Starting phenix.real_space_refine on Fri Jul 3 23:44:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8q6p_18192/07_2026/8q6p_18192.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q6p_18192/07_2026/8q6p_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_18192/07_2026/8q6p_18192.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q6p_18192/07_2026/8q6p_18192.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8q6p_18192/07_2026/8q6p_18192.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q6p_18192/07_2026/8q6p_18192.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8q6p_18192/07_2026/8q6p_18192.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8q6p_18192/07_2026/8q6p_18192.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 3.24, per 1000 atoms: 0.19 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: 1.35 Conformation dependent library (CDL) restraints added in 563.0 milliseconds 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: 0.42 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: 2.60 Time building geometry restraints manager: 1.74 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 - 16.75: 9566 16.75 - 33.51: 725 33.51 - 50.26: 115 50.26 - 67.02: 74 67.02 - 83.77: 10 Dihedral angle restraints: 10490 sinusoidal: 4336 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 10487 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1783 0.029 - 0.057: 513 0.057 - 0.086: 187 0.086 - 0.114: 123 0.114 - 0.143: 11 Chirality restraints: 2617 Sorted by residual: chirality pdb=" CA ILE 6 757 " pdb=" N ILE 6 757 " pdb=" C ILE 6 757 " pdb=" CB ILE 6 757 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.11e-01 chirality pdb=" CA ILE 5 470 " pdb=" N ILE 5 470 " pdb=" C ILE 5 470 " pdb=" CB ILE 5 470 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.97e-01 chirality pdb=" CA ILE 5 401 " pdb=" N ILE 5 401 " pdb=" C ILE 5 401 " pdb=" CB ILE 5 401 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.88e-01 ... (remaining 2614 not shown) Planarity restraints: 2934 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN 6 643 " 0.022 5.00e-02 4.00e+02 3.29e-02 1.73e+00 pdb=" N PRO 6 644 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO 6 644 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO 6 644 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE 2 742 " 0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO 2 743 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO 2 743 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO 2 743 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU 5 431 " 0.006 2.00e-02 2.50e+03 1.31e-02 1.71e+00 pdb=" CD GLU 5 431 " -0.023 2.00e-02 2.50e+03 pdb=" OE1 GLU 5 431 " 0.008 2.00e-02 2.50e+03 pdb=" OE2 GLU 5 431 " 0.008 2.00e-02 2.50e+03 ... (remaining 2931 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2892 2.77 - 3.30: 16336 3.30 - 3.83: 27080 3.83 - 4.37: 30735 4.37 - 4.90: 53184 Nonbonded interactions: 130227 Sorted by model distance: nonbonded pdb=" OG SER 3 352 " pdb=" O2G ATP 3 901 " model vdw 2.234 3.040 nonbonded pdb=" O LEU 6 654 " pdb=" OG SER 6 657 " model vdw 2.275 3.040 nonbonded pdb=" OE2 GLU 2 844 " pdb=" OH TYR 2 863 " model vdw 2.280 3.040 nonbonded pdb=" OG1 THR 3 509 " pdb=" OE2 GLU 3 512 " model vdw 2.288 3.040 nonbonded pdb=" O HIS 7 458 " pdb=" NH2 ARG 7 513 " model vdw 2.304 3.120 ... (remaining 130222 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 13.860 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 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 : 13.109 83.772 6484 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 are 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/Z covalent geometry : bond 0.00227 / 0.12 (17053) covalent geometry : angle 0.48438 / 0.29 (22999) hydrogen bonds : bond 0.15815 / 10.84 ( 897) hydrogen bonds : angle 5.61831 / 3.99 ( 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 : 0.557 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: 0.7509 (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: 0.1508 time to fit residues: 118.2023 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 : 0.492 ------------------------------------------------------------------------------- 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... 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 = 0.4101 r_free = 0.4101 target = 0.153291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.103227 restraints weight = 32152.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.106125 restraints weight = 19920.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.106603 restraints weight = 14652.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.107579 restraints weight = 12943.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.107545 restraints weight = 12298.451| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2982 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 : 0.572 10.056 22999 Z= 0.295 Chirality : 0.040 0.171 2617 Planarity : 0.004 0.086 2934 Dihedral : 4.628 76.356 2305 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.75 % Allowed : 13.19 % 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 are not related in a simple way. whole: 1.52 (0.19), residues: 2068 helix: 2.10 (0.15), residues: 1165 sheet: 0.23 (0.33), residues: 232 loop : -0.66 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG 2 547 TYR 0.025 0.002 TYR 2 863 PHE 0.027 0.002 PHE 6 651 TRP 0.021 0.002 TRP 2 554 HIS 0.010 0.001 HIS 3 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (17053) covalent geometry : angle 0.57150 / 0.30 (22999) hydrogen bonds : bond 0.04150 / 2.77 ( 897) hydrogen bonds : angle 4.65888 / 3.35 ( 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 379 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 