Starting phenix.real_space_refine on Tue Apr 9 15:45:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q6p_18192/04_2024/8q6p_18192_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q6p_18192/04_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_18192/04_2024/8q6p_18192.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q6p_18192/04_2024/8q6p_18192.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q6p_18192/04_2024/8q6p_18192_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q6p_18192/04_2024/8q6p_18192_updated.pdb" } 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-5288/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: 8.46, per 1000 atoms: 0.50 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: 6.99 Conformation dependent library (CDL) restraints added in 2.9 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... running ksdssp... Secondary structure from input PDB file: 95 helices and 16 sheets defined 49.6% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.36 Creating SS restraints... Processing helix chain '2' and resid 443 through 454 Processing helix chain '2' and resid 459 through 465 Processing helix chain '2' and resid 474 through 485 Processing helix chain '2' and resid 515 through 524 Processing helix chain '2' and resid 560 through 564 Processing helix chain '2' and resid 579 through 591 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 628 through 631 No H-bonds generated for 'chain '2' and resid 628 through 631' Processing helix chain '2' and resid 636 through 641 Processing helix chain '2' and resid 654 through 670 Processing helix chain '2' and resid 699 through 710 Processing helix chain '2' and resid 722 through 739 Processing helix chain '2' and resid 746 through 762 Processing helix chain '2' and resid 770 through 786 Processing helix chain '2' and resid 790 through 799 Processing helix chain '2' and resid 803 through 805 No H-bonds generated for 'chain '2' and resid 803 through 805' Processing helix chain '2' and resid 810 through 832 Processing helix chain '2' and resid 844 through 853 Processing helix chain '2' and resid 859 through 864 Processing helix chain '2' and resid 866 through 870 Processing helix chain '3' and resid 278 through 290 Processing helix chain '3' and resid 295 through 303 Processing helix chain '3' and resid 311 through 322 Processing helix chain '3' and resid 351 through 361 Processing helix chain '3' and resid 397 through 400 No H-bonds generated for 'chain '3' and resid 397 through 400' Processing helix chain '3' and resid 416 through 427 removed outlier: 3.740A pdb=" N GLU 3 424 " --> pdb=" O THR 3 420 " (cutoff:3.500A) Processing helix chain '3' and resid 435 through 437 No H-bonds generated for 'chain '3' and resid 435 through 437' Processing helix chain '3' and resid 465 through 469 Processing helix chain '3' and resid 474 through 478 Processing helix chain '3' and resid 491 through 506 Processing helix chain '3' and resid 565 through 577 Processing helix chain '3' and resid 584 through 602 Processing helix chain '3' and resid 615 through 631 Processing helix chain '3' and resid 639 through 654 Processing helix chain '4' and resid 443 through 454 Processing helix chain '4' and resid 458 through 465 Processing helix chain '4' and resid 474 through 485 Processing helix chain '4' and resid 493 through 495 No H-bonds generated for 'chain '4' and resid 493 through 495' Processing helix chain '4' and resid 516 through 526 Processing helix chain '4' and resid 581 through 592 Processing helix chain '4' and resid 630 through 634 Processing helix chain '4' and resid 638 through 643 Processing helix chain '4' and resid 656 through 669 Processing helix chain '4' and resid 674 through 680 Processing helix chain '4' and resid 684 through 696 Processing helix chain '4' and resid 704 through 722 Processing helix chain '4' and resid 731 through 747 Processing helix chain '4' and resid 755 through 769 Processing helix chain '5' and resid 317 through 328 Processing helix chain '5' and resid 332 through 339 Processing helix chain '5' and resid 348 through 359 Processing helix chain '5' and resid 388 through 396 Processing helix chain '5' and resid 409 through 411 No H-bonds generated for 'chain '5' and resid 409 through 411' Processing helix chain '5' and resid 434 through 437 No H-bonds generated for 'chain '5' and resid 434 through 437' Processing helix chain '5' and resid 448 through 450 No H-bonds generated for 'chain '5' and resid 448 through 450' Processing helix chain '5' and resid 453 through 464 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 514 Processing helix chain '5' and resid 527 through 544 Processing helix chain '5' and resid 557 through 570 Processing helix chain '5' and resid 577 through 599 Processing helix chain '5' and resid 611 through 627 Processing helix chain '5' and resid 635 through 655 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 324 through 330 Processing helix chain '6' and resid 333 through 344 Processing helix chain '6' and resid 348 through 356 Processing helix chain '6' and resid 364 through 375 Processing helix chain '6' and resid 404 through 414 removed outlier: 3.744A pdb=" N LEU 6 408 " --> pdb=" O LYS 6 404 " (cutoff:3.500A) Processing helix chain '6' and resid 450 through 453 No H-bonds generated for 'chain '6' and resid 450 through 453' Processing helix chain '6' and resid 464 through 466 No H-bonds generated for 'chain '6' and resid 464 through 466' Processing helix chain '6' and resid 469 through 481 Processing helix chain '6' and resid 518 through 521 No H-bonds generated for 'chain '6' and resid 518 through 521' Processing helix chain '6' and resid 526 through 531 Processing helix chain '6' and resid 544 through 558 Processing helix chain '6' and resid 571 through 583 Processing helix chain '6' and resid 590 through 608 Processing helix chain '6' and resid 620 through 636 Processing helix chain '6' and resid 644 through 657 Processing helix chain '6' and resid 719 through 736 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 755 removed outlier: 3.730A pdb=" N LYS 6 751 " --> pdb=" O ASN 6 747 " (cutoff:3.500A) Processing helix chain '6' and