Starting phenix.real_space_refine on Wed Aug 5 03:16:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rw0_54294/08_2026/9rw0_54294.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rw0_54294/08_2026/9rw0_54294.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9rw0_54294/08_2026/9rw0_54294.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rw0_54294/08_2026/9rw0_54294.map" model { file = "/net/cci-nas-00/data/ceres_data/9rw0_54294/08_2026/9rw0_54294.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rw0_54294/08_2026/9rw0_54294.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 88 5.49 5 S 17 5.16 5 C 4759 2.51 5 N 1509 2.21 5 O 1845 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8218 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 343 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'TRANS': 52} Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 8, 'TYR:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 74 Chain: "B" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 343 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'TRANS': 52} Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 8, 'TYR:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 74 Chain: "D" Number of atoms: 2928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 2928 Classifications: {'peptide': 462} Incomplete info: {'truncation_to_alanine': 233} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 450} Chain breaks: 3 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 830 Unresolved non-hydrogen angles: 1056 Unresolved non-hydrogen dihedrals: 676 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'GLU:plan': 16, 'ASN:plan1': 16, 'TYR:plan': 9, 'TRP:plan': 2, 'GLN:plan1': 20, 'PHE:plan': 8, 'ASP:plan': 13, 'ARG:plan': 11, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 435 Chain: "C" Number of atoms: 2754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 2754 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 278} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 448} Chain breaks: 3 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 994 Unresolved non-hydrogen angles: 1257 Unresolved non-hydrogen dihedrals: 812 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'ASP:plan': 18, 'GLU:plan': 22, 'ASN:plan1': 17, 'TYR:plan': 12, 'TRP:plan': 2, 'GLN:plan1': 20, 'PHE:plan': 8, 'ARG:plan': 15, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 518 Chain: "E" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 925 Classifications: {'RNA': 44} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 21, 'rna3p_pyr': 22} Link IDs: {'rna2p': 1, 'rna3p': 42} Chain: "F" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 925 Classifications: {'RNA': 44} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 21, 'rna3p_pyr': 22} Link IDs: {'rna2p': 1, 'rna3p': 42} Time building chain proxies: 1.63, per 1000 atoms: 0.20 Number of scatterers: 8218 At special positions: 0 Unit cell: (93.192, 93.192, 180.03, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 17 16.00 P 88 15.00 O 1845 8.00 N 1509 7.00 C 4759 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 - 3.00 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 Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 324.7 milliseconds 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1964 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 6 sheets defined 67.9% alpha, 6.2% beta 35 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 695 through 747 removed outlier: 4.152A pdb=" N VAL A 699 " --> pdb=" O CYS A 695 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 747 Processing helix chain 'D' and resid 3 through 25 removed outlier: 3.773A pdb=" N LYS D 24 " --> pdb=" O ARG D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 36 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 43 through 50 Processing helix chain 'D' and resid 53 through 63 Processing helix chain 'D' and resid 95 through 110 Processing helix chain 'D' and resid 119 through 125 removed outlier: 3.719A pdb=" N HIS D 125 " --> pdb=" O SER D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 129 Processing helix chain 'D' and resid 130 through 138 Processing helix chain 'D' and resid 140 through 151 Processing helix chain 'D' and resid 521 through 530 Processing helix chain 'D' and resid 535 through 554 Processing helix chain 'D' and resid 594 through 600 removed outlier: 3.892A pdb=" N THR D 598 " --> pdb=" O PRO D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 608 Processing helix chain 'D' and resid 618 through 628 Processing helix chain 'D' and resid 639 through 652 Processing helix chain 'D' and resid 654 through 658 Processing helix chain 