Starting phenix.real_space_refine on Wed Mar 4 00:05:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6og1_20049/03_2026/6og1_20049.cif Found real_map, /net/cci-nas-00/data/ceres_data/6og1_20049/03_2026/6og1_20049.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6og1_20049/03_2026/6og1_20049.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6og1_20049/03_2026/6og1_20049.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6og1_20049/03_2026/6og1_20049.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6og1_20049/03_2026/6og1_20049.map" } resolution = 3.3 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= 0.008 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 P 9 5.49 5 S 32 5.16 5 C 5749 2.51 5 N 1669 2.21 5 O 1748 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9207 Number of models: 1 Model: "" Number of chains: 4 Chain: "F" Number of atoms: 4518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4518 Classifications: {'peptide': 571} Link IDs: {'PTRANS': 22, 'TRANS': 548} Chain breaks: 2 Chain: "A" Number of atoms: 4577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4577 Classifications: {'peptide': 581} Link IDs: {'PTRANS': 22, 'TRANS': 558} Chain breaks: 1 Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.71, per 1000 atoms: 0.19 Number of scatterers: 9207 At special positions: 0 Unit cell: (108.36, 118.68, 105.264, 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) S 32 16.00 P 9 15.00 O 1748 8.00 N 1669 7.00 C 5749 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: 0.71 Conformation dependent library (CDL) restraints added in 336.1 milliseconds 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2130 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 0 sheets defined 44.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'F' and resid 188 through 193 Processing helix chain 'F' and resid 213 through 221 removed outlier: 3.506A pdb=" N GLU F 217 " --> pdb=" O THR F 213 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU F 219 " --> pdb=" O ILE F 215 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ALA F 220 " --> pdb=" O VAL F 216 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLN F 221 " --> pdb=" O GLU F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 246 removed outlier: 5.236A pdb=" N VAL F 246 " --> pdb=" O MET F 242 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 242 through 246' Processing helix chain 'F' and resid 253 through 268 removed outlier: 4.395A pdb=" N ARG F 258 " --> pdb=" O GLU F 254 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU F 259 " --> pdb=" O PHE F 255 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU F 263 " --> pdb=" O LEU F 259 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN F 264 " --> pdb=" O LYS F 260 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASP F 265 " --> pdb=" O GLY F 261 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N LEU F 266 " --> pdb=" O VAL F 262 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ALA F 267 " --> pdb=" O LEU F 263 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LYS F 268 " --> pdb=" O ASN F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 305 Processing helix chain 'F' and resid 315 through 321 Processing helix chain 'F' and resid 343 through 352 removed outlier: 4.093A pdb=" N ILE F 347 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA F 348 " --> pdb=" O GLU F 344 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE F 349 " --> pdb=" O ASP F 345 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY F 352 " --> pdb=" O ALA F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 362 Processing helix chain 'F' and resid 366 through 371 removed outlier: 3.724A pdb=" N VAL F 371 " --> pdb=" O ASP F 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 379 removed outlier: 6.325A pdb=" N HIS F 378 " --> pdb=" O ALA F 374 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ARG F 379 " --> pdb=" O THR F 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 374 through 379' Processing helix chain 'F' and resid 387 through 405 removed outlier: 3.991A pdb=" N ASP F 392 " --> pdb=" O ASP F 388 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU F 393 " --> pdb=" O LYS F 389 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP F 395 " --> pdb=" O ILE F 391 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ALA F 397 " --> pdb=" O LEU F 393 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER F 400 " --> pdb=" O GLU F 396 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ILE F 401 " --> pdb=" O ALA F 397 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ARG F 402 " --> pdb=" O ALA F 398 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N MET F 403 " --> pdb=" O SER F 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 533 through 541 removed outlier: 3.745A pdb=" N VAL F 539 " --> pdb=" O GLU F 535 " (cutoff:3.500A) Processing helix chain 'F' and resid 547 through 551 removed outlier: 4.608A pdb=" N MET F 551 " --> pdb=" O PRO F 547 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 547 through 551' Processing helix chain 'F' and resid 556 through 560 removed outlier: 4.665A pdb=" N LEU F 560 " --> pdb=" O ARG F 556 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 556 through 560' Processing helix chain 'F' and resid 565 through 569 removed outlier: 3.994A pdb=" N ARG F 569 " --> pdb=" O GLU F 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 565 through 569' Processing helix chain 'F' and resid 573 through 589 removed outlier: 4.643A pdb=" N VAL F 577 " --> pdb=" O GLN F 573 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ASP F 578 " --> pdb=" O ASN F 574 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ALA F 579 " --> pdb=" O GLU F 575 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N VAL F 580 " --> pdb=" O ALA F 576 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ALA F 583 " --> pdb=" O ALA F 579 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ILE F 584 " --> pdb=" O VAL F 580 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ARG F 585 " --> pdb=" O SER F 581 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ARG F 586 " --> pdb=" O ASN F 582 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N SER F 587 " --> pdb=" O ALA F 583 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG F 588 " --> pdb=" O ILE F 584 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ALA F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) Processing helix chain 'F' and resid 610 through 623 removed outlier: 3.546A pdb=" N LEU F 614 " --> pdb=" O GLY F 610 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA F 619 " --> pdb=" O CYS F 615 " (cutoff:3.500A) Processing