Starting phenix.real_space_refine on Sat Dec 28 20:28:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ekm_31170/12_2024/7ekm_31170.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ekm_31170/12_2024/7ekm_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7ekm_31170/12_2024/7ekm_31170.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ekm_31170/12_2024/7ekm_31170.map" model { file = "/net/cci-nas-00/data/ceres_data/7ekm_31170/12_2024/7ekm_31170.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ekm_31170/12_2024/7ekm_31170.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 29 Restraints were copied for chains: B Time building chain proxies: 8.26, per 1000 atoms: 0.91 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: 2.33 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.06 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: 2.51 Time building geometry restraints manager: 2.69 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: 0.00 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: 1.220 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 26.180 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.180 ------------------------------------------------------------------------------- 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= 0.325 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.90 (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 TRP 0.017 0.002 TRP B 299 HIS 0.006 0.002 HIS B 706 PHE 0.028 0.002 PHE B 409 TYR 0.029 0.002 TYR A 465 ARG 0.007 0.001 ARG B 439 *********************** 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 : 1.081 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: 0.2590 time to fit residues: 61.8869 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 : 0.998 ------------------------------------------------------------------------------- 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 97 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 46 optimal weight: 0.0570 chunk 90 optimal weight: 4.9990 chunk 35 optimal weight: 8.9990 chunk 55 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- 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 316 GLN B 596 HIS B 607 GLN B 665 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9298 Z= 0.297 Angle : 0.716 10.160 12612 Z= 0.383 Chirality : 0.046 0.213 1466 Planarity : 0.005 0.040 1590 Dihedral : 6.942 41.535 1293 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.29 % Favored : 94.45 % Rotamer: Outliers : 3.11 % Allowed : 8.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.93 (0.22), residues: 1154 helix: -3.22 (0.17), residues: 642 sheet: 0.27 (0.56), residues: 82 loop : -1.86 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 488 HIS 0.003 0.001 HIS B 665 PHE 0.038 0.003 PHE B 408 TYR 0.025 0.002 TYR A 541 ARG 0.005 0.001 ARG B 739 *********************** 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: 30 poor density : 106 time to evaluate : 1.039 Fit side-chains revert: symmetry clash REVERT: A 792 ASP cc_start: 0.7206 (t70) cc_final: 0.6807 (m-30) REVERT: B 505 ILE cc_start: 0.9011 (tp) cc_final: 0.8649 (tp) REVERT: B 542 MET cc_start: 0.8148 (mtt) cc_final: 0.7927 (mtm) REVERT: B 558 PHE cc_start: 0.7297 (m-80) cc_final: 0.7086 (m-80) REVERT: B 750 LEU cc_start: 0.7931 (mp) cc_final: 0.7652 (tt) outliers start: 30 outliers final: 13 residues processed: 131 average time/residue: 0.1894 time to fit residues: 36.2665 Evaluate side-chains 96 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 58 optimal weight: 10.0000 chunk 32 optimal weight: 0.5980 chunk 87 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 105 optimal weight: 7.9990 chunk 114 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 104 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 84 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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** B 683 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9298 Z= 0.194 Angle : 0.609 10.760 12612 Z= 0.325 Chirality : 0.042 0.142 1466 Planarity : 0.004 0.060 1590 Dihedral : 5.747 39.325 1282 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.68 % Favored : 95.06 % Rotamer: Outliers : 3.01 % Allowed : 11.83 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.23), residues: 1154 helix: -2.74 (0.18), residues: 632 sheet: 0.85 (0.55), residues: 82 loop : -1.55 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 488 HIS 0.002 0.001 HIS B 596 PHE 0.021 0.002 PHE B 408 TYR 0.021 0.002 TYR A 541 ARG 0.003 0.000 ARG B 776 *********************** 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 123 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 94 time to evaluate : 1.023 Fit side-chains revert: symmetry clash REVERT: A 315 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8505 (mp) REVERT: A 397 ASP cc_start: 0.8311 (t0) cc_final: 0.8041 (t0) REVERT: A 792 ASP cc_start: 0.7186 (t70) cc_final: 0.6823 (m-30) REVERT: B 505 ILE cc_start: 0.8909 (tp) cc_final: 0.8589 (tp) REVERT: B 523 GLN cc_start: 0.8354 (mp10) cc_final: 0.8066 (mt0) REVERT: B 565 PHE cc_start: 0.7833 (OUTLIER) cc_final: 0.7087 (t80) REVERT: B 710 MET cc_start: 0.4001 (tpp) cc_final: 0.3175 (mmm) REVERT: B 750 LEU cc_start: 0.8012 (mp) cc_final: 0.7719 (tt) outliers start: 29 outliers final: 14 residues processed: 115 average time/residue: 0.1994 time to fit residues: 33.1426 Evaluate side-chains 98 