Starting phenix.real_space_refine on Sat Dec 9 03:21:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dra_27675/12_2023/8dra_27675.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dra_27675/12_2023/8dra_27675.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dra_27675/12_2023/8dra_27675.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dra_27675/12_2023/8dra_27675.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dra_27675/12_2023/8dra_27675.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dra_27675/12_2023/8dra_27675.pdb" } resolution = 3.98 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= 0.001 sd= 0.045 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: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 6369 2.51 5 N 1713 2.21 5 O 1785 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 703": "OD1" <-> "OD2" Residue "F PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 595": "OE1" <-> "OE2" Residue "F GLU 628": "OE1" <-> "OE2" Residue "F PHE 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 764": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 795": "OD1" <-> "OD2" Residue "F GLU 798": "OE1" <-> "OE2" Residue "F ASP 803": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 9899 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3321 Classifications: {'peptide': 407} Link IDs: {'PTRANS': 18, 'TRANS': 388} Chain: "B" Number of atoms: 3321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3321 Classifications: {'peptide': 407} Link IDs: {'PTRANS': 18, 'TRANS': 388} Chain: "F" Number of atoms: 3257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3257 Classifications: {'peptide': 404} Link IDs: {'PTRANS': 17, 'TRANS': 386} Time building chain proxies: 5.71, per 1000 atoms: 0.58 Number of scatterers: 9899 At special positions: 0 Unit cell: (119.472, 114.232, 92.224, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 32 16.00 O 1785 8.00 N 1713 7.00 C 6369 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: 3.77 Conformation dependent library (CDL) restraints added in 1.7 seconds 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2364 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 9 sheets defined 33.2% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 402 through 411 Processing helix chain 'A' and resid 412 through 420 Processing helix chain 'A' and resid 439 through 444 removed outlier: 3.637A pdb=" N PHE A 443 " --> pdb=" O PRO A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 467 removed outlier: 3.527A pdb=" N ILE A 465 " --> pdb=" O PRO A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 495 Processing helix chain 'A' and resid 536 through 542 removed outlier: 3.889A pdb=" N GLY A 539 " --> pdb=" O VAL A 536 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG A 541 " --> pdb=" O ASP A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 566 removed outlier: 3.694A pdb=" N THR A 563 " --> pdb=" O PRO A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 590 removed outlier: 3.911A pdb=" N LYS A 588 " --> pdb=" O ASN A 585 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS A 589 " --> pdb=" O SER A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 613 Processing helix chain 'A' and resid 629 through 638 removed outlier: 3.954A pdb=" N ILE A 633 " --> pdb=" O GLU A 630 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN A 636 " --> pdb=" O ILE A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 661 Processing helix chain 'A' and resid 680 through 684 removed outlier: 3.606A pdb=" N CYS A 684 " --> pdb=" O LEU A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 706 Processing helix chain 'A' and resid 724 through 730 removed outlier: 3.644A pdb=" N CYS A 730 " --> pdb=" O LEU A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 753 removed outlier: 3.549A pdb=" N VAL A 750 " --> pdb=" O PRO A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 776 removed outlier: 3.655A pdb=" N CYS A 776 " --> pdb=" O LEU A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 793 Processing helix chain 'A' and resid 795 through 808 Processing helix chain 'B' and resid 403 through 411 Processing helix chain 'B' and resid 412 through 419 Processing helix chain 'B' and resid 440 through 445 Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 484 through 495 removed outlier: 3.647A pdb=" N GLU B 493 " --> pdb=" O ALA B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 