Starting phenix.real_space_refine on Tue Jul 29 15:17:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c5z_45238/07_2025/9c5z_45238.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c5z_45238/07_2025/9c5z_45238.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c5z_45238/07_2025/9c5z_45238.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c5z_45238/07_2025/9c5z_45238.map" model { file = "/net/cci-nas-00/data/ceres_data/9c5z_45238/07_2025/9c5z_45238.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c5z_45238/07_2025/9c5z_45238.cif" } resolution = 3.63 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= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 7401 2.51 5 N 1846 2.21 5 O 2144 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11451 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2791 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 12, 'TRANS': 341} Chain breaks: 1 Chain: "B" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2899 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 12, 'TRANS': 354} Chain breaks: 1 Chain: "C" Number of atoms: 2857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2857 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 350} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 2820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2820 Classifications: {'peptide': 358} Link IDs: {'PTRANS': 12, 'TRANS': 345} Chain breaks: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.48, per 1000 atoms: 0.65 Number of scatterers: 11451 At special positions: 0 Unit cell: (120.84, 131.44, 121.9, 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 60 16.00 O 2144 8.00 N 1846 7.00 C 7401 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 750 " - pdb=" SG CYS D 804 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1001 " - " ASN A 546 " " NAG B1001 " - " ASN B 546 " " NAG B1002 " - " ASN B 751 " " NAG C1001 " - " ASN C 751 " " NAG C1002 " - " ASN C 546 " " NAG D1001 " - " ASN D 546 " Time building additional restraints: 2.73 Conformation dependent library (CDL) restraints added in 1.6 seconds 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2648 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 16 sheets defined 51.0% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.84 Creating SS restraints... Processing helix chain 'A' and resid 461 through 475 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 560 through 582 Processing helix chain 'A' and resid 632 through 665 removed outlier: 3.904A pdb=" N GLU A 665 " --> pdb=" O VAL A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 677 removed outlier: 3.546A pdb=" N LYS A 676 " --> pdb=" O ASP A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 696 removed outlier: 3.752A pdb=" N LYS A 696 " --> pdb=" O THR A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 712 Processing helix chain 'A' and resid 723 through 730 removed outlier: 3.756A pdb=" N THR A 730 " --> pdb=" O GLN A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 749 Processing helix chain 'A' and resid 774 through 789 removed outlier: 3.573A pdb=" N ILE A 778 " --> pdb=" O TYR A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 801 removed outlier: 3.578A pdb=" N MET A 793 " --> pdb=" O GLY A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 804 No H-bonds generated for 'chain 'A' and resid 802 through 804' Processing helix chain 'A' and resid 821 through 834 removed outlier: 3.585A pdb=" N SER A 834 " --> pdb=" O GLY A 830 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 457 No H-bonds generated for 'chain 'B' and resid 455 through 457' Processing helix chain 'B' and resid 461 through 474 Processing helix chain 'B' and resid 502 through 507 Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 550 through 557 removed outlier: 4.169A pdb=" N PHE B 555 " --> pdb=" O GLY B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 584 Processing helix chain 'B' and resid 634 through 662 Processing helix chain 'B' and resid 670 through 677 removed outlier: 3.537A pdb=" N GLN B 677 " --> pdb=" O ASP B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 695 Processing helix chain 'B' and resid 702 through 712 removed outlier: 3.742A pdb=" N ARG B 712 " --> pdb=" O PHE B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 731 Processing helix chain 'B' and resid 739 through 749 Processing helix chain 'B' and resid 774 through 789 removed outlier: 4.056A pdb=" N ILE B 780 " --> pdb=" O ASP B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 798 removed outlier: 3.722A pdb=" N TRP B 798 " --> pdb=" O MET B 794 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 842 removed outlier: 3.916A pdb=" N ILE B 825 " --> pdb=" O GLY B 821 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE B 842 " --> pdb=" O ALA B 838 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 457 removed outlier: 4.038A pdb=" N ASP C 457 " --> pdb=" O TYR C 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 454 through 457' Processing helix chain 'C' and resid 461 through 474 Processing helix chain 'C' and resid 499 through 507 removed outlier: 3.819A pdb=" N ARG C 503 " --> pdb=" O ASN C 499 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP C 507 " --> pdb=" O ARG C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 527 removed outlier: 3.997A pdb=" N VAL C 526 " --> pdb=" O VAL