Starting phenix.real_space_refine on Tue Mar 3 22:44:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ekm_31170/03_2026/7ekm_31170.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ekm_31170/03_2026/7ekm_31170.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ekm_31170/03_2026/7ekm_31170.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ekm_31170/03_2026/7ekm_31170.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ekm_31170/03_2026/7ekm_31170.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ekm_31170/03_2026/7ekm_31170.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 5870 2.51 5 N 1574 2.21 5 O 1646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9124 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4562 Classifications: {'peptide': 581} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 12, 'TRANS': 568} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1, 'HIS:plan': 1, 'ARG:plan': 2, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Restraints were copied for chains: B Time building chain proxies: 3.60, per 1000 atoms: 0.39 Number of scatterers: 9124 At special positions: 0 Unit cell: (116.1, 70.52, 137.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 34 16.00 O 1646 8.00 N 1574 7.00 C 5870 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.49 Conformation dependent library (CDL) restraints added in 279.5 milliseconds 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2140 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 4 sheets defined 49.4% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 249 through 253 Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 274 through 278 removed outlier: 3.656A pdb=" N LEU A 278 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 295 Processing helix chain 'A' and resid 298 through 302 Processing helix chain 'A' and resid 306 through 316 removed outlier: 3.619A pdb=" N PHE A 311 " --> pdb=" O THR A 307 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU A 312 " --> pdb=" O SER A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 339 Processing helix chain 'A' and resid 340 through 345 removed outlier: 3.549A pdb=" N ARG A 344 " --> pdb=" O PHE A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 375 removed outlier: 3.533A pdb=" N ASP A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 390 removed outlier: 3.904A pdb=" N VAL A 380 " --> pdb=" O GLY A 376 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR A 381 " --> pdb=" O THR A 377 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLY A 382 " --> pdb=" O SER A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 397 Processing helix chain 'A' and resid 398 through 402 removed outlier: 3.517A pdb=" N ILE A 402 " --> pdb=" O ILE A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 433 removed outlier: 4.125A pdb=" N THR A 428 " --> pdb=" O TYR A 424 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL A 430 " --> pdb=" O THR A 426 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N VAL A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 440 removed outlier: 3.609A pdb=" N ARG A 439 " --> pdb=" O ARG A 435 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG A 440 " --> pdb=" O THR A 436 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 435 through 440' Processing helix chain 'A' and resid 442 through 454 removed outlier: 3.931A pdb=" N ASN A 447 " --> pdb=" O ASN A 443 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ARG A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA A 453 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL A 454 " --> pdb=" O ARG A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 464 removed outlier: 3.989A pdb=" N VAL A 463 " --> pdb=" O ASN A 459 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS A 464 " --> pdb=" O PHE A 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 459 through 464' Processing helix chain 'A' and resid 482 through 486 removed outlier: 3.716A pdb=" N GLY A 485 " --> pdb=" O LYS A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 499 Processing helix chain 'A' and resid 500 through 506 removed outlier: 3.996A pdb=" N ILE A 505 " --> pdb=" O GLN A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 522 Processing helix chain 'A' and resid 530 through 542 removed outlier: 3.550A pdb=" N GLY A 534 " --> pdb=" O TYR A 530 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TYR A 536 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 537 " --> pdb=" O PHE A 533 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE A 538 " --> pdb=" O GLY A 534 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN A 539 " --> pdb=" O THR A 535 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 540 " --> pdb=" O TYR A 536 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N MET A 542 " --> pdb=" O ILE A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 545 No H-bonds generated for 'chain 'A' and resid 543 through 545' Processing helix chain 'A' and resid 549 through 560 removed outlier: 3.649A pdb=" N GLN A 555 " --> pdb=" O TYR A 551 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASN A 557 " --> pdb=" O MET A 553 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE A 558 " --> pdb=" O ILE A 554 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE A 559 " --> pdb=" O GLN A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 566 removed outlier: 3.626A pdb=" N PHE A 565 " --> pdb=" O MET A 561 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP A 566 " --> pdb=" O GLU A 562 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 561 through 566' Processing helix chain 'A' and resid 628 through 636 removed outlier: 3.628A pdb=" N ILE A 632 " --> pdb=" O GLY A 628 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU