Starting phenix.real_space_refine on Sun May 18 12:01:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q6p_18192/05_2025/8q6p_18192.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q6p_18192/05_2025/8q6p_18192.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8q6p_18192/05_2025/8q6p_18192.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q6p_18192/05_2025/8q6p_18192.map" model { file = "/net/cci-nas-00/data/ceres_data/8q6p_18192/05_2025/8q6p_18192.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q6p_18192/05_2025/8q6p_18192.cif" } resolution = 3.53 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= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 103 5.16 5 C 10497 2.51 5 N 2965 2.21 5 O 3214 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 16794 Number of models: 1 Model: "" Number of chains: 12 Chain: "2" Number of atoms: 3419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3419 Classifications: {'peptide': 431} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 416} Chain breaks: 1 Chain: "3" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2900 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 12, 'TRANS': 357} Chain breaks: 1 Chain: "4" Number of atoms: 2189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2189 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 10, 'TRANS': 261} Chain breaks: 2 Chain: "5" Number of atoms: 2455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2455 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 11, 'TRANS': 309} Chain breaks: 2 Chain: "6" Number of atoms: 3175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3175 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 8, 'TRANS': 386} Chain breaks: 3 Chain: "7" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2360 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 13, 'TRANS': 284} Chain breaks: 2 Chain: "L" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 141 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 1, 'TRANS': 15} Chain: "2" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.19, per 1000 atoms: 0.73 Number of scatterers: 16794 At special positions: 0 Unit cell: (141.55, 106.4, 146.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 103 16.00 P 15 15.00 O 3214 8.00 N 2965 7.00 C 10497 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: 3.89 Conformation dependent library (CDL) restraints added in 2.0 seconds 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4006 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 23 sheets defined 58.1% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain '2' and resid 442 through 455 Processing helix chain '2' and resid 458 through 466 Processing helix chain '2' and resid 473 through 486 Processing helix chain '2' and resid 514 through 525 removed outlier: 3.785A pdb=" N LEU 2 518 " --> pdb=" O LYS 2 514 " (cutoff:3.500A) Processing helix chain '2' and resid 561 through 565 removed outlier: 3.508A pdb=" N ASP 2 565 " --> pdb=" O VAL 2 562 " (cutoff:3.500A) Processing helix chain '2' and resid 578 through 592 removed outlier: 4.842A pdb=" N HIS 2 586 " --> pdb=" O ARG 2 582 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLU 2 587 " --> pdb=" O THR 2 583 " (cutoff:3.500A) Processing helix chain '2' and resid 627 through 632 Processing helix chain '2' and resid 635 through 642 removed outlier: 3.694A pdb=" N PHE 2 642 " --> pdb=" O ILE 2 638 " (cutoff:3.500A) Processing helix chain '2' and resid 653 through 671 Processing helix chain '2' and resid 698 through 709 Processing helix chain '2' and resid 721 through 740 Processing helix chain '2' and resid 745 through 763 removed outlier: 3.761A pdb=" N ILE 2 749 " --> pdb=" O THR 2 745 " (cutoff:3.500A) Processing helix chain '2' and resid 769 through 787 Processing helix chain '2' and resid 789 through 800 Processing helix chain '2' and resid 802 through 806 Processing helix chain '2' and resid 809 through 833 Processing helix chain '2' and resid 844 through 854 Processing helix chain '2' and resid 858 through 865 removed outlier: 3.778A pdb=" N PHE 2 862 " --> pdb=" O ASN 2 858 " (cutoff:3.500A) Processing helix chain '2' and resid 865 through 871 removed outlier: 3.552A pdb=" N LYS 2 869 " --> pdb=" O SER 2 865 " (cutoff:3.500A) Processing helix chain '3' and resid 277 through 291 Processing helix chain '3' and resid 294 through 304 removed outlier: 4.587A pdb=" N ALA 3 304 " --> pdb=" O SER 3 300 " (cutoff:3.500A) Processing helix chain '3' and resid 310 through 323 Processing helix chain '3' and resid 350 through 362 removed outlier: 3.802A pdb=" N LEU 3 354 " --> pdb=" O ALA 3 350 " (cutoff:3.500A) Processing helix chain '3' and resid 396 through 401 Processing helix chain '3' and resid 415 through 428 removed outlier: 3.740A pdb=" N GLU 3 424 " --> pdb=" O THR 3 420 " (cutoff:3.500A) Processing helix chain '3' and resid 434 through 438 removed outlier: 3.743A pdb=" N GLY 3 437 " --> pdb=" O ALA 3 434 " (cutoff:3.500A) Processing helix chain '3' and resid 464 through 470 Processing helix chain '3' and resid 473 through 479 removed outlier: 3.602A pdb=" N PHE 3 479 " --> pdb=" O LEU 3 475 " (cutoff:3.500A) Processing helix chain '3' and resid 490 through 506 Processing helix chain '3' and resid 564 through 578 removed outlier: 3.596A pdb=" N ILE 3 578 " --> pdb=" O VAL 3 574 " (cutoff:3.500A) Processing helix chain '3' and resid 583 through 603 Processing helix chain '3' and resid 615 through 633 removed outlier: 4.094A pdb=" N GLU 3 619 " --> pdb=" O ALA 3 615 " (cutoff:3.500A) Processing helix chain '3' and resid 638 through 655 removed outlier: 3.629A pdb=" N ALA 3 642 " --> pdb=" O GLU 3 638 " (cutoff:3.500A) Processing helix chain '4' and resid 442 through 455 Processing helix chain '4' and resid 457 through 466 removed outlier: 3.565A pdb=" N LEU 4 466 " --> pdb=" O LEU 4 462 " (cutoff:3.500A) Processing helix chain '4' and resid 473 through 486 Processing helix chain '4' and resid 492 through 496 Processing helix chain '4' and resid 515 through 527 removed outlier: 3.523A pdb=" N LEU 4 519 " --> pdb=" O SER 4 515 " (cutoff:3.500A) Processing helix chain '4' and resid 580 through 593 removed outlier: 3.658A pdb=" N GLN 4 593 " --> pdb=" O GLU 4 589 " (cutoff:3.500A) Processing helix chain '4' and resid 629 through 635 Processing helix chain '4' and resid 637 through 643 Processing helix chain '4' and resid 655 through 672 Processing helix chain '4' and resid 673 through 681 Processing helix chain '4' and resid 683 through 697 removed outlier: 3.622A pdb=" N LEU 4 687 " --> pdb=" O ASP 4 683 " (cutoff:3.500A) Processing helix chain '4' and resid 703 through 723 removed outlier: 3.654A pdb=" N GLY 4 723 " --> pdb=" O LYS 4 719 " (cutoff:3.500A) Processing helix chain '4' and resid 730 through 748 removed outlier: 3.982A pdb=" N LEU 4 734 " --> pdb=" O TYR 4 730 " (cutoff:3.500A) Processing helix chain '4' and resid 754 through 770 Processing helix chain '5' and resid 316 through 329 removed outlier: 3.726A pdb=" N LYS 5 329 " --> pdb=" O ARG 5 325 " (cutoff:3.500A) Processing helix chain '5' and resid 331 through 340 Processing helix chain '5' and resid 347 through 360 Processing helix chain '5' and resid 387 through 397 removed outlier: 3.614A pdb=" N LEU 5 391 " --> pdb=" O ALA 5 387 " (cutoff:3.500A) Processing helix chain '5' and resid 408 through 412 removed outlier: 3.949A pdb=" N SER 5 411 " --> pdb=" O LYS 5 408 " (cutoff:3.500A) Processing helix chain '5' and resid 433 through 438 Processing helix chain '5' and resid 448 through 451 Processing helix chain '5' and resid 452 through 466 removed outlier: 3.560A pdb=" N GLU 5 464 " --> pdb=" O HIS 5 460 " (cutoff:3.500A) Processing helix chain '5' and resid 509 through 515 Processing helix chain '5' and resid 526 through 543 Processing helix chain '5' and resid 556 through 571 Processing helix chain '5' and resid 576 through 600 Processing helix chain '5' and resid 610 through 628 Processing helix chain '5' and resid 634 through 656 removed outlier: 3.634A pdb=" N VAL 5 638 " --> pdb=" O THR 5 634 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU 5 650 " --> pdb=" O GLN 5 646 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ASP 5 651 " --> pdb=" O VAL 5 647 " (cutoff:3.500A) Processing helix chain '6' and resid 323 through 331 Processing helix chain '6' and resid 332 through 344 Processing helix chain '6' and resid 347 through 357 removed outlier: 3.543A pdb=" N PHE 6 357 " --> pdb=" O CYS 6 353 " (cutoff:3.500A) Processing helix chain '6' and resid 363 through 376 Processing helix chain '6' and resid 403 through 415 removed outlier: 3.809A pdb=" N PHE 6 407 " --> pdb=" O SER 6 403 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU 6 408 " --> pdb=" O LYS 6 404 " (cutoff:3.500A) Processing helix chain '6' and resid 449 through 454 Processing helix chain '6' and resid 463 through 467 removed outlier: 3.753A pdb=" N MET 6 467 " --> pdb=" O PHE 6 464 " (cutoff:3.500A) Processing helix chain '6' and resid 468 through 482 Processing helix chain '6' and resid 517 through 522 Processing helix chain '6' and resid 525 through 532 removed outlier: 3.654A pdb=" N PHE 6 532 " --> pdb=" O ILE 6 528 " (cutoff:3.500A) Processing helix chain '6' and resid 543 through 559 Processing helix chain '6' and resid 570 through 584 removed outlier: 3.521A pdb=" N PHE 6 584 " --> pdb=" O PHE 6 580 " (cutoff:3.500A) Processing helix chain '6' and resid 589 through 609 Processing helix chain '6' and resid 619 through 637 removed outlier: 3.998A pdb=" N LEU 6 623 " --> pdb=" O THR 6 619 " (cutoff:3.500A) Processing helix chain '6' and resid 643 through 658 removed outlier: 3.531A pdb=" N VAL 6 647 " --> pdb=" O GLN 6 643 " (cutoff:3.500A) Processing helix chain '6' and resid 719 through 737 removed outlier: 3.823A pdb=" N VAL 6 725 " --> pdb=" O SER 6 721 " (cutoff:3.500A) Processing helix chain '6' and resid 743 through 754 removed outlier: 3.730A pdb=" N LYS 6 751 " --> pdb=" O ASN 6 747 " (cutoff:3.500A) Processing helix chain '6' and resid 759 through 777 Processing helix chain '7' and resid 319 through 327 Processing helix chain '7' and resid 330 through 339 Processing helix chain '7' and resid 346 through 