Starting phenix.real_space_refine on Thu Feb 13 21:44:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6og1_20049/02_2025/6og1_20049.cif Found real_map, /net/cci-nas-00/data/ceres_data/6og1_20049/02_2025/6og1_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6og1_20049/02_2025/6og1_20049.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6og1_20049/02_2025/6og1_20049.map" model { file = "/net/cci-nas-00/data/ceres_data/6og1_20049/02_2025/6og1_20049.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6og1_20049/02_2025/6og1_20049.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.48, per 1000 atoms: 0.60 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: 2.21 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.75 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: 1.85 Time building geometry restraints manager: 2.50 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 21.480 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.310 ------------------------------------------------------------------------------- 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= 0.466 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.004 0.001 TRP F 543 HIS 0.016 0.002 HIS A 747 PHE 0.020 0.003 PHE F 687 TYR 0.016 0.003 TYR A 653 ARG 0.012 0.001 ARG F 585 *********************** 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 : 1.036 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: 0.0468 (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: 0.7524 (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: 0.7113 (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: 0.2662 time to fit residues: 75.4099 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 : 1.011 ------------------------------------------------------------------------------- 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 97 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 0.0670 chunk 90 optimal weight: 1.9990 chunk 34 optimal weight: 0.0370 chunk 54 optimal weight: 3.9990 chunk 67 optimal weight: 0.4980 chunk 104 optimal weight: 0.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- 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 736 HIS A 794 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4826 r_free = 0.4826 target = 0.265174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.219727 restraints weight = 10902.453| |-----------------------------------------------------------------------------| r_work (start): 0.4397 rms_B_bonded: 3.06 r_work: 0.4088 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.2361 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= 0.190 Angle : 0.712 6.722 12634 Z= 0.357 Chirality : 0.046 0.149 1426 Planarity : 0.006 0.064 1648 Dihedral : 11.381 174.492 1331 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 2.47 % Allowed : 13.09 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.71 (0.20), residues: 1142 helix: -3.86 (0.17), residues: 425 sheet: -3.14 (0.54), residues: 77 loop : -2.62 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 543 HIS 0.005 0.001 HIS A 641 PHE 0.011 0.001 PHE A 621 TYR 0.018 0.001 TYR F 661 ARG 0.006 0.000 ARG F 305 *********************** 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 177 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 0.999 Fit side-chains REVERT: F 242 MET cc_start: 0.3615 (ttm) cc_final: 0.3373 (ttm) REVERT: F 258 ARG cc_start: 0.6461 (mtp-110) cc_final: 0.6069 (mtp180) REVERT: F 276 PHE cc_start: 0.7987 (m-10) cc_final: 0.7611 (m-80) REVERT: F 298 MET cc_start: 0.4518 (mtm) cc_final: 0.4283 (mtm) REVERT: F 318 GLU cc_start: 0.7294 (tm-30) cc_final: 0.6543 (tm-30) REVERT: F 552 MET cc_start: 0.1304 (tmm) cc_final: -0.2058 (mtt) REVERT: F 634 MET cc_start: -0.0218 (mmp) cc_final: -0.1233 (mtt) REVERT: F 638 MET cc_start: 0.0979 (mmp) cc_final: 0.0397 (mmt) REVERT: F 737 MET cc_start: 0.1854 (tpt) cc_final: 0.0753 (ppp) REVERT: A 164 TYR cc_start: 0.7844 (m-80) cc_final: 0.7206 (m-80) REVERT: A 184 ASP cc_start: 0.7749 (t0) cc_final: 0.7514 (m-30) REVERT: A 188 ARG cc_start: 0.7882 (ttp80) cc_final: 0.7588 (tpt170) REVERT: A 395 