A 633 " --> pdb=" O LYS A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 663 removed outlier: 3.555A pdb=" N ARG A 663 " --> pdb=" O GLN A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 685 removed outlier: 3.546A pdb=" N ARG A 685 " --> pdb=" O ALA A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 700 removed outlier: 3.515A pdb=" N ALA A 698 " --> pdb=" O ASP A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 710 removed outlier: 3.947A pdb=" N MET A 710 " --> pdb=" O HIS A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 718 removed outlier: 3.784A pdb=" N ARG A 717 " --> pdb=" O GLU A 714 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR A 718 " --> pdb=" O GLY A 715 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 714 through 718' Processing helix chain 'A' and resid 721 through 725 removed outlier: 3.722A pdb=" N GLY A 724 " --> pdb=" O GLY A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 744 removed outlier: 3.708A pdb=" N VAL A 735 " --> pdb=" O GLU A 731 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA A 736 " --> pdb=" O LYS A 732 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR A 740 " --> pdb=" O ALA A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 770 removed outlier: 3.853A pdb=" N SER A 768 " --> pdb=" O ALA A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 813 removed outlier: 3.514A pdb=" N SER A 813 " --> pdb=" O GLU A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 827 removed outlier: 3.761A pdb=" N GLN A 825 " --> pdb=" O MET A 821 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY A 827 " --> pdb=" O GLN A 823 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 253 Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 274 through 278 removed outlier: 3.655A pdb=" N LEU B 278 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 295 Processing helix chain 'B' and resid 298 through 302 Processing helix chain 'B' and resid 306 through 316 removed outlier: 3.619A pdb=" N PHE B 311 " --> pdb=" O THR B 307 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU B 312 " --> pdb=" O SER B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 339 Processing helix chain 'B' and resid 340 through 345 removed outlier: 3.549A pdb=" N ARG B 344 " --> pdb=" O PHE B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 375 removed outlier: 3.533A pdb=" N ASP B 374 " --> pdb=" O LEU B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 390 removed outlier: 3.903A pdb=" N VAL B 380 " --> pdb=" O GLY B 376 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR B 381 " --> pdb=" O THR B 377 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLY B 382 " --> pdb=" O SER B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 397 Processing helix chain 'B' and resid 398 through 402 removed outlier: 3.516A pdb=" N ILE B 402 " --> pdb=" O ILE B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 433 removed outlier: 4.123A pdb=" N THR B 428 " --> pdb=" O TYR B 424 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL B 430 " --> pdb=" O THR B 426 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N VAL B 431 " --> pdb=" O LEU B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 440 removed outlier: 3.609A pdb=" N ARG B 439 " --> pdb=" O ARG B 435 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG B 440 " --> pdb=" O THR B 436 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 435 through 440' Processing helix chain 'B' and resid 442 through 454 removed outlier: 3.931A pdb=" N ASN B 447 " --> pdb=" O ASN B 443 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ARG B 452 " --> pdb=" O ALA B 448 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA B 453 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL B 454 " --> pdb=" O ARG B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 464 removed outlier: 3.988A pdb=" N VAL B 463 " --> pdb=" O ASN B 459 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS B 464 " --> pdb=" O PHE B 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 459 through 464' Processing helix chain 'B' and resid 482 through 486 removed outlier: 3.716A pdb=" N GLY B 485 " --> pdb=" O LYS B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 499 Processing helix chain 'B' and resid 500 through 506 removed outlier: 3.996A pdb=" N ILE B 505 " --> pdb=" O GLN B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 522 Processing helix chain 'B' and resid 530 through 542 removed outlier: 3.551A pdb=" N GLY B 534 " --> pdb=" O TYR B 530 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR B 536 " --> pdb=" O LEU B 532 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B 537 " --> pdb=" O PHE B 533 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE B 538 " --> pdb=" O GLY B 534 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN B 539 " --> pdb=" O THR B 535 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU B 540 " --> pdb=" O TYR B 536 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N MET B 542 " --> pdb=" O ILE B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 545 No H-bonds generated for 'chain 'B' and resid 543 through 545' Processing helix chain 'B' and resid 549 through 560 removed outlier: 3.649A pdb=" N GLN B 555 " --> pdb=" O TYR B 551 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASN B 557 " --> pdb=" O MET B 553 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE B 558 " --> pdb=" O ILE B 554 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE B 559 " --> pdb=" O GLN B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 566 removed outlier: 3.626A pdb=" N PHE B 565 " --> pdb=" O MET B 561 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP B 566 " --> pdb=" O GLU B 562 