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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 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 323 THR Chi-restraints excluded: chain B residue 370 LEU 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 809 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 0.1980 chunk 79 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 chunk 70 optimal weight: 0.0170 chunk 105 optimal weight: 7.9990 chunk 112 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 chunk 100 optimal weight: 9.9990 chunk 30 optimal weight: 0.1980 overall best weight: 1.0822 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9298 Z= 0.173 Angle : 0.574 12.304 12612 Z= 0.301 Chirality : 0.041 0.142 1466 Planarity : 0.003 0.027 1590 Dihedral : 5.373 37.200 1282 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.42 % Favored : 95.41 % Rotamer: Outliers : 3.32 % Allowed : 12.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.23), residues: 1154 helix: -2.43 (0.19), residues: 628 sheet: 0.96 (0.54), residues: 82 loop : -1.39 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 546 HIS 0.002 0.000 HIS B 808 PHE 0.015 0.001 PHE B 408 TYR 0.017 0.001 TYR A 541 ARG 0.005 0.000 ARG B 359 *********************** 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 127 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 95 time to evaluate : 1.023 Fit side-chains revert: symmetry clash REVERT: A 792 ASP cc_start: 0.7142 (t70) cc_final: 0.6874 (m-30) REVERT: B 315 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8354 (mp) REVERT: B 505 ILE cc_start: 0.8912 (tp) cc_final: 0.8575 (tp) REVERT: B 523 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.8079 (mt0) REVERT: B 565 PHE cc_start: 0.7893 (OUTLIER) cc_final: 0.7163 (t80) REVERT: B 710 MET cc_start: 0.3985 (tpp) cc_final: 0.3389 (mmm) REVERT: B 716 TYR cc_start: 0.1881 (OUTLIER) cc_final: 0.1327 (m-10) REVERT: B 750 LEU cc_start: 0.8031 (mp) cc_final: 0.7746 (tt) outliers start: 32 outliers final: 16 residues processed: 117 average time/residue: 0.1990 time to fit residues: 34.0161 Evaluate side-chains 105 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 1.049 ------------------------------------------------------------------------------- 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 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 315 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 523 GLN 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 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 93 optimal weight: 0.0570 chunk 63 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 95 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 57 optimal weight: 7.9990 chunk 100 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.8902 ------------------------------------------------------------------------------- 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** ** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.4434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9298 Z= 0.156 Angle : 0.552 10.372 12612 Z= 0.289 Chirality : 0.041 0.177 1466 Planarity : 0.003 0.051 1590 Dihedral : 5.090 35.054 1282 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.51 % Favored : 95.32 % Rotamer: Outliers : 2.80 % Allowed : 13.38 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.24), residues: 1154 helix: -2.15 (0.19), residues: 646 sheet: 0.99 (0.56), residues: 84 loop : -1.34 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 546 HIS 0.002 0.000 HIS B 808 PHE 0.015 0.001 PHE A 676 TYR 0.015 0.001 TYR A 541 ARG 0.004 0.000 ARG A 734 *********************** 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 : 0.988 Fit side-chains REVERT: A 315 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8380 (mp) REVERT: A 792 ASP cc_start: 0.7082 (t70) cc_final: 0.6784 (m-30) REVERT: B 315 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8383 (mp) REVERT: B 505 ILE cc_start: 0.8895 (tp) cc_final: 0.8533 (tp) REVERT: B 565 PHE cc_start: 0.7896 (OUTLIER) cc_final: 0.7163 (t80) REVERT: B 710 MET cc_start: 0.4016 (tpp) cc_final: 0.3453 (mmm) outliers start: 27 outliers final: 17 residues processed: 117 average time/residue: 0.1782 time to fit residues: 30.9904 Evaluate side-chains 108 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 1.027 ------------------------------------------------------------------------------- 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 618 THR 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 315 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 461 GLU 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 680 ILE 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 37 optimal weight: 0.9990 chunk 100 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 112 optimal weight: 0.3980 chunk 93 optimal weight: 3.9990 chunk 51 optimal weight: 0.0370 chunk 9 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 108 optimal weight: 6.9990 overall best weight: 1.0662 ------------------------------------------------------------------------------- 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 499 GLN B 693 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.4767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9298 Z= 0.168 Angle : 0.551 9.834 12612 Z= 0.289 Chirality : 0.041 0.165 1466 Planarity : 0.003 0.042 1590 Dihedral : 4.976 33.858 1282 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.11 % Allowed : 13.90 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.24), residues: 1154 helix: -1.96 (0.20), residues: 656 sheet: 1.00 (0.56), residues: 84 loop : -1.48 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 546 HIS 0.002 0.000 HIS B 808 PHE 0.010 0.001 PHE B 639 TYR 0.014 0.001 TYR A 541 ARG 0.015 0.000 ARG B 717 *********************** 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 128 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 98 time to evaluate : 1.018 Fit side-chains revert: symmetry clash REVERT: A 315 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8375 (mp) REVERT: B 315 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8365 (mp) REVERT: B 419 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8572 (mp) REVERT: B 505 ILE cc_start: 0.8912 (tp) cc_final: 0.8530 (tp) REVERT: B 565 PHE cc_start: 0.7894 (OUTLIER) cc_final: 0.7464 (t80) REVERT: B 710 MET cc_start: 0.4173 (tpp) cc_final: 0.3716 (mmm) outliers start: 30 outliers final: 18 residues processed: 118 average time/residue: 0.1742 time to fit residues: 31.5964 Evaluate side-chains 112 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 1.323 ------------------------------------------------------------------------------- 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 618 THR 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 315 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 419 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 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 12 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 94 optimal weight: 9.9990 chunk 62 optimal weight: 0.7980 chunk 111 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 51 optimal weight: 0.0770 chunk 44 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 overall best weight: 1.1342 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.5040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9298 Z= 0.176 Angle : 0.553 9.928 12612 Z= 0.289 Chirality : 0.041 0.149 1466 Planarity : 0.003 0.034 1590 Dihedral : 4.928 33.479 1282 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.80 % Allowed : 14.73 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.24), residues: 1154 helix: -1.78 (0.20), residues: 654 sheet: 0.92 (0.56), residues: 84 loop : -1.42 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 546 HIS 0.002 0.000 HIS B 808 PHE 0.010 0.001 PHE A 565 TYR 0.030 0.001 TYR B 471 ARG 0.006 0.000 ARG B 717 *********************** 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 119 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 0.814 Fit side-chains revert: symmetry clash REVERT: A 315 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8327 (mp) REVERT: B 315 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8364 (mp) REVERT: B 505 ILE cc_start: 0.8919 (tp) cc_final: 0.8542 (tp) REVERT: B 565 PHE cc_start: 0.7895 (OUTLIER) cc_final: 0.7425 (t80) REVERT: B 710 MET cc_start: 0.4347 (tpp) cc_final: 0.3848 (mmm) outliers start: 27 outliers final: 18 residues processed: 112 average time/residue: 0.1766 time to fit residues: 29.6724 Evaluate side-chains 108 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 1.081 ------------------------------------------------------------------------------- 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 618 THR 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 315 LEU 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 668 VAL Chi-restraints excluded: chain B residue 680 ILE 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 33 optimal weight: 20.0000 chunk 21 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 chunk 55 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- 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 683 ASN A 719 GLN B 445 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.5383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9298 Z= 0.263 Angle : 0.614 13.157 12612 Z= 0.320 Chirality : 0.043 0.169 1466 Planarity : 0.003 0.032 1590 Dihedral : 5.212 34.426 1282 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.37 % Favored : 94.54 % Rotamer: Outliers : 2.90 % Allowed : 15.56 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.24), residues: 1154 helix: -1.82 (0.20), residues: 656 sheet: 0.82 (0.57), residues: 82 loop : -1.40 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 546 HIS 0.004 0.001 HIS B 706 PHE 0.011 0.001 PHE B 639 TYR 0.027 0.002 TYR B 471 ARG 0.005 0.000 ARG B 717 *********************** 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 120 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 92 time to evaluate : 1.005 Fit side-chains revert: symmetry clash REVERT: A 315 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8353 (mp) REVERT: A 522 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7581 (mm-30) REVERT: A 710 MET cc_start: 0.2082 (mmm) cc_final: 0.0572 (mmt) REVERT: B 565 PHE cc_start: 0.8029 (OUTLIER) cc_final: 0.7399 (t80) REVERT: B 614 MET cc_start: 0.6274 (ptp) cc_final: 0.5978 (pmm) outliers start: 28 outliers final: 20 residues processed: 112 average time/residue: 0.2134 time to fit residues: 34.0107 Evaluate side-chains 106 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 1.030 ------------------------------------------------------------------------------- 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 618 THR 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 