Starting phenix.real_space_refine on Mon Jul 6 13:07:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8c97_16504/07_2026/8c97_16504.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c97_16504/07_2026/8c97_16504.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8c97_16504/07_2026/8c97_16504.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c97_16504/07_2026/8c97_16504.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8c97_16504/07_2026/8c97_16504.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c97_16504/07_2026/8c97_16504.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8c97_16504/07_2026/8c97_16504.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8c97_16504/07_2026/8c97_16504.cif" } resolution = 4.07 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= 0.017 sd= 0.096 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 1292 5.49 5 S 25 5.16 5 C 17639 2.51 5 N 6738 2.21 5 O 10469 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 36163 Number of models: 1 Model: "" Number of chains: 12 Chain: "0" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 263 Classifications: {'peptide': 33} Modifications used: {'COO': 1} Link IDs: {'TRANS': 32} Chain: "2" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 262 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain breaks: 1 Chain: "A" Number of atoms: 27767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1292, 27767 Classifications: {'RNA': 1292} Modifications used: {'rna2p_pur': 119, 'rna2p_pyr': 70, 'rna3p_pur': 641, 'rna3p_pyr': 462} Link IDs: {'rna2p': 189, 'rna3p': 1102} Chain breaks: 6 Chain: "D" Number of atoms: 1200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1200 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 156} Chain breaks: 1 Chain: "E" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1129 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 143} Chain breaks: 1 Chain: "K" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "N" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "P" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "S" Number of atoms: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 717 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain breaks: 1 Chain: "T" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 722 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 1, 'TRANS': 89} Chain: "U" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "Y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Time building chain proxies: 6.59, per 1000 atoms: 0.18 Number of scatterers: 36163 At special positions: 0 Unit cell: (150, 175, 203.75, 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 25 16.00 P 1292 15.00 O 10469 8.00 N 6738 7.00 C 17639 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: 2.66 Conformation dependent library (CDL) restraints added in 430.3 milliseconds 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2006 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 15 sheets defined 31.6% alpha, 21.4% beta 404 base pairs and 629 stacking pairs defined. Time for finding SS restraints: 5.57 Creating SS restraints... Processing helix chain '2' and resid 11 through 16 Processing helix chain '2' and resid 17 through 24 Processing helix chain '2' and resid 24 through 36 Processing helix chain 'D' and resid 39 through 44 Processing helix chain 'D' and resid 61 through 72 removed outlier: 3.774A pdb=" N LYS D 70 " --> pdb=" O GLY D 66 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 103 removed outlier: 4.326A pdb=" N ASP D 103 " --> pdb=" O LEU D 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 24 through 39 Processing helix chain 'E' and resid 97 through 115 Processing helix chain 'E' and resid 130 through 142 removed outlier: 3.513A pdb=" N LEU E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 160 removed outlier: 3.541A pdb=" N PHE E 158 " --> pdb=" O ASP E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 183 removed outlier: 3.680A pdb=" N PHE E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 201 removed outlier: 4.122A pdb=" N GLN E 195 " --> pdb=" O ASP E 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 113 removed outlier: 3.800A pdb=" N MET K 113 " --> pdb=" O GLU K 110 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 32 removed outlier: 3.542A pdb=" N GLN N 18 " --> pdb=" O SER N 14 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 56 