Starting phenix.real_space_refine on Thu Mar 13 17:30:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ekm_31170/03_2025/7ekm_31170.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ekm_31170/03_2025/7ekm_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_31170/03_2025/7ekm_31170.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ekm_31170/03_2025/7ekm_31170.map" model { file = "/net/cci-nas-00/data/ceres_data/7ekm_31170/03_2025/7ekm_31170.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ekm_31170/03_2025/7ekm_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-5624/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: 8.53, per 1000 atoms: 0.93 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: 2.50 Conformation dependent library (CDL) restraints added in 1.1 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: 1.04 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: 2.41 Time building geometry restraints manager: 2.94 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: 0.05 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 27.330 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.980 ------------------------------------------------------------------------------- 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 : 1.005 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: 0.2553 time to fit residues: 61.0044 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 : 0.945 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.226477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.170045 restraints weight = 10397.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.164323 restraints weight = 11198.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.166356 restraints weight = 10864.603| |-----------------------------------------------------------------------------| r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 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 : 0.936 Fit side-chains revert: symmetry clash REVERT: A 383 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7958 (tp) REVERT: A 792 ASP cc_start: 0.6870 (t70) cc_final: 0.6526 (m-30) REVERT: B 505 ILE cc_start: 0.9036 (tp) cc_final: 0.8661 (tp) REVERT: B 542 MET cc_start: 0.8083 (mtt) cc_final: 0.7864 (mtm) REVERT: B 558 PHE cc_start: 0.7464 (m-80) cc_final: 0.7198 (m-80) REVERT: B 750 LEU cc_start: 0.7928 (mp) cc_final: 0.7344 (tt) outliers start: 30 outliers final: 13 residues processed: 131 average time/residue: 0.1787 time to fit residues: 34.3303 Evaluate side-chains 97 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.927 ------------------------------------------------------------------------------- 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 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 44 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 52 optimal weight: 8.9990 chunk 8 optimal weight: 0.0670 chunk 91 optimal weight: 20.0000 chunk 97 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 63 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 overall best weight: 1.5922 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.224694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.171522 restraints weight = 10473.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.167429 restraints weight = 15263.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.169233 restraints weight = 14061.304| |-----------------------------------------------------------------------------| r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3591 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= 0.235 Angle : 0.632 10.783 12612 Z= 0.338 Chirality : 0.043 0.158 1466 Planarity : 0.004 0.036 1590 Dihedral : 6.018 39.998 1284 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.85 % Favored : 94.89 % Rotamer: Outliers : 3.53 % Allowed : 11.20 % Favored : 85.27 % 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: -3.32 (0.23), residues: 1154 helix: -2.80 (0.18), residues: 632 sheet: 0.81 (0.55), residues: 82 loop : -1.57 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 488 HIS 0.003 0.001 HIS B 808 PHE 0.026 0.002 PHE B 408 TYR 0.017 0.002 TYR B 465 ARG 0.006 0.000 ARG A 734 *********************** 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 125 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 91 time to evaluate : 0.926 Fit side-chains REVERT: A 315 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8235 (mp) REVERT: A 383 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8018 (tt) REVERT: A 397 ASP cc_start: 0.8387 (t0) cc_final: 0.8128 (t0) REVERT: A 792 ASP cc_start: 0.7058 (t70) cc_final: 0.6721 (m-30) REVERT: B 461 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7239 (pt0) REVERT: B 505 ILE cc_start: 0.8985 (tp) cc_final: 0.8660 (tp) REVERT: B 542 MET cc_start: 0.8025 (mtt) cc_final: 0.7824 (mtm) REVERT: B 558 PHE cc_start: 0.7457 (m-80) cc_final: 0.7155 (m-80) REVERT: B 750 LEU cc_start: 0.8092 (mp) cc_final: 0.7563 (tt) outliers start: 34 outliers final: 18 residues processed: 115 average time/residue: 0.1651 time to fit residues: 28.7425 Evaluate side-chains 101 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 542 MET 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 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 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 809 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 101 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 110 optimal weight: 10.0000 chunk 99 optimal weight: 0.9980 chunk 104 optimal weight: 0.0050 chunk 55 optimal weight: 9.9990 chunk 25 optimal weight: 0.7980 chunk 15 optimal weight: 0.0050 chunk 42 optimal weight: 4.9990 chunk 93 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 overall best weight: 0.4608 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.230504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.179125 restraints weight = 10329.