Starting phenix.real_space_refine on Fri May 16 11:22:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pty_17925/05_2025/8pty_17925.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pty_17925/05_2025/8pty_17925.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pty_17925/05_2025/8pty_17925.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pty_17925/05_2025/8pty_17925.map" model { file = "/net/cci-nas-00/data/ceres_data/8pty_17925/05_2025/8pty_17925.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pty_17925/05_2025/8pty_17925.cif" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 Fe 4 7.16 5 S 91 5.16 5 C 9015 2.51 5 N 2461 2.21 5 O 2618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14189 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 643, 5068 Classifications: {'peptide': 643} Link IDs: {'PTRANS': 32, 'TRANS': 610} Chain breaks: 4 Chain: "B" Number of atoms: 5558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 702, 5558 Classifications: {'peptide': 702} Link IDs: {'PTRANS': 27, 'TRANS': 674} Chain breaks: 4 Chain: "C" Number of atoms: 3528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3528 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 21, 'TRANS': 418} Chain breaks: 2 Chain: "C" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {'5AD': 1, 'SF4': 1} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10832 SG CYS C 112 53.234 64.013 71.343 1.00185.15 S ATOM 10732 SG CYS C 99 47.739 63.676 68.874 1.00156.39 S ATOM 10807 SG CYS C 109 48.330 65.527 75.230 1.00173.12 S Time building chain proxies: 7.93, per 1000 atoms: 0.56 Number of scatterers: 14189 At special positions: 0 Unit cell: (82.56, 110.94, 154.8, 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) Fe 4 26.01 S 91 16.00 O 2618 8.00 N 2461 7.00 C 9015 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: 3.06 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 C 601 " pdb="FE4 SF4 C 601 " - pdb=" SG CYS C 109 " pdb="FE3 SF4 C 601 " - pdb=" SG CYS C 99 " pdb="FE1 SF4 C 601 " - pdb=" SG CYS C 112 " Number of angles added : 9 3518 Ramachandran restraints generated. 1759 Oldfield, 0 Emsley, 1759 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3332 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 36 sheets defined 12.8% alpha, 32.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'A' and resid 78 through 81 removed outlier: 3.660A pdb=" N GLU A 81 " --> pdb=" O LEU A 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 78 through 81' Processing helix chain 'A' and resid 702 through 704 No H-bonds generated for 'chain 'A' and resid 702 through 704' Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 467 through 479 removed outlier: 3.791A pdb=" N VAL B 471 " --> pdb=" O PRO B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 555 removed outlier: 3.545A pdb=" N LEU B 551 " --> pdb=" O THR B 547 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR B 555 " --> pdb=" O LEU B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 737 removed outlier: 3.718A pdb=" N GLN B 736 " --> pdb=" O HIS B 733 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ARG B 737 " --> pdb=" O PRO B 734 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 733 through 737' Processing helix chain 'C' and resid 99 through 103 removed outlier: 3.554A pdb=" N ILE C 102 " --> pdb=" O CYS C 99 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER C 103 " --> pdb=" O PRO C 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 99 through 103' Processing helix chain 'C' and resid 131 through 140 removed outlier: 3.837A pdb=" N ALA C 140 " --> pdb=" O ARG C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 158 Processing helix chain 'C' and resid 178 through 195 removed outlier: 3.522A pdb=" N ARG C 182 " --> pdb=" O PRO C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 209 Processing helix chain 'C' and resid 223 through 227 removed outlier: 3.548A pdb=" N CYS C 227 " --> pdb=" O PRO C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 239 Processing helix chain 'C' and resid 251 through 258 removed outlier: 3.734A pdb=" N ALA C 255 " --> pdb=" O TYR C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 278 Processing helix chain 'C' and resid 293 through 307 Processing helix chain 'C' and resid 326 through 334 Processing helix chain 'C' and resid 341 through 356 Processing helix chain 'C' and resid 370 through 374 removed outlier: 3.517A pdb=" N LEU C 373 " --> pdb=" O PRO C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 395 removed outlier: 3.892A pdb=" N LEU C 386 " --> pdb=" O ASN C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 405 Processing helix chain 'C' and resid 496 through 512 removed outlier: 3.624A pdb=" N LEU C 500 " --> pdb=" O GLY C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 533 removed outlier: 3.705A pdb=" N ASN C 528 " --> pdb=" O VAL C 524 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE C 533 " --> pdb=" O TYR C 529 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 8 removed outlier: 6.942A pdb=" N ASP A 372 " --> pdb=" O PHE A 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 3 through 8 removed outlier: 6.942A pdb=" N ASP A 372 " --> pdb=" O PHE A 7 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 44 through 45 Processing sheet with id=AA4, first strand: chain 'A' and resid 71 through 76 removed outlier: 6.678A pdb=" N ALA A 86 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N VAL A 74 " --> pdb=" O CYS A 84 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N CYS A 84 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP A 91 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU A 94 " --> pdb=" O CYS A 104 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N CYS A 104 " --> pdb=" O LEU A 94 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 112 through 117 removed outlier: 3.927A pdb=" N VAL A 114 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N THR A 128 " --> pdb=" O THR A 132 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N THR A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU A 144 " --> pdb=" O MET A 135 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N THR A 137 " --> pdb=" O PRO A 142 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 