Starting phenix.real_space_refine on Thu Jul 2 10:36:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rw0_54294/07_2026/9rw0_54294.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rw0_54294/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9rw0_54294/07_2026/9rw0_54294.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rw0_54294/07_2026/9rw0_54294.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rw0_54294/07_2026/9rw0_54294.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rw0_54294/07_2026/9rw0_54294.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 1.98, per 1000 atoms: 0.24 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: 0.67 Conformation dependent library (CDL) restraints added in 401.5 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: 0.86 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: 1.35 Time building geometry restraints manager: 0.90 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 - 3.06: 11902 3.06 - 6.12: 59 6.12 - 9.17: 3 9.17 - 12.23: 1 12.23 - 15.29: 1 Bond angle restraints: 11966 Sorted by residual: angle pdb=" C3' C E 33 " pdb=" C2' C E 33 " pdb=" O2' C E 33 " ideal model delta sigma weight residual 110.70 125.99 -15.29 1.50e+00 4.44e-01 1.04e+02 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 1.50e+00 4.44e-01 5.87e+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 ... (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 - 0.089: 1449 0.089 - 0.178: 74 0.178 - 0.267: 1 0.267 - 0.356: 0 0.356 - 0.444: 2 Chirality restraints: 1526 Sorted by residual: 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 -2.75 -2.31 -0.44 2.00e-01 2.50e+01 4.94e+00 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=" 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: 0.960 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.550 Find NCS groups from input model: 0.130 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: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.900 ------------------------------------------------------------------------------- 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= 0.356 Angle : 0.743 15.288 11966 Z= 0.648 Chirality : 0.043 0.444 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 0.00531 / 0.36 ( 8482) covalent geometry : angle 0.74287 / 0.65 (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 : 0.277 Fit side-chains revert: symmetry clash REVERT: D 809 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7723 (mmtt) outliers start: 1 outliers final: 0 residues processed: 87 average time/residue: 0.1149 time to fit residues: 12.9848 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 : 0.165 ------------------------------------------------------------------------------- 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: 20.0000 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 = 0.4171 r_free = 0.4171 target = 0.131688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.098620 restraints weight = 21385.646| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 3.20 r_work: 0.3319 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1076 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= 0.179 Angle : 0.536 5.831 11966 Z= 0.314 Chirality : 0.039 0.233 1526 Planarity : 0.004 0.062 1279 Dihedral : 15.722 164.698 2335 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.07 % Favored : 95.83 % Rotamer: Outliers : 2.58 % Allowed : 19.48 % 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: 1.07 (0.27), residues: 1008 helix: 1.91 (0.20), residues: 622 sheet: -2.16 (0.62), residues: 57 loop : -1.11 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 120 TYR 0.011 0.001 TYR C 80 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 0.00376 / 0.18 ( 8482) covalent geometry : angle 0.53597 / 0.31 (11966) hydrogen bonds : bond 0.05275 / 3.85 ( 572) hydrogen bonds : angle 5.06883 / 3.91 ( 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 89 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 160 ASP cc_start: 0.7890 (t0) cc_final: 0.7643 (t0) outliers start: 9 outliers final: 6 residues processed: 89 average time/residue: 0.1000 time to fit residues: 12.0819 Evaluate side-chains 84 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.274 ------------------------------------------------------------------------------- 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: 10.0000 chunk 28 optimal weight: 40.0000 chunk 19 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 57 optimal weight: 0.7980 chunk 37 optimal weight: 30.0000 chunk 24 optimal weight: 5.9990 chunk 43 optimal weight: 40.0000 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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 = 0.4187 r_free = 0.4187 target = 0.132629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.096332 