Starting phenix.real_space_refine on Sat Oct 11 11:50:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pty_17925/10_2025/8pty_17925.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pty_17925/10_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_17925/10_2025/8pty_17925.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pty_17925/10_2025/8pty_17925.map" model { file = "/net/cci-nas-00/data/ceres_data/8pty_17925/10_2025/8pty_17925.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pty_17925/10_2025/8pty_17925.cif" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 3.94, per 1000 atoms: 0.28 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: 1.30 Conformation dependent library (CDL) restraints added in 811.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.69 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: 3.20 Time building geometry restraints manager: 1.74 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: 5.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.970 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.770 ------------------------------------------------------------------------------- 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 : 12.03 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.81 (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 ARG 0.004 0.000 ARG A 693 TYR 0.019 0.001 TYR B 345 PHE 0.015 0.001 PHE C 271 TRP 0.031 0.001 TRP A 375 HIS 0.007 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00460 (14538) covalent geometry : angle 0.64861 (19758) hydrogen bonds : bond 0.17208 ( 418) hydrogen bonds : angle 6.64456 ( 1218) metal coordination : bond 0.01465 ( 3) metal coordination : angle 5.78675 ( 9) *********************** 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 : 0.574 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: 0.1544 time to fit residues: 34.9199 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 : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 A 703 GLN B 102 HIS B 182 ASN ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.117479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.095500 restraints weight = 26210.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.098505 restraints weight = 16936.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.099638 restraints weight = 11736.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.101721 restraints weight = 9724.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.101800 restraints weight = 9127.821| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14541 Z= 0.130 Angle : 0.579 11.635 19767 Z= 0.300 Chirality : 0.046 0.161 2198 Planarity : 0.004 0.044 2524 Dihedral : 6.541 89.909 1934 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 1.08 % Allowed : 6.04 % Favored : 92.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.73 (0.20), residues: 1759 helix: 1.60 (0.38), residues: 194 sheet: -0.55 (0.22), residues: 604 loop : -2.22 (0.19), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 139 TYR 0.012 0.001 TYR A 357 PHE 0.014 0.001 PHE B 452 TRP 0.011 0.001 TRP A 373 HIS 0.004 0.001 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00299 (14538) covalent geometry : angle 0.56582 (19758) hydrogen bonds : bond 0.04370 ( 418) hydrogen bonds : angle 5.12383 ( 1218) metal coordination : bond 0.00513 ( 3) metal coordination : angle 5.82466 ( 9) *********************** 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 127 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.606 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7961 (pmm) cc_final: 0.7720 (pmm) REVERT: A 125 LEU cc_start: 0.9397 (mt) cc_final: 0.9117 (mm) REVERT: A 357 TYR cc_start: 0.9062 (m-80) cc_final: 0.8495 (m-80) REVERT: A 594 LYS cc_start: 0.7741 (ttpt) cc_final: 0.7482 (ttpt) REVERT: B 237 LYS cc_start: 0.6339 (mtmm) cc_final: 0.6118 (tttm) REVERT: B 736 GLN cc_start: 0.7911 (mm110) cc_final: 0.7023 (tm-30) REVERT: C 202 TYR cc_start: 0.7678 (m-80) cc_final: 0.7477 (m-80) REVERT: C 347 GLU cc_start: 0.7920 (tt0) cc_final: 0.7509 (mt-10) REVERT: C 478 TYR cc_start: 0.6682 (p90) cc_final: 0.6416 (p90) REVERT: C 603 MET cc_start: 0.8322 (pmm) cc_final: 0.8018 (pmm) outliers start: 17 outliers final: 13 residues processed: 120 average time/residue: 0.1125 time to fit residues: 21.2053 Evaluate side-chains 97 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.560 ------------------------------------------------------------------------------- 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 165 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 160 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN A 426 GLN A 572 GLN B 182 ASN B 192 GLN ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3595 r_free = 0.3595 target = 0.112582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.089995 restraints weight = 27072.