resid 760 through 776 Processing helix chain '7' and resid 320 through 326 Processing helix chain '7' and resid 331 through 338 Processing helix chain '7' and resid 347 through 358 Processing helix chain '7' and resid 365 through 367 No H-bonds generated for 'chain '7' and resid 365 through 367' Processing helix chain '7' and resid 386 through 396 Processing helix chain '7' and resid 446 through 448 No H-bonds generated for 'chain '7' and resid 446 through 448' Processing helix chain '7' and resid 451 through 463 removed outlier: 3.837A pdb=" N ALA 7 456 " --> pdb=" O SER 7 452 " (cutoff:3.500A) Processing helix chain '7' and resid 500 through 503 No H-bonds generated for 'chain '7' and resid 500 through 503' Processing helix chain '7' and resid 508 through 513 Processing helix chain '7' and resid 526 through 542 Processing helix chain '7' and resid 555 through 567 Processing helix chain '7' and resid 576 through 593 Processing helix chain '7' and resid 602 through 618 Processing helix chain '7' and resid 626 through 643 Processing helix chain 'L' and resid 379 through 384 Processing helix chain 'L' and resid 388 through 390 No H-bonds generated for 'chain 'L' and resid 388 through 390' Processing sheet with id= A, first strand: chain '2' and resid 644 through 647 removed outlier: 3.768A pdb=" N GLY 2 508 " --> pdb=" O SER 2 615 " (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) Processing sheet with id= B, first strand: chain '2' and resid 593 through 598 Processing sheet with id= C, first strand: chain '2' and resid 839 through 843 Processing sheet with id= D, first strand: chain '3' and resid 481 through 485 removed outlier: 3.745A pdb=" N GLY 3 345 " --> pdb=" O ALA 3 452 " (cutoff:3.500A) 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) Processing sheet with id= E, first strand: chain '3' and resid 381 through 384 Processing sheet with id= F, first strand: chain '3' and resid 430 through 433 Processing sheet with id= G, 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: 6.489A pdb=" N LEU 4 646 " --> pdb=" O LEU 4 507 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N CYS 4 509 " --> pdb=" O LEU 4 646 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N PHE 4 648 " --> pdb=" O CYS 4 509 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain '5' and resid 517 through 521 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) Processing sheet with id= I, first strand: chain '5' and resid 418 through 421 Processing sheet with id= J, first strand: chain '5' and resid 469 through 472 Processing sheet with id= K, first strand: chain '6' and resid 396 through 398 removed outlier: 6.658A pdb=" N PHE 6 536 " --> pdb=" O VAL 6 397 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain '6' and resid 419 through 421 Processing sheet with id= M, first strand: chain '6' and resid 433 through 438 Processing sheet with id= N, first strand: chain '6' and resid 483 through 488 Processing sheet with id= O, first strand: chain '7' and resid 363 through 365 Processing sheet with id= P, first strand: chain '7' and resid 516 through 520 removed outlier: 3.734A pdb=" N GLY 7 380 " --> pdb=" O ALA 7 487 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLY 7 439 " --> pdb=" O SER 7 482 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N LEU 7 484 " --> pdb=" O GLY 7 439 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N CYS 7 441 " --> pdb=" O LEU 7 484 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N ALA 7 486 " --> pdb=" O CYS 7 441 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ILE 7 443 " --> pdb=" O ALA 7 486 " (cutoff:3.500A) removed outlier: 8.898A pdb=" N ASN 7 488 " --> pdb=" O ILE 7 443 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN 7 401 " --> pdb=" O VAL 7 440 " (cutoff:3.500A) 759 hydrogen bonds defined for protein. 2148 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: 5.11 Time building geometry restraints manager: 7.41 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: 2910 2.77 - 3.30: 16450 3.30 - 3.83: 27213 3.83 - 4.37: 30979 4.37 - 4.90: 53227 Nonbonded interactions: 130779 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 130774 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: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 32.840 Check model and map are aligned: 0.290 Set scattering table: 0.130 Process input model: 45.480 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.070 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.990 ------------------------------------------------------------------------------- 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= 0.147 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 : 1.934 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: 0.3902 time to fit residues: 304.5701 Evaluate side-chains 302 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 302 time to evaluate : 2.160 ------------------------------------------------------------------------------- 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: 4.9990 chunk 157 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 chunk 106 optimal weight: 8.9990 chunk 84 optimal weight: 5.9990 chunk 163 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 99 optimal weight: 10.0000 chunk 121 optimal weight: 0.9990 chunk 188 optimal weight: 0.0970 overall best weight: 2.3784 ------------------------------------------------------------------------------- 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 7 521 GLN 7 644 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3070 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= 0.356 Angle : 0.634 9.812 22999 Z= 0.327 Chirality : 0.041 0.187 2617 Planarity : 0.005 0.092 2934 Dihedral : 9.153 89.325 2460 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.23 % Allowed : 14.07 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.04 (0.18), residues: 2068 helix: 1.73 (0.15), residues: 1141 sheet: 0.06 (0.32), residues: 250 loop : -0.83 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP 2 554 HIS 0.010 0.002 HIS 3 360 PHE 0.028 0.002 PHE 6 651 TYR 0.025 0.002 TYR 2 863 ARG 0.007 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 