197 through 200 removed outlier: 3.859A pdb=" N ALA A 208 " --> pdb=" O THR A 199 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A 211 " --> pdb=" O LYS A 220 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL A 221 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N THR A 233 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL A 223 " --> pdb=" O GLN A 231 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 245 through 246 removed outlier: 3.767A pdb=" N ALA A 245 " --> pdb=" O ALA A 254 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE A 253 " --> pdb=" O PHE A 268 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 287 through 294 removed outlier: 5.420A pdb=" N VAL A 289 " --> pdb=" O GLU A 306 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLU A 306 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASP A 291 " --> pdb=" O TRP A 304 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN A 334 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N THR A 324 " --> pdb=" O LEU A 332 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N LEU A 332 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 390 through 395 Processing sheet with id=AB1, first strand: chain 'A' and resid 424 through 429 removed outlier: 4.375A pdb=" N GLN A 447 " --> pdb=" O ASP A 443 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE A 490 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N LYS A 452 " --> pdb=" O ILE A 488 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE A 488 " --> pdb=" O LYS A 452 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 507 through 508 removed outlier: 3.642A pdb=" N SER A 548 " --> pdb=" O HIS A 530 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N THR A 532 " --> pdb=" O ASN A 546 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ASN A 546 " --> pdb=" O THR A 532 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 507 through 508 Processing sheet with id=AB4, first strand: chain 'A' and resid 557 through 559 removed outlier: 6.630A pdb=" N GLN A 572 " --> pdb=" O ILE A 558 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 609 through 615 Processing sheet with id=AB6, first strand: chain 'A' and resid 644 through 646 removed outlier: 3.519A pdb=" N LEU A 653 " --> pdb=" O GLN A 661 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG A 689 " --> pdb=" O CYS A 660 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 696 through 701 removed outlier: 5.759A pdb=" N ILE A 697 " --> pdb=" O GLN A 710 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLN A 710 " --> pdb=" O ILE A 697 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR A 699 " --> pdb=" O VAL A 708 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASP C 426 " --> pdb=" O LEU A 716 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N HIS A 720 " --> pdb=" O LEU C 422 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU C 422 " --> pdb=" O HIS A 720 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS C 476 " --> pdb=" O LEU C 450 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU C 474 " --> pdb=" O ARG C 452 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ARG C 454 " --> pdb=" O VAL C 472 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N VAL C 472 " --> pdb=" O ARG C 454 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 696 through 701 removed outlier: 5.759A pdb=" N ILE A 697 " --> pdb=" O GLN A 710 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLN A 710 " --> pdb=" O ILE A 697 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR A 699 " --> pdb=" O VAL A 708 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASP C 426 " --> pdb=" O LEU A 716 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N HIS A 720 " --> pdb=" O LEU C 422 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU C 422 " --> pdb=" O HIS A 720 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY C 449 " --> pdb=" O TYR C 439 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ASP C 441 " --> pdb=" O LEU C 447 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N LEU C 447 " --> pdb=" O ASP C 441 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS C 476 " --> pdb=" O LEU C 450 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU C 474 " --> pdb=" O ARG C 452 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ARG C 454 " --> pdb=" O VAL C 472 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N VAL C 472 " --> pdb=" O ARG C 454 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 7 through 12 removed outlier: 5.569A pdb=" N THR B 8 " --> pdb=" O ARG B 820 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ARG B 820 " --> pdb=" O THR B 8 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE B 807 " --> pdb=" O HIS B 819 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N HIS B 806 " --> pdb=" O TRP B 787 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N TRP B 787 " --> pdb=" O HIS B 806 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ALA B 808 " --> pdb=" O LEU B 785 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LEU B 785 " --> pdb=" O ALA B 808 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N CYS B 810 " --> pdb=" O ARG B 783 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 39 through 43 removed outlier: 3.552A pdb=" N LEU B 42 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR B 52 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 61 through 66 Processing sheet with id=AC3, first strand: chain 'B' and resid 110 through 117 removed outlier: 4.081A pdb=" N ALA B 138 " --> pdb=" O ALA B 134 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N MET B 150 " --> pdb=" O SER B 143 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 110 through 117 removed outlier: 4.081A pdb=" N ALA B 138 " --> pdb=" O ALA B 134 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 165 through 169 removed outlier: 3.583A pdb=" N LEU B 201 " --> pdb=" O ILE B 189 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 210 through 215 Processing sheet with id=AC7, first strand: chain 'B' and resid 286 through 289 removed outlier: 6.539A pdb=" N ALA B 310 " --> pdb=" O ASN B 287 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR B 315 " --> pdb=" O SER B 311 