329 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: 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: 0.7779 (mptt) cc_final: 0.7426 (mttp) REVERT: 2 534 GLN cc_start: 0.7695 (OUTLIER) cc_final: 0.7427 (pp30) REVERT: 2 554 TRP cc_start: 0.7328 (m100) cc_final: 0.7095 (m100) REVERT: 2 580 GLN cc_start: 0.7438 (tp-100) cc_final: 0.7221 (tp-100) REVERT: 2 794 ARG cc_start: 0.7927 (tpp80) cc_final: 0.7672 (tpp80) REVERT: 2 819 LYS cc_start: 0.8446 (tttt) cc_final: 0.8159 (mmmt) REVERT: 2 838 ASP cc_start: 0.7588 (m-30) cc_final: 0.6725 (t0) REVERT: 2 867 LEU cc_start: 0.8670 (mt) cc_final: 0.8447 (mp) REVERT: 3 475 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8540 (tt) REVERT: 4 443 GLU cc_start: 0.7589 (mp0) cc_final: 0.7322 (mm-30) REVERT: 4 578 LYS cc_start: 0.7490 (mmtt) cc_final: 0.6676 (mttp) REVERT: 4 579 MET cc_start: 0.7666 (tpt) cc_final: 0.7111 (tpp) REVERT: 4 677 MET cc_start: -0.1668 (mmm) cc_final: -0.2919 (tmm) REVERT: 4 684 MET cc_start: 0.4802 (mmp) cc_final: 0.4410 (ttm) REVERT: 5 421 ARG cc_start: 0.7882 (ptm160) cc_final: 0.7678 (ptm160) REVERT: 5 512 LEU cc_start: 0.8667 (mt) cc_final: 0.8290 (tt) REVERT: 6 342 MET cc_start: 0.7920 (OUTLIER) cc_final: 0.7712 (mtm) REVERT: 6 345 ASP cc_start: 0.7399 (t0) cc_final: 0.7195 (t0) REVERT: 6 401 SER cc_start: 0.8856 (m) cc_final: 0.8416 (p) REVERT: 6 437 LYS cc_start: 0.8170 (tttt) cc_final: 0.7964 (ptpp) REVERT: 6 443 GLU cc_start: 0.6941 (mt-10) cc_final: 0.6114 (pt0) REVERT: 6 446 ILE cc_start: 0.8665 (mt) cc_final: 0.8446 (mm) REVERT: 6 466 LYS cc_start: 0.8595 (mmtt) cc_final: 0.8283 (tmtt) REVERT: 6 572 GLU cc_start: 0.8712 (pt0) cc_final: 0.8472 (pt0) REVERT: 6 780 TYR cc_start: 0.5738 (m-10) cc_final: 0.5529 (m-80) REVERT: 7 553 MET cc_start: 0.8726 (tpp) cc_final: 0.8473 (tpp) REVERT: 7 587 MET cc_start: 0.8018 (mtt) cc_final: 0.7656 (ttp) REVERT: 7 615 LEU cc_start: 0.8463 (mt) cc_final: 0.8247 (mt) outliers start: 50 outliers final: 24 residues processed: 369 average time/residue: 0.1259 time to fit residues: 68.2594 Evaluate side-chains 296 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 269 time to evaluate : 0.614 ------------------------------------------------------------------------------- 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 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 475 LEU 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 400 SER 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: 10.0000 chunk 41 optimal weight: 6.9990 chunk 145 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 72 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 53 optimal weight: 0.0060 chunk 110 optimal weight: 3.9990 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 534 GLN 3 553 HIS 4 665 HIS 4 751 ASN 5 541 HIS 6 496 ASN 6 558 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.152734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.103726 restraints weight = 32283.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.104457 restraints weight = 20759.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.105664 restraints weight = 16703.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.106342 restraints weight = 13774.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.107143 restraints weight = 12992.074| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17053 Z= 0.120 Angle : 0.567 11.213 22999 Z= 0.286 Chirality : 0.039 0.146 2617 Planarity : 0.004 0.054 2934 Dihedral : 4.587 74.570 2305 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.19 % Allowed : 13.68 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.18), residues: 2068 helix: 2.05 (0.15), residues: 1164 sheet: 0.39 (0.33), residues: 233 loop : -0.64 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 3 430 TYR 0.028 0.002 TYR 7 579 PHE 0.022 0.001 PHE 2 663 TRP 0.017 0.002 TRP 6 748 HIS 0.008 0.001 HIS 3 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (17053) covalent geometry : angle 0.56668 / 0.29 (22999) hydrogen bonds : bond 0.03788 / 2.56 ( 897) hydrogen bonds : angle 4.47668 / 3.22 ( 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 341 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 283 time to evaluate : 0.538 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: 2 452 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7647 (mm) REVERT: 2 509 ASP cc_start: 0.7375 (m-30) cc_final: 0.7140 (t0) REVERT: 2 580 GLN cc_start: 0.7414 (tp-100) cc_final: 0.7183 (tp-100) REVERT: 2 794 ARG cc_start: 0.7917 (tpp80) cc_final: 0.7708 (tpp80) REVERT: 2 819 LYS cc_start: 0.8436 (tttt) cc_final: 0.8152 (mmmt) REVERT: 2 838 ASP cc_start: 0.7636 (m-30) cc_final: 0.6791 (t0) REVERT: 4 443 GLU cc_start: 0.7535 (mp0) cc_final: 0.6959 (mp0) REVERT: 4 518 GLN cc_start: 0.4839 (mm-40) cc_final: 0.3899 (tm-30) REVERT: 4 578 LYS cc_start: 0.7549 (mmtt) cc_final: 0.6510 (mtmm) REVERT: 4 579 MET cc_start: 0.7682 (tpt) cc_final: 0.7022 (tpp) REVERT: 4 677 MET cc_start: -0.1590 (mmm) cc_final: -0.2858 (tmm) REVERT: 4 684 MET cc_start: 0.4974 (mmp) cc_final: 0.4526 (ttm) REVERT: 5 512 LEU cc_start: 0.8546 (mt) cc_final: 0.8285 (tt) REVERT: 6 342 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.7234 (mtt) REVERT: 6 345 ASP cc_start: 0.7544 (t0) cc_final: 0.6510 (t0) REVERT: 6 381 THR cc_start: 0.6837 (m) cc_final: 0.6612 (m) REVERT: 6 401 SER cc_start: 0.8841 (m) cc_final: 0.8439 (p) REVERT: 6 443 GLU cc_start: 0.6904 (mt-10) cc_final: 0.6112 (pt0) REVERT: 6 633 MET cc_start: 0.8313 (mmm) cc_final: 0.8079 (tpp) REVERT: 6 780 TYR cc_start: 0.5912 (m-10) cc_final: 0.5707 (m-80) REVERT: 7 587 MET cc_start: 0.7926 (mtt) cc_final: 0.7672 (ttp) outliers start: 58 outliers final: 26 residues processed: 322 average time/residue: 0.1314 time to