helix chain 'F' and resid 640 through 646 removed outlier: 5.637A pdb=" N SER F 644 " --> pdb=" O LYS F 640 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ARG F 645 " --> pdb=" O HIS F 641 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU F 646 " --> pdb=" O SER F 642 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 640 through 646' Processing helix chain 'F' and resid 660 through 664 removed outlier: 4.175A pdb=" N GLU F 664 " --> pdb=" O GLY F 660 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 660 through 664' Processing helix chain 'F' and resid 684 through 694 removed outlier: 5.350A pdb=" N ASN F 688 " --> pdb=" O PRO F 684 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE F 689 " --> pdb=" O ASP F 685 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N LEU F 690 " --> pdb=" O VAL F 686 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N LEU F 691 " --> pdb=" O PHE F 687 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N GLN F 692 " --> pdb=" O ASN F 688 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N VAL F 693 " --> pdb=" O ILE F 689 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N LEU F 694 " --> pdb=" O LEU F 690 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 684 through 694' Processing helix chain 'F' and resid 722 through 730 removed outlier: 4.467A pdb=" N GLN F 726 " --> pdb=" O SER F 722 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N GLU F 727 " --> pdb=" O ASP F 723 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ARG F 728 " --> pdb=" O LEU F 724 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N PHE F 729 " --> pdb=" O ILE F 725 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N GLY F 730 " --> pdb=" O GLN F 726 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 722 through 730' Processing helix chain 'F' and resid 734 through 748 removed outlier: 5.487A pdb=" N LYS F 738 " --> pdb=" O TYR F 734 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLU F 739 " --> pdb=" O ALA F 735 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU F 740 " --> pdb=" O HIS F 736 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL F 741 " --> pdb=" O MET F 737 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU F 742 " --> pdb=" O LYS F 738 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY F 743 " --> pdb=" O GLU F 739 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N VAL F 744 " --> pdb=" O LEU F 740 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL F 745 " --> pdb=" O VAL F 741 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER F 746 " --> pdb=" O LEU F 742 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N HIS F 747 " --> pdb=" O GLY F 743 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ASN F 748 " --> pdb=" O VAL F 744 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 734 through 748' Processing helix chain 'F' and resid 750 through 756 removed outlier: 5.455A pdb=" N ILE F 754 " --> pdb=" O ARG F 750 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ASN F 755 " --> pdb=" O PRO F 751 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ARG F 756 " --> pdb=" O GLU F 752 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 750 through 756' Processing helix chain 'F' and resid 768 through 784 removed outlier: 3.729A pdb=" N ILE F 774 " --> pdb=" O HIS F 770 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU F 779 " --> pdb=" O ALA F 775 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU F 782 " --> pdb=" O GLN F 778 " (cutoff:3.500A) Processing helix chain 'F' and resid 786 through 790 Processing helix chain 'F' and resid 796 through 806 removed outlier: 3.819A pdb=" N LYS F 801 " --> pdb=" O ASP F 797 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LEU F 803 " --> pdb=" O ALA F 799 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER F 804 " --> pdb=" O LEU F 800 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLU F 805 " --> pdb=" O LYS F 801 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ASN F 806 " --> pdb=" O LEU F 802 " (cutoff:3.500A) Processing helix chain 'F' and resid 817 through 834 removed outlier: 5.251A pdb=" N ASN F 827 " --> pdb=" O GLN F 823 " (cutoff:3.500A) Proline residue: F 828 - end of helix Processing helix chain 'A' and resid 168 through 173 Processing helix chain 'A' and resid 183 through 194 Processing helix chain 'A' and resid 215 through 225 removed outlier: 3.685A pdb=" N GLN A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG A 222 " --> pdb=" O GLY A 218 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 264 removed outlier: 3.626A pdb=" N ARG A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 283 No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 299 through 305 removed outlier: 3.500A pdb=" N ALA A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 320 Processing helix chain 'A' and resid 326 through 331 removed outlier: 3.805A pdb=" N ARG A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 362 removed outlier: 3.618A pdb=" N GLY A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLU A 355 " --> pdb=" O ARG A 351 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ARG A 356 " --> pdb=" O GLY A 352 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR A 357 " --> pdb=" O LEU A 353 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N HIS A 360 " --> pdb=" O ARG A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 381 removed outlier: 3.604A pdb=" N ALA A 373 " --> pdb=" O ALA A 369 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA A 374 " --> pdb=" O ILE A 370 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR A 375 " --> pdb=" O VAL A 371 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 407 removed outlier: 3.680A pdb=" N ILE A 394 " --> pdb=" O ALA A 390 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLN A 404 " --> pdb=" O SER A 400 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP A 406 " --> pdb=" O ARG A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 544 Processing helix chain 'A' and resid 565 through 569 removed outlier: 4.281A pdb=" N ARG A 569 " --> pdb=" O GLU A 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 565 through 569' Processing helix chain 'A' and resid 573 through 589 removed outlier: 4.183A pdb=" N ASN A 582 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A 583 " --> pdb=" O ALA A 579 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER A 587 " --> pdb=" O ALA A 583 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG A 588 " --> pdb=" O ILE A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 623 removed outlier: 3.816A pdb=" N CYS A 615 " --> pdb=" O LYS A 611 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS A 616 " --> pdb=" O THR A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 646 removed outlier: 5.360A pdb=" N SER A 644 " --> pdb=" O LYS A 640 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N ARG A 645 " --> pdb=" O HIS A 641 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N LEU A 646 " --> pdb=" O SER A 642 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 640 through 646' Processing helix chain 'A' and resid 661 through 669 removed outlier: 3.922A pdb=" N ALA A 665 " --> pdb=" O TYR A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 692 removed outlier: 4.583A pdb=" N GLN A 692 " --> pdb=" O ASN A 688 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 688 through 692' Processing helix chain 'A' and resid 710 through 712 No H-bonds generated for 'chain 'A' and resid 710 through 712' Processing helix chain 'A' and resid 722 through 730 removed outlier: 3.863A pdb=" N GLU A 727 " --> pdb=" O ASP A 723 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG A 728 " --> pdb=" O LEU A 724 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE A 729 " --> pdb=" O ILE A 725 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLY A 730 " --> pdb=" O GLN A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 748 removed outlier: 6.009A pdb=" N LYS A 738 " --> pdb=" O TYR A 734 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU A 739 " --> pdb=" O ALA A 735 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N LEU A 740 " --> pdb=" O HIS A 736 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N VAL A 741 " --> pdb=" O MET A 737 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N LEU A 742 " --> pdb=" O LYS A 738 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N GLY A 743 " --> pdb=" O GLU A 739 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N VAL A 744 " --> pdb=" O LEU A 740 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL A 745 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N SER A 746 " --> pdb=" O LEU A 742 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N HIS A 747 " --> pdb=" O GLY A 743 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ASN A 748 " --> pdb=" O VAL A 744 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 734 through 748' Processing helix chain 'A' and resid 750 through 756 removed outlier: 4.517A pdb=" N ILE A 754 " --> pdb=" O ARG A 750 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN A 755 " --> pdb=" O PRO A 751 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ARG A 756 " --> pdb=" O GLU A 752 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 750 through 756' Processing helix chain 'A' and resid 767 through 779 removed outlier: 3.585A pdb=" N ILE A 771 " --> pdb=" O GLY A 767 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N SER A 773 " --> pdb=" O GLN A 769 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N GLN A 776 " --> pdb=" O ALA A 772 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ILE A 777 " --> pdb=" O SER A 773 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N GLN A 778 " --> pdb=" O ILE A 774 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N LEU A 779 " --> pdb=" O ALA A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 785 removed outlier: 5.213A pdb=" N ARG A 785 " --> pdb=" O ARG A 781 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 781 through 785' Processing helix chain 'A' and resid 799 through 807 removed outlier: 4.023A pdb=" N LEU A 803 " --> pdb=" O ALA A 799 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ASN A 806 " --> pdb=" O LEU A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 823 removed outlier: 4.509A pdb=" N LYS A 818 " --> pdb=" O ALA A 814 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ARG A 819 " --> pdb=" O ARG A 815 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 821 " --> pdb=" O LEU A 817 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN A 822 " --> pdb=" O LYS A 818 " (cutoff:3.500A) 147 hydrogen bonds defined for protein. 441 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: 0.86 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 3261 1.36 - 1.51: 2480 1.51 - 1.66: 3548 1.66 - 1.80: 47 1.80 - 1.95: 12 Bond restraints: 9348 Sorted by residual: bond pdb=" C ARG A 815 " pdb=" N PRO A 816 " ideal model delta sigma weight residual 1.337 1.397 -0.060 9.80e-03 1.04e+04 3.81e+01 bond pdb=" C ALA A 682 " pdb=" N HIS A 683 " ideal model delta sigma weight residual 1.330 1.286 0.044 1.47e-02 4.63e+03 9.00e+00 bond pdb=" CA ALA F 775 " pdb=" C ALA F 775 " ideal model delta sigma weight residual 1.522 1.487 0.035 1.37e-02 5.33e+03 6.49e+00 bond pdb=" CA HIS A 747 " pdb=" CB HIS A 747 " ideal model delta sigma weight residual 1.524 1.556 -0.031 1.27e-02 6.20e+03 6.06e+00 bond pdb=" C ALA A 289 " pdb=" N ASP A 290 " ideal model delta sigma weight residual 1.333 1.304 0.029 1.41e-02 5.03e+03 4.36e+00 ... (remaining 9343 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 11634 2.04 - 4.08: 819 4.08 - 6.12: 127 6.12 - 8.16: 44 8.16 - 10.19: 10 Bond angle restraints: 12634 Sorted by residual: angle pdb=" N VAL F 343 " pdb=" CA VAL F 343 " pdb=" C VAL F 343 " ideal model delta sigma weight residual 113.22 105.79 7.43 1.23e+00 6.61e-01 3.65e+01 angle pdb=" N ILE A 215 " pdb=" CA ILE A 215 " pdb=" C ILE A 215 " ideal model delta sigma weight residual 111.81 106.63 5.18 8.60e-01 1.35e+00 3.63e+01 angle pdb=" C ARG A 852 " pdb=" N ILE A 853 " pdb=" CA ILE A 853 " ideal model delta sigma weight residual 120.49 127.77 -7.28 1.38e+00 5.25e-01 2.79e+01 angle pdb=" N ASN A 297 " pdb=" CA ASN A 297 " pdb=" C ASN A 297 " ideal model delta sigma weight residual 114.75 108.27 6.48 1.26e+00 6.30e-01 2.64e+01 angle pdb=" N ILE A 853 " pdb=" CA ILE A 853 " pdb=" C ILE A 853 " ideal model delta sigma weight residual 109.51 116.53 -7.02 1.43e+00 4.89e-01 2.41e+01 ... (remaining 12629 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.03: 5525 33.03 - 66.07: 201 66.07 - 99.10: 18 99.10 - 132.14: 3 132.14 - 165.17: 1 Dihedral angle restraints: 5748 sinusoidal: 2441 harmonic: 3307 Sorted by residual: dihedral pdb=" O1B ADP F 901 " pdb=" O3A ADP F 901 " pdb=" PB ADP F 901 " pdb=" PA ADP F 901 " ideal model delta sinusoidal sigma weight residual -60.00 55.84 -115.84 1 2.00e+01 2.50e-03 3.45e+01 dihedral pdb=" O1B ADP A 902 " pdb=" O3A ADP A 902 " pdb=" PB ADP A 902 " pdb=" PA ADP A 902 " ideal model delta sinusoidal sigma weight residual -60.00 53.33 -113.33 1 2.00e+01 2.50e-03 3.35e+01 dihedral pdb=" CA GLN A 385 " pdb=" C GLN A 385 " pdb=" N LEU A 386 " pdb=" CA LEU A 386 " ideal model delta harmonic sigma weight residual -180.00 -151.32 -28.68 0 5.00e+00 4.00e-02 3.29e+01 ... (remaining 5745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1062 