C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 557 Processing helix chain 'C' and resid 560 through 584 Processing helix chain 'C' and resid 631 through 665 removed outlier: 3.649A pdb=" N GLU C 662 " --> pdb=" O PHE C 658 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG C 663 " --> pdb=" O LEU C 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 677 Processing helix chain 'C' and resid 691 through 697 Processing helix chain 'C' and resid 699 through 712 Processing helix chain 'C' and resid 720 through 731 Processing helix chain 'C' and resid 739 through 749 Processing helix chain 'C' and resid 773 through 789 Processing helix chain 'C' and resid 789 through 800 removed outlier: 3.512A pdb=" N MET C 793 " --> pdb=" O GLY C 789 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 836 removed outlier: 3.814A pdb=" N VAL C 826 " --> pdb=" O GLY C 822 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N PHE C 836 " --> pdb=" O VAL C 832 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 474 Processing helix chain 'D' and resid 520 through 527 Processing helix chain 'D' and resid 553 through 557 removed outlier: 3.710A pdb=" N LEU D 556 " --> pdb=" O PHE D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 580 Processing helix chain 'D' and resid 634 through 665 removed outlier: 3.653A pdb=" N GLU D 665 " --> pdb=" O VAL D 661 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 696 Processing helix chain 'D' and resid 701 through 712 Processing helix chain 'D' and resid 712 through 717 Processing helix chain 'D' and resid 720 through 731 Processing helix chain 'D' and resid 739 through 749 Processing helix chain 'D' and resid 773 through 787 removed outlier: 3.860A pdb=" N LYS D 777 " --> pdb=" O PRO D 773 " (cutoff:3.500A) Processing helix chain 'D' and resid 790 through 800 removed outlier: 3.635A pdb=" N MET D 794 " --> pdb=" O LYS D 790 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 841 removed outlier: 5.964A pdb=" N GLY D 822 " --> pdb=" O GLN D 818 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE D 823 " --> pdb=" O ASN D 819 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N PHE D 824 " --> pdb=" O ILE D 820 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU D 841 " --> pdb=" O VAL D 837 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 435 through 436 removed outlier: 6.801A pdb=" N VAL A 435 " --> pdb=" O ARG A 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 535 through 536 Processing sheet with id=AA3, first strand: chain 'A' and resid 681 through 683 removed outlier: 8.916A pdb=" N TYR A 733 " --> pdb=" O ARG A 543 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ARG A 543 " --> pdb=" O TYR A 733 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE A 735 " --> pdb=" O LEU A 541 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 433 through 437 Processing sheet with id=AA5, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AA6, first strand: chain 'B' and resid 527 through 529 Processing sheet with id=AA7, first strand: chain 'B' and resid 734 through 738 Processing sheet with id=AA8, first strand: chain 'B' and resid 684 through 685 removed outlier: 6.107A pdb=" N ALA B 684 " --> pdb=" O VAL B 718 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 433 through 435 Processing sheet with id=AB1, first strand: chain 'C' and resid 445 through 446 Processing sheet with id=AB2, first strand: chain 'C' and resid 514 through 515 removed outlier: 4.187A pdb=" N ALA C 515 " --> pdb=" O GLY C 765 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLY C 765 " --> pdb=" O ALA C 515 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 735 through 738 Processing sheet with id=AB4, first strand: chain 'D' and resid 479 through 482 removed outlier: 6.325A pdb=" N ILE D 434 " --> pdb=" O LEU D 512 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 445 through 446 Processing sheet with id=AB6, first strand: chain 'D' and resid 534 through 536 Processing sheet with id=AB7, first strand: chain 'D' and resid 681 through 684 removed outlier: 6.813A pdb=" N GLU D 681 " --> pdb=" O ALA D 734 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N LEU D 736 " --> pdb=" O GLU D 681 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N GLY D 683 " --> pdb=" O LEU D 736 " (cutoff:3.500A) removed outlier: 9.418A pdb=" N GLU D 738 " --> pdb=" O GLY D 683 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N TYR D 733 " --> pdb=" O ARG D 543 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ARG D 543 " --> pdb=" O TYR D 733 " (cutoff:3.500A) 541 hydrogen bonds defined for protein. 1590 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: 3.67 Time building geometry restraints manager: 3.