Starting phenix.real_space_refine on Tue Feb 13 21:32:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eij_28158/02_2024/8eij_28158_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eij_28158/02_2024/8eij_28158.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eij_28158/02_2024/8eij_28158.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eij_28158/02_2024/8eij_28158.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eij_28158/02_2024/8eij_28158_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eij_28158/02_2024/8eij_28158_updated.pdb" } resolution = 3.34 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= 0.023 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 Zn 6 6.06 5 S 67 5.16 5 C 4981 2.51 5 N 1358 2.21 5 O 1401 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 697": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7813 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3290 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASN:plan1': 3, 'ARG:plan': 7, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 83 Chain: "B" Number of atoms: 3374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3374 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 413} Chain breaks: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 9, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 58 Chain: "D" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1091 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 141} Chain breaks: 4 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 79 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 135 SG CYS A 435 26.424 27.415 32.413 1.00178.98 S ATOM 155 SG CYS A 438 25.215 31.209 31.853 1.00187.35 S ATOM 285 SG CYS A 455 28.546 30.007 30.785 1.00177.92 S ATOM 307 SG CYS A 458 27.548 30.039 34.660 1.00170.71 S ATOM 486 SG CYS A 478 22.876 28.790 44.559 1.00175.25 S ATOM 506 SG CYS A 481 22.882 30.984 41.410 1.00178.78 S ATOM 634 SG CYS A 500 20.007 31.376 43.847 1.00186.48 S ATOM 656 SG CYS A 503 20.370 28.301 41.694 1.00188.66 S ATOM 562 SG CYS A 490 22.405 22.242 56.090 1.00184.01 S ATOM 594 SG CYS A 495 26.004 21.481 55.050 1.00179.16 S ATOM 802 SG CYS A 524 23.099 20.593 52.676 1.00185.18 S ATOM 828 SG CYS A 527 23.780 18.623 55.673 1.00186.73 S ATOM 3452 SG CYS B 435 62.529 63.225 118.249 1.00149.11 S ATOM 3472 SG CYS B 438 60.666 66.486 118.207 1.00153.62 S ATOM 3599 SG CYS B 455 58.974 63.401 119.750 1.00139.43 S ATOM 3621 SG CYS B 458 59.431 63.631 116.053 1.00135.76 S ATOM 3803 SG CYS B 478 63.011 64.741 105.525 1.00146.43 S ATOM 3823 SG CYS B 481 61.056 66.889 107.659 1.00161.00 S ATOM 3961 SG CYS B 500 63.713 68.585 105.341 1.00161.15 S ATOM 3983 SG CYS B 503 64.726 66.837 108.382 1.00155.41 S ATOM 3888 SG CYS B 490 71.769 59.476 96.562 1.00153.98 S ATOM 3921 SG CYS B 495 70.391 56.345 98.327 1.00159.43 S ATOM 4122 SG CYS B 524 72.350 58.893 100.342 1.00153.71 S ATOM 4148 SG CYS B 527 74.107 56.682 98.006 1.00159.17 S Time building chain proxies: 4.70, per 1000 atoms: 0.60 Number of scatterers: 7813 At special positions: 0 Unit cell: (91.3, 84.7, 135.3, 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) Zn 6 29.99 S 67 16.00 O 1401 8.00 N 1358 7.00 C 4981 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: 2.98 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 902 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 435 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 455 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 458 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 438 " pdb=" ZN A 903 " pdb="ZN ZN A 903 " - pdb=" SG CYS A 503 " pdb="ZN ZN A 903 " - pdb=" SG CYS A 481 " pdb="ZN ZN A 903 " - pdb=" SG CYS A 500 " pdb="ZN ZN A 903 " - pdb=" SG CYS A 478 " pdb=" ZN A 904 " pdb="ZN ZN A 904 " - pdb=" SG CYS A 527 " pdb="ZN ZN A 904 " - pdb=" SG CYS A 495 " pdb="ZN ZN A 904 " - pdb=" SG CYS A 524 " pdb="ZN ZN A 904 " - pdb=" SG CYS A 490 " pdb=" ZN B 902 " pdb="ZN ZN B 902 " - pdb=" SG CYS B 458 " pdb="ZN ZN B 902 " - pdb=" SG CYS B 438 " pdb="ZN ZN B 902 " - pdb=" SG CYS B 455 " pdb="ZN ZN B 902 " - pdb=" SG CYS B 435 " pdb=" ZN B 903 " pdb="ZN ZN B 903 " - pdb=" SG CYS B 481 " pdb="ZN ZN B 903 " - pdb=" SG CYS B 503 " pdb="ZN ZN B 903 " - pdb=" SG CYS B 478 " pdb="ZN ZN B 903 " - pdb=" SG CYS B 500 " pdb=" ZN B 904 " pdb="ZN ZN B 904 " - pdb=" SG CYS B 524 " pdb="ZN ZN B 904 " - pdb=" SG CYS B 527 " pdb="ZN ZN B 904 " - pdb=" SG CYS B 495 " pdb="ZN ZN B 904 " - pdb=" SG CYS B 490 " Number of angles added : 36 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1882 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 41 helices and 8 sheets defined 31.4% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.15 Creating SS restraints... Processing helix chain 'A' and resid 417 through 426 Processing helix chain 'A' and resid 431 through 433 No H-bonds generated for 'chain 'A' and resid 431 through 433' Processing helix chain 'A' and resid 456 through 467 removed outlier: 3.619A pdb=" N ASP A 460 " --> pdb=" O GLN A 456 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ARG A 461 " --> pdb=" O THR A 457 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE A 462 " --> pdb=" O CYS A 458 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE A 466 " --> pdb=" O PHE A 462 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N TYR A 467 " --> pdb=" O LEU