removed outlier: 3.712A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU N 49 " --> pdb=" O ARG N 45 " (cutoff:3.500A) Proline residue: N 50 - end of helix Processing helix chain 'N' and resid 59 through 68 Processing helix chain 'N' and resid 72 through 79 Processing helix chain 'N' and resid 82 through 88 Processing helix chain 'P' and resid 2 through 10 Processing helix chain 'P' and resid 52 through 55 Processing helix chain 'P' and resid 96 through 101 Processing helix chain 'P' and resid 103 through 108 Processing helix chain 'S' and resid 15 through 23 Processing helix chain 'S' and resid 28 through 39 Processing helix chain 'S' and resid 42 through 62 removed outlier: 3.981A pdb=" N LEU S 46 " --> pdb=" O LYS S 42 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 28 Processing helix chain 'T' and resid 39 through 52 Processing helix chain 'U' and resid 65 through 67 No H-bonds generated for 'chain 'U' and resid 65 through 67' Processing helix chain 'Y' and resid 2 through 7 Processing helix chain 'Y' and resid 9 through 33 removed outlier: 4.069A pdb=" N GLN Y 25 " --> pdb=" O LEU Y 21 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N PHE Y 26 " --> pdb=" O LEU Y 22 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLN Y 31 " --> pdb=" O ASN Y 27 " (cutoff:3.500A) Processing helix chain 'Y' and resid 46 through 56 Processing sheet with id=AA1, first strand: chain '0' and resid 28 through 29 Processing sheet with id=AA2, first strand: chain '0' and resid 47 through 48 Processing sheet with id=AA3, first strand: chain 'D' and resid 170 through 176 removed outlier: 5.059A pdb=" N THR D 171 " --> pdb=" O GLY D 111 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N GLY D 111 " --> pdb=" O THR D 171 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N GLN D 173 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL D 109 " --> pdb=" O GLN D 173 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE D 27 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU D 187 " --> pdb=" O ILE D 27 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 12 through 15 Processing sheet with id=AA5, first strand: chain 'D' and resid 34 through 38 removed outlier: 5.653A pdb=" N VAL D 34 " --> pdb=" O THR D 51 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N THR D 51 " --> pdb=" O VAL D 34 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 121 removed outlier: 3.707A pdb=" N ASP E 168 " --> pdb=" O VAL E 146 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 6 through 10 removed outlier: 3.704A pdb=" N VAL K 10 " --> pdb=" O ARG K 17 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ARG K 17 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA K 16 " --> pdb=" O ALA K 46 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ALA K 46 " --> pdb=" O ALA K 16 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ARG K 18 " --> pdb=" O LYS K 44 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N VAL K 24 " --> pdb=" O ILE K 38 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N ILE K 38 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N VAL K 62 " --> pdb=" O VAL K 85 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL K 85 " --> pdb=" O VAL K 62 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N CYS K 84 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ASN K 9 " --> pdb=" O CYS K 84 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N LEU K 86 " --> pdb=" O ASN K 9 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 69 through 70 removed outlier: 3.907A pdb=" N VAL K 69 " --> pdb=" O ILE K 77 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE K 77 " --> pdb=" O VAL K 69 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL K 76 " --> pdb=" O VAL P 72 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA P 48 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ARG P 61 " --> pdb=" O VAL P 46 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N VAL P 46 " --> pdb=" O ARG P 61 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N ILE P 63 " --> pdb=" O GLY P 44 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N GLY P 44 " --> pdb=" O ILE P 63 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL P 46 " --> pdb=" O ASP P 23 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ASP P 23 " --> pdb=" O VAL P 46 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLU P 26 " --> pdb=" O VAL P 85 