fit residues: 63.2055 Evaluate side-chains 276 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 248 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 452 LEU 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 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 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 327 ILE Chi-restraints excluded: chain 6 residue 342 MET Chi-restraints excluded: chain 6 residue 353 CYS Chi-restraints excluded: chain 6 residue 356 LEU Chi-restraints excluded: chain 6 residue 540 ASP Chi-restraints excluded: chain 7 residue 339 ILE 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: 0.8980 chunk 42 optimal weight: 9.9990 chunk 184 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 86 optimal weight: 0.0370 chunk 54 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 189 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 overall best weight: 1.1262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 423 HIS 3 553 HIS 4 473 HIS 4 665 HIS 4 751 ASN 5 541 HIS 6 496 ASN ** 7 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.152334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.106189 restraints weight = 32436.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.105922 restraints weight = 21125.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.105684 restraints weight = 16683.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.106332 restraints weight = 15875.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.106584 restraints weight = 14165.880| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17053 Z= 0.136 Angle : 0.555 8.809 22999 Z= 0.282 Chirality : 0.039 0.154 2617 Planarity : 0.003 0.037 2934 Dihedral : 4.598 73.270 2305 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.08 % Allowed : 15.38 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.19), residues: 2068 helix: 1.99 (0.15), residues: 1163 sheet: 0.21 (0.32), residues: 245 loop : -0.66 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 7 634 TYR 0.022 0.001 TYR 7 579 PHE 0.024 0.001 PHE 2 663 TRP 0.014 0.001 TRP 6 748 HIS 0.023 0.001 HIS 5 541 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (17053) covalent geometry : angle 0.55524 / 0.28 (22999) hydrogen bonds : bond 0.03797 / 2.54 ( 897) hydrogen bonds : angle 4.43980 / 3.21 ( 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 313 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 257 time to evaluate : 0.703 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: 2 509 ASP cc_start: 0.7464 (m-30) cc_final: 0.7244 (t0) REVERT: 2 580 GLN cc_start: 0.7422 (tp-100) cc_final: 0.7163 (tp-100) REVERT: 2 819 LYS cc_start: 0.8508 (tttt) cc_final: 0.8209 (mmmt) REVERT: 2 838 ASP cc_start: 0.7642 (m-30) cc_final: 0.6755 (t0) REVERT: 4 443 GLU cc_start: 0.7538 (mp0) cc_final: 0.7020 (mp0) REVERT: 4 472 GLU cc_start: 0.5696 (OUTLIER) cc_final: 0.5359 (tt0) REVERT: 4 518 GLN cc_start: 0.5012 (mm-40) cc_final: 0.4006 (tm-30) REVERT: 4 579 MET cc_start: 0.7626 (tpt) cc_final: 0.6627 (tpp) REVERT: 4 677 MET cc_start: -0.1467 (mmm) cc_final: -0.2777 (tmm) REVERT: 4 684 MET cc_start: 0.4972 (mmp) cc_final: 0.4675 (mtp) REVERT: 4 735 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7338 (mp0) REVERT: 6 342 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.7397 (mtt) REVERT: 6 381 THR cc_start: 0.7056 (m) cc_final: 0.6821 (m) REVERT: 6 401 SER cc_start: 0.8923 (m) cc_final: 0.8513 (p) REVERT: 6 443 GLU cc_start: 0.6869 (mt-10) cc_final: 0.6172 (pt0) REVERT: 6 780 TYR cc_start: 0.6028 (m-10) cc_final: 0.5745 (m-80) REVERT: 7 321 GLU cc_start: 0.8348 (tp30) cc_final: 0.8144 (tp30) REVERT: 7 587 MET cc_start: 0.8014 (mtt) cc_final: 0.7722 (ttp) outliers start: 56 outliers final: 33 residues processed: 295 average time/residue: 0.1242 time to fit residues: 55.3326 Evaluate side-chains 279 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 243 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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 781 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 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 472 GLU Chi-restraints excluded: chain 4 residue 511 ASP 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 557 LEU 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 63 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 38 optimal weight: 20.0000 chunk 22 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 172 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 182 optimal weight: 0.0670 overall best weight: 0.7918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 534 GLN 2 631 ASN ** 2 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 423 HIS 3 553 HIS ** 4 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 751 ASN ** 7 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 502 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.152189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.100374 restraints weight = 31643.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.104161 restraints weight = 15683.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.106672 restraints weight = 10702.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.108068 restraints weight = 8615.