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.175339 restraints weight = 14866.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.177444 restraints weight = 12555.274| |-----------------------------------------------------------------------------| r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9298 Z= 0.122 Angle : 0.544 9.649 12612 Z= 0.289 Chirality : 0.040 0.198 1466 Planarity : 0.003 0.028 1590 Dihedral : 5.361 37.124 1284 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.99 % Favored : 95.84 % Rotamer: Outliers : 2.90 % Allowed : 12.66 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.23), residues: 1154 helix: -2.39 (0.19), residues: 626 sheet: 0.86 (0.53), residues: 82 loop : -1.34 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 546 HIS 0.002 0.000 HIS B 808 PHE 0.015 0.001 PHE A 639 TYR 0.021 0.001 TYR A 541 ARG 0.004 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 129 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 1.024 Fit side-chains REVERT: A 400 ILE cc_start: 0.8898 (pt) cc_final: 0.8386 (mt) REVERT: A 682 ASP cc_start: 0.5623 (m-30) cc_final: 0.5325 (m-30) REVERT: B 315 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8177 (mp) REVERT: B 461 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6893 (pt0) REVERT: B 505 ILE cc_start: 0.8880 (tp) cc_final: 0.8538 (tp) REVERT: B 565 PHE cc_start: 0.7929 (OUTLIER) cc_final: 0.7181 (t80) REVERT: B 710 MET cc_start: 0.4182 (tpp) cc_final: 0.3629 (mmm) REVERT: B 716 TYR cc_start: 0.1668 (OUTLIER) cc_final: 0.1334 (m-10) REVERT: B 750 LEU cc_start: 0.8068 (mp) cc_final: 0.7590 (tt) outliers start: 28 outliers final: 12 residues processed: 123 average time/residue: 0.1660 time to fit residues: 30.9735 Evaluate side-chains 100 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 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 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 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 102 optimal weight: 9.9990 chunk 105 optimal weight: 0.0270 chunk 68 optimal weight: 0.5980 chunk 113 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 92 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 81 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 97 optimal weight: 8.9990 overall best weight: 1.8642 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.217443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.162106 restraints weight = 10030.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.157068 restraints weight = 13001.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.159295 restraints weight = 12154.974| |-----------------------------------------------------------------------------| r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.4542 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= 0.260 Angle : 0.624 11.133 12612 Z= 0.327 Chirality : 0.044 0.211 1466 Planarity : 0.003 0.028 1590 Dihedral : 5.386 36.166 1282 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.29 % Favored : 94.45 % Rotamer: Outliers : 2.70 % Allowed : 14.00 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.23), residues: 1154 helix: -2.28 (0.19), residues: 650 sheet: 0.86 (0.55), residues: 84 loop : -1.47 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 412 HIS 0.002 0.001 HIS B 808 PHE 0.017 0.002 PHE A 592 TYR 0.016 0.002 TYR B 686 ARG 0.005 0.000 ARG A 359 *********************** 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 119 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 93 time to evaluate : 1.018 Fit side-chains revert: symmetry clash REVERT: A 315 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8224 (mp) REVERT: B 358 LEU cc_start: 0.6402 (tt) cc_final: 0.6155 (tt) REVERT: B 565 PHE cc_start: 0.8088 (OUTLIER) cc_final: 0.7338 (t80) REVERT: B 710 MET cc_start: 0.4307 (tpp) cc_final: 0.3697 (mmm) outliers start: 26 outliers final: 16 residues processed: 110 average time/residue: 0.1930 time to fit residues: 31.0721 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 : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 73 optimal weight: 0.0870 chunk 37 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 112 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 107 optimal weight: 9.9990 chunk 92 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 overall best weight: 1.2164 ------------------------------------------------------------------------------- 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** A 607 GLN A 719 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.207788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.152441 restraints weight = 10304.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.144259 restraints weight = 13260.