REVERT: D 65 ASN cc_start: 0.7943 (m-40) cc_final: 0.7483 (m-40) REVERT: D 73 CYS cc_start: 0.6558 (m) cc_final: 0.6071 (m) REVERT: D 79 LYS cc_start: 0.8238 (tppp) cc_final: 0.6865 (tppp) REVERT: D 80 ILE cc_start: 0.8187 (mm) cc_final: 0.7960 (mm) REVERT: D 82 GLU cc_start: 0.8311 (tt0) cc_final: 0.7661 (tt0) REVERT: D 134 ASN cc_start: 0.7481 (t0) cc_final: 0.7168 (t0) REVERT: C 130 GLU cc_start: 0.8520 (pt0) cc_final: 0.7659 (pm20) REVERT: C 138 GLU cc_start: 0.8536 (mp0) cc_final: 0.8043 (mp0) REVERT: C 288 ILE cc_start: 0.8583 (tt) cc_final: 0.8368 (tt) REVERT: C 304 MET cc_start: 0.4826 (tpt) cc_final: 0.4514 (tpt) REVERT: C 330 LYS cc_start: 0.8579 (mmmt) cc_final: 0.8259 (mmtm) REVERT: C 332 ASN cc_start: 0.7654 (t0) cc_final: 0.7091 (t0) REVERT: C 338 ARG cc_start: 0.7894 (mmm-85) cc_final: 0.6888 (mmm-85) REVERT: C 341 GLU cc_start: 0.7803 (pp20) cc_final: 0.6241 (pp20) REVERT: C 349 TYR cc_start: 0.7683 (t80) cc_final: 0.7368 (t80) REVERT: C 361 LEU cc_start: 0.7285 (tp) cc_final: 0.6808 (tp) REVERT: C 379 TYR cc_start: 0.7566 (t80) cc_final: 0.7180 (t80) REVERT: C 397 ASP cc_start: 0.7775 (t0) cc_final: 0.7554 (t0) REVERT: C 406 GLU cc_start: 0.7416 (tt0) cc_final: 0.7050 (tt0) REVERT: C 407 LEU cc_start: 0.8966 (mt) cc_final: 0.8596 (pp) REVERT: C 410 GLN cc_start: 0.8353 (mm110) cc_final: 0.7314 (mm-40) REVERT: C 447 GLU cc_start: 0.7736 (mp0) cc_final: 0.7501 (tp30) REVERT: C 450 ILE cc_start: 0.8289 (mt) cc_final: 0.7518 (mt) REVERT: C 458 LEU cc_start: 0.8510 (tp) cc_final: 0.8140 (tp) REVERT: C 478 MET cc_start: 0.7799 (mtp) cc_final: 0.7562 (mtp) REVERT: C 493 LEU cc_start: 0.7398 (tp) cc_final: 0.7068 (tp) REVERT: C 501 MET cc_start: 0.7803 (mtt) cc_final: 0.7402 (mtt) REVERT: C 504 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7427 (mm-30) REVERT: C 505 ARG cc_start: 0.8212 (mtt90) cc_final: 0.7751 (mtt90) REVERT: C 507 ILE cc_start: 0.8452 (mt) cc_final: 0.7896 (mp) REVERT: C 522 TYR cc_start: 0.7795 (m-80) cc_final: 0.7338 (m-80) REVERT: C 530 ASP cc_start: 0.7583 (p0) cc_final: 0.7375 (p0) REVERT: C 532 ILE cc_start: 0.8193 (pt) cc_final: 0.7715 (mm) REVERT: C 539 ARG cc_start: 0.8184 (ttm-80) cc_final: 0.7835 (ttm-80) REVERT: C 541 GLU cc_start: 0.8326 (tt0) cc_final: 0.7437 (tt0) REVERT: C 542 MET cc_start: 0.7636 (tpp) cc_final: 0.7061 (tpp) REVERT: C 545 MET cc_start: 0.7599 (mtm) cc_final: 0.7164 (mtm) REVERT: C 553 LYS cc_start: 0.8574 (mtmt) cc_final: 0.8338 (mtpp) REVERT: C 555 LEU cc_start: 0.8456 (tp) cc_final: 0.8070 (tp) REVERT: C 573 GLU cc_start: 0.7873 (pm20) cc_final: 0.7498 (pm20) REVERT: C 576 GLN cc_start: 0.7423 (tm-30) cc_final: 0.6905 (tm-30) REVERT: C 577 LEU cc_start: 0.8625 (mt) cc_final: 0.7895 (mt) REVERT: C 589 MET cc_start: 0.5802 (mmt) cc_final: 0.4186 (mmt) REVERT: C 613 THR cc_start: 0.8332 (m) cc_final: 0.8083 (p) REVERT: C 621 LEU cc_start: 0.8050 (mm) cc_final: 0.7514 (mm) REVERT: C 625 ASN cc_start: 0.8060 (m-40) cc_final: 0.7658 (m110) REVERT: C 626 ASN cc_start: 0.8063 (m110) cc_final: 0.7743 (m110) REVERT: C 635 MET cc_start: 0.7818 (mpp) cc_final: 0.7261 (mpp) REVERT: C 641 LEU cc_start: 0.8361 (mt) cc_final: 0.7999 (mm) REVERT: C 642 MET cc_start: 0.7889 (mmp) cc_final: 0.7535 (mmp) REVERT: C 648 PHE cc_start: 0.8762 (p90) cc_final: 0.8523 (p90) REVERT: C 649 ARG cc_start: 0.8701 (ttm170) cc_final: 0.8477 (ttm110) REVERT: C 651 LEU cc_start: 0.8434 (mt) cc_final: 0.8004 (mt) REVERT: C 658 LEU cc_start: 0.8442 (tp) cc_final: 0.8233 (tp) REVERT: C 663 LYS cc_start: 0.8160 (ttpp) cc_final: 0.7904 (ttpp) REVERT: C 667 GLU cc_start: 0.7915 (pp20) cc_final: 0.7513 (pp20) REVERT: C 712 GLU cc_start: 0.8875 (tt0) cc_final: 0.8373 (tt0) REVERT: C 716 LEU cc_start: 0.8725 (mt) cc_final: 0.8066 (pp) REVERT: C 717 TYR cc_start: 0.8561 (t80) cc_final: 0.8115 (t80) REVERT: C 720 TYR cc_start: 0.7446 (t80) cc_final: 0.6955 (t80) REVERT: C 724 LYS cc_start: 0.7943 (ptpp) cc_final: 0.7611 (pttm) REVERT: C 734 ARG cc_start: 0.8578 (ttt-90) cc_final: 0.8352 (ttm-80) REVERT: C 738 HIS cc_start: 0.7778 (t-90) cc_final: 0.7493 (t70) REVERT: C 743 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7809 (mm-30) REVERT: C 747 LYS cc_start: 0.9081 (mtmt) cc_final: 0.8875 (mmmt) REVERT: C 748 TYR cc_start: 0.6954 (t80) cc_final: 0.6587 (t80) REVERT: C 750 PHE cc_start: 0.7852 (m-80) cc_final: 0.7393 (m-10) REVERT: C 754 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7839 (mp0) REVERT: C 756 GLU cc_start: 0.7098 (tp30) cc_final: 0.6364 (tp30) REVERT: C 791 TRP cc_start: 0.7501 (t60) cc_final: 0.7133 (t60) REVERT: C 792 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7912 (mm-30) REVERT: C 807 GLN cc_start: 0.8533 (tt0) cc_final: 0.7848 (tt0) REVERT: C 822 LYS cc_start: 0.8473 (mmtt) cc_final: 0.8217 (mmtp) REVERT: C 855 LYS cc_start: 0.8770 (tttt) cc_final: 0.8033 (tptt) outliers start: 0 outliers final: 0 residues processed: 521 average time/residue: 0.3389 time to fit residues: 235.6649 Evaluate side-chains 493 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 493 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 52 optimal weight: 0.6980 chunk 141 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 A 768 GLN ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 455 ASN C 723 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.5678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13522 Z= 0.184 Angle : 0.635 10.360 18260 Z= 0.323 Chirality : 0.044 0.198 2014 Planarity : 0.004 0.044 2372 Dihedral : 5.066 21.263 1806 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.07 % Allowed : 1.93 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.21), residues: 1610 helix: -0.41 (0.18), residues: 822 sheet: -2.51 (0.56), residues: 92 loop : -1.13 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP A 328 HIS 0.006 0.001 HIS B 85 PHE 0.019 0.002 PHE A 750 TYR 0.016 0.001 TYR A 464 ARG 0.006 0.000 ARG A 763 *********************** 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 517 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 516 time to evaluate : 1.605 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 22 LEU cc_start: 0.8198 (mm) cc_final: 0.7886 (mm) REVERT: B 49 VAL cc_start: 0.6820 (t) cc_final: 0.6479 (t) REVERT: B 65 ASN cc_start: 0.7571 (m-40) cc_final: 0.7309 (m-40) REVERT: B 73 CYS cc_start: 0.6979 (m) cc_final: 0.6515 (m) REVERT: B 77 TYR cc_start: 0.8052 (m-80) cc_final: 0.7466 (m-80) REVERT: B 79 LYS cc_start: 0.8149 (tppp) cc_final: 0.6679 (tppp) REVERT: B 82 GLU cc_start: 0.8233 (tt0) cc_final: 0.7720 (tt0) REVERT: B 88 TYR cc_start: 0.6818 (p90) cc_final: 0.6586 (p90) REVERT: B 124 ARG cc_start: 0.8455 (ttt-90) cc_final: 0.7947 (ttt-90) REVERT: B 134 ASN cc_start: 0.7332 (t0) cc_final: 0.6676 (t0) REVERT: B 136 ARG cc_start: 0.7468 (mmm160) cc_final: 0.7245 (mmm160) REVERT: A 130 GLU cc_start: 0.8516 (pt0) cc_final: 0.7620 (pm20) REVERT: A 237 ASP cc_start: 0.8428 (m-30) cc_final: 0.7859 (t0) REVERT: A 287 PHE cc_start: 0.6843 (m-80) cc_final: 0.6503 (m-80) REVERT: A 304 MET cc_start: 0.4657 (tpt) cc_final: 0.4013 (tpt) REVERT: A 332 ASN cc_start: 0.7559 (t0) cc_final: 0.7028 (t0) REVERT: A 337 ARG cc_start: 0.8150 (ttm170) cc_final: 0.7126 (ttp80) REVERT: A 338 ARG cc_start: 0.7884 (mtp85) cc_final: 0.7609 (mmm-85) REVERT: A 341 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7604 (mt-10) REVERT: A 344 GLN cc_start: 0.8264 (tp-100) cc_final: 0.7154 (tp-100) REVERT: A 347 ILE cc_start: 0.7512 (mt) cc_final: 0.7130 (mm) REVERT: A 348 THR cc_start: 0.7879 (m) cc_final: 0.7589 (m) REVERT: A 350 LYS cc_start: 0.7600 (mmpt) cc_final: 0.7058 (tptt) REVERT: A 379 TYR cc_start: 0.7566 (t80) cc_final: 0.7218 (t80) REVERT: A 392 HIS cc_start: 0.8069 (m90) cc_final: 0.7730 (m90) REVERT: A 394 GLU cc_start: 0.6654 (mm-30) cc_final: 0.5956 (mm-30) REVERT: A 407 LEU cc_start: 0.8990 (mt) cc_final: 0.8705 (pp) REVERT: A 420 LYS cc_start: 0.7768 (pttp) cc_final: 0.7508 (pttp) REVERT: A 426 ASP cc_start: 0.8480 (t0) cc_final: 0.8213 (t0) REVERT: A 447 GLU cc_start: 0.7798 (mp0) cc_final: 0.7520 (tp30) REVERT: A 450 ILE cc_start: 0.8323 (mt) cc_final: 0.7126 (mt) REVERT: A 458 LEU cc_start: 0.8422 (tp) cc_final: 0.8027 (tt) REVERT: A 478 MET cc_start: 