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N VAL P 85 " --> pdb=" O GLU P 26 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LYS P 28 " --> pdb=" O ILE P 83 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ILE P 83 " --> pdb=" O LYS P 28 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N TRP P 30 " --> pdb=" O ASP P 81 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ASP P 81 " --> pdb=" O TRP P 30 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 33 through 36 removed outlier: 6.649A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 2 through 10 removed outlier: 5.176A pdb=" N ILE S 4 " --> pdb=" O VAL S 107 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL S 107 " --> pdb=" O ILE S 4 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LYS S 6 " --> pdb=" O VAL S 105 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N VAL S 105 " --> pdb=" O LYS S 6 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ARG S 8 " --> pdb=" O ILE S 103 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE S 103 " --> pdb=" O ARG S 8 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N HIS S 102 " --> pdb=" O VAL S 76 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL S 76 " --> pdb=" O HIS S 102 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR S 104 " --> pdb=" O ILE S 74 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ILE S 74 " --> pdb=" O THR S 104 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL S 106 " --> pdb=" O THR S 72 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'T' and resid 13 through 14 removed outlier: 3.811A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TRP T 80 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N VAL T 62 " --> pdb=" O TRP T 80 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LYS T 82 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N THR T 60 " --> pdb=" O LYS T 82 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TYR T 84 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL T 58 " --> pdb=" O TYR T 84 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR T 86 " --> pdb=" O GLU T 56 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'T' and resid 67 through 68 Processing sheet with id=AB4, first strand: chain 'U' and resid 33 through 35 removed outlier: 3.827A pdb=" N ASN U 26 " --> pdb=" O ILE U 34 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N GLU U 9 " --> pdb=" O PHE U 72 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE U 72 " --> pdb=" O GLU U 9 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASN U 73 " --> pdb=" O LYS U 78 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS U 78 " --> pdb=" O ASN U 73 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'U' and resid 40 through 41 removed outlier: 3.520A pdb=" N LYS U 60 " --> pdb=" O VAL U 41 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'U' and resid 82 through 86 311 hydrogen bonds defined for protein. 858 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1029 hydrogen bonds 1648 hydrogen bond angles 0 basepair planarities 404 basepair parallelities 629 stacking parallelities Total time for adding SS restraints: 13.93 Time building geometry restraints manager: 3.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 5958 1.33 - 1.45: 16665 1.45 - 1.57: 14330 1.57 - 1.69: 2578 1.69 - 1.81: 47 Bond restraints: 39578 Sorted by residual: bond pdb=" C1' U A 138 " pdb=" N1 U A 138 " ideal model delta sigma weight residual 1.480 1.573 -0.093 1.50e-02 4.44e+03 3.83e+01 bond pdb=" O5' A A2733 " pdb=" C5' A A2733 " ideal model delta sigma weight residual 1.420 1.457 -0.037 1.50e-02 4.44e+03 5.93e+00 bond pdb=" N GLU T 4 " pdb=" CA GLU T 4 " ideal model delta sigma weight residual 1.453 1.484 -0.031 1.37e-02 5.33e+03 4.97e+00 bond pdb=" N GLU T 5 " pdb=" CA GLU T 5 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.29e-02 6.01e+03 4.92e+00 bond pdb=" O5' A A2734 " pdb=" C5' A A2734 " ideal model delta sigma weight residual 1.420 1.448 -0.028 1.50e-02 4.44e+03 3.49e+00 ... (remaining 39573 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 59769 2.83 - 5.66: 87 5.66 - 8.49: 10 8.49 - 11.32: 0 11.32 - 14.15: 1 Bond angle restraints: 59867 Sorted by residual: angle pdb=" C3' A A2733 " pdb=" O3' A A2733 " pdb=" P A A2734 " ideal model delta sigma weight residual 120.20 106.05 14.15 1.50e+00 4.44e-01 8.89e+01 angle pdb=" N GLU T 4 " pdb=" CA GLU