Starting phenix.real_space_refine on Mon Jul 22 04:41:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q6p_18192/07_2024/8q6p_18192.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q6p_18192/07_2024/8q6p_18192.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q6p_18192/07_2024/8q6p_18192.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q6p_18192/07_2024/8q6p_18192.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q6p_18192/07_2024/8q6p_18192.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q6p_18192/07_2024/8q6p_18192.cif" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 103 5.16 5 C 10497 2.51 5 N 2965 2.21 5 O 3214 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "2 ASP 809": "OD1" <-> "OD2" Residue "5 PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 449": "OD1" <-> "OD2" Residue "6 PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 468": "OD1" <-> "OD2" Residue "7 ASP 596": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 16794 Number of models: 1 Model: "" Number of chains: 12 Chain: "2" Number of atoms: 3419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3419 Classifications: {'peptide': 431} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 416} Chain breaks: 1 Chain: "3" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2900 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 12, 'TRANS': 357} Chain breaks: 1 Chain: "4" Number of atoms: 2189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2189 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 10, 'TRANS': 261} Chain breaks: 2 Chain: "5" Number of atoms: 2455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2455 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 11, 'TRANS': 309} Chain breaks: 2 Chain: "6" Number of atoms: 3175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3175 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 8, 'TRANS': 386} Chain breaks: 3 Chain: "7" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2360 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 13, 'TRANS': 284} Chain breaks: 2 Chain: "L" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 141 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 1, 'TRANS': 15} Chain: "2" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.78, per 1000 atoms: 0.70 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 - 3.50 Amino acid : False - 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: 6.93 Conformation dependent library (CDL) restraints added in 3.1 seconds 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4006 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 23 sheets defined 58.1% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain '2' and resid 442 through 455 Processing helix chain '2' and resid 458 through 466 Processing helix chain '2' and resid 473 through 486 Processing helix chain '2' and resid 514 through 525 removed outlier: 3.785A pdb=" N LEU 2 518 " --> pdb=" O LYS 2 514 " (cutoff:3.500A) Processing helix chain '2' and resid 561 through 565 removed outlier: 3.508A pdb=" N ASP 2 565 " --> pdb=" O VAL 2 562 " (cutoff:3.500A) Processing helix chain '2' and resid 578 through 592 removed outlier: 4.842A pdb=" N HIS 2 586 " --> pdb=" O ARG 2 582 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLU 2 587 " --> pdb=" O THR 2 583 " (cutoff:3.500A) Processing helix chain '2' and resid 627 through 632 Processing helix chain '2' and resid 635 through 642 removed outlier: 3.694A pdb=" N PHE 2 642 " --> pdb=" O ILE 2 638 " (cutoff:3.500A) Processing helix chain '2' and resid 653 through 671 Processing helix chain '2' and resid 698 through 709 Processing helix chain '2' and resid 721 through 740 Processing helix chain '2' and resid 745 through 763 removed outlier: 3.761A pdb=" N ILE 2 749 " --> pdb=" O THR 2 745 " (cutoff:3.500A) Processing helix chain '2' and resid 769 through 787 Processing helix chain '2' and resid 789 through 800 Processing helix chain '2' and resid 802 through 806 Processing helix chain '2' and resid 809 through 833 Processing helix chain '2' and resid 844 through 854 Processing helix chain '2' and resid 858 through 865 removed outlier: 3.778A pdb=" N PHE 2 862 " --> pdb=" O ASN 2 858 " (cutoff:3.500A) Processing helix chain '2' and resid 865 through 871 removed outlier: 3.552A pdb=" N LYS 2 869 " --> pdb=" O SER 2 865 " (cutoff:3.500A) Processing helix chain '3' and resid 277 through 291 Processing helix chain '3' and resid 294 through 304 removed outlier: 4.587A pdb=" N ALA 3 304 " --> pdb=" O SER 3 300 " (cutoff:3.500A) Processing helix chain '3' and resid 310 through 323 Processing helix chain '3' and resid 350 through 362 removed outlier: 3.802A pdb=" N LEU 3 354 " --> pdb=" O ALA 3 350 " (cutoff:3.500A) Processing helix chain '3' and resid 396 through 401 Processing helix chain '3' and resid 415 through 428 removed outlier: 3.740A pdb=" N GLU 3 424 " --> pdb=" O THR 3 420 " (cutoff:3.500A) Processing helix chain '3' and resid 434 through 438 removed outlier: 3.743A pdb=" N GLY 3 437 " --> pdb=" O ALA 3 434 " (cutoff:3.500A) Processing helix chain '3' and resid 464 through 470 Processing helix chain '3' and resid 473 through 479 removed outlier: 3.602A pdb=" N PHE 3 479 " --> pdb=" O LEU 3 475 " (cutoff:3.500A) Processing helix chain '3' and resid 490 through 506 Processing helix chain '3' and resid 564 through 578 removed outlier: 3.596A pdb=" N ILE 3 578 " --> pdb=" O VAL 3 574 " (cutoff:3.500A) Processing helix chain '3' and resid 583 through 603 Processing helix chain '3' and resid 615 through 633 removed outlier: 4.094A pdb=" N GLU 3 619 " --> pdb=" O ALA 3 615 " (cutoff:3.500A) Processing helix chain '3' and resid 638 through 655 removed outlier: 3.629A pdb=" N ALA 3 642 " --> pdb=" O GLU 3 638 " (cutoff:3.500A) Processing helix chain '4' and resid 442 through 455 Processing helix chain '4' and resid 457 through 466 removed outlier: 3.565A pdb=" N LEU 4 466 " --> pdb=" O LEU 4 462 " (cutoff:3.500A) Processing helix chain '4' and resid 473 through 486 Processing helix chain '4' and resid 492 through 496 Processing helix chain '4' and resid 515 through 527 removed outlier: 3.523A pdb=" N LEU 4 519 " --> pdb=" O SER 4 515 " (cutoff:3.500A) Processing helix chain '4' and resid 580 through 593 removed outlier: 3.658A pdb=" N GLN 4 593 " --> pdb=" O GLU 4 589 " (cutoff:3.500A) Processing helix chain '4' and resid 629 through 635 Processing helix chain '4' and resid 637 through 643 Processing helix chain '4' and resid 655 through 672 Processing helix chain '4' and resid 673 through 681 Processing helix chain '4' and resid 683 through 697 removed outlier: 3.622A pdb=" N LEU 4 687 " --> pdb=" O ASP 4 683 " (cutoff:3.500A) Processing helix chain '4' and resid 703 through 723 removed outlier: 3.654A pdb=" N GLY 4 723 " --> pdb=" O LYS 4 719 " (cutoff:3.500A) Processing helix chain '4' and resid 730 through 748 removed outlier: 3.982A pdb=" N LEU 4 734 " --> pdb=" O TYR 4 730 " (cutoff:3.500A) Processing helix chain '4' and resid 754 through 770 Processing helix chain '5' and resid 316 through 329 removed outlier: 3.726A pdb=" N LYS 5 329 " --> pdb=" O ARG 5 325 " (cutoff:3.500A) Processing helix chain '5' and resid 331 through 340 Processing helix chain '5' and resid 347 through 360 Processing helix chain '5' and resid 387 through 397 removed outlier: 3.614A pdb=" N LEU 5 391 " --> pdb=" O ALA 5 387 " (cutoff:3.500A) Processing helix chain '5' and resid 408 through 412 removed outlier: 3.949A pdb=" N SER 5 411 " --> pdb=" O LYS 5 408 " (cutoff:3.500A) Processing helix chain '5' and resid 433 through 438 Processing helix chain '5' and resid 448 through 451 Processing helix chain '5' and resid 452 through 466 removed outlier: 3.560A pdb=" N GLU 5 464 " --> pdb=" O HIS 5 460 " (cutoff:3.500A) Processing helix chain '5' and resid 509 through 515 Processing helix chain '5' and resid 526 through 543 Processing helix chain '5' and resid 556 through 571 Processing helix chain '5' and resid 576 through 600 Processing helix chain '5' and resid 610 through 628 Processing helix chain '5' and resid 634 through 656 removed outlier: 3.634A pdb=" N VAL 5 638 " --> pdb=" O THR 5 634 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU 5 650 " --> pdb=" O GLN 5 646 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ASP 5 651 " --> pdb=" O VAL 5 647 " (cutoff:3.500A) Processing helix chain '6' and resid 323 through 331 Processing helix chain '6' and resid 332 through 344 Processing helix chain '6' and resid 347 through 357 removed outlier: 3.543A pdb=" N PHE 6 357 " --> pdb=" O CYS 6 353 " (cutoff:3.500A) Processing helix chain '6' and resid 363 through 376 Processing helix chain '6' and resid 403 through 415 removed outlier: 3.809A pdb=" N PHE 6 407 " --> pdb=" O SER 6 403 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU 6 408 " --> pdb=" O LYS 6 404 " (cutoff:3.500A) Processing helix chain '6' and resid 449 through 454 Processing helix chain '6' and resid 463 through 467 removed outlier: 3.753A pdb=" N MET 6 467 " --> pdb=" O PHE 6 464 " (cutoff:3.500A) Processing helix chain '6' and resid 468 through 482 Processing helix chain '6' and resid 517 through 522 Processing helix chain '6' and resid 525 through 532 removed outlier: 3.654A pdb=" N PHE 6 532 " --> pdb=" O ILE 6 528 " (cutoff:3.500A) Processing helix chain '6' and resid 543 through 559 Processing helix chain '6' and resid 570 through 584 removed outlier: 3.521A pdb=" N PHE 6 584 " --> pdb=" O PHE 6 580 " (cutoff:3.500A) Processing helix chain '6' and resid 589 through 609 Processing helix chain '6' and resid 619 through 637 removed outlier: 3.998A pdb=" N LEU 6 623 " --> pdb=" O THR 6 619 " (cutoff:3.500A) Processing helix chain '6' and resid 643 through 658 removed outlier: 3.531A pdb=" N VAL 6 647 " --> pdb=" O GLN 6 643 " (cutoff:3.500A) Processing helix chain '6' and resid 719 through 737 removed outlier: 3.823A pdb=" N VAL 6 725 " --> pdb=" O SER 6 721 " (cutoff:3.500A) Processing helix chain '6' and resid 743 through 754 removed outlier: 3.730A pdb=" N LYS 6 751 " --> pdb=" O ASN 6 747 " (cutoff:3.500A) Processing helix chain '6' and resid 759 through 777 Processing helix chain '7' and resid 319 through 327 Processing helix chain '7' and resid 330 through 339 Processing helix chain '7' and resid 346 through 359 Processing helix chain '7' and resid 364 through 368 Processing helix chain '7' and resid 385 through 397 Processing helix chain '7' and resid 445 through 449 removed outlier: 3.741A pdb=" N MET 7 449 " --> pdb=" O PHE 7 446 " (cutoff:3.500A) Processing helix chain '7' and resid 450 through 464 removed outlier: 3.837A pdb=" N ALA 7 456 " --> pdb=" O SER 7 452 " (cutoff:3.500A) Processing helix chain '7' and resid 499 through 504 Processing helix chain '7' and resid 507 through 514 removed outlier: 3.902A pdb=" N PHE 7 514 " --> pdb=" O LEU 7 510 " (cutoff:3.500A) Processing helix chain '7' and resid 525 through 543 Processing helix chain '7' and resid 554 through 568 removed outlier: 3.775A pdb=" N LYS 7 568 " --> pdb=" O MET 7 564 " (cutoff:3.500A) Processing helix chain '7' and resid 573 through 594 removed outlier: 3.656A pdb=" N ALA 7 577 " --> pdb=" O PRO 7 573 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP 7 578 " --> pdb=" O GLU 7 574 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N TYR 7 579 " --> pdb=" O SER 7 575 " (cutoff:3.500A) Processing helix chain '7' and resid 601 through 619 Processing helix chain '7' and resid 625 through 644 removed outlier: 3.503A pdb=" N VAL 7 629 " --> pdb=" O GLU 7 625 " (cutoff:3.500A) Processing helix chain 'L' and resid 379 through 385 removed outlier: 3.526A pdb=" N MET L 385 " --> pdb=" O TRP L 381 " (cutoff:3.500A) Processing helix chain 'L' and resid 387 through 391 Processing sheet with id=AA1, first strand: chain '2' and resid 528 through 530 removed outlier: 6.295A pdb=" N VAL 2 529 " --> pdb=" O LEU 2 570 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N GLY 2 567 " --> pdb=" O THR 2 610 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N ILE 2 612 " --> pdb=" O GLY 2 567 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N CYS 2 569 " --> pdb=" O ILE 2 612 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N ALA 2 614 " --> pdb=" O CYS 2 569 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL 2 504 " --> pdb=" O ALA 2 613 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N SER 2 615 " --> pdb=" O VAL 2 504 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU 2 506 " --> pdb=" O SER 2 615 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LEU 2 505 " --> pdb=" O CYS 2 646 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain '2' and resid 544 through 548 removed outlier: 3.522A pdb=" N THR 2 555 " --> pdb=" O GLN 2 546 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU 2 553 " --> pdb=" O HIS 2 548 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '2' and resid 593 through 598 Processing sheet with id=AA4, first strand: chain '2' and resid 839 through 843 Processing sheet with id=AA5, first strand: chain '3' and resid 327 through 328 removed outlier: 3.599A pdb=" N LYS 3 327 " --> pdb=" O ILE 3 335 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '3' and resid 365 through 368 removed outlier: 3.501A pdb=" N CYS 3 407 " --> pdb=" O ILE 3 366 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR 3 368 " --> pdb=" O CYS 3 407 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP 3 409 " --> pdb=" O THR 3 368 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY 3 345 " --> pdb=" O ALA 3 452 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '3' and resid 381 through 384 Processing sheet with id=AA8, first strand: chain '3' and resid 430 through 433 Processing sheet with id=AA9, first strand: chain '4' and resid 614 through 617 removed outlier: 6.580A pdb=" N ILE 4 506 " --> pdb=" O ALA 4 615 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ALA 4 617 " --> pdb=" O ILE 4 506 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU 4 508 " --> pdb=" O ALA 4 617 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU 4 507 " --> pdb=" O PHE 4 648 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain '4' and resid 701 through 702 removed outlier: 6.384A pdb=" N ARG 4 701 " --> pdb=" O VAL 4 753 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain '5' and resid 364 through 365 Processing sheet with id=AB3, first strand: chain '5' and resid 402 through 406 removed outlier: 3.817A pdb=" N ALA 5 487 " --> pdb=" O LEU 5 378 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY 5 382 " --> pdb=" O ALA 5 489 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU 5 379 " --> pdb=" O PHE 5 519 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL 5 521 " --> pdb=" O LEU 5 379 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU 5 381 " --> pdb=" O VAL 5 521 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '5' and resid 418 through 421 Processing sheet with id=AB5, first strand: chain '5' and resid 469 through 472 Processing sheet with id=AB6, first strand: chain '5' and resid 574 through 575 removed outlier: 7.138A pdb=" N ARG 5 574 " --> pdb=" O ALA 5 633 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain '6' and resid 380 through 381 removed outlier: 3.780A pdb=" N LYS 6 380 " --> pdb=" O LEU 6 388 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '6' and resid 504 through 505 removed outlier: 8.060A pdb=" N ALA 6 505 " --> pdb=" O VAL 6 394 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ILE 6 396 " --> pdb=" O ALA 6 505 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N CYS 6 395 " --> pdb=" O PHE 6 536 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N LEU 6 538 " --> pdb=" O CYS 6 395 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL 6 397 " --> pdb=" O LEU 6 538 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain '6' and resid 419 through 421 Processing sheet with id=AC1, first strand: chain '6' and resid 433 through 438 Processing sheet with id=AC2, first strand: chain '6' and resid 483 through 488 Processing sheet with id=AC3, first strand: chain '6' and resid 613 through 614 Processing sheet with id=AC4, first strand: chain '7' and resid 400 through 403 removed outlier: 3.583A pdb=" N GLN 7 401 " --> pdb=" O VAL 7 440 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY 7 380 " --> pdb=" O ALA 7 487 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N CYS 7 377 " --> pdb=" O TRP 7 518 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ILE 7 520 " --> pdb=" O CYS 7 377 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N MET 7 379 " --> pdb=" O ILE 7 520 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '7' and resid 465 through 466 897 hydrogen bonds defined for protein. 