restraints weight = 21151.453| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.61 r_work: 0.3371 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8482 Z= 0.123 Angle : 0.465 6.704 11966 Z= 0.272 Chirality : 0.037 0.236 1526 Planarity : 0.003 0.051 1279 Dihedral : 15.584 163.495 2331 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.72 % Allowed : 18.05 % 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: 1.69 (0.27), residues: 1008 helix: 2.37 (0.20), residues: 626 sheet: -1.85 (0.63), residues: 54 loop : -0.86 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 799 TYR 0.013 0.001 TYR C 80 PHE 0.015 0.002 PHE D 17 TRP 0.000 0.000 TRP D 522 HIS 0.017 0.002 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 ( 8482) covalent geometry : angle 0.46511 / 0.27 (11966) hydrogen bonds : bond 0.04423 / 3.26 ( 572) hydrogen bonds : angle 4.54808 / 3.52 ( 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 95 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 739 GLU cc_start: 0.8475 (tm-30) cc_final: 0.7923 (tp30) REVERT: C 126 ARG cc_start: 0.8143 (tmm-80) cc_final: 0.7736 (tmm-80) REVERT: C 160 ASP cc_start: 0.7932 (t0) cc_final: 0.7680 (t0) outliers start: 13 outliers final: 10 residues processed: 94 average time/residue: 0.0953 time to fit residues: 12.0485 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 : 0.190 ------------------------------------------------------------------------------- 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 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 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: 0.9990 chunk 64 optimal weight: 0.2980 chunk 70 optimal weight: 2.9990 chunk 29 optimal weight: 40.0000 chunk 34 optimal weight: 40.0000 chunk 85 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 26 optimal weight: 20.0000 chunk 103 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 overall best weight: 3.0186 ------------------------------------------------------------------------------- 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 = 0.4165 r_free = 0.4165 target = 0.131027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.094276 restraints weight = 21582.607| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.62 r_work: 0.3336 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1752 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= 0.184 Angle : 0.496 8.419 11966 Z= 0.285 Chirality : 0.039 0.220 1526 Planarity : 0.003 0.040 1279 Dihedral : 15.584 160.310 2331 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 4.87 % Allowed : 19.48 % 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: 1.65 (0.27), residues: 1008 helix: 2.34 (0.20), residues: 628 sheet: -1.86 (0.63), residues: 54 loop : -0.90 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 736 TYR 0.010 0.001 TYR C 64 PHE 0.015 0.003 PHE D 17 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 0.00401 / 0.18 ( 8482) covalent geometry : angle 0.49571 / 0.28 (11966) hydrogen bonds : bond 0.04727 / 3.46 ( 572) hydrogen bonds : angle 4.46291 / 3.44 ( 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 89 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 739 GLU cc_start: 0.8485 (tm-30) cc_final: 0.7997 (tp30) REVERT: D 109 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8075 (mm) outliers start: 17 outliers final: 11 residues processed: 87 average time/residue: 0.0958 time to fit residues: 11.3114 Evaluate side-chains 82 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.275 ------------------------------------------------------------------------------- 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 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 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: 0.7980 chunk 109 optimal weight: 10.0000 chunk 26 optimal weight: 30.0000 chunk 72 optimal weight: 0.9990 chunk 39 optimal weight: 8.9990 chunk 31 optimal weight: 0.8980 chunk 6 optimal weight: 20.0000 chunk 56 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.132223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.097206 restraints weight = 20968.106| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.59 r_work: 0.3386 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8482 Z= 0.103 Angle : 0.431 7.589 11966 Z= 0.250 Chirality : 0.036 0.210 1526 Planarity : 0.003 0.047 1279 Dihedral : 15.618 161.072 2331 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.58 % Favored : 97.32 % Rotamer: Outliers : 2.58 % Allowed : 21.49 % Favored : 75.93 % 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: 2.13 (0.27), residues: 1008 helix: 2.68 (0.20), residues: 626 sheet: -1.80 (0.62), residues: 54 loop : -0.56 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 47 TYR 0.013 0.001 