Starting phenix.real_space_refine on Sun Aug 24 04:24:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q6p_18192/08_2025/8q6p_18192.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q6p_18192/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8q6p_18192/08_2025/8q6p_18192.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q6p_18192/08_2025/8q6p_18192.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8q6p_18192/08_2025/8q6p_18192.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q6p_18192/08_2025/8q6p_18192.map" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.027 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 3.32, per 1000 atoms: 0.20 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: 1.23 Conformation dependent library (CDL) restraints added in 694.0 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.35 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: 2.40 Time building geometry restraints manager: 1.56 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: 12.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 12.900 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.100 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG 3 506 TYR 0.012 0.001 TYR 6 349 PHE 0.012 0.001 PHE 2 873 TRP 0.004 0.001 TRP L 381 HIS 0.005 0.001 HIS 6 410 Details of bonding type rmsd covalent geometry : bond 0.00227 (17053) covalent geometry : angle 0.48438 (22999) hydrogen bonds : bond 0.15815 ( 897) hydrogen bonds : angle 5.61831 ( 2601) *********************** 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 : 0.581 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: 0.1455 time to fit residues: 113.2875 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 : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 0.1980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 2 672 HIS 2 718 ASN 3 553 HIS 4 623 GLN 4 751 ASN 5 536 HIS 5 630 GLN 6 410 HIS 6 496 ASN 6 521 ASN ** 6 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 521 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.153379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.103091 restraints weight = 32035.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.106805 restraints weight = 19442.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.106983 restraints weight = 13973.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.107591 restraints weight = 12782.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.107863 restraints weight = 11867.137| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17053 Z= 0.130 Angle : 0.574 10.076 22999 Z= 0.298 Chirality : 0.040 0.154 2617 Planarity : 0.004 0.085 2934 Dihedral : 9.222 87.689 2460 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.86 % Allowed : 13.08 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.19), residues: 2068 helix: 2.07 (0.15), residues: 1165 sheet: 0.18 (0.33), residues: 240 loop : -0.67 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 2 547 TYR 0.023 0.002 TYR 2 863 PHE 0.028 0.002 PHE 6 651 TRP 0.021 0.001 TRP 2 554 HIS 0.010 0.001 HIS 3 360 Details of bonding type rmsd covalent geometry : bond 0.00282 (17053) covalent geometry : angle 0.57392 (22999) hydrogen bonds : bond 0.04124 ( 897) hydrogen bonds : angle 4.63350 ( 2601) *********************** 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 381 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 329 time to evaluate : 0.720 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: 2 490 LYS cc_start: 0.7761 (mptt) cc_final: 0.7404 (mttp) REVERT: 2 534 GLN cc_start: 0.7680 (OUTLIER) cc_final: 0.7385 (pp30) REVERT: 2 554 TRP cc_start: 0.7317 (m100) cc_final: 0.7064 (m100) REVERT: 2 580 GLN cc_start: 0.7442 (tp-100) cc_final: 0.7233 (tp-100) REVERT: 2 717 LEU cc_start: 0.7046 (pt) cc_final: 0.6450 (tp) REVERT: 2 794 ARG cc_start: 0.7923 (tpp80) cc_final: 0.7677 (tpp80) REVERT: 2 819 LYS cc_start: 0.8433 (tttt) cc_final: 0.8144 (mmmt) REVERT: 2 838 ASP cc_start: 0.7597 (m-30) cc_final: 0.6734 (t0) REVERT: 4 443 GLU cc_start: 0.7577 (mp0) cc_final: 0.7321 (mm-30) REVERT: 4 578 LYS cc_start: 0.7499 (mmtt) cc_final: 0.6702 (mttp) REVERT: 4 579 MET cc_start: 0.7660 (tpt) cc_final: 0.6880 (tpp) REVERT: 4 677 MET cc_start: -0.1661 (mmm) cc_final: -0.2960 (tmm) REVERT: 4 684 MET cc_start: 0.4857 (mmp) cc_final: 0.4626 (ttm) REVERT: 5 404 TYR cc_start: 0.8891 (t80) cc_final: 0.8643 (t80) REVERT: 5 421 ARG cc_start: 0.7868 (ptm160) cc_final: 0.7641 (ptm160) REVERT: 5 512 LEU cc_start: 0.8678 (mt) cc_final: 0.8288 (tt) REVERT: 6 342 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7409 (mtm) REVERT: 6 345 ASP cc_start: 0.7388 (t0) cc_final: 0.6966 (t0) REVERT: 6 381 THR cc_start: 0.6816 (m) cc_final: 0.6582 (m) REVERT: 6 401 SER cc_start: 0.8854 (m) cc_final: 0.8412 (p) REVERT: 6 437 LYS cc_start: 0.8183 (tttt) cc_final: 0.7921 (ptpp) REVERT: 6 443 GLU cc_start: 0.6941 (mt-10) cc_final: 0.6111 (pt0) REVERT: 6 446 ILE cc_start: 0.8666 (mt) cc_final: 0.8448 (mm) REVERT: 6 466 LYS cc_start: 0.8585 (mmtt) cc_final: 0.8282 (tmtt) REVERT: 6 572 GLU cc_start: 0.8703 (pt0) cc_final: 0.8454 (pt0) REVERT: 7 553 MET cc_start: 0.8720 (tpp) cc_final: 0.8479 (tpp) REVERT: 7 587 MET cc_start: 0.8012 (mtt) cc_final: 0.7681 (ttp) REVERT: 7 615 LEU cc_start: 0.8486 (mt) cc_final: 0.8278 (mt) REVERT: 7 638 MET cc_start: 0.8064 (mtt) cc_final: 0.7824 (mtt) outliers start: 52 outliers final: 24 residues processed: 371 average time/residue: 0.1507 time to fit residues: 81.0410 Evaluate side-chains 297 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 271 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 443 ASP Chi-restraints excluded: chain 2 residue 534 GLN Chi-restraints excluded: chain 2 residue 781 LEU Chi-restraints excluded: chain 3 residue 349 VAL Chi-restraints excluded: chain 3 residue 416 ASP 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 542 LEU Chi-restraints excluded: chain 3 residue 577 LEU Chi-restraints excluded: chain 3 residue 