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 295 through 297 Processing sheet with id=AC9, first strand: chain 'B' and resid 346 through 349 removed outlier: 4.676A pdb=" N LEU B 367 " --> pdb=" O GLU B 381 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 391 through 396 removed outlier: 6.992A pdb=" N VAL B 406 " --> pdb=" O GLN B 392 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LEU B 394 " --> pdb=" O ILE B 404 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ILE B 404 " --> pdb=" O LEU B 394 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR B 411 " --> pdb=" O GLY B 407 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N THR B 412 " --> pdb=" O ARG B 433 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ARG B 433 " --> pdb=" O THR B 412 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LEU B 414 " --> pdb=" O ILE B 431 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR B 427 " --> pdb=" O TRP B 418 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 444 through 448 removed outlier: 6.405A pdb=" N GLN B 451 " --> pdb=" O ILE B 447 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL B 463 " --> pdb=" O GLN B 561 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN B 561 " --> pdb=" O VAL B 463 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N SER B 465 " --> pdb=" O GLU B 559 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLU B 559 " --> pdb=" O SER B 465 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 570 through 575 removed outlier: 6.713A pdb=" N ALA B 585 " --> pdb=" O PHE B 571 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N VAL B 573 " --> pdb=" O ALA B 583 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ALA B 583 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N CYS B 575 " --> pdb=" O LEU B 581 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LEU B 581 " --> pdb=" O CYS B 575 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TRP B 599 " --> pdb=" O LEU B 582 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LEU B 598 " --> pdb=" O VAL B 607 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 617 through 622 removed outlier: 3.982A pdb=" N GLN B 619 " --> pdb=" O VAL B 632 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 672 through 677 Processing sheet with id=AD6, first strand: chain 'B' and resid 723 through 728 removed outlier: 3.633A pdb=" N ALA B 725 " --> pdb=" O GLY B 743 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ILE B 749 " --> pdb=" O GLU B 771 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N GLU B 771 " --> pdb=" O ILE B 749 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N LEU B 751 " --> pdb=" O CYS B 769 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 88 through 93 removed outlier: 6.623A pdb=" N VAL C 165 " --> pdb=" O CYS C 215 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLY C 217 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG C 242 " --> pdb=" O ILE C 218 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 282 through 285 removed outlier: 7.218A pdb=" N LEU C 317 " --> pdb=" O TYR C 363 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 517 through 520 456 hydrogen bonds defined for protein. 1218 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: 5.22 Time building geometry restraints manager: 3.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 6333 1.43 - 1.64: 8077 1.64 - 1.85: 116 1.85 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 14538 Sorted by residual: bond pdb=" N THR A 99 " pdb=" CA THR A 99 " ideal model delta sigma weight residual 1.454 1.492 -0.037 1.31e-02 5.83e+03 8.18e+00 bond pdb=" N GLN A 544 " pdb=" CA GLN A 544 " ideal model delta sigma weight residual 1.456 1.488 -0.031 1.23e-02 6.61e+03 6.43e+00 bond pdb=" N SER A 96 " pdb=" CA SER A 96 " ideal model delta sigma weight residual 1.455 1.484 -0.029 1.25e-02 6.40e+03 5.33e+00 bond pdb=" N THR A 642 " pdb=" CA THR A 642 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.35e-02 5.49e+03 4.66e+00 bond pdb=" CA SER A 82 " pdb=" CB SER A 82 " ideal model delta sigma weight residual 1.533 1.498 0.034 1.65e-02 3.67e+03 4.36e+00 ... (remaining 14533 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 19353 1.97 - 3.93: 374 3.93 - 5.90: 28 5.90 - 7.87: 2 7.87 - 9.84: 1 Bond angle restraints: 19758 Sorted by residual: angle pdb=" N VAL C 365 " pdb=" CA VAL C 365 " pdb=" C VAL C 365 " ideal model delta sigma weight residual 113.20 109.54 3.66 9.60e-01 1.09e+00 1.46e+01 angle pdb=" C VAL B 406 " pdb=" N GLY B 407 " pdb=" CA GLY B 407 " ideal model delta sigma weight residual 121.61 118.76 2.85 7.70e-01 1.69e+00 1.37e+01 angle pdb=" N THR A 642 " pdb=" CA THR A 642 " pdb=" C THR A 642 " ideal model delta sigma weight residual 113.43 108.85 4.58 1.26e+00 6.30e-01 1.32e+01 angle pdb=" N THR A 99 " pdb=" CA THR A 99 " pdb=" C THR A 99 " ideal model delta sigma weight residual 114.31 110.14 4.17 1.29e+00 6.01e-01 1.04e+01 angle pdb=" N GLU C 474 " pdb=" CA GLU C 474 " pdb=" C GLU C 474 " ideal model delta sigma weight residual 108.32 113.40 -5.08 1.64e+00 3.72e-01 9.61e+00 ... (remaining 19753 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 7777 17.90 - 35.81: 668 35.81 - 53.71: 97 53.71 - 71.62: 30 71.62 - 89.52: 18 Dihedral angle restraints: 8590 sinusoidal: 3438 harmonic: 5152 Sorted by residual: dihedral pdb=" CA SER A 657 " pdb=" C SER A 657 " pdb=" N HIS A 658 " pdb=" CA HIS A 658 " ideal model delta harmonic sigma weight residual 180.00 162.15 17.85 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA SER A 639 " pdb=" C SER A 639 " pdb=" N ASN A 640 " pdb=" CA ASN A 640 " ideal model delta harmonic sigma weight residual 180.00 162.18 17.82 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA HIS A 374 " pdb=" C HIS A 374 " pdb=" N TRP A 375 " pdb=" CA TRP A 375 " ideal model delta harmonic sigma weight residual -180.00 -162.40 -17.60 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 8587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1561 0.044 - 0.088: 455 0.088 - 0.131: 175 0.131 - 0.175: 5 0.175 - 0.219: 2 Chirality restraints: 2198 Sorted by residual: chirality pdb=" CG LEU A 252 " pdb=" CB LEU A 252 " pdb=" CD1 LEU A 252 " pdb=" CD2 LEU A 252 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB THR C 173 " pdb=" CA THR C 173 " pdb=" OG1 THR C 173 " pdb=" CG2 THR C 173 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.94e-01 chirality pdb=" CA ILE B 130 " pdb=" N ILE B 130 " pdb=" C ILE B 130 " pdb=" CB ILE B 130 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.25e-01 ... (remaining 2195 not shown) Planarity restraints: 2524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 375 " 0.011 2.00e-02 2.50e+03 1.14e-02 3.23e+00 pdb=" CG TRP A 375 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP A 375 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A 375 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 375 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 375 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 375 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 375 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 375 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 375 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY C 539 " -0.024 5.00e-02 4.00e+02 3.58e-02 2.05e+00 pdb=" N PRO C 540 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO C 540 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 540 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 397 " -0.022 5.00e-02 4.00e+02 3.40e-02 1.84e+00 pdb=" N PRO B 398 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 398 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 398 " -0.019 5.00e-02 4.00e+02 ... (remaining 2521 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 982 2.73 - 3.27: 14062 3.27 - 3.81: 22384 3.81 - 4.36: 26223 4.36 - 4.90: 45985 Nonbonded interactions: 109636 Sorted by model distance: nonbonded pdb=" NE2 GLN B 303 " pdb=" O PRO B 304 " model vdw 2.184 3.120 nonbonded pdb=" OG SER A 118 " pdb=" OD1 ASP A 120 " model vdw 2.207 3.040 nonbonded pdb=" OE1 GLU C 179 " pdb=" NH2 ARG C 182 " model vdw 2.211 3.120 nonbonded pdb=" O SER C 126 " pdb=" NH2 ARG C 367 " model vdw 2.213 3.120 nonbonded pdb=" OD1 ASN B 662 " pdb=" OG1 THR B 665 " model vdw 2.216 3.040 ... (remaining 109631 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 3.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 34.740 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 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 : 0.005 0.043 14541 Z= 0.218 Angle : 0.660 9.917 19767 Z= 0.359 Chirality : 0.046 0.219 2198 Planarity : 0.004 0.041 2524 Dihedral : 14.259 89.524 5258 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 0.13 % Allowed : 0.51 % Favored : 99.36 % 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: -1.81 (0.20), residues: 1759 helix: 1.48 (0.38), residues: 189 sheet: -0.64 (0.21), residues: 613 loop : -2.23 (0.19), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 375 HIS 0.007 0.001 HIS A 360 PHE 0.015 0.001 PHE C 271 TYR 0.019 0.001 TYR B 345 ARG 0.004 0.000 ARG A 693 Details of bonding type rmsd hydrogen bonds : bond 0.17208 ( 418) hydrogen bonds : angle 6.64456 ( 1218) metal coordination : bond 0.01465 ( 3) metal coordination : angle 5.78675 ( 9) covalent geometry : bond 0.00460 (14538) covalent geometry : angle 0.64861 (19758) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3518 Ramachandran restraints generated. 1759 Oldfield, 0 Emsley, 1759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3518 Ramachandran restraints generated. 1759 Oldfield, 0 Emsley, 1759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 158 time to evaluate : 1.517 Fit side-chains REVERT: A 195 ARG cc_start: 0.8960 (ttt180) cc_final: 0.8758 (ttp80) REVERT: A 594 LYS cc_start: 0.8167 (ttpt) cc_final: 0.7862 (ttpt) REVERT: B 214 GLU cc_start: 0.6386 (tm-30) cc_final: 0.5968 (tm-30) REVERT: B 237 LYS cc_start: 0.5395 (mtmm) cc_final: 0.4895 (tttm) REVERT: B 277 THR cc_start: 0.6788 (m) cc_final: 0.6479 (m) REVERT: B 676 ASP cc_start: 0.7417 (t0) cc_final: 0.6941 (t0) REVERT: B 713 CYS cc_start: 0.8228 (t) cc_final: 0.7868 (m) REVERT: B 736 GLN cc_start: 0.8119 (mm110) cc_final: 0.6641 (tm-30) REVERT: B 745 GLU cc_start: 0.8158 (tp30) cc_final: 0.7908 (tp30) REVERT: C 228 MET cc_start: 0.4380 (mpp) cc_final: 0.3999 (mtm) REVERT: C 299 GLU cc_start: 0.6543 (tm-30) cc_final: 0.6324 (tm-30) REVERT: C 347 GLU cc_start: 0.7568 (tt0) cc_final: 0.7232 (mt-10) outliers start: 2 outliers final: 0 residues processed: 160 average time/residue: 0.3101 time to fit residues: 70.2268 Evaluate side-chains 95 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 46 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 53 optimal weight: 0.2980 chunk 84 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 161 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN A 262 GLN A 425 ASN B 102 HIS B 182 ASN C 196 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.118777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.096800 restraints weight = 25897.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.099049 restraints weight = 15167.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.100636 restraints weight = 10984.829| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14541 Z= 0.124 Angle : 0.575 11.598 19767 Z= 0.297 Chirality : 0.046 0.166 2198 Planarity : 0.004 0.043 2524 Dihedral : 6.462 89.778 1934 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 1.02 % Allowed : 5.98 % Favored : 93.00 % 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: -1.68 (0.20), residues: 1759 helix: 1.62 (0.38), residues: 194 sheet: -0.51 (0.21), residues: 619 loop : -2.20 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 373 HIS 0.004 0.001 HIS B 106 PHE 0.013 0.001 PHE A 207 TYR 0.010 0.001 TYR A 357 ARG 0.004 0.000 ARG C 139 Details of bonding type rmsd hydrogen bonds : bond 0.04201 ( 418) hydrogen bonds : angle 5.05319 ( 1218) metal coordination : bond 0.00492 ( 3) metal coordination : angle 5.80082 ( 9) covalent geometry : bond 0.00282 (14538) covalent geometry : angle 0.56178 (19758) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3518 Ramachandran restraints generated. 1759 Oldfield, 0 Emsley, 1759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3518 Ramachandran restraints generated. 