0.7879 (mtp) cc_final: 0.7160 (mtp) REVERT: A 489 LYS cc_start: 0.7976 (mtmm) cc_final: 0.7618 (ptpp) REVERT: A 494 TYR cc_start: 0.7258 (t80) cc_final: 0.7039 (t80) REVERT: A 499 ILE cc_start: 0.7790 (tp) cc_final: 0.7524 (tp) REVERT: A 504 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7005 (mm-30) REVERT: A 505 ARG cc_start: 0.8154 (mtt90) cc_final: 0.7576 (mtt90) REVERT: A 507 ILE cc_start: 0.8483 (mt) cc_final: 0.7948 (mt) REVERT: A 520 ASN cc_start: 0.7387 (t0) cc_final: 0.7145 (p0) REVERT: A 522 TYR cc_start: 0.7934 (m-80) cc_final: 0.7010 (m-80) REVERT: A 530 ASP cc_start: 0.7274 (p0) cc_final: 0.6789 (p0) REVERT: A 533 ILE cc_start: 0.8335 (pt) cc_final: 0.7884 (mp) REVERT: A 538 VAL cc_start: 0.8400 (m) cc_final: 0.8060 (m) REVERT: A 539 ARG cc_start: 0.8130 (ttm-80) cc_final: 0.7615 (ptm-80) REVERT: A 542 MET cc_start: 0.7989 (ptt) cc_final: 0.7301 (ptt) REVERT: A 545 MET cc_start: 0.7462 (mtm) cc_final: 0.7082 (mtm) REVERT: A 550 ASP cc_start: 0.7388 (p0) cc_final: 0.6976 (p0) REVERT: A 552 LYS cc_start: 0.8557 (mmtm) cc_final: 0.8247 (mmtm) REVERT: A 553 LYS cc_start: 0.8643 (mtpp) cc_final: 0.8060 (tppt) REVERT: A 554 GLN cc_start: 0.6964 (tp40) cc_final: 0.6759 (mm110) REVERT: A 555 LEU cc_start: 0.8375 (tp) cc_final: 0.8050 (tp) REVERT: A 576 GLN cc_start: 0.7662 (tp40) cc_final: 0.6934 (tp40) REVERT: A 593 ASP cc_start: 0.7506 (t0) cc_final: 0.7274 (t70) REVERT: A 603 PRO cc_start: 0.7433 (Cg_endo) cc_final: 0.7182 (Cg_exo) REVERT: A 617 ILE cc_start: 0.8409 (mm) cc_final: 0.8117 (mm) REVERT: A 621 LEU cc_start: 0.7841 (mm) cc_final: 0.7322 (mp) REVERT: A 625 ASN cc_start: 0.8199 (m110) cc_final: 0.7755 (m110) REVERT: A 635 MET cc_start: 0.7408 (mpp) cc_final: 0.6816 (mpp) REVERT: A 641 LEU cc_start: 0.8366 (mt) cc_final: 0.8028 (mm) REVERT: A 642 MET cc_start: 0.7744 (mmp) cc_final: 0.7524 (mmp) REVERT: A 651 LEU cc_start: 0.8424 (mt) cc_final: 0.8041 (mt) REVERT: A 658 LEU cc_start: 0.8152 (tp) cc_final: 0.7900 (tp) REVERT: A 660 GLN cc_start: 0.8041 (pp30) cc_final: 0.7337 (pp30) REVERT: A 663 LYS cc_start: 0.8132 (ptmm) cc_final: 0.7458 (mptt) REVERT: A 667 GLU cc_start: 0.8090 (pp20) cc_final: 0.7770 (pp20) REVERT: A 682 ILE cc_start: 0.8519 (tp) cc_final: 0.8020 (tp) REVERT: A 711 LYS cc_start: 0.9261 (mmtt) cc_final: 0.8931 (mmtm) REVERT: A 712 GLU cc_start: 0.8795 (tt0) cc_final: 0.8369 (tt0) REVERT: A 715 ASN cc_start: 0.8674 (m110) cc_final: 0.8431 (m110) REVERT: A 716 LEU cc_start: 0.8746 (mt) cc_final: 0.8439 (mp) REVERT: A 717 TYR cc_start: 0.8482 (t80) cc_final: 0.7951 (t80) REVERT: A 720 TYR cc_start: 0.7291 (t80) cc_final: 0.6897 (t80) REVERT: A 728 LYS cc_start: 0.8197 (ttpt) cc_final: 0.7550 (tmtt) REVERT: A 734 ARG cc_start: 0.8220 (ttt-90) cc_final: 0.7541 (ttm-80) REVERT: A 743 GLU cc_start: 0.7469 (mp0) cc_final: 0.7063 (mp0) REVERT: A 750 PHE cc_start: 0.7469 (m-80) cc_final: 0.7152 (m-10) REVERT: A 753 GLU cc_start: 0.8360 (mp0) cc_final: 0.8047 (mp0) REVERT: A 756 GLU cc_start: 0.7508 (tp30) cc_final: 0.6957 (tp30) REVERT: A 763 ARG cc_start: 0.6673 (ttm110) cc_final: 0.6327 (ttm-80) REVERT: A 788 ARG cc_start: 0.8495 (ptt180) cc_final: 0.7967 (ptt180) REVERT: A 792 GLU cc_start: 0.8379 (mm-30) cc_final: 0.7989 (mm-30) REVERT: A 822 LYS cc_start: 0.8295 (mmtt) cc_final: 0.8047 (mmtm) REVERT: D 22 LEU cc_start: 0.8435 (mm) cc_final: 0.8183 (mm) REVERT: D 65 ASN cc_start: 0.7550 (m-40) cc_final: 0.7240 (m-40) REVERT: D 73 CYS cc_start: 0.6140 (m) cc_final: 0.5911 (m) REVERT: D 79 LYS cc_start: 0.8027 (tppp) cc_final: 0.6713 (tppp) REVERT: D 80 ILE cc_start: 0.7979 (mm) cc_final: 0.7763 (mm) REVERT: D 82 GLU cc_start: 0.8220 (tt0) cc_final: 0.7595 (tt0) REVERT: D 88 TYR cc_start: 0.6745 (p90) cc_final: 0.6370 (p90) REVERT: D 114 GLN cc_start: 0.6784 (mp10) cc_final: 0.6553 (mp10) REVERT: D 132 PHE cc_start: 0.6892 (m-80) cc_final: 0.6361 (m-80) REVERT: D 134 ASN cc_start: 0.7132 (t0) cc_final: 0.6804 (t0) REVERT: D 138 ARG cc_start: 0.6332 (pmt170) cc_final: 0.6058 (pmt170) REVERT: C 130 GLU cc_start: 0.8491 (pt0) cc_final: 0.7605 (pm20) REVERT: C 138 GLU cc_start: 0.8564 (mp0) cc_final: 0.8311 (mm-30) REVERT: C 288 ILE cc_start: 0.8512 (tt) cc_final: 0.8211 (tt) REVERT: C 292 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7497 (mm-30) REVERT: C 304 MET cc_start: 0.4621 (tpt) cc_final: 0.4323 (tpt) REVERT: C 315 LYS cc_start: 0.7983 (mtmm) cc_final: 0.7373 (ptpp) REVERT: C 330 LYS cc_start: 0.8618 (mmmt) cc_final: 0.8295 (mmtm) REVERT: C 332 ASN cc_start: 0.7593 (t0) cc_final: 0.7024 (t0) REVERT: C 341 GLU cc_start: 0.7743 (pp20) cc_final: 0.7276 (pp20) REVERT: C 344 GLN cc_start: 0.8288 (tp-100) cc_final: 0.7272 (tp-100) REVERT: C 349 TYR cc_start: 0.7603 (t80) cc_final: 0.7294 (t80) REVERT: C 361 LEU cc_start: 0.7147 (tp) cc_final: 0.6873 (tp) REVERT: C 379 TYR cc_start: 0.7496 (t80) cc_final: 0.6820 (t80) REVERT: C 382 ASN cc_start: 0.8202 (m110) cc_final: 0.7887 (t0) REVERT: C 394 GLU cc_start: 0.6055 (mm-30) cc_final: 0.5558 (mm-30) REVERT: C 397 ASP cc_start: 0.7801 (t0) cc_final: 0.7304 (t0) REVERT: C 406 GLU cc_start: 0.7360 (tt0) cc_final: 0.6828 (tt0) REVERT: C 407 LEU cc_start: 0.9026 (mt) cc_final: 0.8590 (pp) REVERT: C 450 ILE cc_start: 0.8310 (mt) cc_final: 0.8079 (mt) REVERT: C 478 MET cc_start: 0.7652 (mtp) cc_final: 0.7343 (mtp) REVERT: C 499 ILE cc_start: 0.7939 (tp) cc_final: 0.7399 (tp) REVERT: C 501 MET cc_start: 0.7785 (mtt) cc_final: 0.7319 (mtt) REVERT: C 502 TYR cc_start: 0.6966 (m-10) cc_final: 0.6597 (m-10) REVERT: C 505 ARG cc_start: 0.8199 (mtt90) cc_final: 0.7685 (mtt90) REVERT: C 507 ILE cc_start: 0.8312 (mt) cc_final: 0.8061 (mt) REVERT: C 522 TYR cc_start: 0.7723 (m-80) cc_final: 0.7121 (m-80) REVERT: C 530 ASP cc_start: 0.7595 (p0) cc_final: 0.7395 (p0) REVERT: C 532 ILE cc_start: 0.8140 (pt) cc_final: 0.7639 (mm) REVERT: C 539 ARG cc_start: 0.8148 (ttm-80) cc_final: 0.7783 (ttm-80) REVERT: C 542 MET cc_start: 0.7614 (tpp) cc_final: 0.6992 (tpp) REVERT: C 545 MET cc_start: 0.7559 (mtm) cc_final: 0.7115 (mtm) REVERT: C 553 LYS cc_start: 0.8581 (mtmt) cc_final: 0.8167 (mtpp) REVERT: C 555 LEU cc_start: 0.8429 (tp) cc_final: 0.8059 (tp) REVERT: C 573 GLU cc_start: 0.7816 (pm20) cc_final: 0.7439 (pm20) REVERT: C 576 GLN cc_start: 0.7110 (tm-30) cc_final: 0.6658 (tm-30) REVERT: C 577 LEU cc_start: 0.8403 (mt) cc_final: 0.7998 (pp) REVERT: C 581 GLU cc_start: 0.7841 (pp20) cc_final: 0.7437 (pp20) REVERT: C 589 MET cc_start: 0.5028 (mmt) cc_final: 0.4813 (mmt) REVERT: C 593 ASP cc_start: 0.7114 (t70) cc_final: 0.6912 (t0) REVERT: C 617 ILE cc_start: 0.8437 (mm) cc_final: 0.8056 (mm) REVERT: C 619 LEU cc_start: 0.8673 (tp) cc_final: 0.8447 (tp) REVERT: C 621 LEU cc_start: 0.7948 (mm) cc_final: 0.7431 (mm) REVERT: C 625 ASN cc_start: 0.7971 (m-40) cc_final: 0.7556 (m110) REVERT: C 626 ASN cc_start: 0.8046 (m110) cc_final: 0.7651 (m110) REVERT: C 635 MET cc_start: 0.7733 (mpp) cc_final: 0.7183 (mpp) REVERT: C 640 LYS cc_start: 0.7676 (mtpp) cc_final: 0.7392 (mtpp) REVERT: C 641 LEU cc_start: 0.8401 (mt) cc_final: 0.7944 (mm) REVERT: C 642 MET cc_start: 0.7849 (mmp) cc_final: 0.7500 (mmp) REVERT: C 651 LEU cc_start: 0.8429 (mt) cc_final: 0.8041 (mt) REVERT: C 663 LYS cc_start: 0.8111 (ttpp) cc_final: 0.7875 (ttpp) REVERT: C 664 ASP cc_start: 0.7322 (m-30) cc_final: 0.6819 (m-30) REVERT: C 667 GLU cc_start: 0.8001 (pp20) cc_final: 0.7729 (pp20) REVERT: C 712 GLU cc_start: 0.8785 (tt0) cc_final: 0.8256 (tt0) REVERT: C 716 LEU cc_start: 0.8680 (mt) cc_final: 0.8020 (pp) REVERT: C 717 TYR cc_start: 0.8591 (t80) cc_final: 0.8120 (t80) REVERT: C 720 TYR cc_start: 0.7389 (t80) cc_final: 0.6976 (t80) REVERT: C 724 LYS cc_start: 0.7865 (ptpp) cc_final: 0.7617 (pttm) REVERT: C 730 PHE cc_start: 0.7382 (t80) cc_final: 0.6941 (t80) REVERT: C 738 HIS cc_start: 0.7658 (t-90) cc_final: 0.7112 (t70) REVERT: C 743 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7628 (mm-30) REVERT: C 747 LYS cc_start: 0.8999 (mtpt) cc_final: 0.8705 (mtpt) REVERT: C 748 TYR cc_start: 0.6811 (t80) cc_final: 0.6465 (t80) REVERT: C 750 PHE cc_start: 0.7963 (m-10) cc_final: 0.7703 (m-10) REVERT: C 754 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7784 (mp0) REVERT: C 756 GLU cc_start: 0.6661 (tp30) cc_final: 0.6014 (tp30) REVERT: C 780 TYR cc_start: 0.6324 (t80) cc_final: 0.4155 (t80) REVERT: C 792 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7269 (mm-30) REVERT: C 805 PHE cc_start: 0.8257 (t80) cc_final: 0.7930 (t80) REVERT: C 806 LEU cc_start: 0.8356 (mt) cc_final: 0.7850 (mt) REVERT: C 822 LYS cc_start: 0.8443 (mmtt) cc_final: 0.8091 (mmtm) REVERT: C 855 LYS cc_start: 0.8753 (tttt) cc_final: 0.7876 (tptt) outliers start: 1 outliers final: 0 residues processed: 517 average time/residue: 0.3364 time to fit residues: 235.4524 Evaluate side-chains 498 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 498 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 151 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 114 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 156 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 95 optimal weight: 0.0980 chunk 72 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 A 738 HIS ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 455 ASN C 723 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.6008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13522 Z= 0.181 Angle : 0.648 12.725 18260 Z= 0.326 Chirality : 0.044 0.202 2014 Planarity : 0.004 0.038 2372 Dihedral : 5.048 21.214 1806 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.20), residues: 1610 helix: -0.27 (0.18), residues: 812 sheet: -2.51 (0.59), residues: 72 loop : -1.19 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP A 328 HIS 0.005 0.001 HIS C 655 PHE 0.018 0.002 PHE A 750 TYR 0.017 0.001 TYR C 134 ARG 0.006 0.001 ARG C 337 *********************** 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 525 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 525 time to evaluate : 1.495 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: 0.7727 (mmtm) cc_final: 0.7197 (mmmm) REVERT: B 22 LEU cc_start: 0.8370 (mm) cc_final: 0.8071 (mm) REVERT: B 49 VAL cc_start: 0.6988 (t) cc_final: 0.6619 (t) REVERT: B 65 ASN cc_start: 0.7446 (m-40) cc_final: 0.7210 (m-40) REVERT: B 73 CYS cc_start: 0.6631 (m) cc_final: 0.6228 (m) REVERT: B 77 TYR cc_start: 0.7882 (m-80) cc_final: 0.7409 (m-80) REVERT: B 79 LYS cc_start: 0.8059 (tppp) cc_final: 0.6648 (tppp) REVERT: B 82 GLU cc_start: 0.8202 (tt0) cc_final: 0.7762 (tt0) REVERT: B 114 GLN cc_start: 0.7080 (mp10) cc_final: 0.6784 (mp10) REVERT: B 134 ASN cc_start: 0.7060 (t0) cc_final: 0.6531 (t0) REVERT: B 136 ARG cc_start: 0.7708 (mmm160) cc_final: 0.7409 (mmm160) REVERT: A 130 GLU cc_start: 0.8520 (pt0) cc_final: 0.7659 (pm20) REVERT: A 237 ASP cc_start: 0.8285 (m-30) cc_final: 0.7733 (t0) REVERT: A 291 MET cc_start: 0.8210 (ttt) cc_final: 0.7902 (ptm) REVERT: A 304 MET cc_start: 0.4627 (tpt) cc_final: 0.3981 (tpt) REVERT: A 306 LEU cc_start: 0.6351 (tp) cc_final: 0.5861 (tt) REVERT: A 315 LYS cc_start: 0.8108 (mmtm) cc_final: 0.7670 (mttt) REVERT: A 331 TYR cc_start: 0.6710 (m-10) cc_final: 0.6301 (m-80) REVERT: A 332 ASN cc_start: 0.7576 (t0) cc_final: 0.7001 (t0) REVERT: A 337 ARG cc_start: 0.8143 (ttm170) cc_final: 0.7215 (ttp80) REVERT: A 338 ARG cc_start: 0.7989 (mtp85) cc_final: 0.7671 (mmm-85) REVERT: A 341 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7488 (mt-10) REVERT: A 344 GLN cc_start: 0.8326 (tp-100) cc_final: 0.7226 (tp-100) REVERT: A 348 THR cc_start: 0.7905 (m) cc_final: 0.7635 (m) REVERT: A 350 LYS cc_start: 0.7543 (mmpt) cc_final: 0.7004 (tptt) REVERT: A 379 TYR cc_start: 0.7549 (t80) cc_final: 0.7177 (t80) REVERT: A 392 HIS cc_start: 0.8220 (m90) cc_final: 0.7804 (m90) REVERT: A 395 GLU cc_start: 0.6510 (tm-30) cc_final: 0.6162 (tm-30) REVERT: A 407 LEU cc_start: 0.8926 (mt) cc_final: 0.8605 (mt) REVERT: A 420 LYS cc_start: 0.7724 (pttp) cc_final: 0.7464 (pttp) REVERT: A 447 GLU cc_start: 0.7750 (mp0) cc_final: 0.7490 (tp30) REVERT: A 449 PHE cc_start: 0.7076 (m-10) cc_final: 0.6800 (m-10) REVERT: A 450 ILE cc_start: 0.8237 (mt) cc_final: 0.7063 (mt) REVERT: A 458 LEU cc_start: 0.8363 (tp) cc_final: 0.7927 (tt) REVERT: A 478 MET cc_start: 0.7822 (mtp) cc_final: 0.6629 (mtp) REVERT: A 499 ILE cc_start: 0.7787 (tp) cc_final: 0.7512 (tp) REVERT: A 504 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7088 (mm-30) REVERT: A 505 ARG cc_start: 0.8170 (mtt90) cc_final: 0.7576 (mtt90) REVERT: A 507 ILE cc_start: 0.8491 (mt) cc_final: 0.7981 (mt) REVERT: A 520 ASN cc_start: 0.7269 (t0) cc_final: 0.7052 (p0) REVERT: A 522 TYR cc_start: 0.7954 (m-80) cc_final: 0.6988 (m-80) REVERT: A 530 ASP cc_start: 0.7552 (p0) cc_final: 0.7321 (p0) REVERT: A 532 ILE cc_start: 0.8266 (pt) cc_final: 0.7782 (mm) REVERT: A 533 ILE cc_start: 0.8377 (pt) cc_final: 0.7829 (mp) REVERT: A 538 VAL cc_start: 0.8395 (m) cc_final: 0.8026 (m) REVERT: A 539 ARG cc_start: 0.8131 (ttm-80) cc_final: 0.7567 (ptm160) REVERT: A 540 LEU cc_start: 0.8738 (mm) cc_final: 0.8526 (mm) REVERT: A 542 MET cc_start: 0.7851 (ptt) cc_final: 0.7117 (ptt) REVERT: A 545 MET cc_start: 0.7500 (mtm) cc_final: 0.7066 (mtm) REVERT: A 550 ASP cc_start: 0.7369 (p0) cc_final: 0.6952 (p0) REVERT: A 553 LYS cc_start: 0.8613 (mtpp) cc_final: 0.8069 (tppt) REVERT: A 555 LEU cc_start: 0.8355 (tp) cc_final: 0.8086 (tp) REVERT: A 576 GLN cc_start: 0.7977 (tp40) cc_final: 0.7476 (tp40) REVERT: A 593 ASP cc_start: 0.7512 (t0) cc_final: 0.7283 (t70) REVERT: A 600 TRP cc_start: 0.8359 (t-100) cc_final: 0.8116 (t-100) REVERT: A 603 PRO cc_start: 0.7596 (Cg_endo) cc_final: 0.7356 (Cg_exo) REVERT: A 617 ILE cc_start: 0.8338 (mm) cc_final: 0.8089 (mm) REVERT: A 619 LEU cc_start: 0.8649 (tp) cc_final: 0.8391 (tp) REVERT: A 621 LEU cc_start: 0.7790 (mm) cc_final: 0.7338 (mp) REVERT: A 625 ASN cc_start: 0.8142 (m110) cc_final: 0.7789 (m110) REVERT: A 626 ASN cc_start: 0.7944 (m110) cc_final: 0.7628 (m110) REVERT: A 635 MET cc_start: 0.7579 (mpp) cc_final: 0.6948 (mpp) REVERT: A 641 LEU cc_start: 0.8421 (mt) cc_final: 0.7947 (mm) REVERT: A 642 MET cc_start: 0.7761 (mmp) cc_final: 0.7455 (mmp) REVERT: A 651 LEU cc_start: 0.8436 (mt) cc_final: 0.8042 (mt) REVERT: A 660 GLN cc_start: 0.7938 (pp30) cc_final: 0.7143 (pp30) REVERT: A 663 LYS cc_start: 0.8205 (ptmm) cc_final: 0.7569 (mptt) REVERT: A 667 GLU cc_start: 0.8106 (pp20) cc_final: 0.7755 (pp20) REVERT: A 682 ILE cc_start: 0.8507 (tp) cc_final: 0.8083 (tp) REVERT: A 711 LYS cc_start: 0.9255 (mmtt) cc_final: 0.8833 (mmtm) REVERT: A 712 GLU cc_start: 0.8799 (tt0) cc_final: 0.8299 (tt0) REVERT: A 715 ASN cc_start: 0.8661 (m110) cc_final: 0.8378 (m-40) REVERT: A 716 LEU cc_start: 0.8795 (mt) cc_final: 0.8490 (mp) REVERT: A 717 TYR cc_start: 0.8494 (t80) cc_final: 0.7869 (t80) REVERT: A 719 ASP cc_start: 0.7895 (m-30) cc_final: 0.7618 (m-30) REVERT: A 720 TYR cc_start: 0.7271 (t80) cc_final: 0.6877 (t80) REVERT: A 728 LYS cc_start: 0.8191 (ttpt) cc_final: 0.7533 (tmtt) REVERT: A 734 ARG cc_start: 0.8467 (ttt-90) cc_final: 0.7596 (ttm-80) REVERT: A 743 GLU cc_start: 0.7384 (mp0) cc_final: 0.6930 (mp0) REVERT: A 748 TYR cc_start: 0.6731 (t80) cc_final: 0.6517 (t80) REVERT: A 754 GLU cc_start: 0.8339 (mt-10) cc_final: 0.7900 (mp0) REVERT: A 756 GLU cc_start: 0.7495 (tp30) cc_final: 0.6938 (tp30) REVERT: A 763 ARG cc_start: 0.6732 (ttm110) cc_final: 0.6413 (ttm-80) REVERT: A 788 ARG cc_start: 0.8476 (ptt180) cc_final: 0.7976 (ptt180) REVERT: A 792 GLU cc_start: 0.8384 (mm-30) cc_final: 0.8023 (mm-30) REVERT: D 22 LEU cc_start: 0.8461 (mm) cc_final: 0.8109 (mm) REVERT: D 65 ASN cc_start: 0.7461 (m-40) cc_final: 0.7162 (m-40) REVERT: D 73 CYS cc_start: 0.6396 (m) cc_final: 0.5984 (m) REVERT: D 79 LYS cc_start: 0.8009 (tppp) cc_final: 0.6749 (tppp) REVERT: D 82 GLU cc_start: 0.8154 (tt0) cc_final: 0.7643 (tt0) REVERT: D 98 GLN cc_start: 0.8626 (mp10) cc_final: 0.8121 (mp10) REVERT: D 132 PHE cc_start: 0.7015 (m-80) cc_final: 0.6342 (m-80) REVERT: D 134 ASN cc_start: 0.7175 (t0) cc_final: 0.6713 (t0) REVERT: D 138 ARG cc_start: 0.6397 (pmt170) cc_final: 0.6194 (pmt170) REVERT: C 130 GLU cc_start: 0.8444 (pt0) cc_final: 0.7610 (pm20) REVERT: C 138 GLU cc_start: 0.8562 (mp0) cc_final: 0.8303 (mm-30) REVERT: C 304 MET cc_start: 0.4642 (tpt) cc_final: 0.4293 (tpt) REVERT: C 315 LYS cc_start: 0.8035 (mtmm) cc_final: 0.7382 (ptpp) REVERT: C 330 LYS cc_start: 0.8575 (mmmt) cc_final: 