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3595 1.34 - 1.46: 2800 1.46 - 1.58: 5189 1.58 - 1.70: 0 1.70 - 1.82: 104 Bond restraints: 11688 Sorted by residual: bond pdb=" C1 NAG B1002 " pdb=" O5 NAG B1002 " ideal model delta sigma weight residual 1.406 1.496 -0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" N MET B 664 " pdb=" CA MET B 664 " ideal model delta sigma weight residual 1.456 1.484 -0.028 1.22e-02 6.72e+03 5.20e+00 bond pdb=" N MET D 664 " pdb=" CA MET D 664 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.19e-02 7.06e+03 5.19e+00 bond pdb=" C1 NAG C1001 " pdb=" O5 NAG C1001 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 2.01e+00 bond pdb=" C1 NAG B1001 " pdb=" O5 NAG B1001 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.92e+00 ... (remaining 11683 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 15480 1.70 - 3.40: 276 3.40 - 5.10: 40 5.10 - 6.80: 13 6.80 - 8.50: 8 Bond angle restraints: 15817 Sorted by residual: angle pdb=" CB MET B 793 " pdb=" CG MET B 793 " pdb=" SD MET B 793 " ideal model delta sigma weight residual 112.70 121.20 -8.50 3.00e+00 1.11e-01 8.03e+00 angle pdb=" C GLN D 677 " pdb=" N THR D 678 " pdb=" CA THR D 678 " ideal model delta sigma weight residual 121.54 126.67 -5.13 1.91e+00 2.74e-01 7.20e+00 angle pdb=" N MET D 664 " pdb=" CA MET D 664 " pdb=" C MET D 664 " ideal model delta sigma weight residual 111.07 108.26 2.81 1.07e+00 8.73e-01 6.91e+00 angle pdb=" CA MET D 664 " pdb=" C MET D 664 " pdb=" O MET D 664 " ideal model delta sigma weight residual 120.82 118.19 2.63 1.05e+00 9.07e-01 6.26e+00 angle pdb=" CA MET B 664 " pdb=" C MET B 664 " pdb=" O MET B 664 " ideal model delta sigma weight residual 121.16 118.45 2.71 1.12e+00 7.97e-01 5.84e+00 ... (remaining 15812 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.41: 6483 23.41 - 46.82: 438 46.82 - 70.22: 50 70.22 - 93.63: 16 93.63 - 117.04: 23 Dihedral angle restraints: 7010 sinusoidal: 2869 harmonic: 4141 Sorted by residual: dihedral pdb=" CB CYS D 750 " pdb=" SG CYS D 750 " pdb=" SG CYS D 804 " pdb=" CB CYS D 804 " ideal model delta sinusoidal sigma weight residual -86.00 -172.49 86.49 1 1.00e+01 1.00e-02 9.01e+01 dihedral pdb=" CA MET A 737 " pdb=" C MET A 737 " pdb=" N GLU A 738 " pdb=" CA GLU A 738 " ideal model delta harmonic sigma weight residual -180.00 -157.45 -22.55 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" C2 NAG B1002 " pdb=" C1 NAG B1002 " pdb=" O5 NAG B1002 " pdb=" C5 NAG B1002 " ideal model delta sinusoidal sigma weight residual -62.96 54.08 -117.04 1 3.00e+01 1.11e-03 1.55e+01 ... (remaining 7007 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1652 0.076 - 0.152: 151 0.152 - 0.228: 5 0.228 - 0.305: 1 0.305 - 0.381: 1 Chirality restraints: 1810 Sorted by residual: chirality pdb=" C1 NAG B1002 " pdb=" ND2 ASN B 751 " pdb=" C2 NAG B1002 " pdb=" O5 NAG B1002 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" C1 NAG C1002 " pdb=" ND2 ASN C 546 " pdb=" C2 NAG C1002 " pdb=" O5 NAG C1002 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CB ILE B 820 " pdb=" CA ILE B 820 " pdb=" CG1 ILE B 820 " pdb=" CG2 ILE B 820 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.97e-01 ... (remaining 1807 not shown) Planarity restraints: 1979 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 642 " -0.013 2.00e-02 2.50e+03 1.22e-02 2.62e+00 pdb=" CG PHE A 642 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE A 642 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 642 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE A 642 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE A 642 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 642 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 735 " -0.011 2.00e-02 2.50e+03 1.16e-02 2.34e+00 pdb=" CG PHE A 735 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE A 735 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 735 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 735 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 735 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 735 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 779 " -0.007 2.00e-02 2.50e+03 1.48e-02 2.20e+00 pdb=" C THR C 779 " 0.026 2.00e-02 2.50e+03 pdb=" O THR C 779 " -0.010 2.00e-02 2.50e+03 pdb=" N ILE C 780 " -0.009 2.00e-02 2.50e+03 ... (remaining 1976 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1384 2.75 - 3.29: 12125 3.29 - 3.83: 19335 3.83 - 4.36: 21429 4.36 - 4.90: 36390 Nonbonded interactions: 90663 Sorted by model distance: nonbonded pdb=" O VAL B 716 " pdb=" OH TYR B 733 " model vdw 2.213 3.040 nonbonded pdb=" OG1 THR C 520 " pdb=" NH1 ARG C 523 " model vdw 2.264 3.120 nonbonded pdb=" O GLU D 469 " pdb=" OG1 THR D 472 " model vdw 2.266 3.040 nonbonded pdb=" OG SER D 670 " pdb=" O ASP D 673 " model vdw 2.287 3.040 nonbonded pdb=" O GLU D 738 " pdb=" OG1 THR D 741 " model vdw 2.293 3.040 ... (remaining 90658 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 433 through 580 or resid 633 through 681 or (resid 682 and \ (name N or name CA or name C or name O or name CB )) or resid 683 through 814 o \ r (resid 815 and (name N or name CA or name C or name O or name CB )) or resid 8 \ 16 through 834 or resid 1001)) selection = (chain 'B' and (resid 433 through 580 or resid 633 through 681 or (resid 682 and \ (name N or name CA or name C or name O or name CB )) or resid 683 through 814 o \ r (resid 815 and (name N or name CA or name C or name O or name CB )) or resid 8 \ 16 through 834 or resid 1002)) selection = (chain 'C' and (resid 433 through 580 or resid 633 through 834 or resid 1002)) selection = (chain 'D' and (resid 433 through 681 or (resid 682 and (name N or name CA or na \ me C or name O or name CB )) or resid 683 through 814 or (resid 815 and (name N \ or name CA or name C or name O or name CB )) or resid 816 through 834 or resid 1 \ 001)) } 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: 1.140 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: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 30.730 