1759 Oldfield, 0 Emsley, 1759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 1.716 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7987 (pmm) cc_final: 0.7732 (pmm) REVERT: A 125 LEU cc_start: 0.9400 (mt) cc_final: 0.9113 (mm) REVERT: A 357 TYR cc_start: 0.9062 (m-80) cc_final: 0.8538 (m-80) REVERT: A 594 LYS cc_start: 0.7729 (ttpt) cc_final: 0.7475 (ttpt) REVERT: B 237 LYS cc_start: 0.6289 (mtmm) cc_final: 0.6083 (tttm) REVERT: B 620 MET cc_start: 0.9064 (mtp) cc_final: 0.8789 (mtp) REVERT: B 736 GLN cc_start: 0.7956 (mm110) cc_final: 0.7059 (tm-30) REVERT: C 299 GLU cc_start: 0.7405 (tm-30) cc_final: 0.7200 (tm-30) REVERT: C 347 GLU cc_start: 0.7904 (tt0) cc_final: 0.7500 (mt-10) REVERT: C 478 TYR cc_start: 0.6716 (p90) cc_final: 0.6449 (p90) REVERT: C 603 MET cc_start: 0.8309 (pmm) cc_final: 0.8058 (pmm) outliers start: 16 outliers final: 13 residues processed: 124 average time/residue: 0.2378 time to fit residues: 45.7436 Evaluate side-chains 101 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 375 TRP Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 704 ASP Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 182 ASN Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 733 HIS Chi-restraints excluded: chain B residue 782 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 56 optimal weight: 3.9990 chunk 176 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 66 optimal weight: 0.0980 chunk 149 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 572 GLN B 182 ASN ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.114745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.092649 restraints weight = 26611.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.094777 restraints weight = 17945.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.095888 restraints weight = 13347.168| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14541 Z= 0.179 Angle : 0.596 11.529 19767 Z= 0.313 Chirality : 0.047 0.153 2198 Planarity : 0.004 0.045 2524 Dihedral : 6.426 88.168 1934 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 1.46 % Allowed : 9.80 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.20), residues: 1759 helix: 1.52 (0.37), residues: 194 sheet: -0.49 (0.22), residues: 611 loop : -2.28 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 373 HIS 0.006 0.001 HIS B 206 PHE 0.017 0.002 PHE B 452 TYR 0.012 0.001 TYR B 43 ARG 0.003 0.000 ARG A 219 Details of bonding type rmsd hydrogen bonds : bond 0.04839 ( 418) hydrogen bonds : angle 5.07752 ( 1218) metal coordination : bond 0.00708 ( 3) metal coordination : angle 5.61281 ( 9) covalent geometry : bond 0.00426 (14538) covalent geometry : angle 0.58426 (19758) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3518 Ramachandran restraints generated. 1759 Oldfield, 0 Emsley, 1759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3518 Ramachandran restraints generated. 1759 Oldfield, 0 Emsley, 1759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 1.481 Fit side-chains REVERT: A 357 TYR cc_start: 0.9011 (m-80) cc_final: 0.8571 (m-80) REVERT: A 594 LYS cc_start: 0.7799 (ttpt) cc_final: 0.7569 (ttpt) REVERT: B 237 LYS cc_start: 0.6616 (mtmm) cc_final: 0.6170 (tttm) REVERT: B 736 GLN cc_start: 0.7997 (mm110) cc_final: 0.6989 (tm-30) REVERT: C 299 GLU cc_start: 0.7394 (tm-30) cc_final: 0.7166 (tm-30) REVERT: C 347 GLU cc_start: 0.7982 (tt0) cc_final: 0.7548 (mt-10) outliers start: 23 outliers final: 16 residues processed: 110 average time/residue: 0.2267 time to fit residues: 39.3601 Evaluate side-chains 100 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 375 TRP Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 704 ASP Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 182 ASN Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 733 HIS Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 313 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 35 optimal weight: 1.9990 chunk 171 optimal weight: 0.4980 chunk 130 optimal weight: 8.9990 chunk 64 optimal weight: 0.5980 chunk 93 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 72 optimal weight: 0.0270 chunk 174 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 169 optimal weight: 0.0670 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.118866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.096789 restraints weight = 26267.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.099861 restraints weight = 17037.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.100891 restraints weight = 11787.567| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14541 Z= 0.096 Angle : 0.539 14.242 19767 Z= 0.273 Chirality : 0.045 0.152 2198 Planarity : 0.004 0.042 2524 Dihedral : 5.695 82.080 1934 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 1.46 % Allowed : 11.64 % Favored : 86.90 % 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: -1.56 (0.20), residues: 1759 helix: 1.80 (0.37), residues: 194 sheet: -0.41 (0.22), residues: 617 loop : -2.17 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 224 HIS 0.006 0.001 HIS B 206 PHE 0.014 0.001 PHE B 452 TYR 0.009 0.001 TYR C 184 ARG 0.003 0.000 ARG A 405 Details of bonding type rmsd hydrogen bonds : bond 0.03414 ( 418) hydrogen bonds : angle 4.71449 ( 1218) metal coordination : bond 0.00297 ( 3) metal coordination : angle 6.88656 ( 9) covalent geometry : bond 0.00214 (14538) covalent geometry : angle 0.51895 (19758) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3518 Ramachandran restraints generated. 1759 Oldfield, 0 Emsley, 1759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3518 Ramachandran restraints generated. 1759 Oldfield, 0 Emsley, 1759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 1.530 Fit side-chains REVERT: A 115 MET cc_start: 0.8696 (tmm) cc_final: 0.8477 (tmm) REVERT: A 594 LYS cc_start: 0.7808 (ttpt) cc_final: 0.7551 (ttpt) REVERT: B 620 MET cc_start: 0.8958 (mtp) cc_final: 0.8711 (mtp) REVERT: B 736 GLN cc_start: 0.7962 (mm110) cc_final: 0.6985 (tm-30) REVERT: C 122 TYR cc_start: 0.7301 (OUTLIER) cc_final: 0.6038 (m-80) REVERT: C 299 GLU cc_start: 0.7413 (tm-30) cc_final: 0.7152 (tm-30) REVERT: C 333 LYS cc_start: 0.8741 (tppt) cc_final: 0.8520 (tppt) REVERT: C 347 GLU cc_start: 0.7965 (tt0) cc_final: 0.7525 (mt-10) outliers start: 23 outliers final: 15 residues processed: 114 average time/residue: 0.2279 time to fit residues: 41.0917 Evaluate side-chains 102 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 375 TRP Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 733 HIS Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 814 HIS Chi-restraints excluded: chain C residue 122 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 62 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 171 optimal weight: 3.9990 chunk 165 optimal weight: 1.9990 chunk 162 optimal weight: 9.9990 chunk 89 optimal weight: 4.9990 chunk 172 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN A 426 GLN A 572 GLN A 577 GLN B 10 HIS ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.110177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.087745 restraints weight = 26845.