0.8232 (mptt) REVERT: C 332 ASN cc_start: 0.7678 (t0) cc_final: 0.7113 (t0) REVERT: C 336 ILE cc_start: 0.8158 (mt) cc_final: 0.7918 (mt) REVERT: C 337 ARG cc_start: 0.8019 (ppt170) cc_final: 0.7385 (ttp80) REVERT: C 338 ARG cc_start: 0.7818 (mmm-85) cc_final: 0.6966 (mmm160) REVERT: C 341 GLU cc_start: 0.7631 (pp20) cc_final: 0.7015 (pp20) REVERT: C 344 GLN cc_start: 0.8352 (tp-100) cc_final: 0.7381 (tp-100) REVERT: C 349 TYR cc_start: 0.7615 (t80) cc_final: 0.7285 (t80) REVERT: C 379 TYR cc_start: 0.7473 (t80) cc_final: 0.6934 (t80) REVERT: C 382 ASN cc_start: 0.8221 (m110) cc_final: 0.7876 (t0) REVERT: C 397 ASP cc_start: 0.7630 (t0) cc_final: 0.7360 (t0) REVERT: C 406 GLU cc_start: 0.7377 (tt0) cc_final: 0.6926 (tt0) REVERT: C 407 LEU cc_start: 0.9013 (mt) cc_final: 0.8575 (pp) REVERT: C 409 LEU cc_start: 0.8566 (tp) cc_final: 0.7859 (pp) REVERT: C 438 ASP cc_start: 0.7347 (m-30) cc_final: 0.6882 (m-30) REVERT: C 450 ILE cc_start: 0.8355 (mt) cc_final: 0.8145 (mt) REVERT: C 467 PHE cc_start: 0.8296 (t80) cc_final: 0.8046 (t80) REVERT: C 478 MET cc_start: 0.7643 (mtp) cc_final: 0.7218 (mtp) REVERT: C 499 ILE cc_start: 0.7900 (tp) cc_final: 0.7249 (tp) REVERT: C 501 MET cc_start: 0.7788 (mtt) cc_final: 0.7288 (mtt) REVERT: C 502 TYR cc_start: 0.6894 (m-10) cc_final: 0.6445 (m-10) REVERT: C 505 ARG cc_start: 0.8147 (mtt90) cc_final: 0.7673 (mtt90) REVERT: C 506 ARG cc_start: 0.7902 (mtt90) cc_final: 0.7676 (mtt90) REVERT: C 507 ILE cc_start: 0.8283 (mt) cc_final: 0.8060 (mt) REVERT: C 522 TYR cc_start: 0.7634 (m-80) cc_final: 0.7015 (m-80) REVERT: C 532 ILE cc_start: 0.8137 (pt) cc_final: 0.7656 (mm) REVERT: C 539 ARG cc_start: 0.8133 (ttm-80) cc_final: 0.7842 (ttm-80) REVERT: C 542 MET cc_start: 0.7587 (tpp) cc_final: 0.6965 (tpp) REVERT: C 545 MET cc_start: 0.7536 (mtm) cc_final: 0.7048 (mtm) REVERT: C 553 LYS cc_start: 0.8570 (mtmt) cc_final: 0.8168 (mtpp) REVERT: C 555 LEU cc_start: 0.8436 (tp) cc_final: 0.8098 (tp) REVERT: C 576 GLN cc_start: 0.7115 (tm-30) cc_final: 0.6719 (tm-30) REVERT: C 577 LEU cc_start: 0.8401 (mt) cc_final: 0.7988 (pp) REVERT: C 581 GLU cc_start: 0.7742 (pp20) cc_final: 0.7326 (pp20) REVERT: C 593 ASP cc_start: 0.7163 (t70) cc_final: 0.6952 (t0) REVERT: C 619 LEU cc_start: 0.8658 (tp) cc_final: 0.8432 (tp) REVERT: C 621 LEU cc_start: 0.7945 (mm) cc_final: 0.7473 (mm) REVERT: C 625 ASN cc_start: 0.8098 (m-40) cc_final: 0.7718 (m110) REVERT: C 626 ASN cc_start: 0.8017 (m110) cc_final: 0.7598 (m110) REVERT: C 635 MET cc_start: 0.7759 (mpp) cc_final: 0.7143 (mpp) REVERT: C 641 LEU cc_start: 0.8387 (mt) cc_final: 0.7972 (mm) REVERT: C 642 MET cc_start: 0.7840 (mmp) cc_final: 0.7484 (mmp) REVERT: C 651 LEU cc_start: 0.8414 (mt) cc_final: 0.8021 (mt) REVERT: C 663 LYS cc_start: 0.8143 (ttpp) cc_final: 0.7894 (ttpp) REVERT: C 664 ASP cc_start: 0.7347 (m-30) cc_final: 0.6847 (m-30) REVERT: C 666 LEU cc_start: 0.8655 (mm) cc_final: 0.8453 (mm) REVERT: C 667 GLU cc_start: 0.7998 (pp20) cc_final: 0.7717 (pp20) REVERT: C 693 MET cc_start: 0.6341 (tpt) cc_final: 0.6044 (tpt) REVERT: C 712 GLU cc_start: 0.8805 (tt0) cc_final: 0.8320 (tt0) REVERT: C 713 PHE cc_start: 0.8496 (t80) cc_final: 0.7817 (t80) REVERT: C 716 LEU cc_start: 0.8709 (mt) cc_final: 0.8073 (pp) REVERT: C 717 TYR cc_start: 0.8625 (t80) cc_final: 0.8224 (t80) REVERT: C 720 TYR cc_start: 0.7409 (t80) cc_final: 0.6981 (t80) REVERT: C 730 PHE cc_start: 0.7383 (t80) cc_final: 0.7020 (t80) REVERT: C 738 HIS cc_start: 0.7602 (t-90) cc_final: 0.7153 (t-170) REVERT: C 739 MET cc_start: 0.7324 (ptm) cc_final: 0.7098 (ptm) REVERT: C 743 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7670 (mm-30) REVERT: C 747 LYS cc_start: 0.8975 (mtpt) cc_final: 0.8654 (mtpt) REVERT: C 748 TYR cc_start: 0.6783 (t80) cc_final: 0.6505 (t80) REVERT: C 756 GLU cc_start: 0.6645 (tp30) cc_final: 0.5997 (tp30) REVERT: C 780 TYR cc_start: 0.6280 (t80) cc_final: 0.4178 (t80) REVERT: C 788 ARG cc_start: 0.8181 (tmm160) cc_final: 0.7809 (ttp80) REVERT: C 805 PHE cc_start: 0.8220 (t80) cc_final: 0.7864 (t80) REVERT: C 806 LEU cc_start: 0.8395 (mt) cc_final: 0.7826 (mt) REVERT: C 822 LYS cc_start: 0.8462 (mmtt) cc_final: 0.8083 (mmtm) REVERT: C 855 LYS cc_start: 0.8793 (tttt) cc_final: 0.8426 (tptt) outliers start: 0 outliers final: 0 residues processed: 525 average time/residue: 0.3481 time to fit residues: 245.6007 Evaluate side-chains 498 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 498 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 96 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 93 optimal weight: 3.9990 chunk 47 optimal weight: 0.0070 chunk 30 optimal weight: 0.9990 chunk 99 optimal weight: 0.5980 chunk 106 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 14 optimal weight: 0.0870 chunk 122 optimal weight: 0.5980 chunk 142 optimal weight: 0.9980 overall best weight: 0.4576 ------------------------------------------------------------------------------- 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 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 ASN A 738 HIS ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 455 ASN C 723 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.6258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13522 Z= 0.172 Angle : 0.640 11.129 18260 Z= 0.324 Chirality : 0.044 0.157 2014 Planarity : 0.005 0.112 2372 Dihedral : 4.982 21.371 1806 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.21), residues: 1610 helix: -0.15 (0.18), residues: 806 sheet: -2.55 (0.62), residues: 68 loop : -1.20 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.005 TRP D 139 HIS 0.009 0.001 HIS A 655 PHE 0.031 0.002 PHE C 730 TYR 0.019 0.001 TYR A 494 ARG 0.008 0.001 ARG D 46 *********************** 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 522 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 522 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 18 LYS cc_start: 0.7697 (mmtm) cc_final: 0.7207 (mmmm) REVERT: B 22 LEU cc_start: 0.8384 (mm) cc_final: 0.8079 (mm) REVERT: B 65 ASN cc_start: 0.7221 (m-40) cc_final: 0.7015 (m-40) REVERT: B 73 CYS cc_start: 0.6533 (m) cc_final: 0.6192 (m) REVERT: B 77 TYR cc_start: 0.7917 (m-80) cc_final: 0.7417 (m-80) REVERT: B 79 LYS cc_start: 0.8055 (tppp) cc_final: 0.6752 (tppp) REVERT: B 82 GLU cc_start: 0.8136 (tt0) cc_final: 0.7759 (tt0) REVERT: B 88 TYR cc_start: 0.6799 (p90) cc_final: 0.6548 (p90) REVERT: B 114 GLN cc_start: 0.6984 (mp10) cc_final: 0.6726 (mp10) REVERT: B 124 ARG cc_start: 0.8087 (tmm160) cc_final: 0.7782 (ttp80) REVERT: B 134 ASN cc_start: 0.7142 (t0) cc_final: 0.6663 (t0) REVERT: B 136 ARG cc_start: 0.7673 (mmm160) cc_final: 0.7408 (mmm160) REVERT: A 130 GLU cc_start: 0.8477 (pt0) cc_final: 0.7653 (pm20) REVERT: A 237 ASP cc_start: 0.8280 (m-30) cc_final: 0.7759 (t0) REVERT: A 291 MET cc_start: 0.8028 (ttt) cc_final: 0.7741 (ptm) REVERT: A 304 MET cc_start: 0.4634 (tpt) cc_final: 0.4027 (tpt) REVERT: A 315 LYS cc_start: 0.8055 (mmtm) cc_final: 0.7641 (mttt) REVERT: A 337 ARG cc_start: 0.8125 (ttm170) cc_final: 0.7117 (ttp80) REVERT: A 338 ARG cc_start: 0.7876 (mtp85) cc_final: 0.7587 (mmm-85) REVERT: A 341 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7489 (mt-10) REVERT: A 344 GLN cc_start: 0.8332 (tp-100) cc_final: 0.7224 (tp-100) REVERT: A 348 THR cc_start: 0.7855 (m) cc_final: 0.7612 (m) REVERT: A 350 LYS cc_start: 0.7517 (mmpt) cc_final: 0.7087 (tptt) REVERT: A 377 MET cc_start: 0.8114 (mtt) cc_final: 0.7902 (mtp) REVERT: A 379 TYR cc_start: 0.7456 (t80) cc_final: 0.7130 (t80) REVERT: A 392 HIS cc_start: 0.8230 (m90) cc_final: 0.7814 (m90) REVERT: A 407 LEU cc_start: 0.8962 (mt) cc_final: 0.8697 (pp) REVERT: A 420 LYS cc_start: 0.7779 (pttp) cc_final: 0.7552 (pttp) REVERT: A 426 ASP cc_start: 0.8437 (t0) cc_final: 0.8200 (t0) REVERT: A 438 ASP cc_start: 0.7122 (m-30) cc_final: 0.6452 (m-30) REVERT: A 447 GLU cc_start: 0.7767 (mp0) cc_final: 0.7517 (tp30) REVERT: A 449 PHE cc_start: 0.7018 (m-10) cc_final: 0.6710 (m-10) REVERT: A 450 ILE cc_start: 0.8135 (mt) cc_final: 0.7041 (mt) REVERT: A 455 ASN cc_start: 0.7786 (m-40) cc_final: 0.7553 (m-40) REVERT: A 458 LEU cc_start: 0.8280 (tp) cc_final: 0.7859 (tt) REVERT: A 478 MET cc_start: 0.7802 (mtp) cc_final: 0.7174 (mtp) REVERT: A 499 ILE cc_start: 0.7764 (tp) cc_final: 0.7505 (tp) REVERT: A 504 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7045 (mm-30) REVERT: A 505 ARG cc_start: 0.8187 (mtt90) cc_final: 0.7533 (mtt90) REVERT: A 507 ILE cc_start: 0.8470 (mt) cc_final: 0.7972 (mt) REVERT: A 522 TYR cc_start: 0.7891 (m-80) cc_final: 0.6793 (m-80) REVERT: A 530 ASP cc_start: 0.7126 (p0) cc_final: 0.6701 (p0) REVERT: A 532 ILE cc_start: 0.8299 (pt) cc_final: 0.7947 (mm) REVERT: A 533 ILE cc_start: 0.8332 (pt) cc_final: 0.7820 (mp) REVERT: A 538 VAL cc_start: 0.8381 (m) cc_final: 0.7975 (m) REVERT: A 539 ARG cc_start: 0.8065 (ttm-80) cc_final: 0.7705 (ptm160) REVERT: A 542 MET cc_start: 0.7808 (ptt) cc_final: 0.7021 (ptt) REVERT: A 545 MET cc_start: 0.7477 (mtm) cc_final: 0.7009 (mtm) REVERT: A 550 ASP cc_start: 0.7356 (p0) cc_final: 0.6834 (p0) REVERT: A 553 LYS cc_start: 0.8545 (mtpp) cc_final: 0.7922 (tppp) REVERT: A 572 LYS cc_start: 0.7784 (tptt) cc_final: 0.7301 (tptt) REVERT: A 576 GLN cc_start: 0.7808 (tp40) cc_final: 0.7245 (tp40) REVERT: A 589 MET cc_start: 0.5070 (mtm) cc_final: 0.4247 (mtm) REVERT: A 593 ASP cc_start: 0.7438 (t0) cc_final: 0.7158 (t70) REVERT: A 600 TRP cc_start: 0.8301 (t-100) cc_final: 0.8098 (t-100) REVERT: A 603 PRO cc_start: 0.7616 (Cg_endo) cc_final: 0.7379 (Cg_exo) REVERT: A 611 GLN cc_start: 0.7593 (tm-30) cc_final: 0.6348 (tm-30) REVERT: A 619 LEU cc_start: 0.8629 (tp) cc_final: 0.8383 (tp) REVERT: A 635 MET cc_start: 0.7569 (mpp) cc_final: 0.6935 (mpp) REVERT: A 641 LEU cc_start: 0.8444 (mt) cc_final: 0.8050 (mm) REVERT: A 642 MET cc_start: 0.7812 (mmp) cc_final: 0.7495 (mmp) REVERT: A 651 LEU cc_start: 0.8366 (mt) cc_final: 0.7956 (mt) REVERT: A 660 GLN cc_start: 0.7896 (pp30) cc_final: 0.7094 (pp30) REVERT: A 663 LYS cc_start: 0.8143 (ptmm) cc_final: 0.7537 (mmtm) REVERT: A 667 GLU cc_start: 0.8131 (pp20) cc_final: 0.7805 (pp20) REVERT: A 682 ILE cc_start: 0.8496 (tp) cc_final: 0.8148 (tp) REVERT: A 711 LYS cc_start: 0.9227 (mmtt) cc_final: 0.8841 (mmtm) REVERT: A 712 GLU cc_start: 0.8721 (tt0) cc_final: 0.8255 (tt0) REVERT: A 715 ASN cc_start: 0.8696 (m110) cc_final: 0.8430 (m-40) REVERT: A 716 LEU cc_start: 0.8795 (mt) cc_final: 0.8500 (mp) REVERT: A 717 TYR cc_start: 0.8493 (t80) cc_final: 0.8076 (t80) REVERT: A 719 ASP cc_start: 0.7838 (m-30) cc_final: 0.7587 (m-30) REVERT: A 720 TYR cc_start: 0.7240 (t80) cc_final: 0.6851 (t80) REVERT: A 728 LYS cc_start: 0.8175 (ttpt) cc_final: 0.7461 (tmtt) REVERT: A 734 ARG cc_start: 0.8459 (ttt-90) cc_final: 0.8207 (ttt90) REVERT: A 743 GLU cc_start: 0.7385 (mp0) cc_final: 0.6952 (mp0) REVERT: A 754 GLU cc_start: 0.8327 (mt-10) cc_final: 0.7802 (mp0) REVERT: A 756 GLU cc_start: 0.7407 (tp30) cc_final: 0.6910 (tp30) REVERT: A 788 ARG cc_start: 0.8441 (ptt180) cc_final: 0.7934 (ptt180) REVERT: A 792 GLU cc_start: 0.8403 (mm-30) cc_final: 0.8049 (mm-30) REVERT: A 822 LYS cc_start: 0.8168 (mmtt) cc_final: 0.7930 (mmtm) REVERT: D 18 LYS cc_start: 0.7371 (mmtm) cc_final: 0.6804 (mmmm) REVERT: D 22 LEU cc_start: 0.8498 (mm) cc_final: 0.8134 (mm) REVERT: D 62 ARG cc_start: 0.6392 (mmt-90) cc_final: 0.6096 (mmt-90) REVERT: D 65 ASN cc_start: 0.7268 (m-40) cc_final: 0.6995 (m-40) REVERT: D 73 CYS cc_start: 0.5969 (m) cc_final: 0.5563 (m) REVERT: D 79 LYS cc_start: 0.8007 (tppp) cc_final: 0.6727 (tppp) REVERT: D 82 GLU cc_start: 0.8165 (tt0) cc_final: 0.7686 (tt0) REVERT: D 98 GLN cc_start: 0.8629 (mp10) cc_final: 0.8254 (mp10) REVERT: D 114 GLN cc_start: 0.6611 (mp10) cc_final: 0.6371 (mp10) REVERT: D 132 PHE cc_start: 0.7008 (m-80) cc_final: 0.6425 (m-80) REVERT: C 130 GLU cc_start: 0.8438 (pt0) cc_final: 0.7565 (pm20) REVERT: C 138 GLU cc_start: 0.8556 (mp0) cc_final: 0.8288 (mm-30) REVERT: C 246 LEU cc_start: 0.8010 (tp) cc_final: 0.7790 (tp) REVERT: C 260 LEU cc_start: 0.8781 (mm) cc_final: 0.8502 (pp) REVERT: C 304 MET cc_start: 0.4610 (tpt) cc_final: 0.4266 (tpt) REVERT: C 315 LYS cc_start: 0.7998 (mtmm) cc_final: 0.7315 (ptpp) REVERT: C 336 ILE cc_start: 0.8186 (mt) cc_final: 0.7948 (mt) REVERT: C 337 ARG cc_start: 0.8030 (ppt170) cc_final: 0.7621 (ttp80) REVERT: C 339 MET cc_start: 0.6214 (mmm) cc_final: 0.5872 (mmm) REVERT: C 341 GLU cc_start: 0.7594 (pp20) cc_final: 0.7050 (pp20) REVERT: C 344 GLN cc_start: 0.8328 (tp-100) cc_final: 0.7516 (tp-100) REVERT: C 349 TYR cc_start: 0.7621 (t80) cc_final: 0.7309 (t80) REVERT: C 379 TYR cc_start: 0.7467 (t80) cc_final: 0.6918 (t80) REVERT: C 382 ASN cc_start: 0.8160 (m110) cc_final: 0.7884 (t0) REVERT: C 394 GLU cc_start: 0.6082 (mm-30) cc_final: 0.5730 (mm-30) REVERT: C 397 ASP cc_start: 0.7648 (t0) cc_final: 0.7375 (t0) REVERT: C 407 LEU cc_start: 0.9041 (mt) cc_final: 0.8594 (pp) REVERT: C 450 ILE cc_start: 0.8325 (mt) cc_final: 0.8118 (mt) REVERT: C 467 PHE cc_start: 0.8274 (t80) cc_final: 0.8018 (t80) REVERT: C 478 MET cc_start: 0.7640 (mtp) cc_final: 0.7230 (mtp) REVERT: C 499 ILE cc_start: 0.7895 (tp) cc_final: 0.7239 (tp) REVERT: C 501 MET cc_start: 0.7711 (mtt) cc_final: 0.7329 (mtt) REVERT: C 502 TYR cc_start: 0.6899 (m-10) cc_final: 0.6505 (m-10) REVERT: C 505 ARG cc_start: 0.8183 (mtt90) cc_final: 0.7686 (mtt90) REVERT: C 506 ARG cc_start: 0.7888 (mtt90) cc_final: 0.7662 (mtt90) REVERT: C 507 ILE cc_start: 0.8282 (mt) cc_final: 0.7947 (mt) REVERT: C 522 TYR cc_start: 0.7607 (m-80) cc_final: 0.6999 (m-80) REVERT: C 532 ILE cc_start: 0.8159 (pt) cc_final: 0.7639 (mm) REVERT: C 539 ARG cc_start: 0.8069 (ttm-80) cc_final: 0.7795 (ttm-80) REVERT: C 542 MET cc_start: 0.7558 (tpp) cc_final: 0.6925 (tpp) REVERT: C 545 MET cc_start: 0.7500 (mtm) cc_final: 0.6995 (mtm) REVERT: C 553 LYS cc_start: 0.8538 (mtmt) cc_final: 0.8287 (mtpp) REVERT: C 555 LEU cc_start: 0.8429 (tp) cc_final: 0.8059 (tp) REVERT: C 576 GLN cc_start: 0.7596 (tm-30) cc_final: 0.7153 (tm-30) REVERT: C 577 LEU cc_start: 0.8555 (mt) cc_final: 0.8148 (pp) REVERT: C 581 GLU cc_start: 0.7678 (pp20) cc_final: 0.7222 (pp20) REVERT: C 603 PRO cc_start: 0.7651 (Cg_endo) cc_final: 0.7405 (Cg_exo) REVERT: C 619 LEU cc_start: 0.8659 (tp) cc_final: 0.7933 (tp) REVERT: C 621 LEU cc_start: 0.7890 (mm) cc_final: 0.7394 (mm) REVERT: C 625 ASN cc_start: 0.8080 (m-40) cc_final: 0.7692 (m110) REVERT: C 626 ASN cc_start: 0.8038 (m110) cc_final: 0.7612 (m110) REVERT: C 635 MET cc_start: 0.7738 (mpp) cc_final: 0.7131 (mpp) REVERT: C 641 LEU cc_start: 0.8348 (mt) cc_final: 0.7853 (mm) REVERT: C 642 MET cc_start: 0.7822 (mmp) cc_final: 0.7468 (mmp) REVERT: C 651 LEU cc_start: 0.8452 (mt) cc_final: 0.8104 (mt) REVERT: C 663 LYS cc_start: 0.8137 (ttpp) cc_final: 0.7842 (ttpp) REVERT: C 666 LEU cc_start: 0.8683 (mm) cc_final: 0.8421 (mm) REVERT: C 667 GLU cc_start: 0.7997 (pp20) cc_final: 0.7646 (pp20) REVERT: C 711 LYS cc_start: 0.9232 (mmtt) cc_final: 0.8691 (mmtm) REVERT: C 712 GLU cc_start: 0.8793 (tt0) cc_final: 0.8304 (tt0) REVERT: C 713 PHE cc_start: 0.8425 (t80) cc_final: 0.7714 (t80) REVERT: C 716 LEU cc_start: 0.8726 (mt) cc_final: 0.8096 (pp) REVERT: C 717 TYR cc_start: 0.8586 (t80) cc_final: 0.8222 (t80) REVERT: C 720 TYR cc_start: 0.7308 (t80) cc_final: 0.6887 (t80) REVERT: C 731 LYS cc_start: 0.7796 (pptt) cc_final: 0.7483 (pptt) REVERT: C 737 PHE cc_start: 0.7924 (t80) cc_final: 0.7373 (t80) REVERT: C 738 HIS cc_start: 0.7607 (t-90) cc_final: 0.7096 (t-170) REVERT: C 739 MET cc_start: 0.7296 (ptm) cc_final: 0.7045 (ptm) REVERT: C 743 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7673 (mm-30) REVERT: C 747 LYS cc_start: 0.8945 (mtpt) cc_final: 0.8602 (mmtt) REVERT: C 748 TYR cc_start: 0.6733 (t80) cc_final: 0.6438 (t80) REVERT: C 754 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7710 (mp0) REVERT: C 756 GLU cc_start: 0.6717 (tp30) cc_final: 0.6157 (tp30) REVERT: C 780 TYR cc_start: 0.6254 (t80) cc_final: 0.4154 (t80) REVERT: C 788 ARG cc_start: 0.8226 (tmm160) cc_final: 0.7756 (ttp80) REVERT: C 797 PHE cc_start: 0.6037 (m-80) cc_final: 0.5767 (m-80) REVERT: C 822 LYS cc_start: 0.8395 (mmtt) cc_final: 0.8052 (mmtm) REVERT: C 835 GLU cc_start: 0.7512 (pm20) cc_final: 0.7300 (pm20) REVERT: C 855 LYS cc_start: 0.8823 (tttt) cc_final: 0.8399 (tptt) outliers start: 0 outliers final: 0 residues processed: 522 average time/residue: 0.3438 time