'D' and resid 662 through 670 Processing helix chain 'D' and resid 681 through 688 removed outlier: 3.710A pdb=" N TYR D 685 " --> pdb=" O LEU D 681 " (cutoff:3.500A) Processing helix chain 'D' and resid 698 through 714 removed outlier: 3.901A pdb=" N ASP D 708 " --> pdb=" O TYR D 704 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL D 709 " --> pdb=" O ALA D 705 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N HIS D 714 " --> pdb=" O LEU D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 725 Processing helix chain 'D' and resid 729 through 743 Processing helix chain 'D' and resid 746 through 773 removed outlier: 3.987A pdb=" N THR D 773 " --> pdb=" O LYS D 769 " (cutoff:3.500A) Processing helix chain 'D' and resid 780 through 787 Processing helix chain 'D' and resid 788 through 790 No H-bonds generated for 'chain 'D' and resid 788 through 790' Processing helix chain 'D' and resid 793 through 802 removed outlier: 4.183A pdb=" N GLY D 802 " --> pdb=" O GLU D 798 " (cutoff:3.500A) Processing helix chain 'D' and resid 803 through 816 Processing helix chain 'C' and resid 6 through 25 Processing helix chain 'C' and resid 30 through 36 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 42 through 50 removed outlier: 4.026A pdb=" N MET C 46 " --> pdb=" O PHE C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 62 Processing helix chain 'C' and resid 95 through 109 Processing helix chain 'C' and resid 118 through 127 removed outlier: 3.783A pdb=" N LEU C 122 " --> pdb=" O PRO C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 138 Processing helix chain 'C' and resid 140 through 151 removed outlier: 3.570A pdb=" N HIS C 151 " --> pdb=" O PHE C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 530 removed outlier: 3.817A pdb=" N GLN C 528 " --> pdb=" O ILE C 524 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASN C 529 " --> pdb=" O LYS C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 554 Processing helix chain 'C' and resid 594 through 600 removed outlier: 4.218A pdb=" N THR C 598 " --> pdb=" O PRO C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 608 Processing helix chain 'C' and resid 617 through 628 removed outlier: 4.622A pdb=" N ASP C 621 " --> pdb=" O ASP C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 639 through 652 Processing helix chain 'C' and resid 654 through 658 removed outlier: 3.525A pdb=" N LYS C 657 " --> pdb=" O GLN C 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 669 Processing helix chain 'C' and resid 677 through 680 Processing helix chain 'C' and resid 681 through 688 removed outlier: 4.158A pdb=" N TYR C 685 " --> pdb=" O LEU C 681 " (cutoff:3.500A) Processing helix chain 'C' and resid 698 through 714 removed outlier: 4.086A pdb=" N ASP C 708 " --> pdb=" O TYR C 704 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL C 709 " --> pdb=" O ALA C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 717 through 725 removed outlier: 3.636A pdb=" N ALA C 722 " --> pdb=" O PHE C 718 " (cutoff:3.500A) Processing helix chain 'C' and resid 726 through 728 No H-bonds generated for 'chain 'C' and resid 726 through 728' Processing helix chain 'C' and resid 729 through 743 Processing helix chain 'C' and resid 746 through 773 removed outlier: 4.267A pdb=" N THR C 773 " --> pdb=" O LYS C 769 " (cutoff:3.500A) Processing helix chain 'C' and resid 780 through 787 removed outlier: 3.548A pdb=" N LEU C 787 " --> pdb=" O GLU C 783 " (cutoff:3.500A) Processing helix chain 'C' and resid 788 through 790 No H-bonds generated for 'chain 'C' and resid 788 through 790' Processing helix chain 'C' and resid 793 through 801 Processing helix chain 'C' and resid 803 through 816 removed outlier: 3.707A pdb=" N GLU C 814 " --> pdb=" O LEU C 810 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 28 through 29 Processing sheet with id=AA2, first strand: chain 'D' and resid 117 through 118 Processing sheet with id=AA3, first strand: chain 'D' and resid 531 through 533 removed outlier: 3.668A pdb=" N ILE D 576 " --> pdb=" O PHE D 588 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE D 556 " --> pdb=" O ILE D 612 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N VAL D 614 " --> pdb=" O ILE D 556 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL D 558 " --> pdb=" O VAL D 614 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N PHE D 637 " --> pdb=" O VAL D 611 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LYS D 613 " --> pdb=" O PHE D 637 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 28 through 29 Processing sheet with id=AA5, first strand: chain 'C' and resid 155 through 158 Processing sheet with id=AA6, first strand: chain 'C' and resid 531 through 533 removed outlier: 6.879A pdb=" N VAL C 558 " --> pdb=" O VAL C 614 " (cutoff:3.500A) 498 hydrogen bonds defined for protein. 