0.066 - 0.131: 315 0.131 - 0.196: 41 0.196 - 0.262: 7 0.262 - 0.327: 1 Chirality restraints: 1426 Sorted by residual: chirality pdb=" CB ILE F 571 " pdb=" CA ILE F 571 " pdb=" CG1 ILE F 571 " pdb=" CG2 ILE F 571 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA ASP A 624 " pdb=" N ASP A 624 " pdb=" C ASP A 624 " pdb=" CB ASP A 624 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CG LEU F 280 " pdb=" CB LEU F 280 " pdb=" CD1 LEU F 280 " pdb=" CD2 LEU F 280 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 1423 not shown) Planarity restraints: 1648 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 367 " 0.053 5.00e-02 4.00e+02 8.01e-02 1.03e+01 pdb=" N PRO A 368 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO A 368 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 368 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 207 " -0.048 5.00e-02 4.00e+02 7.18e-02 8.26e+00 pdb=" N PRO A 208 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 208 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 208 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 650 " -0.047 5.00e-02 4.00e+02 7.02e-02 7.89e+00 pdb=" N PRO A 651 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 651 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 651 " -0.039 5.00e-02 4.00e+02 ... (remaining 1645 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1572 2.77 - 3.30: 7900 3.30 - 3.83: 14539 3.83 - 4.37: 17088 4.37 - 4.90: 28044 Nonbonded interactions: 69143 Sorted by model distance: nonbonded pdb=" O ASP A 241 " pdb=" OD1 ASP A 241 " model vdw 2.234 3.040 nonbonded pdb=" O MET F 629 " pdb=" OH TYR F 661 " model vdw 2.262 3.040 nonbonded pdb=" OD2 ASP F 178 " pdb=" O2' ADP F 901 " model vdw 2.272 3.040 nonbonded pdb=" O SER A 804 " pdb=" OG SER A 804 " model vdw 2.297 3.040 nonbonded pdb=" NH2 ARG F 196 " pdb=" OD1 ASP A 392 " model vdw 2.314 3.120 ... (remaining 69138 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 161 through 283 or resid 294 through 857 or resid 902)) selection = (chain 'F' and (resid 161 through 857 or resid 902)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.060 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5811 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 9348 Z= 0.333 Angle : 1.216 10.194 12634 Z= 0.682 Chirality : 0.062 0.327 1426 Planarity : 0.008 0.080 1648 Dihedral : 16.868 165.171 3618 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.60 % Favored : 89.32 % Rotamer: Outliers : 0.52 % Allowed : 9.38 % Favored : 90.10 % 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 are not related in a simple way. whole: -5.53 (0.18), residues: 1142 helix: -4.82 (0.11), residues: 401 sheet: -3.29 (0.44), residues: 80 loop : -3.03 (0.20), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 585 TYR 0.016 0.003 TYR A 653 PHE 0.020 0.003 PHE F 687 TRP 0.004 0.001 TRP F 543 HIS 0.016 0.002 HIS A 747 Details of bonding type rmsd covalent geometry : bond 0.00720 ( 9348) covalent geometry : angle 1.21596 (12634) hydrogen bonds : bond 0.32348 ( 147) hydrogen bonds : angle 12.59379 ( 441) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 212 time to evaluate : 0.348 Fit side-chains REVERT: F 199 LYS cc_start: 0.7673 (ttmt) cc_final: 0.7473 (tttm) REVERT: F 298 MET cc_start: 0.4762 (mtm) cc_final: 0.4284 (mtm) REVERT: F 318 GLU cc_start: 0.7347 (tm-30) cc_final: 0.6207 (tt0) REVERT: F 634 MET cc_start: 0.0469 (mmp) cc_final: -0.0560 (mtm) REVERT: F 638 MET cc_start: 0.1410 (mmp) cc_final: 0.0911 (mmt) REVERT: F 737 MET cc_start: 0.2313 (tpt) cc_final: 0.1104 (ppp) REVERT: F 784 LYS cc_start: 0.8138 (mptt) cc_final: 0.7762 (mmtm) REVERT: F 828 PRO cc_start: 0.7942 (Cg_exo) cc_final: 0.7668 (Cg_endo) REVERT: A 184 ASP cc_start: 0.7735 (t0) cc_final: 0.7525 (t70) REVERT: A 533 ASP cc_start: 0.7691 (p0) cc_final: 0.7243 (t0) REVERT: A 562 MET cc_start: 0.5562 (ttm) cc_final: 0.5351 (ttm) REVERT: A 564 GLN cc_start: 0.7440 (tm-30) cc_final: 0.7008 (tm-30) REVERT: A 616 LYS cc_start: 0.8009 (mttt) cc_final: 0.7796 (mtmt) REVERT: A 708 ASP cc_start: 0.7112 (t70) cc_final: 0.6883 (t70) REVERT: A 710 ARG cc_start: 0.8332 (mpt-90) cc_final: 0.7996 (mtt-85) outliers start: 5 outliers final: 2 residues processed: 216 average time/residue: 0.1095 time to fit residues: 31.1405 Evaluate side-chains 129 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 127 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 777 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 0.4980 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 719 ASN F 770 HIS A 174 GLN ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 719 ASN A 794 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4809 r_free = 0.4809 target = 0.263154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.217313 restraints weight = 10921.846| |-----------------------------------------------------------------------------| r_work (start): 0.4385 rms_B_bonded: 3.03 r_work: 0.4056 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9348 Z= 0.146 Angle : 0.723 6.621 12634 Z= 0.363 Chirality : 0.046 0.181 1426 Planarity : 0.006 0.064 1648 Dihedral : 11.439 173.290 1331 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 2.47 % Allowed : 13.30 % Favored : 84.23 % 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 are not related in a simple way. whole: -4.73 (0.20), residues: 1142 helix: -3.85 (0.17), residues: 426 sheet: -3.18 (0.53), residues: 77 loop : -2.64 (0.22), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 305 TYR 0.017 0.001 TYR F 661 PHE 0.009 0.001 PHE A 621 TRP 0.008 0.001 TRP F 543 HIS 0.005 0.001 HIS A 641 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 9348) covalent geometry : angle 0.72264 (12634) hydrogen bonds : bond 0.04470 ( 147) hydrogen bonds : angle 7.07632 ( 441) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: F 242 MET cc_start: 0.3643 (ttm) cc_final: 0.3402 (ttm) REVERT: F 258 ARG cc_start: 0.6488 (mtp-110) cc_final: 0.6043 (mtp180) REVERT: F 276 PHE cc_start: 0.8055 (m-10) cc_final: 0.7690 (m-80) REVERT: F 298 MET cc_start: 0.4574 (mtm) cc_final: 0.4308 (mtm) REVERT: F 318 GLU cc_start: 0.7444 (tm-30) cc_final: 0.6734 (tm-30) REVERT: F 389 LYS cc_start: 0.5458 (mtpt) cc_final: 0.5177 (mtmt) REVERT: F 552 MET cc_start: 0.1358 (tmm) cc_final: -0.1916 (mtt) REVERT: F 634 MET cc_start: -0.0088 (mmp) cc_final: -0.1180 (mtt) REVERT: F 638 MET cc_start: 0.0961 (mmp) cc_final: 0.0394 (mmt) REVERT: F 737 MET cc_start: 0.1789 (tpt) cc_final: 0.0701 (ppp) REVERT: A 164 TYR cc_start: 0.7930 (m-80) cc_final: 0.7284 (m-80) REVERT: A 184 ASP cc_start: 0.7837 (t0) cc_final: 0.7549 (m-30) REVERT: A 395 ASP cc_start: 0.8318 (OUTLIER) cc_final: 0.7761 (m-30) REVERT: A 710 ARG cc_start: 0.8576 (mpt-90) cc_final: 0.8373 (mtt180) REVERT: A 732 LEU cc_start: 0.6677 (mp) cc_final: 0.5860 (mp) outliers start: 24 outliers final: 12 residues processed: 169 average time/residue: 0.1152 time to fit residues: 25.8844 Evaluate side-chains 135 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 580 VAL Chi-restraints excluded: chain F residue 673 VAL Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 642 SER Chi-restraints excluded: chain A residue 693 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 9 optimal weight: 0.3980 chunk 22 optimal weight: 0.0570 chunk 73 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 40 optimal weight: 0.3980 chunk 79 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 GLN A 573 GLN A 641 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4798 r_free = 0.4798 target = 0.261256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.215521 restraints weight = 10834.542| |-----------------------------------------------------------------------------| r_work (start): 0.4367 rms_B_bonded: 3.06 r_work: 0.4048 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9348 Z= 0.122 Angle : 0.653 6.573 12634 Z= 0.323 Chirality : 0.045 0.144 1426 Planarity : 0.005 0.056 1648 Dihedral : 10.725 177.482 1329 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 2.89 % Allowed : 16.49 % Favored : 80.62 % 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 are not related in a simple way. whole: -4.14 (0.22), residues: 1142 helix: -3.26 (0.19), residues: 438 sheet: -3.14 (0.52), residues: 82 loop : -2.28 (0.23), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 561 TYR 0.009 0.001 TYR F 653 PHE 0.008 0.001 PHE A 621 TRP 0.008 0.001 TRP F 543 HIS 0.008 0.001 HIS A 641 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 9348) covalent geometry : angle 0.65315 (12634) hydrogen bonds : bond 0.03403 ( 147) hydrogen bonds : angle 6.10624 ( 441) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 0.300 Fit side-chains REVERT: F 318 GLU cc_start: 0.7532 (tm-30) cc_final: 0.6650 (tm-30) REVERT: F 337 PHE cc_start: 0.6210 (t80) cc_final: 0.5911 (t80) REVERT: F 614 LEU cc_start: 0.8288 (tt) cc_final: 0.8072 (tt) REVERT: F 629 MET cc_start: 0.4330 (tmm) cc_final: 0.3014 (tpt) REVERT: F 634 MET cc_start: -0.0196 (mmp) cc_final: -0.1290 (mtt) REVERT: F 638 MET cc_start: 0.1050 (mmp) cc_final: 0.0423 (mmt) REVERT: F 737 MET cc_start: 0.1518 (tpt) cc_final: 0.0447 (ppp) REVERT: A 184 ASP cc_start: 0.7863 (t0) cc_final: 0.7558 (m-30) REVERT: A 395 ASP cc_start: 0.8260 (OUTLIER) cc_final: 0.7625 (m-30) REVERT: A 710 ARG cc_start: 0.8590 (mpt-90) cc_final: 0.8334 (mtt180) outliers start: 28 outliers final: 14 residues processed: 145 average time/residue: 0.0979 time to fit residues: 19.3670 Evaluate side-chains 129 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 580 VAL Chi-restraints excluded: chain F residue 673 VAL Chi-restraints excluded: chain F residue 771 ILE Chi-restraints excluded: chain F residue 800 LEU Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain A residue 777 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 9 optimal weight: 0.1980 chunk 32 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 1 optimal weight: 0.0030 chunk 72 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 281 HIS A 641 HIS A 719 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4815 r_free = 0.4815 target = 0.263462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.218651 restraints weight = 10949.232| |-----------------------------------------------------------------------------| r_work (start): 0.4391 rms_B_bonded: 3.24 r_work: 0.4060 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9348 Z= 0.117 Angle : 0.637 7.354 12634 Z= 0.310 Chirality : 0.045 0.140 1426 Planarity : 0.004 0.057 1648 Dihedral : 10.176 165.720 1329 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 3.30 % Allowed : 17.63 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.72 (0.23), residues: 1142 helix: -2.88 (0.20), residues: 439 sheet: -3.05 (0.51), residues: 86 loop : -2.02 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 728 TYR 0.013 0.001 TYR F 661 PHE 0.011 0.001 PHE A 621 TRP 0.007 0.001 TRP F 543 HIS 0.008 0.001 HIS A 641 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 9348) covalent geometry : angle 0.63692 (12634) hydrogen bonds : bond 0.02987 ( 147) hydrogen bonds : angle 5.65798 ( 441) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 127 time to evaluate : 0.335 Fit side-chains REVERT: F 614 LEU cc_start: 0.8314 (tt) cc_final: 0.8083 (tt) REVERT: F 629 MET cc_start: 0.4155 (tmm) cc_final: 0.2950 (tpt) REVERT: F 634 MET cc_start: 0.0139 (mmp) cc_final: -0.1434 (mtt) REVERT: F 716 MET cc_start: 0.5807 (tpt) cc_final: 0.4717 (mpp) REVERT: F 737 MET cc_start: 0.1570 (tpt) cc_final: 0.0500 (ppp) REVERT: A 184 ASP cc_start: 0.7970 (t0) cc_final: 0.7675 (m-30) REVERT: A 321 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.7679 (pp30) REVERT: A 395 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7609 (m-30) REVERT: A 563 GLU cc_start: 0.7364 (mt-10) cc_final: 0.6976 (mt-10) REVERT: A 678 GLU cc_start: 0.7447 (mp0) cc_final: 0.7137 (mp0) REVERT: A 710 ARG cc_start: 0.8505 (mpt-90) cc_final: 0.8285 (mtt-85) REVERT: A 728 ARG cc_start: 0.7658 (mtp85) cc_final: 0.7034 (mtp85) outliers start: 32 outliers final: 17 residues processed: 150 average time/residue: 0.1033 time to fit residues: 21.0554 Evaluate side-chains 135 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 242 MET Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 347 ILE Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 580 VAL Chi-restraints excluded: chain F residue 673 VAL Chi-restraints excluded: chain F residue 800 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 642 SER Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 777 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 104 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 17 optimal weight: 8.9990 chunk 108 optimal weight: 9.9990 chunk 83 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 20 optimal weight: 0.2980 chunk 55 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 174 GLN A 641 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4788 r_free = 0.4788 target = 0.259883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.214379 restraints weight = 10790.127| |-----------------------------------------------------------------------------| r_work (start): 0.4372 rms_B_bonded: 3.03 r_work: 0.4029 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9348 Z= 0.133 Angle : 0.643 7.691 12634 Z= 0.310 Chirality : 0.045 0.142 1426 Planarity : 0.004 0.054 1648 Dihedral : 9.767 153.191 