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.090682 restraints weight = 17254.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.092546 restraints weight = 11574.497| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.057 14541 Z= 0.360 Angle : 0.768 13.060 19767 Z= 0.404 Chirality : 0.052 0.218 2198 Planarity : 0.005 0.059 2524 Dihedral : 7.009 81.335 1934 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.78 % Favored : 90.22 % Rotamer: Outliers : 2.61 % Allowed : 12.53 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.07 (0.20), residues: 1759 helix: 0.94 (0.36), residues: 194 sheet: -0.65 (0.21), residues: 636 loop : -2.51 (0.19), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 373 HIS 0.011 0.002 HIS B 106 PHE 0.025 0.003 PHE B 452 TYR 0.018 0.002 TYR B 43 ARG 0.007 0.001 ARG A 219 Details of bonding type rmsd hydrogen bonds : bond 0.06575 ( 418) hydrogen bonds : angle 5.56828 ( 1218) metal coordination : bond 0.01749 ( 3) metal coordination : angle 7.49596 ( 9) covalent geometry : bond 0.00875 (14538) covalent geometry : angle 0.75093 (19758) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3518 Ramachandran restraints generated. 1759 Oldfield, 0 Emsley, 1759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3518 Ramachandran restraints generated. 1759 Oldfield, 0 Emsley, 1759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 85 time to evaluate : 1.635 Fit side-chains REVERT: A 594 LYS cc_start: 0.7785 (ttpt) cc_final: 0.7378 (ttpp) REVERT: A 653 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8642 (pp) REVERT: B 237 LYS cc_start: 0.6813 (mtmm) cc_final: 0.6287 (tttt) REVERT: B 736 GLN cc_start: 0.7939 (mm110) cc_final: 0.6857 (tm-30) REVERT: C 122 TYR cc_start: 0.7821 (OUTLIER) cc_final: 0.6110 (m-80) REVERT: C 299 GLU cc_start: 0.7563 (tm-30) cc_final: 0.7297 (tm-30) REVERT: C 347 GLU cc_start: 0.7975 (tt0) cc_final: 0.7616 (mt-10) outliers start: 41 outliers final: 26 residues processed: 117 average time/residue: 0.2310 time to fit residues: 43.0649 Evaluate side-chains 111 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 83 time to evaluate : 2.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 375 TRP Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 733 HIS Chi-restraints excluded: chain B residue 814 HIS Chi-restraints excluded: chain C residue 122 TYR Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain C residue 478 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 1 optimal weight: 0.3980 chunk 19 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 165 optimal weight: 3.9990 chunk 95 optimal weight: 0.4980 chunk 68 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 159 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 192 GLN ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.115763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.093667 restraints weight = 26543.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.096836 restraints weight = 17336.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.097969 restraints weight = 11685.483| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14541 Z= 0.115 Angle : 0.562 11.889 19767 Z= 0.290 Chirality : 0.046 0.205 2198 Planarity : 0.004 0.047 2524 Dihedral : 6.154 85.894 1934 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.10 % Allowed : 13.17 % Favored : 84.73 % 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: -1.77 (0.20), residues: 1759 helix: 1.45 (0.37), residues: 194 sheet: -0.48 (0.21), residues: 620 loop : -2.33 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 224 HIS 0.003 0.001 HIS C 272 PHE 0.019 0.001 PHE B 452 TYR 0.010 0.001 TYR B 43 ARG 0.003 0.000 ARG B 120 Details of bonding type rmsd hydrogen bonds : bond 0.03848 ( 418) hydrogen bonds : angle 4.90648 ( 1218) metal coordination : bond 0.00445 ( 3) metal coordination : angle 5.61271 ( 9) covalent geometry : bond 0.00264 (14538) covalent geometry : angle 0.54883 (19758) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3518 Ramachandran restraints generated. 1759 Oldfield, 0 Emsley, 1759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3518 Ramachandran restraints generated. 1759 Oldfield, 0 Emsley, 1759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 90 time to evaluate : 1.633 Fit side-chains REVERT: A 503 LEU cc_start: 0.7305 (OUTLIER) cc_final: 0.7087 (mm) REVERT: B 237 LYS cc_start: 0.6369 (mtmm) cc_final: 0.5916 (tttm) REVERT: B 736 GLN cc_start: 0.7897 (mm110) cc_final: 0.6852 (tm-30) REVERT: C 122 TYR cc_start: 0.7516 (OUTLIER) cc_final: 0.6204 (m-80) REVERT: C 299 GLU cc_start: 0.7376 (tm-30) cc_final: 0.7155 (tm-30) REVERT: C 347 GLU cc_start: 0.7960 (tt0) cc_final: 0.7524 (mt-10) REVERT: C 603 MET cc_start: 0.8847 (pmm) cc_final: 0.8635 (pmm) outliers start: 33 outliers final: 22 residues processed: 117 average time/residue: 0.2236 time to fit residues: 41.5334 Evaluate side-chains 110 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 375 TRP Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 733 HIS Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain C residue 122 TYR Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain C residue 478 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 133 optimal weight: 4.9990 chunk 128 optimal weight: 0.5980 chunk 135 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 143 optimal weight: 0.0030 chunk 145 optimal weight: 2.9990 chunk 123 optimal weight: 10.0000 chunk 144 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 572 GLN B 192 GLN ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.115544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.093740 restraints weight = 26484.