A residue 781 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 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 641 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 81 optimal weight: 0.0870 chunk 31 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 98 optimal weight: 30.0000 chunk 103 optimal weight: 4.9990 chunk 68 optimal weight: 0.5980 chunk 110 optimal weight: 6.9990 chunk 67 optimal weight: 0.5980 overall best weight: 0.5960 ------------------------------------------------------------------------------- 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 A 683 ASN B 596 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.5536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9298 Z= 0.134 Angle : 0.569 14.436 12612 Z= 0.287 Chirality : 0.040 0.143 1466 Planarity : 0.003 0.027 1590 Dihedral : 4.857 33.497 1282 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.39 % Allowed : 16.49 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.24), residues: 1154 helix: -1.64 (0.20), residues: 650 sheet: 0.85 (0.57), residues: 82 loop : -1.40 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 546 HIS 0.002 0.001 HIS B 706 PHE 0.008 0.001 PHE A 611 TYR 0.025 0.001 TYR B 471 ARG 0.006 0.000 ARG A 685 *********************** 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 113 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.944 Fit side-chains revert: symmetry clash REVERT: A 710 MET cc_start: 0.1880 (mmm) cc_final: 0.0895 (mmt) REVERT: B 505 ILE cc_start: 0.8882 (tp) cc_final: 0.8498 (tp) REVERT: B 565 PHE cc_start: 0.7944 (OUTLIER) cc_final: 0.7510 (t80) outliers start: 23 outliers final: 17 residues processed: 106 average time/residue: 0.2014 time to fit residues: 30.9333 Evaluate side-chains 106 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 1.065 ------------------------------------------------------------------------------- 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 618 THR Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain A residue 781 VAL 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 668 VAL Chi-restraints excluded: chain B residue 680 ILE 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 52 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 115 optimal weight: 5.9990 chunk 106 optimal weight: 10.0000 chunk 92 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 56 optimal weight: 30.0000 chunk 73 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 693 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.5698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9298 Z= 0.213 Angle : 0.598 14.456 12612 Z= 0.306 Chirality : 0.043 0.161 1466 Planarity : 0.003 0.039 1590 Dihedral : 4.986 33.937 1282 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.07 % Allowed : 16.70 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.24), residues: 1154 helix: -1.65 (0.20), residues: 658 sheet: 0.76 (0.57), residues: 82 loop : -1.38 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 546 HIS 0.004 0.001 HIS B 706 PHE 0.015 0.001 PHE B 408 TYR 0.026 0.001 TYR B 471 ARG 0.004 0.000 ARG B 717 ********************** 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 111 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: A 315 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8332 (mp) REVERT: A 710 MET cc_start: 0.1865 (mmm) cc_final: 0.1138 (mmt) REVERT: B 565 PHE cc_start: 0.8021 (OUTLIER) cc_final: 0.7540 (t80) REVERT: B 614 MET cc_start: 0.6349 (ptp) cc_final: 0.6045 (pmm) outliers start: 20 outliers final: 17 residues processed: 106 average time/residue: 0.1933 time to fit residues: 30.2850 Evaluate side-chains 104 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 1.065 ------------------------------------------------------------------------------- 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 618 THR Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain A residue 781 VAL 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 668 VAL Chi-restraints excluded: chain B residue 680 ILE 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 84 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 92 optimal weight: 8.9990 chunk 38 optimal weight: 8.9990 chunk 94 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 66 optimal weight: 0.0870 overall best weight: 1.4164 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.208401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.152853 restraints weight = 10167.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.147034 restraints weight = 12790.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.141304 restraints weight = 6634.243| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.5837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9298 Z= 0.207 Angle : 0.602 14.369 12612 Z= 0.307 Chirality : 0.042 0.170 1466 Planarity : 0.003 0.027 1590 Dihedral : 5.016 34.706 1282 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.87 % Allowed : 17.43 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.24), residues: 1154 helix: -1.59 (0.20), residues: 658 sheet: 0.85 (0.67), residues: 58 loop : -1.28 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 546 HIS 0.004 0.001 HIS B 706 PHE 0.017 0.001 PHE B 408 TYR 0.026 0.001 TYR B 471 ARG 0.005 0.000 ARG A 685 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1798.73 seconds wall clock time: 33 minutes 41.27 seconds (2021.27 seconds total)