1329 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 4.12 % Allowed : 18.14 % Favored : 77.73 % 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 are not related in a simple way. whole: -3.39 (0.23), residues: 1142 helix: -2.57 (0.22), residues: 430 sheet: -3.05 (0.54), residues: 82 loop : -1.86 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 561 TYR 0.012 0.001 TYR F 322 PHE 0.011 0.001 PHE F 276 TRP 0.006 0.001 TRP F 543 HIS 0.008 0.001 HIS A 641 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 9348) covalent geometry : angle 0.64264 (12634) hydrogen bonds : bond 0.03026 ( 147) hydrogen bonds : angle 5.45150 ( 441) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 122 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: F 283 MET cc_start: 0.0531 (ppp) cc_final: -0.0076 (ppp) REVERT: F 322 TYR cc_start: 0.7789 (m-80) cc_final: 0.7428 (m-80) REVERT: F 376 LEU cc_start: 0.4227 (OUTLIER) cc_final: 0.3489 (mt) REVERT: F 552 MET cc_start: 0.0242 (tmm) cc_final: -0.0014 (tmm) REVERT: F 614 LEU cc_start: 0.8192 (tt) cc_final: 0.7912 (tt) REVERT: F 629 MET cc_start: 0.4056 (tmm) cc_final: 0.3118 (tpt) REVERT: F 634 MET cc_start: -0.0153 (mmp) cc_final: -0.1561 (mpp) REVERT: F 716 MET cc_start: 0.5741 (tpt) cc_final: 0.4713 (mpp) REVERT: F 737 MET cc_start: 0.1494 (tpt) cc_final: 0.0454 (ppp) REVERT: A 184 ASP cc_start: 0.8081 (t0) cc_final: 0.7771 (m-30) REVERT: A 321 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.7533 (pp30) REVERT: A 395 ASP cc_start: 0.8269 (OUTLIER) cc_final: 0.7684 (m-30) REVERT: A 645 ARG cc_start: 0.7691 (ttt90) cc_final: 0.7279 (mmt-90) REVERT: A 678 GLU cc_start: 0.7473 (mp0) cc_final: 0.7147 (mp0) REVERT: A 834 LEU cc_start: -0.2525 (OUTLIER) cc_final: -0.2908 (tt) outliers start: 40 outliers final: 23 residues processed: 149 average time/residue: 0.1007 time to fit residues: 20.4625 Evaluate side-chains 146 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 242 MET Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 347 ILE Chi-restraints excluded: chain F residue 376 LEU Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 580 VAL Chi-restraints excluded: chain F residue 673 VAL Chi-restraints excluded: chain F residue 800 LEU Chi-restraints excluded: chain F residue 824 GLN Chi-restraints excluded: chain F residue 846 LEU Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 642 SER Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 834 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 2 optimal weight: 0.1980 chunk 72 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 17 optimal weight: 0.2980 chunk 67 optimal weight: 0.0020 chunk 38 optimal weight: 3.9990 chunk 108 optimal weight: 0.0070 chunk 36 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 overall best weight: 0.2206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 174 GLN A 641 HIS A 719 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4844 r_free = 0.4844 target = 0.266852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.222139 restraints weight = 10850.407| |-----------------------------------------------------------------------------| r_work (start): 0.4389 rms_B_bonded: 2.94 r_work: 0.4099 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9348 Z= 0.096 Angle : 0.603 6.583 12634 Z= 0.290 Chirality : 0.044 0.148 1426 Planarity : 0.004 0.052 1648 Dihedral : 9.285 137.412 1329 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.09 % Allowed : 19.07 % Favored : 77.84 % 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 are not related in a simple way. whole: -3.00 (0.24), residues: 1142 helix: -2.25 (0.23), residues: 430 sheet: -2.85 (0.54), residues: 82 loop : -1.62 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 569 TYR 0.009 0.001 TYR F 322 PHE 0.009 0.001 PHE F 276 TRP 0.008 0.001 TRP F 543 HIS 0.009 0.001 HIS A 641 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 9348) covalent geometry : angle 0.60284 (12634) hydrogen bonds : bond 0.02708 ( 147) hydrogen bonds : angle 5.28036 ( 441) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: F 213 THR cc_start: 0.5376 (m) cc_final: 0.5113 (p) REVERT: F 322 TYR cc_start: 0.7751 (m-80) cc_final: 0.7299 (m-80) REVERT: F 376 LEU cc_start: 0.4175 (OUTLIER) cc_final: 0.3431 (mt) REVERT: F 614 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7775 (tt) REVERT: F 629 MET cc_start: 0.4090 (tmm) cc_final: 0.3302 (tpt) REVERT: F 716 MET cc_start: 0.5623 (tpt) cc_final: 0.4490 (mpp) REVERT: F 737 MET cc_start: 0.1375 (tpt) cc_final: 0.0449 (ppp) REVERT: A 184 ASP cc_start: 0.7871 (t0) cc_final: 0.7632 (m-30) REVERT: A 316 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7754 (mt) REVERT: A 321 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.7433 (pp30) REVERT: A 395 ASP cc_start: 0.8091 (t0) cc_final: 0.7514 (m-30) REVERT: A 678 GLU cc_start: 0.7291 (mp0) cc_final: 0.7035 (mp0) REVERT: A 728 ARG cc_start: 0.7493 (mtp85) cc_final: 0.7196 (mtp85) REVERT: A 834 LEU cc_start: -0.2425 (OUTLIER) cc_final: -0.2770 (tt) outliers start: 30 outliers final: 16 residues processed: 147 average time/residue: 0.1057 time to fit residues: 20.9923 Evaluate side-chains 137 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 376 LEU Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 614 LEU Chi-restraints excluded: chain F residue 673 VAL Chi-restraints excluded: chain F residue 824 GLN Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 642 SER Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 834 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 94 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 chunk 15 optimal weight: 8.9990 chunk 60 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 6 optimal weight: 0.0030 chunk 87 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 chunk 45 optimal weight: 6.9990 chunk 41 optimal weight: 8.