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 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 0.090 11695 Z= 0.132 Angle : 0.605 8.669 15837 Z= 0.297 Chirality : 0.043 0.381 1810 Planarity : 0.003 0.031 1973 Dihedral : 16.882 117.041 4359 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.16 % Allowed : 0.24 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.23), residues: 1426 helix: 1.39 (0.21), residues: 680 sheet: -1.81 (0.44), residues: 137 loop : -1.85 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 798 HIS 0.002 0.001 HIS C 792 PHE 0.028 0.001 PHE A 642 TYR 0.023 0.001 TYR C 521 ARG 0.003 0.000 ARG A 800 Details of bonding type rmsd link_NAG-ASN : bond 0.00877 ( 6) link_NAG-ASN : angle 3.46419 ( 18) hydrogen bonds : bond 0.11539 ( 541) hydrogen bonds : angle 5.17741 ( 1590) SS BOND : bond 0.00004 ( 1) SS BOND : angle 0.34914 ( 2) covalent geometry : bond 0.00277 (11688) covalent geometry : angle 0.59393 (15817) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 232 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 676 LYS cc_start: 0.8952 (ptmt) cc_final: 0.8732 (ptmm) REVERT: A 677 GLN cc_start: 0.7700 (pp30) cc_final: 0.7295 (pp30) REVERT: B 793 MET cc_start: 0.7698 (mmm) cc_final: 0.7489 (mmt) REVERT: C 737 MET cc_start: 0.6903 (ptt) cc_final: 0.6565 (ptt) REVERT: D 793 MET cc_start: 0.7924 (ttt) cc_final: 0.6886 (mpp) outliers start: 2 outliers final: 0 residues processed: 232 average time/residue: 0.2264 time to fit residues: 79.7002 Evaluate side-chains 188 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 1.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 0.3980 chunk 107 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 67 optimal weight: 0.4980 chunk 82 optimal weight: 0.7980 chunk 128 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 GLN A 714 GLN A 819 ASN B 497 GLN ** B 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 802 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.157304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.124584 restraints weight = 22366.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.126265 restraints weight = 22961.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.127165 restraints weight = 19236.553| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11695 Z= 0.129 Angle : 0.618 10.651 15837 Z= 0.299 Chirality : 0.044 0.331 1810 Planarity : 0.003 0.032 1973 Dihedral : 8.918 75.390 1679 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.89 % Allowed : 11.73 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.23), residues: 1426 helix: 1.37 (0.20), residues: 690 sheet: -1.89 (0.45), residues: 136 loop : -1.83 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 641 HIS 0.001 0.001 HIS C 792 PHE 0.013 0.001 PHE A 735 TYR 0.011 0.001 TYR B 733 ARG 0.006 0.000 ARG C 800 Details of bonding type rmsd link_NAG-ASN : bond 0.00726 ( 6) link_NAG-ASN : angle 3.17663 ( 18) hydrogen bonds : bond 0.03148 ( 541) hydrogen bonds : angle 4.34573 ( 1590) SS BOND : bond 0.00008 ( 1) SS BOND : angle 0.05101 ( 2) covalent geometry : bond 0.00300 (11688) covalent geometry : angle 0.60921 (15817) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 207 time to evaluate : 1.742 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 564 TRP cc_start: 0.4655 (t60) cc_final: 0.4403 (t60) REVERT: B 542 TYR cc_start: 0.7738 (t80) cc_final: 0.7271 (t80) REVERT: D 793 MET cc_start: 0.7987 (ttt) cc_final: 0.6796 (mpp) outliers start: 11 outliers final: 8 residues processed: 211 average time/residue: 0.2941 time to fit residues: 94.0744 Evaluate side-chains 191 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 183 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 737 MET Chi-restraints excluded: chain D residue 794 MET Chi-restraints excluded: chain D residue 802 ASN Chi-restraints excluded: chain D residue 826 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 89 optimal weight: 1.9990 chunk 125 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 138 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 40 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 chunk 59 optimal weight: 0.2980 chunk 37 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 GLN A 819 ASN ** D 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 792 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.154385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.115379 restraints weight = 22555.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.114692 restraints weight = 15303.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.114731 restraints weight = 13334.395| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11695 Z= 0.198 Angle : 0.646 9.153 15837 Z= 0.317 Chirality : 0.044 0.342 1810 Planarity : 0.003 0.031 1973 Dihedral : 5.903 55.571 1679 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.78 % Allowed : 15.29 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.23), residues: 1426 helix: 1.23 (0.20), residues: 690 sheet: -2.06 (0.43), residues: 149 loop : -1.81 (0.25), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 641 HIS 0.003 0.001 HIS C 508 PHE 0.024 0.002 PHE C 533 TYR 0.015 0.001 TYR C 774 ARG 0.006 0.000 ARG C 800 Details of bonding type rmsd link_NAG-ASN : bond 0.00644 ( 6) link_NAG-ASN : angle 3.16167 ( 18) hydrogen bonds : bond 0.03287 ( 541) hydrogen bonds : angle 4.44374 ( 1590) SS BOND : bond 