597 ILE Chi-restraints excluded: chain 4 residue 524 PHE Chi-restraints excluded: chain 4 residue 582 SER Chi-restraints excluded: chain 4 residue 751 ASN Chi-restraints excluded: chain 5 residue 370 LEU Chi-restraints excluded: chain 5 residue 468 ILE 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 496 ASN Chi-restraints excluded: chain 6 residue 540 ASP Chi-restraints excluded: chain 6 residue 558 HIS Chi-restraints excluded: chain 7 residue 379 MET Chi-restraints excluded: chain 7 residue 434 VAL Chi-restraints excluded: chain 7 residue 466 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 42 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 72 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 53 optimal weight: 0.0030 chunk 110 optimal weight: 3.9990 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 534 GLN 3 553 HIS ** 4 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 541 HIS 6 496 ASN 6 558 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.152564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.104690 restraints weight = 32281.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.105747 restraints weight = 21070.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.106112 restraints weight = 14633.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.106884 restraints weight = 14704.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.106977 restraints weight = 13120.933| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17053 Z= 0.123 Angle : 0.568 11.530 22999 Z= 0.288 Chirality : 0.039 0.149 2617 Planarity : 0.004 0.053 2934 Dihedral : 8.770 86.806 2460 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.02 % Allowed : 13.96 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.18), residues: 2068 helix: 2.05 (0.15), residues: 1163 sheet: 0.34 (0.33), residues: 235 loop : -0.63 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 3 430 TYR 0.017 0.001 TYR 7 579 PHE 0.023 0.001 PHE 2 663 TRP 0.015 0.002 TRP 6 748 HIS 0.008 0.001 HIS 4 744 Details of bonding type rmsd covalent geometry : bond 0.00272 (17053) covalent geometry : angle 0.56849 (22999) hydrogen bonds : bond 0.03796 ( 897) hydrogen bonds : angle 4.46094 ( 2601) *********************** 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 335 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 280 time to evaluate : 0.667 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: 2 509 ASP cc_start: 0.7322 (m-30) cc_final: 0.7104 (t0) REVERT: 2 534 GLN cc_start: 0.7803 (OUTLIER) cc_final: 0.7507 (pp30) REVERT: 2 580 GLN cc_start: 0.7419 (tp-100) cc_final: 0.7173 (tp-100) REVERT: 2 717 LEU cc_start: 0.7085 (pt) cc_final: 0.6496 (tp) REVERT: 2 786 ASP cc_start: 0.8473 (OUTLIER) cc_final: 0.8273 (m-30) REVERT: 2 794 ARG cc_start: 0.7935 (tpp80) cc_final: 0.7725 (tpp80) REVERT: 2 819 LYS cc_start: 0.8446 (tttt) cc_final: 0.8167 (mmmt) REVERT: 2 838 ASP cc_start: 0.7639 (m-30) cc_final: 0.6800 (t0) REVERT: 4 443 GLU cc_start: 0.7553 (mp0) cc_final: 0.6972 (mp0) REVERT: 4 578 LYS cc_start: 0.7512 (mmtt) cc_final: 0.6511 (mtmm) REVERT: 4 579 MET cc_start: 0.7642 (tpt) cc_final: 0.7005 (tpp) REVERT: 4 677 MET cc_start: -0.1602 (mmm) cc_final: -0.2893 (tmm) REVERT: 4 684 MET cc_start: 0.4971 (mmp) cc_final: 0.4539 (ttm) REVERT: 5 421 ARG cc_start: 0.7852 (ptm160) cc_final: 0.7634 (ptm160) REVERT: 5 512 LEU cc_start: 0.8578 (mt) cc_final: 0.8307 (tt) REVERT: 6 342 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7381 (mtt) REVERT: 6 345 ASP cc_start: 0.7471 (t0) cc_final: 0.7193 (t0) REVERT: 6 381 THR cc_start: 0.6880 (m) cc_final: 0.6657 (m) REVERT: 6 401 SER cc_start: 0.8879 (m) cc_final: 0.8472 (p) REVERT: 6 437 LYS cc_start: 0.8148 (tttt) cc_final: 0.7862 (ptpp) REVERT: 6 443 GLU cc_start: 0.6844 (mt-10) cc_final: 0.6067 (pt0) REVERT: 6 572 GLU cc_start: 0.8756 (pt0) cc_final: 0.8493 (pt0) REVERT: 6 780 TYR cc_start: 0.5970 (m-10) cc_final: 0.5740 (m-80) REVERT: 7 587 MET cc_start: 0.7934 (mtt) cc_final: 0.7674 (ttp) outliers start: 55 outliers final: 25 residues processed: 316 average time/residue: 0.1198 time to fit residues: 56.6026 Evaluate side-chains 277 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 249 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 534 GLN Chi-restraints excluded: chain 2 residue 547 ARG 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 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 577 LEU Chi-restraints excluded: chain 3 residue 597 ILE Chi-restraints excluded: chain 3 residue 631 VAL Chi-restraints excluded: chain 4 residue 511 ASP Chi-restraints excluded: chain 5 residue 370 LEU Chi-restraints excluded: chain 5 residue 517 MET Chi-restraints excluded: chain 5 residue 541 HIS 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 518 LEU Chi-restraints excluded: chain 6 residue 540 ASP Chi-restraints excluded: chain 7 residue 339 ILE Chi-restraints excluded: chain 7 residue 400 SER Chi-restraints excluded: chain 7 residue 434 VAL Chi-restraints excluded: chain 7 residue 450 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 187 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 184 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 44 optimal weight: 0.5980 chunk 46 optimal weight: 4.9990 chunk 189 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 423 HIS 3 553 HIS 3 640 GLN 4 473 HIS ** 4 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 751 ASN 5 541 HIS 6 496 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.149086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.100030 restraints weight = 31640.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.101954 restraints weight = 17990.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.103705 restraints weight = 12000.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.104153 restraints weight = 10611.