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.108978 restraints weight = 7632.528| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17053 Z= 0.118 Angle : 0.542 9.487 22999 Z= 0.274 Chirality : 0.039 0.154 2617 Planarity : 0.003 0.045 2934 Dihedral : 4.569 72.813 2305 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.97 % Allowed : 15.77 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.19), residues: 2068 helix: 1.96 (0.15), residues: 1164 sheet: 0.55 (0.33), residues: 237 loop : -0.73 (0.23), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG 7 324 TYR 0.019 0.001 TYR 7 579 PHE 0.024 0.001 PHE 2 663 TRP 0.015 0.001 TRP 2 554 HIS 0.010 0.001 HIS 7 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (17053) covalent geometry : angle 0.54226 / 0.27 (22999) hydrogen bonds : bond 0.03541 / 2.38 ( 897) hydrogen bonds : angle 4.32048 / 3.12 ( 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 312 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 258 time to evaluate : 0.750 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: 2 509 ASP cc_start: 0.7735 (m-30) cc_final: 0.7475 (t0) REVERT: 2 580 GLN cc_start: 0.7346 (tp-100) cc_final: 0.7048 (tp-100) REVERT: 2 712 LYS cc_start: 0.8122 (mttt) cc_final: 0.7901 (mtmm) REVERT: 2 819 LYS cc_start: 0.8494 (tttt) cc_final: 0.8240 (mmmt) REVERT: 2 838 ASP cc_start: 0.7743 (m-30) cc_final: 0.6848 (t0) REVERT: 2 855 ASN cc_start: 0.8544 (m-40) cc_final: 0.8135 (t0) REVERT: 4 443 GLU cc_start: 0.7845 (mp0) cc_final: 0.7354 (mp0) REVERT: 4 472 GLU cc_start: 0.5691 (OUTLIER) cc_final: 0.5350 (tt0) REVERT: 4 579 MET cc_start: 0.7635 (tpt) cc_final: 0.6613 (tpp) REVERT: 4 677 MET cc_start: -0.1497 (mmm) cc_final: -0.2806 (tmm) REVERT: 4 684 MET cc_start: 0.4944 (mmp) cc_final: 0.4713 (mtp) REVERT: 4 735 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7425 (mp0) REVERT: 5 426 ARG cc_start: 0.8493 (mtp-110) cc_final: 0.8238 (tpp80) REVERT: 6 342 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7430 (mtt) REVERT: 6 381 THR cc_start: 0.7042 (m) cc_final: 0.6800 (m) REVERT: 6 401 SER cc_start: 0.8929 (m) cc_final: 0.8601 (p) REVERT: 6 443 GLU cc_start: 0.6865 (mt-10) cc_final: 0.6132 (pt0) REVERT: 6 633 MET cc_start: 0.8083 (mmm) cc_final: 0.7690 (tpp) REVERT: 7 587 MET cc_start: 0.8134 (mtt) cc_final: 0.7688 (tpt) outliers start: 54 outliers final: 34 residues processed: 297 average time/residue: 0.1254 time to fit residues: 57.1713 Evaluate side-chains 281 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 244 time to evaluate : 0.681 ------------------------------------------------------------------------------- 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 781 LEU 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 542 LEU Chi-restraints excluded: chain 3 residue 546 GLU Chi-restraints excluded: chain 3 residue 568 ILE Chi-restraints excluded: chain 3 residue 572 ILE Chi-restraints excluded: chain 3 residue 577 LEU Chi-restraints excluded: chain 3 residue 597 ILE Chi-restraints excluded: chain 3 residue 631 VAL Chi-restraints excluded: chain 4 residue 472 GLU Chi-restraints excluded: chain 4 residue 511 ASP Chi-restraints excluded: chain 4 residue 735 GLU Chi-restraints excluded: chain 4 residue 751 ASN Chi-restraints excluded: chain 4 residue 765 HIS Chi-restraints excluded: chain 5 residue 370 LEU Chi-restraints excluded: chain 5 residue 551 VAL Chi-restraints excluded: chain 5 residue 557 LEU Chi-restraints excluded: chain 5 residue 609 ILE Chi-restraints excluded: chain 6 residue 327 ILE Chi-restraints excluded: chain 6 residue 342 MET Chi-restraints excluded: chain 6 residue 353 CYS Chi-restraints excluded: chain 6 residue 356 LEU Chi-restraints excluded: chain 6 residue 378 VAL Chi-restraints excluded: chain 6 residue 535 PHE Chi-restraints excluded: chain 6 residue 540 ASP Chi-restraints excluded: chain 7 residue 326 ILE Chi-restraints excluded: chain 7 residue 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: 1.9990 chunk 112 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 203 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 145 optimal weight: 6.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 423 HIS 3 553 HIS ** 4 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 751 ASN 7 502 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.152163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.100062 restraints weight = 31875.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.103883 restraints weight = 15874.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.106315 restraints weight = 10843.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.107748 restraints weight = 8772.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.108718 restraints weight = 7762.152| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.4312 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= 0.118 Angle : 0.539 9.488 22999 Z= 0.274 Chirality : 0.039 0.163 2617 Planarity : 0.003 0.052 2934 Dihedral : 4.569 72.641 2305 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.80 % Allowed : 16.87 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.19), residues: 2068 helix: 1.95 (0.15), residues: 1170 sheet: 0.41 (0.33), residues: 253 loop : -0.69 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG 7 634 TYR 0.016 0.001 TYR 6 569 PHE 0.023 0.001 PHE 2 663 TRP 0.019 0.001 TRP 2 554 HIS 0.008 0.001 HIS 4 744 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (17053) covalent geometry : angle 0.53946 / 0.27 (22999) hydrogen bonds : bond 0.03457 / 2.33 ( 897) hydrogen bonds : angle 4.28221 / 3.09 ( 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: 51 poor density : 254 time to evaluate : 0.666 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: 0.7789 (m-30) cc_final: 0.7484 (t0) REVERT: 2 580 GLN cc_start: 0.7368 (tp-100) cc_final: 0.7056 (tp-100) REVERT: 2 712 LYS cc_start: 0.8029 (mttt) cc_final: 0.7712 (tttt) REVERT: 2 819 LYS cc_start: 0.8646 (tttt) cc_final: 0.8300 (mmtt) REVERT: 2 838 ASP cc_start: 0.7764 (m-30) cc_final: 0.6838 (t0) REVERT: 2 855 ASN cc_start: 0.8554 (m-40) cc_final: 0.8133 (t0) REVERT: 4 472 GLU cc_start: 0.5682 (OUTLIER) cc_final: 0.5371 (tt0) REVERT: 4 579 MET cc_start: 0.7747 (tpt) cc_final: 0.6958 (tpp) REVERT: 4 648 PHE cc_start: 0.6186 (m-80) cc_final: 0.5813 (m-80) REVERT: 4 650 MET cc_start: 0.2661 (tmm) cc_final: 0.2195 (tmm) REVERT: 4 677 MET cc_start: -0.1494 (mmm) cc_final: -0.2806 (tmm) REVERT: 4 684 MET cc_start: 0.4991 (mmp) cc_final: 0.4704 (mtp) REVERT: 4 735 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7403 (mp0) REVERT: 4 753 VAL cc_start: 0.7560 (t) cc_final: 0.7260 (p) REVERT: 5 426 ARG cc_start: 0.8513 (mtp-110) cc_final: 0.8247 (tpp80) REVERT: 5 508 MET cc_start: 0.6669 (tmm) cc_final: 0.6133 (tpp) REVERT: 6 342 MET cc_start: 0.8226 (OUTLIER) cc_final: 0.7312 (mtt) REVERT: 6 381 THR cc_start: 0.6965 (m) cc_final: 0.6726 (m) REVERT: 6 401 SER cc_start: 0.8922 (m) cc_final: 0.8603 (p) REVERT: 6 443 GLU cc_start: 0.6912 (mt-10) cc_final: 0.6221 (pt0) REVERT: 6 633 MET cc_start: 0.8054 (mmm) cc_final: 0.7661 (tpp) REVERT: 6 780 TYR cc_start: 0.5959 (m-10) cc_final: 0.5755 (m-80) REVERT: 7 587 MET cc_start: 0.8115 (mtt) cc_final: 0.7698 (tpt) outliers start: 51 outliers final: 37 residues processed: 290 average time/residue: 0.1233 time to fit residues: 54.4155 Evaluate side-chains 278 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 238 time to evaluate : 0.633 ------------------------------------------------------------------------------- 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 781 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 542 LEU Chi-restraints excluded: chain 3 residue 546 GLU 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 472 GLU Chi-restraints excluded: chain 4 residue 511 ASP 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 470 ILE Chi-restraints excluded: chain 5 residue 478 THR Chi-restraints excluded: chain 5 residue 551 VAL Chi-restraints excluded: chain 5 residue 609 ILE Chi-restraints excluded: chain 5 residue 651 ASP Chi-restraints excluded: chain 6 residue 327 ILE Chi-restraints excluded: chain 6 residue 342 MET Chi-restraints excluded: chain 6 residue 353 CYS Chi-restraints excluded: chain 6 residue 356 LEU Chi-restraints excluded: chain 6 residue 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 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 500 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 111 optimal weight: 0.0270 chunk 157 optimal weight: 5.9990 chunk 145 optimal weight: 0.8980 chunk 151 optimal weight: 0.8980 chunk 75 optimal weight: 0.0770 chunk 188 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 201 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 120 optimal weight: 0.7980 chunk 186 optimal weight: 5.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 534 GLN ** 2 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 423 HIS 3 553 HIS 3 640 GLN 4 665 HIS 4 751 ASN 5 541 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.153090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.101381 restraints weight = 31380.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.105249 restraints weight = 15574.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.107692 restraints weight = 10638.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.109120 restraints weight = 8591.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.109842 restraints weight = 7605.862| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.4487 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= 0.104 Angle : 0.550 16.774 22999 Z= 0.274 Chirality : 0.039 0.148 2617 Planarity : 0.003 0.042 2934 Dihedral : 4.505 71.921 2305 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.69 % Allowed : 17.36 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.19), residues: 2068 helix: 1.95 (0.15), residues: 1171 sheet: 0.57 (0.34), residues: 239 loop : -0.60 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 4 643 TYR 0.015 0.001 TYR 6 569 PHE 0.049 0.001 PHE 2 868 TRP 0.024 0.001 TRP 2 554 HIS 0.011 0.001 HIS 3 423 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (17053) covalent geometry : angle 0.54992 / 0.27 (22999) hydrogen bonds : bond 0.03235 / 2.19 ( 897) hydrogen bonds : angle 4.20266 / 3.02 ( 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 304 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 255 time to evaluate : 0.646 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: 0.7726 (m-30) cc_final: 0.7440 (t0) REVERT: 2 580 GLN cc_start: 0.7343 (tp-100) cc_final: 0.7028 (tp-100) REVERT: 2 819 LYS cc_start: 0.8655 (tttt) cc_final: 0.8314 (mmtt) REVERT: 2 838 ASP cc_start: 0.7783 (m-30) cc_final: 0.6845 (t0) REVERT: 2 855 ASN cc_start: 0.8551 (m-40) cc_final: 0.8148 (t0) REVERT: 4 472 GLU cc_start: 0.5743 (OUTLIER) cc_final: 0.5400 (tt0) REVERT: 4 499 LYS cc_start: 0.7299 (OUTLIER) cc_final: 0.6946 (pttm) REVERT: 4 579 MET cc_start: 0.7698 (tpt) cc_final: 0.6959 (tpp) REVERT: 4 650 MET cc_start: 0.2478 (tmm) cc_final: 0.2005 (tmm) REVERT: 4 677 MET cc_start: -0.1791 (mmm) cc_final: -0.2919 (tmm) REVERT: 4 684 MET cc_start: 0.5070 (mmp) cc_final: 0.4840 (mtp) REVERT: 4 753 VAL cc_start: 0.7408 (t) cc_final: 0.7110 (p) REVERT: 5 420 MET cc_start: 0.6802 (mmm) cc_final: 0.6499 (mpp) REVERT: 5 426 ARG cc_start: 0.8526 (mtp-110) cc_final: 0.8234 (tpp80) REVERT: 6 342 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7413 (mtt) REVERT: 6 381 THR cc_start: 0.7119 (m) cc_final: 0.6893 (m) REVERT: 6 401 SER cc_start: 0.8905 (m) cc_final: 0.8600 (p) REVERT: 6 437 LYS cc_start: 0.8157 (mptt) cc_final: 0.7741 (mtmm) REVERT: 6 443 GLU cc_start: 0.7049 (mt-10) cc_final: 0.6301 (pt0) REVERT: 6 444 PHE cc_start: 0.6775 (m-10) cc_final: 0.6368 (m-10) REVERT: 7 446 PHE cc_start: 0.8533 (t80) cc_final: 0.8300 (t80) REVERT: 7 587 MET cc_start: 0.8160 (mtt) cc_final: 0.7723 (tpt) outliers start: 49 outliers final: 32 residues processed: 289 average time/residue: 0.1225 time to fit residues: 54.4897 Evaluate