508 removed outlier: 3.878A pdb=" N GLU B 507 " --> pdb=" O ASP B 504 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE B 508 " --> pdb=" O ILE B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 566 Processing helix chain 'B' and resid 567 through 569 No H-bonds generated for 'chain 'B' and resid 567 through 569' Processing helix chain 'B' and resid 586 through 590 removed outlier: 4.011A pdb=" N LYS B 589 " --> pdb=" O SER B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 613 removed outlier: 3.512A pdb=" N LEU B 613 " --> pdb=" O ILE B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 638 removed outlier: 3.756A pdb=" N HIS B 637 " --> pdb=" O SER B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 661 removed outlier: 3.718A pdb=" N ILE B 658 " --> pdb=" O PRO B 655 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU B 661 " --> pdb=" O ILE B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 684 removed outlier: 3.866A pdb=" N CYS B 684 " --> pdb=" O LEU B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 705 removed outlier: 3.619A pdb=" N ILE B 704 " --> pdb=" O PRO B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 729 Processing helix chain 'B' and resid 747 through 752 removed outlier: 3.638A pdb=" N VAL B 750 " --> pdb=" O PRO B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 776 removed outlier: 3.510A pdb=" N CYS B 776 " --> pdb=" O LEU B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 792 Processing helix chain 'B' and resid 795 through 808 Processing helix chain 'F' and resid 401 through 409 Processing helix chain 'F' and resid 410 through 418 Processing helix chain 'F' and resid 460 through 466 removed outlier: 3.649A pdb=" N ILE F 463 " --> pdb=" O PRO F 460 " (cutoff:3.500A) Processing helix chain 'F' and resid 482 through 493 Processing helix chain 'F' and resid 502 through 506 Processing helix chain 'F' and resid 508 through 513 removed outlier: 3.710A pdb=" N TYR F 511 " --> pdb=" O PRO F 508 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU F 513 " --> pdb=" O MET F 510 " (cutoff:3.500A) Processing helix chain 'F' and resid 534 through 540 removed outlier: 4.042A pdb=" N ARG F 539 " --> pdb=" O GLU F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 557 through 563 removed outlier: 3.573A pdb=" N VAL F 561 " --> pdb=" O PRO F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 582 through 587 Processing helix chain 'F' and resid 605 through 610 Processing helix chain 'F' and resid 629 through 636 removed outlier: 4.564A pdb=" N GLN F 634 " --> pdb=" O VAL F 631 " (cutoff:3.500A) Processing helix chain 'F' and resid 653 through 659 removed outlier: 3.797A pdb=" N ILE F 656 " --> pdb=" O PRO F 653 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU F 659 " --> pdb=" O ILE F 656 " (cutoff:3.500A) Processing helix chain 'F' and resid 676 through 682 removed outlier: 3.938A pdb=" N PHE F 680 " --> pdb=" O PRO F 676 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N CYS F 682 " --> pdb=" O HIS F 678 " (cutoff:3.500A) Processing helix chain 'F' and resid 699 through 705 removed outlier: 3.537A pdb=" N ILE F 702 " --> pdb=" O PRO F 699 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLY F 703 " --> pdb=" O PRO F 700 " (cutoff:3.500A) Processing helix chain 'F' and resid 724 through 728 Processing helix chain 'F' and resid 768 through 774 removed outlier: 3.696A pdb=" N CYS F 774 " --> pdb=" O LEU F 771 " (cutoff:3.500A) Processing helix chain 'F' and resid 785 through 791 Processing helix chain 'F' and resid 793 through 802 removed outlier: 3.839A pdb=" N MET F 800 " --> pdb=" O VAL F 796 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 421 through 422 removed outlier: 6.379A pdb=" N LEU A 428 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LYS A 452 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU A 430 " --> pdb=" O LYS A 452 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N GLU A 454 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LEU A 432 " --> pdb=" O GLU A 454 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU A 451 " --> pdb=" O TRP A 475 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N TYR A 477 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU A 453 " --> pdb=" O TYR A 477 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU A 572 " --> pdb=" O GLU A 597 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE A 599 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ILE A 574 " --> pdb=" O ILE A 599 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU A 596 " --> pdb=" O ASP A 620 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ILE A 619 " --> pdb=" O LYS A 645 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 459 through 461 removed outlier: 6.351A pdb=" N VAL A 459 " --> pdb=" O LYS A 482 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 666 through 668 removed outlier: 3.660A pdb=" N ASP A 691 " --> pdb=" O LEU A 667 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 759 through 760 removed outlier: 6.341A pdb=" N ILE A 759 " --> pdb=" O VAL A 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 420 through 422 removed outlier: 6.518A pdb=" N LEU B 428 " --> pdb=" O VAL B 450 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LYS B 452 " --> pdb=" O LEU B 428 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LEU B 430 " --> pdb=" O LYS B 452 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLU B 454 " --> pdb=" O LEU B 430 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU B 432 " --> pdb=" O GLU B 454 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LEU B 451 " --> pdb=" O TRP B 475 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N TYR B 477 " --> pdb=" O LEU B 451 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU B 453 " --> pdb=" O TYR B 477 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU B 474 " --> pdb=" O HIS B 499 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N LYS B 501 " --> pdb=" O LEU B 474 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N LEU B 476 " --> pdb=" O LYS B 501 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU B 498 " --> pdb=" O HIS B 522 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N THR B 524 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE B 500 " --> pdb=" O THR B 524 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER B 573 " --> pdb=" O LEU B 549 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU B 644 " --> pdb=" O TYR B 668 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU B 667 " --> pdb=" O ASP B 691 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 459 through 461 Processing sheet with id=AA7, first strand: chain 'B' and resid 712 through 714 removed outlier: 7.029A pdb=" N LEU B 713 " --> pdb=" O HIS B 737 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 419 through 420 removed outlier: 6.080A pdb=" N LEU F 426 " --> pdb=" O SER F 448 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LYS F 450 " --> pdb=" O LEU F 426 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N LEU F 428 " --> pdb=" O LYS F 450 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLU F 452 " --> pdb=" O LEU F 428 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU F 430 " --> pdb=" O GLU F 452 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU F 449 " --> pdb=" O CYS F 473 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N HIS F 475 " --> pdb=" O LEU F 449 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU F 451 " --> pdb=" O HIS F 475 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU F 472 " --> pdb=" O SER F 497 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N LYS F 499 " --> pdb=" O LEU F 472 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU F 474 " --> pdb=" O LYS F 499 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N MET F 570 " --> pdb=" O GLU F 595 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL F 597 " --> pdb=" O MET F 570 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N VAL F 572 " --> pdb=" O VAL F 597 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU F 617 " --> pdb=" O LYS F 643 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS F 735 " --> pdb=" O PHE F 711 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP F 758 " --> pdb=" O LEU F 734 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LEU F 757 " --> pdb=" O VAL F 783 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 457 through 459 removed outlier: 5.735A pdb=" N VAL F 457 " --> pdb=" O LYS F 480 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 238 hydrogen bonds defined for protein. 504 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.71 Time building geometry restraints manager: 4.