A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 507 removed outlier: 4.486A pdb=" N GLU A 505 " --> pdb=" O VAL A 501 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL A 506 " --> pdb=" O GLU A 502 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 507 " --> pdb=" O CYS A 503 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 501 through 507' Processing helix chain 'A' and resid 513 through 518 removed outlier: 3.927A pdb=" N LYS A 517 " --> pdb=" O ALA A 513 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU A 518 " --> pdb=" O ALA A 514 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 513 through 518' Processing helix chain 'A' and resid 542 through 551 removed outlier: 4.375A pdb=" N GLN A 547 " --> pdb=" O ASN A 543 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA A 548 " --> pdb=" O VAL A 544 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE A 550 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 594 Processing helix chain 'A' and resid 608 through 616 removed outlier: 3.613A pdb=" N ALA A 612 " --> pdb=" O GLU A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 630 No H-bonds generated for 'chain 'A' and resid 628 through 630' Processing helix chain 'A' and resid 633 through 639 removed outlier: 4.356A pdb=" N GLU A 637 " --> pdb=" O LYS A 633 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU A 638 " --> pdb=" O LYS A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 682 removed outlier: 3.756A pdb=" N HIS A 677 " --> pdb=" O GLU A 674 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 678 " --> pdb=" O PHE A 675 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR A 681 " --> pdb=" O LEU A 678 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER A 682 " --> pdb=" O LEU A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 707 No H-bonds generated for 'chain 'A' and resid 704 through 707' Processing helix chain 'A' and resid 709 through 713 Processing helix chain 'A' and resid 723 through 725 No H-bonds generated for 'chain 'A' and resid 723 through 725' Processing helix chain 'A' and resid 756 through 758 No H-bonds generated for 'chain 'A' and resid 756 through 758' Processing helix chain 'A' and resid 802 through 808 removed outlier: 4.282A pdb=" N GLU A 806 " --> pdb=" O CYS A 802 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ARG A 807 " --> pdb=" O THR A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 828 removed outlier: 3.738A pdb=" N LYS A 828 " --> pdb=" O GLY A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 848 removed outlier: 3.540A pdb=" N HIS A 841 " --> pdb=" O PRO A 837 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A 842 " --> pdb=" O VAL A 838 " (cutoff:3.500A) Proline residue: A 845 - end of helix removed outlier: 5.497A pdb=" N ASP A 848 " --> pdb=" O ALA A 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 425 Processing helix chain 'B' and resid 431 through 433 No H-bonds generated for 'chain 'B' and resid 431 through 433' Processing helix chain 'B' and resid 456 through 459 No H-bonds generated for 'chain 'B' and resid 456 through 459' Processing helix chain 'B' and resid 462 through 465 No H-bonds generated for 'chain 'B' and resid 462 through 465' Processing helix chain 'B' and resid 502 through 508 removed outlier: 4.577A pdb=" N LEU B 507 " --> pdb=" O CYS B 503 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL B 508 " --> pdb=" O LEU B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 518 Processing helix chain 'B' and resid 542 through 550 removed outlier: 3.654A pdb=" N ALA B 548 " --> pdb=" O VAL B 544 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE B 550 " --> pdb=" O LEU B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 594 Processing helix chain 'B' and resid 608 through 616 Processing helix chain 'B' and resid 628 through 630 No H-bonds generated for 'chain 'B' and resid 628 through 630' Processing helix chain 'B' and resid 633 through 639 Processing helix chain 'B' and resid 667 through 682 removed outlier: 3.682A pdb=" N TYR B 681 " --> pdb=" O LEU B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 714 Processing helix chain 'B' and resid 723 through 725 No H-bonds generated for 'chain 'B' and resid 723 through 725' Processing helix chain 'B' and resid 756 through 759 Processing helix chain 'B' and resid 802 through 808 removed outlier: 3.588A pdb=" N ARG B 807 " --> pdb=" O THR B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 823 through 831 Processing helix chain 'B' and resid 836 through 848 Proline residue: B 845 - end of helix removed outlier: 5.257A pdb=" N ASP B 848 " --> pdb=" O ALA B 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 593 Processing helix chain 'D' and resid 633 through 639 Processing helix chain 'D' and resid 668 through 682 removed outlier: 4.140A pdb=" N GLU D 674 " --> pdb=" O ARG D 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 704 through 714 Processing helix chain 'D' and resid 836 through 847 Proline residue: D 845 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 487 through 489 Processing sheet with id= B, first strand: chain 'A' and resid 695 through 699 removed outlier: 3.841A pdb=" N PHE A 696 " --> pdb=" O TRP A 736 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG A 733 " --> pdb=" O ILE A 721 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE A 721 " --> pdb=" O ARG A 733 