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.093117 restraints weight = 17223.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.096110 restraints weight = 11498.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.095536 restraints weight = 8772.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.095889 restraints weight = 8910.037| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 14541 Z= 0.237 Angle : 0.660 12.374 19767 Z= 0.347 Chirality : 0.049 0.162 2198 Planarity : 0.005 0.049 2524 Dihedral : 6.834 89.005 1934 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 1.91 % Allowed : 9.86 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.89 (0.20), residues: 1759 helix: 1.26 (0.37), residues: 194 sheet: -0.57 (0.21), residues: 617 loop : -2.37 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 219 TYR 0.015 0.002 TYR B 43 PHE 0.019 0.002 PHE B 452 TRP 0.014 0.002 TRP A 373 HIS 0.007 0.001 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00571 (14538) covalent geometry : angle 0.64640 (19758) hydrogen bonds : bond 0.05599 ( 418) hydrogen bonds : angle 5.32024 ( 1218) metal coordination : bond 0.01013 ( 3) metal coordination : angle 6.39165 ( 9) *********************** 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 120 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 90 time to evaluate : 0.692 Fit side-chains REVERT: A 357 TYR cc_start: 0.9057 (m-80) cc_final: 0.8562 (m-80) REVERT: A 594 LYS cc_start: 0.7792 (ttpt) cc_final: 0.7519 (ttpt) REVERT: B 237 LYS cc_start: 0.6617 (mtmm) cc_final: 0.6166 (tttm) REVERT: B 736 GLN cc_start: 0.7899 (mm110) cc_final: 0.6883 (tm-30) REVERT: C 122 TYR cc_start: 0.7491 (OUTLIER) cc_final: 0.5991 (m-80) REVERT: C 347 GLU cc_start: 0.7942 (tt0) cc_final: 0.7546 (mt-10) outliers start: 30 outliers final: 19 residues processed: 113 average time/residue: 0.1129 time to fit residues: 20.1710 Evaluate side-chains 100 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.615 ------------------------------------------------------------------------------- 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 95 ASN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 182 ASN Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 277 THR 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 122 TYR 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 143 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 176 optimal weight: 0.7980 chunk 163 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 151 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 140 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 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 = 0.3636 r_free = 0.3636 target = 0.115627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.093249 restraints weight = 26836.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.096967 restraints weight = 17538.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.097910 restraints weight = 11690.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.098119 restraints weight = 10204.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.098314 restraints weight = 9977.554| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14541 Z= 0.126 Angle : 0.565 13.907 19767 Z= 0.292 Chirality : 0.046 0.152 2198 Planarity : 0.004 0.043 2524 Dihedral : 6.110 84.025 1934 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 1.91 % Allowed : 11.70 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.74 (0.20), residues: 1759 helix: 1.57 (0.37), residues: 194 sheet: -0.52 (0.21), residues: 617 loop : -2.27 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 413 TYR 0.010 0.001 TYR B 43 PHE 0.018 0.001 PHE B 452 TRP 0.009 0.001 TRP A 224 HIS 0.004 0.001 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00294 (14538) covalent geometry : angle 0.54774 (19758) hydrogen bonds : bond 0.04057 ( 418) hydrogen bonds : angle 4.94167 ( 1218) metal coordination : bond 0.00460 ( 3) metal coordination : angle 6.58228 ( 9) *********************** 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 121 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 91 time to evaluate : 0.674 Fit side-chains REVERT: A 594 LYS cc_start: 0.7839 (ttpt) cc_final: 0.7630 (tmmt) REVERT: B 237 LYS cc_start: 0.6385 (mtmm) cc_final: 0.5976 (tttm) REVERT: B 620 MET cc_start: 0.9022 (mtp) cc_final: 0.8789 (mtp) REVERT: B 736 GLN cc_start: 0.7922 (mm110) cc_final: 0.6856 (tm-30) REVERT: C 122 TYR cc_start: 0.7362 (OUTLIER) cc_final: 0.6094 (m-80) REVERT: C 170 MET cc_start: 0.8128 (mtm) cc_final: 0.7909 (ptp) REVERT: C 347 GLU cc_start: 0.7896 (tt0) cc_final: 0.7496 (mt-10) outliers start: 30 outliers final: 18 residues processed: 113 average time/residue: 0.1114 time to fit residues: 19.8526 Evaluate side-chains 102 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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 A residue 704 ASP Chi-restraints excluded: chain B residue 50 VAL 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 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 C residue 122 TYR Chi-restraints excluded: chain C residue 313 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 134 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 572 GLN A 577 GLN ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.112838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.090768 restraints weight = 26689.