373 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 296 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 580 GLN cc_start: 0.7631 (tp-100) cc_final: 0.7418 (tp-100) REVERT: 2 633 ASP cc_start: 0.7875 (t70) cc_final: 0.7531 (t70) REVERT: 2 794 ARG cc_start: 0.8106 (tpp80) cc_final: 0.7811 (tpp80) REVERT: 2 810 ASN cc_start: 0.8787 (OUTLIER) cc_final: 0.8539 (p0) REVERT: 2 819 LYS cc_start: 0.8482 (tttt) cc_final: 0.8213 (mmmt) REVERT: 2 838 ASP cc_start: 0.7635 (m-30) cc_final: 0.6793 (t0) REVERT: 3 646 LEU cc_start: 0.9194 (tp) cc_final: 0.8886 (tt) REVERT: 4 451 GLU cc_start: 0.8377 (tt0) cc_final: 0.7983 (tm-30) REVERT: 4 677 MET cc_start: -0.1260 (mmm) cc_final: -0.2847 (tmm) REVERT: 5 421 ARG cc_start: 0.7999 (ptm160) cc_final: 0.7466 (ptm160) REVERT: 5 512 LEU cc_start: 0.8885 (mt) cc_final: 0.8573 (tt) REVERT: 5 535 LYS cc_start: 0.9000 (mttt) cc_final: 0.8796 (mtmt) REVERT: 5 568 ARG cc_start: 0.9103 (OUTLIER) cc_final: 0.7594 (mtm-85) REVERT: 6 342 MET cc_start: 0.7908 (OUTLIER) cc_final: 0.7464 (mtm) REVERT: 6 401 SER cc_start: 0.8961 (m) cc_final: 0.8481 (p) REVERT: 6 446 ILE cc_start: 0.8731 (mt) cc_final: 0.8515 (mm) REVERT: 6 466 LYS cc_start: 0.8683 (mmtt) cc_final: 0.8203 (tmtt) REVERT: 6 572 GLU cc_start: 0.8630 (pt0) cc_final: 0.8403 (pt0) REVERT: 6 633 MET cc_start: 0.8492 (mmm) cc_final: 0.8284 (tpp) REVERT: 7 320 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8407 (tp30) REVERT: 7 326 ILE cc_start: 0.6527 (OUTLIER) cc_final: 0.5912 (mt) REVERT: 7 615 LEU cc_start: 0.8492 (mt) cc_final: 0.8268 (mt) REVERT: 7 620 LEU cc_start: 0.8157 (mt) cc_final: 0.7879 (tt) REVERT: 7 640 LYS cc_start: 0.8860 (ptmt) cc_final: 0.8638 (ptpp) outliers start: 77 outliers final: 43 residues processed: 358 average time/residue: 0.3268 time to fit residues: 169.5865 Evaluate side-chains 296 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 249 time to evaluate : 1.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 446 VAL Chi-restraints excluded: chain 2 residue 458 ILE Chi-restraints excluded: chain 2 residue 586 HIS Chi-restraints excluded: chain 2 residue 739 THR Chi-restraints excluded: chain 2 residue 768 VAL Chi-restraints excluded: chain 2 residue 781 LEU Chi-restraints excluded: chain 2 residue 810 ASN Chi-restraints excluded: chain 3 residue 279 ASP 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 542 LEU Chi-restraints excluded: chain 3 residue 577 LEU Chi-restraints excluded: chain 3 residue 597 ILE Chi-restraints excluded: chain 4 residue 577 ASP Chi-restraints excluded: chain 4 residue 582 SER Chi-restraints excluded: chain 4 residue 751 ASN Chi-restraints excluded: chain 5 residue 370 LEU Chi-restraints excluded: chain 5 residue 398 CYS 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 568 ARG Chi-restraints excluded: chain 5 residue 609 ILE Chi-restraints excluded: chain 6 residue 342 MET Chi-restraints excluded: chain 6 residue 353 CYS Chi-restraints excluded: chain 6 residue 356 LEU Chi-restraints excluded: chain 6 residue 366 ILE Chi-restraints excluded: chain 6 residue 432 THR Chi-restraints excluded: chain 6 residue 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 363 HIS Chi-restraints excluded: chain 7 residue 379 MET Chi-restraints excluded: chain 7 residue 400 SER Chi-restraints excluded: chain 7 residue 434 VAL Chi-restraints excluded: chain 7 residue 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 Chi-restraints excluded: chain 7 residue 599 PHE 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: 0.5980 chunk 157 optimal weight: 5.9990 chunk 128 optimal weight: 0.0770 chunk 52 optimal weight: 0.0470 chunk 189 optimal weight: 3.9990 chunk 204 optimal weight: 0.9980 chunk 168 optimal weight: 2.9990 chunk 187 optimal weight: 4.9990 chunk 64 optimal weight: 0.1980 chunk 151 optimal weight: 6.9990 overall best weight: 0.3836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 534 GLN 4 665 HIS 4 751 ASN 5 541 HIS 6 496 ASN 6 558 HIS 7 644 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3497 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= 0.147 Angle : 0.541 11.357 22999 Z= 0.275 Chirality : 0.038 0.154 2617 Planarity : 0.004 0.064 2934 Dihedral : 8.614 88.964 2460 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.19 % Allowed : 15.44 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.19), residues: 2068 helix: 1.91 (0.16), residues: 1137 sheet: 0.19 (0.34), residues: 240 loop : -0.77 (0.22), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP 2 554 HIS 0.009 0.001 HIS 3 360 PHE 0.020 0.001 PHE 2 663 TYR 0.016 0.001 TYR 5 404 ARG 0.009 0.000 ARG 5 421 *********************** 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 342 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 284 time to evaluate : 2.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 509 ASP cc_start: 0.7395 (m-30) cc_final: 0.7137 (t0) REVERT: 2 580 GLN cc_start: 0.7558 (tp-100) cc_final: 0.7320 (tp-100) REVERT: 2 707 MET cc_start: 0.8693 (mmm) cc_final: 0.8424 (mmm) REVERT: 2 794 ARG cc_start: 0.7944 (tpp80) cc_final: 0.7720 (tpp80) REVERT: 2 819 LYS cc_start: 0.8410 (tttt) cc_final: 0.8201 (mmmt) REVERT: 2 838 ASP cc_start: 0.7755 (m-30) cc_final: 0.6964 (t0) REVERT: 4 443 GLU cc_start: 0.7680 (mp0) cc_final: 0.6949 (tt0) REVERT: 4 451 GLU cc_start: 0.8313 (tt0) cc_final: 0.7998 (tm-30) REVERT: 4 492 PHE cc_start: 0.6798 (m-80) cc_final: 0.5338 (t80) REVERT: 4 677 MET cc_start: -0.1454 (mmm) cc_final: -0.2891 (tmm) REVERT: 5 421 ARG cc_start: 0.7793 (ptm160) cc_final: 0.7451 (ptm-80) REVERT: 6 342 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.7254 (mtt) REVERT: 6 401 SER cc_start: 0.8816 (m) cc_final: 0.8386 (p) REVERT: 6 443 GLU cc_start: 0.6965 (mt-10) cc_final: 0.6194 (pt0) REVERT: 7 620 LEU cc_start: 0.8061 (mt) cc_final: 0.7832 (tt) outliers start: 58 outliers final: 30 residues processed: 322 average time/residue: 0.3102 time to fit residues: 147.4080 Evaluate side-chains 285 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 254 time to evaluate : 1.