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.7692 (m-30) REVERT: A 564 GLN cc_start: 0.7716 (tm-30) cc_final: 0.7396 (tm-30) outliers start: 24 outliers final: 11 residues processed: 166 average time/residue: 0.2543 time to fit residues: 56.4722 Evaluate side-chains 135 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.989 ------------------------------------------------------------------------------- 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 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 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 693 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 26 optimal weight: 0.0570 chunk 78 optimal weight: 0.2980 chunk 5 optimal weight: 0.1980 chunk 12 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 chunk 24 optimal weight: 0.7980 chunk 112 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 83 optimal weight: 0.0060 overall best weight: 0.2514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 281 HIS 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 = 0.4827 r_free = 0.4827 target = 0.264726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.220015 restraints weight = 11027.809| |-----------------------------------------------------------------------------| r_work (start): 0.4404 rms_B_bonded: 3.09 r_work: 0.4087 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9348 Z= 0.158 Angle : 0.638 6.583 12634 Z= 0.315 Chirality : 0.045 0.137 1426 Planarity : 0.004 0.056 1648 Dihedral : 10.524 173.775 1329 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 2.68 % Allowed : 16.29 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.12 (0.21), residues: 1142 helix: -3.25 (0.19), residues: 436 sheet: -2.81 (0.52), residues: 86 loop : -2.31 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 543 HIS 0.008 0.001 HIS A 641 PHE 0.007 0.001 PHE A 621 TYR 0.008 0.001 TYR F 653 ARG 0.014 0.000 ARG A 561 *********************** 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 157 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.940 Fit side-chains REVERT: F 242 MET cc_start: 0.3646 (ttm) cc_final: 0.3392 (ttm) REVERT: F 276 PHE cc_start: 0.8028 (m-10) cc_final: 0.7583 (m-80) REVERT: F 298 MET cc_start: 0.4440 (mtm) cc_final: 0.4210 (mtm) REVERT: F 318 GLU cc_start: 0.7469 (tm-30) cc_final: 0.6522 (tm-30) REVERT: F 337 PHE cc_start: 0.5993 (t80) cc_final: 0.5782 (t80) REVERT: F 376 LEU cc_start: 0.3761 (OUTLIER) cc_final: 0.2710 (mt) REVERT: F 552 MET cc_start: 0.1441 (tmm) cc_final: -0.1594 (mtm) REVERT: F 614 LEU cc_start: 0.8230 (tt) cc_final: 0.8011 (tt) REVERT: F 629 MET cc_start: 0.4326 (tmm) cc_final: 0.3045 (tpt) REVERT: F 634 MET cc_start: -0.0312 (mmp) cc_final: -0.1355 (mtt) REVERT: F 638 MET cc_start: 0.1081 (mmp) cc_final: 0.0445 (mmt) REVERT: F 737 MET cc_start: 0.1607 (tpt) cc_final: 0.0450 (ppp) REVERT: A 164 TYR cc_start: 0.7813 (m-80) cc_final: 0.7150 (m-80) REVERT: A 184 ASP cc_start: 0.7845 (t0) cc_final: 0.7591 (m-30) REVERT: A 188 ARG cc_start: 0.7964 (ttp80) cc_final: 0.7588 (tpt170) REVERT: A 395 ASP cc_start: 0.8214 (OUTLIER) cc_final: 0.7567 (m-30) REVERT: A 564 GLN cc_start: 0.7890 (tm-30) cc_final: 0.7605 (tm-30) REVERT: A 732 LEU cc_start: 0.6550 (mp) cc_final: 0.6140 (mt) outliers start: 26 outliers final: 12 residues processed: 149 average time/residue: 0.2531 time to fit residues: 50.2678 Evaluate side-chains 135 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 580 VAL Chi-restraints excluded: chain F residue 673 VAL Chi-restraints excluded: chain F residue 771 ILE 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 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 54 optimal weight: 0.1980 chunk 74 optimal weight: 1.9990 chunk 35 optimal weight: 0.0370 chunk 88 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 overall best weight: 0.6260 ------------------------------------------------------------------------------- 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 A 719 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4818 r_free = 0.4818 target = 0.263765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.218671 restraints