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.094137 restraints weight = 17266.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.095194 restraints weight = 11629.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.095448 restraints weight = 10199.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.095581 restraints weight = 9497.958| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 14541 Z= 0.208 Angle : 0.620 12.571 19767 Z= 0.326 Chirality : 0.047 0.155 2198 Planarity : 0.004 0.050 2524 Dihedral : 6.499 88.280 1934 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 2.74 % Allowed : 12.21 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.83 (0.20), residues: 1759 helix: 1.37 (0.37), residues: 194 sheet: -0.52 (0.21), residues: 623 loop : -2.36 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 219 TYR 0.013 0.001 TYR B 43 PHE 0.020 0.002 PHE B 452 TRP 0.011 0.001 TRP A 373 HIS 0.007 0.001 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00500 (14538) covalent geometry : angle 0.60703 (19758) hydrogen bonds : bond 0.05065 ( 418) hydrogen bonds : angle 5.13472 ( 1218) metal coordination : bond 0.00973 ( 3) metal coordination : angle 6.02509 ( 9) *********************** 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 128 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 85 time to evaluate : 0.591 Fit side-chains REVERT: A 594 LYS cc_start: 0.7792 (ttpt) cc_final: 0.7558 (tmmt) REVERT: A 653 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8597 (pp) REVERT: B 237 LYS cc_start: 0.6752 (mtmm) cc_final: 0.6149 (tttt) REVERT: B 736 GLN cc_start: 0.7861 (mm110) cc_final: 0.6802 (tm-30) REVERT: C 122 TYR cc_start: 0.7596 (OUTLIER) cc_final: 0.6151 (m-80) REVERT: C 170 MET cc_start: 0.8138 (mtm) cc_final: 0.7927 (ptp) REVERT: C 347 GLU cc_start: 0.7938 (tt0) cc_final: 0.7511 (mt-10) REVERT: C 603 MET cc_start: 0.8994 (pmm) cc_final: 0.8541 (pmm) outliers start: 43 outliers final: 25 residues processed: 119 average time/residue: 0.1058 time to fit residues: 20.2659 Evaluate side-chains 108 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 81 time to evaluate : 0.571 ------------------------------------------------------------------------------- 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 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 659 THR Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 704 ASP 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 733 HIS Chi-restraints excluded: chain C residue 122 TYR 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 13 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 164 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 111 optimal weight: 0.0030 chunk 43 optimal weight: 3.9990 chunk 3 optimal weight: 0.4980 chunk 112 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.115506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.093232 restraints weight = 26617.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.095925 restraints weight = 17524.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.097152 restraints weight = 12459.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.098933 restraints weight = 10369.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.099070 restraints weight = 9857.708| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2274 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= 0.128 Angle : 0.562 12.281 19767 Z= 0.291 Chirality : 0.045 0.201 2198 Planarity : 0.004 0.043 2524 Dihedral : 6.110 86.056 1934 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 2.29 % Allowed : 12.98 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.67 (0.20), residues: 1759 helix: 1.61 (0.37), residues: 194 sheet: -0.42 (0.22), residues: 619 loop : -2.28 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 367 TYR 0.011 0.001 TYR B 43 PHE 0.019 0.001 PHE B 452 TRP 0.009 0.001 TRP B 24 HIS 0.004 0.001 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00301 (14538) covalent geometry : angle 0.54978 (19758) hydrogen bonds : bond 0.04028 ( 418) hydrogen bonds : angle 4.86163 ( 1218) metal coordination : bond 0.00555 ( 3) metal coordination : angle 5.50126 ( 9) *********************** 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 