2601 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.20 Time building geometry restraints manager: 7.55 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: 99.26 - 107.37: 564 107.37 - 115.49: 10677 115.49 - 123.60: 11373 123.60 - 131.72: 363 131.72 - 139.83: 22 Bond angle restraints: 22999 Sorted by residual: angle pdb=" C GLU 4 472 " pdb=" CA GLU 4 472 " pdb=" CB GLU 4 472 " ideal model delta sigma weight residual 116.54 109.88 6.66 1.15e+00 7.56e-01 3.36e+01 angle pdb=" CA GLU 4 472 " pdb=" C GLU 4 472 " pdb=" N HIS 4 473 " ideal model delta sigma weight residual 119.52 116.53 2.99 7.90e-01 1.60e+00 1.43e+01 angle pdb=" CA LEU 4 466 " pdb=" CB LEU 4 466 " pdb=" CG LEU 4 466 " ideal model delta sigma weight residual 116.30 126.64 -10.34 3.50e+00 8.16e-02 8.73e+00 angle pdb=" C VAL 7 384 " pdb=" N ALA 7 385 " pdb=" CA ALA 7 385 " ideal model delta sigma weight residual 122.74 126.86 -4.12 1.44e+00 4.82e-01 8.17e+00 angle pdb=" C ALA 5 413 " pdb=" CA ALA 5 413 " pdb=" CB ALA 5 413 " ideal model delta sigma weight residual 110.42 115.81 -5.39 1.99e+00 2.53e-01 7.32e+00 ... (remaining 22994 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 9651 17.34 - 34.68: 741 34.68 - 52.02: 158 52.02 - 69.37: 81 69.37 - 86.71: 14 Dihedral angle restraints: 10645 sinusoidal: 4491 harmonic: 6154 Sorted by residual: dihedral pdb=" CA ASP 3 294 " pdb=" CB ASP 3 294 " pdb=" CG ASP 3 294 " pdb=" OD1 ASP 3 294 " ideal model delta sinusoidal sigma weight residual -30.00 -85.02 55.02 1 2.00e+01 2.50e-03 1.02e+01 dihedral pdb=" CA ASP 4 645 " pdb=" CB ASP 4 645 " pdb=" CG ASP 4 645 " pdb=" OD1 ASP 4 645 " ideal model delta sinusoidal sigma weight residual -30.00 -83.80 53.80 1 2.00e+01 2.50e-03 9.83e+00 dihedral pdb=" CB MET 7 379 " pdb=" CG MET 7 379 " pdb=" SD MET 7 379 " pdb=" CE MET 7 379 " ideal model delta sinusoidal sigma weight residual 180.00 123.56 56.44 3 1.50e+01 4.44e-03 9.40e+00 ... (remaining 10642 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1783 0.029 - 0.057: 513 0.057 - 0.086: 187 0.086 - 0.114: 123 0.114 - 0.143: 11 Chirality restraints: 2617 Sorted by residual: chirality pdb=" CA ILE 6 757 " pdb=" N ILE 6 757 " pdb=" C ILE 6 757 " pdb=" CB ILE 6 757 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.11e-01 chirality pdb=" CA ILE 5 470 " pdb=" N ILE 5 470 " pdb=" C ILE 5 470 " pdb=" CB ILE 5 470 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.97e-01 chirality pdb=" CA ILE 5 401 " pdb=" N ILE 5 401 " pdb=" C ILE 5 401 " pdb=" CB ILE 5 401 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.88e-01 ... (remaining 2614 not shown) Planarity restraints: 2934 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN 6 643 " 0.022 5.00e-02 4.00e+02 3.29e-02 1.73e+00 pdb=" N PRO 6 644 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO 6 644 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO 6 644 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE 2 742 " 0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO 2 743 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO 2 743 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO 2 743 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU 5 431 " 0.006 2.00e-02 2.50e+03 1.31e-02 1.71e+00 pdb=" CD GLU 5 431 " -0.023 2.00e-02 2.50e+03 pdb=" OE1 GLU 5 431 " 0.008 2.00e-02 2.50e+03 pdb=" OE2 GLU 5 431 " 0.008 2.00e-02 2.50e+03 ... (remaining 2931 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2892 2.77 - 3.30: 16336 3.30 - 3.83: 27080 3.83 - 4.37: 30735 4.37 - 4.90: 53184 Nonbonded interactions: 130227 Sorted by model distance: nonbonded pdb=" OG SER 3 352 " pdb=" O2G ATP 3 901 " model vdw 2.234 2.440 nonbonded pdb=" O LEU 6 654 " pdb=" OG SER 6 657 " model vdw 2.275 2.440 nonbonded pdb=" OE2 GLU 2 844 " pdb=" OH TYR 2 863 " model vdw 2.280 2.440 nonbonded pdb=" OG1 THR 3 509 " pdb=" OE2 GLU 3 512 " model vdw 2.288 2.440 nonbonded pdb=" O HIS 7 458 " pdb=" NH2 ARG 7 513 " model vdw 2.304 2.520 ... (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 ========== 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 16.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.760 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 48.460 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17053 Z= 0.149 Angle : 0.484 10.343 22999 Z= 0.286 Chirality : 0.037 0.143 2617 Planarity : 0.003 0.033 2934 Dihedral : 14.142 86.707 6639 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.11 % Allowed : 6.70 % Favored : 93.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.19), residues: 2068 helix: 2.22 (0.15), residues: 1146 sheet: -0.34 (0.32), residues: 249 loop : -0.62 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L 381 HIS 0.005 0.001 HIS 6 410 PHE 0.012 0.001 PHE 2 873 TYR 0.012 0.001 TYR 6 349 ARG 0.002 0.000 ARG 3 506 *********************** 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 fitting. rotamer outliers: 2 poor density : 555 time to evaluate : 2.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 490 LYS cc_start: 0.8023 (mptt) cc_final: 0.7582 (pttm) REVERT: 2 580 GLN cc_start: 0.7508 (tp-100) cc_final: 0.7299 (tp-100) REVERT: 2 633 ASP cc_start: 0.7799 (t70) cc_final: 0.7524 (t70) REVERT: 2 808 ARG cc_start: 0.6864 (mtp180) cc_final: 0.6458 (tpt-90) REVERT: 2 810 ASN cc_start: 0.8570 (m-40) cc_final: 0.8296 (p0) REVERT: 2 819 LYS cc_start: 0.8422 (tttt) cc_final: 0.8218 (mmmt) REVERT: 2 838 ASP cc_start: 0.7569 (m-30) cc_final: 0.6810 (t0) REVERT: 4 490 LYS cc_start: 0.7861 (mttt) cc_final: 0.7539 (tmtt) REVERT: 4 677 MET cc_start: -0.0879 (mmm) cc_final: -0.2840 (tmm) REVERT: 4 684 MET cc_start: 0.4970 (mmp) cc_final: 0.4698 (ttm) REVERT: 4 697 TYR cc_start: 0.4701 (m-80) cc_final: 0.4386 (m-10) REVERT: 5 512 LEU cc_start: 0.8667 (mt) cc_final: 0.8385 (tt) REVERT: 6 345 ASP cc_start: 0.7518 (t0) cc_final: 0.7278 (t70) REVERT: 6 401 SER cc_start: 0.8963 (m) cc_final: 0.8438 (p) REVERT: 6 436 VAL cc_start: 0.7708 (t) cc_final: 0.7463 (m) REVERT: 6 437 LYS cc_start: 0.8344 (tttt) cc_final: 0.8046 (ptpp) REVERT: 6 443 GLU cc_start: 0.7045 (mt-10) cc_final: 0.6206 (pt0) REVERT: 6 446 ILE cc_start: 0.8727 (mt) cc_final: 0.8506 (mm) REVERT: 6 580 PHE cc_start: 0.9177 (t80) cc_final: 0.8947 (t80) REVERT: 7 517 LEU cc_start: 0.7990 (tt) cc_final: 0.7248 (tt) REVERT: 7 587 MET cc_start: 0.7938 (mtt) cc_final: 0.7634 (ttp) REVERT: 7 615 LEU cc_start: 0.8439 (mt) cc_final: 0.8207 (mt) REVERT: 7 620 LEU cc_start: 0.8015 (mt) cc_final: 0.7655 (mp) outliers start: 2 outliers final: 0 residues processed: 556 average time/residue: 0.3509 time to fit residues: 271.2376 Evaluate side-chains 302 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 302 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 0.5980 chunk 157 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 chunk 106 optimal weight: 9.9990 chunk 84 optimal weight: 6.9990 chunk 163 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 99 optimal weight: 7.9990 chunk 121 optimal weight: 0.8980 chunk 188 optimal weight: 4.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 534 GLN 4 473 HIS ** 4 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** 7 521 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 17053 Z= 0.345 Angle : 0.633 10.330 22999 Z= 0.328 Chirality : 0.041 0.161 2617 Planarity : 0.005 0.094 2934 Dihedral : 9.169 88.599 2460 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.12 % Allowed : 13.79 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.19), residues: 2068 helix: 1.93 (0.15), residues: 1156 sheet: 0.15 (0.32), residues: 251 loop : -0.74 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP 2 554 HIS 0.010 0.002 HIS 3 360 PHE 0.027 0.002 PHE 6 651 TYR 0.026 0.002 TYR 2 863 ARG 0.006 0.001 ARG 2 547 *********************** 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 377 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 302 time to evaluate : 1.878 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: 2 554 TRP cc_start: 0.7383 (m100) cc_final: 0.7120 (m100) REVERT: 2 580 GLN cc_start: 0.7590 (tp-100) cc_final: 0.7352 (tp-100) REVERT: 2 633 ASP cc_start: 0.7824 (t70) cc_final: 0.7550 (t70) REVERT: 2 786 ASP cc_start: 0.8550 (OUTLIER) cc_final: 0.8334 (m-30) REVERT: 2 810 ASN cc_start: 0.8728 (OUTLIER) cc_final: 0.8397 (p0) REVERT: 2 819 LYS cc_start: 0.8496 (tttt) cc_final: 0.8225 (mmmt) REVERT: 2 838 ASP cc_start: 0.7619 (m-30) cc_final: 0.6790 (t0) REVERT: 3 475 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8696 (tt) REVERT: 4 443 GLU cc_start: 0.7620 (mp0) cc_final: 0.6995 (mp0) REVERT: 4 677 MET cc_start: -0.1113 (mmm) cc_final: -0.2641 (tmm) REVERT: 4 684 MET cc_start: 0.4869 (mmp) cc_final: 0.4590 (ttm) REVERT: 5 421 ARG cc_start: 0.7990 (ptm160) cc_final: 0.7773 (ptm160) REVERT: 5 512 LEU cc_start: 0.8863 (mt) cc_final: 0.8537 (tt) REVERT: 6 342 MET cc_start: 0.7889 (OUTLIER) cc_final: 0.7177 (mtt) REVERT: 6 401 SER cc_start: 0.8951 (m) cc_final: 0.8480 (p) REVERT: 6 446 ILE cc_start: 0.8732 (mt) cc_final: 0.8527 (mm) REVERT: 6 466 LYS cc_start: 0.8760 (mmtt) cc_final: 0.8335 (tmtt) REVERT: 6 572 GLU cc_start: 0.8590 (pt0) cc_final: 0.8377 (pt0) REVERT: 6 780 TYR cc_start: 0.5798 (m-10) cc_final: 0.5592 (m-80) REVERT: 7 326 ILE cc_start: 0.6517 (OUTLIER) cc_final: 0.5911 (mt) REVERT: 7 587 MET cc_start: 0.7886 (mtt) cc_final: 0.7680 (tpt) REVERT: 7 620 LEU cc_start: 0.8098 (mt) cc_final: 0.7854 (tt) outliers start: 75 outliers final: 38 residues processed: 363 average time/residue: 0.3127 time to fit residues: 166.3832 Evaluate side-chains 291 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 248 time to evaluate : 1.