359 Processing helix chain '7' and resid 364 through 368 Processing helix chain '7' and resid 385 through 397 Processing helix chain '7' and resid 445 through 449 removed outlier: 3.741A pdb=" N MET 7 449 " --> pdb=" O PHE 7 446 " (cutoff:3.500A) Processing helix chain '7' and resid 450 through 464 removed outlier: 3.837A pdb=" N ALA 7 456 " --> pdb=" O SER 7 452 " (cutoff:3.500A) Processing helix chain '7' and resid 499 through 504 Processing helix chain '7' and resid 507 through 514 removed outlier: 3.902A pdb=" N PHE 7 514 " --> pdb=" O LEU 7 510 " (cutoff:3.500A) Processing helix chain '7' and resid 525 through 543 Processing helix chain '7' and resid 554 through 568 removed outlier: 3.775A pdb=" N LYS 7 568 " --> pdb=" O MET 7 564 " (cutoff:3.500A) Processing helix chain '7' and resid 573 through 594 removed outlier: 3.656A pdb=" N ALA 7 577 " --> pdb=" O PRO 7 573 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP 7 578 " --> pdb=" O GLU 7 574 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N TYR 7 579 " --> pdb=" O SER 7 575 " (cutoff:3.500A) Processing helix chain '7' and resid 601 through 619 Processing helix chain '7' and resid 625 through 644 removed outlier: 3.503A pdb=" N VAL 7 629 " --> pdb=" O GLU 7 625 " (cutoff:3.500A) Processing helix chain 'L' and resid 379 through 385 removed outlier: 3.526A pdb=" N MET L 385 " --> pdb=" O TRP L 381 " (cutoff:3.500A) Processing helix chain 'L' and resid 387 through 391 Processing sheet with id=AA1, first strand: chain '2' and resid 528 through 530 removed outlier: 6.295A pdb=" N VAL 2 529 " --> pdb=" O LEU 2 570 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N GLY 2 567 " --> pdb=" O THR 2 610 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N ILE 2 612 " --> pdb=" O GLY 2 567 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N CYS 2 569 " --> pdb=" O ILE 2 612 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N ALA 2 614 " --> pdb=" O CYS 2 569 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL 2 504 " --> pdb=" O ALA 2 613 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N SER 2 615 " --> pdb=" O VAL 2 504 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU 2 506 " --> pdb=" O SER 2 615 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LEU 2 505 " --> pdb=" O CYS 2 646 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain '2' and resid 544 through 548 removed outlier: 3.522A pdb=" N THR 2 555 " --> pdb=" O GLN 2 546 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU 2 553 " --> pdb=" O HIS 2 548 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '2' and resid 593 through 598 Processing sheet with id=AA4, first strand: chain '2' and resid 839 through 843 Processing sheet with id=AA5, first strand: chain '3' and resid 327 through 328 removed outlier: 3.599A pdb=" N LYS 3 327 " --> pdb=" O ILE 3 335 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '3' and resid 365 through 368 removed outlier: 3.501A pdb=" N CYS 3 407 " --> pdb=" O ILE 3 366 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR 3 368 " --> pdb=" O CYS 3 407 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP 3 409 " --> pdb=" O THR 3 368 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY 3 345 " --> pdb=" O ALA 3 452 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '3' and resid 381 through 384 Processing sheet with id=AA8, first strand: chain '3' and resid 430 through 433 Processing sheet with id=AA9, first strand: chain '4' and resid 614 through 617 removed outlier: 6.580A pdb=" N ILE 4 506 " --> pdb=" O ALA 4 615 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ALA 4 617 " --> pdb=" O ILE 4 506 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU 4 508 " --> pdb=" O ALA 4 617 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU 4 507 " --> pdb=" O PHE 4 648 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain '4' and resid 701 through 702 removed outlier: 6.384A pdb=" N ARG 4 701 " --> pdb=" O VAL 4 753 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain '5' and resid 364 through 365 Processing sheet with id=AB3, first strand: chain '5' and resid 402 through 406 removed outlier: 3.817A pdb=" N ALA 5 487 " --> pdb=" O LEU 5 378 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY 5 382 " --> pdb=" O ALA 5 489 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU 5 379 " --> pdb=" O PHE 5 519 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL 5 521 " --> pdb=" O LEU 5 379 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU 5 381 " --> pdb=" O VAL 5 521 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '5' and resid 418 through 421 Processing sheet with id=AB5, first strand: chain '5' and resid 469 through 472 Processing sheet with id=AB6, first strand: chain '5' and resid 574 through 575 removed outlier: 7.138A pdb=" N ARG 5 574 " --> pdb=" O ALA 5 633 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain '6' and resid 380 through 381 removed outlier: 3.780A pdb=" N LYS 6 380 " --> pdb=" O LEU 6 388 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '6' and resid 504 through 505 removed outlier: 8.060A pdb=" N ALA 6 505 " --> pdb=" O VAL 6 394 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ILE 6 396 " --> pdb=" O ALA 6 505 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N CYS 6 395 " --> pdb=" O PHE 6 536 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N LEU 6 538 " --> pdb=" O CYS 6 395 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL 6 397 " --> pdb=" O LEU 6 538 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain '6' and resid 419 through 421 Processing sheet with id=AC1, first strand: chain '6' and resid 433 through 438 Processing sheet with id=AC2, first strand: chain '6' and resid 483 through 488 Processing sheet with id=AC3, first strand: chain '6' and resid 613 through 614 Processing sheet with id=AC4, first strand: chain '7' and resid 400 through 403 removed outlier: 3.583A pdb=" N GLN 7 401 " --> pdb=" O VAL 7 440 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY 7 380 " --> pdb=" O ALA 7 487 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N CYS 7 377 " --> pdb=" O TRP 7 518 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ILE 7 520 " --> pdb=" O CYS 7 377 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N MET 7 379 " --> pdb=" O ILE 7 520 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '7' and resid 465 through 466 897 hydrogen bonds defined for protein. 2601 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: 5.07 Time building geometry restraints manager: 4.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5635 1.34 - 1.46: 2612 1.46 - 1.58: 8603 1.58 - 1.69: 25 1.69 - 1.81: 178 Bond restraints: 17053 Sorted by residual: bond pdb=" C ALA 4 729 " pdb=" N TYR 4 730 " ideal model delta sigma weight residual 1.327 1.343 -0.017 1.39e-02 5.18e+03 1.44e+00 bond pdb=" CA VAL 2 602 " pdb=" CB VAL 2 602 " ideal model delta sigma weight residual 1.540 1.525 0.015 1.36e-02 5.41e+03 1.23e+00 bond pdb=" N GLN 6 482 " pdb=" CA GLN 6 482 " ideal model delta sigma weight residual 1.457 1.470 -0.013 1.29e-02 6.01e+03 9.99e-01 bond pdb=" CA VAL 6 491 " pdb=" CB VAL 6 491 " ideal model delta sigma weight residual 1.531 1.541 -0.010 1.11e-02 8.12e+03 8.52e-01 bond pdb=" CA VAL 3 613 " pdb=" CB VAL 3 613 " ideal model delta sigma weight residual 1.527 1.539 -0.012 1.31e-02 5.83e+03 8.18e-01 ... (remaining 17048 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 22812 2.07 - 4.14: 177 4.14 - 6.21: 7 6.21 - 8.27: 2 8.27 - 10.34: 1 Bond angle restraints: 22999 Sorted by residual: angle pdb=" C GLU 4 472 " pdb=" CA GLU 4 472 " pdb=" CB GLU 4 472 " ideal model delta sigma weight residual 116.54 109.88 6.66 1.15e+00 7.56e-01 3.36e+01 angle pdb=" CA GLU 4 472 " pdb=" C GLU 4 472 " pdb=" N HIS 4 473 " ideal model delta sigma weight residual 119.52 116.53 2.99 7.90e-01 1.60e+00 1.43e+01 angle pdb=" CA LEU 4 466 " pdb=" CB LEU 4 466 " pdb=" CG LEU 4 466 " ideal model delta sigma weight residual 116.30 126.64 -10.34 3.50e+00 8.16e-02 8.73e+00 angle pdb=" C VAL 7 384 " pdb=" N ALA 7 385 " pdb=" CA ALA 7 385 " ideal model delta sigma weight residual 122.74 126.86 -4.12 1.44e+00 4.82e-01 8.17e+00 angle pdb=" C ALA 5 413 " pdb=" CA ALA 5 413 " pdb=" CB ALA 5 413 " ideal model delta sigma weight residual 110.42 115.81 -5.39 1.99e+00 2.53e-01 7.32e+00 ... (remaining 22994 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 9651 17.34 - 34.68: 741 34.68 - 52.02: 158 52.02 - 69.37: 81 69.37 - 86.71: 14 Dihedral angle restraints: 10645 sinusoidal: 4491 harmonic: 6154 Sorted by residual: dihedral pdb=" CA ASP 3 294 " pdb=" CB ASP 3 294 " pdb=" CG ASP 3 294 " pdb=" OD1 ASP 3 294 " ideal model delta sinusoidal sigma weight residual -30.00 -85.02 55.02 1 2.00e+01 2.50e-03 1.02e+01 dihedral pdb=" CA ASP 4 645 " pdb=" CB ASP 4 645 " pdb=" CG ASP 4 645 " pdb=" OD1 ASP 4 645 " ideal model delta sinusoidal sigma weight residual -30.00 -83.80 53.80 1 2.00e+01 2.50e-03 9.83e+00 dihedral pdb=" CB MET 7 379 " pdb=" CG MET 7 379 " pdb=" SD MET 7 379 " pdb=" CE MET 7 379 " ideal model delta sinusoidal sigma weight residual 180.00 123.56 56.44 3 1.50e+01 4.44e-03 9.40e+00 ... (remaining 10642 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1783 0.029 - 0.057: 513 0.057 - 0.086: 187 0.086 - 0.114: 123 0.114 - 0.143: 11 Chirality restraints: 2617 Sorted by residual: chirality pdb=" CA ILE 6 757 " pdb=" N ILE 6 757 " pdb=" C ILE 6 757 " pdb=" CB ILE 6 757 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.11e-01 chirality pdb=" CA ILE 5 470 " pdb=" N ILE 5 470 " pdb=" C ILE 5 470 " pdb=" CB ILE 5 470 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.97e-01 chirality pdb=" CA ILE 5 401 " pdb=" N ILE 5 401 " pdb=" C ILE 5 401 " pdb=" CB ILE 5 401 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.88e-01 ... (remaining 2614 not shown) Planarity restraints: 2934 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN 6 643 " 0.022 5.00e-02 4.00e+02 3.29e-02 1.73e+00 pdb=" N PRO 6 644 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO 6 644 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO 6 644 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE 2 742 " 0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO 2 743 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO 2 743 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO 2 743 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU 5 431 " 0.006 2.00e-02 2.50e+03 1.31e-02 1.71e+00 pdb=" CD GLU 5 431 " -0.023 2.00e-02 2.50e+03 pdb=" OE1 GLU 5 431 " 0.008 2.00e-02 2.50e+03 pdb=" OE2 GLU 5 431 " 0.008 2.00e-02 2.50e+03 ... (remaining 2931 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2892 2.77 - 3.30: 16336 3.30 - 3.83: 27080 3.83 - 4.37: 30735 4.37 - 4.90: 53184 Nonbonded interactions: 130227 Sorted by model distance: nonbonded pdb=" OG SER 3 352 " pdb=" O2G ATP 3 901 " model vdw 2.234 3.040 nonbonded pdb=" O LEU 6 654 " pdb=" OG SER 6 657 " model vdw 2.275 3.040 nonbonded pdb=" OE2 GLU 2 844 " pdb=" OH TYR 2 863 " model vdw 2.280 3.040 nonbonded pdb=" OG1 THR 3 509 " pdb=" OE2 GLU 3 512 " model vdw 2.288 3.040 nonbonded pdb=" O HIS 7 458 " pdb=" NH2 ARG 7 513 " model vdw 2.304 3.120 ... (remaining 130222 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 10.