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.104248 restraints weight = 9238.799| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17053 Z= 0.207 Angle : 0.621 14.246 22999 Z= 0.316 Chirality : 0.041 0.172 2617 Planarity : 0.004 0.041 2934 Dihedral : 8.477 81.972 2460 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.63 % Allowed : 14.67 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.18), residues: 2068 helix: 1.79 (0.15), residues: 1161 sheet: 0.23 (0.31), residues: 268 loop : -0.73 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG 4 501 TYR 0.015 0.002 TYR 7 579 PHE 0.023 0.002 PHE 2 663 TRP 0.011 0.001 TRP 6 748 HIS 0.019 0.001 HIS 5 541 Details of bonding type rmsd covalent geometry : bond 0.00488 (17053) covalent geometry : angle 0.62090 (22999) hydrogen bonds : bond 0.04490 ( 897) hydrogen bonds : angle 4.64720 ( 2601) *********************** 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 319 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 253 time to evaluate : 0.613 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: 2 509 ASP cc_start: 0.7840 (m-30) cc_final: 0.7557 (t0) REVERT: 2 580 GLN cc_start: 0.7412 (tp-100) cc_final: 0.7111 (tp-100) REVERT: 2 717 LEU cc_start: 0.7013 (pt) cc_final: 0.6473 (tp) REVERT: 2 786 ASP cc_start: 0.8610 (OUTLIER) cc_final: 0.8387 (m-30) REVERT: 2 819 LYS cc_start: 0.8536 (tttt) cc_final: 0.8239 (mmtt) REVERT: 2 838 ASP cc_start: 0.7699 (m-30) cc_final: 0.6775 (t0) REVERT: 3 514 ASP cc_start: 0.8383 (OUTLIER) cc_final: 0.8131 (t0) REVERT: 4 443 GLU cc_start: 0.7853 (mp0) cc_final: 0.7357 (mp0) REVERT: 4 579 MET cc_start: 0.7654 (tpt) cc_final: 0.6686 (tpp) REVERT: 4 677 MET cc_start: -0.1569 (mmm) cc_final: -0.2763 (tmm) REVERT: 4 684 MET cc_start: 0.5014 (mmp) cc_final: 0.4478 (ttm) REVERT: 4 735 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7340 (mp0) REVERT: 5 421 ARG cc_start: 0.8082 (ptm160) cc_final: 0.6883 (ptm160) REVERT: 5 568 ARG cc_start: 0.9138 (OUTLIER) cc_final: 0.8088 (mtm-85) REVERT: 6 342 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.7649 (mtt) REVERT: 6 345 ASP cc_start: 0.7628 (t0) cc_final: 0.7075 (t0) REVERT: 6 381 THR cc_start: 0.7163 (m) cc_final: 0.6944 (m) REVERT: 6 443 GLU cc_start: 0.6965 (mt-10) cc_final: 0.6204 (pt0) REVERT: 6 488 LYS cc_start: 0.8616 (mmtm) cc_final: 0.8410 (mptt) REVERT: 6 780 TYR cc_start: 0.6150 (m-10) cc_final: 0.5839 (m-80) REVERT: 7 587 MET cc_start: 0.8136 (mtt) cc_final: 0.7850 (ttp) REVERT: 7 633 MET cc_start: 0.8820 (ptp) cc_final: 0.8612 (ptp) REVERT: 7 638 MET cc_start: 0.8199 (mtp) cc_final: 0.7847 (mtt) outliers start: 66 outliers final: 41 residues processed: 298 average time/residue: 0.1297 time to fit residues: 56.6967 Evaluate side-chains 281 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 235 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 534 GLN Chi-restraints excluded: chain 2 residue 547 ARG Chi-restraints excluded: chain 2 residue 585 ILE Chi-restraints excluded: chain 2 residue 586 HIS Chi-restraints excluded: chain 2 residue 596 ILE 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 400 LEU Chi-restraints excluded: chain 3 residue 416 ASP 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 514 ASP 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 3 residue 631 VAL Chi-restraints excluded: chain 4 residue 511 ASP Chi-restraints excluded: chain 4 residue 667 VAL Chi-restraints excluded: chain 4 residue 735 GLU Chi-restraints excluded: chain 5 residue 370 LEU Chi-restraints excluded: chain 5 residue 478 THR Chi-restraints excluded: chain 5 residue 517 MET 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 496 ASN Chi-restraints excluded: chain 6 residue 518 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 339 ILE Chi-restraints excluded: chain 7 residue 363 HIS 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 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 63 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 38 optimal weight: 30.0000 chunk 22 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 131 optimal weight: 3.9990 chunk 4 optimal weight: 0.0870 chunk 172 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 182 optimal weight: 5.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 534 GLN 2 631 ASN ** 2 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 423 HIS 3 553 HIS 4 751 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.151789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.103337 restraints weight = 31614.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.105142 restraints weight = 18235.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.109161 restraints weight = 11799.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.108910 restraints weight = 9978.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.108970 restraints weight = 8523.039| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17053 Z= 0.111 Angle : 0.540 9.836 22999 Z= 0.275 Chirality : 0.039 0.146 2617 Planarity : 0.003 0.045 2934 Dihedral : 8.239 84.779 2460 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.13 % Allowed : 16.10 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.19), residues: 2068 helix: 1.93 (0.15), residues: 1162 sheet: 0.20 (0.32), residues: 264 loop : -0.67 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 5 426 TYR 0.015 0.001 TYR 6 569 PHE 0.023 0.001 PHE 2 663 TRP 0.016 0.001 TRP 2 554 HIS 0.016 0.001 HIS 3 423 Details of bonding type rmsd covalent geometry : bond 0.00239 (17053) covalent geometry : angle 0.54010 (22999) hydrogen bonds : bond 0.03515 ( 897) hydrogen bonds : angle 4.32651 ( 2601) *********************** 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 308 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 251 time to evaluate : 0.637 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: 0.7758 (m-30) cc_final: 0.7468 (t0) REVERT: 2 580 GLN cc_start: 0.7336 (tp-100) cc_final: 0.7001 (tp-100) REVERT: 2 717 LEU cc_start: 0.7035 (pt) cc_final: 0.6442 (tp) REVERT: 2 786 ASP cc_start: 0.8601 (OUTLIER) cc_final: 0.8392 (m-30) REVERT: 2 819 LYS