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 446 VAL Chi-restraints excluded: chain 2 residue 458 ILE Chi-restraints excluded: chain 2 residue 586 HIS Chi-restraints excluded: chain 2 residue 739 THR Chi-restraints excluded: chain 2 residue 781 LEU Chi-restraints excluded: chain 2 residue 786 ASP Chi-restraints excluded: chain 2 residue 810 ASN Chi-restraints excluded: chain 3 residue 349 VAL Chi-restraints excluded: chain 3 residue 369 THR 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 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 577 ASP 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 478 THR Chi-restraints excluded: chain 5 residue 555 VAL 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 432 THR Chi-restraints excluded: chain 6 residue 465 ASP Chi-restraints excluded: chain 6 residue 496 ASN Chi-restraints excluded: chain 6 residue 499 THR Chi-restraints excluded: chain 6 residue 558 HIS Chi-restraints excluded: chain 6 residue 609 SER Chi-restraints excluded: chain 7 residue 326 ILE Chi-restraints excluded: chain 7 residue 379 MET Chi-restraints excluded: chain 7 residue 400 SER Chi-restraints excluded: chain 7 residue 434 VAL Chi-restraints excluded: chain 7 residue 440 VAL Chi-restraints excluded: chain 7 residue 466 ILE Chi-restraints excluded: chain 7 residue 527 ASP Chi-restraints excluded: chain 7 residue 596 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 104 optimal weight: 5.9990 chunk 58 optimal weight: 0.0570 chunk 157 optimal weight: 3.9990 chunk 128 optimal weight: 0.4980 chunk 52 optimal weight: 4.9990 chunk 189 optimal weight: 0.9980 chunk 204 optimal weight: 0.9980 chunk 168 optimal weight: 2.9990 chunk 187 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 151 optimal weight: 7.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 534 GLN 3 553 HIS 4 665 HIS 4 751 ASN ** 5 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 496 ASN 6 558 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17053 Z= 0.169 Angle : 0.554 11.557 22999 Z= 0.284 Chirality : 0.039 0.145 2617 Planarity : 0.003 0.059 2934 Dihedral : 8.691 89.134 2460 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.30 % Allowed : 15.71 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.19), residues: 2068 helix: 2.01 (0.15), residues: 1162 sheet: 0.25 (0.34), residues: 229 loop : -0.66 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP 2 554 HIS 0.009 0.001 HIS 3 360 PHE 0.021 0.001 PHE 2 663 TYR 0.026 0.002 TYR 7 579 ARG 0.005 0.000 ARG 3 430 *********************** 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 339 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 279 time to evaluate : 2.106 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: 2 509 ASP cc_start: 0.7434 (m-30) cc_final: 0.7170 (t0) REVERT: 2 580 GLN cc_start: 0.7557 (tp-100) cc_final: 0.7290 (tp-100) REVERT: 2 819 LYS cc_start: 0.8435 (tttt) cc_final: 0.8211 (mmmt) REVERT: 2 838 ASP cc_start: 0.7683 (m-30) cc_final: 0.6897 (t0) REVERT: 4 443 GLU cc_start: 0.7552 (mp0) cc_final: 0.6952 (mp0) REVERT: 4 677 MET cc_start: -0.1080 (mmm) cc_final: -0.2692 (tmm) REVERT: 4 753 VAL cc_start: 0.8167 (t) cc_final: 0.7883 (p) REVERT: 5 512 LEU cc_start: 0.8657 (mt) cc_final: 0.8428 (tt) REVERT: 5 568 ARG cc_start: 0.9108 (OUTLIER) cc_final: 0.7612 (mtm-85) REVERT: 6 342 MET cc_start: 0.7911 (OUTLIER) cc_final: 0.7234 (mtt) REVERT: 6 381 THR cc_start: 0.6809 (m) cc_final: 0.6604 (m) REVERT: 6 401 SER cc_start: 0.8854 (m) cc_final: 0.8414 (p) REVERT: 6 443 GLU cc_start: 0.6964 (mt-10) cc_final: 0.6180 (pt0) REVERT: 6 569 TYR cc_start: 0.8434 (m-80) cc_final: 0.8038 (m-80) REVERT: 7 620 LEU cc_start: 0.8041 (mt) cc_final: 0.7797 (tt) outliers start: 60 outliers final: 32 residues processed: 318 average time/residue: 0.3093 time to fit residues: 144.1652 Evaluate side-chains 282 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 248 time to evaluate : 1.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 458 ILE 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 369 THR 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 426 MET 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 582 SER Chi-restraints excluded: chain 4 residue 765 HIS Chi-restraints excluded: chain 5 residue 370 LEU Chi-restraints excluded: chain 5 residue 468 ILE Chi-restraints excluded: chain 5 residue 551 VAL Chi-restraints excluded: chain 5 residue 568 ARG Chi-restraints excluded: chain 5 residue 609 ILE Chi-restraints excluded: chain 6 residue 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 609 SER Chi-restraints excluded: chain 7 residue 339 ILE Chi-restraints excluded: chain 7 residue 400 SER Chi-restraints excluded: chain 7 residue 434 VAL Chi-restraints excluded: chain 7 residue 450 MET Chi-restraints excluded: chain 7 residue 527 ASP Chi-restraints excluded: chain 7 residue 558 MET Chi-restraints excluded: chain 7 residue 596 ASP Chi-restraints excluded: chain 7 residue 629 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 186 optimal weight: 0.7980 chunk 142 optimal weight: 1.9990 chunk 98 optimal weight: 9.9990 chunk 20 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 chunk 127 optimal weight: 4.9990 chunk 189 optimal weight: 6.9990 chunk 201 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 179 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 553 HIS 4 665 HIS 4 751 ASN 6 496 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17053 Z= 0.251 Angle : 0.571 9.074 22999 Z= 0.292 Chirality : 0.040 0.155 2617 Planarity : 0.003 0.043 2934 Dihedral : 8.324 89.811 2460 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 4.34 % Allowed : 15.27 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.18), residues: 2068 helix: 1.91 (0.15), residues: 1159 sheet: 0.25 (0.32), residues: 254 loop : -0.73 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 6 748 HIS 0.008 0.001 HIS 3 360 PHE 0.023 0.002 PHE 2 663 TYR 0.023 0.002 TYR 6 780 ARG 0.008 0.001 ARG 7 634 *********************** 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 330 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 251 time to evaluate : 2.047 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: 2 509 ASP cc_start: 0.7589 (m-30) cc_final: 0.7326 (t0) REVERT: 2 580 GLN cc_start: 0.7595 (tp-100) cc_final: 0.7292 (tp-100) REVERT: 2 819 LYS cc_start: 0.8494 (tttt) cc_final: 0.8256 (mmmt) REVERT: 2 838 ASP cc_start: 0.7831 (m-30) cc_final: 0.6999 (t0) REVERT: 2 855 ASN cc_start: 0.8137 (OUTLIER) cc_final: 0.7905 (t0) REVERT: 4 443 GLU cc_start: 0.7742 (mp0) cc_final: 0.7209 (mp0) REVERT: 4 499 LYS cc_start: 0.7379 (OUTLIER) cc_final: 0.6932 (pttm) REVERT: 4 677 MET cc_start: -0.1122 (mmm) cc_final: -0.2763 (tmm) REVERT: 5 568 ARG cc_start: 0.9138 (OUTLIER) cc_final: 0.7576 (mtm-85) REVERT: 6 342 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.7344 (mtt) REVERT: 6 401 SER cc_start: 0.8929 (m) cc_final: 0.8469 (p) REVERT: 6 437 LYS cc_start: 0.8190 (ptpp) cc_final: 0.7893 (mtmm) REVERT: 6 444 PHE cc_start: 0.6899 (m-80) cc_final: 0.6052 (m-10) REVERT: 6 569 TYR cc_start: 0.8580 (m-80) cc_final: 0.8268 (m-80) REVERT: 7 620 LEU cc_start: 0.8068 (mt) cc_final: 0.7796 (tt) outliers start: 79 outliers final: 49 residues processed: 309 average time/residue: 0.2887 time to fit residues: 133.0357 Evaluate side-chains 286 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 233 time to evaluate : 1.990 ------------------------------------------------------------------------------- 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 2 residue 855 ASN Chi-restraints excluded: chain 3 residue 349 VAL Chi-restraints excluded: chain 3 residue 369 THR 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 489 MET Chi-restraints excluded: chain 3 residue 492 ASP Chi-restraints excluded: chain 3 residue 542 LEU Chi-restraints excluded: chain 3 