1443 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 74 hydrogen bonds 140 hydrogen bond angles 0 basepair planarities 35 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 1.02 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1261 1.30 - 1.43: 2526 1.43 - 1.56: 4491 1.56 - 1.68: 174 1.68 - 1.81: 30 Bond restraints: 8482 Sorted by residual: bond pdb=" C LYS D 101 " pdb=" O LYS D 101 " ideal model delta sigma weight residual 1.237 1.175 0.061 1.19e-02 7.06e+03 2.65e+01 bond pdb=" CA LYS D 101 " pdb=" C LYS D 101 " ideal model delta sigma weight residual 1.524 1.476 0.047 1.29e-02 6.01e+03 1.33e+01 bond pdb=" CA LYS D 809 " pdb=" C LYS D 809 " ideal model delta sigma weight residual 1.523 1.474 0.049 1.37e-02 5.33e+03 1.27e+01 bond pdb=" C LYS D 809 " pdb=" O LYS D 809 " ideal model delta sigma weight residual 1.236 1.198 0.038 1.29e-02 6.01e+03 8.77e+00 bond pdb=" N LYS D 101 " pdb=" CA LYS D 101 " ideal model delta sigma weight residual 1.459 1.424 0.035 1.23e-02 6.61e+03 8.31e+00 ... (remaining 8477 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 11787 2.54 - 5.08: 166 5.08 - 7.61: 11 7.61 - 10.15: 0 10.15 - 12.69: 2 Bond angle restraints: 11966 Sorted by residual: angle pdb=" O3' C E 33 " pdb=" C3' C E 33 " pdb=" C2' C E 33 " ideal model delta sigma weight residual 113.70 125.20 -11.50 1.60e+00 3.91e-01 5.16e+01 angle pdb=" N6 A F 31 " pdb=" C6 A F 31 " pdb=" N1 A F 31 " ideal model delta sigma weight residual 118.60 115.22 3.38 6.00e-01 2.78e+00 3.18e+01 angle pdb=" N6 A F 39 " pdb=" C6 A F 39 " pdb=" N1 A F 39 " ideal model delta sigma weight residual 118.60 115.32 3.28 6.00e-01 2.78e+00 2.99e+01 angle pdb=" N6 A F 38 " pdb=" C6 A F 38 " pdb=" N1 A F 38 " ideal model delta sigma weight residual 118.60 115.38 3.22 6.00e-01 2.78e+00 2.88e+01 angle pdb=" N6 A F 22 " pdb=" C6 A F 22 " pdb=" N1 A F 22 " ideal model delta sigma weight residual 118.60 115.43 3.17 6.00e-01 2.78e+00 2.79e+01 ... (remaining 11961 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 4928 35.91 - 71.82: 184 71.82 - 107.73: 11 107.73 - 143.64: 2 143.64 - 179.55: 1 Dihedral angle restraints: 5126 sinusoidal: 2125 harmonic: 3001 Sorted by residual: dihedral pdb=" C4' C F 33 " pdb=" C3' C F 33 " pdb=" O3' C F 33 " pdb=" P U F 34 " ideal model delta sinusoidal sigma weight residual -140.00 39.55 -179.55 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CA LYS D 659 " pdb=" C LYS D 659 " pdb=" N TYR D 660 " pdb=" CA TYR D 660 " ideal model delta harmonic sigma weight residual -180.00 -160.71 -19.29 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" C4' C E 33 " pdb=" C3' C E 33 " pdb=" O3' C E 33 " pdb=" P U E 34 " ideal model delta sinusoidal sigma weight residual 220.00 90.90 129.10 1 3.50e+01 8.16e-04 1.28e+01 ... (remaining 5123 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1326 0.076 - 0.151: 190 0.151 - 0.227: 7 0.227 - 0.303: 1 0.303 - 0.378: 2 Chirality restraints: 1526 Sorted by residual: chirality pdb=" C3' C E 33 " pdb=" C4' C E 33 " pdb=" O3' C E 33 " pdb=" C2' C E 33 " both_signs ideal model delta sigma weight residual False -2.48 -2.10 -0.38 2.00e-01 2.50e+01 3.58e+00 chirality pdb=" C2' C E 33 " pdb=" C3' C E 33 " pdb=" O2' C E 33 " pdb=" C1' C E 33 " both_signs ideal model delta sigma weight residual False -2.62 -2.31 -0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" CA HIS C 31 " pdb=" N HIS C 31 " pdb=" C HIS C 31 " pdb=" CB HIS C 31 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 1523 not shown) Planarity restraints: 1279 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U F 9 " -0.042 2.00e-02 2.50e+03 2.37e-02 1.26e+01 pdb=" N1 U F 9 " -0.001 2.00e-02 2.50e+03 pdb=" C2 U F 9 " -0.000 2.00e-02 2.50e+03 pdb=" O2 U F 9 " 0.036 2.00e-02 2.50e+03 pdb=" N3 U F 9 " -0.017 2.00e-02 2.50e+03 pdb=" C4 U F 9 " -0.006 2.00e-02 2.50e+03 pdb=" O4 U F 9 " -0.019 2.00e-02 2.50e+03 pdb=" C5 U F 9 " 0.022 2.00e-02 2.50e+03 pdb=" C6 U F 9 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A F 18 " 0.041 2.00e-02 2.50e+03 1.92e-02 1.01e+01 pdb=" N9 A F 18 " -0.008 2.00e-02 2.50e+03 pdb=" C8 A F 18 " -0.016 2.00e-02 2.50e+03 pdb=" N7 A F 18 " -0.012 2.00e-02 2.50e+03 pdb=" C5 A F 18 " -0.009 2.00e-02 2.50e+03 pdb=" C6 A F 18 " -0.006 2.00e-02 2.50e+03 pdb=" N6 A F 18 " 0.039 2.00e-02 2.50e+03 pdb=" N1 A F 18 " -0.004 2.00e-02 2.50e+03 pdb=" C2 A F 18 " -0.008 2.00e-02 2.50e+03 pdb=" N3 A F 18 " -0.008 2.00e-02 2.50e+03 pdb=" C4 A F 18 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G F 8 " -0.039 2.00e-02 2.50e+03 1.73e-02 8.96e+00 pdb=" N9 G F 8 " 0.018 2.00e-02 