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 561 through 566' Processing helix chain 'B' and resid 628 through 636 removed outlier: 3.628A pdb=" N ILE B 632 " --> pdb=" O GLY B 628 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU B 633 " --> pdb=" O LYS B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 658 through 663 removed outlier: 3.555A pdb=" N ARG B 663 " --> pdb=" O GLN B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 685 removed outlier: 3.546A pdb=" N ARG B 685 " --> pdb=" O ALA B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 700 removed outlier: 3.515A pdb=" N ALA B 698 " --> pdb=" O ASP B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 710 removed outlier: 3.947A pdb=" N MET B 710 " --> pdb=" O HIS B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 718 removed outlier: 3.784A pdb=" N ARG B 717 " --> pdb=" O GLU B 714 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR B 718 " --> pdb=" O GLY B 715 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 714 through 718' Processing helix chain 'B' and resid 721 through 725 removed outlier: 3.722A pdb=" N GLY B 724 " --> pdb=" O GLY B 721 " (cutoff:3.500A) Processing helix chain 'B' and resid 730 through 744 removed outlier: 3.707A pdb=" N VAL B 735 " --> pdb=" O GLU B 731 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA B 736 " --> pdb=" O LYS B 732 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR B 740 " --> pdb=" O ALA B 736 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 770 removed outlier: 3.853A pdb=" N SER B 768 " --> pdb=" O ALA B 764 " (cutoff:3.500A) Processing helix chain 'B' and resid 808 through 813 removed outlier: 3.513A pdb=" N SER B 813 " --> pdb=" O GLU B 809 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 827 removed outlier: 3.761A pdb=" N GLN B 825 " --> pdb=" O MET B 821 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY B 827 " --> pdb=" O GLN B 823 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 606 through 613 removed outlier: 7.087A pdb=" N GLN A 607 " --> pdb=" O HIS A 596 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N HIS A 596 " --> pdb=" O GLN A 607 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N VAL A 609 " --> pdb=" O ASN A 594 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE A 611 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL A 595 " --> pdb=" O SER A 644 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N SER A 644 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 666 through 669 removed outlier: 5.924A pdb=" N LEU A 619 " --> pdb=" O VAL A 780 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N THR A 618 " --> pdb=" O GLN A 793 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N LEU A 795 " --> pdb=" O THR A 618 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA A 620 " --> pdb=" O LEU A 795 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N ILE A 797 " --> pdb=" O ALA A 620 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL A 622 " --> pdb=" O ILE A 797 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLU A 804 " --> pdb=" O VAL A 796 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 606 through 613 removed outlier: 7.087A pdb=" N GLN B 607 " --> pdb=" O HIS B 596 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N HIS B 596 " --> pdb=" O GLN B 607 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N VAL B 609 " --> pdb=" O ASN B 594 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE B 611 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N VAL B 595 " --> pdb=" O SER B 644 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N SER B 644 " --> pdb=" O VAL B 595 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 666 through 669 removed outlier: 5.924A pdb=" N LEU B 619 " --> pdb=" O VAL B 780 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N THR B 618 " --> pdb=" O GLN B 793 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N LEU B 795 " --> pdb=" O THR B 618 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA B 620 " --> pdb=" O LEU B 795 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N ILE B 797 " --> pdb=" O ALA B 620 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL B 622 " --> pdb=" O ILE B 797 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLU B 804 " --> pdb=" O VAL B 796 " (cutoff:3.500A) 252 hydrogen bonds defined for protein. 678 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: 1.31 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2916 1.34 - 1.45: 1288 1.45 - 1.57: 5036 1.57 - 1.69: 2 1.69 - 1.81: 56 Bond restraints: 9298 Sorted by residual: bond pdb=" CB GLU B 275 " pdb=" CG GLU B 275 " ideal model delta sigma weight residual 1.520 1.587 -0.067 3.00e-02 1.11e+03 5.01e+00 bond pdb=" CB GLU A 275 " pdb=" CG GLU A 275 " ideal model delta sigma weight residual 1.520 1.586 -0.066 3.00e-02 1.11e+03 4.91e+00 bond pdb=" CA ASN A 328 " pdb=" CB ASN A 328 " ideal model delta sigma weight residual 1.530 1.563 -0.033 1.54e-02 4.22e+03 4.61e+00 bond pdb=" CA ASN B 328 " pdb=" CB ASN B 328 " ideal model delta sigma weight residual 1.530 1.563 -0.033 1.54e-02 4.22e+03 4.61e+00 bond pdb=" CG GLU B 474 " pdb=" CD GLU B 474 " ideal model delta sigma weight residual 1.516 1.569 -0.053 2.50e-02 1.60e+03 4.41e+00 ... (remaining 9293 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 11628 2.01 - 4.01: 858 4.01 - 6.02: 77 6.02 - 8.03: 33 8.03 - 10.04: 16 Bond angle restraints: 12612 Sorted by residual: angle pdb=" N TRP B 412 " pdb=" CA TRP B 412 " pdb=" C TRP B 412 " ideal model delta sigma weight residual 113.88 104.25 9.63 1.23e+00 6.61e-01 6.13e+01 angle pdb=" N TRP A 412 " pdb=" CA TRP A 412 " pdb=" C TRP A 412 " ideal model delta sigma weight residual 113.88 104.27 9.61 1.23e+00 6.61e-01 6.10e+01 