residue 572 ILE Chi-restraints excluded: chain 3 residue 577 LEU Chi-restraints excluded: chain 3 residue 597 ILE Chi-restraints excluded: chain 3 residue 631 VAL Chi-restraints excluded: chain 4 residue 499 LYS Chi-restraints excluded: chain 4 residue 577 ASP Chi-restraints excluded: chain 4 residue 582 SER Chi-restraints excluded: chain 4 residue 751 ASN Chi-restraints excluded: chain 4 residue 765 HIS Chi-restraints excluded: chain 5 residue 331 ASP Chi-restraints excluded: chain 5 residue 370 LEU Chi-restraints excluded: chain 5 residue 468 ILE Chi-restraints excluded: chain 5 residue 478 THR Chi-restraints excluded: chain 5 residue 517 MET Chi-restraints excluded: chain 5 residue 551 VAL Chi-restraints excluded: chain 5 residue 557 LEU Chi-restraints excluded: chain 5 residue 568 ARG Chi-restraints excluded: chain 5 residue 609 ILE Chi-restraints excluded: chain 6 residue 342 MET Chi-restraints excluded: chain 6 residue 353 CYS Chi-restraints excluded: chain 6 residue 356 LEU Chi-restraints excluded: chain 6 residue 432 THR Chi-restraints excluded: chain 6 residue 465 ASP Chi-restraints excluded: chain 6 residue 488 LYS Chi-restraints excluded: chain 6 residue 518 LEU Chi-restraints excluded: chain 6 residue 535 PHE Chi-restraints excluded: chain 6 residue 558 HIS Chi-restraints excluded: chain 6 residue 609 SER Chi-restraints excluded: chain 7 residue 326 ILE Chi-restraints excluded: chain 7 residue 339 ILE Chi-restraints excluded: chain 7 residue 363 HIS Chi-restraints excluded: chain 7 residue 400 SER Chi-restraints excluded: chain 7 residue 434 VAL Chi-restraints excluded: chain 7 residue 440 VAL Chi-restraints excluded: chain 7 residue 450 MET Chi-restraints excluded: chain 7 residue 596 ASP Chi-restraints excluded: chain 7 residue 599 PHE Chi-restraints excluded: chain 7 residue 629 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 167 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 149 optimal weight: 7.9990 chunk 82 optimal weight: 20.0000 chunk 171 optimal weight: 1.9990 chunk 138 optimal weight: 0.0020 chunk 0 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 chunk 180 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 overall best weight: 1.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 553 HIS 4 665 HIS 4 751 ASN ** 5 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 541 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17053 Z= 0.301 Angle : 0.596 8.993 22999 Z= 0.306 Chirality : 0.040 0.163 2617 Planarity : 0.004 0.039 2934 Dihedral : 8.225 87.494 2460 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.89 % Allowed : 15.71 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.18), residues: 2068 helix: 1.79 (0.15), residues: 1153 sheet: 0.22 (0.32), residues: 259 loop : -0.86 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP 2 554 HIS 0.008 0.001 HIS 2 586 PHE 0.023 0.002 PHE 2 663 TYR 0.019 0.002 TYR 7 579 ARG 0.007 0.000 ARG 7 634 *********************** 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 334 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 245 time to evaluate : 2.015 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: 0.7660 (m-30) cc_final: 0.7385 (t0) REVERT: 2 580 GLN cc_start: 0.7673 (tp-100) cc_final: 0.7359 (tp-100) REVERT: 2 819 LYS cc_start: 0.8600 (tttt) cc_final: 0.8340 (mmtt) REVERT: 2 838 ASP cc_start: 0.7874 (m-30) cc_final: 0.6976 (t0) REVERT: 4 472 GLU cc_start: 0.5867 (OUTLIER) cc_final: 0.5222 (tt0) REVERT: 4 499 LYS cc_start: 0.7466 (OUTLIER) cc_final: 0.7019 (pttm) REVERT: 4 518 GLN cc_start: 0.4708 (mm-40) cc_final: 0.3836 (tm-30) REVERT: 4 579 MET cc_start: 0.7674 (tpt) cc_final: 0.6933 (tpp) REVERT: 4 677 MET cc_start: -0.1234 (mmm) cc_final: -0.2812 (tmm) REVERT: 4 753 VAL cc_start: 0.8100 (t) cc_final: 0.7796 (p) REVERT: 5 568 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.7567 (mtm-85) REVERT: 6 342 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.7362 (mtt) REVERT: 6 401 SER cc_start: 0.8951 (m) cc_final: 0.8544 (p) REVERT: 6 569 TYR cc_start: 0.8679 (m-80) cc_final: 0.8435 (m-80) REVERT: 7 320 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8389 (tp30) REVERT: 7 620 LEU cc_start: 0.8150 (mt) cc_final: 0.7815 (tt) outliers start: 89 outliers final: 62 residues processed: 313 average time/residue: 0.2958 time to fit residues: 138.2801 Evaluate side-chains 299 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 233 time to evaluate : 1.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 462 ILE Chi-restraints excluded: chain 2 residue 547 ARG Chi-restraints excluded: chain 2 residue 581 ASP 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 369 THR 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 489 MET Chi-restraints excluded: chain 3 residue 492 ASP Chi-restraints excluded: chain 3 residue 542 LEU Chi-restraints excluded: chain 3 residue 568 ILE Chi-restraints excluded: chain 3 residue 572 ILE Chi-restraints excluded: chain 3 residue 577 LEU Chi-restraints excluded: chain 3 residue 597 ILE Chi-restraints excluded: chain 3 residue 631 VAL Chi-restraints excluded: chain 4 residue 472 GLU Chi-restraints excluded: chain 4 residue 499 LYS Chi-restraints excluded: chain 4 residue 511 ASP Chi-restraints excluded: chain 4 residue 577 ASP Chi-restraints excluded: chain 4 residue 582 SER Chi-restraints excluded: chain 4 residue 631 ILE Chi-restraints excluded: chain 4 residue 751 ASN Chi-restraints excluded: chain 4 residue 765 HIS Chi-restraints excluded: chain 5 residue 316 THR Chi-restraints excluded: chain 5 residue 331 ASP Chi-restraints excluded: chain 5 residue 370 LEU Chi-restraints excluded: chain 5 residue 468 ILE Chi-restraints excluded: chain 5 residue 478 THR Chi-restraints excluded: chain 5 residue 517 MET Chi-restraints excluded: chain 5 residue 541 HIS Chi-restraints excluded: chain 5 residue 546 THR Chi-restraints excluded: chain 5 residue 551 VAL Chi-restraints excluded: chain 5 residue 557 LEU Chi-restraints excluded: chain 5 residue 568 ARG Chi-restraints excluded: chain 5 residue 609 ILE Chi-restraints excluded: chain 6 residue 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 432 THR Chi-restraints excluded: chain 6 residue 465 ASP Chi-restraints excluded: chain 6 residue 488 LYS 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 6 residue 609 SER Chi-restraints excluded: chain 6 residue 614 SER Chi-restraints excluded: chain 6 residue 623 LEU Chi-restraints excluded: chain 7 residue 326 ILE Chi-restraints excluded: chain 7 residue 331 PHE Chi-restraints excluded: chain 7 residue 339 ILE Chi-restraints excluded: chain 7 residue 393 ILE Chi-restraints excluded: chain 7 residue 400 SER Chi-restraints excluded: chain 7 residue 440 VAL Chi-restraints excluded: chain 7 residue 450 MET Chi-restraints excluded: chain 7 residue 527 ASP Chi-restraints excluded: chain 7 residue 581 THR Chi-restraints excluded: chain 7 residue 596 ASP Chi-restraints excluded: chain 7 residue 599 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 67 optimal weight: 3.9990 chunk 181 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 118 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 201 optimal weight: 0.8980 chunk 167 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 16 optimal weight: 0.3980 chunk 66 optimal weight: 2.9990 chunk 105 optimal weight: 8.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 751 ASN 5 541 HIS ** 6 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17053 Z= 0.172 Angle : 0.540 9.339 22999 Z= 0.277 Chirality : 0.039 0.148 2617 Planarity : 0.003 0.038 2934 Dihedral : 8.004 89.751 2460 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.18 % Allowed : 17.09 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.19), residues: 2068 helix: 1.87 (0.15), residues: 1165 sheet: 0.38 (0.33), residues: 248 loop : -0.71 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP 2 554 HIS 0.008 0.001 HIS 3 360 PHE 0.048 0.001 PHE 2 868 TYR 0.015 0.001 TYR 7 579 ARG 0.005 0.000 ARG 7 634 *********************** 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 324 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 248 time to evaluate : 1.