2.50e+03 pdb=" C8 G F 8 " 0.024 2.00e-02 2.50e+03 pdb=" N7 G F 8 " 0.012 2.00e-02 2.50e+03 pdb=" C5 G F 8 " -0.000 2.00e-02 2.50e+03 pdb=" C6 G F 8 " -0.010 2.00e-02 2.50e+03 pdb=" O6 G F 8 " -0.017 2.00e-02 2.50e+03 pdb=" N1 G F 8 " -0.006 2.00e-02 2.50e+03 pdb=" C2 G F 8 " -0.005 2.00e-02 2.50e+03 pdb=" N2 G F 8 " 0.024 2.00e-02 2.50e+03 pdb=" N3 G F 8 " -0.000 2.00e-02 2.50e+03 pdb=" C4 G F 8 " 0.001 2.00e-02 2.50e+03 ... (remaining 1276 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 51 2.56 - 3.14: 6987 3.14 - 3.73: 13378 3.73 - 4.31: 16870 4.31 - 4.90: 26225 Nonbonded interactions: 63511 Sorted by model distance: nonbonded pdb=" OD1 ASP C 153 " pdb=" OG1 THR C 154 " model vdw 1.970 3.040 nonbonded pdb=" O2' C E 36 " pdb=" OP1 A E 38 " model vdw 2.108 3.040 nonbonded pdb=" O THR D 773 " pdb=" NH1 ARG D 799 " model vdw 2.128 3.120 nonbonded pdb=" O ASP C 160 " pdb=" OD1 ASP C 160 " model vdw 2.148 3.040 nonbonded pdb=" NE2 GLN C 139 " pdb=" OP1 A F 30 " model vdw 2.223 3.120 ... (remaining 63506 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' selection = chain 'B' } ncs_group { reference = (chain 'C' and (resid 5 through 81 or resid 92 through 816)) selection = (chain 'D' and (resid 5 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 57 or (resid 58 and (name N or name \ CA or name C or name O or name CB )) or resid 59 through 148 or (resid 149 and \ (name N or name CA or name C or name O or name CB )) or resid 150 through 158 or \ (resid 159 and (name N or name CA or name C or name O or name CB )) or resid 16 \ 0 through 394 or (resid 520 through 563 and (name N or name CA or name C or name \ O or name CB )) or (resid 564 through 801 and (name N or name CA or name C or n \ ame O or name CB )) or resid 802 or (resid 803 through 816 and (name N or name C \ A or name C or name O or name CB )))) } ncs_group { reference = chain 'E' selection = chain 'F' } 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: 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.450 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 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 : 0.005 0.061 8482 Z= 0.380 Angle : 0.795 12.688 11966 Z= 0.687 Chirality : 0.049 0.378 1526 Planarity : 0.004 0.060 1279 Dihedral : 17.667 179.553 3162 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 0.29 % Allowed : 21.49 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.26), residues: 1008 helix: 0.78 (0.21), residues: 603 sheet: -2.57 (0.54), residues: 62 loop : -1.40 (0.31), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 120 TYR 0.014 0.002 TYR D 64 PHE 0.015 0.002 PHE C 60 TRP 0.000 0.000 TRP D 522 HIS 0.006 0.001 HIS C 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00536 / 0.38 ( 8482) covalent geometry : angle 0.79472 / 0.69 (11966) hydrogen bonds : bond 0.16836 / 12.22 ( 572) hydrogen bonds : angle 6.85728 / 5.19 ( 1583) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: D 809 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7690 (mmtp) outliers start: 1 outliers final: 0 residues processed: 87 average time/residue: 0.0957 time to fit residues: 10.8871 Evaluate side-chains 74 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 809 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 30.0000 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 40.0000 chunk 33 optimal weight: 0.0770 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 20.0000 chunk 100 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 overall best weight: 2.5942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 720 ASN B 721 GLN D 128 GLN C 82 HIS C 128 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.130986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.095239 restraints weight = 21245.827| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.62 r_work: 0.3349 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8482 Z= 0.176 Angle : 0.555 6.432 11966 Z= 0.318 Chirality : 0.040 0.295 1526 Planarity : 0.004 0.060 1279 Dihedral : 15.626 166.684 2335 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.87 % Allowed : 19.20 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.27), residues: 1008 helix: 1.89 (0.20), residues: 622 sheet: -2.14 (0.62), residues: 57 loop : -1.11 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 799 TYR 0.010 0.001 TYR C 80 PHE 0.018 0.002 PHE D 17 TRP 0.000 0.000 TRP D 522 HIS 0.003 0.001 HIS C 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.18 ( 8482) covalent geometry : angle 0.55473 / 0.32 (11966) hydrogen bonds : bond 0.05357 / 3.91 ( 572) hydrogen bonds : angle 5.02400 / 3.88 ( 1583) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 160 ASP cc_start: 