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3172 1.34 - 1.46: 1052 1.46 - 1.57: 5803 1.57 - 1.69: 0 1.69 - 1.81: 44 Bond restraints: 10071 Sorted by residual: bond pdb=" N ASP F 540 " pdb=" CA ASP F 540 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.23e-02 6.61e+03 5.56e+00 bond pdb=" N ASN F 456 " pdb=" CA ASN F 456 " ideal model delta sigma weight residual 1.457 1.480 -0.022 1.29e-02 6.01e+03 3.03e+00 bond pdb=" CB TRP B 411 " pdb=" CG TRP B 411 " ideal model delta sigma weight residual 1.498 1.538 -0.040 3.10e-02 1.04e+03 1.70e+00 bond pdb=" CB PRO F 507 " pdb=" CG PRO F 507 " ideal model delta sigma weight residual 1.492 1.556 -0.064 5.00e-02 4.00e+02 1.65e+00 bond pdb=" C PRO A 607 " pdb=" O PRO A 607 " ideal model delta sigma weight residual 1.235 1.219 0.016 1.30e-02 5.92e+03 1.52e+00 ... (remaining 10066 not shown) Histogram of bond angle deviations from ideal: 98.95 - 106.07: 229 106.07 - 113.19: 5743 113.19 - 120.31: 3616 120.31 - 127.43: 3958 127.43 - 134.55: 96 Bond angle restraints: 13642 Sorted by residual: angle pdb=" CA LYS F 555 " pdb=" CB LYS F 555 " pdb=" CG LYS F 555 " ideal model delta sigma weight residual 114.10 122.88 -8.78 2.00e+00 2.50e-01 1.93e+01 angle pdb=" N ILE F 713 " pdb=" CA ILE F 713 " pdb=" C ILE F 713 " ideal model delta sigma weight residual 112.17 108.09 4.08 9.50e-01 1.11e+00 1.85e+01 angle pdb=" CA VAL B 715 " pdb=" CB VAL B 715 " pdb=" CG1 VAL B 715 " ideal model delta sigma weight residual 110.40 116.85 -6.45 1.70e+00 3.46e-01 1.44e+01 angle pdb=" C SER B 553 " pdb=" N ASN B 554 " pdb=" CA ASN B 554 " ideal model delta sigma weight residual 121.54 128.42 -6.88 1.91e+00 2.74e-01 1.30e+01 angle pdb=" CA MET F 581 " pdb=" CB MET F 581 " pdb=" CG MET F 581 " ideal model delta sigma weight residual 114.10 121.28 -7.18 2.00e+00 2.50e-01 1.29e+01 ... (remaining 13637 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 5469 17.83 - 35.65: 595 35.65 - 53.48: 157 53.48 - 71.30: 24 71.30 - 89.13: 5 Dihedral angle restraints: 6250 sinusoidal: 2646 harmonic: 3604 Sorted by residual: dihedral pdb=" CA ASP B 703 " pdb=" C ASP B 703 " pdb=" N ILE B 704 " pdb=" CA ILE B 704 " ideal model delta harmonic sigma weight residual 180.00 159.66 20.34 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA PRO B 747 " pdb=" C PRO B 747 " pdb=" N SER B 748 " pdb=" CA SER B 748 " ideal model delta harmonic sigma weight residual -180.00 -160.82 -19.18 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA GLN B 758 " pdb=" C GLN B 758 " pdb=" N ILE B 759 " pdb=" CA ILE B 759 " ideal model delta harmonic sigma weight residual 180.00 161.93 18.07 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 6247 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1325 0.056 - 0.111: 267 0.111 - 0.167: 34 0.167 - 0.222: 5 0.222 - 0.278: 2 Chirality restraints: 1633 Sorted by residual: chirality pdb=" CB ILE B 677 " pdb=" CA ILE B 677 " pdb=" CG1 ILE B 677 " pdb=" CG2 ILE B 677 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CB ILE B 456 " pdb=" CA ILE B 456 " pdb=" CG1 ILE B 456 " pdb=" CG2 ILE B 456 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA ASN F 456 " pdb=" N ASN F 456 " pdb=" C ASN F 456 " pdb=" CB ASN F 456 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.98e-01 ... (remaining 1630 not shown) Planarity restraints: 1715 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 795 " 0.047 5.00e-02 4.00e+02 7.16e-02 8.20e+00 pdb=" N PRO A 796 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 796 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 796 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 438 " -0.040 5.00e-02 4.00e+02 6.03e-02 5.81e+00 pdb=" N PRO B 439 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 439 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 439 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 475 " -0.009 2.00e-02 2.50e+03 1.45e-02 5.27e+00 pdb=" CG TRP A 475 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP A 475 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP A 475 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 475 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP A 475 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 475 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 475 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 475 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP A 475 " 0.004 2.00e-02 2.50e+03 ... (remaining 1712 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2095 