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.650 Check model and map are aligned: 0.110 Set scattering table: 0.240 Process input model: 39.210 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 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 : 0.002 0.029 17053 Z= 0.119 Angle : 0.484 10.343 22999 Z= 0.286 Chirality : 0.037 0.143 2617 Planarity : 0.003 0.033 2934 Dihedral : 14.142 86.707 6639 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.11 % Allowed : 6.70 % Favored : 93.19 % 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: 1.50 (0.19), residues: 2068 helix: 2.22 (0.15), residues: 1146 sheet: -0.34 (0.32), residues: 249 loop : -0.62 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L 381 HIS 0.005 0.001 HIS 6 410 PHE 0.012 0.001 PHE 2 873 TYR 0.012 0.001 TYR 6 349 ARG 0.002 0.000 ARG 3 506 Details of bonding type rmsd hydrogen bonds : bond 0.15815 ( 897) hydrogen bonds : angle 5.61831 ( 2601) covalent geometry : bond 0.00227 (17053) covalent geometry : angle 0.48438 (22999) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 555 time to evaluate : 1.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 490 LYS cc_start: 0.8023 (mptt) cc_final: 0.7582 (pttm) REVERT: 2 580 GLN cc_start: 0.7508 (tp-100) cc_final: 0.7299 (tp-100) REVERT: 2 633 ASP cc_start: 0.7799 (t70) cc_final: 0.7524 (t70) REVERT: 2 808 ARG cc_start: 0.6864 (mtp180) cc_final: 0.6458 (tpt-90) REVERT: 2 810 ASN cc_start: 0.8570 (m-40) cc_final: 0.8296 (p0) REVERT: 2 819 LYS cc_start: 0.8422 (tttt) cc_final: 0.8218 (mmmt) REVERT: 2 838 ASP cc_start: 0.7569 (m-30) cc_final: 0.6810 (t0) REVERT: 4 490 LYS cc_start: 0.7861 (mttt) cc_final: 0.7539 (tmtt) REVERT: 4 677 MET cc_start: -0.0879 (mmm) cc_final: -0.2840 (tmm) REVERT: 4 684 MET cc_start: 0.4970 (mmp) cc_final: 0.4698 (ttm) REVERT: 4 697 TYR cc_start: 0.4701 (m-80) cc_final: 0.4386 (m-10) REVERT: 5 512 LEU cc_start: 0.8667 (mt) cc_final: 0.8385 (tt) REVERT: 6 345 ASP cc_start: 0.7518 (t0) cc_final: 0.7278 (t70) REVERT: 6 401 SER cc_start: 0.8963 (m) cc_final: 0.8438 (p) REVERT: 6 436 VAL cc_start: 0.7708 (t) cc_final: 0.7463 (m) REVERT: 6 437 LYS cc_start: 0.8344 (tttt) cc_final: 0.8046 (ptpp) REVERT: 6 443 GLU cc_start: 0.7045 (mt-10) cc_final: 0.6206 (pt0) REVERT: 6 446 ILE cc_start: 0.8727 (mt) cc_final: 0.8506 (mm) REVERT: 6 580 PHE cc_start: 0.9177 (t80) cc_final: 0.8947 (t80) REVERT: 7 517 LEU cc_start: 0.7990 (tt) cc_final: 0.7248 (tt) REVERT: 7 587 MET cc_start: 0.7938 (mtt) cc_final: 0.7634 (ttp) REVERT: 7 615 LEU cc_start: 0.8439 (mt) cc_final: 0.8207 (mt) REVERT: 7 620 LEU cc_start: 0.8015 (mt) cc_final: 0.7655 (mp) outliers start: 2 outliers final: 0 residues processed: 556 average time/residue: 0.3536 time to fit residues: 272.1694 Evaluate side-chains 302 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 1.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 8.9990 chunk 157 optimal weight: 4.9990 chunk 87 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 106 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 163 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 188 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 534 GLN ** 2 671 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 672 HIS 2 718 ASN ** 2 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 628 HIS 3 640 GLN 4 623 GLN ** 4 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 751 ASN 5 536 HIS 5 541 HIS 5 630 GLN 6 410 HIS 6 496 ASN 6 521 ASN ** 6 558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 521 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.146108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.097364 restraints weight = 31807.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.099333 restraints weight = 17314.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.099747 restraints weight = 11962.646| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 17053 Z= 0.354 Angle : 0.795 12.899 22999 Z= 0.412 Chirality : 0.046 0.174 2617 Planarity : 0.006 0.095 2934 Dihedral : 9.337 89.072 2460 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.73 % Allowed : 13.90 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.62 (0.18), residues: 2068 helix: 1.40 (0.15), residues: 1150 sheet: -0.20 (0.31), residues: 262 loop : -1.05 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP 2 554 HIS 0.014 0.002 HIS 3 310 PHE 0.026 0.003 PHE 6 651 TYR 0.024 0.003 TYR 6 780 ARG 0.012 0.001 ARG 2 547 Details of bonding type rmsd hydrogen bonds : bond 0.06150 ( 897) hydrogen bonds : angle 5.31997 ( 2601) covalent geometry : bond 0.00831 (17053) covalent geometry : angle 0.79462 (22999) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 289 time to evaluate : 1.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 580 GLN cc_start: 0.7547 (tp-100) cc_final: 0.7306 (tp-100) REVERT: 2 659 MET cc_start: 0.7842 (tpp) cc_final: 0.7565 (tmm) REVERT: 2 786 ASP cc_start: 0.8629 (OUTLIER) cc_final: 0.8359 (m-30) REVERT: 2 819 LYS cc_start: 0.8615 (tttt) cc_final: 0.8282 (mmmt) REVERT: 2 838 ASP cc_start: 0.7599 (m-30) cc_final: 0.6579 (t0) REVERT: 3 339 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8421 (mt) REVERT: 3 463 ARG cc_start: 0.6957 (mtt-85) cc_final: 0.6708 (mmm-85) REVERT: 3 475 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8673 (tt) REVERT: 3 489 MET cc_start: 0.7736 (pmm) cc_final: 0.7242 (mpp) REVERT: 3 546 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8233 (tt0) REVERT: 3 646 LEU cc_start: 0.9213 (tp) cc_final: 0.9013 (tt) REVERT: 4 443 GLU cc_start: 0.7634 (mp0) cc_final: 0.7038 (mp0) REVERT: 4 492 PHE cc_start: 0.6426 (m-80) cc_final: 0.5369 (m-10) REVERT: 4 579 MET cc_start: 0.7400 (tpt) cc_final: 0.6615 (tpp) REVERT: 4 624 TRP cc_start: 0.7638 (t-100) cc_final: 0.7283 (t-100) REVERT: 4 648 PHE cc_start: 0.6747 (m-80) cc_final: 0.6433 (m-80) REVERT: 4 677 MET cc_start: -0.1324 (mmm) cc_final: -0.2478 (tmm) REVERT: 4 684 MET cc_start: 0.5025 (mmp) cc_final: 0.4805 (ttm) REVERT: 4 735 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7538 (mp0) REVERT: 5 421 ARG cc_start: 0.8199 (ptm160) cc_final: 0.6921 (ptm160) REVERT: 5 426 ARG cc_start: 0.8520 (mtp-110) cc_final: 0.8273 (mtp-110) REVERT: 5 472 LYS cc_start: 0.7767 (tttt) cc_final: 0.7540 (tmtt) REVERT: 5 568 ARG cc_start: 0.9268 (OUTLIER) cc_final: 0.8150 (mtm-85) REVERT: 6 342 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.7902 (mtt) REVERT: 6 443 GLU cc_start: 0.6925 (mt-10) cc_final: 0.6120 (pt0) REVERT: 6 446 ILE cc_start: 0.8542 (mt) cc_final: 0.8253 (mm) REVERT: 6 466 LYS cc_start: 0.8620 (mmtt) cc_final: 0.8199 (tmtt) REVERT: 6 580 PHE cc_start: 0.9384 (t80) cc_final: 0.9172 (t80) REVERT: 6 780 TYR cc_start: 0.6140 (m-10) cc_final: 0.5798 (m-80) REVERT: 7 320 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8412 (tp30) REVERT: 7 445 GLU cc_start: 0.6701 (tp30) cc_final: 0.6449 (tp30) REVERT: 7 587 MET cc_start: 0.8137 (mtt) cc_final: 0.7766 (tpt) outliers start: 86 outliers final: 41 residues processed: 358 average time/residue: 0.3154 time to fit residues: 161.8491 Evaluate side-chains 292 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 244 time to evaluate : 1.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 446 VAL Chi-restraints excluded: chain 2 residue 458 ILE Chi-restraints excluded: chain 2 residue 586 HIS Chi-restraints excluded: chain 2 residue 739 THR Chi-restraints excluded: chain 2 residue 768 VAL Chi-restraints excluded: chain 2 residue 781 LEU Chi-restraints excluded: chain 2 residue 786 ASP Chi-restraints excluded: chain 3 residue 279 ASP Chi-restraints excluded: chain 3 residue 339 ILE Chi-restraints excluded: chain 3 residue 349 VAL Chi-restraints excluded: chain 3 residue 360 HIS Chi-restraints excluded: chain 3 residue 422 ILE Chi-restraints excluded: chain 3 residue 423 HIS Chi-restraints excluded: chain 3 residue 424 GLU Chi-restraints excluded: chain 3 residue 475 LEU Chi-restraints excluded: chain 3 residue 542 LEU Chi-restraints excluded: chain 3 residue 546 GLU Chi-restraints excluded: chain 3 residue 568 ILE Chi-restraints excluded: chain 3 residue 577 LEU Chi-restraints excluded: chain 3 residue 597 ILE Chi-restraints excluded: chain 4 residue 577 ASP Chi-restraints excluded: chain 4 residue 582 SER Chi-restraints excluded: chain 4 residue 735 GLU Chi-restraints excluded: chain 4 residue 751 ASN Chi-restraints excluded: chain 5 residue 316 THR Chi-restraints excluded: chain 5 residue 370 LEU Chi-restraints excluded: chain 5 residue 378 LEU Chi-restraints excluded: chain 5 residue 478 THR Chi-restraints excluded: chain 5 residue 551 VAL Chi-restraints excluded: chain 5 residue 555 VAL Chi-restraints excluded: chain 5 residue 568 ARG Chi-restraints excluded: chain 5 residue 609 ILE Chi-restraints excluded: chain 6 residue 342 MET Chi-restraints excluded: chain 6 residue 353 CYS Chi-restraints excluded: chain 6 residue 356 LEU Chi-restraints excluded: chain 6 residue 366 ILE Chi-restraints excluded: chain 6 residue 432 THR Chi-restraints excluded: chain 6 residue 496 ASN Chi-restraints excluded: chain 6 residue 535 PHE Chi-restraints excluded: chain 6 residue 540 ASP Chi-restraints excluded: chain 6 residue 558 HIS Chi-restraints excluded: chain 7 residue 326 ILE Chi-restraints excluded: chain 7 residue 379 MET Chi-restraints excluded: chain 7 residue 400 SER Chi-restraints excluded: chain 7 residue 440 VAL Chi-restraints excluded: chain 7 residue 466 ILE Chi-restraints excluded: chain 7 residue 599 PHE Chi-restraints excluded: chain 7 residue 629 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 10 optimal weight: 0.6980 chunk 146 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 190 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 106 optimal weight: 20.0000 chunk 203 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 37 optimal weight: 9.