T 4 " pdb=" C GLU T 4 " ideal model delta sigma weight residual 110.41 104.28 6.13 1.23e+00 6.61e-01 2.48e+01 angle pdb=" C3' G A2732 " pdb=" O3' G A2732 " pdb=" P A A2733 " ideal model delta sigma weight residual 120.20 112.76 7.44 1.50e+00 4.44e-01 2.46e+01 angle pdb=" CA GLU T 4 " pdb=" C GLU T 4 " pdb=" O GLU T 4 " ideal model delta sigma weight residual 121.99 116.68 5.31 1.14e+00 7.69e-01 2.17e+01 angle pdb=" O2' A A2733 " pdb=" C2' A A2733 " pdb=" C1' A A2733 " ideal model delta sigma weight residual 108.40 114.33 -5.93 1.50e+00 4.44e-01 1.57e+01 ... (remaining 59862 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 20124 35.91 - 71.82: 576 71.82 - 107.73: 64 107.73 - 143.64: 14 143.64 - 179.54: 4 Dihedral angle restraints: 20782 sinusoidal: 17702 harmonic: 3080 Sorted by residual: dihedral pdb=" O4' U A1340 " pdb=" C1' U A1340 " pdb=" N1 U A1340 " pdb=" C2 U A1340 " ideal model delta sinusoidal sigma weight residual -128.00 42.32 -170.32 1 1.70e+01 3.46e-03 6.60e+01 dihedral pdb=" O4' U A1313 " pdb=" C1' U A1313 " pdb=" N1 U A1313 " pdb=" C2 U A1313 " ideal model delta sinusoidal sigma weight residual 200.00 95.41 104.59 1 1.50e+01 4.44e-03 5.34e+01 dihedral pdb=" O4' C A 323 " pdb=" C1' C A 323 " pdb=" N1 C A 323 " pdb=" C2 C A 323 " ideal model delta sinusoidal sigma weight residual -128.00 -18.41 -109.59 1 1.70e+01 3.46e-03 4.44e+01 ... (remaining 20779 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 7660 0.092 - 0.184: 126 0.184 - 0.276: 1 0.276 - 0.368: 1 0.368 - 0.460: 2 Chirality restraints: 7790 Sorted by residual: chirality pdb=" P G A2732 " pdb=" OP1 G A2732 " pdb=" OP2 G A2732 " pdb=" O5' G A2732 " both_signs ideal model delta sigma weight residual True 2.41 -2.87 -0.46 2.00e-01 2.50e+01 5.29e+00 chirality pdb=" P A A2733 " pdb=" OP1 A A2733 " pdb=" OP2 A A2733 " pdb=" O5' A A2733 " both_signs ideal model delta sigma weight residual True 2.41 -2.87 -0.46 2.00e-01 2.50e+01 5.18e+00 chirality pdb=" P A A2734 " pdb=" OP1 A A2734 " pdb=" OP2 A A2734 " pdb=" O5' A A2734 " both_signs ideal model delta sigma weight residual True 2.41 -2.75 -0.34 2.00e-01 2.50e+01 2.92e+00 ... (remaining 7787 not shown) Planarity restraints: 2745 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C A1575 " 0.003 2.00e-02 2.50e+03 1.94e-02 8.44e+00 pdb=" N1 C A1575 " -0.006 2.00e-02 2.50e+03 pdb=" C2 C A1575 " -0.047 2.00e-02 2.50e+03 pdb=" O2 C A1575 " 0.031 2.00e-02 2.50e+03 pdb=" N3 C A1575 " 0.002 2.00e-02 2.50e+03 pdb=" C4 C A1575 " -0.002 2.00e-02 2.50e+03 pdb=" N4 C A1575 " 0.003 2.00e-02 2.50e+03 pdb=" C5 C A1575 " 0.007 2.00e-02 2.50e+03 pdb=" C6 C A1575 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 305 " -0.005 2.00e-02 2.50e+03 1.55e-02 5.42e+00 pdb=" N1 C A 305 " 0.010 2.00e-02 2.50e+03 pdb=" C2 C A 305 " -0.038 2.00e-02 2.50e+03 pdb=" O2 C A 305 " 0.023 2.00e-02 2.50e+03 pdb=" N3 C A 305 " 0.003 2.00e-02 2.50e+03 pdb=" C4 C A 305 " -0.006 2.00e-02 2.50e+03 pdb=" N4 C A 305 " 0.004 2.00e-02 2.50e+03 pdb=" C5 C A 305 " 0.004 2.00e-02 2.50e+03 pdb=" C6 C A 305 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 363 " -0.004 2.00e-02 2.50e+03 1.14e-02 3.92e+00 pdb=" N9 G A 363 " 0.004 2.00e-02 2.50e+03 pdb=" C8 G A 363 " 0.001 2.00e-02 2.50e+03 pdb=" N7 G A 363 " -0.005 2.00e-02 2.50e+03 pdb=" C5 G A 363 " -0.003 2.00e-02 2.50e+03 pdb=" C6 G A 363 " -0.005 2.00e-02 2.50e+03 pdb=" O6 G A 363 " 0.001 2.00e-02 2.50e+03 pdb=" N1 G A 363 " 0.004 2.00e-02 2.50e+03 pdb=" C2 G A 363 " 0.030 2.00e-02 2.50e+03 pdb=" N2 G A 363 " -0.024 2.00e-02 2.50e+03 pdb=" N3 G A 363 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G A 363 " -0.001 2.00e-02 2.50e+03 ... (remaining 2742 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 256 2.50 - 3.10: 25207 3.10 - 3.70: 68095 3.70 - 4.30: 95019 4.30 - 4.90: 129330 Nonbonded interactions: 317907 Sorted by model distance: nonbonded pdb=" O2' G A1734 " pdb=" OP1 A A1735 " model vdw 1.904 3.040 nonbonded pdb=" O2' G A2692 " pdb=" O2' U A2847 " model vdw 1.926 3.040 nonbonded pdb=" O2' C A1351 " pdb=" O2' A A1571 " model vdw 1.931 3.040 nonbonded pdb=" O2' G A2859 " pdb=" O4' A A2860 " model vdw 1.943 3.040 nonbonded pdb=" OP2 G A1521 " pdb=" O2' A A1522 " model vdw 1.976 3.040 ... (remaining 317902 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.480 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 38.550 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 