angle pdb=" N SER B 406 " pdb=" CA SER B 406 " pdb=" C SER B 406 " ideal model delta sigma weight residual 112.68 103.73 8.95 1.33e+00 5.65e-01 4.53e+01 angle pdb=" N SER A 406 " pdb=" CA SER A 406 " pdb=" C SER A 406 " ideal model delta sigma weight residual 112.68 103.75 8.93 1.33e+00 5.65e-01 4.51e+01 angle pdb=" N ILE A 480 " pdb=" CA ILE A 480 " pdb=" C ILE A 480 " ideal model delta sigma weight residual 113.43 106.86 6.57 1.09e+00 8.42e-01 3.63e+01 ... (remaining 12607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.00: 5005 15.00 - 30.00: 312 30.00 - 45.00: 103 45.00 - 60.00: 48 60.00 - 75.00: 8 Dihedral angle restraints: 5476 sinusoidal: 2134 harmonic: 3342 Sorted by residual: dihedral pdb=" CA ASN B 328 " pdb=" C ASN B 328 " pdb=" N LEU B 329 " pdb=" CA LEU B 329 " ideal model delta harmonic sigma weight residual 180.00 151.20 28.80 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA ASN A 328 " pdb=" C ASN A 328 " pdb=" N LEU A 329 " pdb=" CA LEU A 329 " ideal model delta harmonic sigma weight residual 180.00 151.22 28.78 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA GLY B 324 " pdb=" C GLY B 324 " pdb=" N PHE B 325 " pdb=" CA PHE B 325 " ideal model delta harmonic sigma weight residual -180.00 -154.69 -25.31 0 5.00e+00 4.00e-02 2.56e+01 ... (remaining 5473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1066 0.048 - 0.097: 279 0.097 - 0.145: 93 0.145 - 0.194: 16 0.194 - 0.242: 12 Chirality restraints: 1466 Sorted by residual: chirality pdb=" CA ASN A 328 " pdb=" N ASN A 328 " pdb=" C ASN A 328 " pdb=" CB ASN A 328 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA ASN B 328 " pdb=" N ASN B 328 " pdb=" C ASN B 328 " pdb=" CB ASN B 328 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA VAL B 388 " pdb=" N VAL B 388 " pdb=" C VAL B 388 " pdb=" CB VAL B 388 " both_signs ideal model delta sigma weight residual False 2.44 2.21 0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 1463 not shown) Planarity restraints: 1590 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 542 " 0.044 5.00e-02 4.00e+02 6.62e-02 7.01e+00 pdb=" N PRO B 543 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO B 543 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 543 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 542 " -0.044 5.00e-02 4.00e+02 6.62e-02 7.00e+00 pdb=" N PRO A 543 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 543 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 543 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 314 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.60e+00 pdb=" C PHE A 314 " 0.041 2.00e-02 2.50e+03 pdb=" O PHE A 314 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU A 315 " -0.014 2.00e-02 2.50e+03 ... (remaining 1587 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1569 2.75 - 3.29: 7832 3.29 - 3.83: 13916 3.83 - 4.36: 17175 4.36 - 4.90: 28678 Nonbonded interactions: 69170 Sorted by model distance: nonbonded pdb=" O MET B 407 " pdb=" CD2 PHE B 408 " model vdw 2.215 3.340 nonbonded pdb=" O MET A 407 " pdb=" CD2 PHE A 408 " model vdw 2.216 3.340 nonbonded pdb=" O ASN A 683 " pdb=" CD ARG A 739 " model vdw 2.237 3.440 nonbonded pdb=" O ASN B 683 " pdb=" CD ARG B 739 " model vdw 2.237 3.440 nonbonded pdb=" OD1 ASN A 328 " pdb=" NE2 GLN B 499 " model vdw 2.318 3.120 ... (remaining 69165 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 10.600 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 9298 Z= 0.270 Angle : 1.186 10.036 12612 Z= 0.758 Chirality : 0.054 0.242 1466 Planarity : 0.006 0.066 1590 Dihedral : 13.127 75.005 3336 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.69 % Allowed : 6.41 % Favored : 92.89 % Rotamer: Outliers : 4.77 % Allowed : 4.36 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.90 (0.20), residues: 1154 helix: -3.67 (0.16), residues: 678 sheet: -0.16 (0.62), residues: 82 loop : -2.74 (0.23), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 439 TYR 0.029 0.002 TYR A 465 PHE 0.028 0.002 PHE B 409 TRP 0.017 0.002 TRP B 299 HIS 0.006 0.002 HIS B 706 Details of bonding type rmsd covalent geometry : bond 0.00502 ( 9298) covalent geometry : angle 1.18558 (12612) hydrogen bonds : bond 0.31894 ( 252) hydrogen bonds : angle 9.31468 ( 678) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 150 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 362 LEU cc_start: 0.4386 (OUTLIER) cc_final: 0.4152 (mp) REVERT: A 383 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7912 (tt) REVERT: B 323 THR cc_start: 0.8864 (m) cc_final: 0.8503 (p) REVERT: B 499 GLN cc_start: 0.8679 (mm-40) cc_final: 0.7939 (mm110) REVERT: B 505 ILE cc_start: 0.8998 (tp) cc_final: 0.8760 (tp) REVERT: B 542 MET cc_start: 0.8105 (mtt) cc_final: 0.7902 (mtm) outliers start: 46 outliers final: 6 residues processed: 179 average time/residue: 0.1032 time to fit residues: 24.7482 Evaluate side-chains 89 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain B residue 406 SER Chi-restraints excluded: chain B residue 532 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 20.0000 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 0.6980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN A 665 HIS B 596 HIS B 607 GLN B 665 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.228590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.183957 restraints weight = 10471.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.181545 restraints weight = 14908.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.182296 restraints weight = 14921.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.182157 restraints weight = 9211.