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 534 GLN ** 2 671 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 360 HIS 4 473 HIS 4 665 HIS 4 751 ASN 5 460 HIS 5 541 HIS 6 496 ASN ** 6 558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.149611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.098135 restraints weight = 31499.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.102152 restraints weight = 17403.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.102799 restraints weight = 11780.272| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17053 Z= 0.145 Angle : 0.581 13.100 22999 Z= 0.302 Chirality : 0.040 0.150 2617 Planarity : 0.004 0.068 2934 Dihedral : 8.854 84.049 2460 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.24 % Allowed : 15.77 % Favored : 80.99 % 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: 1.01 (0.18), residues: 2068 helix: 1.68 (0.15), residues: 1162 sheet: 0.03 (0.33), residues: 242 loop : -0.86 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP 2 554 HIS 0.010 0.001 HIS 3 360 PHE 0.021 0.001 PHE 2 663 TYR 0.020 0.002 TYR 2 863 ARG 0.006 0.000 ARG 2 714 Details of bonding type rmsd hydrogen bonds : bond 0.04299 ( 897) hydrogen bonds : angle 4.65170 ( 2601) covalent geometry : bond 0.00329 (17053) covalent geometry : angle 0.58103 (22999) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 272 time to evaluate : 1.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 509 ASP cc_start: 0.7882 (m-30) cc_final: 0.7583 (t0) REVERT: 2 580 GLN cc_start: 0.7395 (tp-100) cc_final: 0.7082 (tp-100) REVERT: 2 659 MET cc_start: 0.7943 (tpp) cc_final: 0.7669 (tmm) REVERT: 2 786 ASP cc_start: 0.8625 (OUTLIER) cc_final: 0.8397 (m-30) REVERT: 2 794 ARG cc_start: 0.8312 (tpp80) cc_final: 0.7951 (tpp-160) REVERT: 2 819 LYS cc_start: 0.8605 (tttt) cc_final: 0.8259 (mmmt) REVERT: 2 838 ASP cc_start: 0.7768 (m-30) cc_final: 0.6784 (t0) REVERT: 3 489 MET cc_start: 0.7568 (pmm) cc_final: 0.7304 (mpp) REVERT: 3 646 LEU cc_start: 0.9058 (tp) cc_final: 0.8755 (tt) REVERT: 4 443 GLU cc_start: 0.7597 (mp0) cc_final: 0.7064 (mp0) REVERT: 4 518 GLN cc_start: 0.5343 (mm-40) cc_final: 0.4184 (tm-30) REVERT: 4 578 LYS cc_start: 0.7710 (tptt) cc_final: 0.6962 (mmtp) REVERT: 4 579 MET cc_start: 0.7550 (tpt) cc_final: 0.7069 (tpt) REVERT: 4 677 MET cc_start: -0.1545 (mmm) cc_final: -0.2711 (tmm) REVERT: 4 684 MET cc_start: 0.4973 (mmp) cc_final: 0.4700 (ttm) REVERT: 4 735 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7712 (mp0) REVERT: 5 421 ARG cc_start: 0.8176 (ptm160) cc_final: 0.6251 (ptm160) REVERT: 5 535 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8954 (mtpp) REVERT: 5 568 ARG cc_start: 0.9156 (OUTLIER) cc_final: 0.7993 (mtm-85) REVERT: 6 342 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.7854 (mtm) REVERT: 6 345 ASP cc_start: 0.7726 (t0) cc_final: 0.7011 (t70) REVERT: 6 443 GLU cc_start: 0.6969 (mt-10) cc_final: 0.6280 (pt0) REVERT: 6 444 PHE cc_start: 0.6846 (m-80) cc_final: 0.6407 (m-80) REVERT: 6 446 ILE cc_start: 0.8651 (mt) cc_final: 0.8414 (mm) REVERT: 6 580 PHE cc_start: 0.9384 (t80) cc_final: 0.9146 (t80) REVERT: 6 753 MET cc_start: 0.5951 (tmm) cc_final: 0.5677 (tmm) REVERT: 7 638 MET cc_start: 0.8263 (mtt) cc_final: 0.7821 (mtt) outliers start: 59 outliers final: 35 residues processed: 314 average time/residue: 0.3041 time to fit residues: 139.0041 Evaluate side-chains 283 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 243 time to evaluate : 1.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 458 ILE Chi-restraints excluded: chain 2 residue 585 ILE Chi-restraints excluded: chain 2 residue 586 HIS Chi-restraints excluded: chain 2 residue 781 LEU Chi-restraints excluded: chain 2 residue 786 ASP Chi-restraints excluded: chain 3 residue 349 VAL Chi-restraints excluded: chain 3 residue 422 ILE Chi-restraints excluded: chain 3 residue 423 HIS Chi-restraints excluded: chain 3 residue 424 GLU Chi-restraints excluded: chain 3 residue 572 ILE Chi-restraints excluded: chain 3 residue 577 LEU Chi-restraints excluded: chain 3 residue 597 ILE Chi-restraints excluded: chain 4 residue 511 ASP Chi-restraints excluded: chain 4 residue 735 GLU Chi-restraints excluded: chain 4 residue 765 HIS Chi-restraints excluded: chain 5 residue 370 LEU Chi-restraints excluded: chain 5 residue 517 MET Chi-restraints excluded: chain 5 residue 535 LYS Chi-restraints excluded: chain 5 residue 546 THR Chi-restraints excluded: chain 5 residue 568 ARG Chi-restraints excluded: chain 5 residue 609 ILE Chi-restraints excluded: chain 5 residue 618 VAL Chi-restraints excluded: chain 6 residue 342 MET Chi-restraints excluded: chain 6 residue 353 CYS Chi-restraints excluded: chain 6 residue 356 LEU Chi-restraints excluded: chain 6 residue 535 PHE Chi-restraints excluded: chain 6 residue 540 ASP Chi-restraints excluded: chain 6 residue 558 HIS Chi-restraints excluded: chain 7 residue 326 ILE Chi-restraints excluded: chain 7 residue 331 PHE Chi-restraints excluded: chain 7 residue 339 ILE Chi-restraints excluded: chain 7 residue 363 HIS Chi-restraints excluded: chain 7 residue 379 MET Chi-restraints excluded: chain 7 residue 393 ILE Chi-restraints excluded: chain 7 residue 400 SER Chi-restraints excluded: chain 7 residue 434 VAL Chi-restraints excluded: chain 7 residue 440 VAL Chi-restraints excluded: chain 7 residue 558 MET Chi-restraints excluded: chain 7 residue 581 THR Chi-restraints excluded: chain 7 residue 599 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 117 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 76 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 75 optimal weight: 0.0980 chunk 107 optimal weight: 0.0270 chunk 113 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 chunk 145 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 overall best weight: 0.9642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 665 HIS 4 751 ASN ** 5 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 496 ASN ** 6 558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.149193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.097090 restraints weight = 31349.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.100732 restraints weight = 15681.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.102980 restraints weight = 10782.827| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17053 Z= 0.130 Angle : 0.561 12.530 22999 Z= 0.288 Chirality : 0.039 0.133 2617 Planarity : 0.004 0.061 2934 Dihedral : 8.541 83.325 2460 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.52 % Allowed : 16.26 % Favored : 80.22 % 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: 1.17 (0.18), residues: 2068 helix: 1.83 (0.15), residues: 1161 sheet: 0.08 (0.34), residues: 232 loop : -0.80 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 2 554 HIS 0.010 0.001 HIS 4 744 PHE 0.022 0.001 PHE 2 663 TYR 0.017 0.002 TYR 6 569 ARG 0.024 0.000 ARG 5 421 Details of bonding type rmsd hydrogen bonds : bond 0.03862 ( 897) hydrogen bonds : angle 4.46304 ( 2601) covalent geometry : bond 0.00292 (17053) covalent geometry : angle 0.56081 (22999) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 256 time to evaluate : 2.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 509 ASP cc_start: 0.7851 (m-30) cc_final: 0.7518 (t0) REVERT: 2 580 GLN cc_start: 0.7405 (tp-100) cc_final: 0.7069 (tp-100) REVERT: 2 720 MET cc_start: 0.7215 (ppp) cc_final: 0.6997 (ppp) REVERT: 2 794 ARG cc_start: 0.8217 (tpp80) cc_final: 0.7898 (tpp-160) REVERT: 2 819 LYS cc_start: 0.8626 (tttt) cc_final: 0.8280 (mmtt) REVERT: 2 838 ASP cc_start: 0.7900 (m-30) cc_final: 0.6900 (t0) REVERT: 3 514 ASP cc_start: 0.8365 (OUTLIER) cc_final: 0.8146 (t0) REVERT: 4 443 GLU cc_start: 0.7833 (mp0) cc_final: 0.7357 (mp0) REVERT: 4 451 GLU cc_start: 0.8392 (tt0) cc_final: 0.7925 (tp30) REVERT: 4 578 LYS cc_start: 0.7441 (tptt) cc_final: 0.6661 (mmtp) REVERT: 4 579 MET cc_start: 0.7723 (tpt) cc_final: 0.7198 (tpt) REVERT: 4 677 MET cc_start: -0.1491 (mmm) cc_final: -0.2733 (tmm) REVERT: 4 684 MET cc_start: 0.4987 (mmp) cc_final: 0.4556 (mtp) REVERT: 5 451 MET cc_start: 0.8361 (mmm) cc_final: 0.8126 (mmm) REVERT: 5 535 LYS cc_start: 0.9174 (mtmt) cc_final: 0.8963 (mtpp) REVERT: 5 568 ARG cc_start: 0.9123 (OUTLIER) cc_final: 0.7957 (mtm-85) REVERT: 6 342 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.7545 (mtt) REVERT: 6 381 THR cc_start: 0.7067 (m) cc_final: 0.6839 (m) REVERT: 6 443 GLU cc_start: 0.6950 (mt-10) cc_final: 0.6278 (pt0) REVERT: 6 444 PHE cc_start: 0.7020 (m-80) cc_final: 0.6605 (m-80) REVERT: 6 580 PHE cc_start: 0.9388 (t80) cc_final: 0.9100 (t80) REVERT: 7 638 MET cc_start: 0.8271 (mtt) cc_final: 0.8044 (mtp) outliers start: 64 outliers final: 46 residues processed: 300 average time/residue: 0.3045 time to fit residues: 134.5732 Evaluate side-chains 285 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 236 time to evaluate : 1.