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 586 HIS Chi-restraints excluded: chain 2 residue 781 LEU Chi-restraints excluded: chain 3 residue 416 ASP Chi-restraints excluded: chain 3 residue 422 ILE Chi-restraints excluded: chain 3 residue 423 HIS Chi-restraints excluded: chain 3 residue 424 GLU Chi-restraints excluded: chain 3 residue 475 LEU Chi-restraints excluded: chain 3 residue 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 577 LEU Chi-restraints excluded: chain 3 residue 597 ILE Chi-restraints excluded: chain 3 residue 631 VAL 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 557 LEU Chi-restraints excluded: chain 6 residue 342 MET Chi-restraints excluded: chain 6 residue 353 CYS Chi-restraints excluded: chain 6 residue 356 LEU Chi-restraints excluded: chain 6 residue 465 ASP 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 363 HIS 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 558 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 186 optimal weight: 0.8980 chunk 142 optimal weight: 0.9980 chunk 98 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 127 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 chunk 201 optimal weight: 0.7980 chunk 99 optimal weight: 6.9990 chunk 179 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- 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** 3 423 HIS 3 553 HIS 4 665 HIS 4 751 ASN 5 541 HIS 6 496 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17053 Z= 0.229 Angle : 0.556 8.953 22999 Z= 0.284 Chirality : 0.039 0.143 2617 Planarity : 0.004 0.044 2934 Dihedral : 8.269 89.941 2460 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.07 % Allowed : 14.95 % 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: 1.11 (0.19), residues: 2068 helix: 1.78 (0.16), residues: 1130 sheet: 0.16 (0.33), residues: 253 loop : -0.76 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 2 554 HIS 0.009 0.001 HIS 7 458 PHE 0.023 0.002 PHE 4 500 TYR 0.024 0.002 TYR 6 780 ARG 0.005 0.000 ARG 6 498 *********************** 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 337 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 263 time to evaluate : 1.985 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: 0.7601 (m-30) cc_final: 0.7374 (t0) REVERT: 2 580 GLN cc_start: 0.7604 (tp-100) cc_final: 0.7321 (tp-100) REVERT: 2 819 LYS cc_start: 0.8423 (tttt) cc_final: 0.8217 (mmmt) REVERT: 2 838 ASP cc_start: 0.7826 (m-30) cc_final: 0.6991 (t0) REVERT: 3 339 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8413 (mt) REVERT: 4 443 GLU cc_start: 0.7593 (mp0) cc_final: 0.7022 (mp0) REVERT: 4 472 GLU cc_start: 0.5434 (OUTLIER) cc_final: 0.5167 (tt0) REVERT: 4 677 MET cc_start: -0.1627 (mmm) cc_final: -0.2946 (tmm) REVERT: 5 421 ARG cc_start: 0.7813 (ptm160) cc_final: 0.7573 (ptm160) REVERT: 5 429 ILE cc_start: 0.8942 (pt) cc_final: 0.8674 (pt) REVERT: 5 431 GLU cc_start: 0.7729 (mp0) cc_final: 0.7444 (mp0) REVERT: 5 451 MET cc_start: 0.8237 (mmm) cc_final: 0.8031 (mmm) REVERT: 5 568 ARG cc_start: 0.9090 (OUTLIER) cc_final: 0.7612 (mtm-85) REVERT: 6 342 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7273 (mtt) REVERT: 6 401 SER cc_start: 0.8902 (m) cc_final: 0.8462 (p) REVERT: 6 443 GLU cc_start: 0.6941 (mt-10) cc_final: 0.6224 (pt0) REVERT: 6 569 TYR cc_start: 0.8523 (m-80) cc_final: 0.8194 (m-80) REVERT: 7 320 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8397 (tp30) REVERT: 7 620 LEU cc_start: 0.8103 (mt) cc_final: 0.7725 (tt) outliers start: 74 outliers final: 43 residues processed: 315 average time/residue: 0.3021 time to fit residues: 141.7904 Evaluate side-chains 288 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 241 time to evaluate : 1.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 462 ILE Chi-restraints excluded: chain 2 residue 577 MET Chi-restraints excluded: chain 2 residue 586 HIS Chi-restraints excluded: chain 2 residue 768 VAL Chi-restraints excluded: chain 2 residue 781 LEU Chi-restraints excluded: chain 3 residue 339 ILE 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 751 ASN Chi-restraints excluded: chain 5 residue 370 LEU Chi-restraints excluded: chain 5 residue 478 THR Chi-restraints excluded: chain 5 residue 541 HIS Chi-restraints excluded: chain 5 residue 551 VAL Chi-restraints excluded: chain 5 residue 568 ARG Chi-restraints excluded: chain 5 residue 609 ILE Chi-restraints excluded: chain 6 residue 342 MET Chi-restraints excluded: chain 6 residue 353 CYS Chi-restraints excluded: chain 6 residue 356 LEU Chi-restraints excluded: chain 6 residue 366 ILE Chi-restraints excluded: chain 6 residue 432 THR Chi-restraints excluded: chain 6 residue 465 ASP Chi-restraints excluded: chain 6 residue 496 ASN 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 331 PHE 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 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: 0.9990 chunk 2 optimal weight: 0.9980 chunk 149 optimal weight: 4.9990 chunk 82 optimal weight: 9.9990 chunk 171 optimal weight: 4.9990 chunk 138 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 102 optimal weight: 20.0000 chunk 180 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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** 3 423 HIS 3 553 HIS 4 665 HIS 4 751 ASN 5 541 HIS 6 496 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17053 Z= 0.193 Angle : 0.543 9.968 22999 Z= 0.274 Chirality : 0.039 0.156 2617 Planarity : 0.003 0.041 2934 Dihedral : 8.110 89.893 2460 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.68 % Allowed : 16.26 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.11 (0.19), residues: 2068 helix: 1.76 (0.16), residues: 1131 sheet: 0.16 (0.33), residues: 253 loop : -0.73 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP 2 554 HIS 0.008 0.001 HIS 7 458 PHE 0.027 0.001 PHE 4 500 TYR 0.031 0.001 TYR 6 780 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 325 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 258 time to evaluate : 1.