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL A 719 " --> pdb=" O PHE A 735 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 764 through 766 removed outlier: 3.813A pdb=" N VAL A 791 " --> pdb=" O ASP A 798 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 644 through 646 removed outlier: 4.108A pdb=" N LEU B 644 " --> pdb=" O ARG B 576 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY B 599 " --> pdb=" O ILE B 575 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N VAL B 577 " --> pdb=" O GLY B 599 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N TYR B 601 " --> pdb=" O VAL B 577 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N SER B 579 " --> pdb=" O TYR B 601 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ALA B 603 " --> pdb=" O SER B 579 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LYS B 623 " --> pdb=" O ALA B 603 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 695 through 699 removed outlier: 4.073A pdb=" N PHE B 696 " --> pdb=" O TRP B 736 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN B 698 " --> pdb=" O TYR B 734 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 791 through 793 removed outlier: 3.583A pdb=" N VAL B 791 " --> pdb=" O ASP B 798 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 697 through 699 removed outlier: 3.697A pdb=" N ILE D 721 " --> pdb=" O ARG D 733 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 575 through 577 removed outlier: 7.693A pdb=" N VAL D 577 " --> pdb=" O GLY D 599 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N TYR D 601 " --> pdb=" O VAL D 577 " (cutoff:3.500A) 151 hydrogen bonds defined for protein. 375 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: 1.78 Time building geometry restraints manager: 3.22 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: 2554 1.34 - 1.46: 1868 1.46 - 1.58: 3484 1.58 - 1.70: 0 1.70 - 1.82: 89 Bond restraints: 7995 Sorted by residual: bond pdb=" C2 SAH A 901 " pdb=" N3 SAH A 901 " ideal model delta sigma weight residual 1.322 1.381 -0.059 2.00e-02 2.50e+03 8.62e+00 bond pdb=" C2 SAH B 901 " pdb=" N3 SAH B 901 " ideal model delta sigma weight residual 1.322 1.380 -0.058 2.00e-02 2.50e+03 8.34e+00 bond pdb=" CA HIS D 677 " pdb=" C HIS D 677 " ideal model delta sigma weight residual 1.524 1.489 0.034 1.27e-02 6.20e+03 7.30e+00 bond pdb=" C8 SAH A 901 " pdb=" N7 SAH A 901 " ideal model delta sigma weight residual 1.299 1.353 -0.054 2.00e-02 2.50e+03 7.18e+00 bond pdb=" C8 SAH B 901 " pdb=" N7 SAH B 901 " ideal model delta sigma weight residual 1.299 1.352 -0.053 2.00e-02 2.50e+03 7.14e+00 ... (remaining 7990 not shown) Histogram of bond angle deviations from ideal: 89.83 - 98.66: 2 98.66 - 107.49: 321 107.49 - 116.32: 4932 116.32 - 125.15: 5450 125.15 - 133.98: 147 Bond angle restraints: 10852 Sorted by residual: angle pdb=" CA GLU B 715 " pdb=" CB GLU B 715 " pdb=" CG GLU B 715 " ideal model delta sigma weight residual 114.10 124.02 -9.92 2.00e+00 2.50e-01 2.46e+01 angle pdb=" N ASP D 706 " pdb=" CA ASP D 706 " pdb=" C ASP D 706 " ideal model delta sigma weight residual 111.07 105.97 5.10 1.07e+00 8.73e-01 2.28e+01 angle pdb=" C ASN B 442 " pdb=" N PRO B 443 " pdb=" CA PRO B 443 " ideal model delta sigma weight residual 119.84 125.15 -5.31 1.25e+00 6.40e-01 1.80e+01 angle pdb=" CG SAH B 901 " pdb=" SD SAH B 901 " pdb=" C5' SAH B 901 " ideal model delta sigma weight residual 101.77 89.83 11.94 3.00e+00 1.11e-01 1.58e+01 angle pdb=" C GLU B 715 " pdb=" CA GLU B 715 " pdb=" CB GLU B 715 " ideal model delta sigma weight residual 112.27 119.13 -6.86 1.75e+00 3.27e-01 1.54e+01 ... (remaining 10847 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 4104 17.94 - 35.87: 486 35.87 - 53.80: 95 53.80 - 71.74: 9 71.74 - 89.67: 4 Dihedral angle restraints: 4698 sinusoidal: 1771 harmonic: 2927 Sorted by residual: dihedral pdb=" CA ASN D 626 " pdb=" C ASN D 626 " pdb=" N ASP D 627 " pdb=" CA ASP D 627 " ideal model delta harmonic sigma weight residual 180.00 160.12 19.88 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" C GLU B 715 " pdb=" N GLU B 715 " pdb=" CA GLU B 715 " pdb=" CB GLU B 715 " ideal model delta harmonic sigma weight residual -122.60 -131.92 9.32 0 2.50e+00 1.60e-01 1.39e+01 dihedral pdb=" CA GLU A 464 " pdb=" C GLU A 464 " pdb=" N LEU A 465 " pdb=" CA LEU A 465 " ideal model delta harmonic sigma weight residual 180.00 -161.87 -18.13 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 4695 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1041 0.063 - 0.126: 137 0.126 - 0.188: 3 0.188 - 0.251: 1 0.251 - 0.314: 1 Chirality restraints: 1183 Sorted by residual: chirality pdb=" CA ASN B 442 " pdb=" N ASN B 442 " pdb=" C ASN B 442 " pdb=" CB ASN B 442 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CA GLU B 715 " pdb=" N GLU B 715 " pdb=" C GLU B 715 " pdb=" CB GLU B 715 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.23e-01 chirality pdb=" CA ASP D 706 " pdb=" N ASP D 706 " pdb=" C ASP D 706 " pdb=" CB ASP D 706 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.12e-01 ... (remaining 1180 not shown) Planarity restraints: 1407 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 441 " 0.014 2.00e-02 2.50e+03 2.83e-02 8.03e+00 pdb=" C LYS B 441 " -0.049 2.00e-02 2.50e+03 pdb=" O LYS B 441 " 0.018 2.00e-02 2.50e+03 pdb=" N ASN B 442 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY D 640 " 0.028 