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.096034 restraints weight = 17438.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.097085 restraints weight = 12811.105| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14541 Z= 0.129 Angle : 0.566 15.274 19767 Z= 0.290 Chirality : 0.046 0.237 2198 Planarity : 0.004 0.043 2524 Dihedral : 5.966 83.416 1934 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 2.16 % Allowed : 13.49 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1759 helix: 1.60 (0.37), residues: 194 sheet: -0.40 (0.21), residues: 622 loop : -2.30 (0.19), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 24 HIS 0.005 0.001 HIS B 106 PHE 0.017 0.001 PHE B 452 TYR 0.010 0.001 TYR B 43 ARG 0.003 0.000 ARG B 120 Details of bonding type rmsd hydrogen bonds : bond 0.04062 ( 418) hydrogen bonds : angle 4.81380 ( 1218) metal coordination : bond 0.00538 ( 3) metal coordination : angle 5.38041 ( 9) covalent geometry : bond 0.00302 (14538) covalent geometry : angle 0.55470 (19758) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3518 Ramachandran restraints generated. 1759 Oldfield, 0 Emsley, 1759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3518 Ramachandran restraints generated. 1759 Oldfield, 0 Emsley, 1759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 89 time to evaluate : 1.614 Fit side-chains REVERT: A 503 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.7090 (mm) REVERT: A 594 LYS cc_start: 0.7684 (ttpt) cc_final: 0.7414 (tmmt) REVERT: A 653 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8592 (pp) REVERT: B 150 MET cc_start: 0.7974 (pmm) cc_final: 0.7494 (pmm) REVERT: B 237 LYS cc_start: 0.6441 (mtmm) cc_final: 0.5887 (tttm) REVERT: B 736 GLN cc_start: 0.7900 (mm110) cc_final: 0.6850 (tm-30) REVERT: C 122 TYR cc_start: 0.7538 (OUTLIER) cc_final: 0.6204 (m-80) REVERT: C 299 GLU cc_start: 0.7415 (tm-30) cc_final: 0.7214 (tm-30) REVERT: C 347 GLU cc_start: 0.7909 (tt0) cc_final: 0.7473 (mt-10) REVERT: C 603 MET cc_start: 0.8890 (pmm) cc_final: 0.8660 (pmm) outliers start: 34 outliers final: 25 residues processed: 117 average time/residue: 0.2275 time to fit residues: 42.4644 Evaluate side-chains 114 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 86 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 375 TRP Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 192 GLN Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 733 HIS Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain C residue 122 TYR Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain C residue 478 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 16 optimal weight: 0.0050 chunk 130 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 148 optimal weight: 0.6980 chunk 99 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 overall best weight: 1.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.115187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.093035 restraints weight = 26688.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.094931 restraints weight = 18735.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.096032 restraints weight = 13835.779| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14541 Z= 0.145 Angle : 0.571 15.013 19767 Z= 0.294 Chirality : 0.046 0.223 2198 Planarity : 0.004 0.044 2524 Dihedral : 6.008 83.679 1934 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 2.10 % Allowed : 13.74 % Favored : 84.16 % 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: -1.66 (0.20), residues: 1759 helix: 1.62 (0.37), residues: 194 sheet: -0.38 (0.22), residues: 616 loop : -2.30 (0.19), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 375 HIS 0.005 0.001 HIS B 106 PHE 0.018 0.001 PHE B 452 TYR 0.011 0.001 TYR B 43 ARG 0.003 0.000 ARG B 120 Details of bonding type rmsd hydrogen bonds : bond 0.04186 ( 418) hydrogen bonds : angle 4.82856 ( 1218) metal coordination : bond 0.00614 ( 3) metal coordination : angle 5.20844 ( 9) covalent geometry : bond 0.00342 (14538) covalent geometry : angle 0.55983 (19758) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3518 Ramachandran restraints generated. 1759 Oldfield, 0 Emsley, 1759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3518 Ramachandran restraints generated. 1759 Oldfield, 0 Emsley, 1759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 89 time to evaluate : 1.497 Fit side-chains REVERT: A 503 LEU cc_start: 0.7359 (OUTLIER) cc_final: 0.7132 (mm) REVERT: A 594 LYS cc_start: 0.7603 (ttpt) cc_final: 0.7224 (ttpp) REVERT: A 653 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8594 (pp) REVERT: B 237 LYS cc_start: 0.6565 (mtmm) cc_final: 0.5958 (tttm) REVERT: B 736 GLN cc_start: 0.7895 (mm110) cc_final: 0.6845 (tm-30) REVERT: C 122 TYR cc_start: 0.7570 (OUTLIER) cc_final: 0.6179 (m-80) REVERT: C 299 GLU cc_start: 0.7392 (tm-30) cc_final: 0.7184 (tm-30) REVERT: C 347 GLU cc_start: 0.7923 (tt0) cc_final: 0.7479 (mt-10) REVERT: C 603 MET cc_start: 0.8861 (pmm) cc_final: 0.8624 (pmm) outliers start: 33 outliers final: 26 residues processed: 115 average time/residue: 0.2189 time to fit residues: 40.0790 Evaluate side-chains 117 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 88 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 375 TRP Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 733 HIS Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain C residue 122 TYR Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain C residue 478 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 116 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 167 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.115064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.093229 restraints weight = 26337.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.095341 restraints weight = 17671.