cc_start: 0.8569 (tttt) cc_final: 0.8227 (mmtt) REVERT: 2 838 ASP cc_start: 0.7740 (m-30) cc_final: 0.6826 (t0) REVERT: 3 514 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.8049 (t0) REVERT: 4 443 GLU cc_start: 0.7912 (mp0) cc_final: 0.7425 (mp0) REVERT: 4 579 MET cc_start: 0.7690 (tpt) cc_final: 0.6678 (tpp) REVERT: 4 677 MET cc_start: -0.1653 (mmm) cc_final: -0.2827 (tmm) REVERT: 4 684 MET cc_start: 0.4991 (mmp) cc_final: 0.4712 (mtp) REVERT: 4 735 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7413 (mp0) REVERT: 5 420 MET cc_start: 0.6880 (mmm) cc_final: 0.6669 (mmm) REVERT: 5 421 ARG cc_start: 0.8093 (ptm160) cc_final: 0.7892 (ptm160) REVERT: 5 517 MET cc_start: 0.8584 (mtp) cc_final: 0.8295 (mtm) REVERT: 5 568 ARG cc_start: 0.9094 (OUTLIER) cc_final: 0.8873 (mtm-85) REVERT: 6 342 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.7477 (mtt) REVERT: 6 345 ASP cc_start: 0.7474 (t0) cc_final: 0.6594 (t0) REVERT: 6 381 THR cc_start: 0.7228 (m) cc_final: 0.7001 (m) REVERT: 6 443 GLU cc_start: 0.6918 (mt-10) cc_final: 0.6323 (pt0) REVERT: 6 569 TYR cc_start: 0.8478 (m-80) cc_final: 0.8015 (m-80) REVERT: 6 780 TYR cc_start: 0.6135 (m-10) cc_final: 0.5803 (m-80) REVERT: 7 320 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8378 (tp30) REVERT: 7 344 TYR cc_start: 0.8770 (t80) cc_final: 0.8499 (t80) REVERT: 7 565 CYS cc_start: 0.8349 (t) cc_final: 0.7697 (m) REVERT: 7 587 MET cc_start: 0.8137 (mtt) cc_final: 0.7691 (tpt) REVERT: L 383 GLU cc_start: 0.8779 (tp30) cc_final: 0.8565 (mt-10) outliers start: 57 outliers final: 31 residues processed: 293 average time/residue: 0.1239 time to fit residues: 54.9064 Evaluate side-chains 274 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 238 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 534 GLN Chi-restraints excluded: chain 2 residue 547 ARG Chi-restraints excluded: chain 2 residue 585 ILE Chi-restraints excluded: chain 2 residue 586 HIS Chi-restraints excluded: chain 2 residue 596 ILE 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 349 VAL Chi-restraints excluded: chain 3 residue 422 ILE Chi-restraints excluded: chain 3 residue 424 GLU Chi-restraints excluded: chain 3 residue 514 ASP 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 582 SER Chi-restraints excluded: chain 4 residue 735 GLU Chi-restraints excluded: chain 4 residue 751 ASN Chi-restraints excluded: chain 5 residue 370 LEU Chi-restraints excluded: chain 5 residue 551 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 535 PHE Chi-restraints excluded: chain 6 residue 540 ASP Chi-restraints excluded: chain 6 residue 558 HIS Chi-restraints excluded: chain 6 residue 750 LEU Chi-restraints excluded: chain 7 residue 339 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 5 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 203 optimal weight: 6.9990 chunk 24 optimal weight: 0.6980 chunk 119 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 145 optimal weight: 0.0870 chunk 57 optimal weight: 0.0980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 423 HIS 4 751 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.152266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.100449 restraints weight = 31682.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.104295 restraints weight = 15754.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.106716 restraints weight = 10760.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.108087 restraints weight = 8686.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.108997 restraints weight = 7708.219| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 17053 Z= 0.107 Angle : 0.532 9.923 22999 Z= 0.271 Chirality : 0.038 0.132 2617 Planarity : 0.003 0.046 2934 Dihedral : 8.102 87.882 2460 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.75 % Allowed : 17.14 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.19), residues: 2068 helix: 1.92 (0.15), residues: 1170 sheet: 0.30 (0.32), residues: 265 loop : -0.63 (0.24), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 2 747 TYR 0.022 0.001 TYR 7 579 PHE 0.023 0.001 PHE 2 663 TRP 0.021 0.001 TRP 2 554 HIS 0.009 0.001 HIS 4 744 Details of bonding type rmsd covalent geometry : bond 0.00231 (17053) covalent geometry : angle 0.53179 (22999) hydrogen bonds : bond 0.03284 ( 897) hydrogen bonds : angle 4.21270 ( 2601) *********************** 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 305 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 255 time to evaluate : 0.741 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: 0.7726 (m-30) cc_final: 0.7458 (t0) REVERT: 2 580 GLN cc_start: 0.7334 (tp-100) cc_final: 0.6987 (tp-100) REVERT: 2 717 LEU cc_start: 0.6993 (pt) cc_final: 0.6433 (tp) REVERT: 2 786 ASP cc_start: 0.8554 (OUTLIER) cc_final: 0.8331 (m-30) REVERT: 2 819 LYS cc_start: 0.8569 (tttt) cc_final: 0.8231 (mmtt) REVERT: 2 838 ASP cc_start: 0.7774 (m-30) cc_final: 0.6864 (t0) REVERT: 3 514 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.8058 (t0) REVERT: 4 499 LYS cc_start: 0.7100 (OUTLIER) cc_final: 0.6653 (pttm) REVERT: 4 579 MET cc_start: 0.7678 (tpt) cc_final: 0.6853 (tpp) REVERT: 4 650 MET cc_start: 0.2600 (tmm) cc_final: 0.2115 (tmm) REVERT: 4 677 MET cc_start: -0.1713 (mmm) cc_final: -0.2880 (tmm) REVERT: 4 684 MET cc_start: 0.4933 (mmp) cc_final: 0.4722 (mtp) REVERT: 4 735 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7383 (mp0) REVERT: 5 420 MET cc_start: 0.6905 (mmm) cc_final: 0.6611 (mpp) REVERT: 5 508 MET cc_start: 0.6625 (tmm) cc_final: 0.6277 (tpp) REVERT: 5 517 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.8279 (mtm) REVERT: 5 568 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.8845 (mtm-85) REVERT: 6 342 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7509 (mtt) REVERT: 6 345 ASP cc_start: 0.7516 (t0) cc_final: 0.6628 (t0) REVERT: 6 381 THR cc_start: 0.7096 (m) cc_final: 0.6869 (m) REVERT: 6 437 LYS cc_start: 0.8116 (ptpp) cc_final: 0.7757 (mptp) REVERT: 6 443 GLU