2.79 - 3.31: 9310 3.31 - 3.84: 17119 3.84 - 4.37: 21342 4.37 - 4.90: 33726 Nonbonded interactions: 83592 Sorted by model distance: nonbonded pdb=" O ILE F 556 " pdb=" ND2 ASN F 584 " model vdw 2.257 2.520 nonbonded pdb=" O TRP A 411 " pdb=" OG1 THR A 441 " model vdw 2.272 2.440 nonbonded pdb=" O GLN A 560 " pdb=" OG1 THR A 563 " model vdw 2.278 2.440 nonbonded pdb=" O GLU F 790 " pdb=" NH2 ARG F 797 " model vdw 2.309 2.520 nonbonded pdb=" NH1 ARG B 749 " pdb=" OE1 GLU B 752 " model vdw 2.313 2.520 ... (remaining 83587 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 4.840 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: 14.960 Check model and map are aligned: 0.150 Set scattering table: 0.120 Process input model: 28.850 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 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 : 0.003 0.064 10071 Z= 0.218 Angle : 0.766 9.779 13642 Z= 0.399 Chirality : 0.046 0.278 1633 Planarity : 0.006 0.072 1715 Dihedral : 15.743 89.126 3886 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.35 % Allowed : 21.09 % Favored : 78.56 % 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: -3.01 (0.23), residues: 1212 helix: -2.86 (0.22), residues: 369 sheet: -2.58 (0.37), residues: 182 loop : -1.18 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP A 475 HIS 0.009 0.001 HIS B 499 PHE 0.029 0.002 PHE F 609 TYR 0.016 0.001 TYR F 756 ARG 0.006 0.000 ARG B 749 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 377 time to evaluate : 1.265 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 outliers start: 4 outliers final: 0 residues processed: 378 average time/residue: 0.2601 time to fit residues: 130.3713 Evaluate side-chains 205 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 1.220 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.2388 > 50: distance: 49 - 164: 28.934 distance: 52 - 178: 30.115 distance: 65 - 181: 21.260 distance: 92 - 112: 36.155 distance: 95 - 101: 34.420 distance: 101 - 102: 56.650 distance: 102 - 103: 40.583 distance: 102 - 105: 21.166 distance: 103 - 104: 51.541 distance: 103 - 112: 39.567 distance: 105 - 106: 32.965 distance: 106 - 107: 17.244 distance: 106 - 108: 40.979 distance: 107 - 109: 26.279 distance: 108 - 110: 50.010 distance: 109 - 111: 43.405 distance: 110 - 111: 27.430 distance: 112 - 113: 57.560 distance: 113 - 114: 23.524 distance: 113 - 116: 13.890 distance: 114 - 115: 53.434 distance: 114 - 118: 42.972 distance: 116 - 117: 28.070 distance: 118 - 119: 46.126 distance: 119 - 120: 42.411 distance: 119 - 122: 38.465 distance: 120 - 121: 20.052 distance: 120 - 126: 57.368 distance: 122 - 123: 54.783 distance: 123 - 124: 11.351 distance: 123 - 125: 51.868 distance: 126 - 127: 60.774 distance: 127 - 128: 32.271 distance: 127 - 130: 41.196 distance: 128 - 129: 7.125 distance: 128 - 136: 44.994 distance: 130 - 131: 28.654 distance: 131 - 132: 40.474 distance: 131 - 133: 39.400 distance: 132 - 134: 11.611 distance: 133 - 135: 38.319 distance: 134 - 135: 28.484 distance: 136 - 137: 32.215 distance: 137 - 138: 48.007 distance: 137 - 140: 24.482 distance: 138 - 139: 30.048 distance: 138 - 144: 55.899 distance: 140 - 141: 54.039 distance: 141 - 142: 29.663 distance: 141 - 143: 5.462 distance: 144 - 145: 24.501 distance: 145 - 146: 10.626 distance: 145 - 148: 21.416 distance: 146 - 147: 43.079 distance: 146 - 152: 10.195 distance: 148 - 149: 17.945 distance: 152 - 153: 29.412 distance: 153 - 154: 39.857 distance: 153 - 156: 3.659 distance: 154 - 155: 38.411 distance: 154 - 161: 56.018 distance: 156 - 157: 38.372 distance: 157 - 158: 4.862 distance: 158 - 159: 3.234 distance: 158 - 160: 36.155 distance: 161 - 162: 32.457 distance: 162 - 163: 6.740 distance: 162 - 165: 52.071 distance: 163 - 164: 60.453 distance: 163 - 170: 60.807 distance: 165 - 166: 42.712 distance: 166 - 167: 34.735 distance: 167 - 168: 43.963 distance: 167 - 169: 42.026 distance: 170 - 171: 37.056 distance: 170 - 258: 30.395 distance: 171 - 172: 14.988 distance: 171 - 174: 6.752 distance: 172 - 173: 8.254 distance: 172 - 178: 51.870 distance: 173 - 268: 35.324 distance: 174 - 175: 43.537 distance: 174 - 176: 43.304 distance: 175 - 177: 14.531 distance: 178 - 179: 43.112 distance: 179 - 180: 16.535 distance: 179 - 182: 17.228 distance: 180 - 181: 9.113 distance: 180 - 186: 22.766 distance: 182 - 183: 49.764 distance: 183 - 184: 12.131 distance: 183 - 185: 41.280