weight = 10794.675| |-----------------------------------------------------------------------------| r_work (start): 0.4396 rms_B_bonded: 3.13 r_work: 0.4054 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.3506 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= 0.191 Angle : 0.630 6.598 12634 Z= 0.309 Chirality : 0.045 0.144 1426 Planarity : 0.004 0.059 1648 Dihedral : 10.032 162.450 1329 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.20 % Allowed : 17.53 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.66 (0.22), residues: 1142 helix: -2.83 (0.21), residues: 433 sheet: -2.97 (0.51), residues: 86 loop : -2.00 (0.24), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 543 HIS 0.008 0.001 HIS A 641 PHE 0.009 0.001 PHE A 621 TYR 0.013 0.001 TYR F 661 ARG 0.009 0.000 ARG A 561 *********************** 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 164 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 0.927 Fit side-chains REVERT: F 258 ARG cc_start: 0.6537 (mtp-110) cc_final: 0.6194 (mtp-110) REVERT: F 614 LEU cc_start: 0.8345 (tt) cc_final: 0.8110 (tt) REVERT: F 629 MET cc_start: 0.4013 (tmm) cc_final: 0.2890 (tpt) REVERT: F 634 MET cc_start: 0.0096 (mmp) cc_final: -0.1447 (mtt) REVERT: F 716 MET cc_start: 0.5493 (tpt) cc_final: 0.4647 (mpp) REVERT: F 737 MET cc_start: 0.1440 (tpt) cc_final: 0.0348 (ppp) REVERT: A 164 TYR cc_start: 0.7916 (m-80) cc_final: 0.7240 (m-80) REVERT: A 184 ASP cc_start: 0.7938 (t0) cc_final: 0.7635 (m-30) REVERT: A 395 ASP cc_start: 0.8236 (OUTLIER) cc_final: 0.7632 (m-30) REVERT: A 564 GLN cc_start: 0.8011 (tm-30) cc_final: 0.7492 (tm-30) REVERT: A 667 ARG cc_start: 0.8008 (mtm110) cc_final: 0.7627 (mtm110) REVERT: A 728 ARG cc_start: 0.7673 (mtp85) cc_final: 0.7150 (mtp85) outliers start: 31 outliers final: 15 residues processed: 156 average time/residue: 0.2339 time to fit residues: 49.7504 Evaluate side-chains 135 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 1.097 ------------------------------------------------------------------------------- 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 280 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 815 ARG 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 642 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 63 optimal weight: 0.0170 chunk 43 optimal weight: 10.0000 chunk 74 optimal weight: 0.3980 chunk 51 optimal weight: 0.6980 chunk 105 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- 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 641 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4821 r_free = 0.4821 target = 0.264042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.217957 restraints weight = 10891.859| |-----------------------------------------------------------------------------| r_work (start): 0.4393 rms_B_bonded: 3.22 r_work: 0.4052 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9348 Z= 0.179 Angle : 0.623 7.437 12634 Z= 0.301 Chirality : 0.044 0.155 1426 Planarity : 0.004 0.055 1648 Dihedral : 9.610 149.656 1329 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 3.20 % Allowed : 18.25 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.23), residues: 1142 helix: -2.60 (0.21), residues: 440 sheet: -2.96 (0.51), residues: 86 loop : -1.80 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 543 HIS 0.008 0.001 HIS A 641 PHE 0.011 0.001 PHE F 276 TYR 0.010 0.001 TYR F 661 ARG 0.009 0.000 ARG A 561 *********************** 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 159 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 242 MET cc_start: 0.3607 (ttm) cc_final: 0.3362 (ttm) REVERT: F 283 MET cc_start: 0.0270 (ppp) cc_final: -0.0059 (ppp) REVERT: F 533 ASP cc_start: 0.4869 (t70) cc_final: 0.4381 (p0) REVERT: F 552 MET cc_start: 0.0349 (tmm) cc_final: 0.0144 (tmm) REVERT: F 614 LEU cc_start: 0.8223 (tt) cc_final: 0.7948 (tt) REVERT: F 629 MET cc_start: 0.4004 (tmm) cc_final: 0.3124 (tpt) REVERT: F 634 MET cc_start: -0.0213 (mmp) cc_final: -0.1539 (mpp) REVERT: F 716 MET cc_start: 0.5600 (tpt) cc_final: 0.4615 (mpp) REVERT: F 737 MET cc_start: 0.1417 (tpt) cc_final: 0.0457 (ppp) REVERT: F 763 PHE cc_start: 0.1886 (OUTLIER) cc_final: 0.1199 (m-80) REVERT: A 184 ASP cc_start: 0.7943 (t0) cc_final: 0.7670 (m-30) REVERT: A 321 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.7649 (pp30) REVERT: A 395 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.7614 (m-30) REVERT: A 563 GLU cc_start: 0.7415 (mt-10) cc_final: 0.6970 (mt-10) REVERT: A 667 ARG cc_start: 0.8056 (mtm110) cc_final: 0.7708 (mtm110) REVERT: A 678 GLU cc_start: 0.7420 (mp0) cc_final: 0.7112 (mp0) REVERT: A 834 LEU cc_start: -0.2548 (OUTLIER) cc_final: -0.2939 (tt) outliers start: 31 outliers final: 18 residues processed: 150 average time/residue: 0.2444 time to fit residues: 49.2179 Evaluate side-chains 141 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 203 VAL 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 763 PHE Chi-restraints excluded: chain F residue 815 ARG 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 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 29 optimal weight: 7.9990 chunk 114 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 65 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 40 optimal weight: 0.1980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4793 r_free = 0.4793 target = 0.260807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.214927 restraints weight = 10656.618| |-----------------------------------------------------------------------------| r_work (start): 0.4360 rms_B_bonded: 3.14 r_work: 0.4034 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9348 Z= 0.194 Angle : 0.622 6.936 12634 Z= 0.300 Chirality : 0.045 0.142 1426 Planarity : 0.004 0.054 1648 Dihedral : 9.381 140.729 1329 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 3.71 % Allowed : 19.28 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.23), residues: 1142 helix: -2.37 (0.22), residues: 440 sheet: -2.90 (0.52), residues: 82 loop : -1.67 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 543 HIS 0.008 0.001 HIS A 641 PHE 0.012 0.001 PHE F 276 TYR 0.008 0.001 TYR A 322 ARG 0.007 0.000 ARG F 320 *********************** 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 167 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 131 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 322 TYR cc_start: 0.7799 (m-80) cc_final: 0.7404 (m-80) REVERT: F 376 LEU cc_start: 0.4206 (OUTLIER) cc_final: 0.3203 (mt) REVERT: F 533 ASP cc_start: 0.5080 (OUTLIER) cc_final: 0.4424 (p0) REVERT: F 614 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7860 (tt) REVERT: F 629 MET cc_start: 0.4230 (tmm) cc_final: 0.3376 (tpt) REVERT: F 716 MET cc_start: 0.5784 (tpt) cc_final: 0.4673 (mpp) REVERT: F 737 MET cc_start: 0.1309 (tpt) cc_final: 0.0418 (ppp) REVERT: A 184 ASP cc_start: 0.8093 (t0) cc_final: 0.7785 (m-30) REVERT: A 321 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.7918 (pp30) REVERT: A 395 ASP cc_start: 0.8314 (OUTLIER) cc_final: 0.7708 (m-30) REVERT: A 678 GLU cc_start: 0.7418 (mp0) cc_final: 0.7105 (mp0) REVERT: A 728 ARG cc_start: 0.7532 (mtp85) cc_final: 0.7147 (mtp85) REVERT: A 834 LEU cc_start: -0.2443 (OUTLIER) cc_final: -0.2772 (tt) outliers start: 36 outliers final: 19 residues processed: 156 average time/residue: 0.2507 time to fit residues: 52.5062 Evaluate side-chains 149 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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 376 LEU Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 533 ASP 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 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 308 LEU 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 693 VAL Chi-restraints excluded: chain A residue 723 ASP 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 90 optimal weight: 0.9990 chunk 44 optimal weight: 20.0000 chunk 109 optimal weight: 10.0000 chunk 9 optimal weight: 0.0270 chunk 25 optimal weight: 3.9990 chunk 65 optimal weight: 0.4980 chunk 66 optimal weight: 0.5980 chunk 91 optimal weight: 0.1980 chunk 24 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 overall best weight: 0.4038 ------------------------------------------------------------------------------- 