120 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 84 time to evaluate : 0.577 Fit side-chains REVERT: A 503 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.7092 (mm) REVERT: A 653 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8584 (pp) REVERT: B 237 LYS cc_start: 0.6487 (mtmm) cc_final: 0.5948 (tttm) REVERT: B 620 MET cc_start: 0.9035 (mtp) cc_final: 0.8817 (mtp) REVERT: B 736 GLN cc_start: 0.7838 (mm110) cc_final: 0.6813 (tm-30) REVERT: C 122 TYR cc_start: 0.7440 (OUTLIER) cc_final: 0.6126 (m-80) REVERT: C 347 GLU cc_start: 0.7885 (tt0) cc_final: 0.7485 (mt-10) outliers start: 36 outliers final: 23 residues processed: 114 average time/residue: 0.1051 time to fit residues: 19.2899 Evaluate side-chains 106 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 80 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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 394 ILE 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 121 THR Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 228 SER 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 5 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 76 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 172 optimal weight: 4.9990 chunk 103 optimal weight: 0.0000 chunk 85 optimal weight: 0.9990 chunk 152 optimal weight: 0.6980 chunk 165 optimal weight: 6.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN B 192 GLN ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.116900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.094910 restraints weight = 26561.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.096919 restraints weight = 17830.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.098131 restraints weight = 13292.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.099698 restraints weight = 10849.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.099838 restraints weight = 10107.393| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14541 Z= 0.109 Angle : 0.547 15.246 19767 Z= 0.279 Chirality : 0.045 0.187 2198 Planarity : 0.004 0.042 2524 Dihedral : 5.850 85.063 1934 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 2.35 % Allowed : 13.42 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.55 (0.20), residues: 1759 helix: 1.80 (0.37), residues: 194 sheet: -0.33 (0.22), residues: 617 loop : -2.22 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 139 TYR 0.009 0.001 TYR B 43 PHE 0.016 0.001 PHE B 452 TRP 0.009 0.001 TRP A 375 HIS 0.003 0.001 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00250 (14538) covalent geometry : angle 0.53629 (19758) hydrogen bonds : bond 0.03656 ( 418) hydrogen bonds : angle 4.70522 ( 1218) metal coordination : bond 0.00430 ( 3) metal coordination : angle 5.15684 ( 9) *********************** 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: 37 poor density : 86 time to evaluate : 0.624 Fit side-chains REVERT: A 503 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.7064 (mm) REVERT: A 594 LYS cc_start: 0.7700 (ttpt) cc_final: 0.7315 (ttpt) REVERT: A 653 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8561 (pp) REVERT: B 150 MET cc_start: 0.7932 (pmm) cc_final: 0.7488 (pmm) REVERT: B 237 LYS cc_start: 0.6406 (mtmm) cc_final: 0.5838 (tttm) REVERT: B 620 MET cc_start: 0.8973 (mtp) cc_final: 0.8741 (mtp) REVERT: B 736 GLN cc_start: 0.7846 (mm110) cc_final: 0.6815 (tm-30) REVERT: C 122 TYR cc_start: 0.7414 (OUTLIER) cc_final: 0.6224 (m-80) REVERT: C 347 GLU cc_start: 0.7945 (tt0) cc_final: 0.7470 (mt-10) outliers start: 37 outliers final: 25 residues processed: 117 average time/residue: 0.1057 time to fit residues: 19.7353 Evaluate side-chains 109 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 81 time to evaluate : 0.603 ------------------------------------------------------------------------------- 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 36 THR 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 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 34 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 6 optimal weight: 0.0980 chunk 26 optimal weight: 0.9980 chunk 165 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 123 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 15 optimal weight: 0.0670 chunk 71 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.116876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.094774 restraints weight = 26463.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.096877 restraints weight = 18279.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.098024 restraints weight = 13432.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.099824 restraints weight = 10870.