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 509 ASP cc_start: 0.7586 (m-30) cc_final: 0.7283 (t0) REVERT: 2 580 GLN cc_start: 0.7647 (tp-100) cc_final: 0.7317 (tp-100) REVERT: 2 819 LYS cc_start: 0.8582 (tttt) cc_final: 0.8304 (mmmt) REVERT: 2 838 ASP cc_start: 0.7920 (m-30) cc_final: 0.7017 (t0) REVERT: 4 451 GLU cc_start: 0.8170 (tt0) cc_final: 0.7628 (tp30) REVERT: 4 472 GLU cc_start: 0.5996 (OUTLIER) cc_final: 0.5356 (tt0) REVERT: 4 499 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.7357 (pttm) REVERT: 4 518 GLN cc_start: 0.4828 (mm-40) cc_final: 0.3928 (tm-30) REVERT: 4 579 MET cc_start: 0.7712 (tpt) cc_final: 0.7007 (tpp) REVERT: 4 753 VAL cc_start: 0.7979 (t) cc_final: 0.7683 (p) REVERT: 5 568 ARG cc_start: 0.9101 (OUTLIER) cc_final: 0.7593 (mtm-85) REVERT: 6 342 MET cc_start: 0.7923 (OUTLIER) cc_final: 0.7317 (mtt) REVERT: 6 381 THR cc_start: 0.6827 (m) cc_final: 0.6604 (m) REVERT: 6 401 SER cc_start: 0.8886 (m) cc_final: 0.8472 (p) REVERT: 6 443 GLU cc_start: 0.7085 (mt-10) cc_final: 0.6282 (pt0) REVERT: 7 620 LEU cc_start: 0.8126 (mt) cc_final: 0.7758 (tt) outliers start: 76 outliers final: 56 residues processed: 302 average time/residue: 0.2781 time to fit residues: 127.0608 Evaluate side-chains 295 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 235 time to evaluate : 1.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 462 ILE 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 369 THR 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 489 MET Chi-restraints excluded: chain 3 residue 492 ASP Chi-restraints excluded: chain 3 residue 568 ILE Chi-restraints excluded: chain 3 residue 572 ILE Chi-restraints excluded: chain 3 residue 577 LEU Chi-restraints excluded: chain 3 residue 597 ILE Chi-restraints excluded: chain 3 residue 631 VAL Chi-restraints excluded: chain 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 4 residue 650 MET Chi-restraints excluded: chain 4 residue 751 ASN Chi-restraints excluded: chain 4 residue 765 HIS Chi-restraints excluded: chain 5 residue 316 THR Chi-restraints excluded: chain 5 residue 331 ASP Chi-restraints excluded: chain 5 residue 370 LEU Chi-restraints excluded: chain 5 residue 468 ILE Chi-restraints excluded: chain 5 residue 517 MET Chi-restraints excluded: chain 5 residue 541 HIS Chi-restraints excluded: chain 5 residue 551 VAL Chi-restraints excluded: chain 5 residue 557 LEU Chi-restraints excluded: chain 5 residue 568 ARG Chi-restraints excluded: chain 5 residue 590 MET 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 432 THR Chi-restraints excluded: chain 6 residue 465 ASP Chi-restraints excluded: chain 6 residue 488 LYS Chi-restraints excluded: chain 6 residue 535 PHE Chi-restraints excluded: chain 6 residue 558 HIS Chi-restraints excluded: chain 6 residue 609 SER Chi-restraints excluded: chain 6 residue 614 SER Chi-restraints excluded: chain 7 residue 326 ILE Chi-restraints excluded: chain 7 residue 331 PHE Chi-restraints excluded: chain 7 residue 339 ILE Chi-restraints excluded: chain 7 residue 393 ILE Chi-restraints excluded: chain 7 residue 400 SER Chi-restraints excluded: chain 7 residue 434 VAL Chi-restraints excluded: chain 7 residue 440 VAL Chi-restraints excluded: chain 7 residue 450 MET Chi-restraints excluded: chain 7 residue 527 ASP Chi-restraints excluded: chain 7 residue 581 THR Chi-restraints excluded: chain 7 residue 596 ASP Chi-restraints excluded: chain 7 residue 599 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 194 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 146 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 169 optimal weight: 6.9990 chunk 112 optimal weight: 0.8980 chunk 200 optimal weight: 0.8980 chunk 125 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 92 optimal weight: 6.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 631 ASN ** 2 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 751 ASN ** 7 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.4647 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= 0.176 Angle : 0.548 13.602 22999 Z= 0.277 Chirality : 0.039 0.130 2617 Planarity : 0.003 0.033 2934 Dihedral : 7.885 89.169 2460 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 4.12 % Allowed : 17.42 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.19), residues: 2068 helix: 1.87 (0.15), residues: 1165 sheet: 0.39 (0.33), residues: 250 loop : -0.67 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP 2 554 HIS 0.011 0.001 HIS 5 541 PHE 0.035 0.001 PHE 2 868 TYR 0.024 0.001 TYR 6 569 ARG 0.003 0.000 ARG 2 747 *********************** 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 323 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 248 time to evaluate : 1.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 509 ASP cc_start: 0.7602 (m-30) cc_final: 0.7292 (t0) REVERT: 2 580 GLN cc_start: 0.7663 (tp-100) cc_final: 0.7336 (tp-100) REVERT: 2 819 LYS cc_start: 0.8591 (tttt) cc_final: 0.8320 (mmmt) REVERT: 2 838 ASP cc_start: 0.7965 (m-30) cc_final: 0.7046 (t0) REVERT: 4 451 GLU cc_start: 0.8121 (tt0) cc_final: 0.7639 (tp30) REVERT: 4 472 GLU cc_start: 0.5968 (OUTLIER) cc_final: 0.5341 (tt0) REVERT: 4 499 LYS cc_start: 0.7692 (OUTLIER) cc_final: 0.7356 (pttm) REVERT: 4 579 MET cc_start: 0.7717 (tpt) cc_final: 0.7022 (tpp) REVERT: 4 677 MET cc_start: -0.3383 (tpt) cc_final: -0.4705 (tmm) REVERT: 4 753 VAL cc_start: 0.7987 (t) cc_final: 0.7697 (p) REVERT: 4 769 LEU cc_start: 0.7441 (mt) cc_final: 0.7112 (tt) REVERT: 5 568 ARG cc_start: 0.9110 (OUTLIER) cc_final: 0.7546 (mtm-85) REVERT: 6 342 MET cc_start: 0.7962 (OUTLIER) cc_final: 0.7133 (mtt) REVERT: 6 401 SER cc_start: 0.8875 (m) cc_final: 0.8459 (p) REVERT: 6 443 GLU cc_start: 0.7053 (mt-10) cc_final: 0.6228 (pt0) REVERT: 7 620 LEU cc_start: 0.8138 (mt) cc_final: 0.7777 (tt) outliers start: 75 outliers final: 59 residues processed: 302 average time/residue: 0.2670 time to fit residues: 123.8504 Evaluate side-chains 298 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 235 time to evaluate : 1.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 462 ILE Chi-restraints excluded: chain 2 residue 547 ARG Chi-restraints excluded: chain 2 residue 581 ASP 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 369 THR 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 489 MET Chi-restraints excluded: chain 3 residue 492 ASP Chi-restraints excluded: chain 3 residue 568 ILE Chi-restraints excluded: chain 3 residue 572 ILE Chi-restraints excluded: chain 3 residue 577 LEU Chi-restraints excluded: chain 3 residue 597 ILE Chi-restraints excluded: chain 3 residue 631 VAL Chi-restraints excluded: chain 4 residue 472 GLU Chi-restraints excluded: chain 4 residue 499 LYS Chi-restraints excluded: chain 4 residue 511 ASP Chi-restraints excluded: chain 4 residue 577 ASP Chi-restraints excluded: chain 4 residue 582 SER Chi-restraints excluded: chain 4 residue 631 ILE Chi-restraints excluded: chain 4 residue 650 MET Chi-restraints excluded: chain 4 residue 751 ASN Chi-restraints excluded: chain 4 residue 765 HIS Chi-restraints excluded: chain 5 residue 316 THR Chi-restraints excluded: chain 5 residue 331 ASP Chi-restraints excluded: chain 5 residue 370 LEU Chi-restraints excluded: chain 5 residue 415 LEU Chi-restraints excluded: chain 5 residue 468 ILE Chi-restraints excluded: chain 5 residue 517 MET Chi-restraints excluded: chain 5 residue 551 VAL Chi-restraints excluded: chain 5 residue 557 LEU Chi-restraints excluded: chain 5 residue 568 ARG Chi-restraints excluded: chain 5 residue 609 ILE Chi-restraints excluded: chain 5 residue 618 VAL Chi-restraints excluded: chain 6 residue 327 ILE Chi-restraints excluded: chain 6 residue 342 MET Chi-restraints excluded: chain 6 residue 353 CYS Chi-restraints excluded: chain 6 residue 356 LEU Chi-restraints excluded: chain 6 residue 432 THR Chi-restraints excluded: chain 6 residue 465 ASP Chi-restraints excluded: chain 6 residue 488 LYS Chi-restraints excluded: chain 6 residue 535 PHE Chi-restraints excluded: chain 6 residue 540 ASP Chi-restraints excluded: chain 6 residue 558 HIS Chi-restraints excluded: chain 6 residue 609 SER Chi-restraints excluded: chain 6 residue 614 SER Chi-restraints excluded: chain 7 residue 326 ILE Chi-restraints excluded: chain 7 residue 331 PHE Chi-restraints excluded: chain 7 residue 339 ILE Chi-restraints excluded: chain 7 residue 393 ILE Chi-restraints excluded: chain 7 residue 400 SER Chi-restraints excluded: chain 7 residue 434 VAL Chi-restraints excluded: chain 7 residue 440 VAL Chi-restraints excluded: chain 7 residue 450 MET Chi-restraints excluded: chain 7 residue 527 ASP Chi-restraints excluded: chain 7 residue 596 ASP Chi-restraints excluded: chain 7 residue 599 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 124 optimal weight: 0.5980 chunk 80 optimal weight: 9.9990 chunk 119 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 136 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 157 optimal weight: 30.