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 = 0.4805 r_free = 0.4805 target = 0.262197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.216469 restraints weight = 10798.203| |-----------------------------------------------------------------------------| r_work (start): 0.4369 rms_B_bonded: 3.24 r_work: 0.4048 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.4407 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= 0.167 Angle : 0.605 6.747 12634 Z= 0.290 Chirality : 0.044 0.133 1426 Planarity : 0.004 0.053 1648 Dihedral : 9.165 133.304 1329 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.20 % Allowed : 19.38 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.24), residues: 1142 helix: -2.11 (0.22), residues: 437 sheet: -3.05 (0.55), residues: 70 loop : -1.51 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 543 HIS 0.008 0.001 HIS A 641 PHE 0.017 0.001 PHE A 621 TYR 0.009 0.001 TYR F 791 ARG 0.008 0.000 ARG A 645 *********************** 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 157 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 178 ASP cc_start: 0.7945 (m-30) cc_final: 0.7241 (p0) REVERT: F 322 TYR cc_start: 0.7698 (m-80) cc_final: 0.7352 (m-80) REVERT: F 376 LEU cc_start: 0.4405 (OUTLIER) cc_final: 0.3365 (mt) REVERT: F 569 ARG cc_start: 0.6026 (ptt90) cc_final: 0.4376 (ptm-80) REVERT: F 614 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7901 (tt) REVERT: F 629 MET cc_start: 0.3959 (tmm) cc_final: 0.3433 (tpt) REVERT: F 716 MET cc_start: 0.5550 (tpt) cc_final: 0.4558 (mpp) REVERT: F 737 MET cc_start: 0.1280 (tpt) cc_final: 0.0440 (ppp) REVERT: F 791 TYR cc_start: 0.7984 (m-80) cc_final: 0.7656 (m-80) REVERT: A 184 ASP cc_start: 0.7970 (t0) cc_final: 0.7713 (m-30) REVERT: A 316 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8191 (mt) REVERT: A 321 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7460 (pp30) REVERT: A 395 ASP cc_start: 0.8196 (t0) cc_final: 0.7591 (m-30) REVERT: A 667 ARG cc_start: 0.8214 (mtm110) cc_final: 0.7844 (mtm110) REVERT: A 678 GLU cc_start: 0.7348 (mp0) cc_final: 0.7105 (mp0) REVERT: A 728 ARG cc_start: 0.7688 (mtp85) cc_final: 0.7356 (mtp85) REVERT: A 834 LEU cc_start: -0.2374 (OUTLIER) cc_final: -0.2743 (tt) outliers start: 31 outliers final: 19 residues processed: 148 average time/residue: 0.2515 time to fit residues: 49.8161 Evaluate side-chains 144 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.989 ------------------------------------------------------------------------------- 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 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 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 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 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 110 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 65 optimal weight: 0.2980 chunk 55 optimal weight: 0.0170 chunk 22 optimal weight: 0.7980 chunk 60 optimal weight: 0.0570 chunk 106 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.3736 ------------------------------------------------------------------------------- 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 A 719 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4806 r_free = 0.4806 target = 0.262416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.217566 restraints weight = 10909.194| |-----------------------------------------------------------------------------| r_work (start): 0.4381 rms_B_bonded: 3.08 r_work: 0.4055 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.4640 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= 0.157 Angle : 0.610 10.041 12634 Z= 0.290 Chirality : 0.044 0.156 1426 Planarity : 0.004 0.052 1648 Dihedral : 9.011 128.468 1329 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 2.89 % Allowed : 20.00 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.24), residues: 1142 helix: -1.89 (0.23), residues: 435 sheet: -2.74 (0.56), residues: 70 loop : -1.48 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 543 HIS 0.008 0.001 HIS A 641 PHE 0.019 0.001 PHE A 621 TYR 0.008 0.001 TYR F 791 