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.099891 restraints weight = 9985.034| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2388 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= 0.116 Angle : 0.550 14.594 19767 Z= 0.282 Chirality : 0.045 0.176 2198 Planarity : 0.004 0.042 2524 Dihedral : 5.731 79.892 1934 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 2.10 % Allowed : 14.06 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.48 (0.20), residues: 1759 helix: 1.87 (0.37), residues: 194 sheet: -0.29 (0.22), residues: 621 loop : -2.18 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 120 TYR 0.009 0.001 TYR B 43 PHE 0.017 0.001 PHE B 452 TRP 0.009 0.001 TRP A 375 HIS 0.004 0.001 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00268 (14538) covalent geometry : angle 0.53908 (19758) hydrogen bonds : bond 0.03738 ( 418) hydrogen bonds : angle 4.67477 ( 1218) metal coordination : bond 0.00475 ( 3) metal coordination : angle 5.20205 ( 9) *********************** 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 118 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 85 time to evaluate : 0.596 Fit side-chains REVERT: A 503 LEU cc_start: 0.7303 (OUTLIER) cc_final: 0.7086 (mm) REVERT: A 594 LYS cc_start: 0.7608 (ttpt) cc_final: 0.7231 (ttpp) REVERT: A 653 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8627 (pp) REVERT: B 237 LYS cc_start: 0.6437 (mtmm) cc_final: 0.5864 (tttm) REVERT: B 620 MET cc_start: 0.8952 (mtp) cc_final: 0.8724 (mtp) REVERT: B 736 GLN cc_start: 0.7816 (mm110) cc_final: 0.6809 (tm-30) REVERT: C 122 TYR cc_start: 0.7446 (OUTLIER) cc_final: 0.6243 (m-80) REVERT: C 347 GLU cc_start: 0.7917 (tt0) cc_final: 0.7488 (mt-10) REVERT: C 542 MET cc_start: 0.7591 (mmt) cc_final: 0.6754 (mmt) REVERT: C 603 MET cc_start: 0.9127 (pmm) cc_final: 0.8903 (pmm) outliers start: 33 outliers final: 24 residues processed: 112 average time/residue: 0.1016 time to fit residues: 18.3745 Evaluate side-chains 111 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 84 time to evaluate : 0.532 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 61 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 75 optimal weight: 0.6980 chunk 162 optimal weight: 8.9990 chunk 82 optimal weight: 3.9990 chunk 122 optimal weight: 0.1980 chunk 177 optimal weight: 0.9990 chunk 17 optimal weight: 0.3980 chunk 153 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN B 192 GLN B 350 ASN B 764 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.117688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.095536 restraints weight = 26590.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.097831 restraints weight = 17743.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.099082 restraints weight = 13138.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.100504 restraints weight = 10649.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.100617 restraints weight = 10066.416| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14541 Z= 0.105 Angle : 0.541 14.075 19767 Z= 0.277 Chirality : 0.045 0.170 2198 Planarity : 0.004 0.042 2524 Dihedral : 5.503 75.564 1934 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 2.16 % Allowed : 14.38 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.42 (0.20), residues: 1759 helix: 1.97 (0.37), residues: 194 sheet: -0.24 (0.22), residues: 620 loop : -2.16 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 120 TYR 0.009 0.001 TYR C 184 PHE 0.018 0.001 PHE A 599 TRP 0.009 0.001 TRP A 375 HIS 0.003 0.001 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00241 (14538) covalent geometry : angle 0.53086 (19758) hydrogen bonds : bond 0.03535 ( 418) hydrogen bonds : angle 4.59496 ( 1218) metal coordination : bond 0.00423 ( 3) metal coordination : angle 5.00805 ( 9) *********************** 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 123 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 89 time to evaluate : 0.382 Fit side-chains REVERT: A 394 ILE cc_start: 0.8897 (OUTLIER) cc_final: 0.8696 (mt) REVERT: A 503 LEU cc_start: 0.7289 (OUTLIER) cc_final: 0.7077 (mm) REVERT: A 594 LYS cc_start: 0.7626 (ttpt) cc_final: 0.7244 (ttpp) REVERT: A 653 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8645 (pp) REVERT: B 150 MET cc_start: 0.7902 (pmm) cc_final: 0.7499 (pmm) REVERT: B 237 LYS cc_start: 0.6384 (mtmm) cc_final: 0.5822 (tttm) REVERT: B 620 MET cc_start: 0.8921 (mtp) cc_final: 0.8685 (mtp) REVERT: B 736 GLN cc_start: 0.7844 (mm110) cc_final: 0.6812 (tm-30) REVERT: C 122 TYR cc_start: 0.7418 (OUTLIER) cc_final: 0.6281 (m-80) REVERT: C 347 GLU cc_start: 0.7962 (tt0) cc_final: 0.7520 (mt-10) REVERT: C 603 MET cc_start: 0.9127 (pmm) cc_final: 0.8852 (pmm) outliers start: 34 outliers final: 26 residues processed: 116 average time/residue: 0.1005 time to fit residues: 18.6205 Evaluate side-chains 115 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 85 time to evaluate : 0.616 ------------------------------------------------------------------------------- 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 394 ILE 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 36 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 101 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 166 optimal weight: 0.0040 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 172 optimal weight: 0.8980 chunk 171 optimal weight: 0.0770 chunk 126 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.5550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.117486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.095484 restraints weight = 26497.