0.7895 (t0) cc_final: 0.7683 (t0) outliers start: 10 outliers final: 6 residues processed: 90 average time/residue: 0.0927 time to fit residues: 11.2611 Evaluate side-chains 83 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 82 HIS Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 123 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 106 optimal weight: 20.0000 chunk 28 optimal weight: 40.0000 chunk 19 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 66 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 chunk 57 optimal weight: 0.6980 chunk 37 optimal weight: 30.0000 chunk 24 optimal weight: 0.9980 chunk 43 optimal weight: 40.0000 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 735 GLN D 48 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.132086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.106343 restraints weight = 21088.780| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 3.94 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8482 Z= 0.139 Angle : 0.492 6.896 11966 Z= 0.281 Chirality : 0.038 0.283 1526 Planarity : 0.003 0.052 1279 Dihedral : 15.473 165.904 2331 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.27 % Favored : 96.63 % Rotamer: Outliers : 3.15 % Allowed : 18.05 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.27), residues: 1008 helix: 2.28 (0.20), residues: 626 sheet: -1.82 (0.64), residues: 54 loop : -0.95 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 799 TYR 0.012 0.001 TYR C 80 PHE 0.016 0.002 PHE D 17 TRP 0.000 0.000 TRP D 522 HIS 0.009 0.001 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 ( 8482) covalent geometry : angle 0.49169 / 0.28 (11966) hydrogen bonds : bond 0.04715 / 3.46 ( 572) hydrogen bonds : angle 4.62577 / 3.58 ( 1583) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 720 ASN cc_start: 0.7892 (t0) cc_final: 0.7673 (t0) REVERT: B 739 GLU cc_start: 0.8340 (tm-30) cc_final: 0.7874 (tp30) REVERT: D 101 LYS cc_start: 0.8511 (ttmt) cc_final: 0.8289 (ttmm) REVERT: C 122 LEU cc_start: 0.7836 (mm) cc_final: 0.7636 (mm) REVERT: C 126 ARG cc_start: 0.8041 (tmm-80) cc_final: 0.7685 (tmm-80) outliers start: 11 outliers final: 8 residues processed: 92 average time/residue: 0.0693 time to fit residues: 8.8996 Evaluate side-chains 86 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 780 SER Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 125 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 45 optimal weight: 20.0000 chunk 56 optimal weight: 0.7980 chunk 64 optimal weight: 0.4980 chunk 70 optimal weight: 1.9990 chunk 29 optimal weight: 40.0000 chunk 34 optimal weight: 50.0000 chunk 85 optimal weight: 10.0000 chunk 46 optimal weight: 50.0000 chunk 26 optimal weight: 20.0000 chunk 103 optimal weight: 20.0000 chunk 10 optimal weight: 0.7980 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 735 GLN D 54 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.131008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.094235 restraints weight = 21584.513| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.63 r_work: 0.3337 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8482 Z= 0.174 Angle : 0.500 7.023 11966 Z= 0.285 Chirality : 0.039 0.284 1526 Planarity : 0.003 0.043 1279 Dihedral : 15.509 163.136 2331 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.97 % Favored : 95.93 % Rotamer: Outliers : 5.44 % Allowed : 18.34 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.27), residues: 1008 helix: 2.36 (0.20), residues: 628 sheet: -1.87 (0.63), residues: 54 loop : -0.90 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 120 TYR 0.011 0.001 TYR C 161 PHE 0.017 0.002 PHE D 17 TRP 0.000 0.000 TRP D 522 HIS 0.005 0.001 HIS C 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 ( 8482) covalent geometry : angle 0.50040 / 0.29 (11966) hydrogen bonds : bond 0.04713 / 3.46 ( 572) hydrogen bonds : angle 4.45768 / 3.43 ( 1583) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 739 GLU cc_start: 0.8476 (tm-30) cc_final: 0.7988 (tp30) REVERT: D 109 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8111 (mm) REVERT: C 126 ARG cc_start: 0.8348 (tmm-80) cc_final: 0.7902 (tmm-80) outliers start: 19 outliers final: 13 residues processed: 91 average time/residue: 0.0803 time to fit residues: 10.0201 Evaluate side-chains 86 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 780 SER Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 64 TYR Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 125 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 10 optimal weight: 0.3980 chunk 109 optimal weight: 20.0000 chunk 26 optimal weight: 20.0000 chunk 72 optimal weight: 0.7980 chunk 39 optimal weight: 9.9990 chunk 31 optimal weight: 40.0000 chunk 6 optimal weight: 20.0000 chunk 56 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 41 optimal weight: 30.0000 chunk 17 optimal weight: 4.