ARG 0.006 0.000 ARG A 645 *********************** 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 156 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 178 ASP cc_start: 0.7962 (m-30) cc_final: 0.7208 (p0) REVERT: F 322 TYR cc_start: 0.7706 (m-80) cc_final: 0.7203 (m-80) REVERT: F 376 LEU cc_start: 0.4378 (OUTLIER) cc_final: 0.3353 (mt) REVERT: F 629 MET cc_start: 0.4034 (tmm) cc_final: 0.3524 (tpt) REVERT: F 716 MET cc_start: 0.5557 (tpt) cc_final: 0.4548 (mpp) REVERT: F 737 MET cc_start: 0.1266 (tpt) cc_final: 0.0442 (ppp) REVERT: F 791 TYR cc_start: 0.7996 (m-80) cc_final: 0.7706 (m-80) REVERT: A 184 ASP cc_start: 0.7976 (t0) cc_final: 0.7713 (m-30) REVERT: A 321 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7652 (pp30) REVERT: A 678 GLU cc_start: 0.7478 (mp0) cc_final: 0.7202 (mp0) REVERT: A 728 ARG cc_start: 0.7739 (mtp85) cc_final: 0.7272 (mtp85) REVERT: A 834 LEU cc_start: -0.2545 (OUTLIER) cc_final: -0.2888 (tt) outliers start: 28 outliers final: 18 residues processed: 147 average time/residue: 0.2450 time to fit residues: 48.5589 Evaluate side-chains 142 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.964 ------------------------------------------------------------------------------- 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 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 744 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 48 optimal weight: 5.9990 chunk 100 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 54 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 106 optimal weight: 0.0870 overall best weight: 0.7160 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4793 r_free = 0.4793 target = 0.261136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.213034 restraints weight = 10861.606| |-----------------------------------------------------------------------------| r_work (start): 0.4339 rms_B_bonded: 2.73 r_work: 0.4047 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.4776 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= 0.197 Angle : 0.627 8.730 12634 Z= 0.298 Chirality : 0.045 0.174 1426 Planarity : 0.004 0.052 1648 Dihedral : 9.066 131.652 1329 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 2.37 % Allowed : 20.82 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.24), residues: 1142 helix: -1.85 (0.23), residues: 439 sheet: -2.63 (0.58), residues: 68 loop : -1.41 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 543 HIS 0.009 0.001 HIS A 641 PHE 0.014 0.001 PHE A 621 TYR 0.009 0.001 TYR A 322 ARG 0.008 0.000 ARG A 561 *********************** 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 145 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 178 ASP cc_start: 0.7968 (m-30) cc_final: 0.7216 (p0) REVERT: F 322 TYR cc_start: 0.7794 (m-80) cc_final: 0.7299 (m-80) REVERT: F 376 LEU cc_start: 0.4400 (OUTLIER) cc_final: 0.3338 (mt) REVERT: F 629 MET cc_start: 0.3979 (tmm) cc_final: 0.3557 (tpt) REVERT: F 716 MET cc_start: 0.5678 (tpt) cc_final: 0.4614 (mpp) REVERT: F 737 MET cc_start: 0.1182 (tpt) cc_final: 0.0772 (ppp) REVERT: F 791 TYR cc_start: 0.8052 (m-80) cc_final: 0.7794 (m-80) REVERT: A 184 ASP cc_start: 0.7955 (t0) cc_final: 0.7687 (m-30) REVERT: A 321 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.7787 (pp30) REVERT: A 395 ASP cc_start: 0.8285 (t0) cc_final: 0.7664 (m-30) REVERT: A 564 GLN cc_start: 0.8062 (tm-30) cc_final: 0.7433 (tm-30) REVERT: A 678 GLU cc_start: 0.7401 (mp0) cc_final: 0.7113 (mp0) REVERT: A 737 MET cc_start: 0.7493 (mmm) cc_final: 0.6582 (mtt) REVERT: A 834 LEU cc_start: -0.2600 (OUTLIER) cc_final: -0.2910 (tt) outliers start: 23 outliers final: 18 residues processed: 141 average time/residue: 0.2729 time to fit residues: 52.0726 Evaluate side-chains 141 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.959 ------------------------------------------------------------------------------- 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 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 744 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 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 723 ASP 