TYR C 161 PHE 0.015 0.002 PHE D 17 TRP 0.000 0.000 TRP D 522 HIS 0.002 0.000 HIS D 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.10 ( 8482) covalent geometry : angle 0.43066 / 0.25 (11966) hydrogen bonds : bond 0.03819 / 2.82 ( 572) hydrogen bonds : angle 4.09108 / 3.16 ( 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 86 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 739 GLU cc_start: 0.8429 (tm-30) cc_final: 0.7959 (tp30) REVERT: D 109 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8086 (mm) REVERT: D 158 THR cc_start: 0.8262 (m) cc_final: 0.7811 (p) REVERT: C 15 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8787 (mp) REVERT: C 73 ASP cc_start: 0.8021 (t70) cc_final: 0.7732 (t70) REVERT: C 126 ARG cc_start: 0.8128 (tmm-80) cc_final: 0.7473 (tmm-80) REVERT: C 160 ASP cc_start: 0.7891 (t0) cc_final: 0.7446 (t0) outliers start: 9 outliers final: 5 residues processed: 84 average time/residue: 0.0958 time to fit residues: 11.1271 Evaluate side-chains 80 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.289 ------------------------------------------------------------------------------- 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 117 VAL Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 123 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 109 optimal weight: 10.0000 chunk 83 optimal weight: 20.0000 chunk 102 optimal weight: 10.0000 chunk 77 optimal weight: 0.0980 chunk 100 optimal weight: 20.0000 chunk 38 optimal weight: 20.0000 chunk 39 optimal weight: 20.0000 chunk 99 optimal weight: 0.9990 chunk 79 optimal weight: 30.0000 chunk 17 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 overall best weight: 4.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.130036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.093021 restraints weight = 21100.799| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.67 r_work: 0.3315 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 8482 Z= 0.254 Angle : 0.554 8.228 11966 Z= 0.315 Chirality : 0.040 0.204 1526 Planarity : 0.004 0.041 1279 Dihedral : 15.689 158.765 2331 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.17 % Favored : 95.73 % Rotamer: Outliers : 4.58 % Allowed : 20.63 % Favored : 74.79 % 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: 1.58 (0.27), residues: 1008 helix: 2.19 (0.20), residues: 638 sheet: -1.84 (0.64), residues: 55 loop : -0.81 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 47 TYR 0.015 0.002 TYR C 80 PHE 0.018 0.003 PHE C 60 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 0.00558 / 0.25 ( 8482) covalent geometry : angle 0.55401 / 0.32 (11966) hydrogen bonds : bond 0.05357 / 3.90 ( 572) hydrogen bonds : angle 4.48680 / 3.45 ( 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 87 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 739 GLU cc_start: 0.8466 (tm-30) cc_final: 0.7950 (tp30) REVERT: D 109 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8092 (mm) REVERT: C 12 MET cc_start: 0.8839 (mmm) cc_final: 0.8355 (tpt) REVERT: C 160 ASP cc_start: 0.7753 (t0) cc_final: 0.7496 (t0) outliers start: 16 outliers final: 11 residues processed: 82 average time/residue: 0.0816 time to fit residues: 9.2558 Evaluate side-chains 81 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.258 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 8.9990 chunk 49 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 81 optimal weight: 50.0000 chunk 66 optimal weight: 0.8980 chunk 87 optimal weight: 50.0000 chunk 73 optimal weight: 40.0000 chunk 74 optimal weight: 50.0000 chunk 36 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 125 HIS ** 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 = 0.4170 r_free = 0.4170 target = 0.131475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.104847 restraints weight = 21177.000| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 3.83 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8482 Z= 0.160 Angle : 0.472 7.941 11966 Z= 0.272 Chirality : 0.038 0.205 1526 Planarity : 0.003 0.050 1279 Dihedral : 15.776 159.474 2331 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.98 % Favored : 96.92 % Rotamer: Outliers : 3.72 % Allowed : 22.35 % Favored : 73.93 % 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: 1.88 (0.27), residues: 1008 helix: 2.42 (0.20), residues: 639 sheet: -1.89 (0.61), residues: 55 loop : -0.66 (0.36), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 126 TYR 0.010 0.001 TYR D 103 PHE 0.018 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 0.00348 / 0.16 ( 8482) covalent geometry : angle 0.47156 / 0.27 (11966) hydrogen bonds : bond 0.04285 / 3.16 ( 572) hydrogen bonds : angle 4.23686 / 3.27 ( 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: 13 poor density : 72 