to fit residues: 242.2322 Evaluate side-chains 491 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 491 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 149 optimal weight: 3.9990 chunk 136 optimal weight: 0.0030 chunk 145 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 114 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 131 optimal weight: 0.4980 chunk 137 optimal weight: 0.8980 chunk 144 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- 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 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 ASN A 738 HIS ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 723 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.6462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13522 Z= 0.179 Angle : 0.643 10.239 18260 Z= 0.328 Chirality : 0.044 0.220 2014 Planarity : 0.005 0.100 2372 Dihedral : 4.959 21.027 1806 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.21), residues: 1610 helix: -0.26 (0.18), residues: 822 sheet: -1.97 (0.66), residues: 64 loop : -1.14 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.004 TRP D 139 HIS 0.006 0.001 HIS C 655 PHE 0.031 0.002 PHE C 730 TYR 0.015 0.001 TYR A 624 ARG 0.007 0.000 ARG A 326 *********************** 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 510 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 510 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 18 LYS cc_start: 0.7593 (mmtm) cc_final: 0.7223 (mmmm) REVERT: B 22 LEU cc_start: 0.8372 (mm) cc_final: 0.8062 (mm) REVERT: B 77 TYR cc_start: 0.7984 (m-80) cc_final: 0.7537 (m-80) REVERT: B 124 ARG cc_start: 0.8143 (tmm160) cc_final: 0.7793 (ttp80) REVERT: B 134 ASN cc_start: 0.7112 (t0) cc_final: 0.6628 (t0) REVERT: A 130 GLU cc_start: 0.8457 (pt0) cc_final: 0.7626 (pm20) REVERT: A 237 ASP cc_start: 0.8325 (m-30) cc_final: 0.7791 (t0) REVERT: A 291 MET cc_start: 0.7928 (ttt) cc_final: 0.7593 (ptm) REVERT: A 304 MET cc_start: 0.4350 (tpt) cc_final: 0.3674 (tpt) REVERT: A 337 ARG cc_start: 0.8189 (ttm170) cc_final: 0.7108 (ttp80) REVERT: A 338 ARG cc_start: 0.7866 (mtp85) cc_final: 0.7544 (mmm-85) REVERT: A 341 GLU cc_start: 0.8340 (mt-10) cc_final: 0.7529 (mt-10) REVERT: A 344 GLN cc_start: 0.8265 (tp-100) cc_final: 0.7204 (tp-100) REVERT: A 350 LYS cc_start: 0.7632 (mmpt) cc_final: 0.6965 (tptt) REVERT: A 377 MET cc_start: 0.8135 (mtt) cc_final: 0.7905 (mtp) REVERT: A 379 TYR cc_start: 0.7470 (t80) cc_final: 0.7186 (t80) REVERT: A 392 HIS cc_start: 0.8264 (m90) cc_final: 0.7850 (m90) REVERT: A 395 GLU cc_start: 0.6550 (pp20) cc_final: 0.6263 (tm-30) REVERT: A 407 LEU cc_start: 0.8960 (mt) cc_final: 0.8679 (mt) REVERT: A 424 ARG cc_start: 0.7982 (mmm-85) cc_final: 0.7551 (mtp85) REVERT: A 426 ASP cc_start: 0.8441 (t0) cc_final: 0.8193 (t0) REVERT: A 447 GLU cc_start: 0.7773 (mp0) cc_final: 0.7509 (tp30) REVERT: A 449 PHE cc_start: 0.6981 (m-10) cc_final: 0.6688 (m-10) REVERT: A 450 ILE cc_start: 0.8175 (mt) cc_final: 0.7062 (mt) REVERT: A 458 LEU cc_start: 0.8274 (tp) cc_final: 0.7850 (tt) REVERT: A 464 TYR cc_start: 0.6848 (t80) cc_final: 0.6589 (t80) REVERT: A 478 MET cc_start: 0.7799 (mtp) cc_final: 0.7503 (ttm) REVERT: A 499 ILE cc_start: 0.7745 (tp) cc_final: 0.7480 (tp) REVERT: A 504 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7072 (mm-30) REVERT: A 505 ARG cc_start: 0.8180 (mtt90) cc_final: 0.7503 (mtt90) REVERT: A 507 ILE cc_start: 0.8499 (mt) cc_final: 0.7981 (mt) REVERT: A 515 GLN cc_start: 0.7109 (pp30) cc_final: 0.6858 (pp30) REVERT: A 522 TYR cc_start: 0.7861 (m-80) cc_final: 0.6877 (m-80) REVERT: A 530 ASP cc_start: 0.7256 (p0) cc_final: 0.6941 (p0) REVERT: A 532 ILE cc_start: 0.8314 (pt) cc_final: 0.7956 (mm) REVERT: A 533 ILE cc_start: 0.8294 (pt) cc_final: 0.7864 (mp) REVERT: A 538 VAL cc_start: 0.8337 (m) cc_final: 0.7969 (m) REVERT: A 539 ARG cc_start: 0.8101 (ttm-80) cc_final: 0.7723 (ptm160) REVERT: A 542 MET cc_start: 0.7849 (ptt) cc_final: 0.7191 (ptt) REVERT: A 545 MET cc_start: 0.7476 (mtm) cc_final: 0.7080 (mtm) REVERT: A 550 ASP cc_start: 0.7353 (p0) cc_final: 0.6757 (p0) REVERT: A 553 LYS cc_start: 0.8054 (mtpp) cc_final: 0.7463 (ttmt) REVERT: A 572 LYS cc_start: 0.7711 (tptt) cc_final: 0.7241 (tptt) REVERT: A 576 GLN cc_start: 0.7829 (tp40) cc_final: 0.7170 (tp40) REVERT: A 589 MET cc_start: 0.5143 (mtm) cc_final: 0.4694 (mtm) REVERT: A 593 ASP cc_start: 0.7469 (t0) cc_final: 0.7212 (t70) REVERT: A 600 TRP cc_start: 0.8358 (t-100) cc_final: 0.8054 (t-100) REVERT: A 603 PRO cc_start: 0.7621 (Cg_endo) cc_final: 0.7374 (Cg_exo) REVERT: A 619 LEU cc_start: 0.8617 (tp) cc_final: 0.7922 (tp) REVERT: A 625 ASN cc_start: 0.7733 (p0) cc_final: 0.7214 (p0) REVERT: A 635 MET cc_start: 0.7636 (mpp) cc_final: 0.6982 (mpp) REVERT: A 641 LEU cc_start: 0.8471 (mt) cc_final: 0.8123 (mm) REVERT: A 642 MET cc_start: 0.7853 (mmp) cc_final: 0.7532 (mmp) REVERT: A 651 LEU cc_start: 0.8371 (mt) cc_final: 0.7969 (mt) REVERT: A 660 GLN cc_start: 0.7890 (pp30) cc_final: 0.7055 (pp30) REVERT: A 663 LYS cc_start: 0.8163 (ptmm) cc_final: 0.7604 (mptt) REVERT: A 667 GLU cc_start: 0.8157 (pp20) cc_final: 0.7843 (pp20) REVERT: A 682 ILE cc_start: 0.8487 (tp) cc_final: 0.8177 (tp) REVERT: A 712 GLU cc_start: 0.8697 (tt0) cc_final: 0.8431 (tt0) REVERT: A 715 ASN cc_start: 0.8830 (m110) cc_final: 0.8411 (m110) REVERT: A 716 LEU cc_start: 0.8801 (mt) cc_final: 0.8340 (tp) REVERT: A 717 TYR cc_start: 0.8476 (t80) cc_final: 0.8166 (t80) REVERT: A 719 ASP cc_start: 0.7858 (m-30) cc_final: 0.7631 (m-30) REVERT: A 728 LYS cc_start: 0.8198 (ttpt) cc_final: 0.7279 (ptmm) REVERT: A 734 ARG cc_start: 0.8547 (ttt-90) cc_final: 0.8227 (ttt90) REVERT: A 737 PHE cc_start: 0.7918 (t80) cc_final: 0.7571 (t80) REVERT: A 739 MET cc_start: 0.7305 (ptm) cc_final: 0.7089 (ptm) REVERT: A 756 GLU cc_start: 0.7429 (tp30) cc_final: 0.6919 (tp30) REVERT: A 788 ARG cc_start: 0.8383 (ptt180) cc_final: 0.7899 (ptt180) REVERT: A 792 GLU cc_start: 0.8375 (mm-30) cc_final: 0.8040 (mm-30) REVERT: A 822 LYS cc_start: 0.8202 (mmtt) cc_final: 0.7927 (mmtm) REVERT: D 18 LYS cc_start: 0.7418 (mmtm) cc_final: 0.6788 (mmmm) REVERT: D 22 LEU cc_start: 0.8538 (mm) cc_final: 0.8167 (mm) REVERT: D 62 ARG cc_start: 0.6315 (mmt-90) cc_final: 0.6064 (mmt-90) REVERT: D 65 ASN cc_start: 0.7253 (m-40) cc_final: 0.6966 (m-40) REVERT: D 73 CYS cc_start: 0.6091 (m) cc_final: 0.5709 (m) REVERT: D 79 LYS cc_start: 0.7972 (tppp) cc_final: 0.6850 (tppp) REVERT: D 82 GLU cc_start: 0.8231 (tt0) cc_final: 0.7820 (tt0) REVERT: D 132 PHE cc_start: 0.7082 (m-80) cc_final: 0.6576 (m-80) REVERT: C 130 GLU cc_start: 0.8440 (pt0) cc_final: 0.7590 (pm20) REVERT: C 138 GLU cc_start: 0.8544 (mp0) cc_final: 0.8234 (mm-30) REVERT: C 246 LEU cc_start: 0.8069 (tp) cc_final: 0.7864 (tp) REVERT: C 260 LEU cc_start: 0.8784 (mm) cc_final: 0.8451 (pp) REVERT: C 304 MET cc_start: 0.4608 (tpt) cc_final: 0.4281 (tpt) REVERT: C 315 LYS cc_start: 0.8038 (mtmm) cc_final: 0.7368 (ptpp) REVERT: C 330 LYS cc_start: 0.8621 (mmmt) cc_final: 0.8283 (mptt) REVERT: C 336 ILE cc_start: 0.8165 (mt) cc_final: 0.7943 (mt) REVERT: C 337 ARG cc_start: 0.8046 (ppt170) cc_final: 0.7468 (ttp80) REVERT: C 338 ARG cc_start: 0.7993 (mmm-85) cc_final: 0.7543 (mmt90) REVERT: C 341 GLU cc_start: 0.7545 (pp20) cc_final: 0.7091 (pp20) REVERT: C 349 TYR cc_start: 0.7606 (t80) cc_final: 0.7297 (t80) REVERT: C 379 TYR cc_start: 0.7413 (t80) cc_final: 0.6933 (t80) REVERT: C 380 TYR cc_start: 0.7909 (m-10) cc_final: 0.7685 (m-10) REVERT: C 382 ASN cc_start: 0.8188 (m110) cc_final: 0.7897 (t0) REVERT: C 397 ASP cc_start: 0.7648 (t0) cc_final: 0.7321 (t0) REVERT: C 407 LEU cc_start: 0.9059 (mt) cc_final: 0.8565 (pp) REVERT: C 410 GLN cc_start: 0.8350 (mm110) cc_final: 0.6397 (mm-40) REVERT: C 438 ASP cc_start: 0.7525 (m-30) cc_final: 0.6952 (m-30) REVERT: C 450 ILE cc_start: 0.8298 (mt) cc_final: 0.7357 (mm) REVERT: C 477 PHE cc_start: 0.7269 (m-80) cc_final: 0.6914 (m-80) REVERT: C 478 MET cc_start: 0.7761 (mtp) cc_final: 0.7338 (mtp) REVERT: C 482 PHE cc_start: 0.8048 (p90) cc_final: 0.7816 (p90) REVERT: C 499 ILE cc_start: 0.7923 (tp) cc_final: 0.7260 (tp) REVERT: C 501 MET cc_start: 0.7710 (mtt) cc_final: 0.7359 (mtt) REVERT: C 502 TYR cc_start: 0.6884 (m-10) cc_final: 0.6629 (m-10) REVERT: C 505 ARG cc_start: 0.8164 (mtt90) cc_final: 0.7626 (mtt90) REVERT: C 507 ILE cc_start: 0.8325 (mt) cc_final: 0.8005 (mt) REVERT: C 522 TYR cc_start: 0.7605 (m-80) cc_final: 0.6936 (m-80) REVERT: C 539 ARG cc_start: 0.8053 (ttm-80) cc_final: 0.7799 (ttm-80) REVERT: C 542 MET cc_start: 0.7578 (tpp) cc_final: 0.7091 (tpp) REVERT: C 545 MET cc_start: 0.7475 (mtm) cc_final: 0.7208 (mtm) REVERT: C 553 LYS cc_start: 0.8585 (mtmt) cc_final: 0.8313 (mtpp) REVERT: C 555 LEU cc_start: 0.8446 (tp) cc_final: 0.8101 (tp) REVERT: C 576 GLN cc_start: 0.7491 (tm-30) cc_final: 0.7015 (tm-30) REVERT: C 577 LEU cc_start: 0.8421 (mt) cc_final: 0.7936 (pp) REVERT: C 581 GLU cc_start: 0.7711 (pp20) cc_final: 0.7410 (pp20) REVERT: C 603 PRO cc_start: 0.7691 (Cg_endo) cc_final: 0.7475 (Cg_exo) REVERT: C 619 LEU cc_start: 0.8693 (tp) cc_final: 0.8493 (tp) REVERT: C 621 LEU cc_start: 0.7882 (mm) cc_final: 0.7433 (mm) REVERT: C 625 ASN cc_start: 0.8039 (m-40) cc_final: 0.7670 (m110) REVERT: C 626 ASN cc_start: 0.8061 (m110) cc_final: 0.7542 (m110) REVERT: C 635 MET cc_start: 0.7730 (mpp) cc_final: 0.7135 (mpp) REVERT: C 641 LEU cc_start: 0.8405 (mt) cc_final: 0.8077 (mt) REVERT: C 642 MET cc_start: 0.7858 (mmp) cc_final: 0.7602 (mmp) REVERT: C 651 LEU cc_start: 0.8465 (mt) cc_final: 0.8128 (mt) REVERT: C 660 GLN cc_start: 0.8080 (pp30) cc_final: 0.7621 (pp30) REVERT: C 663 LYS cc_start: 0.8149 (ttpp) cc_final: 0.7806 (ttpp) REVERT: C 666 LEU cc_start: 0.8680 (mm) cc_final: 0.8457 (mm) REVERT: C 667 GLU cc_start: 0.7993 (pp20) cc_final: 0.7643 (pp20) REVERT: C 707 ASN cc_start: 0.8041 (p0) cc_final: 0.7480 (m-40) REVERT: C 712 GLU cc_start: 0.8774 (tt0) cc_final: 0.8409 (tt0) REVERT: C 716 LEU cc_start: 0.8761 (mt) cc_final: 0.8144 (pp) REVERT: C 717 TYR cc_start: 0.8620 (t80) cc_final: 0.8268 (t80) REVERT: C 720 TYR cc_start: 0.7299 (t80) cc_final: 0.6838 (t80) REVERT: C 730 PHE cc_start: 0.7509 (t80) cc_final: 0.7139 (t80) REVERT: C 738 HIS cc_start: 0.7612 (t-90) cc_final: 0.7084 (t-170) REVERT: C 739 MET cc_start: 0.7289 (ptm) cc_final: 0.7086 (ptm) REVERT: C 743 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7742 (mm-30) REVERT: C 747 LYS cc_start: 0.8931 (mtpt) cc_final: 0.8622 (mmtt) REVERT: C 748 TYR cc_start: 0.6702 (t80) cc_final: 0.6444 (t80) REVERT: C 754 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7524 (mp0) REVERT: C 756 GLU cc_start: 0.6681 (tp30) cc_final: 0.6353 (tp30) REVERT: C 780 TYR cc_start: 0.6309 (t80) cc_final: 0.4303 (t80) REVERT: C 788 ARG cc_start: 0.8256 (tmm160) cc_final: 0.7755 (ttp80) REVERT: C 797 PHE cc_start: 0.5991 (m-80) cc_final: 0.5756 (m-80) REVERT: C 822 LYS cc_start: 0.8381 (mmtt) cc_final: 0.8058 (mmtm) REVERT: C 855 LYS cc_start: 0.8849 (tttt) cc_final: 0.8433 (tptt) outliers start: 0 outliers final: 0 residues processed: 510 average time/residue: 0.3521 time to fit residues: 244.9949 Evaluate side-chains 478 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 478 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 153 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 161 optimal weight: 0.3980 chunk 148 optimal weight: 0.2980 chunk 128 optimal weight: 0.7980 chunk 13 optimal weight: 0.4980 chunk 99 optimal weight: 4.9990 chunk 78 optimal weight: 0.4980 chunk 102 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 ASN ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 723 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.6661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13522 Z= 0.174 Angle : 0.642 9.861 18260 Z= 0.327 Chirality : 0.044 0.208 2014 Planarity : 0.005 0.078 2372 Dihedral : 4.889 20.967 1806 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.21), residues: 1610 helix: -0.14 (0.18), residues: 808 sheet: -1.88 (0.67), residues: 64 loop : -1.04 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP B 139 HIS 0.007 0.001 HIS C 655 PHE 0.031 0.002 PHE A 574 TYR 0.017 0.001 TYR A 494 ARG 0.006 0.000 ARG A 763 ********************** 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 513 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 513 time to evaluate : 1.454 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 18 LYS cc_start: 0.7537 (mmtm) cc_final: 0.7214 (mmmm) REVERT: B 22 LEU cc_start: 0.8395 (mm) cc_final: 0.8119 (mm) REVERT: B 73 CYS cc_start: 0.6251 (m) cc_final: 0.5956 (m) REVERT: B 77 TYR cc_start: 0.7846 (m-80) cc_final: 0.7559 (m-80) REVERT: B 88 TYR cc_start: 0.6876 (p90) cc_final: 0.6624 (p90) REVERT: B 114 GLN cc_start: 0.6732 (mp10) cc_final: 0.6285 (mp10) REVERT: B 124 ARG cc_start: 0.8133 (tmm160) cc_final: 0.7804 (ttp80) REVERT: B 134 ASN cc_start: 0.7218 (t0) cc_final: 0.6937 (t0) REVERT: A 130 GLU cc_start: 0.8445 (pt0) cc_final: 0.7601 (pm20) REVERT: A 237 ASP cc_start: 0.8329 (m-30) cc_final: 0.7839 (t0) REVERT: A 287 PHE cc_start: 0.6605 (m-80) cc_final: 0.5560 (m-80) REVERT: A 304 MET cc_start: 0.4297 (tpt) cc_final: 0.3767 (tpt) REVERT: A 332 ASN cc_start: 0.7566 (t0) cc_final: 0.7166 (t0) REVERT: A 337 ARG cc_start: 0.8211 (ttm170) cc_final: 0.7105 (ttp80) REVERT: A 338 ARG cc_start: 0.7897 (mtp85) cc_final: 0.7578 (mmm-85) REVERT: A 341 GLU cc_start: 0.8318 (mt-10) cc_final: 0.7477 (mt-10) REVERT: A 343 PHE cc_start: 0.8164 (m-10) cc_final: 0.7843 (m-10) REVERT: A 349 TYR cc_start: 0.7473 (t80) cc_final: 0.7245 (t80) REVERT: A 356 PHE cc_start: 0.7434 (m-80) cc_final: 0.5543 (m-80) REVERT: A 377 MET cc_start: 0.8067 (mtt) cc_final: 0.7860 (mtp) REVERT: A 379 TYR cc_start: 0.7443 (t80) cc_final: 0.7218 (t80) REVERT: A 392 HIS cc_start: 0.8212 (m90) cc_final: 0.7860 (m90) REVERT: A 407 LEU cc_start: 0.9019 (mt) cc_final: 0.8748 (mt) REVERT: A 424 ARG cc_start: 0.8033 (mmm-85) cc_final: 0.7481 (tpt-90) REVERT: A 446 PHE cc_start: 0.7666 (m-80) cc_final: 0.7387 (m-80) REVERT: A 447 GLU cc_start: 0.7743 (mp0) cc_final: 0.7522 (tp30) REVERT: A 449 PHE cc_start: 0.6905 (m-10) cc_final: 0.6622 (m-10) REVERT: A 450 ILE cc_start: 0.8152 (mt) cc_final: 0.7181 (mt) REVERT: A 458 LEU cc_start: 0.8236 (tp) cc_final: 0.7868 (tt) REVERT: A 478 MET cc_start: 0.7768 (mtp) cc_final: 0.7492 (ttm) REVERT: A 493 LEU cc_start: 0.7150 (tp) cc_final: 0.6622 (tp) REVERT: A 497 ASN cc_start: 0.7394 (m-40) cc_final: 0.7103 (m-40) REVERT: A 499 ILE cc_start: 0.7785 (tp) cc_final: 0.7549 (tp) REVERT: A 504 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7001 (mm-30) REVERT: A 505 ARG cc_start: 0.8174 (mtt90) cc_final: 0.7485 (mtt90) REVERT: A 507 ILE cc_start: 0.8527 (mt) cc_final: 0.8098 (mt) REVERT: A 522 TYR cc_start: 0.7795 (m-80) cc_final: 0.6950 (m-80) REVERT: A 530 ASP cc_start: 0.7087 (p0) cc_final: 0.6764 (p0) REVERT: A 532 ILE cc_start: 0.8328 (pt) cc_final: 0.8013 (mm) REVERT: A 533 ILE cc_start: 0.8339 (pt) cc_final: 0.7882 (mp) REVERT: A 539 ARG cc_start: 0.7997 (ttm-80) cc_final: 0.7641 (ptm160) REVERT: A 542 MET cc_start: 0.7879 (ptt) cc_final: 0.7333 (ptt) REVERT: A 545 MET cc_start: 0.7394 (mtm) cc_final: 0.7012 (mtm) REVERT: A 550 ASP cc_start: 0.7349 (p0) cc_final: 0.6777 (p0) REVERT: A 552 LYS cc_start: 0.8454 (mmtm) cc_final: 0.7970 (mmtm) REVERT: A 553 LYS cc_start: 0.8237 (mtpp) cc_final: 0.7703 (ttmt) REVERT: A 555 LEU cc_start: 0.8305 (tp) cc_final: 0.7771 (tp) REVERT: A 572 LYS cc_start: 0.7674 (tptt) cc_final: 0.7252 (tptt) REVERT: A 576 GLN cc_start: 0.7766 (tp40) cc_final: 0.7126 (tp40) REVERT: A 589 MET cc_start: 0.5132 (mtm) cc_final: 0.4672 (mtm) REVERT: A 593 ASP cc_start: 0.7403 (t0) cc_final: 0.7112 (t70) REVERT: A 600 TRP cc_start: 0.8357 (t-100) cc_final: 0.8022 (t-100) REVERT: A 603 PRO cc_start: 0.7612 (Cg_endo) cc_final: 0.7407 (Cg_exo) REVERT: A 619 LEU cc_start: 0.8583 (tp) cc_final: 0.7997 (tp) REVERT: A 625 ASN cc_start: 0.7521 (p0) cc_final: 0.6904 (p0) REVERT: A 635 MET cc_start: 0.7569 (mpp) cc_final: 0.6936 (mpp) REVERT: A 640 LYS cc_start: 0.7554 (mtpp) cc_final: 0.7132 (ttmm) REVERT: A 641 LEU cc_start: 0.8565 (mt) cc_final: 0.8175 (mm) REVERT: A 642 MET cc_start: 0.7811 (mmp) cc_final: 0.7496 (mmp) REVERT: A 651 LEU cc_start: 0.8366 (mt) cc_final: 0.7965 (mt) REVERT: A 660 GLN cc_start: 0.7910 (pp30) cc_final: 0.7099 (pp30) REVERT: A 663 LYS cc_start: 0.8167 (ptmm) cc_final: 