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 423 HIS 4 751 ASN 5 460 HIS 5 541 HIS ** 7 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.4774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17053 Z= 0.196 Angle : 0.551 10.223 22999 Z= 0.278 Chirality : 0.038 0.130 2617 Planarity : 0.003 0.034 2934 Dihedral : 7.854 89.776 2460 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.23 % Allowed : 17.36 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.19), residues: 2068 helix: 1.85 (0.15), residues: 1167 sheet: 0.43 (0.34), residues: 248 loop : -0.67 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP 2 554 HIS 0.010 0.001 HIS 5 541 PHE 0.030 0.001 PHE 2 868 TYR 0.019 0.001 TYR 6 569 ARG 0.004 0.000 ARG 7 634 *********************** 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 312 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 235 time to evaluate : 1.996 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: 0.7621 (m-30) cc_final: 0.7309 (t0) REVERT: 2 580 GLN cc_start: 0.7699 (tp-100) cc_final: 0.7378 (tp-100) REVERT: 2 720 MET cc_start: 0.6970 (ppp) cc_final: 0.6656 (ppp) REVERT: 2 819 LYS cc_start: 0.8610 (tttt) cc_final: 0.8331 (mmmt) REVERT: 2 838 ASP cc_start: 0.7963 (m-30) cc_final: 0.7015 (t0) REVERT: 4 472 GLU cc_start: 0.5932 (OUTLIER) cc_final: 0.5300 (tt0) REVERT: 4 499 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7390 (pttm) REVERT: 4 591 MET cc_start: 0.6092 (ttp) cc_final: 0.5839 (tmm) REVERT: 4 644 PHE cc_start: 0.7038 (m-80) cc_final: 0.6679 (t80) REVERT: 4 648 PHE cc_start: 0.6486 (m-80) cc_final: 0.5933 (m-80) REVERT: 4 677 MET cc_start: -0.3288 (tpt) cc_final: -0.4636 (tmm) REVERT: 4 753 VAL cc_start: 0.7950 (t) cc_final: 0.7666 (p) REVERT: 4 769 LEU cc_start: 0.7422 (mt) cc_final: 0.7099 (tt) REVERT: 5 568 ARG cc_start: 0.9102 (OUTLIER) cc_final: 0.7553 (mtm-85) REVERT: 6 342 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7129 (mtt) REVERT: 6 401 SER cc_start: 0.8897 (m) cc_final: 0.8492 (p) REVERT: 6 443 GLU cc_start: 0.7097 (mt-10) cc_final: 0.6310 (pt0) REVERT: 7 620 LEU cc_start: 0.8133 (mt) cc_final: 0.7809 (tt) outliers start: 77 outliers final: 60 residues processed: 289 average time/residue: 0.2757 time to fit residues: 122.6061 Evaluate side-chains 295 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 231 time to evaluate : 1.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 462 ILE Chi-restraints excluded: chain 2 residue 547 ARG Chi-restraints excluded: chain 2 residue 581 ASP 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 369 THR 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 489 MET Chi-restraints excluded: chain 3 residue 492 ASP Chi-restraints excluded: chain 3 residue 568 ILE Chi-restraints excluded: chain 3 residue 572 ILE Chi-restraints excluded: chain 3 residue 577 LEU Chi-restraints excluded: chain 3 residue 597 ILE Chi-restraints excluded: chain 3 residue 631 VAL Chi-restraints excluded: chain 3 residue 656 LYS Chi-restraints excluded: chain 4 residue 472 GLU Chi-restraints excluded: chain 4 residue 499 LYS Chi-restraints excluded: chain 4 residue 511 ASP Chi-restraints excluded: chain 4 residue 519 LEU Chi-restraints excluded: chain 4 residue 577 ASP Chi-restraints excluded: chain 4 residue 631 ILE Chi-restraints excluded: chain 4 residue 650 MET Chi-restraints excluded: chain 4 residue 751 ASN Chi-restraints excluded: chain 4 residue 765 HIS Chi-restraints excluded: chain 5 residue 316 THR Chi-restraints excluded: chain 5 residue 331 ASP Chi-restraints excluded: chain 5 residue 370 LEU Chi-restraints excluded: chain 5 residue 415 LEU Chi-restraints excluded: chain 5 residue 421 ARG Chi-restraints excluded: chain 5 residue 468 ILE Chi-restraints excluded: chain 5 residue 478 THR Chi-restraints excluded: chain 5 residue 517 MET Chi-restraints excluded: chain 5 residue 551 VAL Chi-restraints excluded: chain 5 residue 557 LEU Chi-restraints excluded: chain 5 residue 568 ARG Chi-restraints excluded: chain 5 residue 609 ILE Chi-restraints excluded: chain 5 residue 618 VAL Chi-restraints excluded: chain 6 residue 327 ILE Chi-restraints excluded: chain 6 residue 342 MET Chi-restraints excluded: chain 6 residue 353 CYS Chi-restraints excluded: chain 6 residue 356 LEU Chi-restraints excluded: chain 6 residue 432 THR Chi-restraints excluded: chain 6 residue 465 ASP Chi-restraints excluded: chain 6 residue 535 PHE Chi-restraints excluded: chain 6 residue 558 HIS Chi-restraints excluded: chain 6 residue 609 SER Chi-restraints excluded: chain 6 residue 614 SER Chi-restraints excluded: chain 7 residue 331 PHE Chi-restraints excluded: chain 7 residue 339 ILE Chi-restraints excluded: chain 7 residue 393 ILE Chi-restraints excluded: chain 7 residue 400 SER Chi-restraints excluded: chain 7 residue 434 VAL Chi-restraints excluded: chain 7 residue 440 VAL Chi-restraints excluded: chain 7 residue 450 MET Chi-restraints excluded: chain 7 residue 511 LEU Chi-restraints excluded: chain 7 residue 527 ASP Chi-restraints excluded: chain 7 residue 596 ASP Chi-restraints excluded: chain 7 residue 599 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 182 optimal weight: 6.9990 chunk 192 optimal weight: 0.9990 chunk 175 optimal weight: 7.9990 chunk 186 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 81 optimal weight: 3.9990 chunk 146 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 168 optimal weight: 0.9990 chunk 176 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 423 HIS 4 751 ASN 7 401 GLN 7 521 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.4877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17053 Z= 0.182 Angle : 0.564 13.067 22999 Z= 0.281 Chirality : 0.038 0.129 2617 Planarity : 0.003 0.034 2934 Dihedral : 7.817 89.641 2460 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.12 % Allowed : 17.69 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.19), residues: 2068 helix: 1.86 (0.15), residues: 1170 sheet: 0.39 (0.34), residues: 250 loop : -0.66 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP 2 554 HIS 0.011 0.001 HIS 7 363 PHE 0.028 0.001 PHE 2 868 TYR 0.020 0.001 TYR 6 569 ARG 0.003 0.000 ARG 7 634 *********************** 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 318 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 243 time to evaluate : 2.010 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: 0.7626 (m-30) cc_final: 0.7307 (t0) REVERT: 2 580 GLN cc_start: 0.7697 (tp-100) cc_final: 0.7379 (tp-100) REVERT: 2 720 MET cc_start: 0.6975 (ppp) cc_final: 0.6651 (ppp) REVERT: 2 819 LYS cc_start: 0.8634 (tttt) cc_final: 0.8357 (mmmt) REVERT: 2 838 ASP cc_start: 0.7973 (m-30) cc_final: 0.7020 (t0) REVERT: 4 455 LYS cc_start: 0.5345 (mtpt) cc_final: 0.4822 (mtmm) REVERT: 4 472 GLU cc_start: 0.5894 (OUTLIER) cc_final: 0.5397 (tt0) REVERT: 4 499 LYS cc_start: 0.7687 (OUTLIER) cc_final: 0.7352 (pttm) REVERT: 4 579 MET cc_start: 0.7473 (tpt) cc_final: 0.6762 (tpp) REVERT: 4 644 PHE cc_start: 0.6950 (m-80) cc_final: 0.6648 (t80) REVERT: 4 648 PHE cc_start: 0.6458 (m-80) cc_final: 0.5917 (m-80) REVERT: 4 677 MET cc_start: -0.3337 (tpt) cc_final: -0.4655 (tmm) REVERT: 4 753 VAL cc_start: 0.7941 (t) cc_final: 0.7658 (p) REVERT: 4 769 LEU cc_start: 0.7245 (mt) cc_final: 0.6964 (tt) REVERT: 5 568 ARG cc_start: 0.9107 (OUTLIER) cc_final: 0.7572 (mtm-85) REVERT: 6 342 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7124 (mtt) REVERT: 6 401 SER cc_start: 0.8889 (m) cc_final: 0.8495 (p) REVERT: 6 443 GLU cc_start: 0.7073 (mt-10) cc_final: 0.6308 (pt0) REVERT: 7 363 HIS cc_start: 0.4873 (t70) cc_final: 0.4603 (t-90) REVERT: 7 620 LEU cc_start: 0.8154 (mt) cc_final: 0.7785 (tt) REVERT: L 383 GLU cc_start: 0.8641 (tp30) cc_final: 0.8304 (tp30) outliers start: 75 outliers final: 59 residues processed: 293 average time/residue: 0.2652 time to fit residues: 119.9408 Evaluate side-chains 297 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 234 time to evaluate : 2.