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.182939 restraints weight = 8228.859| |-----------------------------------------------------------------------------| r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9298 Z= 0.188 Angle : 0.698 9.849 12612 Z= 0.376 Chirality : 0.044 0.197 1466 Planarity : 0.005 0.041 1590 Dihedral : 6.832 41.441 1293 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.94 % Favored : 94.80 % Rotamer: Outliers : 3.01 % Allowed : 8.92 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.93 (0.22), residues: 1154 helix: -3.22 (0.17), residues: 642 sheet: 0.26 (0.56), residues: 82 loop : -1.85 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 739 TYR 0.023 0.002 TYR A 541 PHE 0.030 0.002 PHE B 408 TRP 0.016 0.001 TRP A 488 HIS 0.005 0.001 HIS B 596 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 9298) covalent geometry : angle 0.69816 (12612) hydrogen bonds : bond 0.04869 ( 252) hydrogen bonds : angle 5.61630 ( 678) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 107 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: A 383 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.8026 (tp) REVERT: A 792 ASP cc_start: 0.7168 (t70) cc_final: 0.6866 (m-30) REVERT: B 505 ILE cc_start: 0.9053 (tp) cc_final: 0.8689 (tp) REVERT: B 542 MET cc_start: 0.8116 (mtt) cc_final: 0.7871 (mtm) REVERT: B 558 PHE cc_start: 0.7341 (m-80) cc_final: 0.7068 (m-80) REVERT: B 710 MET cc_start: 0.3935 (tpp) cc_final: 0.3168 (mmm) REVERT: B 750 LEU cc_start: 0.7985 (mp) cc_final: 0.7626 (tt) outliers start: 29 outliers final: 13 residues processed: 131 average time/residue: 0.0761 time to fit residues: 14.7531 Evaluate side-chains 99 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 593 GLU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 781 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 55 optimal weight: 7.9990 chunk 30 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 72 optimal weight: 0.7980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 GLN B 316 GLN ** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 683 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.221703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.168732 restraints weight = 10442.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.161970 restraints weight = 12312.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.164104 restraints weight = 12180.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.163801 restraints weight = 7517.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.166267 restraints weight = 6362.183| |-----------------------------------------------------------------------------| r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9298 Z= 0.193 Angle : 0.671 11.633 12612 Z= 0.360 Chirality : 0.045 0.173 1466 Planarity : 0.004 0.055 1590 Dihedral : 6.149 40.277 1284 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.46 % Favored : 94.28 % Rotamer: Outliers : 4.36 % Allowed : 10.06 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.50 (0.22), residues: 1154 helix: -2.86 (0.18), residues: 650 sheet: 0.79 (0.55), residues: 82 loop : -1.74 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 776 TYR 0.021 0.002 TYR B 465 PHE 0.023 0.002 PHE B 408 TRP 0.016 0.001 TRP A 488 HIS 0.003 0.001 HIS B 808 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 9298) covalent geometry : angle 0.67140 (12612) hydrogen bonds : bond 0.05011 ( 252) hydrogen bonds : angle 5.13548 ( 678) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 101 time to evaluate : 0.340 Fit side-chains REVERT: A 315 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8358 (mp) REVERT: A 397 ASP cc_start: 0.8337 (t0) cc_final: 0.8016 (t0) REVERT: A 652 GLN cc_start: 0.5755 (OUTLIER) cc_final: 0.5528 (mt0) REVERT: A 682 ASP cc_start: 0.6021 (m-30) cc_final: 0.5810 (m-30) REVERT: B 315 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8382 (mp) REVERT: B 558 PHE cc_start: 0.7479 (m-80) cc_final: 0.7225 (m-80) REVERT: B 565 PHE cc_start: 0.8034 (OUTLIER) cc_final: 0.7266 (t80) REVERT: B 750 LEU cc_start: 0.8055 (mp) cc_final: 0.7447 (tt) outliers start: 42 outliers final: 21 residues processed: 133 average time/residue: 0.0748 time to fit residues: 14.9113 Evaluate side-chains 109 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 593 GLU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 652 GLN Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 547 PHE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 809 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 102 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 60 optimal weight: 0.0170 chunk 62 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 42 optimal weight: 0.0980 chunk 25 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 HIS A 652 GLN ** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.227936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.175162 restraints weight = 10511.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.168709 restraints weight = 13859.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.171444 restraints weight = 11503.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.171587 restraints weight = 6751.