side-chains 274 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 239 time to evaluate : 0.603 ------------------------------------------------------------------------------- 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 739 THR Chi-restraints excluded: chain 2 residue 781 LEU 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 542 LEU Chi-restraints excluded: chain 3 residue 577 LEU Chi-restraints excluded: chain 3 residue 597 ILE Chi-restraints excluded: chain 3 residue 631 VAL Chi-restraints excluded: chain 4 residue 472 GLU Chi-restraints excluded: chain 4 residue 499 LYS Chi-restraints excluded: chain 4 residue 511 ASP Chi-restraints excluded: chain 4 residue 582 SER Chi-restraints excluded: chain 4 residue 631 ILE Chi-restraints excluded: chain 5 residue 470 ILE Chi-restraints excluded: chain 5 residue 541 HIS Chi-restraints excluded: chain 5 residue 551 VAL Chi-restraints excluded: chain 6 residue 327 ILE Chi-restraints excluded: chain 6 residue 342 MET Chi-restraints excluded: chain 6 residue 353 CYS Chi-restraints excluded: chain 6 residue 356 LEU Chi-restraints excluded: chain 6 residue 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 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 500 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 0.7980 chunk 144 optimal weight: 0.5980 chunk 164 optimal weight: 8.9990 chunk 171 optimal weight: 3.9990 chunk 189 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 119 optimal weight: 5.9990 chunk 59 optimal weight: 0.0070 chunk 2 optimal weight: 0.0670 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4125 r_free = 0.4125 target = 0.153272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.101566 restraints weight = 31601.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.105359 restraints weight = 15699.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.107822 restraints weight = 10704.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.109302 restraints weight = 8616.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.110289 restraints weight = 7611.811| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.4632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 17053 Z= 0.105 Angle : 0.560 15.623 22999 Z= 0.279 Chirality : 0.039 0.157 2617 Planarity : 0.003 0.043 2934 Dihedral : 4.484 71.743 2305 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.47 % Allowed : 17.47 % 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 are not related in a simple way. whole: 1.48 (0.19), residues: 2068 helix: 1.93 (0.15), residues: 1173 sheet: 0.42 (0.33), residues: 262 loop : -0.54 (0.25), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 7 634 TYR 0.035 0.001 TYR 6 600 PHE 0.036 0.001 PHE 2 868 TRP 0.024 0.001 TRP 2 554 HIS 0.009 0.001 HIS 7 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (17053) covalent geometry : angle 0.56028 / 0.28 (22999) hydrogen bonds : bond 0.03208 / 2.17 ( 897) hydrogen bonds : angle 4.17809 / 2.99 ( 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 292 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 247 time to evaluate : 0.664 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: 0.7722 (m-30) cc_final: 0.7438 (t0) REVERT: 2 580 GLN cc_start: 0.7342 (tp-100) cc_final: 0.7028 (tp-100) REVERT: 2 720 MET cc_start: 0.7019 (ppp) cc_final: 0.6587 (ppp) REVERT: 2 819 LYS cc_start: 0.8654 (tttt) cc_final: 0.8318 (mmtt) REVERT: 2 836 GLN cc_start: 0.6562 (mm-40) cc_final: 0.5621 (pm20) REVERT: 2 838 ASP cc_start: 0.7825 (m-30) cc_final: 0.6911 (t0) REVERT: 2 855 ASN cc_start: 0.8596 (m-40) cc_final: 0.8183 (t0) REVERT: 4 472 GLU cc_start: 0.5650 (OUTLIER) cc_final: 0.5374 (tt0) REVERT: 4 499 LYS cc_start: 0.7386 (OUTLIER) cc_final: 0.7053 (pttm) REVERT: 4 579 MET cc_start: 0.7722 (tpt) cc_final: 0.6955 (tpp) REVERT: 4 648 PHE cc_start: 0.5982 (m-80) cc_final: 0.5727 (m-80) REVERT: 4 650 MET cc_start: 0.2294 (tmm) cc_final: 0.1870 (tmm) REVERT: 4 677 MET cc_start: -0.1681 (mmm) cc_final: -0.2873 (tmm) REVERT: 4 684 MET cc_start: 0.5192 (mmp) cc_final: 0.4852 (mtp) REVERT: 4 732 ARG cc_start: 0.8227 (mtm-85) cc_final: 0.7894 (ptm160) REVERT: 5 426 ARG cc_start: 0.8525 (mtp-110) cc_final: 0.8236 (tpp80) REVERT: 5 508 MET cc_start: 0.6696 (tmm) cc_final: 0.6177 (tpp) REVERT: 6 342 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7251 (mtt) REVERT: 6 401 SER cc_start: 0.8906 (m) cc_final: 0.8680 (p) REVERT: 6 443 GLU cc_start: 0.7142 (mt-10) cc_final: 0.6428 (pt0) REVERT: 7 446 PHE cc_start: 0.8512 (t80) cc_final: 0.8293 (t80) REVERT: 7 587 MET cc_start: 0.8158 (mtt) cc_final: 0.7728 (tpt) outliers start: 45 outliers final: 35 residues processed: 280 average time/residue: 0.1240 time to fit residues: 53.8517 Evaluate side-chains 269 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 231 time to evaluate : 0.650 ------------------------------------------------------------------------------- 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 739 THR Chi-restraints excluded: chain 2 residue 781 LEU 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 542 LEU Chi-restraints excluded: chain 3 residue 568 ILE Chi-restraints excluded: chain 3 residue 577 LEU Chi-restraints excluded: chain 3 residue 597 ILE Chi-restraints excluded: chain 3 residue 631 VAL Chi-restraints excluded: chain 4 residue 472 GLU Chi-restraints excluded: chain 4 residue 499 LYS Chi-restraints excluded: chain 4 residue 511 ASP Chi-restraints excluded: chain 4 residue 631 ILE Chi-restraints excluded: chain 4 residue 751 ASN Chi-restraints excluded: chain 5 residue 316 THR Chi-restraints excluded: chain 5 residue 470 ILE Chi-restraints excluded: chain 5 residue 551 VAL Chi-restraints excluded: chain 5 residue 609 ILE Chi-restraints excluded: chain 6 residue 327 ILE Chi-restraints excluded: chain 6 residue 342 MET Chi-restraints excluded: chain 6 residue 353 CYS Chi-restraints excluded: chain 6 residue 356 LEU Chi-restraints excluded: chain 6 residue 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 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 500 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 173 optimal weight: 4.9990 chunk 129 optimal weight: 0.6980 chunk 203 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 152 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 42 optimal weight: 8.9990 chunk 101 optimal weight: 0.9980 chunk 146 optimal weight: 2.