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 139 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.131269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.095747 restraints weight = 21166.268| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.62 r_work: 0.3367 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8482 Z= 0.125 Angle : 0.450 7.835 11966 Z= 0.257 Chirality : 0.037 0.275 1526 Planarity : 0.003 0.045 1279 Dihedral : 15.525 163.225 2331 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.98 % Favored : 96.92 % Rotamer: Outliers : 4.30 % Allowed : 20.06 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.27), residues: 1008 helix: 2.57 (0.20), residues: 633 sheet: -1.76 (0.63), residues: 54 loop : -0.63 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 120 TYR 0.008 0.001 TYR D 103 PHE 0.017 0.002 PHE D 17 TRP 0.000 0.000 TRP D 522 HIS 0.002 0.001 HIS D 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 8482) covalent geometry : angle 0.44971 / 0.26 (11966) hydrogen bonds : bond 0.04117 / 3.04 ( 572) hydrogen bonds : angle 4.15625 / 3.21 ( 1583) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 739 GLU cc_start: 0.8438 (tm-30) cc_final: 0.7965 (tp30) REVERT: D 109 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8102 (mm) REVERT: D 158 THR cc_start: 0.8253 (m) cc_final: 0.7801 (p) REVERT: C 15 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8776 (mp) REVERT: C 73 ASP cc_start: 0.8071 (t70) cc_final: 0.7758 (t70) REVERT: C 126 ARG cc_start: 0.8233 (tmm-80) cc_final: 0.7509 (tmm-80) REVERT: C 160 ASP cc_start: 0.7969 (t0) cc_final: 0.7459 (t0) outliers start: 15 outliers final: 9 residues processed: 89 average time/residue: 0.0681 time to fit residues: 8.3388 Evaluate side-chains 84 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 780 SER Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 125 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 109 optimal weight: 20.0000 chunk 83 optimal weight: 50.0000 chunk 102 optimal weight: 20.0000 chunk 77 optimal weight: 0.9990 chunk 100 optimal weight: 20.0000 chunk 38 optimal weight: 20.0000 chunk 39 optimal weight: 10.0000 chunk 99 optimal weight: 40.0000 chunk 79 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 overall best weight: 5.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 735 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.128937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.091662 restraints weight = 21186.925| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.60 r_work: 0.3291 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 8482 Z= 0.317 Angle : 0.648 8.479 11966 Z= 0.353 Chirality : 0.045 0.279 1526 Planarity : 0.004 0.044 1279 Dihedral : 15.776 160.230 2331 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.46 % Favored : 95.44 % Rotamer: Outliers : 5.73 % Allowed : 20.06 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.27), residues: 1008 helix: 1.89 (0.20), residues: 637 sheet: -1.90 (0.64), residues: 55 loop : -0.97 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 120 TYR 0.015 0.002 TYR C 80 PHE 0.020 0.003 PHE C 60 TRP 0.000 0.000 TRP D 522 HIS 0.010 0.002 HIS C 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00695 / 0.32 ( 8482) covalent geometry : angle 0.64797 / 0.35 (11966) hydrogen bonds : bond 0.06004 / 4.36 ( 572) hydrogen bonds : angle 4.72401 / 3.62 ( 1583) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 70 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 739 GLU cc_start: 0.8502 (tm-30) cc_final: 0.7963 (tp30) REVERT: D 109 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8138 (mm) REVERT: C 120 ARG cc_start: 0.7890 (tmt-80) cc_final: 0.7583 (tmt-80) outliers start: 20 outliers final: 14 residues processed: 84 average time/residue: 0.0728 time to fit residues: 8.6139 Evaluate side-chains 83 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 790 MET Chi-restraints excluded: chain C residue 35 CYS Chi-restraints excluded: chain C residue 64 TYR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 154 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 9.9990 chunk 49 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 81 optimal weight: 50.0000 chunk 66 optimal weight: 0.4980 chunk 87 optimal weight: 50.0000 chunk 73 optimal weight: 40.0000 chunk 74 optimal weight: 50.0000 chunk 36 optimal weight: 7.9990 chunk 63 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 735 GLN ** C 125 HIS ** 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 = 0.4183 r_free = 0.4183 target = 0.132277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.099934 restraints weight = 20944.327| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 3.24 r_work: 0.3318 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8482 Z= 0.121 Angle : 0.466 7.448 11966 Z= 0.265 Chirality : 0.037 0.272 1526 Planarity : 0.003 0.055 1279 Dihedral : 15.765 162.715 2331 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.88 % Favored : 97.02 % Rotamer: Outliers : 2.87 % Allowed : 23.78 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.27), residues: 1008 helix: 2.49 (0.20), residues: 639 sheet: -1.95 (0.61), residues: 55 loop : -0.56 (0.37), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 126 TYR 0.009 0.001 TYR D 6 PHE 0.018 0.002 PHE D 17 TRP 0.000 0.000 TRP D 522 HIS 0.004 0.001 HIS C 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 8482) covalent geometry : angle 0.46551 / 0.27 (11966) hydrogen bonds : bond 0.04171 / 3.10 ( 572) hydrogen bonds : angle 4.17807 / 3.23 ( 1583) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 739 GLU cc_start: 0.8541 (tm-30) cc_final: 0.8040 (tp30) REVERT: D 158 THR cc_start: 0.8291 (m) cc_final: 0.7801 (p) REVERT: C 12 MET cc_start: 0.8856 (mmm) cc_final: 0.8354 (tpt) REVERT: C 73 ASP cc_start: 0.8176 (t70) cc_final: 0.7869 (t70) REVERT: C 106 ASN cc_start: 0.7885 (t0) cc_final: 0.7628 (t0) REVERT: C 126 ARG cc_start: 0.8272 (tmm-80) cc_final: 0.7643 (tmm-80) REVERT: C 160 ASP cc_start: 0.7842 (t70) cc_final: 0.7276 (t0) outliers start: 10 outliers final: 7 residues processed: 83 average time/residue: 0.0783 time to fit residues: 9.0249 Evaluate side-chains 81 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 109 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 8 optimal weight: 0.9980 chunk 103 optimal weight: 20.0000 chunk 51 optimal weight: 7.9990 chunk 50 optimal weight: 20.0000 chunk 107 optimal weight: 20.0000 chunk 94 optimal weight: 8.9990 chunk 84 optimal weight: 9.9990 chunk 83 optimal weight: 20.0000 chunk 36 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.129648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.102967 restraints weight = 21296.802| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 3.85 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8482 Z= 0.247 Angle : 0.570 8.419 11966 Z= 0.315 Chirality : 0.041 0.268 1526 Planarity : 0.004 0.043 1279 Dihedral : 15.798 161.016 2331 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.17 % Favored : 95.73 % Rotamer: Outliers : 4.01 % Allowed : 22.92 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.27), residues: 1008 helix: 2.17 (0.20), residues: 645 sheet: -2.01 (0.63), residues: 55 loop : -0.69 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 47 TYR 0.013 0.002 TYR C 80 PHE 0.019 0.003 PHE C 17 TRP 0.000 0.000 TRP D 522 HIS 0.007 0.001 HIS C 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.25 ( 8482) covalent geometry : angle 0.56977 / 0.31 (11966) hydrogen bonds : bond 0.05353 / 3.92 ( 572) hydrogen bonds : angle 4.46970 / 3.44 ( 1583) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 739 GLU cc_start: 0.8359 (tm-30) cc_final: 0.7930 (tp30) REVERT: C 12 MET cc_start: 0.8160 (mmm) cc_final: 0.7670 (tpt) REVERT: C 126 ARG cc_start: 0.8439 (tmm-80) cc_final: 0.7922 (tmm-80) REVERT: C 160 ASP cc_start: 0.7645 (t70) cc_final: 0.7131 (t0) outliers start: 14 outliers final: 13 residues processed: 84 average time/residue: 0.0870 time to fit residues: 10.0707 Evaluate side-chains 83 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain C residue 35 CYS Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 64 TYR Chi-restraints excluded: chain C residue 109 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 89 optimal weight: 40.0000 chunk 36 optimal weight: 9.9990 chunk 56 optimal weight: 0.9990 chunk 38 optimal weight: 30.0000 chunk 43 optimal weight: 40.0000 chunk 8 optimal weight: 0.9990 chunk 96 optimal weight: 20.0000 chunk 62 optimal weight: 0.9990 chunk 84 optimal weight: 8.9990 chunk 12 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.132268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.106121 restraints weight = 21293.101| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 3.89 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 8482 Z= 0.112 Angle : 0.473 8.383 11966 Z= 0.268 Chirality : 0.036 0.261 1526 Planarity : 0.003 0.050 1279 Dihedral : 15.803 163.416 2331 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.78 % Favored : 97.12 % Rotamer: Outliers : 1.72 % Allowed : 25.21 % Favored : 73.07 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.27), residues: 1008 helix: 2.57 (0.20), residues: 