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 739 GLU cc_start: 0.8330 (tm-30) cc_final: 0.7935 (tp30) REVERT: D 109 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8045 (mm) REVERT: D 158 THR cc_start: 0.8359 (m) cc_final: 0.7989 (p) REVERT: C 12 MET cc_start: 0.8142 (mmm) cc_final: 0.7639 (tpt) REVERT: C 73 ASP cc_start: 0.8021 (t70) cc_final: 0.7701 (t70) REVERT: C 126 ARG cc_start: 0.8183 (tmm-80) cc_final: 0.7587 (tmm-80) outliers start: 13 outliers final: 9 residues processed: 81 average time/residue: 0.0918 time to fit residues: 10.2979 Evaluate side-chains 82 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.250 ------------------------------------------------------------------------------- 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 117 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 35 CYS Chi-restraints excluded: chain C residue 64 TYR 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: 0.9990 chunk 103 optimal weight: 10.0000 chunk 51 optimal weight: 30.0000 chunk 50 optimal weight: 20.0000 chunk 107 optimal weight: 10.0000 chunk 94 optimal weight: 0.9980 chunk 84 optimal weight: 7.9990 chunk 83 optimal weight: 20.0000 chunk 36 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- 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 = 0.4157 r_free = 0.4157 target = 0.130384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.104144 restraints weight = 21273.525| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 3.86 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8482 Z= 0.181 Angle : 0.485 7.959 11966 Z= 0.280 Chirality : 0.038 0.199 1526 Planarity : 0.004 0.060 1279 Dihedral : 15.788 159.581 2331 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.97 % Favored : 95.93 % Rotamer: Outliers : 3.44 % Allowed : 24.07 % Favored : 72.49 % 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: 1.89 (0.27), residues: 1008 helix: 2.38 (0.20), residues: 645 sheet: -2.01 (0.61), residues: 60 loop : -0.52 (0.37), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 47 TYR 0.010 0.001 TYR C 80 PHE 0.016 0.002 PHE D 17 TRP 0.000 0.000 TRP D 522 HIS 0.008 0.001 HIS C 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 ( 8482) covalent geometry : angle 0.48460 / 0.28 (11966) hydrogen bonds : bond 0.04475 / 3.29 ( 572) hydrogen bonds : angle 4.23635 / 3.26 ( 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 85 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 739 GLU cc_start: 0.8343 (tm-30) cc_final: 0.7958 (tp30) REVERT: D 109 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7992 (mm) REVERT: D 158 THR cc_start: 0.8305 (m) cc_final: 0.7939 (p) REVERT: C 12 MET cc_start: 0.8156 (mmm) cc_final: 0.7644 (tpt) REVERT: C 73 ASP cc_start: 0.7979 (t70) cc_final: 0.7734 (t70) REVERT: C 126 ARG cc_start: 0.8195 (tmm-80) cc_final: 0.7488 (tmm-80) outliers start: 12 outliers final: 10 residues processed: 83 average time/residue: 0.0816 time to fit residues: 9.4199 Evaluate side-chains 82 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.260 ------------------------------------------------------------------------------- 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 35 CYS Chi-restraints excluded: chain C residue 64 TYR 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: 5.9990 chunk 56 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 43 optimal weight: 40.0000 chunk 8 optimal weight: 0.7980 chunk 96 optimal weight: 20.0000 chunk 62 optimal weight: 0.2980 chunk 84 optimal weight: 10.0000 chunk 12 optimal weight: 0.0570 chunk 9 optimal weight: 0.9990 overall best weight: 0.6300 ------------------------------------------------------------------------------- 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 = 0.4186 r_free = 0.4186 target = 0.132379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.106550 restraints weight = 21273.419| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 3.84 r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8482 Z= 0.098 Angle : 0.437 7.266 11966 Z= 0.253 Chirality : 0.036 0.193 1526 Planarity : 0.003 0.042 1279 Dihedral : 15.790 160.673 2331 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.68 % Favored : 97.22 % Rotamer: Outliers : 2.58 % Allowed : 23.78 % Favored : 73.64 % 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: 2.33 (0.27), residues: 1008 helix: 2.67 (0.20), residues: 646 sheet: -1.87 (0.61), residues: 63 loop : -0.20 (0.39), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 126 TYR 0.009 0.001 TYR D 6 PHE 0.013 0.001 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 0.00192 / 0.10 ( 8482) covalent geometry : angle 0.43723 / 0.25 (11966) hydrogen bonds : bond 0.03704 / 2.75 ( 572) hydrogen bonds : angle 3.96684 / 3.06 ( 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 