0.7622 (mmtt) REVERT: A 667 GLU cc_start: 0.8189 (pp20) cc_final: 0.7895 (pp20) REVERT: A 682 ILE cc_start: 0.8485 (tp) cc_final: 0.8184 (tp) REVERT: A 712 GLU cc_start: 0.8690 (tt0) cc_final: 0.8432 (tt0) REVERT: A 715 ASN cc_start: 0.8874 (m110) cc_final: 0.8475 (m110) REVERT: A 716 LEU cc_start: 0.8808 (mt) cc_final: 0.8262 (tt) REVERT: A 717 TYR cc_start: 0.8454 (t80) cc_final: 0.8201 (t80) REVERT: A 719 ASP cc_start: 0.7814 (m-30) cc_final: 0.7595 (m-30) REVERT: A 734 ARG cc_start: 0.8518 (ttt-90) cc_final: 0.7706 (ttm-80) REVERT: A 737 PHE cc_start: 0.7934 (t80) cc_final: 0.7610 (t80) REVERT: A 738 HIS cc_start: 0.7803 (t-90) cc_final: 0.7594 (t-170) REVERT: A 743 GLU cc_start: 0.7371 (mp0) cc_final: 0.7003 (mp0) REVERT: A 754 GLU cc_start: 0.8353 (mt-10) cc_final: 0.7938 (mp0) REVERT: A 756 GLU cc_start: 0.7599 (tp30) cc_final: 0.7073 (tp30) REVERT: A 767 PHE cc_start: 0.7923 (m-10) cc_final: 0.7568 (m-80) REVERT: A 788 ARG cc_start: 0.8388 (ptt180) cc_final: 0.8071 (ptt180) REVERT: A 792 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7948 (mm-30) REVERT: A 820 LEU cc_start: 0.7401 (mm) cc_final: 0.6961 (mm) REVERT: A 822 LYS cc_start: 0.8175 (mmtt) cc_final: 0.7928 (mmtm) REVERT: D 18 LYS cc_start: 0.7493 (mmtm) cc_final: 0.6827 (mmmm) REVERT: D 22 LEU cc_start: 0.8544 (mm) cc_final: 0.8199 (mm) REVERT: D 62 ARG cc_start: 0.6383 (mmt-90) cc_final: 0.6175 (mmt-90) REVERT: D 73 CYS cc_start: 0.6075 (m) cc_final: 0.5734 (m) REVERT: D 79 LYS cc_start: 0.8033 (tppp) cc_final: 0.7562 (tppp) REVERT: D 114 GLN cc_start: 0.6536 (mp10) cc_final: 0.6290 (mp10) REVERT: D 132 PHE cc_start: 0.7094 (m-80) cc_final: 0.6553 (m-80) REVERT: D 138 ARG cc_start: 0.6332 (pmt170) cc_final: 0.5926 (pmt170) REVERT: C 130 GLU cc_start: 0.8476 (pt0) cc_final: 0.7560 (pm20) REVERT: C 304 MET cc_start: 0.4531 (tpt) cc_final: 0.4205 (tpt) REVERT: C 330 LYS cc_start: 0.8648 (mmmt) cc_final: 0.8281 (mmtm) REVERT: C 332 ASN cc_start: 0.7642 (t0) cc_final: 0.7370 (t0) REVERT: C 336 ILE cc_start: 0.8162 (mt) cc_final: 0.7947 (mt) REVERT: C 337 ARG cc_start: 0.8018 (ppt170) cc_final: 0.7452 (ttp80) REVERT: C 338 ARG cc_start: 0.7936 (mmm-85) cc_final: 0.7476 (mmt90) REVERT: C 341 GLU cc_start: 0.7605 (pp20) cc_final: 0.7296 (pp20) REVERT: C 349 TYR cc_start: 0.7571 (t80) cc_final: 0.7318 (t80) REVERT: C 379 TYR cc_start: 0.7422 (t80) cc_final: 0.6960 (t80) REVERT: C 380 TYR cc_start: 0.7897 (m-10) cc_final: 0.7614 (m-10) REVERT: C 382 ASN cc_start: 0.8235 (m110) cc_final: 0.7926 (t0) REVERT: C 397 ASP cc_start: 0.7622 (t0) cc_final: 0.7347 (t0) REVERT: C 406 GLU cc_start: 0.6729 (mt-10) cc_final: 0.5674 (mt-10) REVERT: C 407 LEU cc_start: 0.9019 (mt) cc_final: 0.8548 (pp) REVERT: C 409 LEU cc_start: 0.8383 (tp) cc_final: 0.7797 (pp) REVERT: C 410 GLN cc_start: 0.8409 (mm110) cc_final: 0.6219 (mm-40) REVERT: C 438 ASP cc_start: 0.7499 (m-30) cc_final: 0.6999 (m-30) REVERT: C 447 GLU cc_start: 0.7635 (tp30) cc_final: 0.6883 (tp30) REVERT: C 450 ILE cc_start: 0.8262 (mt) cc_final: 0.7649 (mt) REVERT: C 477 PHE cc_start: 0.7443 (m-80) cc_final: 0.7099 (m-80) REVERT: C 478 MET cc_start: 0.7747 (mtp) cc_final: 0.7129 (mtp) REVERT: C 499 ILE cc_start: 0.7894 (tp) cc_final: 0.7211 (tp) REVERT: C 501 MET cc_start: 0.7705 (mtt) cc_final: 0.7163 (mtt) REVERT: C 502 TYR cc_start: 0.6880 (m-10) cc_final: 0.6532 (m-10) REVERT: C 505 ARG cc_start: 0.8170 (mtt90) cc_final: 0.7567 (mtt90) REVERT: C 506 ARG cc_start: 0.7884 (mtt90) cc_final: 0.7664 (mtt90) REVERT: C 507 ILE cc_start: 0.8217 (mt) cc_final: 0.7992 (mt) REVERT: C 522 TYR cc_start: 0.7612 (m-80) cc_final: 0.6824 (m-80) REVERT: C 539 ARG cc_start: 0.8017 (ttm-80) cc_final: 0.7777 (ttm-80) REVERT: C 542 MET cc_start: 0.7572 (tpp) cc_final: 0.7047 (tpp) REVERT: C 545 MET cc_start: 0.7497 (mtm) cc_final: 0.7226 (mtm) REVERT: C 553 LYS cc_start: 0.8559 (mtmt) cc_final: 0.7943 (mtpp) REVERT: C 554 GLN cc_start: 0.7232 (tt0) cc_final: 0.5795 (tt0) REVERT: C 555 LEU cc_start: 0.8455 (tp) cc_final: 0.8114 (tp) REVERT: C 576 GLN cc_start: 0.7471 (tm-30) cc_final: 0.7030 (tm-30) REVERT: C 577 LEU cc_start: 0.8367 (mt) cc_final: 0.8139 (pp) REVERT: C 581 GLU cc_start: 0.7696 (pp20) cc_final: 0.7383 (pp20) REVERT: C 589 MET cc_start: 0.4947 (mmp) cc_final: 0.4682 (mmp) REVERT: C 621 LEU cc_start: 0.7909 (mm) cc_final: 0.7455 (mm) REVERT: C 625 ASN cc_start: 0.8033 (m-40) cc_final: 0.7633 (m110) REVERT: C 626 ASN cc_start: 0.8036 (m110) cc_final: 0.7744 (m110) REVERT: C 635 MET cc_start: 0.7696 (mpp) cc_final: 0.7082 (mpp) REVERT: C 639 ARG cc_start: 0.7624 (mtp85) cc_final: 0.7237 (mtp85) REVERT: C 641 LEU cc_start: 0.8416 (mt) cc_final: 0.8209 (mt) REVERT: C 642 MET cc_start: 0.7823 (mmp) cc_final: 0.7621 (mmp) REVERT: C 651 LEU cc_start: 0.8467 (mt) cc_final: 0.8217 (mt) REVERT: C 660 GLN cc_start: 0.7996 (pp30) cc_final: 0.7551 (pp30) REVERT: C 663 LYS cc_start: 0.8118 (ttpp) cc_final: 0.7801 (ttpp) REVERT: C 666 LEU cc_start: 0.8658 (mm) cc_final: 0.8431 (mm) REVERT: C 667 GLU cc_start: 0.7933 (pp20) cc_final: 0.7582 (pp20) REVERT: C 693 MET cc_start: 0.6358 (tpt) cc_final: 0.6103 (tpt) REVERT: C 712 GLU cc_start: 0.8763 (tt0) cc_final: 0.8429 (tt0) REVERT: C 715 ASN cc_start: 0.8763 (m-40) cc_final: 0.8531 (m-40) REVERT: C 716 LEU cc_start: 0.8773 (mt) cc_final: 0.7790 (tp) REVERT: C 719 ASP cc_start: 0.7835 (m-30) cc_final: 0.7568 (p0) REVERT: C 720 TYR cc_start: 0.7453 (t80) cc_final: 0.6948 (t80) REVERT: C 730 PHE cc_start: 0.7493 (t80) cc_final: 0.7159 (t80) REVERT: C 738 HIS cc_start: 0.7509 (t-90) cc_final: 0.7001 (t-170) REVERT: C 739 MET cc_start: 0.7292 (ptm) cc_final: 0.7051 (ptm) REVERT: C 743 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7704 (mm-30) REVERT: C 747 LYS cc_start: 0.8930 (mtpt) cc_final: 0.8621 (mtpt) REVERT: C 748 TYR cc_start: 0.6687 (t80) cc_final: 0.6390 (t80) REVERT: C 754 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7583 (mp0) REVERT: C 756 GLU cc_start: 0.6682 (tp30) cc_final: 0.6336 (tp30) REVERT: C 780 TYR cc_start: 0.6254 (t80) cc_final: 0.4275 (t80) REVERT: C 792 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7674 (mm-30) REVERT: C 797 PHE cc_start: 0.5926 (m-80) cc_final: 0.5678 (m-80) REVERT: C 822 LYS cc_start: 0.8388 (mmtt) cc_final: 0.8018 (mmtm) REVERT: C 835 GLU cc_start: 0.7486 (pm20) cc_final: 0.7269 (pm20) REVERT: C 855 LYS cc_start: 0.8841 (tttt) cc_final: 0.8255 (tppt) outliers start: 0 outliers final: 0 residues processed: 513 average time/residue: 0.3502 time to fit residues: 244.8755 Evaluate side-chains 479 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 479 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 128 optimal weight: 0.5980 chunk 53 optimal weight: 0.0470 chunk 132 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 113 optimal weight: 0.9980 overall best weight: 0.6680 ------------------------------------------------------------------------------- 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 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 554 GLN ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 ASN ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 HIS ** C 382 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 = 0.4123 r_free = 0.4123 target = 0.142708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.116507 restraints weight = 29597.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.121181 restraints weight = 17838.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.124517 restraints weight = 12121.120| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.6824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13522 Z= 0.186 Angle : 0.657 9.403 18260 Z= 0.335 Chirality : 0.044 0.192 2014 Planarity : 0.005 0.067 2372 Dihedral : 4.932 20.991 1806 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.21), residues: 1610 helix: -0.17 (0.18), residues: 802 sheet: -1.80 (0.66), residues: 64 loop : -1.04 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.004 TRP B 139 HIS 0.010 0.001 HIS C 297 PHE 0.031 0.002 PHE C 633 TYR 0.027 0.001 TYR B 39 ARG 0.006 0.000 ARG A 763 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4169.22 seconds wall clock time: 76 minutes 43.94 seconds (4603.94 seconds total)