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.172252 restraints weight = 6506.158| |-----------------------------------------------------------------------------| r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.4129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9298 Z= 0.098 Angle : 0.564 9.832 12612 Z= 0.299 Chirality : 0.040 0.162 1466 Planarity : 0.003 0.028 1590 Dihedral : 5.519 37.657 1284 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.73 % Favored : 96.10 % Rotamer: Outliers : 2.80 % Allowed : 12.66 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.23), residues: 1154 helix: -2.50 (0.19), residues: 630 sheet: 0.86 (0.54), residues: 82 loop : -1.40 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 734 TYR 0.023 0.001 TYR B 471 PHE 0.015 0.001 PHE B 408 TRP 0.011 0.001 TRP A 546 HIS 0.002 0.000 HIS B 808 Details of bonding type rmsd covalent geometry : bond 0.00206 ( 9298) covalent geometry : angle 0.56390 (12612) hydrogen bonds : bond 0.03077 ( 252) hydrogen bonds : angle 4.69082 ( 678) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.287 Fit side-chains REVERT: A 383 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.8027 (tt) REVERT: A 397 ASP cc_start: 0.8370 (t0) cc_final: 0.7935 (t0) REVERT: A 792 ASP cc_start: 0.6903 (t70) cc_final: 0.6661 (m-30) REVERT: B 505 ILE cc_start: 0.8901 (tp) cc_final: 0.8570 (tp) REVERT: B 523 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.8047 (mt0) REVERT: B 565 PHE cc_start: 0.7990 (OUTLIER) cc_final: 0.7239 (t80) REVERT: B 710 MET cc_start: 0.4211 (tpp) cc_final: 0.3591 (mmm) REVERT: B 716 TYR cc_start: 0.1761 (OUTLIER) cc_final: 0.1382 (m-10) REVERT: B 750 LEU cc_start: 0.8013 (mp) cc_final: 0.7474 (tt) outliers start: 27 outliers final: 12 residues processed: 124 average time/residue: 0.0805 time to fit residues: 14.6438 Evaluate side-chains 108 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 523 GLN Chi-restraints excluded: chain B residue 547 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 716 TYR Chi-restraints excluded: chain B residue 809 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 65 optimal weight: 0.0170 chunk 48 optimal weight: 9.9990 chunk 13 optimal weight: 0.1980 chunk 80 optimal weight: 6.9990 overall best weight: 0.8422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 GLN B 499 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.225906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.174272 restraints weight = 10464.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.170267 restraints weight = 14418.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.172272 restraints weight = 12815.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.172076 restraints weight = 7969.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.172763 restraints weight = 7433.353| |-----------------------------------------------------------------------------| r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.4435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9298 Z= 0.109 Angle : 0.560 10.199 12612 Z= 0.294 Chirality : 0.041 0.180 1466 Planarity : 0.003 0.049 1590 Dihedral : 5.257 35.822 1284 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.03 % Favored : 94.80 % Rotamer: Outliers : 2.80 % Allowed : 13.59 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.60 (0.24), residues: 1154 helix: -2.17 (0.20), residues: 632 sheet: 0.91 (0.56), residues: 84 loop : -1.26 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 734 TYR 0.021 0.001 TYR B 471 PHE 0.012 0.001 PHE B 408 TRP 0.006 0.001 TRP A 546 HIS 0.002 0.000 HIS B 808 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 9298) covalent geometry : angle 0.55986 (12612) hydrogen bonds : bond 0.03165 ( 252) hydrogen bonds : angle 4.48331 ( 678) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: A 397 ASP cc_start: 0.8473 (t0) cc_final: 0.7995 (t0) REVERT: A 677 ASN cc_start: 0.7964 (t0) cc_final: 0.7542 (p0) REVERT: A 792 ASP cc_start: 0.6998 (t70) cc_final: 0.6727 (m-30) REVERT: B 505 ILE cc_start: 0.8903 (tp) cc_final: 0.8540 (tp) REVERT: B 565 PHE cc_start: 0.8018 (OUTLIER) cc_final: 0.7476 (t80) REVERT: B 710 MET cc_start: 0.4428 (tpp) cc_final: 0.3815 (mmm) outliers start: 27 outliers final: 16 residues processed: 115 average time/residue: 0.0808 time to fit residues: 13.8852 Evaluate side-chains 108 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 547 PHE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 809 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 48 optimal weight: 9.9990 chunk 102 optimal weight: 9.9990 chunk 52 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 113 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN B 693 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.211001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.155094 restraints weight = 10293.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.149751 restraints weight = 14611.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.152185 restraints weight = 12171.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.151971 restraints weight = 7568.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.152647 restraints weight = 7099.034| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 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 : 0.002 0.025 9298 Z= 0.105 Angle : 0.554 11.328 12612 Z= 0.284 Chirality : 0.040 0.160 1466 Planarity : 0.003 0.045 1590 Dihedral : 4.911 33.890 1282 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.28 % Allowed : 14.63 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.24), residues: 1154 helix: -1.95 (0.20), residues: 634 sheet: 0.99 (0.56), residues: 84 loop : -1.24 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 717 TYR 0.019 0.001 TYR B 471 PHE 0.009 0.001 PHE B 408 TRP 0.011 0.001 TRP A 546 HIS 0.002 0.000 HIS B 808 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 9298) covalent geometry : angle 0.55414 (12612) hydrogen bonds : bond 0.02919 ( 252) hydrogen bonds : angle 4.36978 ( 678) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: A 397 ASP cc_start: 0.8468 (t0) cc_final: 0.7965 (t0) REVERT: A 677 ASN cc_start: 0.7853 (t0) cc_final: 0.7647 (p0) REVERT: B 461 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.7173 (pm20) REVERT: B 505 ILE cc_start: 0.8891 (tp) cc_final: 0.8514 (tp) REVERT: B 565 PHE cc_start: 0.7999 (OUTLIER) cc_final: 0.7503 (t80) REVERT: B 710 MET cc_start: 0.4763 (tpp) cc_final: 0.4113 (mmm) outliers start: 22 outliers final: 16 residues processed: 111 average time/residue: 0.0866 time to fit residues: 14.1203 Evaluate side-chains 108 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 547 PHE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 809 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 109 optimal weight: 9.9990 chunk 51 optimal weight: 0.0670 chunk 32 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 89 optimal weight: 9.9990 chunk 8 optimal weight: 0.0770 chunk 19 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.212879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.158141 restraints weight = 10373.