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 585 ILE Chi-restraints excluded: chain 2 residue 586 HIS Chi-restraints excluded: chain 2 residue 781 LEU Chi-restraints excluded: chain 3 residue 419 ARG Chi-restraints excluded: chain 3 residue 422 ILE Chi-restraints excluded: chain 3 residue 423 HIS Chi-restraints excluded: chain 3 residue 424 GLU Chi-restraints excluded: chain 3 residue 438 ILE Chi-restraints excluded: chain 3 residue 514 ASP Chi-restraints excluded: chain 3 residue 542 LEU Chi-restraints excluded: chain 3 residue 572 ILE Chi-restraints excluded: chain 3 residue 577 LEU Chi-restraints excluded: chain 3 residue 597 ILE Chi-restraints excluded: chain 3 residue 631 VAL Chi-restraints excluded: chain 3 residue 648 LEU Chi-restraints excluded: chain 4 residue 499 LYS Chi-restraints excluded: chain 4 residue 511 ASP Chi-restraints excluded: chain 4 residue 631 ILE Chi-restraints excluded: chain 4 residue 751 ASN Chi-restraints excluded: chain 4 residue 765 HIS Chi-restraints excluded: chain 5 residue 370 LEU Chi-restraints excluded: chain 5 residue 415 LEU Chi-restraints excluded: chain 5 residue 475 ILE Chi-restraints excluded: chain 5 residue 517 MET Chi-restraints excluded: chain 5 residue 546 THR Chi-restraints excluded: chain 5 residue 568 ARG Chi-restraints excluded: chain 5 residue 609 ILE Chi-restraints excluded: chain 5 residue 618 VAL Chi-restraints excluded: chain 6 residue 342 MET Chi-restraints excluded: chain 6 residue 353 CYS Chi-restraints excluded: chain 6 residue 356 LEU Chi-restraints excluded: chain 6 residue 488 LYS Chi-restraints excluded: chain 6 residue 496 ASN Chi-restraints excluded: chain 6 residue 533 ASP Chi-restraints excluded: chain 6 residue 535 PHE Chi-restraints excluded: chain 6 residue 540 ASP Chi-restraints excluded: chain 6 residue 558 HIS Chi-restraints excluded: chain 7 residue 326 ILE Chi-restraints excluded: chain 7 residue 331 PHE Chi-restraints excluded: chain 7 residue 339 ILE Chi-restraints excluded: chain 7 residue 393 ILE Chi-restraints excluded: chain 7 residue 400 SER Chi-restraints excluded: chain 7 residue 434 VAL Chi-restraints excluded: chain 7 residue 440 VAL Chi-restraints excluded: chain 7 residue 450 MET Chi-restraints excluded: chain 7 residue 465 THR Chi-restraints excluded: chain 7 residue 565 CYS Chi-restraints excluded: chain 7 residue 599 PHE Chi-restraints excluded: chain 7 residue 626 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 178 optimal weight: 5.9990 chunk 182 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 93 optimal weight: 9.9990 chunk 169 optimal weight: 1.9990 chunk 138 optimal weight: 0.4980 chunk 198 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 151 optimal weight: 0.8980 chunk 54 optimal weight: 7.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 665 HIS 4 751 ASN ** 5 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 541 HIS 6 496 ASN 6 558 HIS ** 6 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.147264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.095432 restraints weight = 31963.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.098989 restraints weight = 16125.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.101217 restraints weight = 11131.861| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 17053 Z= 0.205 Angle : 0.610 10.406 22999 Z= 0.314 Chirality : 0.041 0.183 2617 Planarity : 0.004 0.060 2934 Dihedral : 8.553 89.984 2460 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.18 % Allowed : 16.59 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.96 (0.18), residues: 2068 helix: 1.64 (0.15), residues: 1166 sheet: -0.02 (0.31), residues: 262 loop : -0.91 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 2 554 HIS 0.010 0.001 HIS 7 458 PHE 0.023 0.002 PHE 2 663 TYR 0.016 0.002 TYR 7 579 ARG 0.006 0.001 ARG 6 498 Details of bonding type rmsd hydrogen bonds : bond 0.04483 ( 897) hydrogen bonds : angle 4.62849 ( 2601) covalent geometry : bond 0.00480 (17053) covalent geometry : angle 0.60992 (22999) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 241 time to evaluate : 1.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 509 ASP cc_start: 0.8010 (m-30) cc_final: 0.7679 (t0) REVERT: 2 580 GLN cc_start: 0.7513 (tp-100) cc_final: 0.7189 (tp-100) REVERT: 2 786 ASP cc_start: 0.8646 (OUTLIER) cc_final: 0.8407 (m-30) REVERT: 2 819 LYS cc_start: 0.8692 (tttt) cc_final: 0.8345 (mmtt) REVERT: 2 838 ASP cc_start: 0.7794 (m-30) cc_final: 0.6729 (t0) REVERT: 2 855 ASN cc_start: 0.8357 (m-40) cc_final: 0.8061 (t0) REVERT: 3 353 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.7276 (mp10) REVERT: 3 514 ASP cc_start: 0.8383 (OUTLIER) cc_final: 0.8176 (t0) REVERT: 4 443 GLU cc_start: 0.7905 (mp0) cc_final: 0.7434 (mp0) REVERT: 4 451 GLU cc_start: 0.8416 (tt0) cc_final: 0.7950 (tp30) REVERT: 4 578 LYS cc_start: 0.7296 (tptt) cc_final: 0.6841 (tptp) REVERT: 4 579 MET cc_start: 0.7465 (tpt) cc_final: 0.6804 (tpp) REVERT: 4 650 MET cc_start: 0.2472 (tmm) cc_final: 0.2245 (tmm) REVERT: 4 677 MET cc_start: -0.1693 (mmm) cc_final: -0.2823 (tmm) REVERT: 4 684 MET cc_start: 0.4995 (mmp) cc_final: 0.4549 (mtp) REVERT: 5 535 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8960 (mtpp) REVERT: 5 568 ARG cc_start: 0.9135 (OUTLIER) cc_final: 0.7989 (mtm-85) REVERT: 6 342 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.7556 (mtt) REVERT: 6 381 THR cc_start: 0.6932 (m) cc_final: 0.6711 (m) REVERT: 6 443 GLU cc_start: 0.7010 (mt-10) cc_final: 0.6243 (pt0) REVERT: 6 444 PHE cc_start: 0.7172 (m-80) cc_final: 0.6734 (m-80) REVERT: 6 580 PHE cc_start: 0.9399 (t80) cc_final: 0.9083 (t80) REVERT: 7 320 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8359 (tp30) REVERT: 7 638 MET cc_start: 0.8272 (mtt) cc_final: 0.8026 (mtp) outliers start: 76 outliers final: 50 residues processed: 295 average time/residue: 0.2981 time to fit residues: 131.8006 Evaluate side-chains 286 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 230 time to evaluate : 1.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 585 ILE Chi-restraints excluded: chain 2 residue 586 HIS Chi-restraints excluded: chain 2 residue 781 LEU Chi-restraints excluded: chain 2 residue 786 ASP Chi-restraints excluded: chain 3 residue 279 ASP Chi-restraints excluded: chain 3 residue 349 VAL Chi-restraints excluded: chain 3 residue 353 GLN Chi-restraints excluded: chain 3 residue 419 ARG Chi-restraints excluded: chain 3 residue 422 ILE Chi-restraints excluded: chain 3 residue 423 HIS Chi-restraints excluded: chain 3 residue 424 GLU Chi-restraints excluded: chain 3 residue 438 ILE Chi-restraints excluded: chain 3 residue 514 ASP Chi-restraints excluded: chain 3 residue 542 LEU Chi-restraints excluded: chain 3 residue 568 ILE Chi-restraints excluded: chain 3 residue 572 ILE Chi-restraints excluded: chain 3 residue 577 LEU Chi-restraints excluded: chain 3 residue 597 ILE Chi-restraints excluded: chain 3 residue 631 VAL Chi-restraints excluded: chain 3 residue 648 LEU Chi-restraints excluded: chain 4 residue 499 LYS Chi-restraints excluded: chain 4 residue 511 ASP Chi-restraints excluded: chain 4 residue 577 ASP Chi-restraints excluded: chain 4 residue 631 ILE Chi-restraints excluded: chain 4 residue 751 ASN Chi-restraints excluded: chain 4 residue 765 HIS Chi-restraints excluded: chain 5 residue 370 LEU Chi-restraints excluded: chain 5 residue 415 LEU Chi-restraints excluded: chain 5 residue 468 ILE Chi-restraints excluded: chain 5 residue 475 ILE Chi-restraints excluded: chain 5 residue 478 THR Chi-restraints excluded: chain 5 residue 517 MET Chi-restraints excluded: chain 5 residue 535 LYS Chi-restraints excluded: chain 5 residue 546 THR Chi-restraints excluded: chain 5 residue 551 VAL Chi-restraints excluded: chain 5 residue 557 LEU Chi-restraints excluded: chain 5 residue 568 ARG Chi-restraints excluded: chain 5 residue 609 ILE Chi-restraints excluded: chain 5 residue 618 VAL Chi-restraints excluded: chain 6 residue 327 ILE Chi-restraints excluded: chain 6 residue 342 MET Chi-restraints excluded: chain 6 residue 353 CYS Chi-restraints excluded: chain 6 residue 356 LEU Chi-restraints excluded: chain 6 residue 488 LYS Chi-restraints excluded: chain 6 residue 518 LEU Chi-restraints excluded: chain 6 residue 533 ASP Chi-restraints excluded: chain 6 residue 535 PHE Chi-restraints excluded: chain 6 residue 540 ASP Chi-restraints excluded: chain 7 residue 326 ILE Chi-restraints excluded: chain 7 residue 331 PHE Chi-restraints excluded: chain 7 residue 339 ILE Chi-restraints excluded: chain 7 residue 393 ILE Chi-restraints excluded: chain 7 residue 400 SER Chi-restraints excluded: chain 7 residue 440 VAL Chi-restraints excluded: chain 7 residue 599 PHE Chi-restraints excluded: chain 7 residue 629 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 98 optimal weight: 7.9990 chunk 189 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 203 optimal weight: 8.9990 chunk 188 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 103 optimal weight: 9.9990 chunk 118 optimal weight: 0.6980 chunk 183 optimal weight: 0.9980 chunk 87 optimal weight: 0.0870 chunk 137 optimal weight: 3.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 631 ASN ** 2 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 751 ASN 5 541 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.150112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.098636 restraints weight = 31792.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.102326 restraints weight = 15781.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.104642 restraints weight = 10788.697| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17053 Z= 0.116 Angle : 0.552 14.485 22999 Z= 0.281 Chirality : 0.039 0.161 2617 Planarity : 0.003 0.034 2934 Dihedral : 8.291 85.362 2460 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.85 % Allowed : 16.92 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.21 (0.19), residues: 2068 helix: 1.85 (0.15), residues: 1163 sheet: 0.09 (0.33), residues: 245 loop : -0.78 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP 2 554 HIS 0.008 0.001 HIS 4 744 PHE 0.023 0.001 PHE 2 663 TYR 0.024 0.001 TYR 7 579 ARG 0.007 0.000 ARG 5 426 Details of bonding type rmsd hydrogen bonds : bond 0.03566 ( 897) hydrogen bonds : angle 4.35136 ( 2601) covalent geometry : bond 0.00254 (17053) covalent geometry : angle 0.55245 (22999) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 248 time to evaluate : 1.