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 74 optimal weight: 0.5980 chunk 93 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 103 optimal weight: 0.0970 chunk 3 optimal weight: 0.9980 chunk 60 optimal weight: 0.0980 chunk 18 optimal weight: 0.3980 chunk 82 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 overall best weight: 0.3578 ------------------------------------------------------------------------------- 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 281 HIS A 567 HIS A 582 ASN A 641 HIS A 719 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4903 r_free = 0.4903 target = 0.269238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.224160 restraints weight = 11320.504| |-----------------------------------------------------------------------------| r_work (start): 0.4485 rms_B_bonded: 2.82 r_work: 0.4182 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.4182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.4977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 9348 Z= 0.166 Angle : 0.614 8.769 12634 Z= 0.291 Chirality : 0.044 0.162 1426 Planarity : 0.004 0.052 1648 Dihedral : 8.882 132.006 1329 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 2.27 % Allowed : 21.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.24), residues: 1142 helix: -1.66 (0.24), residues: 434 sheet: -2.66 (0.56), residues: 70 loop : -1.36 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 543 HIS 0.009 0.001 HIS A 641 PHE 0.026 0.001 PHE A 621 TYR 0.010 0.001 TYR F 319 ARG 0.007 0.000 ARG F 569 ********************** 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 149 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 178 ASP cc_start: 0.8015 (m-30) cc_final: 0.7271 (p0) REVERT: F 322 TYR cc_start: 0.7795 (m-80) cc_final: 0.7330 (m-80) REVERT: F 376 LEU cc_start: 0.4430 (OUTLIER) cc_final: 0.3373 (mt) REVERT: F 629 MET cc_start: 0.3912 (tmm) cc_final: 0.3548 (tpt) REVERT: F 716 MET cc_start: 0.5663 (tpt) cc_final: 0.4602 (mpp) REVERT: F 737 MET cc_start: 0.1206 (tpt) cc_final: 0.0820 (ppp) REVERT: A 321 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7673 (pp30) REVERT: A 395 ASP cc_start: 0.8118 (t0) cc_final: 0.7490 (m-30) REVERT: A 564 GLN cc_start: 0.7808 (tm-30) cc_final: 0.7496 (mm-40) REVERT: A 678 GLU cc_start: 0.7399 (mp0) cc_final: 0.7164 (mp0) REVERT: A 737 MET cc_start: 0.7471 (mmm) cc_final: 0.6634 (mtt) REVERT: A 834 LEU cc_start: -0.2661 (OUTLIER) cc_final: -0.2935 (tt) outliers start: 22 outliers final: 16 residues processed: 144 average time/residue: 0.2478 time to fit residues: 47.9368 Evaluate side-chains 141 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.974 ------------------------------------------------------------------------------- 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 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 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 98 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 104 optimal weight: 0.4980 chunk 3 optimal weight: 0.8980 chunk 109 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4882 r_free = 0.4882 target = 0.266714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.221457 restraints weight = 11200.955| |-----------------------------------------------------------------------------| r_work (start): 0.4445 rms_B_bonded: 2.68 r_work: 0.4134 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.5124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9348 Z= 0.213 Angle : 0.645 8.485 12634 Z= 0.305 Chirality : 0.045 0.169 1426 Planarity : 0.004 0.052 1648 Dihedral : 8.994 134.832 1329 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 2.16 % Allowed : 21.34 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.24), residues: 1142 helix: -1.62 (0.23), residues: 437 sheet: -2.53 (0.58), residues: 68 loop : -1.36 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 543 HIS 0.009 0.001 HIS A 641 PHE 0.027 0.001 PHE A 621 TYR 0.010 0.001 TYR A 319 ARG 0.008 0.001 ARG A 561 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4783.47 seconds wall clock time: 85 minutes 12.62 seconds (5112.62 seconds total)