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 423 HIS 3 553 HIS 3 640 GLN 4 751 ASN 5 460 HIS 5 541 HIS ** 6 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.149204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.096960 restraints weight = 31841.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.100560 restraints weight = 16142.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.102878 restraints weight = 11144.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.104223 restraints weight = 9046.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.105005 restraints weight = 8041.458| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 17053 Z= 0.197 Angle : 0.633 15.138 22999 Z= 0.318 Chirality : 0.041 0.152 2617 Planarity : 0.004 0.094 2934 Dihedral : 4.780 81.816 2305 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.86 % Allowed : 17.25 % 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 are not related in a simple way. whole: 1.23 (0.19), residues: 2068 helix: 1.73 (0.15), residues: 1169 sheet: 0.27 (0.33), residues: 263 loop : -0.61 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG 4 643 TYR 0.036 0.002 TYR 6 600 PHE 0.033 0.002 PHE 2 868 TRP 0.021 0.001 TRP 2 554 HIS 0.009 0.001 HIS 7 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.20 (17053) covalent geometry : angle 0.63287 / 0.32 (22999) hydrogen bonds : bond 0.04206 / 2.82 ( 897) hydrogen bonds : angle 4.46848 / 3.20 ( 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 281 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 229 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 580 GLN cc_start: 0.7493 (tp-100) cc_final: 0.7154 (tp-100) REVERT: 2 720 MET cc_start: 0.6845 (ppp) cc_final: 0.6493 (ppp) REVERT: 2 819 LYS cc_start: 0.8716 (tttt) cc_final: 0.8377 (mmtt) REVERT: 2 838 ASP cc_start: 0.7883 (m-30) cc_final: 0.6900 (t0) REVERT: 2 855 ASN cc_start: 0.8527 (m-40) cc_final: 0.8142 (t0) REVERT: 3 423 HIS cc_start: 0.8890 (OUTLIER) cc_final: 0.8613 (t70) REVERT: 3 424 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8341 (pp20) REVERT: 3 633 MET cc_start: 0.8792 (mmt) cc_final: 0.8559 (mmt) REVERT: 4 499 LYS cc_start: 0.7360 (OUTLIER) cc_final: 0.7008 (pttm) REVERT: 4 579 MET cc_start: 0.7777 (tpt) cc_final: 0.6991 (tpp) REVERT: 4 648 PHE cc_start: 0.6341 (m-80) cc_final: 0.5974 (m-80) REVERT: 4 650 MET cc_start: 0.2425 (tmm) cc_final: 0.1973 (tmm) REVERT: 4 677 MET cc_start: -0.1705 (mmm) cc_final: -0.2881 (tmm) REVERT: 4 684 MET cc_start: 0.5217 (mmp) cc_final: 0.4720 (mtp) REVERT: 4 753 VAL cc_start: 0.7426 (t) cc_final: 0.7116 (p) REVERT: 5 420 MET cc_start: 0.6910 (mmm) cc_final: 0.6578 (mpp) REVERT: 5 426 ARG cc_start: 0.8563 (mtp-110) cc_final: 0.8243 (tpp80) REVERT: 6 342 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7435 (mtt) REVERT: 6 443 GLU cc_start: 0.7111 (mt-10) cc_final: 0.6455 (pt0) REVERT: 6 780 TYR cc_start: 0.5683 (m-80) cc_final: 0.5444 (m-80) REVERT: 7 363 HIS cc_start: 0.5258 (t70) cc_final: 0.4834 (t70) REVERT: 7 587 MET cc_start: 0.8208 (mtt) cc_final: 0.7787 (tpt) outliers start: 52 outliers final: 36 residues processed: 265 average time/residue: 0.1233 time to fit residues: 50.3563 Evaluate side-chains 258 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 218 time to evaluate : 0.638 ------------------------------------------------------------------------------- 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 739 THR Chi-restraints excluded: chain 2 residue 781 LEU Chi-restraints excluded: chain 3 residue 303 LEU 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 542 LEU Chi-restraints excluded: chain 3 residue 568 ILE Chi-restraints excluded: chain 3 residue 577 LEU Chi-restraints excluded: chain 3 residue 597 ILE Chi-restraints excluded: chain 3 residue 631 VAL Chi-restraints excluded: chain 4 residue 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 478 THR Chi-restraints excluded: chain 5 residue 541 HIS Chi-restraints excluded: chain 5 residue 551 VAL Chi-restraints excluded: chain 5 residue 609 ILE Chi-restraints excluded: chain 5 residue 651 ASP Chi-restraints excluded: chain 6 residue 327 ILE Chi-restraints excluded: chain 6 residue 342 MET Chi-restraints excluded: chain 6 residue 353 CYS Chi-restraints excluded: chain 6 residue 356 LEU Chi-restraints excluded: chain 6 residue 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 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 500 VAL 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: 4.9990 chunk 15 optimal weight: 1.9990 chunk 197 optimal weight: 0.0270 chunk 140 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 chunk 133 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 40 optimal weight: 0.0980 chunk 201 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.5640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 534 GLN 3 423 HIS 3 553 HIS 4 751 ASN 5 541 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.152994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.107222 restraints weight = 32176.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.106629 restraints weight = 19128.