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 509 ASP cc_start: 0.7551 (m-30) cc_final: 0.7307 (t0) REVERT: 2 580 GLN cc_start: 0.7578 (tp-100) cc_final: 0.7312 (tp-100) REVERT: 2 819 LYS cc_start: 0.8441 (tttt) cc_final: 0.8228 (mmmt) REVERT: 2 838 ASP cc_start: 0.7828 (m-30) cc_final: 0.6985 (t0) REVERT: 3 339 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8401 (mt) REVERT: 4 443 GLU cc_start: 0.7580 (mp0) cc_final: 0.6993 (mp0) REVERT: 4 451 GLU cc_start: 0.8311 (tt0) cc_final: 0.7957 (tm-30) REVERT: 4 472 GLU cc_start: 0.5428 (OUTLIER) cc_final: 0.5215 (tt0) REVERT: 4 677 MET cc_start: -0.1451 (mmm) cc_final: -0.2884 (tmm) REVERT: 5 421 ARG cc_start: 0.7738 (ptm160) cc_final: 0.7330 (ptm160) REVERT: 5 429 ILE cc_start: 0.8904 (pt) cc_final: 0.8540 (pt) REVERT: 5 431 GLU cc_start: 0.7636 (mp0) cc_final: 0.7138 (mp0) REVERT: 5 451 MET cc_start: 0.8299 (mmm) cc_final: 0.8065 (mmm) REVERT: 5 568 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.7609 (mtm-85) REVERT: 6 342 MET cc_start: 0.7974 (OUTLIER) cc_final: 0.7316 (mtt) REVERT: 6 401 SER cc_start: 0.8886 (m) cc_final: 0.8452 (p) REVERT: 6 443 GLU cc_start: 0.6964 (mt-10) cc_final: 0.6164 (pt0) REVERT: 6 569 TYR cc_start: 0.8544 (m-80) cc_final: 0.8262 (m-80) REVERT: 7 620 LEU cc_start: 0.8131 (mt) cc_final: 0.7736 (tt) outliers start: 67 outliers final: 51 residues processed: 309 average time/residue: 0.2945 time to fit residues: 136.0885 Evaluate side-chains 292 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 237 time to evaluate : 2.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 462 ILE Chi-restraints excluded: chain 2 residue 577 MET Chi-restraints excluded: chain 2 residue 581 ASP 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 339 ILE 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 438 ILE Chi-restraints excluded: chain 3 residue 489 MET Chi-restraints excluded: chain 3 residue 490 ASP 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 491 ASP 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 5 residue 316 THR 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 541 HIS Chi-restraints excluded: chain 5 residue 551 VAL Chi-restraints excluded: chain 5 residue 568 ARG Chi-restraints excluded: chain 5 residue 609 ILE Chi-restraints excluded: chain 5 residue 651 ASP Chi-restraints excluded: chain 6 residue 342 MET Chi-restraints excluded: chain 6 residue 353 CYS Chi-restraints excluded: chain 6 residue 356 LEU Chi-restraints excluded: chain 6 residue 366 ILE 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 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 339 ILE Chi-restraints excluded: chain 7 residue 363 HIS 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 466 ILE Chi-restraints excluded: chain 7 residue 527 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 67 optimal weight: 4.9990 chunk 181 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 chunk 118 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 201 optimal weight: 0.5980 chunk 167 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 423 HIS 3 553 HIS 4 665 HIS 4 751 ASN 5 460 HIS 6 496 ASN 7 401 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17053 Z= 0.195 Angle : 0.554 16.056 22999 Z= 0.276 Chirality : 0.039 0.129 2617 Planarity : 0.003 0.045 2934 Dihedral : 8.005 89.539 2460 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.79 % Allowed : 17.25 % Favored : 78.96 % 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: 1.08 (0.19), residues: 2068 helix: 1.66 (0.16), residues: 1137 sheet: 0.28 (0.33), residues: 251 loop : -0.67 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP 2 554 HIS 0.011 0.001 HIS 5 541 PHE 0.023 0.001 PHE 2 663 TYR 0.038 0.001 TYR 6 780 ARG 0.008 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 319 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 250 time to evaluate : 2.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 509 ASP cc_start: 0.7600 (m-30) cc_final: 0.7308 (t0) REVERT: 2 580 GLN cc_start: 0.7612 (tp-100) cc_final: 0.7318 (tp-100) REVERT: 2 819 LYS cc_start: 0.8433 (tttt) cc_final: 0.8170 (mmmt) REVERT: 2 838 ASP cc_start: 0.7847 (m-30) cc_final: 0.6984 (t0) REVERT: 3 339 ILE cc_start: 0.8621 (OUTLIER) cc_final: 0.8408 (mt) REVERT: 4 443 GLU cc_start: 0.7576 (mp0) cc_final: 0.6990 (mp0) REVERT: 4 451 GLU cc_start: 0.8330 (tt0) cc_final: 0.7977 (tm-30) REVERT: 4 472 GLU cc_start: 0.5458 (OUTLIER) cc_final: 0.5170 (tt0) REVERT: 4 677 MET cc_start: -0.1381 (mmm) cc_final: -0.2875 (tmm) REVERT: 5 429 ILE cc_start: 0.8881 (pt) cc_final: 0.8499 (pt) REVERT: 5 431 GLU cc_start: 0.7625 (mp0) cc_final: 0.7038 (mp0) REVERT: 6 342 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.7311 (mtt) REVERT: 6 401 SER cc_start: 0.8851 (m) cc_final: 0.8436 (p) REVERT: 6 443 GLU cc_start: 0.7160 (mt-10) cc_final: 0.6380 (pt0) REVERT: 6 569 TYR cc_start: 0.8628 (m-80) cc_final: 0.8305 (m-80) REVERT: 7 620 LEU cc_start: 0.8146 (mt) cc_final: 0.7731 (tt) REVERT: 7 633 MET cc_start: 0.7974 (ptt) cc_final: 0.7611 (ptp) outliers start: 69 outliers final: 56 residues processed: 303 average time/residue: 0.2909 time to fit residues: 134.4793 Evaluate side-chains 296 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 237 time to evaluate : 2.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 462 ILE Chi-restraints excluded: chain 2 residue 581 ASP Chi-restraints excluded: chain 2 residue 586 HIS Chi-restraints excluded: chain 2 residue 739 THR Chi-restraints excluded: chain 2 residue 768 VAL Chi-restraints excluded: chain 2 residue 781 LEU Chi-restraints excluded: chain 3 residue 339 ILE 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 438 ILE Chi-restraints excluded: chain 3 residue 489 MET Chi-restraints excluded: chain 3 residue 490 ASP 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 491 ASP 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 5 residue 316 THR Chi-restraints excluded: chain 5 residue 370 LEU Chi-restraints excluded: chain 5 residue 398 CYS Chi-restraints excluded: chain 5 residue 468 ILE Chi-restraints excluded: chain 5 residue 478 THR Chi-restraints excluded: chain 5 residue 546 THR Chi-restraints excluded: chain 5 residue 551 VAL Chi-restraints excluded: chain 5 residue 609 ILE Chi-restraints excluded: chain 5 residue 651 ASP Chi-restraints excluded: chain 6 residue 342 MET Chi-restraints excluded: chain 6 residue 353 CYS Chi-restraints excluded: chain 6 residue 356 LEU Chi-restraints excluded: chain 6 residue 366 ILE Chi-restraints excluded: chain 6 residue 432 THR Chi-restraints excluded: chain 6 residue 465 ASP Chi-restraints excluded: chain 6 residue 499 THR 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 326 ILE Chi-restraints excluded: chain 7 residue 339 ILE Chi-restraints excluded: chain 7 residue 363 HIS 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 194 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 114 optimal weight: 0.9980 chunk 146 optimal weight: 0.9990 chunk 113 optimal weight: 0.7980 chunk 169 optimal weight: 8.9990 chunk 112 optimal weight: 0.9990 chunk 200 optimal weight: 7.9990 chunk 125 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 92 optimal weight: 8.