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.146707 restraints weight = 11334.760| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.4909 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= 0.182 Angle : 0.565 9.614 12612 Z= 0.294 Chirality : 0.041 0.173 1466 Planarity : 0.003 0.052 1590 Dihedral : 5.135 34.946 1282 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.80 % Allowed : 14.94 % Favored : 82.26 % 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: -2.50 (0.24), residues: 1154 helix: -2.00 (0.20), residues: 636 sheet: 0.85 (0.55), residues: 84 loop : -1.35 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 412 HIS 0.002 0.000 HIS B 808 PHE 0.014 0.001 PHE B 408 TYR 0.016 0.001 TYR A 541 ARG 0.009 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: 27 poor density : 101 time to evaluate : 0.999 Fit side-chains revert: symmetry clash REVERT: A 677 ASN cc_start: 0.7760 (t0) cc_final: 0.7552 (p0) REVERT: B 358 LEU cc_start: 0.6536 (tt) cc_final: 0.6280 (tt) REVERT: B 505 ILE cc_start: 0.8924 (tp) cc_final: 0.8560 (tp) REVERT: B 565 PHE cc_start: 0.8070 (OUTLIER) cc_final: 0.7566 (t80) REVERT: B 710 MET cc_start: 0.4838 (tpp) cc_final: 0.4252 (mmm) outliers start: 27 outliers final: 19 residues processed: 119 average time/residue: 0.1630 time to fit residues: 29.4842 Evaluate side-chains 119 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 1.176 ------------------------------------------------------------------------------- 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 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 374 ASP Chi-restraints excluded: chain B residue 432 THR 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 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 3 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 112 optimal weight: 0.0370 chunk 59 optimal weight: 0.4980 chunk 36 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 overall best weight: 0.8460 ------------------------------------------------------------------------------- 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 = 0.4416 r_free = 0.4416 target = 0.208398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.152567 restraints weight = 10355.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.143978 restraints weight = 12954.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.145904 restraints weight = 11255.128| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.5096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9298 Z= 0.148 Angle : 0.542 10.062 12612 Z= 0.283 Chirality : 0.040 0.171 1466 Planarity : 0.003 0.032 1590 Dihedral : 4.931 33.839 1282 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.28 % Allowed : 16.49 % 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: -2.38 (0.24), residues: 1154 helix: -1.83 (0.20), residues: 650 sheet: 0.86 (0.56), residues: 84 loop : -1.39 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 412 HIS 0.002 0.000 HIS B 808 PHE 0.013 0.001 PHE B 408 TYR 0.029 0.001 TYR B 471 ARG 0.005 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 122 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 1.082 Fit side-chains revert: symmetry clash REVERT: A 652 GLN cc_start: 0.6134 (OUTLIER) cc_final: 0.5804 (mt0) REVERT: B 505 ILE cc_start: 0.8958 (tp) cc_final: 0.8588 (tp) REVERT: B 565 PHE cc_start: 0.8050 (OUTLIER) cc_final: 0.7590 (t80) REVERT: B 710 MET cc_start: 0.4880 (tpp) cc_final: 0.4233 (mmm) outliers start: 22 outliers final: 17 residues processed: 113 average time/residue: 0.1845 time to fit residues: 30.9435 Evaluate side-chains 112 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.982 ------------------------------------------------------------------------------- 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 652 GLN 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 374 ASP 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 809 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 2 optimal weight: 0.7980 chunk 112 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 105 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.4396 r_free = 0.4396 target = 0.206177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.152844 restraints weight = 10455.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.148191 restraints weight = 16369.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.151009 restraints weight = 13476.527| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.5361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9298 Z= 0.200 Angle : 0.579 13.309 12612 Z= 0.302 Chirality : 0.042 0.178 1466 Planarity : 0.003 0.038 1590 Dihedral : 5.024 33.706 1282 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.59 % Allowed : 16.80 % Favored : 80.60 % 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: -1.76 (0.20), residues: 642 sheet: 0.77 (0.57), residues: 82 loop : -1.45 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 546 HIS 0.002 0.001 HIS B 706 PHE 0.011 0.001 PHE B 408 TYR 0.027 0.001 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 116 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 0.993 Fit side-chains revert: symmetry clash REVERT: A 315 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8127 (mp) REVERT: A 675 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7317 (tt) REVERT: A 710 MET cc_start: 0.2403 (mmm) cc_final: 0.0512 (mmt) REVERT: B 565 PHE cc_start: 0.8137 (OUTLIER) cc_final: 0.7674 (t80) outliers start: 25 outliers final: 18 residues processed: 105 average time/residue: 0.2036 time to fit residues: 30.9774 Evaluate side-chains 110 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU 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 675 LEU 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 374 ASP 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 809 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 94 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 64 optimal weight: 0.5980 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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 445 GLN B 596 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.207078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.153767 restraints weight = 10289.