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 509 ASP cc_start: 0.7875 (m-30) cc_final: 0.7528 (t0) REVERT: 2 580 GLN cc_start: 0.7448 (tp-100) cc_final: 0.7101 (tp-100) REVERT: 2 786 ASP cc_start: 0.8613 (OUTLIER) cc_final: 0.8386 (m-30) REVERT: 2 819 LYS cc_start: 0.8656 (tttt) cc_final: 0.8284 (mmtt) REVERT: 2 838 ASP cc_start: 0.7882 (m-30) cc_final: 0.6790 (t0) REVERT: 2 855 ASN cc_start: 0.8332 (m-40) cc_final: 0.7991 (t0) REVERT: 3 353 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.7157 (mp10) REVERT: 3 514 ASP cc_start: 0.8397 (OUTLIER) cc_final: 0.8146 (t0) REVERT: 4 451 GLU cc_start: 0.8366 (tt0) cc_final: 0.7931 (tp30) REVERT: 4 472 GLU cc_start: 0.6425 (OUTLIER) cc_final: 0.5666 (tt0) REVERT: 4 578 LYS cc_start: 0.7290 (tptt) cc_final: 0.6849 (tptp) REVERT: 4 579 MET cc_start: 0.7539 (tpt) cc_final: 0.6890 (tpp) REVERT: 4 593 GLN cc_start: 0.0887 (OUTLIER) cc_final: 0.0234 (pm20) REVERT: 4 650 MET cc_start: 0.2382 (tmm) cc_final: 0.2161 (tmm) REVERT: 4 677 MET cc_start: -0.1818 (mmm) cc_final: -0.2922 (tmm) REVERT: 4 684 MET cc_start: 0.4977 (mmp) cc_final: 0.4516 (mtp) REVERT: 5 451 MET cc_start: 0.8433 (mmm) cc_final: 0.8186 (mmm) REVERT: 5 535 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8843 (mtpp) REVERT: 5 568 ARG cc_start: 0.9085 (OUTLIER) cc_final: 0.8877 (mtm-85) REVERT: 6 342 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.7589 (mtt) REVERT: 6 443 GLU cc_start: 0.7029 (mt-10) cc_final: 0.6336 (pt0) REVERT: 6 444 PHE cc_start: 0.7092 (m-80) cc_final: 0.6540 (m-80) REVERT: 6 580 PHE cc_start: 0.9400 (t80) cc_final: 0.9105 (t80) REVERT: 7 638 MET cc_start: 0.8321 (mtt) cc_final: 0.8067 (mtp) outliers start: 70 outliers final: 44 residues processed: 298 average time/residue: 0.2840 time to fit residues: 126.6639 Evaluate side-chains 283 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 231 time to evaluate : 1.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 585 ILE Chi-restraints excluded: chain 2 residue 586 HIS Chi-restraints excluded: chain 2 residue 781 LEU Chi-restraints excluded: chain 2 residue 786 ASP Chi-restraints excluded: chain 3 residue 279 ASP Chi-restraints excluded: chain 3 residue 349 VAL Chi-restraints excluded: chain 3 residue 353 GLN Chi-restraints excluded: chain 3 residue 416 ASP Chi-restraints excluded: chain 3 residue 419 ARG Chi-restraints excluded: chain 3 residue 422 ILE Chi-restraints excluded: chain 3 residue 423 HIS Chi-restraints excluded: chain 3 residue 424 GLU Chi-restraints excluded: chain 3 residue 438 ILE Chi-restraints excluded: chain 3 residue 509 THR Chi-restraints excluded: chain 3 residue 514 ASP Chi-restraints excluded: chain 3 residue 542 LEU Chi-restraints excluded: chain 3 residue 568 ILE Chi-restraints excluded: chain 3 residue 572 ILE Chi-restraints excluded: chain 3 residue 577 LEU Chi-restraints excluded: chain 3 residue 597 ILE Chi-restraints excluded: chain 3 residue 631 VAL Chi-restraints excluded: chain 3 residue 648 LEU Chi-restraints excluded: chain 4 residue 472 GLU Chi-restraints excluded: chain 4 residue 499 LYS Chi-restraints excluded: chain 4 residue 511 ASP Chi-restraints excluded: chain 4 residue 577 ASP Chi-restraints excluded: chain 4 residue 582 SER Chi-restraints excluded: chain 4 residue 593 GLN Chi-restraints excluded: chain 4 residue 631 ILE Chi-restraints excluded: chain 5 residue 415 LEU Chi-restraints excluded: chain 5 residue 475 ILE Chi-restraints excluded: chain 5 residue 535 LYS Chi-restraints excluded: chain 5 residue 541 HIS Chi-restraints excluded: chain 5 residue 546 THR Chi-restraints excluded: chain 5 residue 551 VAL Chi-restraints excluded: chain 5 residue 557 LEU Chi-restraints excluded: chain 5 residue 568 ARG Chi-restraints excluded: chain 5 residue 609 ILE Chi-restraints excluded: chain 6 residue 342 MET Chi-restraints excluded: chain 6 residue 353 CYS Chi-restraints excluded: chain 6 residue 356 LEU Chi-restraints excluded: chain 6 residue 488 LYS Chi-restraints excluded: chain 6 residue 533 ASP Chi-restraints excluded: chain 6 residue 535 PHE Chi-restraints excluded: chain 6 residue 540 ASP Chi-restraints excluded: chain 6 residue 558 HIS Chi-restraints excluded: chain 7 residue 331 PHE Chi-restraints excluded: chain 7 residue 339 ILE Chi-restraints excluded: chain 7 residue 393 ILE Chi-restraints excluded: chain 7 residue 400 SER Chi-restraints excluded: chain 7 residue 450 MET Chi-restraints excluded: chain 7 residue 499 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 76 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 126 optimal weight: 0.4980 chunk 178 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 423 HIS ** 4 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 751 ASN 5 541 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.148442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.097657 restraints weight = 31589.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.102148 restraints weight = 17131.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.102618 restraints weight = 10324.072| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.4809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17053 Z= 0.157 Angle : 0.576 11.414 22999 Z= 0.295 Chirality : 0.040 0.288 2617 Planarity : 0.003 0.042 2934 Dihedral : 8.235 89.628 2460 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.79 % Allowed : 18.02 % Favored : 78.19 % 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: 1.07 (0.19), residues: 2068 helix: 1.74 (0.15), residues: 1168 sheet: -0.06 (0.32), residues: 257 loop : -0.84 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP 2 554 HIS 0.008 0.001 HIS 7 363 PHE 0.022 0.001 PHE 2 663 TYR 0.048 0.002 TYR 2 863 ARG 0.009 0.000 ARG 6 776 Details of bonding type rmsd hydrogen bonds : bond 0.03955 ( 897) hydrogen bonds : angle 4.44639 ( 2601) covalent geometry : bond 0.00364 (17053) covalent geometry : angle 0.57558 (22999) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 237 time to evaluate : 1.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 509 ASP cc_start: 0.7972 (m-30) cc_final: 0.7635 (t0) REVERT: 2 580 GLN cc_start: 0.7506 (tp-100) cc_final: 0.7153 (tp-100) REVERT: 2 656 GLN cc_start: 0.8125 (tt0) cc_final: 0.7892 (pt0) REVERT: 2 786 ASP cc_start: 0.8628 (OUTLIER) cc_final: 0.8398 (m-30) REVERT: 2 819 LYS cc_start: 0.8685 (tttt) cc_final: 0.8337 (mmtt) REVERT: 2 838 ASP cc_start: 0.7813 (m-30) cc_final: 0.6722 (t0) REVERT: 3 353 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.7267 (mp10) REVERT: 3 514 ASP cc_start: 0.8367 (OUTLIER) cc_final: 0.8135 (t0) REVERT: 4 444 GLU cc_start: 0.9134 (tp30) cc_final: 0.8464 (tm-30) REVERT: 4 451 GLU cc_start: 0.8385 (tt0) cc_final: 0.7906 (tp30) REVERT: 4 579 MET cc_start: 0.7509 (tpt) cc_final: 0.6495 (tpp) REVERT: 4 650 MET cc_start: 0.2455 (tmm) cc_final: 0.2207 (tmm) REVERT: 4 677 MET cc_start: -0.1854 (mmm) cc_final: -0.2927 (tmm) REVERT: 4 684 MET cc_start: 0.5037 (mmp) cc_final: 0.4514 (mtp) REVERT: 5 451 MET cc_start: 0.8372 (mmm) cc_final: 0.8119 (mmm) REVERT: 5 535 LYS cc_start: 0.9239 (OUTLIER) cc_final: 0.9000 (mtpp) REVERT: 5 568 ARG cc_start: 0.9122 (OUTLIER) cc_final: 0.7983 (mtm-85) REVERT: 6 342 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.7641 (mtt) REVERT: 6 443 GLU cc_start: 0.7021 (mt-10) cc_final: 0.6305 (pt0) REVERT: 6 580 PHE cc_start: 0.9407 (t80) cc_final: 0.9106 (t80) REVERT: 7 363 HIS cc_start: 0.5390 (t70) cc_final: 0.5138 (t-90) REVERT: 7 599 PHE cc_start: 0.7294 (t80) cc_final: 0.7093 (t80) outliers start: 69 outliers final: 51 residues processed: 291 average time/residue: 0.2827 time to fit residues: 124.3566 Evaluate side-chains 284 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 227 time to evaluate : 1.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 462 ILE Chi-restraints excluded: chain 2 residue 585 ILE Chi-restraints excluded: chain 2 residue 586 HIS Chi-restraints excluded: chain 2 residue 739 THR Chi-restraints excluded: chain 2 residue 781 LEU Chi-restraints excluded: chain 2 residue 786 ASP Chi-restraints excluded: chain 3 residue 279 ASP Chi-restraints excluded: chain 3 residue 349 VAL Chi-restraints excluded: chain 3 residue 353 GLN Chi-restraints excluded: chain 3 residue 416 ASP Chi-restraints excluded: chain 3 residue 419 ARG Chi-restraints excluded: chain 3 residue 422 ILE Chi-restraints excluded: chain 3 residue 423 HIS Chi-restraints excluded: chain 3 residue 424 GLU Chi-restraints excluded: chain 3 residue 438 ILE Chi-restraints excluded: chain 3 residue 509 THR Chi-restraints excluded: chain 3 residue 514 ASP Chi-restraints excluded: chain 3 residue 542 LEU Chi-restraints excluded: chain 3 residue 568 ILE Chi-restraints excluded: chain 3 residue 572 ILE Chi-restraints excluded: chain 3 residue 577 LEU Chi-restraints excluded: chain 3 residue 597 ILE Chi-restraints excluded: chain 3 residue 631 VAL Chi-restraints excluded: chain 3 residue 648 LEU Chi-restraints excluded: chain 4 residue 499 LYS Chi-restraints excluded: chain 4 residue 511 ASP Chi-restraints excluded: chain 4 residue 577 ASP Chi-restraints excluded: chain 4 residue 631 ILE Chi-restraints excluded: chain 4 residue 751 ASN Chi-restraints excluded: chain 5 residue 415 LEU Chi-restraints excluded: chain 5 residue 475 ILE Chi-restraints excluded: chain 5 residue 517 MET Chi-restraints excluded: chain 5 residue 535 LYS Chi-restraints excluded: chain 5 residue 546 THR Chi-restraints excluded: chain 5 residue 551 VAL Chi-restraints excluded: chain 5 residue 557 LEU Chi-restraints excluded: chain 5 residue 568 ARG Chi-restraints excluded: chain 5 residue 609 ILE Chi-restraints excluded: chain 5 residue 647 VAL Chi-restraints excluded: chain 6 residue 342 MET Chi-restraints excluded: chain 6 residue 353 CYS Chi-restraints excluded: chain 6 residue 356 LEU Chi-restraints excluded: chain 6 residue 488 LYS Chi-restraints excluded: chain 6 residue 533 ASP Chi-restraints excluded: chain 6 residue 535 PHE Chi-restraints excluded: chain 6 residue 540 ASP Chi-restraints excluded: chain 6 residue 558 HIS Chi-restraints excluded: chain 6 residue 614 SER Chi-restraints excluded: chain 6 residue 620 VAL Chi-restraints excluded: chain 7 residue 326 ILE Chi-restraints excluded: chain 7 residue 331 PHE Chi-restraints excluded: chain 7 residue 339 ILE Chi-restraints excluded: chain 7 residue 393 ILE Chi-restraints excluded: chain 7 residue 400 SER Chi-restraints excluded: chain 7 residue 440 VAL Chi-restraints excluded: chain 7 residue 450 MET Chi-restraints excluded: chain 7 residue 499 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 204 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 2 optimal weight: 0.0060 chunk 36 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 89 optimal weight: 10.0000 chunk 140 optimal weight: 3.9990 chunk 187 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 chunk 150 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 overall best weight: 1.