cc_start: 0.6992 (mt-10) cc_final: 0.6224 (pt0) REVERT: 6 444 PHE cc_start: 0.6708 (m-10) cc_final: 0.5678 (m-80) REVERT: 6 569 TYR cc_start: 0.8461 (m-80) cc_final: 0.7999 (m-80) REVERT: 7 344 TYR cc_start: 0.8729 (t80) cc_final: 0.8464 (t80) REVERT: 7 565 CYS cc_start: 0.8250 (t) cc_final: 0.7722 (m) REVERT: 7 587 MET cc_start: 0.8173 (mtt) cc_final: 0.7731 (tpt) REVERT: 7 638 MET cc_start: 0.8221 (mtp) cc_final: 0.8018 (mtp) outliers start: 50 outliers final: 32 residues processed: 288 average time/residue: 0.1254 time to fit residues: 54.5327 Evaluate side-chains 280 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 241 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 547 ARG Chi-restraints excluded: chain 2 residue 585 ILE Chi-restraints excluded: chain 2 residue 586 HIS Chi-restraints excluded: chain 2 residue 596 ILE 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 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 514 ASP 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 631 ILE Chi-restraints excluded: chain 4 residue 735 GLU Chi-restraints excluded: chain 4 residue 751 ASN Chi-restraints excluded: chain 5 residue 370 LEU Chi-restraints excluded: chain 5 residue 517 MET Chi-restraints excluded: chain 5 residue 551 VAL Chi-restraints excluded: chain 5 residue 568 ARG 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 339 ILE Chi-restraints excluded: chain 7 residue 356 LEU 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 511 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 111 optimal weight: 0.4980 chunk 157 optimal weight: 0.5980 chunk 145 optimal weight: 9.9990 chunk 151 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 188 optimal weight: 1.9990 chunk 57 optimal weight: 0.0470 chunk 201 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 186 optimal weight: 6.9990 overall best weight: 0.8282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 534 GLN ** 2 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 423 HIS 4 751 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.151696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.103038 restraints weight = 31368.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.105778 restraints weight = 16828.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.108290 restraints weight = 11098.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.108136 restraints weight = 10549.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.108103 restraints weight = 8729.464| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.4565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17053 Z= 0.116 Angle : 0.546 16.288 22999 Z= 0.275 Chirality : 0.038 0.128 2617 Planarity : 0.003 0.046 2934 Dihedral : 8.030 87.901 2460 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.91 % Allowed : 17.20 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.19), residues: 2068 helix: 1.89 (0.15), residues: 1172 sheet: 0.37 (0.32), residues: 261 loop : -0.63 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 2 747 TYR 0.016 0.001 TYR 7 579 PHE 0.049 0.002 PHE 2 868 TRP 0.022 0.001 TRP 2 554 HIS 0.009 0.001 HIS 4 744 Details of bonding type rmsd covalent geometry : bond 0.00259 (17053) covalent geometry : angle 0.54600 (22999) hydrogen bonds : bond 0.03356 ( 897) hydrogen bonds : angle 4.21151 ( 2601) *********************** 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 295 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 242 time to evaluate : 0.702 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: 2 509 ASP cc_start: 0.7734 (m-30) cc_final: 0.7477 (t0) REVERT: 2 580 GLN cc_start: 0.7366 (tp-100) cc_final: 0.7015 (tp-100) REVERT: 2 717 LEU cc_start: 0.7009 (pt) cc_final: 0.6332 (tp) REVERT: 2 720 MET cc_start: 0.6933 (ppp) cc_final: 0.6606 (ppp) REVERT: 2 786 ASP cc_start: 0.8570 (OUTLIER) cc_final: 0.8358 (m-30) REVERT: 2 819 LYS cc_start: 0.8577 (tttt) cc_final: 0.8211 (mmmt) REVERT: 2 838 ASP cc_start: 0.7738 (m-30) cc_final: 0.6819 (t0) REVERT: 3 424 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8233 (pp20) REVERT: 3 514 ASP cc_start: 0.8291 (OUTLIER) cc_final: 0.8062 (t0) REVERT: 4 499 LYS cc_start: 0.7332 (OUTLIER) cc_final: 0.6969 (pttm) REVERT: 4 579 MET cc_start: 0.7675 (tpt) cc_final: 0.6903 (tpp) REVERT: 4 650 MET cc_start: 0.2469 (tmm) cc_final: 0.1952 (tmm) REVERT: 4 677 MET cc_start: -0.1858 (mmm) cc_final: -0.2938 (tmm) REVERT: 4 684 MET cc_start: 0.5026 (mmp) cc_final: 0.4685 (mtp) REVERT: 5 508 MET cc_start: 0.6723 (tmm) cc_final: 0.6273 (tpp) REVERT: 5 517 MET cc_start: 0.8547 (OUTLIER) cc_final: 0.8268 (mtm) REVERT: 5 568 ARG cc_start: 0.9117 (OUTLIER) cc_final: 0.8912 (mtm-85) REVERT: 6 342 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.7595 (mtt) REVERT: 6 345 ASP cc_start: 0.7507 (t0) cc_final: 0.6730 (t0) REVERT: 6 437 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7909 (mttp) REVERT: 6 443 GLU cc_start: 0.6978 (mt-10) cc_final: 0.6265 (pt0) REVERT: 6 444 PHE cc_start: 0.6602 (m-10) cc_final: 0.6213 (m-80) REVERT: 6 569 TYR cc_start: 0.8501 (m-80) cc_final: 0.8110 (m-80) REVERT: 6 780 TYR cc_start: 0.5634 (m-80) cc_final: 0.5373 (m-80) REVERT: 7 344 TYR cc_start: 0.8734 (t80) cc_final: 0.8486 (t80) REVERT: 7 587 MET cc_start: 0.8176 (mtt) cc_final: 0.7738 (tpt) outliers start: 53 outliers final: 35 residues processed: 277 average time/residue: 0.1288 time to fit residues: 54.3720 Evaluate side-chains 277 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 234 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 462 ILE Chi-restraints excluded: chain 2 residue 534 GLN Chi-restraints excluded: chain 2 residue 547 ARG Chi-restraints excluded: chain 2 residue 585 ILE Chi-restraints excluded: chain 2 residue 586 HIS Chi-restraints excluded: chain 2 residue 596 ILE 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 349 VAL Chi-restraints excluded: chain 3 residue 422 ILE Chi-restraints excluded: chain 3 residue 424 GLU Chi-restraints