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 : 0.002 0.093 39578 Z= 0.087 Angle : 0.391 14.146 59867 Z= 0.205 Chirality : 0.027 0.460 7790 Planarity : 0.002 0.025 2745 Dihedral : 13.880 179.544 18776 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.58 % Favored : 95.22 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.72 (0.28), residues: 1047 helix: 2.05 (0.34), residues: 301 sheet: 0.67 (0.36), residues: 233 loop : -0.57 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG U 85 TYR 0.004 0.001 TYR N 112 PHE 0.008 0.001 PHE U 95 TRP 0.003 0.000 TRP T 80 HIS 0.002 0.000 HIS S 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00153 / 0.09 (39578) covalent geometry : angle 0.39119 / 0.21 (59867) hydrogen bonds : bond 0.09439 / 5.87 ( 1340) hydrogen bonds : angle 4.76139 / 3.21 ( 2506) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 11 MET cc_start: 0.7337 (ptm) cc_final: 0.7043 (ppp) REVERT: E 1 MET cc_start: 0.9193 (tmm) cc_final: 0.8787 (tmm) REVERT: K 4 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7523 (mp0) REVERT: K 20 MET cc_start: 0.8023 (ttt) cc_final: 0.7681 (tpp) REVERT: K 109 SER cc_start: 0.8242 (t) cc_final: 0.7994 (p) REVERT: K 113 MET cc_start: 0.8764 (mmp) cc_final: 0.8478 (mmm) REVERT: S 68 ASP cc_start: 0.8803 (t0) cc_final: 0.8233 (t0) REVERT: S 110 ARG cc_start: 0.8923 (tmm-80) cc_final: 0.8481 (ttp80) REVERT: U 38 ILE cc_start: 0.9062 (mm) cc_final: 0.8835 (mm) REVERT: Y 30 MET cc_start: 0.8937 (mmp) cc_final: 0.8427 (mmp) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.2199 time to fit residues: 21.8273 Evaluate side-chains 40 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 30.0000 chunk 194 optimal weight: 20.0000 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 30.0000 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 50.0000 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 50.0000 chunk 103 optimal weight: 20.0000 chunk 200 optimal weight: 9.9990 overall best weight: 13.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 0 41 HIS D 36 GLN E 115 GLN N 62 ASN S 31 GLN S 61 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.044819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.032225 restraints weight = 477490.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 78)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.031903 restraints weight = 220878.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.032136 restraints weight = 152186.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.032279 restraints weight = 130592.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.032354 restraints weight = 121775.223| |-----------------------------------------------------------------------------| r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.088 39578 Z= 0.408 Angle : 0.852 10.712 59867 Z= 0.419 Chirality : 0.042 0.269 7790 Planarity : 0.006 0.058 2745 Dihedral : 15.860 179.967 16658 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 23.72 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.35 % Favored : 92.36 % Rotamer: Outliers : 0.33 % Allowed : 4.55 % Favored : 95.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.89 (0.25), residues: 1047 helix: -0.06 (0.29), residues: 317 sheet: -0.27 (0.33), residues: 241 loop : -1.03 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Y 7 TYR 0.012 0.002 TYR P 98 PHE 0.035 0.003 PHE N 87 TRP 0.012 0.003 TRP P 30 HIS 0.009 0.002 HIS 2 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00779 / 0.41 (39578) covalent geometry : angle 0.85211 / 0.42 (59867) hydrogen bonds : bond 0.12248 / 7.96 ( 1340) hydrogen bonds : angle 4.47365 / 2.96 ( 2506) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 1 MET cc_start: 0.9034 (tmm) cc_final: 0.8677 (tmm) REVERT: K 20 MET cc_start: 0.8035 (ttt) cc_final: 0.7387 (tpp) REVERT: K 109 SER cc_start: 0.8025 (t) cc_final: 0.7735 (t) REVERT: N 1 MET cc_start: 0.2677 (ttt) cc_final: 0.2260 (ttp) REVERT: P 12 MET cc_start: 0.7479 (mmt) cc_final: 0.6933 (mmt) REVERT: Y 30 MET cc_start: 0.8998 (mmp) cc_final: 0.8413 (mmp) outliers start: 3 outliers final: 2 residues processed: 42 average time/residue: 0.1997 time to fit residues: 14.3431 Evaluate side-chains 36 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 105 optimal weight: 30.0000 chunk 184 optimal weight: 3.9990 chunk 60 optimal weight: 50.0000 chunk 34 optimal weight: 20.0000 chunk 133 optimal weight: 9.9990 chunk 192 optimal weight: 10.0000 chunk 96 optimal weight: 30.0000 chunk 111 optimal weight: 30.0000 chunk 81 optimal weight: 30.0000 chunk 119 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 overall best weight: 8.