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 855 ASN 3 423 HIS ** 4 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 751 ASN 5 541 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.148534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.097175 restraints weight = 31449.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.100774 restraints weight = 15771.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.103051 restraints weight = 10811.764| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.4927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17053 Z= 0.153 Angle : 0.590 12.385 22999 Z= 0.297 Chirality : 0.040 0.241 2617 Planarity : 0.003 0.045 2934 Dihedral : 8.201 88.531 2460 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.85 % Allowed : 18.08 % Favored : 78.08 % 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: 1.03 (0.19), residues: 2068 helix: 1.70 (0.15), residues: 1168 sheet: -0.09 (0.32), residues: 255 loop : -0.84 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP 2 554 HIS 0.010 0.001 HIS 7 458 PHE 0.020 0.001 PHE 2 663 TYR 0.045 0.002 TYR 2 863 ARG 0.008 0.000 ARG 6 776 Details of bonding type rmsd hydrogen bonds : bond 0.03907 ( 897) hydrogen bonds : angle 4.41775 ( 2601) covalent geometry : bond 0.00355 (17053) covalent geometry : angle 0.59022 (22999) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 234 time to evaluate : 2.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 509 ASP cc_start: 0.7960 (m-30) cc_final: 0.7620 (t0) REVERT: 2 580 GLN cc_start: 0.7487 (tp-100) cc_final: 0.7123 (tp-100) REVERT: 2 656 GLN cc_start: 0.8097 (tt0) cc_final: 0.7855 (tm-30) REVERT: 2 786 ASP cc_start: 0.8621 (OUTLIER) cc_final: 0.8395 (m-30) REVERT: 2 819 LYS cc_start: 0.8679 (tttt) cc_final: 0.8286 (mmmt) REVERT: 2 838 ASP cc_start: 0.7862 (m-30) cc_final: 0.6795 (t0) REVERT: 3 339 ILE cc_start: 0.8840 (OUTLIER) cc_final: 0.8567 (mt) REVERT: 3 353 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.7271 (mp10) REVERT: 3 424 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8285 (pp20) REVERT: 3 514 ASP cc_start: 0.8395 (OUTLIER) cc_final: 0.8146 (t0) REVERT: 4 444 GLU cc_start: 0.9116 (tp30) cc_final: 0.8486 (tm-30) REVERT: 4 451 GLU cc_start: 0.8433 (tt0) cc_final: 0.8011 (tp30) REVERT: 4 579 MET cc_start: 0.7528 (tpt) cc_final: 0.6507 (tpp) REVERT: 4 648 PHE cc_start: 0.6440 (m-80) cc_final: 0.5981 (m-80) REVERT: 4 650 MET cc_start: 0.2478 (tmm) cc_final: 0.2226 (tmm) REVERT: 4 677 MET cc_start: -0.1824 (mmm) cc_final: -0.2057 (mmt) REVERT: 4 684 MET cc_start: 0.5025 (mmp) cc_final: 0.4791 (mtp) REVERT: 5 451 MET cc_start: 0.8468 (mmm) cc_final: 0.8191 (mmm) REVERT: 5 535 LYS cc_start: 0.9231 (OUTLIER) cc_final: 0.9029 (mtpp) REVERT: 5 568 ARG cc_start: 0.9105 (OUTLIER) cc_final: 0.7958 (mtm-85) REVERT: 6 342 MET cc_start: 0.8339 (OUTLIER) cc_final: 0.7617 (mtt) REVERT: 6 443 GLU cc_start: 0.6978 (mt-10) cc_final: 0.6486 (pt0) REVERT: 6 580 PHE cc_start: 0.9385 (t80) cc_final: 0.9065 (t80) REVERT: 7 320 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8471 (tp30) REVERT: 7 363 HIS cc_start: 0.5736 (t70) cc_final: 0.5427 (t-90) REVERT: 7 638 MET cc_start: 0.8032 (mtp) cc_final: 0.7780 (mtp) outliers start: 70 outliers final: 52 residues processed: 286 average time/residue: 0.2693 time to fit residues: 116.2343 Evaluate side-chains 281 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 221 time to evaluate : 2.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 462 ILE Chi-restraints excluded: chain 2 residue 471 TYR Chi-restraints excluded: chain 2 residue 585 ILE Chi-restraints excluded: chain 2 residue 586 HIS Chi-restraints excluded: chain 2 residue 739 THR Chi-restraints excluded: chain 2 residue 781 LEU Chi-restraints excluded: chain 2 residue 786 ASP Chi-restraints excluded: chain 3 residue 279 ASP Chi-restraints excluded: chain 3 residue 339 ILE Chi-restraints excluded: chain 3 residue 349 VAL Chi-restraints excluded: chain 3 residue 353 GLN Chi-restraints excluded: chain 3 residue 416 ASP Chi-restraints excluded: chain 3 residue 419 ARG Chi-restraints excluded: chain 3 residue 422 ILE Chi-restraints excluded: chain 3 residue 424 GLU Chi-restraints excluded: chain 3 residue 438 ILE Chi-restraints excluded: chain 3 residue 509 THR Chi-restraints excluded: chain 3 residue 514 ASP Chi-restraints excluded: chain 3 residue 542 LEU Chi-restraints excluded: chain 3 residue 568 ILE Chi-restraints excluded: chain 3 residue 572 ILE Chi-restraints excluded: chain 3 residue 577 LEU Chi-restraints excluded: chain 3 residue 597 ILE Chi-restraints excluded: chain 3 residue 631 VAL Chi-restraints excluded: chain 3 residue 648 LEU Chi-restraints excluded: chain 4 residue 499 LYS Chi-restraints excluded: chain 4 residue 511 ASP Chi-restraints excluded: chain 4 residue 577 ASP Chi-restraints excluded: chain 4 residue 631 ILE Chi-restraints excluded: chain 4 residue 751 ASN Chi-restraints excluded: chain 5 residue 415 LEU Chi-restraints excluded: chain 5 residue 475 ILE Chi-restraints excluded: chain 5 residue 517 MET Chi-restraints excluded: chain 5 residue 535 LYS Chi-restraints excluded: chain 5 residue 541 HIS Chi-restraints excluded: chain 5 residue 546 THR Chi-restraints excluded: chain 5 residue 551 VAL Chi-restraints excluded: chain 5 residue 557 LEU Chi-restraints excluded: chain 5 residue 568 ARG Chi-restraints excluded: chain 5 residue 609 ILE Chi-restraints excluded: chain 5 residue 618 VAL Chi-restraints excluded: chain 5 residue 647 VAL Chi-restraints excluded: chain 6 residue 342 MET Chi-restraints excluded: chain 6 residue 353 CYS Chi-restraints excluded: chain 6 residue 356 LEU Chi-restraints excluded: chain 6 residue 533 ASP Chi-restraints excluded: chain 6 residue 535 PHE Chi-restraints excluded: chain 6 residue 540 ASP Chi-restraints excluded: chain 6 residue 558 HIS Chi-restraints excluded: chain 6 residue 614 SER Chi-restraints excluded: chain 6 residue 620 VAL Chi-restraints excluded: chain 7 residue 326 ILE Chi-restraints excluded: chain 7 residue 331 PHE Chi-restraints excluded: chain 7 residue 339 ILE Chi-restraints excluded: chain 7 residue 393 ILE Chi-restraints excluded: chain 7 residue 400 SER Chi-restraints excluded: chain 7 residue 440 VAL Chi-restraints excluded: chain 7 residue 450 MET Chi-restraints excluded: chain 7 residue 499 THR Chi-restraints excluded: chain 7 residue 511 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 198 optimal weight: 0.0020 chunk 163 optimal weight: 0.7980 chunk 83 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 193 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 151 optimal weight: 0.0770 chunk 131 optimal weight: 0.8980 overall best weight: 0.5146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 423 HIS ** 4 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 751 ASN 5 541 HIS ** 6 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.150749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.100174 restraints weight = 31787.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.104462 restraints weight = 17125.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.105486 restraints weight = 10482.115| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.5005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17053 Z= 0.109 Angle : 0.597 16.676 22999 Z= 0.293 Chirality : 0.039 0.193 2617 Planarity : 0.003 0.049 2934 Dihedral : 8.074 88.930 2460 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.24 % Allowed : 18.52 % Favored : 78.24 % 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: 1.19 (0.19), residues: 2068 helix: 1.79 (0.16), residues: 1166 sheet: 0.16 (0.33), residues: 248 loop : -0.76 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP 2 554 HIS 0.009 0.001 HIS 4 744 PHE 0.019 0.001 PHE 2 663 TYR 0.044 0.001 TYR 2 863 ARG 0.008 0.000 ARG 6 498 Details of bonding type rmsd hydrogen bonds : bond 0.03375 ( 897) hydrogen bonds : angle 4.25690 ( 2601) covalent geometry : bond 0.00230 (17053) covalent geometry : angle 0.59730 (22999) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 236 time to evaluate : 1.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 509 ASP cc_start: 0.7856 (m-30) cc_final: 0.7506 (t0) REVERT: 2 580 GLN cc_start: 0.7437 (tp-100) cc_final: 0.7060 (tp-100) REVERT: 2 656 GLN cc_start: 0.8270 (tt0) cc_final: 0.7958 (tm-30) REVERT: 2 720 MET cc_start: 0.6704 (ppp) cc_final: 0.6366 (ppp) REVERT: 2 786 ASP cc_start: 0.8623 (OUTLIER) cc_final: 0.8395 (m-30) REVERT: 2 819 LYS cc_start: 0.8725 (tttt) cc_final: 0.8360 (mmmt) REVERT: 2 838 ASP cc_start: 0.7954 (m-30) cc_final: 0.6911 (t0) REVERT: 3 353 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.7203 (mp10) REVERT: 3 424 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8163 (pp20) REVERT: 3 514 ASP cc_start: 0.8347 (OUTLIER) cc_final: 0.8063 (t0) REVERT: 4 444 GLU cc_start: 0.9114 (tp30) cc_final: 0.8392 (tm-30) REVERT: 4 472 GLU cc_start: 0.6407 (OUTLIER) cc_final: 0.5700 (tt0) REVERT: 4 579 MET cc_start: 0.7407 (tpt) cc_final: 0.6368 (tpp) REVERT: 4 648 PHE cc_start: 0.6295 (m-80) cc_final: 0.5834 (m-80) REVERT: 4 650 MET cc_start: 0.2271 (tmm) cc_final: 0.2046 (tmm) REVERT: 4 677 MET cc_start: -0.1891 (mmm) cc_final: -0.2140 (mmt) REVERT: 4 684 MET cc_start: 0.5071 (mmp) cc_final: 0.4775 (mtp) REVERT: 4 732 ARG cc_start: 0.8249 (mtm-85) cc_final: 0.7940 (mtp180) REVERT: 5 451 MET cc_start: 0.8392 (mmm) cc_final: 0.8181 (mmm) REVERT: 5 535 LYS cc_start: 0.9256 (OUTLIER) cc_final: 0.8942 (mmmm) REVERT: 6 342 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.7640 (mtt) REVERT: 6 443 GLU cc_start: 0.7014 (mt-10) cc_final: 0.6696 (pt0) REVERT: 6 580 PHE cc_start: 0.9386 (t80) cc_final: 0.9072 (t80) REVERT: 7 320 GLU cc_start: 0.8855 (mt-10) cc_final: 0.8484 (tp30) REVERT: 7 324 ARG cc_start: 0.7794 (ptp-170) cc_final: 0.7538 (ptp-170) REVERT: 7 363 HIS cc_start: 0.5822 (t70) cc_final: 0.5528 (t-90) REVERT: 7 640 LYS cc_start: 0.8619 (pttm) cc_final: 0.8296 (pptt) outliers start: 59 outliers final: 42 residues processed: 276 average time/residue: 0.2750 time to fit residues: 114.2657 Evaluate side-chains 274 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 225 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 462 ILE Chi-restraints excluded: chain 2 residue 585 ILE Chi-restraints excluded: chain 2 residue 586 HIS Chi-restraints excluded: chain 2 residue 739 THR Chi-restraints excluded: chain 2 residue 781 LEU Chi-restraints excluded: chain 2 residue 786 ASP Chi-restraints excluded: chain 3 residue 279 ASP Chi-restraints excluded: chain 3 residue 349 VAL Chi-restraints excluded: chain 3 residue 353 GLN Chi-restraints excluded: chain 3 residue 416 ASP Chi-restraints excluded: chain 3 residue 419 ARG Chi-restraints excluded: chain 3 residue 422 ILE Chi-restraints excluded: chain 3 residue 423 HIS Chi-restraints excluded: chain 3 residue 424 GLU Chi-restraints excluded: chain 3 residue 509 THR Chi-restraints excluded: chain 3 residue 514 ASP Chi-restraints excluded: chain 3 residue 542 LEU Chi-restraints excluded: chain 3 residue 568 ILE Chi-restraints excluded: chain 3 residue 577 LEU Chi-restraints excluded: chain 3 residue 597 ILE Chi-restraints excluded: chain 3 residue 631 VAL Chi-restraints excluded: chain 4 residue 472 GLU Chi-restraints excluded: chain 4 residue 499 LYS Chi-restraints excluded: chain 4 residue 511 ASP Chi-restraints excluded: chain 4 residue 577 ASP Chi-restraints excluded: chain 4 residue 631 ILE Chi-restraints excluded: chain 5 residue 415 LEU Chi-restraints excluded: chain 5 residue 475 ILE Chi-restraints excluded: chain 5 residue 517 MET Chi-restraints excluded: chain 5 residue 535 LYS Chi-restraints excluded: chain 5 residue 541 HIS Chi-restraints excluded: chain 5 residue 546 THR Chi-restraints excluded: chain 5 residue 551 VAL Chi-restraints excluded: chain 5 residue 557 LEU Chi-restraints excluded: chain 6 residue 342 MET Chi-restraints excluded: chain 6 residue 353 CYS Chi-restraints excluded: chain 6 residue 356 LEU Chi-restraints excluded: chain 6 residue 535 PHE Chi-restraints excluded: chain 6 residue 540 ASP Chi-restraints excluded: chain 6 residue 558 HIS Chi-restraints excluded: chain 6 residue 614 SER Chi-restraints excluded: chain 6 residue 620 VAL Chi-restraints excluded: chain 7 residue 326 ILE Chi-restraints excluded: chain 7 residue 331 PHE Chi-restraints excluded: chain 7 residue 400 SER Chi-restraints excluded: chain 7 residue 440 VAL Chi-restraints excluded: chain 7 residue 450 MET Chi-restraints excluded: chain 7 residue 499 THR Chi-restraints excluded: chain 7 residue 511 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 164 optimal weight: 6.9990 chunk 168 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 185 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 62 optimal weight: 0.0870 chunk 105 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 160 optimal weight: 0.9990 chunk 175 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 423 HIS ** 4 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 751 ASN ** 6 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.150545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.099155 restraints weight = 31561.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.102836 restraints weight = 15750.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.105101 restraints weight = 10782.636| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.5075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17053 Z= 0.115 Angle : 0.600 15.752 22999 Z= 0.294 Chirality : 0.039 0.175 2617 Planarity : 0.003 0.048 2934 Dihedral : 8.009 89.986 2460 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.97 % Allowed : 19.29 % Favored : 77.75 % 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: 1.12 (0.19), residues: 2068 helix: 1.75 (0.15), residues: 1165 sheet: 0.06 (0.32), residues: 258 loop : -0.80 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP 2 554 HIS 0.009 0.001 HIS 4 744 PHE 0.053 0.001 PHE 2 868 TYR 0.042 0.002 TYR 2 863 ARG 0.009 0.000 ARG 5 426 Details of bonding type rmsd hydrogen bonds : bond 0.03404 ( 897) hydrogen bonds : angle 4.25711 ( 2601) covalent geometry : bond 0.00254 (17053) covalent geometry : angle 0.60039 (22999) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 232 time to evaluate : 1.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 509 ASP cc_start: 0.7889 (m-30) cc_final: 0.7533 (t0) REVERT: 2 580 GLN cc_start: 0.7473 (tp-100) cc_final: 0.7123 (tp-100) REVERT: 2 656 GLN cc_start: 0.8240 (tt0) cc_final: 0.7871 (tm-30) REVERT: 2 720 MET cc_start: 0.6767 (ppp) cc_final: 0.6420 (ppp) REVERT: 2 786 ASP cc_start: 0.8632 (OUTLIER) cc_final: 0.8406 (m-30) REVERT: 2 819 LYS cc_start: 0.8712 (tttt) cc_final: 0.8351 (mmmt) REVERT: 2 838 ASP cc_start: 0.7948 (m-30) cc_final: 0.6884 (t0) REVERT: 3 353 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.7176 (mp10) REVERT: 3 514 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.8073 (t0) REVERT: 4 444 GLU cc_start: 0.9046 (tp30) cc_final: 0.8376 (tm-30) REVERT: 4 578 LYS cc_start: 0.7257 (tptt) cc_final: 0.6618 (tptp) REVERT: 4 579 MET cc_start: 0.7444 (tpt) cc_final: 0.6452 (tpp) REVERT: 4 650 MET cc_start: 0.1932 (tmm) cc_final: 0.1729 (tmm) REVERT: 4 677 MET cc_start: -0.1855 (mmm) cc_final: -0.2100 (mmt) REVERT: 4 684 MET cc_start: 0.5166 (mmp) cc_final: 0.4853 (mtp) REVERT: 4 732 ARG cc_start: 0.8265 (mtm-85) cc_final: 0.8000 (ptm160) REVERT: 5 451 MET cc_start: 0.8417 (mmm) cc_final: 0.8198 (mmm) REVERT: 6 342 MET cc_start: 0.8328 (OUTLIER) cc_final: 0.7600 (mtt) REVERT: 6 443 GLU cc_start: 0.7158 (mt-10) cc_final: 0.6864 (pt0) REVERT: 6 580 PHE cc_start: 0.9392 (t80) cc_final: 0.9050 (t80) REVERT: 7 320 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8472 (tp30) outliers start: 54 outliers final: 43 residues processed: 270 average time/residue: 0.2834 time to fit residues: 114.9894 Evaluate side-chains 273 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 226 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 462 ILE Chi-restraints excluded: chain 2 residue 585 ILE Chi-restraints excluded: chain 2 residue 586 HIS Chi-restraints excluded: chain 2 residue 739 THR Chi-restraints excluded: chain 2 residue 781 LEU Chi-restraints excluded: chain 2 residue 786 ASP Chi-restraints excluded: chain 3 residue 279 ASP Chi-restraints excluded: chain 3 residue 349 VAL Chi-restraints excluded: chain 3 residue 353 GLN Chi-restraints excluded: chain 3 residue 419 ARG Chi-restraints excluded: chain 3 residue 423 HIS Chi-restraints excluded: chain 3 residue 509 THR Chi-restraints excluded: chain 3 residue 514 ASP Chi-restraints excluded: chain 3 residue 542 LEU Chi-restraints excluded: chain 3 residue 568 ILE Chi-restraints excluded: chain 3 residue 572 ILE Chi-restraints excluded: chain 3 residue 577 LEU Chi-restraints excluded: chain 3 residue 597 ILE Chi-restraints excluded: chain 3 residue 631 VAL Chi-restraints excluded: chain 4 residue 499 LYS Chi-restraints excluded: chain 4 residue 511 ASP Chi-restraints excluded: chain 4 residue 577 ASP Chi-restraints excluded: chain 4 residue 631 ILE Chi-restraints excluded: chain 4 residue 751 ASN Chi-restraints excluded: chain 5 residue 415 LEU Chi-restraints excluded: chain 5 residue 475 ILE Chi-restraints excluded: chain 5 residue 517 MET Chi-restraints excluded: chain 5 residue 546 THR Chi-restraints excluded: chain 5 residue 551 VAL Chi-restraints excluded: chain 5 residue 557 LEU Chi-restraints excluded: chain 5 residue 647 VAL Chi-restraints excluded: chain 6 residue 342 MET Chi-restraints excluded: chain 6 residue 353 CYS Chi-restraints excluded: chain 6 residue 356 LEU Chi-restraints excluded: chain 6 residue 535 PHE Chi-restraints excluded: chain 6 residue 540 ASP Chi-restraints excluded: chain 6 residue 558 HIS Chi-restraints excluded: chain 6 residue 614 SER Chi-restraints excluded: chain 6 residue 620 VAL Chi-restraints excluded: chain 7 residue 326 ILE Chi-restraints excluded: chain 7 residue 331 PHE Chi-restraints excluded: chain 7 residue 339 ILE Chi-restraints excluded: chain 7 residue 400 SER Chi-restraints excluded: chain 7 residue 440 VAL Chi-restraints excluded: chain 7 residue 450 MET Chi-restraints excluded: chain 7 residue 499 THR Chi-restraints excluded: chain 7 residue 511 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 125 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 chunk 134 optimal weight: 0.4980 chunk 40 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 198 optimal weight: 0.2980 chunk 1 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 chunk 178 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 423 HIS ** 4 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 751 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.149636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.098129 restraints weight = 31694.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.101772 restraints weight = 15871.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.104079 restraints weight = 10907.836| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.5143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17053 Z= 0.136 Angle : 0.609 15.660 22999 Z= 0.300 Chirality : 0.040 0.161 2617 Planarity : 0.003 0.047 2934 Dihedral : 7.991 87.078 2460 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.02 % Allowed : 19.12 % Favored : 77.86 % 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: 1.09 (0.19), residues: 2068 helix: 1.70 (0.15), residues: 1167 sheet: 0.07 (0.32), residues: 255 loop : -0.77 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP 2 554 HIS 0.010 0.001 HIS 3 423 PHE 0.043 0.001 PHE 2 868 TYR 0.042 0.002 TYR 2 863 ARG 0.009 0.000 ARG 5 426 Details of bonding type rmsd hydrogen bonds : bond 0.03720 ( 897) hydrogen bonds : angle 4.30141 ( 2601) covalent geometry : bond 0.00311 (17053) covalent geometry : angle 0.60898 (22999) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6706.88 seconds wall clock time: 119 minutes 35.58 seconds (7175.58 seconds total)