excluded: chain 3 residue 514 ASP 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 656 LYS 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 5 residue 370 LEU Chi-restraints excluded: chain 5 residue 470 ILE Chi-restraints excluded: chain 5 residue 517 MET Chi-restraints excluded: chain 5 residue 551 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 437 LYS 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 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 511 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 0.9990 chunk 144 optimal weight: 3.9990 chunk 164 optimal weight: 7.9990 chunk 171 optimal weight: 4.9990 chunk 189 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 59 optimal weight: 0.0040 chunk 2 optimal weight: 0.9980 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 534 GLN ** 2 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 423 HIS 4 751 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.150669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.101897 restraints weight = 31800.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.104376 restraints weight = 17038.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.105833 restraints weight = 11466.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.105966 restraints weight = 11037.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.105924 restraints weight = 9593.421| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.4736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17053 Z= 0.139 Angle : 0.569 15.075 22999 Z= 0.285 Chirality : 0.039 0.180 2617 Planarity : 0.003 0.047 2934 Dihedral : 8.048 86.183 2460 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.08 % Allowed : 16.87 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.19), residues: 2068 helix: 1.83 (0.15), residues: 1171 sheet: 0.29 (0.33), residues: 269 loop : -0.61 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 7 619 TYR 0.016 0.001 TYR 7 579 PHE 0.037 0.002 PHE 2 868 TRP 0.025 0.001 TRP 2 554 HIS 0.010 0.001 HIS 4 744 Details of bonding type rmsd covalent geometry : bond 0.00319 (17053) covalent geometry : angle 0.56860 (22999) hydrogen bonds : bond 0.03560 ( 897) hydrogen bonds : angle 4.24241 ( 2601) *********************** 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 295 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 239 time to evaluate : 0.719 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: 0.7789 (m-30) cc_final: 0.7511 (t0) REVERT: 2 580 GLN cc_start: 0.7395 (tp-100) cc_final: 0.7060 (tp-100) REVERT: 2 717 LEU cc_start: 0.6985 (pt) cc_final: 0.6350 (tp) REVERT: 2 722 GLN cc_start: 0.8875 (pt0) cc_final: 0.8638 (tt0) REVERT: 2 786 ASP cc_start: 0.8596 (OUTLIER) cc_final: 0.8378 (m-30) REVERT: 2 819 LYS cc_start: 0.8617 (tttt) cc_final: 0.8253 (mmmt) REVERT: 2 838 ASP cc_start: 0.7746 (m-30) cc_final: 0.6810 (t0) REVERT: 3 514 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.8088 (t0) REVERT: 4 499 LYS cc_start: 0.7437 (OUTLIER) cc_final: 0.7097 (pttm) REVERT: 4 579 MET cc_start: 0.7686 (tpt) cc_final: 0.6957 (tpp) REVERT: 4 648 PHE cc_start: 0.6251 (m-80) cc_final: 0.5916 (m-80) REVERT: 4 650 MET cc_start: 0.2359 (tmm) cc_final: 0.1836 (tmm) REVERT: 4 677 MET cc_start: -0.1847 (mmm) cc_final: -0.2927 (tmm) REVERT: 4 684 MET cc_start: 0.5157 (mmp) cc_final: 0.4632 (mtp) REVERT: 4 753 VAL cc_start: 0.7276 (t) cc_final: 0.6970 (p) REVERT: 5 517 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.8316 (mtm) REVERT: 5 539 ASN cc_start: 0.9083 (m-40) cc_final: 0.8866 (m-40) REVERT: 5 568 ARG cc_start: 0.9117 (OUTLIER) cc_final: 0.7965 (mtm-85) REVERT: 6 342 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.7589 (mtt) REVERT: 6 345 ASP cc_start: 0.7588 (t0) cc_final: 0.6799 (t0) REVERT: 6 443 GLU cc_start: 0.6945 (mt-10) cc_final: 0.6271 (pt0) REVERT: 6 569 TYR cc_start: 0.8515 (m-80) cc_final: 0.8128 (m-80) REVERT: 6 780 TYR cc_start: 0.5671 (m-80) cc_final: 0.5428 (m-10) REVERT: 7 344 TYR cc_start: 0.8775 (t80) cc_final: 0.8533 (t80) REVERT: 7 363 HIS cc_start: 0.5431 (t70) cc_final: 0.5056 (t-90) REVERT: 7 587 MET cc_start: 0.8230 (mtt) cc_final: 0.7804 (tpt) REVERT: 7 638 MET cc_start: 0.8255 (mtp) cc_final: 0.8025 (mtp) outliers start: 56 outliers final: 42 residues processed: 275 average time/residue: 0.1324 time to fit residues: 55.3845 Evaluate side-chains 276 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 228 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 462 ILE Chi-restraints excluded: chain 2 residue 534 GLN Chi-restraints excluded: chain 2 residue 547 ARG Chi-restraints excluded: chain 2 residue 585 ILE Chi-restraints excluded: chain 2 residue 586 HIS Chi-restraints excluded: chain 2 residue 596 ILE 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 303 LEU 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 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 656 LYS 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 5 residue 316 THR Chi-restraints excluded: chain 5 residue 370 LEU Chi-restraints excluded: chain 5 residue 470 ILE Chi-restraints excluded: chain 5 residue 517 MET Chi-restraints excluded: chain 5 residue 551 VAL Chi-restraints excluded: chain 5 residue 568 ARG Chi-restraints excluded: chain 5 residue 609 ILE Chi-restraints excluded: chain 5 residue 651 ASP 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 400 SER Chi-restraints excluded: chain 7 residue 440 VAL Chi-restraints excluded: chain 7 residue 450 MET Chi-restraints excluded: chain 7 residue 511 LEU Chi-restraints excluded: chain 7 residue 599 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 173 optimal weight: 5.9990 chunk 129 optimal weight: 0.3980 chunk 203 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 chunk 152 optimal weight: 3.9990 chunk 92 optimal weight: 8.9990 chunk 85 optimal weight: 0.1980 chunk 81 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 534 GLN ** 2 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 423 HIS 4 751 ASN 5 460 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.149312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.100109 restraints weight = 31865.