5.00e-02 4.00e+02 4.26e-02 2.91e+00 pdb=" N PRO D 641 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO D 641 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 641 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 705 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C GLY D 705 " -0.029 2.00e-02 2.50e+03 pdb=" O GLY D 705 " 0.011 2.00e-02 2.50e+03 pdb=" N ASP D 706 " 0.010 2.00e-02 2.50e+03 ... (remaining 1404 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 336 2.72 - 3.26: 7739 3.26 - 3.81: 11626 3.81 - 4.35: 14229 4.35 - 4.90: 23756 Nonbonded interactions: 57686 Sorted by model distance: nonbonded pdb=" O ASN B 738 " pdb=" ND2 ASN B 738 " model vdw 2.172 2.520 nonbonded pdb=" OG SER B 491 " pdb=" O TRP B 522 " model vdw 2.227 2.440 nonbonded pdb=" OD1 ASP A 709 " pdb=" NH2 ARG A 712 " model vdw 2.260 2.520 nonbonded pdb=" O SER D 649 " pdb=" OG SER D 649 " model vdw 2.297 2.440 nonbonded pdb=" OE2 GLU B 605 " pdb=" O2' SAH B 901 " model vdw 2.300 2.440 ... (remaining 57681 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' and (resid 415 through 441 or (resid 442 and (name N or name CA or na \ me C or name O or name CB )) or resid 443 through 504 or (resid 505 and (name N \ or name CA or name C or name O or name CB )) or resid 506 through 509 or (resid \ 510 and (name N or name CA or name C or name O or name CB )) or resid 511 throug \ h 518 or (resid 519 and (name N or name CA or name C or name O or name CB )) or \ resid 520 through 556 or (resid 557 and (name N or name CA or name C or name O o \ r name CB )) or resid 558 or (resid 559 through 560 and (name N or name CA or na \ me C or name O or name CB )) or resid 561 through 633 or (resid 634 and (name N \ or name CA or name C or name O or name CB )) or resid 635 through 724 or (resid \ 725 and (name N or name CA or name C or name O or name CB )) or resid 726 throug \ h 773 or resid 777 or resid 788 through 796 or (resid 797 and (name N or name CA \ or name C or name O or name CB )) or resid 798 through 853 or resid 901 or resi \ d 902 through 904)) selection = (chain 'B' and ((resid 415 and (name N or name CA or name C or name O or name CB \ )) or resid 416 through 426 or (resid 427 through 430 and (name N or name CA or \ name C or name O or name CB )) or resid 431 through 432 or (resid 433 and (name \ N or name CA or name C or name O or name CB )) or resid 434 through 471 or (res \ id 472 and (name N or name CA or name C or name O or name CB )) or resid 473 thr \ ough 484 or (resid 485 through 487 and (name N or name CA or name C or name O or \ name CB )) or resid 488 through 493 or (resid 494 and (name N or name CA or nam \ e C or name O or name CB )) or resid 495 through 517 or (resid 518 through 519 a \ nd (name N or name CA or name C or name O or name CB )) or resid 520 through 529 \ or (resid 530 through 531 and (name N or name CA or name C or name O or name CB \ )) or resid 532 through 536 or (resid 537 through 538 and (name N or name CA or \ name C or name O or name CB )) or resid 539 or (resid 540 through 541 and (name \ N or name CA or name C or name O or name CB )) or resid 542 through 572 or (res \ id 573 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name NE )) or resid 574 through 651 or (resid 652 and (name N or name CA o \ r name C or name O or name CB )) or resid 653 through 656 or (resid 657 through \ 658 and (name N or name CA or name C or name O or name CB )) or resid 659 throug \ h 660 or (resid 661 through 662 and (name N or name CA or name C or name O or na \ me CB )) or resid 663 through 665 or (resid 666 and (name N or name CA or name C \ or name O or name CB )) or resid 667 through 702 or (resid 703 and (name N or n \ ame CA or name C or name O or name CB )) or resid 704 through 766 or (resid 767 \ and (name N or name CA or name C or name O or name CB or name CG or name CD )) o \ r resid 768 through 773 or resid 785 or resid 788 through 795 or (resid 796 thro \ ugh 797 and (name N or name CA or name C or name O or name CB )) or resid 798 th \ rough 852 or (resid 853 and (name N or name CA or name C or name O or name CB )) \ or resid 901 or resid 902 through 904)) } 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 individual isotropic 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: 7.230 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: 0.000 Extract box with map and model: 16.580 Check model and map are aligned: 1.580 Set scattering table: 0.000 Process input model: 24.280 Find NCS groups from input model: 0.460 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 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 0.062 7995 Z= 0.224 Angle : 0.731 11.942 10852 Z= 0.385 Chirality : 0.042 0.314 1183 Planarity : 0.004 0.043 1407 Dihedral : 15.166 89.671 2816 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.38 % Allowed : 13.17 % Favored : 86.45 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 10.20 % 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: -1.92 (0.27), residues: 997 helix: -0.43 (0.34), residues: 253 sheet: -2.92 (0.52), residues: 88 loop : -1.42 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 639 HIS 0.003 0.001 HIS D 677 PHE 0.018 0.001 PHE D 672 TYR 0.008 0.001 TYR B 588 ARG 0.004 0.000 ARG B 440 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 94 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 497 ARG