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.153312 restraints weight = 14465.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.154646 restraints weight = 13072.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.158222 restraints weight = 8609.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.157839 restraints weight = 6856.306| |-----------------------------------------------------------------------------| r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.4982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9298 Z= 0.088 Angle : 0.531 10.405 12612 Z= 0.272 Chirality : 0.040 0.156 1466 Planarity : 0.002 0.026 1590 Dihedral : 4.672 32.426 1282 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.80 % Allowed : 14.83 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.24), residues: 1154 helix: -1.69 (0.20), residues: 634 sheet: 0.96 (0.56), residues: 84 loop : -1.27 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 717 TYR 0.018 0.001 TYR B 471 PHE 0.009 0.001 PHE A 639 TRP 0.009 0.001 TRP A 546 HIS 0.002 0.000 HIS B 808 Details of bonding type rmsd covalent geometry : bond 0.00188 ( 9298) covalent geometry : angle 0.53139 (12612) hydrogen bonds : bond 0.02565 ( 252) hydrogen bonds : angle 4.26405 ( 678) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: A 397 ASP cc_start: 0.8451 (t0) cc_final: 0.8110 (t0) REVERT: B 505 ILE cc_start: 0.8846 (tp) cc_final: 0.8462 (tp) REVERT: B 558 PHE cc_start: 0.7448 (m-80) cc_final: 0.7109 (m-80) REVERT: B 565 PHE cc_start: 0.7913 (OUTLIER) cc_final: 0.7504 (t80) REVERT: B 710 MET cc_start: 0.4668 (tpp) cc_final: 0.4192 (mmm) outliers start: 27 outliers final: 18 residues processed: 118 average time/residue: 0.0648 time to fit residues: 11.8296 Evaluate side-chains 113 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 542 MET Chi-restraints excluded: chain B residue 547 PHE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 809 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 94 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 84 optimal weight: 0.0370 chunk 53 optimal weight: 0.5980 chunk 96 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 90 optimal weight: 0.0270 chunk 10 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 GLN A 719 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.213961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.158261 restraints weight = 10278.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.152087 restraints weight = 11922.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.153828 restraints weight = 12817.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.154617 restraints weight = 7398.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.155353 restraints weight = 6425.260| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.5161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9298 Z= 0.087 Angle : 0.533 12.482 12612 Z= 0.272 Chirality : 0.040 0.155 1466 Planarity : 0.002 0.024 1590 Dihedral : 4.505 31.533 1282 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.07 % Allowed : 15.35 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.25), residues: 1154 helix: -1.49 (0.21), residues: 648 sheet: 0.92 (0.56), residues: 84 loop : -1.06 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 717 TYR 0.017 0.001 TYR B 471 PHE 0.016 0.001 PHE B 408 TRP 0.007 0.000 TRP A 546 HIS 0.001 0.000 HIS B 808 Details of bonding type rmsd covalent geometry : bond 0.00182 ( 9298) covalent geometry : angle 0.53346 (12612) hydrogen bonds : bond 0.02480 ( 252) hydrogen bonds : angle 4.22142 ( 678) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 397 ASP cc_start: 0.8359 (t0) cc_final: 0.7987 (t0) REVERT: B 505 ILE cc_start: 0.8923 (tp) cc_final: 0.8517 (tp) REVERT: B 565 PHE cc_start: 0.7941 (OUTLIER) cc_final: 0.7527 (t80) REVERT: B 710 MET cc_start: 0.4811 (tpp) cc_final: 0.4104 (mmm) outliers start: 20 outliers final: 18 residues processed: 111 average time/residue: 0.0649 time to fit residues: 11.2035 Evaluate side-chains 110 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 542 MET Chi-restraints excluded: chain B residue 547 PHE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 809 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 23 optimal weight: 0.0570 chunk 63 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.7302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 596 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.212004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.157031 restraints weight = 10264.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.150864 restraints weight = 13543.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.153186 restraints weight = 12530.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.153227 restraints weight = 6981.