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.102156 restraints weight = 19062.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.102727 restraints weight = 13257.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.103565 restraints weight = 11706.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.103569 restraints weight = 10470.219| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.4859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17053 Z= 0.177 Angle : 0.609 14.758 22999 Z= 0.306 Chirality : 0.040 0.181 2617 Planarity : 0.004 0.070 2934 Dihedral : 8.120 83.854 2460 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.97 % Allowed : 17.25 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.19), residues: 2068 helix: 1.72 (0.15), residues: 1169 sheet: 0.25 (0.33), residues: 264 loop : -0.69 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG 4 732 TYR 0.018 0.002 TYR 7 579 PHE 0.033 0.002 PHE 2 868 TRP 0.027 0.002 TRP 2 554 HIS 0.010 0.001 HIS 4 744 Details of bonding type rmsd covalent geometry : bond 0.00413 (17053) covalent geometry : angle 0.60924 (22999) hydrogen bonds : bond 0.03936 ( 897) hydrogen bonds : angle 4.38246 ( 2601) *********************** 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 280 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 226 time to evaluate : 0.442 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: 0.7848 (m-30) cc_final: 0.7562 (t0) REVERT: 2 580 GLN cc_start: 0.7484 (tp-100) cc_final: 0.7143 (tp-100) REVERT: 2 717 LEU cc_start: 0.6867 (pt) cc_final: 0.6138 (tp) REVERT: 2 720 MET cc_start: 0.7045 (ppp) cc_final: 0.6589 (ppp) REVERT: 2 722 GLN cc_start: 0.8873 (pt0) cc_final: 0.8547 (tt0) REVERT: 2 786 ASP cc_start: 0.8623 (OUTLIER) cc_final: 0.8398 (m-30) REVERT: 2 819 LYS cc_start: 0.8656 (tttt) cc_final: 0.8288 (mmmt) REVERT: 2 838 ASP cc_start: 0.7811 (m-30) cc_final: 0.6874 (t0) REVERT: 2 855 ASN cc_start: 0.8423 (m-40) cc_final: 0.8092 (t0) REVERT: 3 424 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8297 (pp20) REVERT: 3 490 ASP cc_start: 0.6856 (t0) cc_final: 0.6592 (t70) REVERT: 3 514 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.8129 (t0) REVERT: 4 499 LYS cc_start: 0.7381 (OUTLIER) cc_final: 0.7002 (pttm) REVERT: 4 579 MET cc_start: 0.7752 (tpt) cc_final: 0.7064 (tpp) REVERT: 4 677 MET cc_start: -0.1830 (mmm) cc_final: -0.2931 (tmm) REVERT: 4 684 MET cc_start: 0.5237 (mmp) cc_final: 0.4685 (mtp) REVERT: 4 753 VAL cc_start: 0.7300 (t) cc_final: 0.6982 (p) REVERT: 5 421 ARG cc_start: 0.7922 (ptm160) cc_final: 0.7005 (ptm160) REVERT: 5 517 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8342 (mtm) REVERT: 5 539 ASN cc_start: 0.9101 (m-40) cc_final: 0.8879 (m-40) REVERT: 5 568 ARG cc_start: 0.9144 (OUTLIER) cc_final: 0.7915 (mtm-85) REVERT: 6 342 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.7600 (mtt) REVERT: 6 345 ASP cc_start: 0.7668 (t0) cc_final: 0.7056 (t70) REVERT: 6 443 GLU cc_start: 0.6971 (mt-10) cc_final: 0.6324 (pt0) REVERT: 6 569 TYR cc_start: 0.8558 (m-80) cc_final: 0.8286 (m-80) REVERT: 6 780 TYR cc_start: 0.5680 (m-80) cc_final: 0.5418 (m-10) REVERT: 7 363 HIS cc_start: 0.5800 (t70) cc_final: 0.5465 (t-90) REVERT: 7 561 TYR cc_start: 0.8259 (t80) cc_final: 0.8034 (t80) REVERT: 7 587 MET cc_start: 0.8247 (mtt) cc_final: 0.7839 (tpt) REVERT: 7 638 MET cc_start: 0.8252 (mtp) cc_final: 0.8009 (mtp) outliers start: 54 outliers final: 38 residues processed: 262 average time/residue: 0.1185 time to fit residues: 46.9887 Evaluate side-chains 266 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 221 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 462 ILE Chi-restraints excluded: chain 2 residue 534 GLN Chi-restraints excluded: chain 2 residue 547 ARG Chi-restraints excluded: chain 2 residue 585 ILE Chi-restraints excluded: chain 2 residue 586 HIS Chi-restraints excluded: chain 2 residue 596 ILE Chi-restraints excluded: chain 2 residue 660 LEU 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 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 514 ASP 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 656 LYS 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 5 residue 316 THR Chi-restraints excluded: chain 5 residue 370 LEU Chi-restraints excluded: chain 5 residue 517 MET Chi-restraints excluded: chain 5 residue 551 VAL Chi-restraints excluded: chain 5 residue 568 ARG Chi-restraints excluded: chain 5 residue 590 MET 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 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 400 SER Chi-restraints excluded: chain 7 residue 440 VAL Chi-restraints excluded: chain 7 residue 450 MET Chi-restraints excluded: chain 7 residue 599 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 148 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 197 optimal weight: 4.9990 chunk 140 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 133 optimal weight: 1.9990 chunk 118 optimal weight: 0.0980 chunk 123 optimal weight: 3.9990 chunk 40 optimal weight: 20.0000 chunk 201 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 534 GLN ** 2 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 423 HIS 4 751 ASN 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 = 0.150820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.102375 restraints weight = 31327.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.102872 restraints weight = 19148.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.104312 restraints weight = 12880.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.105379 restraints weight = 10837.