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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 3 423 HIS 4 665 HIS 4 751 ASN 5 390 GLN 6 496 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.4440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17053 Z= 0.181 Angle : 0.567 14.492 22999 Z= 0.279 Chirality : 0.039 0.178 2617 Planarity : 0.003 0.029 2934 Dihedral : 7.894 89.128 2460 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.90 % Allowed : 17.86 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.19), residues: 2068 helix: 1.65 (0.16), residues: 1134 sheet: 0.21 (0.32), residues: 254 loop : -0.65 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP 2 554 HIS 0.012 0.001 HIS 3 423 PHE 0.050 0.002 PHE 2 868 TYR 0.031 0.001 TYR 6 780 ARG 0.007 0.000 ARG 6 498 *********************** 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 315 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 244 time to evaluate : 2.190 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: 0.7560 (m-30) cc_final: 0.7254 (t0) REVERT: 2 580 GLN cc_start: 0.7641 (tp-100) cc_final: 0.7362 (tp-100) REVERT: 2 838 ASP cc_start: 0.7863 (m-30) cc_final: 0.6979 (t0) REVERT: 4 443 GLU cc_start: 0.7801 (mp0) cc_final: 0.7218 (mp0) REVERT: 4 451 GLU cc_start: 0.8329 (tt0) cc_final: 0.7979 (tm-30) REVERT: 4 579 MET cc_start: 0.7778 (tpt) cc_final: 0.7108 (tpp) REVERT: 4 677 MET cc_start: -0.1272 (mmm) cc_final: -0.2801 (tmm) REVERT: 5 429 ILE cc_start: 0.8917 (pt) cc_final: 0.8521 (pt) REVERT: 5 431 GLU cc_start: 0.7648 (mp0) cc_final: 0.6988 (mp0) REVERT: 5 512 LEU cc_start: 0.8934 (tt) cc_final: 0.8714 (tt) REVERT: 5 568 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.7604 (mtm-85) REVERT: 6 342 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.7304 (mtt) REVERT: 6 401 SER cc_start: 0.8808 (m) cc_final: 0.8399 (p) REVERT: 6 443 GLU cc_start: 0.7144 (mt-10) cc_final: 0.6444 (pt0) REVERT: 6 569 TYR cc_start: 0.8667 (m-80) cc_final: 0.8348 (m-80) REVERT: 7 620 LEU cc_start: 0.8175 (mt) cc_final: 0.7748 (tt) outliers start: 71 outliers final: 52 residues processed: 300 average time/residue: 0.2913 time to fit residues: 132.2324 Evaluate side-chains 286 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 232 time to evaluate : 2.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 462 ILE Chi-restraints excluded: chain 2 residue 581 ASP Chi-restraints excluded: chain 2 residue 586 HIS Chi-restraints excluded: chain 2 residue 739 THR Chi-restraints excluded: chain 2 residue 768 VAL Chi-restraints excluded: chain 2 residue 781 LEU Chi-restraints excluded: chain 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 438 ILE Chi-restraints excluded: chain 3 residue 489 MET Chi-restraints excluded: chain 3 residue 490 ASP 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 491 ASP 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 5 residue 316 THR Chi-restraints excluded: chain 5 residue 331 ASP Chi-restraints excluded: chain 5 residue 378 LEU Chi-restraints excluded: chain 5 residue 468 ILE Chi-restraints excluded: chain 5 residue 478 THR Chi-restraints excluded: chain 5 residue 546 THR Chi-restraints excluded: chain 5 residue 551 VAL Chi-restraints excluded: chain 5 residue 568 ARG Chi-restraints excluded: chain 5 residue 609 ILE Chi-restraints excluded: chain 5 residue 651 ASP Chi-restraints excluded: chain 6 residue 342 MET Chi-restraints excluded: chain 6 residue 353 CYS Chi-restraints excluded: chain 6 residue 356 LEU Chi-restraints excluded: chain 6 residue 366 ILE 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 535 PHE Chi-restraints excluded: chain 6 residue 558 HIS Chi-restraints excluded: chain 6 residue 609 SER Chi-restraints excluded: chain 7 residue 339 ILE Chi-restraints excluded: chain 7 residue 363 HIS 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 124 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 119 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 127 optimal weight: 0.9980 chunk 136 optimal weight: 0.4980 chunk 99 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 157 optimal weight: 30.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 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: 0.7912 moved from start: 0.4633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17053 Z= 0.266 Angle : 0.617 13.827 22999 Z= 0.305 Chirality : 0.040 0.260 2617 Planarity : 0.004 0.031 2934 Dihedral : 7.976 88.749 2460 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.52 % Allowed : 18.08 % 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: 0.85 (0.19), residues: 2068 helix: 1.43 (0.16), residues: 1136 sheet: 0.29 (0.32), residues: 250 loop : -0.75 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP 7 518 HIS 0.008 0.001 HIS 2 586 PHE 0.039 0.002 PHE 2 868 TYR 0.030 0.002 TYR 6 780 ARG 0.010 0.000 ARG 6 498 *********************** 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 298 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 234 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: 2 509 ASP cc_start: 0.7689 (m-30) cc_final: 0.7382 (t0) REVERT: 2 580 GLN cc_start: 0.7676 (tp-100) cc_final: 0.7427 (tp-100) REVERT: 2 838 ASP cc_start: 0.7963 (m-30) cc_final: 0.7023 (t0) REVERT: 4 443 GLU cc_start: 0.7805 (mp0) cc_final: 0.7224 (mp0) REVERT: 4 451 GLU cc_start: 0.8296 (tt0) cc_final: 0.7941 (tm-30) REVERT: 4 579 MET cc_start: 0.7767 (tpt) cc_final: 0.7097 (tpp) REVERT: 4 650 MET cc_start: 0.3463 (ttm) cc_final: 0.3159 (ptm) REVERT: 4 677 MET cc_start: -0.1323 (mmm) cc_final: -0.2775 (tmm) REVERT: 5 429 ILE cc_start: 0.8903 (pt) cc_final: 0.8543 (pt) REVERT: 5 431 GLU cc_start: 0.7630 (mp0) cc_final: 0.7005 (mp0) REVERT: 5 568 ARG cc_start: 0.9079 (OUTLIER) cc_final: 0.7584 (mtm-85) REVERT: 6 342 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7311 (mtt) REVERT: 6 401 SER cc_start: 0.8865 (m) cc_final: 0.8502 (p) REVERT: 6 443 GLU cc_start: 0.7194 (mt-10) cc_final: 0.6522 (pt0) REVERT: 6 569 TYR cc_start: 0.8696 (m-80) cc_final: 0.8340 (m-80) outliers start: 64 outliers final: 54 residues processed: 284 average time/residue: 0.3046 time to fit residues: 129.0481 Evaluate side-chains 283 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 227 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 462 ILE 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 768 VAL Chi-restraints excluded: chain 2 residue 781 LEU Chi-restraints excluded: chain 3 residue 303 LEU Chi-restraints excluded: chain 3 residue 349 VAL Chi-restraints excluded: chain 3 residue 369 THR Chi-restraints excluded: chain 3 residue 416 ASP Chi-restraints excluded: chain 3 residue 438 ILE Chi-restraints excluded: chain 3 residue 489 MET Chi-restraints excluded: chain 3 residue 490 ASP 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 491 ASP Chi-restraints excluded: chain 4 residue 499 LYS Chi-restraints excluded: chain 4 residue 511 ASP Chi-restraints excluded: chain 4 residue 577 ASP Chi-restraints excluded: chain 4 residue 631 ILE Chi-restraints excluded: chain 4 residue 751 ASN Chi-restraints excluded: chain 5 residue 316 THR Chi-restraints excluded: chain 5 residue 331 ASP Chi-restraints excluded: chain 5 residue 468 ILE Chi-restraints excluded: chain 5 residue 478 THR Chi-restraints excluded: chain 5 residue 546 THR Chi-restraints excluded: chain 5 residue 551 VAL Chi-restraints excluded: chain 5 residue 568 ARG Chi-restraints excluded: chain 5 residue 609 ILE Chi-restraints excluded: chain 6 residue 342 MET Chi-restraints excluded: chain 6 residue 353 CYS Chi-restraints excluded: chain 6 residue 356 LEU Chi-restraints excluded: chain 6 residue 366 ILE 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 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 331 PHE Chi-restraints excluded: chain 7 residue 339 ILE Chi-restraints excluded: chain 7 residue 363 HIS 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 596 ASP Chi-restraints excluded: chain L residue 387 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 182 optimal weight: 8.9990 chunk 192 optimal weight: 2.9990 chunk 175 optimal weight: 5.9990 chunk 186 optimal weight: 0.0980 chunk 112 optimal weight: 0.0980 chunk 81 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 chunk 57 optimal weight: 0.4980 chunk 168 optimal weight: 3.9990 chunk 176 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 665 HIS 4 751 ASN ** 5 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 496 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.4782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17053 Z= 0.182 Angle : 0.583 13.265 22999 Z= 0.287 Chirality : 0.039 0.205 2617 Planarity : 0.003 0.040 2934 Dihedral : 7.895 89.111 2460 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.08 % Allowed : 19.07 % 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: 0.93 (0.19), residues: 2068 helix: 1.46 (0.16), residues: 1135 sheet: 0.62 (0.33), residues: 238 loop : -0.74 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP 2 554 HIS 0.007 0.001 HIS 2 586 PHE 0.036 0.001 PHE 2 868 TYR 0.027 0.001 TYR 6 780 ARG 0.009 0.000 ARG 6 498 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 239 time to evaluate : 1.813 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: 0.7644 (m-30) cc_final: 0.7323 (t0) REVERT: 2 580 GLN cc_start: 0.7621 (tp-100) cc_final: 0.7341 (tp-100) REVERT: 2 838 ASP cc_start: 0.7995 (m-30) cc_final: 0.7066 (t0) REVERT: 4 443 GLU cc_start: 0.7794 (mp0) cc_final: 0.7208 (mp0) REVERT: 4 451 GLU cc_start: 0.8309 (tt0) cc_final: 0.7987 (tm-30) REVERT: 4 472 GLU cc_start: 0.5996 (OUTLIER) cc_final: 0.5402 (tt0) REVERT: 4 579 MET cc_start: 0.7774 (tpt) cc_final: 0.7095 (tpp) REVERT: 4 644 PHE cc_start: 0.7048 (m-80) cc_final: 0.6719 (t80) REVERT: 4 650 MET cc_start: 0.3402 (OUTLIER) cc_final: 0.3089 (ptm) REVERT: 4 677 MET cc_start: -0.1237 (mmm) cc_final: -0.2762 (tmm) REVERT: 5 429 ILE cc_start: 0.8902 (pt) cc_final: 0.8482 (pt) REVERT: 5 431 GLU cc_start: 0.7580 (mp0) cc_final: 0.6850 (mp0) REVERT: 5 568 ARG cc_start: 0.9052 (OUTLIER) cc_final: 0.7567 (mtm-85) REVERT: 6 342 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.7323 (mtt) REVERT: 6 401 SER cc_start: 0.8855 (m) cc_final: 0.8463 (p) REVERT: 6 443 GLU cc_start: 0.7193 (mt-10) cc_final: 0.6537 (pt0) REVERT: 6 569 TYR cc_start: 0.8673 (m-80) cc_final: 0.8366 (m-80) REVERT: 6 633 MET cc_start: 0.8639 (mmm) cc_final: 0.8376 (tpp) REVERT: 7 511 LEU cc_start: 0.8888 (mt) cc_final: 0.8679 (pp) REVERT: 7 640 LYS cc_start: 0.8606 (pttm) cc_final: 0.8315 (pttm) outliers start: 56 outliers final: 47 residues processed: 281 average time/residue: 0.2878 time to fit residues: 122.3915 Evaluate side-chains 280 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 229 time to evaluate : 2.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 462 ILE Chi-restraints excluded: chain 2 residue 581 ASP Chi-restraints excluded: chain 2 residue 586 HIS Chi-restraints excluded: chain 2 residue 739 THR Chi-restraints excluded: chain 2 residue 768 VAL Chi-restraints excluded: chain 2 residue 781 LEU Chi-restraints excluded: chain 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 438 ILE 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 491 ASP Chi-restraints excluded: chain 4 residue 499 LYS Chi-restraints excluded: chain 4 residue 511 ASP Chi-restraints excluded: chain 4 residue 577 ASP Chi-restraints excluded: chain 4 residue 631 ILE Chi-restraints excluded: chain 4 residue 650 MET Chi-restraints excluded: chain 4 residue 751 ASN Chi-restraints excluded: chain 5 residue 331 ASP Chi-restraints excluded: chain 5 residue 468 ILE Chi-restraints excluded: chain 5 residue 478 THR Chi-restraints excluded: chain 5 residue 551 VAL Chi-restraints