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 462 ILE Chi-restraints excluded: chain 2 residue 547 ARG Chi-restraints excluded: chain 2 residue 581 ASP 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 369 THR Chi-restraints excluded: chain 3 residue 416 ASP Chi-restraints excluded: chain 3 residue 422 ILE Chi-restraints excluded: chain 3 residue 424 GLU Chi-restraints excluded: chain 3 residue 489 MET Chi-restraints excluded: chain 3 residue 492 ASP Chi-restraints excluded: chain 3 residue 568 ILE Chi-restraints excluded: chain 3 residue 572 ILE Chi-restraints excluded: chain 3 residue 577 LEU Chi-restraints excluded: chain 3 residue 597 ILE Chi-restraints excluded: chain 3 residue 631 VAL Chi-restraints excluded: chain 3 residue 656 LYS Chi-restraints excluded: chain 4 residue 472 GLU Chi-restraints excluded: chain 4 residue 499 LYS Chi-restraints excluded: chain 4 residue 511 ASP Chi-restraints excluded: chain 4 residue 519 LEU Chi-restraints excluded: chain 4 residue 577 ASP Chi-restraints excluded: chain 4 residue 631 ILE Chi-restraints excluded: chain 4 residue 650 MET Chi-restraints excluded: chain 4 residue 751 ASN Chi-restraints excluded: chain 4 residue 765 HIS Chi-restraints excluded: chain 5 residue 316 THR Chi-restraints excluded: chain 5 residue 331 ASP Chi-restraints excluded: chain 5 residue 370 LEU Chi-restraints excluded: chain 5 residue 415 LEU Chi-restraints excluded: chain 5 residue 421 ARG Chi-restraints excluded: chain 5 residue 455 ASP Chi-restraints excluded: chain 5 residue 468 ILE Chi-restraints excluded: chain 5 residue 478 THR Chi-restraints excluded: chain 5 residue 517 MET Chi-restraints excluded: chain 5 residue 551 VAL Chi-restraints excluded: chain 5 residue 557 LEU Chi-restraints excluded: chain 5 residue 568 ARG Chi-restraints excluded: chain 5 residue 609 ILE Chi-restraints excluded: chain 5 residue 618 VAL Chi-restraints excluded: chain 6 residue 327 ILE Chi-restraints excluded: chain 6 residue 342 MET Chi-restraints excluded: chain 6 residue 353 CYS Chi-restraints excluded: chain 6 residue 356 LEU Chi-restraints excluded: chain 6 residue 432 THR Chi-restraints excluded: chain 6 residue 465 ASP Chi-restraints excluded: chain 6 residue 535 PHE Chi-restraints excluded: chain 6 residue 558 HIS Chi-restraints excluded: chain 6 residue 609 SER Chi-restraints excluded: chain 6 residue 614 SER Chi-restraints excluded: chain 7 residue 331 PHE Chi-restraints excluded: chain 7 residue 339 ILE Chi-restraints excluded: chain 7 residue 393 ILE Chi-restraints excluded: chain 7 residue 400 SER Chi-restraints excluded: chain 7 residue 440 VAL Chi-restraints excluded: chain 7 residue 450 MET Chi-restraints excluded: chain 7 residue 511 LEU Chi-restraints excluded: chain 7 residue 527 ASP Chi-restraints excluded: chain 7 residue 596 ASP 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 197 optimal weight: 0.5980 chunk 120 optimal weight: 0.9980 chunk 93 optimal weight: 0.0370 chunk 137 optimal weight: 1.9990 chunk 207 optimal weight: 0.6980 chunk 190 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 127 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 131 optimal weight: 0.3980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 423 HIS 4 751 ASN ** 6 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.5004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17053 Z= 0.151 Angle : 0.554 14.428 22999 Z= 0.276 Chirality : 0.038 0.131 2617 Planarity : 0.003 0.040 2934 Dihedral : 7.708 89.391 2460 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.52 % Allowed : 18.35 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.19), residues: 2068 helix: 1.91 (0.15), residues: 1172 sheet: 0.52 (0.34), residues: 248 loop : -0.66 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP 2 554 HIS 0.007 0.001 HIS 3 360 PHE 0.026 0.001 PHE 2 868 TYR 0.021 0.001 TYR 6 569 ARG 0.008 0.000 ARG 7 634 ********************** 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 310 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 246 time to evaluate : 1.988 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: 0.7551 (m-30) cc_final: 0.7228 (t0) REVERT: 2 580 GLN cc_start: 0.7682 (tp-100) cc_final: 0.7350 (tp-100) REVERT: 2 720 MET cc_start: 0.6914 (ppp) cc_final: 0.6647 (ppp) REVERT: 2 819 LYS cc_start: 0.8627 (tttt) cc_final: 0.8350 (mmmt) REVERT: 2 838 ASP cc_start: 0.7989 (m-30) cc_final: 0.7062 (t0) REVERT: 4 444 GLU cc_start: 0.9138 (tp30) cc_final: 0.8386 (tm-30) REVERT: 4 472 GLU cc_start: 0.5940 (OUTLIER) cc_final: 0.5424 (tt0) REVERT: 4 499 LYS cc_start: 0.7833 (OUTLIER) cc_final: 0.7519 (pttm) REVERT: 4 579 MET cc_start: 0.7514 (tpt) cc_final: 0.6840 (tpp) REVERT: 4 644 PHE cc_start: 0.6770 (m-80) cc_final: 0.6562 (t80) REVERT: 4 648 PHE cc_start: 0.6462 (m-80) cc_final: 0.5948 (m-80) REVERT: 4 650 MET cc_start: 0.3376 (OUTLIER) cc_final: 0.3039 (ptm) REVERT: 4 677 MET cc_start: -0.3326 (tpt) cc_final: -0.4659 (tmm) REVERT: 4 753 VAL cc_start: 0.7842 (t) cc_final: 0.7562 (p) REVERT: 4 769 LEU cc_start: 0.7371 (mt) cc_final: 0.7092 (tt) REVERT: 5 541 HIS cc_start: 0.7539 (t-90) cc_final: 0.7217 (m-70) REVERT: 5 568 ARG cc_start: 0.9095 (OUTLIER) cc_final: 0.7581 (mtm-85) REVERT: 6 342 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.7096 (mtt) REVERT: 6 401 SER cc_start: 0.8832 (m) cc_final: 0.8503 (p) REVERT: 6 443 GLU cc_start: 0.7167 (mt-10) cc_final: 0.6448 (pt0) REVERT: 7 620 LEU cc_start: 0.8139 (mt) cc_final: 0.7762 (tt) outliers start: 64 outliers final: 44 residues processed: 289 average time/residue: 0.2663 time to fit residues: 119.2888 Evaluate side-chains 288 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 239 time to evaluate : 2.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 462 ILE 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 369 THR Chi-restraints excluded: chain 3 residue 416 ASP Chi-restraints excluded: chain 3 residue 423 HIS Chi-restraints excluded: chain 3 residue 424 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 499 LYS Chi-restraints excluded: chain 4 residue 511 ASP Chi-restraints excluded: chain 4 residue 519 LEU Chi-restraints excluded: chain 4 residue 577 ASP Chi-restraints excluded: chain 4 residue 631 ILE Chi-restraints excluded: chain 4 residue 650 MET Chi-restraints excluded: chain 4 residue 751 ASN Chi-restraints excluded: chain 4 residue 765 HIS Chi-restraints excluded: chain 5 residue 316 THR Chi-restraints excluded: chain 5 residue 415 LEU Chi-restraints excluded: chain 5 residue 455 ASP Chi-restraints excluded: chain 5 residue 551 VAL Chi-restraints excluded: chain 5 residue 557 LEU Chi-restraints excluded: chain 5 residue 568 ARG Chi-restraints excluded: chain 5 residue 618 VAL Chi-restraints excluded: chain 6 residue 327 ILE Chi-restraints excluded: chain 6 residue 342 MET Chi-restraints excluded: chain 6 residue 353 CYS Chi-restraints excluded: chain 6 residue 356 LEU Chi-restraints excluded: chain 6 residue 432 THR Chi-restraints excluded: chain 6 residue 465 ASP Chi-restraints excluded: chain 6 residue 535 PHE Chi-restraints excluded: chain 6 residue 540 ASP Chi-restraints excluded: chain 6 residue 558 HIS Chi-restraints excluded: chain 6 residue 609 SER Chi-restraints excluded: chain 7 residue 331 PHE Chi-restraints excluded: chain 7 residue 339 ILE Chi-restraints excluded: chain 7 residue 400 SER Chi-restraints excluded: chain 7 residue 440 VAL Chi-restraints excluded: chain 7 residue 450 MET Chi-restraints excluded: chain 7 residue 511 LEU Chi-restraints excluded: chain 7 residue 527 ASP Chi-restraints excluded: chain 7 residue 596 ASP 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 175 optimal weight: 8.9990 chunk 50 optimal weight: 0.7980 chunk 152 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 165 optimal weight: 2.9990 chunk 69 optimal weight: 0.0970 chunk 169 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 145 optimal weight: 0.0870 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 423 HIS ** 4 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 751 ASN ** 6 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.151734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.105153 restraints weight = 32069.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.104882 restraints weight = 20678.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.105242 restraints weight = 16315.784| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.5077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17053 Z= 0.150 Angle : 0.562 13.734 22999 Z= 0.279 Chirality : 0.038 0.158 2617 Planarity : 0.003 0.046 2934 Dihedral : 7.661 89.080 2460 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.86 % Allowed : 19.29 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.19), residues: 2068 helix: 1.88 (0.15), residues: 1171 sheet: 0.60 (0.34), residues: 250 loop : -0.63 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP 2 554 HIS 0.008 0.001 HIS 3 360 PHE 0.025 0.001 PHE 2 868 TYR 0.020 0.001 TYR 6 569 ARG 0.006 0.000 ARG 7 324 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3996.58 seconds wall clock time: 72 minutes 11.68 seconds (4331.68 seconds total)