cc_start: 0.7028 (mtt90) cc_final: 0.6314 (mtm-85) REVERT: B 754 LEU cc_start: 0.7510 (tp) cc_final: 0.6982 (mp) REVERT: B 772 GLN cc_start: 0.7067 (OUTLIER) cc_final: 0.6817 (pp30) REVERT: D 842 LEU cc_start: 0.8504 (mm) cc_final: 0.8139 (mm) outliers start: 3 outliers final: 1 residues processed: 94 average time/residue: 0.2369 time to fit residues: 29.4521 Evaluate side-chains 85 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 83 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 497 ARG Chi-restraints excluded: chain B residue 772 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 40 optimal weight: 0.4980 chunk 79 optimal weight: 0.0970 chunk 30 optimal weight: 0.2980 chunk 48 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 HIS ** A 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 772 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6722 moved from start: 0.0784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7995 Z= 0.167 Angle : 0.537 5.903 10852 Z= 0.275 Chirality : 0.040 0.135 1183 Planarity : 0.004 0.039 1407 Dihedral : 5.398 59.902 1117 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 1.66 % Allowed : 16.88 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % 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: -1.68 (0.27), residues: 997 helix: -0.09 (0.34), residues: 261 sheet: -2.96 (0.50), residues: 97 loop : -1.28 (0.26), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 694 HIS 0.003 0.001 HIS D 677 PHE 0.016 0.001 PHE D 675 TYR 0.008 0.001 TYR D 849 ARG 0.003 0.000 ARG D 629 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 92 time to evaluate : 0.939 Fit side-chains revert: symmetry clash REVERT: A 542 TRP cc_start: 0.6923 (p-90) cc_final: 0.6710 (p-90) REVERT: B 497 ARG cc_start: 0.6956 (mtt90) cc_final: 0.6744 (mtm110) REVERT: B 754 LEU cc_start: 0.7544 (tp) cc_final: 0.7014 (mp) REVERT: B 772 GLN cc_start: 0.7075 (pp30) cc_final: 0.6837 (pp30) REVERT: D 842 LEU cc_start: 0.8430 (mm) cc_final: 0.8026 (mm) outliers start: 13 outliers final: 8 residues processed: 102 average time/residue: 0.2260 time to fit residues: 30.6671 Evaluate side-chains 90 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 82 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 HIS Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain B residue 526 MET Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain D residue 668 THR Chi-restraints excluded: chain D residue 711 SER Chi-restraints excluded: chain D residue 722 ASP Chi-restraints excluded: chain D residue 848 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 91 optimal weight: 0.8980 chunk 99 optimal weight: 0.0470 chunk 81 optimal weight: 0.9990 chunk 31 optimal weight: 0.0980 chunk 73 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 738 ASN D 680 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7995 Z= 0.165 Angle : 0.523 6.232 10852 Z= 0.267 Chirality : 0.040 0.136 1183 Planarity : 0.004 0.037 1407 Dihedral : 4.902 58.248 1110 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.30 % Allowed : 17.90 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % 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: -1.60 (0.28), residues: 997 helix: 0.02 (0.34), residues: 261 sheet: -2.87 (0.51), residues: 98 loop : -1.24 (0.26), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 694 HIS 0.005 0.001 HIS A 447 PHE 0.018 0.001 PHE A 735 TYR 0.007 0.001 TYR D 849 ARG 0.003 0.000 ARG D 629 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 85 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: A 542 TRP cc_start: 0.6849 (p-90) cc_final: 0.6648 (p-90) REVERT: A 674 GLU cc_start: 0.7730 (mp0) cc_final: 0.7476 (mp0) REVERT: A 772 GLN cc_start: 0.7134 (pp30) cc_final: 0.6866 (pp30) REVERT: B 497 ARG cc_start: 0.6954 (mtt90) cc_final: 0.6732 (mtm110) REVERT: B 531 ARG cc_start: 0.6121 (OUTLIER) cc_final: 0.5862 (mmp-170) REVERT: B 754 LEU cc_start: 0.7473 (tp) cc_final: 0.6992 (mp) REVERT: D 624 TYR cc_start: 0.6296 (OUTLIER) cc_final: 0.5565 (m-80) REVERT: D 695 MET cc_start: 0.8524 (tpt) cc_final: 0.8303 (tpt) REVERT: D 702 MET cc_start: 0.2584 (OUTLIER) cc_final: 0.1459 (ppp) REVERT: D 842 LEU cc_start: 0.8476 (mm) cc_final: 0.8053 (mm) outliers start: 18 outliers final: 8 residues processed: 97 average time/residue: 0.2402 time to fit residues: 32.0138 Evaluate side-chains 93 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 82 time to evaluate : 2.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 497 ARG Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 481 CYS Chi-restraints excluded: chain B residue 531 ARG Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain D residue 624 TYR Chi-restraints excluded: chain D residue 668 THR Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain D residue 848 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 0.5980 chunk 47 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 92 optimal weight: 8.9990 chunk 97 optimal weight: 0.1980 chunk 48 optimal weight: 0.1980 chunk 87 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 HIS ** A 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 772 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7995 Z= 0.162 Angle : 0.513 6.447 10852 Z= 0.260 Chirality : 0.040 0.165 1183 Planarity : 0.003 0.036 1407 Dihedral : 4.833 55.646 1110 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 