excluded: chain 5 residue 568 ARG Chi-restraints excluded: chain 5 residue 609 ILE Chi-restraints excluded: chain 6 residue 342 MET Chi-restraints excluded: chain 6 residue 353 CYS Chi-restraints excluded: chain 6 residue 356 LEU Chi-restraints excluded: chain 6 residue 366 ILE Chi-restraints excluded: chain 6 residue 432 THR Chi-restraints excluded: chain 6 residue 465 ASP Chi-restraints excluded: chain 6 residue 499 THR 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 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 L residue 387 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 197 optimal weight: 0.0040 chunk 120 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 137 optimal weight: 0.8980 chunk 207 optimal weight: 0.0770 chunk 190 optimal weight: 2.9990 chunk 165 optimal weight: 7.9990 chunk 17 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 131 optimal weight: 0.9980 overall best weight: 0.5750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 665 HIS 4 751 ASN 6 496 ASN 7 521 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.4887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17053 Z= 0.150 Angle : 0.580 12.804 22999 Z= 0.282 Chirality : 0.038 0.185 2617 Planarity : 0.003 0.051 2934 Dihedral : 7.775 89.940 2460 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.75 % Allowed : 19.45 % Favored : 77.80 % 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: 1.02 (0.19), residues: 2068 helix: 1.55 (0.16), residues: 1134 sheet: 0.56 (0.33), residues: 242 loop : -0.69 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP 6 616 HIS 0.007 0.001 HIS 3 360 PHE 0.033 0.001 PHE 2 868 TYR 0.021 0.001 TYR 6 780 ARG 0.009 0.000 ARG 6 498 ********************** 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 297 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 247 time to evaluate : 2.105 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: 0.7560 (m-30) cc_final: 0.7258 (t0) REVERT: 2 580 GLN cc_start: 0.7550 (tp-100) cc_final: 0.7305 (tp-100) REVERT: 2 838 ASP cc_start: 0.8002 (m-30) cc_final: 0.7099 (t0) REVERT: 4 443 GLU cc_start: 0.7793 (mp0) cc_final: 0.7211 (mp0) REVERT: 4 451 GLU cc_start: 0.8317 (tt0) cc_final: 0.8006 (tm-30) REVERT: 4 472 GLU cc_start: 0.6053 (OUTLIER) cc_final: 0.5477 (tt0) REVERT: 4 579 MET cc_start: 0.7812 (tpt) cc_final: 0.7112 (tpp) REVERT: 4 644 PHE cc_start: 0.7039 (m-80) cc_final: 0.6747 (t80) REVERT: 4 648 PHE cc_start: 0.6440 (m-80) cc_final: 0.6038 (m-80) REVERT: 4 650 MET cc_start: 0.3299 (ttm) cc_final: 0.2986 (ptm) REVERT: 4 677 MET cc_start: -0.1275 (mmm) cc_final: -0.2784 (tmm) REVERT: 5 429 ILE cc_start: 0.8815 (pt) cc_final: 0.8401 (pt) REVERT: 5 431 GLU cc_start: 0.7536 (mp0) cc_final: 0.6847 (mp0) REVERT: 5 568 ARG cc_start: 0.8985 (OUTLIER) cc_final: 0.7524 (mtm-85) REVERT: 6 342 MET cc_start: 0.7859 (OUTLIER) cc_final: 0.7039 (mtt) REVERT: 6 401 SER cc_start: 0.8777 (m) cc_final: 0.8446 (p) REVERT: 6 436 VAL cc_start: 0.7472 (p) cc_final: 0.6997 (m) REVERT: 6 443 GLU cc_start: 0.7174 (mt-10) cc_final: 0.6531 (pt0) REVERT: 6 569 TYR cc_start: 0.8648 (m-80) cc_final: 0.8404 (m-80) REVERT: 6 633 MET cc_start: 0.8507 (mmm) cc_final: 0.8253 (tpp) REVERT: 7 640 LYS cc_start: 0.8698 (pttm) cc_final: 0.8464 (pttm) outliers start: 50 outliers final: 41 residues processed: 285 average time/residue: 0.3175 time to fit residues: 137.7359 Evaluate side-chains 283 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 239 time to evaluate : 2.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 462 ILE Chi-restraints excluded: chain 2 residue 586 HIS Chi-restraints excluded: chain 2 residue 739 THR Chi-restraints excluded: chain 2 residue 768 VAL Chi-restraints excluded: chain 2 residue 781 LEU Chi-restraints excluded: chain 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 438 ILE 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 511 ASP Chi-restraints excluded: chain 4 residue 577 ASP Chi-restraints excluded: chain 4 residue 631 ILE Chi-restraints excluded: chain 4 residue 751 ASN Chi-restraints excluded: chain 5 residue 331 ASP Chi-restraints excluded: chain 5 residue 478 THR Chi-restraints excluded: chain 5 residue 551 VAL Chi-restraints excluded: chain 5 residue 568 ARG Chi-restraints excluded: chain 5 residue 609 ILE Chi-restraints excluded: chain 6 residue 342 MET Chi-restraints excluded: chain 6 residue 353 CYS Chi-restraints excluded: chain 6 residue 356 LEU Chi-restraints excluded: chain 6 residue 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 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 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 L residue 387 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 152 optimal weight: 6.9990 chunk 24 optimal weight: 0.2980 chunk 45 optimal weight: 0.6980 chunk 165 optimal weight: 7.9990 chunk 69 optimal weight: 0.5980 chunk 169 optimal weight: 0.2980 chunk 20 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 145 optimal weight: 6.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 665 HIS 4 751 ASN 6 496 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.152085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.103915 restraints weight = 32186.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.104600 restraints weight = 21627.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.104823 restraints weight = 15534.767| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.4988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17053 Z= 0.151 Angle : 0.586 13.688 22999 Z= 0.285 Chirality : 0.039 0.170 2617 Planarity : 0.003 0.054 2934 Dihedral : 7.716 89.996 2460 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.80 % Allowed : 19.40 % Favored : 77.80 % 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: 1.00 (0.19), residues: 2068 helix: 1.52 (0.16), residues: 1134 sheet: 0.61 (0.33), residues: 242 loop : -0.71 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP 6 616 HIS 0.009 0.001 HIS 7 363 PHE 0.038 0.001 PHE 6 580 TYR 0.017 0.001 TYR 7 584 ARG 0.008 0.000 ARG 6 498 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4076.44 seconds wall clock time: 75 minutes 49.81 seconds (4549.81 seconds total)