85 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 739 GLU cc_start: 0.8313 (tm-30) cc_final: 0.7932 (tp30) REVERT: D 109 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7995 (mm) REVERT: D 158 THR cc_start: 0.8348 (m) cc_final: 0.7997 (p) REVERT: C 73 ASP cc_start: 0.7873 (t70) cc_final: 0.7568 (t70) REVERT: C 126 ARG cc_start: 0.8105 (tmm-80) cc_final: 0.7399 (tmm-80) outliers start: 9 outliers final: 6 residues processed: 84 average time/residue: 0.0832 time to fit residues: 9.6565 Evaluate side-chains 82 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.250 ------------------------------------------------------------------------------- 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 152 THR Chi-restraints excluded: chain D residue 780 SER Chi-restraints excluded: chain C residue 123 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: 5.9990 chunk 73 optimal weight: 50.0000 chunk 45 optimal weight: 20.0000 chunk 92 optimal weight: 30.0000 chunk 30 optimal weight: 50.0000 chunk 70 optimal weight: 0.9990 chunk 33 optimal weight: 40.0000 chunk 11 optimal weight: 0.5980 chunk 98 optimal weight: 0.0040 overall best weight: 2.1198 ------------------------------------------------------------------------------- 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 = 0.4171 r_free = 0.4171 target = 0.131344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.099628 restraints weight = 21098.755| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 3.10 r_work: 0.3323 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 8482 Z= 0.148 Angle : 0.471 8.201 11966 Z= 0.271 Chirality : 0.037 0.189 1526 Planarity : 0.003 0.039 1279 Dihedral : 15.693 160.697 2331 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.57 % Favored : 96.33 % Rotamer: Outliers : 2.01 % Allowed : 24.64 % Favored : 73.35 % 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: 2.28 (0.27), residues: 1008 helix: 2.61 (0.20), residues: 647 sheet: -1.71 (0.65), residues: 61 loop : -0.24 (0.38), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 126 TYR 0.018 0.001 TYR C 161 PHE 0.016 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 0.00324 / 0.15 ( 8482) covalent geometry : angle 0.47149 / 0.27 (11966) hydrogen bonds : bond 0.04007 / 2.96 ( 572) hydrogen bonds : angle 3.99338 / 3.07 ( 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 80 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 739 GLU cc_start: 0.8458 (tm-30) cc_final: 0.7959 (tp30) REVERT: D 109 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8097 (mm) REVERT: D 158 THR cc_start: 0.8266 (m) cc_final: 0.7810 (p) REVERT: C 73 ASP cc_start: 0.8121 (t70) cc_final: 0.7877 (t70) REVERT: C 120 ARG cc_start: 0.7519 (tmt-80) cc_final: 0.7264 (tmt-80) REVERT: C 126 ARG cc_start: 0.8408 (tmm-80) cc_final: 0.7634 (tmm-80) outliers start: 7 outliers final: 6 residues processed: 79 average time/residue: 0.0934 time to fit residues: 10.0107 Evaluate side-chains 79 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.267 ------------------------------------------------------------------------------- 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 152 THR Chi-restraints excluded: chain D residue 780 SER Chi-restraints excluded: chain C residue 123 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 6 optimal weight: 20.0000 chunk 90 optimal weight: 20.0000 chunk 79 optimal weight: 20.0000 chunk 3 optimal weight: 8.9990 chunk 36 optimal weight: 50.0000 chunk 78 optimal weight: 5.9990 chunk 47 optimal weight: 50.0000 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 125 HIS ** 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 = 0.4150 r_free = 0.4150 target = 0.129920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.103333 restraints weight = 21252.476| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 3.88 r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 8482 Z= 0.236 Angle : 0.542 8.749 11966 Z= 0.310 Chirality : 0.040 0.186 1526 Planarity : 0.004 0.040 1279 Dihedral : 15.836 162.058 2331 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.07 % Favored : 95.83 % Rotamer: Outliers : 2.58 % Allowed : 24.36 % 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: 1.95 (0.27), residues: 1008 helix: 2.35 (0.20), residues: 647 sheet: -1.79 (0.65), residues: 63 loop : -0.36 (0.38), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 47 TYR 0.013 0.002 TYR C 80 PHE 0.021 0.003 PHE D 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 0.00522 / 0.24 ( 8482) covalent geometry : angle 0.54188 / 0.31 (11966) hydrogen bonds : bond 0.04823 / 3.54 ( 572) hydrogen bonds : angle 4.25718 / 3.27 ( 1583) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1790.05 seconds wall clock time: 31 minutes 20.15 seconds (1880.15 seconds total)