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.106055 restraints weight = 17087.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.106525 restraints weight = 15547.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.106816 restraints weight = 14333.148| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.4909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17053 Z= 0.112 Angle : 0.592 14.555 22999 Z= 0.294 Chirality : 0.039 0.165 2617 Planarity : 0.003 0.059 2934 Dihedral : 4.727 87.619 2305 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.14 % Allowed : 17.97 % 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 are not related in a simple way. whole: 1.34 (0.19), residues: 2068 helix: 1.81 (0.15), residues: 1170 sheet: 0.45 (0.33), residues: 252 loop : -0.61 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 2 754 TYR 0.025 0.001 TYR 6 600 PHE 0.031 0.001 PHE 2 868 TRP 0.020 0.001 TRP 2 554 HIS 0.010 0.001 HIS 3 423 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (17053) covalent geometry : angle 0.59234 / 0.29 (22999) hydrogen bonds : bond 0.03347 / 2.25 ( 897) hydrogen bonds : angle 4.26725 / 3.05 ( 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 275 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 236 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 580 GLN cc_start: 0.7481 (tp-100) cc_final: 0.7125 (tp-100) REVERT: 2 720 MET cc_start: 0.7161 (ppp) cc_final: 0.6843 (ppp) REVERT: 2 722 GLN cc_start: 0.8804 (pt0) cc_final: 0.8548 (tt0) REVERT: 2 819 LYS cc_start: 0.8717 (tttt) cc_final: 0.8388 (mmtt) REVERT: 2 836 GLN cc_start: 0.6578 (mm-40) cc_final: 0.5570 (pm20) REVERT: 2 838 ASP cc_start: 0.7949 (m-30) cc_final: 0.7035 (t0) REVERT: 2 855 ASN cc_start: 0.8500 (m-40) cc_final: 0.8050 (t0) REVERT: 4 499 LYS cc_start: 0.7445 (OUTLIER) cc_final: 0.7139 (pttm) REVERT: 4 579 MET cc_start: 0.7714 (tpt) cc_final: 0.6982 (tpp) REVERT: 4 648 PHE cc_start: 0.6311 (m-80) cc_final: 0.5972 (m-80) REVERT: 4 650 MET cc_start: 0.2410 (tmm) cc_final: 0.1978 (tmm) REVERT: 4 677 MET cc_start: -0.1678 (mmm) cc_final: -0.1914 (mmt) REVERT: 4 684 MET cc_start: 0.5280 (mmp) cc_final: 0.4812 (mtp) REVERT: 5 420 MET cc_start: 0.7099 (mmm) cc_final: 0.6798 (mpp) REVERT: 5 426 ARG cc_start: 0.8511 (mtp-110) cc_final: 0.8277 (tpp80) REVERT: 6 342 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7282 (mtt) REVERT: 6 401 SER cc_start: 0.8943 (m) cc_final: 0.8588 (p) REVERT: 6 443 GLU cc_start: 0.7062 (mt-10) cc_final: 0.6448 (pt0) REVERT: 6 766 LYS cc_start: 0.7930 (ttmm) cc_final: 0.7667 (mtpp) REVERT: 7 363 HIS cc_start: 0.5206 (t70) cc_final: 0.4772 (t70) REVERT: 7 587 MET cc_start: 0.8167 (mtt) cc_final: 0.7778 (tpt) outliers start: 39 outliers final: 28 residues processed: 265 average time/residue: 0.1175 time to fit residues: 48.0461 Evaluate side-chains 258 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 228 time to evaluate : 0.655 ------------------------------------------------------------------------------- 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 586 HIS Chi-restraints excluded: chain 2 residue 781 LEU Chi-restraints excluded: chain 3 residue 349 VAL 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 751 ASN Chi-restraints excluded: chain 5 residue 316 THR Chi-restraints excluded: chain 5 residue 551 VAL Chi-restraints excluded: chain 5 residue 609 ILE Chi-restraints excluded: chain 6 residue 327 ILE Chi-restraints excluded: chain 6 residue 342 MET Chi-restraints excluded: chain 6 residue 353 CYS Chi-restraints excluded: chain 6 residue 356 LEU Chi-restraints excluded: chain 6 residue 535 PHE Chi-restraints excluded: chain 6 residue 540 ASP Chi-restraints excluded: chain 6 residue 558 HIS Chi-restraints excluded: chain 7 residue 318 LEU Chi-restraints excluded: chain 7 residue 326 ILE 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 500 VAL 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: 3.9990 chunk 115 optimal weight: 0.9980 chunk 83 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 186 optimal weight: 6.9990 chunk 201 optimal weight: 0.9990 chunk 151 optimal weight: 0.0070 overall best weight: 0.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 3 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 630 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.153198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.107236 restraints weight = 32579.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.106139 restraints weight = 21530.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.106720 restraints weight = 16491.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.107379 restraints weight = 15180.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.107890 restraints weight = 14277.913| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.4932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.244 17053 Z= 0.235 Angle : 0.873 59.199 22999 Z= 0.495 Chirality : 0.039 0.253 2617 Planarity : 0.005 0.155 2934 Dihedral : 4.742 87.668 2305 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.87 % Allowed : 18.46 % Favored : 79.67 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.19), residues: 2068 helix: 1.77 (0.15), residues: 1171 sheet: 0.45 (0.33), residues: 252 loop : -0.60 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.063 0.001 ARG 2 547 TYR 0.058 0.002 TYR 6 780 PHE 0.028 0.001 PHE 2 868 TRP 0.098 0.005 TRP 2 554 HIS 0.012 0.001 HIS 3 423 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.24 (17053) covalent geometry : angle 0.87274 / 0.50 (22999) hydrogen bonds : bond 0.03368 / 2.27 ( 897) hydrogen bonds : angle 4.28210 / 3.06 ( 2601) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3538.59 seconds wall clock time: 61 minutes 43.70 seconds (3703.70 seconds total)