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.096513 restraints weight = 13060.535| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14541 Z= 0.141 Angle : 0.568 14.317 19767 Z= 0.293 Chirality : 0.046 0.218 2198 Planarity : 0.004 0.043 2524 Dihedral : 5.989 83.369 1934 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 2.10 % Allowed : 14.25 % Favored : 83.65 % 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: -1.63 (0.20), residues: 1759 helix: 1.65 (0.37), residues: 194 sheet: -0.35 (0.22), residues: 619 loop : -2.29 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 375 HIS 0.005 0.001 HIS B 106 PHE 0.018 0.001 PHE B 452 TYR 0.011 0.001 TYR B 43 ARG 0.003 0.000 ARG B 120 Details of bonding type rmsd hydrogen bonds : bond 0.04149 ( 418) hydrogen bonds : angle 4.80593 ( 1218) metal coordination : bond 0.00590 ( 3) metal coordination : angle 5.27458 ( 9) covalent geometry : bond 0.00333 (14538) covalent geometry : angle 0.55723 (19758) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3518 Ramachandran restraints generated. 1759 Oldfield, 0 Emsley, 1759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3518 Ramachandran restraints generated. 1759 Oldfield, 0 Emsley, 1759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 88 time to evaluate : 1.650 Fit side-chains REVERT: A 503 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.7145 (mm) REVERT: A 653 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8600 (pp) REVERT: B 237 LYS cc_start: 0.6574 (mtmm) cc_final: 0.5963 (tttm) REVERT: B 736 GLN cc_start: 0.7884 (mm110) cc_final: 0.6858 (tm-30) REVERT: C 122 TYR cc_start: 0.7579 (OUTLIER) cc_final: 0.6193 (m-80) REVERT: C 347 GLU cc_start: 0.7915 (tt0) cc_final: 0.7509 (mt-10) REVERT: C 542 MET cc_start: 0.7671 (mmt) cc_final: 0.6780 (mmt) outliers start: 33 outliers final: 26 residues processed: 114 average time/residue: 0.2263 time to fit residues: 41.3163 Evaluate side-chains 114 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 85 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 375 TRP Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 733 HIS Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain C residue 122 TYR Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain C residue 478 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 167 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 44 optimal weight: 0.0870 chunk 10 optimal weight: 6.9990 chunk 18 optimal weight: 0.1980 chunk 132 optimal weight: 3.9990 chunk 79 optimal weight: 0.5980 chunk 177 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.117558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.095803 restraints weight = 26249.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.097953 restraints weight = 17240.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.098962 restraints weight = 12924.635| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 14541 Z= 0.100 Angle : 0.544 13.851 19767 Z= 0.277 Chirality : 0.045 0.189 2198 Planarity : 0.004 0.042 2524 Dihedral : 5.667 80.852 1934 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 1.97 % Allowed : 14.44 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.20), residues: 1759 helix: 1.85 (0.37), residues: 194 sheet: -0.33 (0.21), residues: 625 loop : -2.21 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 375 HIS 0.003 0.001 HIS B 814 PHE 0.016 0.001 PHE B 452 TYR 0.009 0.001 TYR C 184 ARG 0.003 0.000 ARG B 120 Details of bonding type rmsd hydrogen bonds : bond 0.03465 ( 418) hydrogen bonds : angle 4.59952 ( 1218) metal coordination : bond 0.00329 ( 3) metal coordination : angle 5.28793 ( 9) covalent geometry : bond 0.00226 (14538) covalent geometry : angle 0.53215 (19758) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3518 Ramachandran restraints generated. 1759 Oldfield, 0 Emsley, 1759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3518 Ramachandran restraints generated. 1759 Oldfield, 0 Emsley, 1759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 88 time to evaluate : 1.525 Fit side-chains REVERT: A 503 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.7062 (mm) REVERT: A 653 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8594 (pp) REVERT: B 150 MET cc_start: 0.7905 (pmm) cc_final: 0.7395 (pmm) REVERT: B 237 LYS cc_start: 0.6298 (mtmm) cc_final: 0.5753 (tttm) REVERT: B 736 GLN cc_start: 0.7904 (mm110) cc_final: 0.6848 (tm-30) REVERT: C 122 TYR cc_start: 0.7486 (OUTLIER) cc_final: 0.6229 (m-80) REVERT: C 347 GLU cc_start: 0.7944 (tt0) cc_final: 0.7484 (mt-10) REVERT: C 542 MET cc_start: 0.7565 (mmt) cc_final: 0.6715 (mmt) outliers start: 31 outliers final: 23 residues processed: 113 average time/residue: 0.2179 time to fit residues: 39.2979 Evaluate side-chains 112 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 86 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 375 TRP Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 733 HIS Chi-restraints excluded: chain C residue 122 TYR Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 478 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 67 optimal weight: 0.3980 chunk 64 optimal weight: 0.6980 chunk 4 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 170 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.113673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.091317 restraints weight = 26780.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.094163 restraints weight = 17785.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.095130 restraints weight = 12409.484| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14541 Z= 0.193 Angle : 0.612 13.734 19767 Z= 0.317 Chirality : 0.047 0.235 2198 Planarity : 0.004 0.044 2524 Dihedral : 6.215 84.472 1934 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 1.84 % Allowed : 14.57 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.20), residues: 1759 helix: 1.62 (0.37), residues: 194 sheet: -0.33 (0.22), residues: 613 loop : -2.31 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 373 HIS 0.006 0.001 HIS B 106 PHE 0.019 0.002 PHE B 452 TYR 0.013 0.001 TYR B 43 ARG 0.003 0.000 ARG A 219 Details of bonding type rmsd hydrogen bonds : bond 0.04769 ( 418) hydrogen bonds : angle 4.92739 ( 1218) metal coordination : bond 0.00775 ( 3) metal coordination : angle 5.77329 ( 9) covalent geometry : bond 0.00462 (14538) covalent geometry : angle 0.59935 (19758) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3601.59 seconds wall clock time: 64 minutes 48.64 seconds (3888.64 seconds total)