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.157010 restraints weight = 6161.601| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.5289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9298 Z= 0.100 Angle : 0.552 14.259 12612 Z= 0.278 Chirality : 0.041 0.159 1466 Planarity : 0.003 0.024 1590 Dihedral : 4.504 31.760 1282 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.07 % Allowed : 15.98 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.25), residues: 1154 helix: -1.38 (0.21), residues: 646 sheet: 0.90 (0.55), residues: 84 loop : -1.22 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 717 TYR 0.017 0.001 TYR B 471 PHE 0.045 0.001 PHE A 460 TRP 0.006 0.001 TRP A 546 HIS 0.002 0.000 HIS B 596 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 9298) covalent geometry : angle 0.55162 (12612) hydrogen bonds : bond 0.02733 ( 252) hydrogen bonds : angle 4.23082 ( 678) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: A 315 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8198 (mp) REVERT: A 397 ASP cc_start: 0.8400 (t0) cc_final: 0.8083 (t0) REVERT: A 710 MET cc_start: 0.2652 (mmm) cc_final: 0.0982 (mmt) REVERT: B 505 ILE cc_start: 0.8922 (tp) cc_final: 0.8501 (tp) REVERT: B 710 MET cc_start: 0.4978 (tpp) cc_final: 0.4268 (mmm) outliers start: 20 outliers final: 18 residues processed: 105 average time/residue: 0.0709 time to fit residues: 11.2257 Evaluate side-chains 107 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 542 MET Chi-restraints excluded: chain B residue 547 PHE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 809 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 105 optimal weight: 6.9990 chunk 56 optimal weight: 30.0000 chunk 52 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 81 optimal weight: 0.5980 chunk 38 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 55 optimal weight: 0.0870 chunk 48 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 overall best weight: 1.7364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 596 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.205837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.151002 restraints weight = 10358.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.144847 restraints weight = 15530.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.147451 restraints weight = 12488.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.148071 restraints weight = 7034.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.148887 restraints weight = 6505.230| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.5528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9298 Z= 0.167 Angle : 0.614 14.386 12612 Z= 0.314 Chirality : 0.044 0.163 1466 Planarity : 0.003 0.029 1590 Dihedral : 4.881 32.875 1282 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.18 % Allowed : 16.08 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.24), residues: 1154 helix: -1.51 (0.20), residues: 652 sheet: 0.81 (0.56), residues: 84 loop : -1.26 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 776 TYR 0.018 0.002 TYR B 471 PHE 0.035 0.002 PHE A 460 TRP 0.007 0.001 TRP A 546 HIS 0.003 0.001 HIS B 706 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 9298) covalent geometry : angle 0.61434 (12612) hydrogen bonds : bond 0.03816 ( 252) hydrogen bonds : angle 4.44024 ( 678) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: A 315 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8226 (mp) REVERT: A 397 ASP cc_start: 0.8375 (t0) cc_final: 0.8008 (t0) REVERT: A 675 LEU cc_start: 0.7713 (tp) cc_final: 0.7385 (tt) REVERT: A 710 MET cc_start: 0.2385 (mmm) cc_final: 0.1076 (mmt) REVERT: B 614 MET cc_start: 0.6876 (ptp) cc_final: 0.6472 (pmm) outliers start: 21 outliers final: 20 residues processed: 106 average time/residue: 0.0672 time to fit residues: 11.0304 Evaluate side-chains 105 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 542 MET Chi-restraints excluded: chain B residue 547 PHE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 641 ASP Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 809 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 96 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 44 optimal weight: 9.9990 chunk 75 optimal weight: 0.9980 chunk 99 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 69 optimal weight: 0.0170 chunk 54 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 114 optimal weight: 10.0000 overall best weight: 0.9620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 596 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.208436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.154053 restraints weight = 10244.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.148559 restraints weight = 15931.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.150858 restraints weight = 13089.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.151138 restraints weight = 7237.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.155343 restraints weight = 6544.008| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.5653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9298 Z= 0.113 Angle : 0.578 14.143 12612 Z= 0.293 Chirality : 0.041 0.180 1466 Planarity : 0.003 0.024 1590 Dihedral : 4.746 32.316 1282 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.28 % Allowed : 16.29 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.25), residues: 1154 helix: -1.39 (0.21), residues: 650 sheet: 0.77 (0.56), residues: 82 loop : -1.25 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 717 TYR 0.022 0.001 TYR A 541 PHE 0.036 0.001 PHE A 460 TRP 0.007 0.001 TRP A 412 HIS 0.003 0.001 HIS B 706 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 9298) covalent geometry : angle 0.57779 (12612) hydrogen bonds : bond 0.03013 ( 252) hydrogen bonds : angle 4.34920 ( 678) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1394.33 seconds wall clock time: 24 minutes 39.28 seconds (1479.28 seconds total)