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.097709 restraints weight = 17786.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.098756 restraints weight = 13216.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.100642 restraints weight = 10788.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.100750 restraints weight = 9551.431| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.115 14541 Z= 0.122 Angle : 0.768 59.179 19767 Z= 0.431 Chirality : 0.045 0.165 2198 Planarity : 0.004 0.042 2524 Dihedral : 5.509 75.527 1934 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 1.97 % Allowed : 14.63 % Favored : 83.40 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.42 (0.20), residues: 1759 helix: 1.97 (0.37), residues: 194 sheet: -0.24 (0.22), residues: 620 loop : -2.16 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 120 TYR 0.016 0.001 TYR A 416 PHE 0.016 0.001 PHE B 452 TRP 0.009 0.001 TRP A 375 HIS 0.003 0.001 HIS B 57 Details of bonding type rmsd covalent geometry : bond 0.00271 (14538) covalent geometry : angle 0.76054 (19758) hydrogen bonds : bond 0.03526 ( 418) hydrogen bonds : angle 4.59459 ( 1218) metal coordination : bond 0.00414 ( 3) metal coordination : angle 5.00707 ( 9) ********************** 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 116 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 85 time to evaluate : 0.568 Fit side-chains REVERT: A 503 LEU cc_start: 0.7288 (OUTLIER) cc_final: 0.7079 (mm) REVERT: A 594 LYS cc_start: 0.7577 (ttpt) cc_final: 0.7213 (ttpp) REVERT: A 653 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8650 (pp) REVERT: B 150 MET cc_start: 0.7900 (pmm) cc_final: 0.7493 (pmm) REVERT: B 237 LYS cc_start: 0.6383 (mtmm) cc_final: 0.5824 (tttm) REVERT: B 620 MET cc_start: 0.8921 (mtp) cc_final: 0.8685 (mtp) REVERT: B 736 GLN cc_start: 0.7828 (mm110) cc_final: 0.6813 (tm-30) REVERT: C 122 TYR cc_start: 0.7418 (OUTLIER) cc_final: 0.6279 (m-80) REVERT: C 347 GLU cc_start: 0.7945 (tt0) cc_final: 0.7518 (mt-10) REVERT: C 603 MET cc_start: 0.9127 (pmm) cc_final: 0.8854 (pmm) outliers start: 31 outliers final: 23 residues processed: 109 average time/residue: 0.1025 time to fit residues: 18.0536 Evaluate side-chains 109 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 83 time to evaluate : 0.603 ------------------------------------------------------------------------------- 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 32 optimal weight: 3.9990 chunk 158 optimal weight: 0.8980 chunk 128 optimal weight: 0.9990 chunk 127 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 143 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 144 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN 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 = 0.117584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.095569 restraints weight = 26320.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.097716 restraints weight = 17984.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.098825 restraints weight = 13385.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.100563 restraints weight = 10862.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.100599 restraints weight = 10019.422| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.115 14541 Z= 0.122 Angle : 0.768 59.179 19767 Z= 0.431 Chirality : 0.045 0.165 2198 Planarity : 0.004 0.042 2524 Dihedral : 5.509 75.527 1934 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 1.72 % Allowed : 14.89 % Favored : 83.40 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.42 (0.20), residues: 1759 helix: 1.97 (0.37), residues: 194 sheet: -0.24 (0.22), residues: 620 loop : -2.16 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 120 TYR 0.016 0.001 TYR A 416 PHE 0.016 0.001 PHE B 452 TRP 0.009 0.001 TRP A 375 HIS 0.003 0.001 HIS B 57 Details of bonding type rmsd covalent geometry : bond 0.00271 (14538) covalent geometry : angle 0.76054 (19758) hydrogen bonds : bond 0.03526 ( 418) hydrogen bonds : angle 4.59459 ( 1218) metal coordination : bond 0.00414 ( 3) metal coordination : angle 5.00707 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2014.25 seconds wall clock time: 35 minutes 57.63 seconds (2157.63 seconds total)