3.20 % Allowed : 19.05 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % 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 (0.28), residues: 997 helix: 0.06 (0.34), residues: 264 sheet: -2.75 (0.53), residues: 97 loop : -1.18 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 694 HIS 0.002 0.001 HIS A 677 PHE 0.017 0.001 PHE A 735 TYR 0.008 0.001 TYR B 525 ARG 0.003 0.000 ARG B 576 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 84 time to evaluate : 0.872 Fit side-chains revert: symmetry clash REVERT: A 542 TRP cc_start: 0.6860 (p-90) cc_final: 0.6656 (p-90) REVERT: A 772 GLN cc_start: 0.7383 (pp30) cc_final: 0.7094 (pp30) REVERT: A 830 LEU cc_start: 0.7006 (OUTLIER) cc_final: 0.6790 (mt) REVERT: B 497 ARG cc_start: 0.6975 (mtt90) cc_final: 0.6744 (mtm110) REVERT: B 754 LEU cc_start: 0.7372 (tp) cc_final: 0.6906 (mp) REVERT: D 624 TYR cc_start: 0.6264 (OUTLIER) cc_final: 0.5444 (m-80) REVERT: D 695 MET cc_start: 0.8513 (tpt) cc_final: 0.8269 (tpt) REVERT: D 702 MET cc_start: 0.2579 (OUTLIER) cc_final: 0.1433 (ppp) REVERT: D 842 LEU cc_start: 0.8483 (mm) cc_final: 0.8051 (mm) outliers start: 25 outliers final: 14 residues processed: 102 average time/residue: 0.2202 time to fit residues: 30.2039 Evaluate side-chains 95 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 78 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 HIS Chi-restraints excluded: chain A residue 497 ARG Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 651 CYS Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain D residue 624 TYR Chi-restraints excluded: chain D residue 635 ASN Chi-restraints excluded: chain D residue 668 THR Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain D residue 711 SER Chi-restraints excluded: chain D residue 848 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 72 optimal weight: 0.9980 chunk 40 optimal weight: 0.0370 chunk 83 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 49 optimal weight: 0.8980 chunk 87 optimal weight: 10.0000 chunk 24 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 overall best weight: 0.9060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 HIS ** A 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 738 ASN ** B 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7995 Z= 0.223 Angle : 0.546 5.943 10852 Z= 0.281 Chirality : 0.041 0.144 1183 Planarity : 0.004 0.036 1407 Dihedral : 5.005 51.528 1110 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 3.32 % Allowed : 19.82 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % 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: -1.59 (0.28), residues: 997 helix: 0.02 (0.34), residues: 263 sheet: -2.85 (0.53), residues: 97 loop : -1.24 (0.26), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 694 HIS 0.009 0.001 HIS A 447 PHE 0.017 0.001 PHE A 735 TYR 0.007 0.001 TYR A 676 ARG 0.003 0.000 ARG B 576 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 79 time to evaluate : 0.970 Fit side-chains revert: symmetry clash REVERT: A 542 TRP cc_start: 0.6884 (p-90) cc_final: 0.6683 (p-90) REVERT: A 830 LEU cc_start: 0.7103 (OUTLIER) cc_final: 0.6842 (mt) REVERT: D 624 TYR cc_start: 0.6377 (OUTLIER) cc_final: 0.5548 (m-80) REVERT: D 702 MET cc_start: 0.2543 (OUTLIER) cc_final: 0.1400 (ppp) REVERT: D 842 LEU cc_start: 0.8502 (mm) cc_final: 0.8073 (mm) outliers start: 26 outliers final: 17 residues processed: 97 average time/residue: 0.2315 time to fit residues: 30.3249 Evaluate side-chains 98 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 78 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 HIS Chi-restraints excluded: chain A residue 497 ARG Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 651 CYS Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 481 CYS Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain D residue 624 TYR Chi-restraints excluded: chain D residue 668 THR Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain D residue 711 SER Chi-restraints excluded: chain D residue 848 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 24 optimal weight: 0.0670 chunk 97 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 8 optimal weight: 0.2980 chunk 32 optimal weight: 0.8980 chunk 51 optimal weight: 0.1980 chunk 94 optimal weight: 1.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 HIS ** A 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7995 Z= 0.155 Angle : 0.510 6.464 10852 Z= 0.259 Chirality : 0.040 0.137 1183 Planarity : 0.003 0.035 1407 Dihedral : 4.837 52.380 1110 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.81 % Allowed : 21.61 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % 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: -1.47 (0.28), residues: 997 helix: 0.08 (0.34), residues: 265 sheet: -2.74 (0.54), residues: 97 loop : -1.16 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 694 HIS 0.009 0.001 HIS A 447 PHE 0.025 0.001 PHE D 675 TYR 0.005 0.001 TYR D 849 ARG 0.002 0.000 ARG B 576 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 82 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 715 GLU cc_start: 0.7291 (tm-30) cc_final: 0.6976 (tm-30) REVERT: B 754 LEU cc_start: 0.7388 (tp) cc_final: 0.6926 (mp) REVERT: B 835 SER cc_start: 0.8556 (OUTLIER) cc_final: 0.8286 (t) REVERT: D 624 TYR cc_start: 0.6318 (OUTLIER) cc_final: 0.5472 (m-80) REVERT: D 695 MET cc_start: 