647 sheet: -1.99 (0.61), residues: 63 loop : -0.22 (0.38), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 126 TYR 0.009 0.001 TYR D 6 PHE 0.014 0.002 PHE D 17 TRP 0.000 0.000 TRP D 522 HIS 0.002 0.001 HIS D 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 ( 8482) covalent geometry : angle 0.47332 / 0.27 (11966) hydrogen bonds : bond 0.03933 / 2.92 ( 572) hydrogen bonds : angle 4.07087 / 3.14 ( 1583) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 739 GLU cc_start: 0.8379 (tm-30) cc_final: 0.7996 (tp30) REVERT: D 109 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7989 (mm) REVERT: D 158 THR cc_start: 0.8351 (m) cc_final: 0.7972 (p) REVERT: C 126 ARG cc_start: 0.8113 (tmm-80) cc_final: 0.7476 (tmm-80) REVERT: C 160 ASP cc_start: 0.7695 (t70) cc_final: 0.7174 (t0) outliers start: 6 outliers final: 4 residues processed: 77 average time/residue: 0.0760 time to fit residues: 8.2079 Evaluate side-chains 77 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain C residue 109 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 58 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 4 optimal weight: 4.9990 chunk 73 optimal weight: 50.0000 chunk 45 optimal weight: 20.0000 chunk 92 optimal weight: 20.0000 chunk 30 optimal weight: 40.0000 chunk 70 optimal weight: 5.9990 chunk 33 optimal weight: 40.0000 chunk 11 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 735 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.129618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.103171 restraints weight = 20902.020| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 3.73 r_work: 0.3308 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 8482 Z= 0.191 Angle : 0.516 8.491 11966 Z= 0.288 Chirality : 0.039 0.256 1526 Planarity : 0.003 0.040 1279 Dihedral : 15.736 161.869 2331 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.57 % Favored : 96.33 % Rotamer: Outliers : 1.43 % Allowed : 25.79 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.27), residues: 1008 helix: 2.44 (0.20), residues: 647 sheet: -1.98 (0.62), residues: 63 loop : -0.34 (0.38), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 47 TYR 0.011 0.001 TYR C 80 PHE 0.017 0.003 PHE C 17 TRP 0.000 0.000 TRP D 522 HIS 0.007 0.001 HIS C 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.19 ( 8482) covalent geometry : angle 0.51601 / 0.29 (11966) hydrogen bonds : bond 0.04676 / 3.45 ( 572) hydrogen bonds : angle 4.22108 / 3.24 ( 1583) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.156 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 739 GLU cc_start: 0.8484 (tm-30) cc_final: 0.7956 (tp30) REVERT: D 158 THR cc_start: 0.8376 (m) cc_final: 0.7905 (p) REVERT: C 12 MET cc_start: 0.8917 (mmm) cc_final: 0.8394 (tpt) REVERT: C 126 ARG cc_start: 0.8534 (tmm-80) cc_final: 0.7890 (tmm-80) REVERT: C 160 ASP cc_start: 0.7793 (t70) cc_final: 0.7225 (t0) outliers start: 5 outliers final: 5 residues processed: 77 average time/residue: 0.0756 time to fit residues: 7.9562 Evaluate side-chains 76 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain C residue 109 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 40.0000 chunk 76 optimal weight: 40.0000 chunk 38 optimal weight: 0.9990 chunk 52 optimal weight: 0.0010 chunk 6 optimal weight: 20.0000 chunk 90 optimal weight: 7.9990 chunk 79 optimal weight: 20.0000 chunk 3 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 47 optimal weight: 50.0000 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 735 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.132278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.105399 restraints weight = 21050.434| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 3.74 r_work: 0.3348 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 8482 Z= 0.106 Angle : 0.462 7.471 11966 Z= 0.260 Chirality : 0.036 0.250 1526 Planarity : 0.003 0.043 1279 Dihedral : 15.749 163.559 2331 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.78 % Favored : 97.12 % Rotamer: Outliers : 2.01 % Allowed : 25.21 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.39 (0.27), residues: 1008 helix: 2.69 (0.20), residues: 647 sheet: -1.82 (0.62), residues: 63 loop : -0.12 (0.39), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 126 TYR 0.008 0.001 TYR D 6 PHE 0.012 0.001 PHE D 17 TRP 0.000 0.000 TRP D 522 HIS 0.002 0.001 HIS D 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.11 ( 8482) covalent geometry : angle 0.46192 / 0.26 (11966) hydrogen bonds : bond 0.03743 / 2.77 ( 572) hydrogen bonds : angle 3.97166 / 3.06 ( 1583) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1572.92 seconds wall clock time: 27 minutes 25.83 seconds (1645.83 seconds total)