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.105496 restraints weight = 9836.286| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.4924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17053 Z= 0.127 Angle : 0.584 14.391 22999 Z= 0.292 Chirality : 0.039 0.161 2617 Planarity : 0.003 0.072 2934 Dihedral : 8.052 84.831 2460 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.75 % Allowed : 17.36 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.19), residues: 2068 helix: 1.79 (0.15), residues: 1169 sheet: 0.28 (0.33), residues: 269 loop : -0.65 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 4 584 TYR 0.016 0.001 TYR 7 579 PHE 0.032 0.001 PHE 2 868 TRP 0.023 0.001 TRP 2 554 HIS 0.009 0.001 HIS 4 744 Details of bonding type rmsd covalent geometry : bond 0.00286 (17053) covalent geometry : angle 0.58448 (22999) hydrogen bonds : bond 0.03498 ( 897) hydrogen bonds : angle 4.27445 ( 2601) ********************** 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 274 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 224 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 490 LYS cc_start: 0.8044 (pttm) cc_final: 0.7583 (pttm) REVERT: 2 509 ASP cc_start: 0.7818 (m-30) cc_final: 0.7473 (t0) REVERT: 2 580 GLN cc_start: 0.7449 (tp-100) cc_final: 0.7109 (tp-100) REVERT: 2 717 LEU cc_start: 0.6940 (pt) cc_final: 0.6198 (tp) REVERT: 2 720 MET cc_start: 0.7064 (ppp) cc_final: 0.6634 (ppp) REVERT: 2 722 GLN cc_start: 0.8857 (pt0) cc_final: 0.8537 (tt0) REVERT: 2 786 ASP cc_start: 0.8612 (OUTLIER) cc_final: 0.8392 (m-30) REVERT: 2 819 LYS cc_start: 0.8659 (tttt) cc_final: 0.8297 (mmmt) REVERT: 2 838 ASP cc_start: 0.7851 (m-30) cc_final: 0.6896 (t0) REVERT: 3 424 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8263 (pp20) REVERT: 3 514 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.8113 (t0) REVERT: 4 499 LYS cc_start: 0.7412 (OUTLIER) cc_final: 0.7090 (pttm) REVERT: 4 579 MET cc_start: 0.7713 (tpt) cc_final: 0.7017 (tpp) REVERT: 4 648 PHE cc_start: 0.6564 (m-80) cc_final: 0.6131 (m-80) REVERT: 4 677 MET cc_start: -0.1742 (mmm) cc_final: -0.2870 (tmm) REVERT: 4 684 MET cc_start: 0.5153 (mmp) cc_final: 0.4552 (mtp) REVERT: 4 753 VAL cc_start: 0.7218 (t) cc_final: 0.6902 (p) REVERT: 5 517 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8349 (mtm) REVERT: 5 539 ASN cc_start: 0.9103 (m-40) cc_final: 0.8870 (m-40) REVERT: 5 568 ARG cc_start: 0.9106 (OUTLIER) cc_final: 0.7732 (mtm-85) REVERT: 6 342 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.7560 (mtt) REVERT: 6 345 ASP cc_start: 0.7612 (t0) cc_final: 0.7021 (t70) REVERT: 6 443 GLU cc_start: 0.6902 (mt-10) cc_final: 0.6204 (pt0) REVERT: 6 569 TYR cc_start: 0.8546 (m-80) cc_final: 0.8321 (m-80) REVERT: 6 780 TYR cc_start: 0.5846 (m-80) cc_final: 0.5606 (m-10) REVERT: 7 363 HIS cc_start: 0.5803 (t70) cc_final: 0.5478 (t-90) REVERT: 7 587 MET cc_start: 0.8220 (mtt) cc_final: 0.7844 (tpt) REVERT: 7 638 MET cc_start: 0.8257 (mtp) cc_final: 0.8052 (mtp) REVERT: L 383 GLU cc_start: 0.8771 (tp30) cc_final: 0.8452 (mp0) outliers start: 50 outliers final: 36 residues processed: 254 average time/residue: 0.1247 time to fit residues: 48.6379 Evaluate side-chains 260 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 217 time to evaluate : 0.587 ------------------------------------------------------------------------------- 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 596 ILE 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 349 VAL Chi-restraints excluded: chain 3 residue 423 HIS Chi-restraints excluded: chain 3 residue 424 GLU 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 656 LYS 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 5 residue 316 THR Chi-restraints excluded: chain 5 residue 370 LEU Chi-restraints excluded: chain 5 residue 517 MET Chi-restraints excluded: chain 5 residue 551 VAL Chi-restraints excluded: chain 5 residue 568 ARG Chi-restraints excluded: chain 5 residue 590 MET 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 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 400 SER Chi-restraints excluded: chain 7 residue 440 VAL Chi-restraints excluded: chain 7 residue 450 MET Chi-restraints excluded: chain 7 residue 599 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 119 optimal weight: 1.9990 chunk 115 optimal weight: 0.0770 chunk 83 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 49 optimal weight: 0.0980 chunk 39 optimal weight: 8.9990 chunk 76 optimal weight: 0.6980 chunk 186 optimal weight: 5.9990 chunk 201 optimal weight: 0.9990 chunk 151 optimal weight: 6.9990 overall best weight: 0.7742 ------------------------------------------------------------------------------- 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 4 751 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.151401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.099433 restraints weight = 31625.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.103183 restraints weight = 15903.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.105570 restraints weight = 10896.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.106885 restraints weight = 8797.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.107858 restraints weight = 7844.143| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.4999 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= 0.117 Angle : 0.578 14.032 22999 Z= 0.290 Chirality : 0.039 0.148 2617 Planarity : 0.004 0.079 2934 Dihedral : 7.994 85.711 2460 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.53 % Allowed : 17.97 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.19), residues: 2068 helix: 1.82 (0.15), residues: 1167 sheet: 0.43 (0.33), residues: 265 loop : -0.67 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 7 324 TYR 0.016 0.001 TYR 7 579 PHE 0.036 0.001 PHE 6 580 TRP 0.012 0.001 TRP 2 554 HIS 0.009 0.001 HIS 4 744 Details of bonding type rmsd covalent geometry : bond 0.00261 (17053) covalent geometry : angle 0.57788 (22999) hydrogen bonds : bond 0.03359 ( 897) hydrogen bonds : angle 4.21186 ( 2601) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3478.45 seconds wall clock time: 60 minutes 40.66 seconds (3640.66 seconds total)