0.00273 ( 1) SS BOND : angle 0.33176 ( 2) covalent geometry : bond 0.00468 (11688) covalent geometry : angle 0.63781 (15817) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 199 time to evaluate : 1.927 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 737 MET cc_start: 0.7025 (ppp) cc_final: 0.6767 (ppp) REVERT: B 542 TYR cc_start: 0.7920 (t80) cc_final: 0.7362 (t80) REVERT: B 669 ASP cc_start: 0.8135 (t0) cc_final: 0.7910 (t0) REVERT: B 787 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7589 (mt-10) REVERT: D 793 MET cc_start: 0.8196 (ttt) cc_final: 0.7036 (mpp) outliers start: 22 outliers final: 11 residues processed: 212 average time/residue: 0.2485 time to fit residues: 80.0211 Evaluate side-chains 194 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 183 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 737 MET Chi-restraints excluded: chain D residue 794 MET Chi-restraints excluded: chain D residue 826 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 70 optimal weight: 3.9990 chunk 121 optimal weight: 9.9990 chunk 69 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 137 optimal weight: 6.9990 chunk 127 optimal weight: 0.6980 chunk 122 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 GLN ** D 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 784 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 = 0.4094 r_free = 0.4094 target = 0.153995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.114252 restraints weight = 22402.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.113241 restraints weight = 15515.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.114072 restraints weight = 15204.476| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11695 Z= 0.173 Angle : 0.625 9.160 15837 Z= 0.307 Chirality : 0.044 0.319 1810 Planarity : 0.003 0.033 1973 Dihedral : 5.514 55.857 1679 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.10 % Allowed : 17.72 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.23), residues: 1426 helix: 1.18 (0.20), residues: 690 sheet: -2.14 (0.42), residues: 150 loop : -1.87 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 798 HIS 0.002 0.001 HIS C 508 PHE 0.018 0.001 PHE C 533 TYR 0.019 0.001 TYR B 443 ARG 0.008 0.000 ARG A 503 Details of bonding type rmsd link_NAG-ASN : bond 0.00652 ( 6) link_NAG-ASN : angle 2.99626 ( 18) hydrogen bonds : bond 0.03153 ( 541) hydrogen bonds : angle 4.39242 ( 1590) SS BOND : bond 0.00054 ( 1) SS BOND : angle 0.18791 ( 2) covalent geometry : bond 0.00410 (11688) covalent geometry : angle 0.61758 (15817) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 195 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 542 TYR cc_start: 0.7809 (t80) cc_final: 0.7413 (t80) REVERT: B 669 ASP cc_start: 0.8036 (t0) cc_final: 0.7821 (t0) REVERT: D 579 PHE cc_start: 0.8476 (t80) cc_final: 0.8270 (t80) REVERT: D 786 GLN cc_start: 0.7670 (tp40) cc_final: 0.7367 (mp10) outliers start: 26 outliers final: 16 residues processed: 212 average time/residue: 0.2536 time to fit residues: 82.9691 Evaluate side-chains 195 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 179 time to evaluate : 2.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 737 MET Chi-restraints excluded: chain D residue 746 THR Chi-restraints excluded: chain D residue 826 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 41 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 111 optimal weight: 9.9990 chunk 116 optimal weight: 7.9990 chunk 107 optimal weight: 9.9990 chunk 84 optimal weight: 0.6980 chunk 50 optimal weight: 20.0000 chunk 20 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 GLN ** D 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 784 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 = 0.4003 r_free = 0.4003 target = 0.146780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.106918 restraints weight = 22060.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.104983 restraints weight = 16268.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.105619 restraints weight = 15282.767| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.091 11695 Z= 0.420 Angle : 0.848 11.712 15837 Z= 0.431 Chirality : 0.052 0.320 1810 Planarity : 0.005 0.064 1973 Dihedral : 6.155 53.160 1679 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 19.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 3.24 % Allowed : 20.31 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.22), residues: 1426 helix: 0.66 (0.19), residues: 682 sheet: -2.53 (0.40), residues: 151 loop : -2.09 (0.24), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 798 HIS 0.005 0.001 HIS C 508 PHE 0.034 0.003 PHE B 735 TYR 0.027 0.002 TYR B 443 ARG 0.009 0.001 ARG B 713 Details of bonding type rmsd link_NAG-ASN : bond 0.00536 ( 6) link_NAG-ASN : angle 3.42567 ( 18) hydrogen bonds : bond 0.04247 ( 541) hydrogen bonds : angle 5.10197 ( 1590) SS BOND : bond 0.00088 ( 1) SS BOND : angle 0.26377 ( 2) covalent geometry : bond 0.00983 (11688) covalent geometry : angle 0.84034 (15817) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 183 time to evaluate : 1.969 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 542 TYR cc_start: 0.7984 (t80) cc_final: 0.7493 (t80) REVERT: B 669 ASP cc_start: 0.8157 (t0) cc_final: 0.7867 (t0) REVERT: B 799 TRP cc_start: 0.8850 (OUTLIER) cc_final: 0.7279 (m-90) REVERT: B 825 ILE cc_start: 0.8610 (OUTLIER) cc_final: 0.8388 (mp) REVERT: D 454 TYR cc_start: 0.8181 (OUTLIER) cc_final: 0.7818 (p90) outliers start: 40 outliers final: 26 residues processed: 207 average time/residue: 0.2643 time to fit residues: 86.1230 Evaluate side-chains 203 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 174 time to evaluate : 1.