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4786 r_free = 0.4786 target = 0.259846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.213172 restraints weight = 10898.485| |-----------------------------------------------------------------------------| r_work (start): 0.4347 rms_B_bonded: 3.18 r_work: 0.4037 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.4474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9348 Z= 0.125 Angle : 0.617 6.316 12634 Z= 0.298 Chirality : 0.045 0.153 1426 Planarity : 0.004 0.055 1648 Dihedral : 9.247 134.838 1329 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 3.09 % Allowed : 19.38 % Favored : 77.53 % 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 are not related in a simple way. whole: -2.83 (0.24), residues: 1142 helix: -2.16 (0.23), residues: 431 sheet: -3.03 (0.54), residues: 77 loop : -1.46 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 258 TYR 0.011 0.001 TYR F 322 PHE 0.017 0.001 PHE F 276 TRP 0.006 0.001 TRP F 543 HIS 0.008 0.001 HIS A 641 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 9348) covalent geometry : angle 0.61651 (12634) hydrogen bonds : bond 0.02887 ( 147) hydrogen bonds : angle 5.13644 ( 441) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: F 213 THR cc_start: 0.5422 (m) cc_final: 0.5144 (p) REVERT: F 322 TYR cc_start: 0.7760 (m-80) cc_final: 0.7175 (m-80) REVERT: F 376 LEU cc_start: 0.4251 (OUTLIER) cc_final: 0.3514 (mt) REVERT: F 614 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7854 (tt) REVERT: F 629 MET cc_start: 0.4080 (tmm) cc_final: 0.3472 (tpt) REVERT: F 716 MET cc_start: 0.5695 (tpt) cc_final: 0.4618 (mpp) REVERT: F 737 MET cc_start: 0.1256 (tpt) cc_final: 0.0453 (ppp) REVERT: F 791 TYR cc_start: 0.8098 (m-80) cc_final: 0.7726 (m-80) REVERT: A 184 ASP cc_start: 0.7988 (t0) cc_final: 0.7723 (m-30) REVERT: A 316 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.7864 (mt) REVERT: A 321 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.7812 (pp30) REVERT: A 395 ASP cc_start: 0.8297 (t0) cc_final: 0.7693 (m-30) REVERT: A 678 GLU cc_start: 0.7427 (mp0) cc_final: 0.7094 (mp0) REVERT: A 728 ARG cc_start: 0.7591 (mtp85) cc_final: 0.7261 (mtp85) REVERT: A 834 LEU cc_start: -0.2402 (OUTLIER) cc_final: -0.2750 (tt) outliers start: 30 outliers final: 19 residues processed: 142 average time/residue: 0.1031 time to fit residues: 19.9920 Evaluate side-chains 141 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 215 ILE Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 376 LEU Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 614 LEU Chi-restraints excluded: chain F residue 621 PHE Chi-restraints excluded: chain F residue 673 VAL Chi-restraints excluded: chain F residue 824 GLN Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 642 SER Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 834 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 48 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 56 optimal weight: 0.0770 chunk 21 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 78 optimal weight: 0.3980 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 297 ASN A 641 HIS A 719 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4781 r_free = 0.4781 target = 0.259598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.213443 restraints weight = 10873.818| |-----------------------------------------------------------------------------| r_work (start): 0.4342 rms_B_bonded: 3.12 r_work: 0.4022 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.4732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9348 Z= 0.124 Angle : 0.616 6.431 12634 Z= 0.297 Chirality : 0.044 0.164 1426 Planarity : 0.004 0.053 1648 Dihedral : 9.171 133.042 1329 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 2.99 % Allowed : 20.72 % Favored : 76.29 % 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 are not related in a simple way. whole: -2.71 (0.24), residues: 1142 helix: -2.00 (0.23), residues: 431 sheet: -2.70 (0.53), residues: 82 loop : -1.45 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 351 TYR 0.010 0.001 TYR F 322 PHE 0.017 0.001 PHE A 621 TRP 0.006 0.001 TRP F 543 HIS 0.008 0.001 HIS A 641 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 9348) covalent geometry : angle 0.61578 (12634) hydrogen bonds : bond 0.02907 ( 147) hydrogen bonds : angle 5.07124 ( 441) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: F 178 ASP cc_start: 0.7852 (m-30) cc_final: 0.7166 (p0) REVERT: F 322 TYR cc_start: 0.7794 (m-80) cc_final: 0.7475 (m-80) REVERT: F 376 LEU cc_start: 0.4403 (OUTLIER) cc_final: 0.3649 (mt) REVERT: F 614 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7850 (tt) REVERT: F 629 MET cc_start: 0.4093 (tmm) cc_final: 0.3584 (tpt) REVERT: F 716 MET cc_start: 0.5809 (tpt) cc_final: 0.4605 (mpp) REVERT: F 737 MET cc_start: 0.1229 (tpt) cc_final: 0.0441 (ppp) REVERT: F 791 TYR cc_start: 0.8000 (m-80) cc_final: 0.7734 (m-80) REVERT: A 184 ASP cc_start: 0.7961 (t0) cc_final: 0.7680 (m-30) REVERT: A 316 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.7948 (mt) REVERT: A 321 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.7669 (pp30) REVERT: A 395 ASP cc_start: 0.8278 (t0) cc_final: 0.7636 (m-30) REVERT: A 552 MET cc_start: 0.3294 (ttp) cc_final: 0.3049 (mmm) REVERT: A 678 GLU cc_start: 0.7426 (mp0) cc_final: 0.7176 (mp0) REVERT: A 728 ARG cc_start: 0.7686 (mtp85) cc_final: 0.7392 (mtp85) REVERT: A 834 LEU cc_start: -0.2539 (OUTLIER) cc_final: -0.2864 (tt) outliers start: 29 outliers final: 20 residues processed: 137 average time/residue: 0.0994 time to fit residues: 18.7720 Evaluate side-chains 137 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 215 ILE Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 376 LEU Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 580 VAL Chi-restraints excluded: chain F residue 614 LEU Chi-restraints excluded: chain F residue 673 VAL Chi-restraints excluded: chain F residue 771 ILE Chi-restraints excluded: chain F residue 824 GLN Chi-restraints excluded: chain F residue 846 LEU Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 642 SER Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 834 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 43 optimal weight: 0.0570 chunk 89 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 17 optimal weight: 0.4980 chunk 79 optimal weight: 0.5980 chunk 113 optimal weight: 9.9990 chunk 12 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 794 HIS A 641 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.259976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.212780 restraints weight = 10847.967| |-----------------------------------------------------------------------------| r_work (start): 0.4336 rms_B_bonded: 2.76 r_work: 0.4057 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.4910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9348 Z= 0.112 Angle : 0.607 6.585 12634 Z= 0.290 Chirality : 0.044 0.160 1426 Planarity : 0.004 0.054 1648 Dihedral : 9.042 133.139 1329 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 2.78 % Allowed : 21.03 % Favored : 76.19 % 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 are not related in a simple way. whole: -2.51 (0.24), residues: 1142 helix: -1.82 (0.23), residues: 427 sheet: -2.47 (0.58), residues: 76 loop : -1.40 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 351 TYR 0.009 0.001 TYR F 319 PHE 0.016 0.001 PHE A 621 TRP 0.007 0.001 TRP F 543 HIS 0.009 0.001 HIS A 641 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 9348) covalent geometry : angle 0.60680 (12634) hydrogen bonds : bond 0.02813 ( 147) hydrogen bonds : angle 5.00297 ( 441) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: F 178 ASP cc_start: 0.7808 (m-30) cc_final: 0.7136 (p0) REVERT: F 322 TYR cc_start: 0.7727 (m-80) cc_final: 0.7303 (m-80) REVERT: F 376 LEU cc_start: 0.4262 (OUTLIER) cc_final: 0.3532 (mt) REVERT: F 629 MET cc_start: 0.4031 (tmm) cc_final: 0.3559 (tpt) REVERT: F 716 MET cc_start: 0.5875 (tpt) cc_final: 0.4741 (mpp) REVERT: F 737 MET cc_start: 0.1264 (tpt) cc_final: 0.0856 (ppp) REVERT: F 791 TYR cc_start: 0.7942 (m-80) cc_final: 0.7722 (m-80) REVERT: A 184 ASP cc_start: 0.7815 (t0) cc_final: 0.7580 (m-30) REVERT: A 316 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7837 (mt) REVERT: A 321 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.7658 (pp30) REVERT: A 395 ASP cc_start: 0.8230 (t0) cc_final: 0.7557 (m-30) REVERT: A 571 ILE cc_start: 0.9325 (mm) cc_final: 0.9107 (mt) REVERT: A 678 GLU cc_start: 0.7483 (mp0) cc_final: 0.7231 (mp0) REVERT: A 728 ARG cc_start: 0.7655 (mtp85) cc_final: 0.7374 (mtp85) REVERT: A 834 LEU cc_start: -0.2679 (OUTLIER) cc_final: -0.2959 (tt) outliers start: 27 outliers final: 18 residues processed: 140 average time/residue: 0.1112 time to fit residues: 21.1913 Evaluate side-chains 138 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 215 ILE Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 376 LEU Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 580 VAL Chi-restraints excluded: chain F residue 673 VAL Chi-restraints excluded: chain F residue 771 ILE Chi-restraints excluded: chain F residue 824 GLN Chi-restraints excluded: chain F residue 846 LEU Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 642 SER Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 834 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 53 optimal weight: 0.0770 chunk 0 optimal weight: 7.9990 chunk 74 optimal weight: 0.6980 chunk 94 optimal weight: 0.0030 chunk 21 optimal weight: 2.9990 chunk 108 optimal weight: 0.0470 chunk 29 optimal weight: 8.9990 chunk 43 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 chunk 105 optimal weight: 0.5980 chunk 114 optimal weight: 0.7980 overall best weight: 0.2846 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 HIS A 719 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.262404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.215754 restraints weight = 10889.778| |-----------------------------------------------------------------------------| r_work (start): 0.4337 rms_B_bonded: 2.56 r_work: 0.4087 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.4087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.5018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9348 Z= 0.098 Angle : 0.607 9.199 12634 Z= 0.289 Chirality : 0.044 0.158 1426 Planarity : 0.004 0.053 1648 Dihedral : 8.884 133.030 1329 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 2.37 % Allowed : 21.34 % Favored : 76.29 % 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 are not related in a simple way. whole: -2.37 (0.24), residues: 1142 helix: -1.66 (0.24), residues: 427 sheet: -2.37 (0.59), residues: 76 loop : -1.35 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 351 TYR 0.009 0.001 TYR F 322 PHE 0.021 0.001 PHE A 621 TRP 0.007 0.001 TRP F 543 HIS 0.009 0.001 HIS A 641 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 9348) covalent geometry : angle 0.60663 (12634) hydrogen bonds : bond 0.02747 ( 147) hydrogen bonds : angle 4.91254 ( 441) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: F 178 ASP cc_start: 0.7733 (m-30) cc_final: 0.7088 (p0) REVERT: F 322 TYR cc_start: 0.7741 (m-80) cc_final: 0.7434 (m-80) REVERT: F 376 LEU cc_start: 0.4368 (OUTLIER) cc_final: 0.3638 (mt) REVERT: F 562 MET cc_start: 0.3704 (mmm) cc_final: 0.3222 (mmt) REVERT: F 629 MET cc_start: 0.4245 (tmm) cc_final: 0.3779 (tpt) REVERT: F 716 MET cc_start: 0.5737 (tpt) cc_final: 0.4622 (mpp) REVERT: F 719 ASN cc_start: 0.5359 (m-40) cc_final: 0.4935 (m-40) REVERT: F 737 MET cc_start: 0.1339 (tpt) cc_final: 0.0895 (ppp) REVERT: A 316 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.7836 (mt) REVERT: A 321 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.7521 (pp30) REVERT: A 395 ASP cc_start: 0.8086 (t0) cc_final: 0.7484 (m-30) REVERT: A 678 GLU cc_start: 0.7354 (mp0) cc_final: 0.7117 (mp0) REVERT: A 728 ARG cc_start: 0.7604 (mtp85) cc_final: 0.7188 (mtp85) REVERT: A 834 LEU cc_start: -0.2573 (OUTLIER) cc_final: -0.2817 (tt) outliers start: 23 outliers final: 16 residues processed: 134 average time/residue: 0.0989 time to fit residues: 18.1153 Evaluate side-chains 137 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 376 LEU Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 673 VAL Chi-restraints excluded: chain F residue 771 ILE Chi-restraints excluded: chain F residue 824 GLN Chi-restraints excluded: chain F residue 846 LEU Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 642 SER Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 834 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 51 optimal weight: 0.3980 chunk 25 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 113 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 43 optimal weight: 0.0060 chunk 83 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 105 optimal weight: 0.3980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.262885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.216399 restraints weight = 10702.354| |-----------------------------------------------------------------------------| r_work (start): 0.4340 rms_B_bonded: 2.44 r_work: 0.4076 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.4076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.5137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9348 Z= 0.109 Angle : 0.622 8.669 12634 Z= 0.292 Chirality : 0.044 0.153 1426 Planarity : 0.004 0.053 1648 Dihedral : 8.849 134.004 1329 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 2.37 % Allowed : 21.24 % Favored : 76.39 % 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 are not related in a simple way. whole: -2.29 (0.24), residues: 1142 helix: -1.57 (0.24), residues: 427 sheet: -2.35 (0.59), residues: 76 loop : -1.31 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 351 TYR 0.011 0.001 TYR F 319 PHE 0.019 0.001 PHE A 621 TRP 0.006 0.001 TRP F 543 HIS 0.009 0.001 HIS A 641 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 9348) covalent geometry : angle 0.62196 (12634) hydrogen bonds : bond 0.02741 ( 147) hydrogen bonds : angle 4.87615 ( 441) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2345.70 seconds wall clock time: 40 minutes 40.42 seconds (2440.42 seconds total)