0.8537 (tpt) cc_final: 0.8270 (tpt) REVERT: D 702 MET cc_start: 0.2628 (OUTLIER) cc_final: 0.1469 (ppp) REVERT: D 842 LEU cc_start: 0.8509 (mm) cc_final: 0.8034 (mm) outliers start: 22 outliers final: 14 residues processed: 97 average time/residue: 0.2258 time to fit residues: 29.7309 Evaluate side-chains 95 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 78 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 HIS Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 651 CYS Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 481 CYS Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain D residue 624 TYR Chi-restraints excluded: chain D residue 668 THR Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain D residue 848 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.9980 chunk 55 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 820 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7995 Z= 0.221 Angle : 0.546 7.953 10852 Z= 0.278 Chirality : 0.041 0.172 1183 Planarity : 0.004 0.036 1407 Dihedral : 5.001 56.886 1110 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.81 % Allowed : 23.02 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % 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: -1.58 (0.28), residues: 997 helix: 0.03 (0.34), residues: 263 sheet: -2.78 (0.54), residues: 97 loop : -1.25 (0.26), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 694 HIS 0.006 0.001 HIS A 447 PHE 0.017 0.001 PHE D 675 TYR 0.013 0.001 TYR D 676 ARG 0.003 0.000 ARG B 576 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 82 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 526 MET cc_start: 0.8033 (mpp) cc_final: 0.7650 (mpp) REVERT: A 715 GLU cc_start: 0.7557 (tm-30) cc_final: 0.7211 (tm-30) REVERT: B 497 ARG cc_start: 0.7014 (mtm110) cc_final: 0.6811 (mtm110) REVERT: D 624 TYR cc_start: 0.6399 (OUTLIER) cc_final: 0.5443 (m-80) REVERT: D 695 MET cc_start: 0.8527 (tpt) cc_final: 0.8215 (tpt) REVERT: D 702 MET cc_start: 0.2487 (OUTLIER) cc_final: 0.1362 (ppp) REVERT: D 842 LEU cc_start: 0.8507 (mm) cc_final: 0.8034 (mm) outliers start: 22 outliers final: 16 residues processed: 97 average time/residue: 0.2160 time to fit residues: 28.4261 Evaluate side-chains 97 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 79 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 651 CYS Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 481 CYS Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain D residue 624 TYR Chi-restraints excluded: chain D residue 668 THR Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain D residue 711 SER Chi-restraints excluded: chain D residue 848 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 9 optimal weight: 0.0980 chunk 76 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 85 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 HIS ** A 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7995 Z= 0.173 Angle : 0.523 7.232 10852 Z= 0.267 Chirality : 0.041 0.174 1183 Planarity : 0.003 0.035 1407 Dihedral : 4.931 59.843 1110 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.81 % Allowed : 22.51 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % 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: -1.51 (0.28), residues: 997 helix: 0.05 (0.34), residues: 263 sheet: -2.69 (0.55), residues: 96 loop : -1.21 (0.26), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 694 HIS 0.002 0.001 HIS A 677 PHE 0.026 0.001 PHE D 675 TYR 0.014 0.001 TYR D 676 ARG 0.002 0.000 ARG B 576 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 81 time to evaluate : 0.911 Fit side-chains revert: symmetry clash REVERT: A 526 MET cc_start: 0.8025 (mpp) cc_final: 0.7631 (mpp) REVERT: A 715 GLU cc_start: 0.7471 (tm-30) cc_final: 0.7143 (tm-30) REVERT: B 772 GLN cc_start: 0.7102 (pp30) cc_final: 0.6675 (pp30) REVERT: B 835 SER cc_start: 0.8580 (OUTLIER) cc_final: 0.8303 (t) REVERT: D 624 TYR cc_start: 0.6317 (OUTLIER) cc_final: 0.5421 (m-80) REVERT: D 695 MET cc_start: 0.8499 (tpt) cc_final: 0.8192 (tpt) REVERT: D 702 MET cc_start: 0.2237 (OUTLIER) cc_final: 0.1162 (ppp) REVERT: D 842 LEU cc_start: 0.8441 (mm) cc_final: 0.8001 (mm) outliers start: 22 outliers final: 16 residues processed: 96 average time/residue: 0.2102 time to fit residues: 27.5435 Evaluate side-chains 100 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 81 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 HIS Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 651 CYS Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 706 ASP Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 481 CYS Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain D residue 624 TYR Chi-restraints excluded: chain D residue 668 THR Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain D residue 848 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 54 optimal weight: 0.0010 chunk 39 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 27 optimal weight: 0.0980 chunk 81 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 HIS ** A 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6747 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7995 Z= 0.173 Angle : 0.530 8.509 10852 Z= 0.270 Chirality : 0.040 0.173 1183 Planarity : 0.003 0.035 1407 Dihedral : 4.885 59.090 1110 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.94 % Allowed : 22.63 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % 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 (0.28), residues: 997 helix: 0.08 (0.34), residues: 263 sheet: -2.69 (0.55), residues: 97 loop : -1.20 (0.26), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 694 HIS 0.007 0.001 HIS A 447 PHE 0.024 0.001 PHE D 675 TYR 0.013 0.001 TYR D 676 ARG 0.002 0.000 ARG B 576 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 83 time to evaluate : 0.842 Fit side-chains revert: symmetry clash REVERT: A 461 ARG cc_start: 0.4236 (mtm180) cc_final: 0.3995 (mtm-85) REVERT: A 526 MET cc_start: 0.8023 (mpp) cc_final: 0.7619 (mpp) REVERT: A 715 GLU cc_start: 0.7443 (tm-30) cc_final: 0.7120 (tm-30) REVERT: B 772 GLN cc_start: 0.7106 (pp30) cc_final: 0.6678 (pp30) REVERT: B 835 SER cc_start: 0.8565 (OUTLIER) cc_final: 0.8290 (t) REVERT: D 624 TYR cc_start: 0.6310 (OUTLIER) cc_final: 0.5406 (m-80) REVERT: D 695 MET cc_start: 0.8498 (tpt) cc_final: 0.8200 (tpt) REVERT: D 702 MET cc_start: 0.2317 (OUTLIER) cc_final: 0.1214 (ppp) REVERT: D 842 LEU cc_start: 0.8396 (mm) cc_final: 0.7945 (mm) outliers start: 23 outliers final: 15 residues processed: 99 average time/residue: 0.1998 time to fit residues: 27.3318 Evaluate side-chains 96 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 78 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 HIS Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 651 CYS Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 706 ASP Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 481 CYS Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain D residue 624 TYR Chi-restraints excluded: chain D residue 668 THR Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain D residue 848 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 8 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 24 optimal weight: 9.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 HIS ** A 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6760 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7995 Z= 0.195 Angle : 0.545 8.861 10852 Z= 0.279 Chirality : 0.041 0.167 1183 Planarity : 0.004 0.035 1407 Dihedral : 4.902 57.234 1110 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.43 % Allowed : 23.15 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % 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: -1.52 (0.28), residues: 997 helix: 0.05 (0.34), residues: 263 sheet: -2.77 (0.54), residues: 97 loop : -1.19 (0.26), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 694 HIS 0.006 0.001 HIS A 447 PHE 0.030 0.002 PHE D 675 TYR 0.006 0.001 TYR A 676 ARG 0.002 0.000 ARG B 576 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 76 time to evaluate : 0.947 Fit side-chains revert: symmetry clash REVERT: A 461 ARG cc_start: 0.4259 (mtm180) cc_final: 0.4032 (mtm-85) REVERT: A 526 MET cc_start: 0.8021 (mpp) cc_final: 0.7609 (mpp) REVERT: A 674 GLU cc_start: 0.7743 (mp0) cc_final: 0.7518 (mp0) REVERT: A 715 GLU cc_start: 0.7487 (tm-30) cc_final: 0.7155 (tm-30) REVERT: B 772 GLN cc_start: 0.7107 (pp30) cc_final: 0.6684 (pp30) REVERT: B 835 SER cc_start: 0.8589 (OUTLIER) cc_final: 0.8308 (t) REVERT: D 624 TYR cc_start: 0.6492 (OUTLIER) cc_final: 0.5552 (m-80) REVERT: D 702 MET cc_start: 0.2210 (OUTLIER) cc_final: 0.1137 (ppp) REVERT: D 842 LEU cc_start: 0.8390 (mm) cc_final: 0.7951 (mm) outliers start: 19 outliers final: 16 residues processed: 88 average time/residue: 0.2077 time to fit residues: 25.0462 Evaluate side-chains 95 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 76 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 HIS Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 651 CYS Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 706 ASP Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 481 CYS Chi-restraints excluded: chain B residue 531 ARG Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain D residue 624 TYR Chi-restraints excluded: chain D residue 668 THR Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain D residue 848 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 0.3980 chunk 11 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 80 optimal weight: 0.0970 chunk 33 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 57 optimal weight: 0.0060 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 HIS ** A 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.190675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.134328 restraints weight = 10200.013| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 3.36 r_work: 0.3735 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6746 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 7995 Z= 0.157 Angle : 0.523 8.591 10852 Z= 0.267 Chirality : 0.040 0.170 1183 Planarity : 0.003 0.035 1407 Dihedral : 4.791 56.589 1110 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.56 % Allowed : 23.27 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % 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: -1.41 (0.28), residues: 997 helix: 0.13 (0.34), residues: 263 sheet: -2.70 (0.54), residues: 97 loop : -1.12 (0.26), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 694 HIS 0.009 0.001 HIS A 447 PHE 0.029 0.001 PHE D 675 TYR 0.005 0.001 TYR D 849 ARG 0.002 0.000 ARG B 576 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2052.24 seconds wall clock time: 38 minutes 26.74 seconds (2306.74 seconds total)