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 566 TYR Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 750 CYS Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 799 TRP Chi-restraints excluded: chain B residue 825 ILE Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 511 ASP Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain D residue 454 TYR Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 737 MET Chi-restraints excluded: chain D residue 742 ILE Chi-restraints excluded: chain D residue 746 THR Chi-restraints excluded: chain D residue 802 ASN Chi-restraints excluded: chain D residue 826 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 100 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 73 optimal weight: 0.0060 chunk 16 optimal weight: 1.9990 chunk 6 optimal weight: 20.0000 chunk 81 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 29 optimal weight: 8.9990 chunk 22 optimal weight: 7.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 654 ASN A 714 GLN ** D 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.152950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.117739 restraints weight = 22094.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.115842 restraints weight = 17654.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.116052 restraints weight = 15903.064| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11695 Z= 0.133 Angle : 0.637 9.246 15837 Z= 0.315 Chirality : 0.044 0.301 1810 Planarity : 0.003 0.036 1973 Dihedral : 5.473 57.024 1679 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.18 % Allowed : 21.93 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.22), residues: 1426 helix: 0.97 (0.20), residues: 687 sheet: -2.22 (0.40), residues: 159 loop : -2.05 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 641 HIS 0.002 0.000 HIS C 792 PHE 0.018 0.001 PHE C 555 TYR 0.023 0.001 TYR B 443 ARG 0.004 0.000 ARG A 503 Details of bonding type rmsd link_NAG-ASN : bond 0.00701 ( 6) link_NAG-ASN : angle 3.01074 ( 18) hydrogen bonds : bond 0.03233 ( 541) hydrogen bonds : angle 4.49540 ( 1590) SS BOND : bond 0.00022 ( 1) SS BOND : angle 0.09917 ( 2) covalent geometry : bond 0.00307 (11688) covalent geometry : angle 0.62952 (15817) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 202 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 642 PHE cc_start: 0.7146 (OUTLIER) cc_final: 0.6890 (m-80) REVERT: B 799 TRP cc_start: 0.8651 (OUTLIER) cc_final: 0.7214 (m-90) REVERT: D 434 ILE cc_start: 0.7346 (OUTLIER) cc_final: 0.7078 (tp) REVERT: D 454 TYR cc_start: 0.8066 (OUTLIER) cc_final: 0.7687 (p90) REVERT: D 741 THR cc_start: 0.8796 (OUTLIER) cc_final: 0.8324 (m) outliers start: 27 outliers final: 15 residues processed: 221 average time/residue: 0.2451 time to fit residues: 83.4422 Evaluate side-chains 196 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 642 PHE Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 799 TRP Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 538 ILE Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 454 TYR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 746 THR Chi-restraints excluded: chain D residue 826 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 84 optimal weight: 0.7980 chunk 19 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 64 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 133 optimal weight: 0.9990 chunk 44 optimal weight: 0.3980 chunk 139 optimal weight: 7.9990 chunk 88 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 GLN A 819 ASN ** D 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.153574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.113885 restraints weight = 22792.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.112963 restraints weight = 18186.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.114039 restraints weight = 15202.593| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11695 Z= 0.137 Angle : 0.669 14.449 15837 Z= 0.326 Chirality : 0.044 0.295 1810 Planarity : 0.003 0.035 1973 Dihedral : 5.243 56.510 1679 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.18 % Allowed : 23.62 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.23), residues: 1426 helix: 1.04 (0.20), residues: 689 sheet: -2.29 (0.40), residues: 163 loop : -1.97 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 641 HIS 0.002 0.000 HIS C 792 PHE 0.025 0.001 PHE C 658 TYR 0.020 0.001 TYR B 443 ARG 0.007 0.000 ARG A 503 Details of bonding type rmsd link_NAG-ASN : bond 0.00690 ( 6) link_NAG-ASN : angle 2.81618 ( 18) hydrogen bonds : bond 0.03207 ( 541) hydrogen bonds : angle 4.40211 ( 1590) SS BOND : bond 0.00022 ( 1) SS BOND : angle 0.05402 ( 2) covalent geometry : bond 0.00320 (11688) covalent geometry : angle 0.66299 (15817) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 184 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 514 VAL cc_start: 0.7652 (t) cc_final: 0.7422 (p) REVERT: A 645 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7854 (tt) REVERT: B 799 TRP cc_start: 0.8620 (OUTLIER) cc_final: 0.7201 (m-90) REVERT: C 665 GLU cc_start: 0.7594 (pp20) cc_final: 0.7348 (pp20) REVERT: D 434 ILE cc_start: 0.7322 (OUTLIER) cc_final: 0.7055 (tp) REVERT: D 454 TYR cc_start: 0.8085 (OUTLIER) cc_final: 0.7730 (p90) REVERT: D 579 PHE cc_start: 0.8365 (t80) cc_final: 0.8153 (t80) outliers start: 27 outliers final: 16 residues processed: 204 average time/residue: 0.1854 time to fit residues: 58.5530 Evaluate side-chains 196 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 764 TYR Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 799 TRP Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 538 ILE Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 454 TYR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 746 THR Chi-restraints excluded: chain D residue 826 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 79 optimal weight: 0.2980 chunk 134 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 28 optimal weight: 0.4980 chunk 33 optimal weight: 0.0570 chunk 54 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 GLN A 819 ASN ** D 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.155669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.118048 restraints weight = 22614.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.117172 restraints weight = 15382.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.117021 restraints weight = 14644.094| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11695 Z= 0.122 Angle : 0.644 10.927 15837 Z= 0.317 Chirality : 0.044 0.286 1810 Planarity : 0.003 0.035 1973 Dihedral : 5.029 56.209 1679 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.43 % Allowed : 23.62 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.23), residues: 1426 helix: 1.11 (0.20), residues: 690 sheet: -2.00 (0.41), residues: 159 loop : -2.02 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 641 HIS 0.002 0.000 HIS C 792 PHE 0.028 0.001 PHE A 533 TYR 0.019 0.001 TYR B 443 ARG 0.005 0.000 ARG A 503 Details of bonding type rmsd link_NAG-ASN : bond 0.00714 ( 6) link_NAG-ASN : angle 2.56024 ( 18) hydrogen bonds : bond 0.03056 ( 541) hydrogen bonds : angle 4.32088 ( 1590) SS BOND : bond 0.00006 ( 1) SS BOND : angle 0.03593 ( 2) covalent geometry : bond 0.00279 (11688) covalent geometry : angle 0.63824 (15817) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 199 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 514 VAL cc_start: 0.7680 (t) cc_final: 0.7426 (p) REVERT: A 645 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7500 (tt) REVERT: A 649 SER cc_start: 0.8961 (m) cc_final: 0.8720 (m) REVERT: A 737 MET cc_start: 0.7485 (ppp) cc_final: 0.7268 (ppp) REVERT: A 819 ASN cc_start: 0.6895 (m-40) cc_final: 0.6652 (m110) REVERT: B 733 TYR cc_start: 0.6961 (t80) cc_final: 0.6270 (t80) REVERT: C 517 LEU cc_start: 0.8258 (tp) cc_final: 0.8021 (tp) REVERT: C 726 GLN cc_start: 0.8116 (mm-40) cc_final: 0.7858 (mm-40) REVERT: D 434 ILE cc_start: 0.7381 (OUTLIER) cc_final: 0.7130 (tp) REVERT: D 454 TYR cc_start: 0.8063 (OUTLIER) cc_final: 0.7828 (p90) outliers start: 30 outliers final: 18 residues processed: 216 average time/residue: 0.1887 time to fit residues: 62.5430 Evaluate side-chains 207 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 186 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 764 TYR Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 538 ILE Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 454 TYR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 742 ILE Chi-restraints excluded: chain D residue 746 THR Chi-restraints excluded: chain D residue 826 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 47 optimal weight: 0.0980 chunk 74 optimal weight: 0.6980 chunk 125 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 114 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 GLN ** D 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 784 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 = 0.4108 r_free = 0.4108 target = 0.155476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.118349 restraints weight = 22688.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.116935 restraints weight = 16372.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.116808 restraints weight = 16100.454| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11695 Z= 0.133 Angle : 0.656 10.722 15837 Z= 0.323 Chirality : 0.044 0.283 1810 Planarity : 0.003 0.035 1973 Dihedral : 4.962 56.363 1679 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.10 % Allowed : 24.11 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.23), residues: 1426 helix: 1.18 (0.20), residues: 689 sheet: -2.06 (0.40), residues: 166 loop : -2.07 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 641 HIS 0.002 0.000 HIS C 792 PHE 0.032 0.001 PHE B 642 TYR 0.018 0.001 TYR B 443 ARG 0.005 0.000 ARG A 503 Details of bonding type rmsd link_NAG-ASN : bond 0.00692 ( 6) link_NAG-ASN : angle 2.54274 ( 18) hydrogen bonds : bond 0.03078 ( 541) hydrogen bonds : angle 4.31239 ( 1590) SS BOND : bond 0.00013 ( 1) SS BOND : angle 0.06353 ( 2) covalent geometry : bond 0.00311 (11688) covalent geometry : angle 0.65035 (15817) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 186 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 514 VAL cc_start: 0.7557 (t) cc_final: 0.7309 (p) REVERT: A 737 MET cc_start: 0.7606 (ppp) cc_final: 0.7353 (ppp) REVERT: A 819 ASN cc_start: 0.6867 (m-40) cc_final: 0.6601 (m110) REVERT: B 733 TYR cc_start: 0.6902 (t80) cc_final: 0.6290 (t80) REVERT: B 799 TRP cc_start: 0.8573 (OUTLIER) cc_final: 0.7368 (m-90) REVERT: C 726 GLN cc_start: 0.8154 (mm-40) cc_final: 0.7889 (mm-40) outliers start: 26 outliers final: 20 residues processed: 200 average time/residue: 0.1798 time to fit residues: 56.3616 Evaluate side-chains 204 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 183 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 764 TYR Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 641 TRP Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 799 TRP Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 664 MET Chi-restraints excluded: chain D residue 742 ILE Chi-restraints excluded: chain D residue 746 THR Chi-restraints excluded: chain D residue 826 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 2 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 57 optimal weight: 0.0980 chunk 33 optimal weight: 0.8980 chunk 47 optimal weight: 0.3980 chunk 125 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 136 optimal weight: 7.9990 chunk 124 optimal weight: 0.4980 chunk 5 optimal weight: 9.9990 chunk 52 optimal weight: 0.4980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.157077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.119452 restraints weight = 22530.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.118142 restraints weight = 16154.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.119557 restraints weight = 15712.887| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11695 Z= 0.121 Angle : 0.659 10.608 15837 Z= 0.322 Chirality : 0.044 0.283 1810 Planarity : 0.003 0.036 1973 Dihedral : 4.849 56.453 1679 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.94 % Allowed : 24.27 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.23), residues: 1426 helix: 1.21 (0.20), residues: 689 sheet: -1.86 (0.42), residues: 158 loop : -2.02 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP D 706 HIS 0.002 0.001 HIS C 792 PHE 0.051 0.001 PHE B 642 TYR 0.019 0.001 TYR B 454 ARG 0.005 0.000 ARG A 503 Details of bonding type rmsd link_NAG-ASN : bond 0.00705 ( 6) link_NAG-ASN : angle 2.63420 ( 18) hydrogen bonds : bond 0.03021 ( 541) hydrogen bonds : angle 4.29591 ( 1590) SS BOND : bond 0.00004 ( 1) SS BOND : angle 0.04485 ( 2) covalent geometry : bond 0.00279 (11688) covalent geometry : angle 0.65337 (15817) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 197 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 514 VAL cc_start: 0.7593 (t) cc_final: 0.7309 (p) REVERT: A 649 SER cc_start: 0.8873 (m) cc_final: 0.8636 (m) REVERT: A 819 ASN cc_start: 0.6837 (m-40) cc_final: 0.6582 (m110) REVERT: B 733 TYR cc_start: 0.6855 (t80) cc_final: 0.6320 (t80) REVERT: B 799 TRP cc_start: 0.8441 (OUTLIER) cc_final: 0.7267 (m-90) REVERT: C 517 LEU cc_start: 0.8440 (tp) cc_final: 0.8145 (tp) REVERT: C 665 GLU cc_start: 0.7520 (pp20) cc_final: 0.7282 (pp20) REVERT: C 726 GLN cc_start: 0.8005 (mm-40) cc_final: 0.7776 (mm-40) REVERT: D 793 MET cc_start: 0.8195 (ttt) cc_final: 0.7802 (tpp) outliers start: 24 outliers final: 20 residues processed: 210 average time/residue: 0.1723 time to fit residues: 56.8622 Evaluate side-chains 209 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 188 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 764 TYR Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 641 TRP Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 799 TRP Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 538 ILE Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 664 MET Chi-restraints excluded: chain D residue 742 ILE Chi-restraints excluded: chain D residue 746 THR Chi-restraints excluded: chain D residue 826 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 25 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 47 optimal weight: 0.0980 chunk 136 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 29 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 819 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.156958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.124483 restraints weight = 22375.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.126056 restraints weight = 21818.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.126966 restraints weight = 18966.494| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 11695 Z= 0.129 Angle : 0.665 10.797 15837 Z= 0.326 Chirality : 0.044 0.285 1810 Planarity : 0.003 0.035 1973 Dihedral : 4.897 56.319 1679 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.35 % Allowed : 24.51 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.23), residues: 1426 helix: 1.24 (0.20), residues: 687 sheet: -1.86 (0.43), residues: 152 loop : -2.04 (0.25), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 706 HIS 0.002 0.000 HIS C 792 PHE 0.026 0.001 PHE C 658 TYR 0.016 0.001 TYR B 443 ARG 0.005 0.000 ARG A 503 Details of bonding type rmsd link_NAG-ASN : bond 0.00699 ( 6) link_NAG-ASN : angle 2.60194 ( 18) hydrogen bonds : bond 0.03097 ( 541) hydrogen bonds : angle 4.30632 ( 1590) SS BOND : bond 0.00001 ( 1) SS BOND : angle 0.05986 ( 2) covalent geometry : bond 0.00306 (11688) covalent geometry : angle 0.66005 (15817) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4088.86 seconds wall clock time: 76 minutes 55.97 seconds (4615.97 seconds total)