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.145997 restraints weight = 8334.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.148361 restraints weight = 8396.017| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.5565 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= 0.170 Angle : 0.565 14.276 12612 Z= 0.291 Chirality : 0.041 0.167 1466 Planarity : 0.003 0.025 1590 Dihedral : 4.872 33.060 1282 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.28 % Allowed : 17.53 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.23 (0.24), residues: 1154 helix: -1.65 (0.20), residues: 650 sheet: 0.75 (0.57), residues: 82 loop : -1.37 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 546 HIS 0.003 0.001 HIS B 706 PHE 0.012 0.001 PHE B 408 TYR 0.026 0.001 TYR B 471 ARG 0.003 0.000 ARG B 717 *********************** 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 117 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.982 Fit side-chains revert: symmetry clash REVERT: A 315 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8170 (mp) REVERT: A 675 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.6812 (tt) REVERT: A 682 ASP cc_start: 0.7084 (m-30) cc_final: 0.6670 (m-30) REVERT: A 710 MET cc_start: 0.3047 (mmm) cc_final: 0.1903 (mmt) REVERT: B 505 ILE cc_start: 0.8896 (tp) cc_final: 0.8485 (tp) REVERT: B 558 PHE cc_start: 0.7525 (m-80) cc_final: 0.7287 (m-80) REVERT: B 614 MET cc_start: 0.7318 (ptp) cc_final: 0.6810 (pmm) REVERT: B 710 MET cc_start: 0.5426 (tpp) cc_final: 0.4877 (mmm) outliers start: 22 outliers final: 17 residues processed: 110 average time/residue: 0.1799 time to fit residues: 29.6247 Evaluate side-chains 108 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU 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 675 LEU 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 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 547 PHE Chi-restraints excluded: chain B residue 549 THR 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 107 optimal weight: 8.9990 chunk 13 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 7 optimal weight: 0.3980 chunk 90 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.206848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.153619 restraints weight = 10310.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.149133 restraints weight = 16192.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.151994 restraints weight = 13898.676| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.5720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9298 Z= 0.170 Angle : 0.574 14.392 12612 Z= 0.295 Chirality : 0.041 0.174 1466 Planarity : 0.003 0.024 1590 Dihedral : 4.883 33.482 1282 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.07 % Allowed : 17.84 % Favored : 80.08 % 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: -2.17 (0.24), residues: 1154 helix: -1.56 (0.21), residues: 646 sheet: 0.73 (0.57), residues: 82 loop : -1.41 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 546 HIS 0.003 0.000 HIS B 706 PHE 0.017 0.001 PHE A 408 TYR 0.025 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 110 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 1.611 Fit side-chains revert: symmetry clash REVERT: A 315 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8064 (mp) REVERT: A 522 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7415 (mm-30) REVERT: A 710 MET cc_start: 0.2579 (mmm) cc_final: 0.1080 (mmt) REVERT: B 505 ILE cc_start: 0.8920 (tp) cc_final: 0.8507 (tp) REVERT: B 558 PHE cc_start: 0.7400 (m-80) cc_final: 0.7178 (m-80) REVERT: B 614 MET cc_start: 0.6888 (ptp) cc_final: 0.6491 (pmm) outliers start: 20 outliers final: 18 residues processed: 103 average time/residue: 0.1970 time to fit residues: 31.0585 Evaluate side-chains 101 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU 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 732 LYS 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 374 ASP 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 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 81 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 64 optimal weight: 0.3980 chunk 63 optimal weight: 2.9990 chunk 89 optimal weight: 0.0770 chunk 31 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 113 optimal weight: 0.0370 chunk 102 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 overall best weight: 0.4416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.210579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.157112 restraints weight = 10236.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.154184 restraints weight = 14868.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.155683 restraints weight = 14952.875| |-----------------------------------------------------------------------------| r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.5850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9298 Z= 0.124 Angle : 0.549 13.873 12612 Z= 0.279 Chirality : 0.040 0.171 1466 Planarity : 0.002 0.024 1590 Dihedral : 4.630 32.446 1282 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.97 % Allowed : 17.95 % Favored : 80.08 % 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: -1.93 (0.25), residues: 1154 helix: -1.39 (0.21), residues: 650 sheet: 0.79 (0.57), residues: 82 loop : -1.27 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 412 HIS 0.002 0.000 HIS B 706 PHE 0.010 0.001 PHE A 408 TYR 0.024 0.001 TYR B 471 ARG 0.002 0.000 ARG B 717 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2742.95 seconds wall clock time: 49 minutes 8.56 seconds (2948.56 seconds total)