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 29 GLN ** K 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.044635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.032389 restraints weight = 478836.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.033024 restraints weight = 228465.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.032600 restraints weight = 145475.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.032643 restraints weight = 134984.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.032647 restraints weight = 135432.117| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.4468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 39578 Z= 0.261 Angle : 0.639 9.076 59867 Z= 0.322 Chirality : 0.035 0.251 7790 Planarity : 0.005 0.036 2745 Dihedral : 16.090 178.000 16658 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.88 % Favored : 92.74 % Rotamer: Outliers : 0.11 % Allowed : 3.77 % Favored : 96.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.01 (0.25), residues: 1047 helix: -0.09 (0.29), residues: 314 sheet: -0.42 (0.33), residues: 232 loop : -1.10 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 2 34 TYR 0.010 0.002 TYR S 38 PHE 0.012 0.002 PHE N 87 TRP 0.008 0.001 TRP D 80 HIS 0.007 0.002 HIS S 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.26 (39578) covalent geometry : angle 0.63908 / 0.32 (59867) hydrogen bonds : bond 0.08757 / 5.62 ( 1340) hydrogen bonds : angle 4.10982 / 2.75 ( 2506) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.625 Fit side-chains REVERT: E 1 MET cc_start: 0.8858 (tmm) cc_final: 0.8511 (tmm) REVERT: E 100 MET cc_start: 0.9322 (ptt) cc_final: 0.9069 (ppp) REVERT: K 20 MET cc_start: 0.8410 (ttt) cc_final: 0.7530 (tpp) REVERT: K 113 MET cc_start: 0.8693 (mmp) cc_final: 0.8445 (mmm) REVERT: Y 30 MET cc_start: 0.8974 (mmp) cc_final: 0.8333 (mmp) outliers start: 1 outliers final: 0 residues processed: 37 average time/residue: 0.2210 time to fit residues: 14.1785 Evaluate side-chains 32 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 151 optimal weight: 40.0000 chunk 47 optimal weight: 50.0000 chunk 31 optimal weight: 40.0000 chunk 158 optimal weight: 0.9990 chunk 138 optimal weight: 30.0000 chunk 171 optimal weight: 50.0000 chunk 40 optimal weight: 10.0000 chunk 225 optimal weight: 9.9990 chunk 96 optimal weight: 40.0000 chunk 163 optimal weight: 7.9990 chunk 75 optimal weight: 30.0000 overall best weight: 11.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 29 GLN K 29 HIS P 40 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.044116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.031529 restraints weight = 479937.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.031390 restraints weight = 216812.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.031581 restraints weight = 149448.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.031749 restraints weight = 130615.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.031852 restraints weight = 120644.455| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.5681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 39578 Z= 0.359 Angle : 0.786 11.957 59867 Z= 0.391 Chirality : 0.040 0.280 7790 Planarity : 0.006 0.043 2745 Dihedral : 16.903 178.348 16658 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 25.04 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.60 % Favored : 91.12 % Rotamer: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.79 (0.25), residues: 1047 helix: -0.90 (0.27), residues: 326 sheet: -1.02 (0.33), residues: 231 loop : -1.35 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG 2 34 TYR 0.014 0.002 TYR N 112 PHE 0.018 0.002 PHE Y 26 TRP 0.008 0.001 TRP D 80 HIS 0.007 0.002 HIS 0 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00687 / 0.36 (39578) covalent geometry : angle 0.78589 / 0.39 (59867) hydrogen bonds : bond 0.11812 / 7.61 ( 1340) hydrogen bonds : angle 4.47007 / 2.97 ( 2506) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: E 1 MET cc_start: 0.9010 (tmm) cc_final: 0.8587 (tmm) REVERT: K 20 MET cc_start: 0.8201 (ttt) cc_final: 0.7618 (tpp) REVERT: Y 30 MET cc_start: 0.9041 (mmp) cc_final: 0.8580 (mmp) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.2154 time to fit residues: 12.8824 Evaluate side-chains 31 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 78 optimal weight: 10.0000 chunk 224 optimal weight: 7.9990 chunk 214 optimal weight: 7.9990 chunk 20 optimal weight: 30.0000 chunk 103 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 233 optimal weight: 5.9990 chunk 187 optimal weight: 0.0470 chunk 49 optimal weight: 20.0000 chunk 89 optimal weight: 30.0000 chunk 223 optimal weight: 20.0000 overall best weight: 6.4088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 31 GLN ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.044259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.031800 restraints weight = 479892.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.031716 restraints weight = 207606.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.031986 restraints weight = 141212.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.032079 restraints weight = 120113.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.032195 restraints weight = 113462.926| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.5503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 39578 Z= 0.207 Angle : 0.606 9.510 59867 Z= 0.306 Chirality : 0.034 0.241 7790 Planarity : 0.004 0.039 2745 Dihedral : 16.484 178.355 16658 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.97 % Favored : 92.74 % Rotamer: Outliers : 0.11 % Allowed : 2.77 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.48 (0.25), residues: 1047 helix: -0.45 (0.29), residues: 319 sheet: -0.99 (0.33), residues: 234 loop : -1.24 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG 2 34 TYR 0.010 0.001 TYR N 112 PHE 0.011 0.002 PHE 2 18 TRP 0.007 0.001 TRP D 80 HIS 0.006 0.001 HIS S 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.21 (39578) covalent geometry : angle 0.60637 / 0.31 (59867) hydrogen bonds : bond 0.08502 / 5.46 ( 1340) hydrogen bonds : angle 4.04149 / 2.69 ( 2506) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.670 Fit side-chains revert: symmetry clash REVERT: E 1 MET cc_start: 0.9148 (tmm) cc_final: 0.8724 (tmm) REVERT: E 100 MET cc_start: 0.9252 (ptt) cc_final: 0.9042 (ppp) REVERT: K 20 MET cc_start: 0.8113 (ttt) cc_final: 0.7591 (tpp) REVERT: N 1 MET cc_start: 0.2337 (ttt) cc_final: 0.1892 (ttp) REVERT: N 20 MET cc_start: 0.9521 (tmm) cc_final: 0.9228 (tmm) REVERT: Y 30 MET cc_start: 0.8971 (mmp) cc_final: 0.8239 (mmp) outliers start: 1 outliers final: 0 residues processed: 36 average time/residue: 0.2238 time to fit residues: 14.1810 Evaluate side-chains 31 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 142 optimal weight: 30.0000 chunk 57 optimal weight: 20.0000 chunk 211 optimal weight: 10.0000 chunk 205 optimal weight: 4.9990 chunk 41 optimal weight: 30.0000 chunk 225 optimal weight: 6.9990 chunk 104 optimal weight: 20.0000 chunk 143 optimal weight: 20.0000 chunk 147 optimal weight: 0.8980 chunk 196 optimal weight: 20.0000 chunk 179 optimal weight: 3.9990 overall best weight: 5.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 11 GLN ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.044432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.032031 restraints weight = 477002.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.031916 restraints weight = 206349.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.032160 restraints weight = 139551.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.032218 restraints weight = 119910.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.032218 restraints weight = 114524.436| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.5509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 39578 Z= 0.183 Angle : 0.572 9.527 59867 Z= 0.288 Chirality : 0.032 0.241 7790 Planarity : 0.004 0.039 2745 Dihedral : 16.247 177.851 16658 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.16 % Favored : 92.55 % Rotamer: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.38 (0.25), residues: 1047 helix: -0.22 (0.29), residues: 319 sheet: -0.98 (0.33), residues: 234 loop : -1.26 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 2 34 TYR 0.009 0.001 TYR S 38 PHE 0.013 0.001 PHE Y 26 TRP 0.005 0.001 TRP D 80 HIS 0.005 0.001 HIS S 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.18 (39578) covalent geometry : angle 0.57208 / 0.29 (59867) hydrogen bonds : bond 0.07944 / 5.09 ( 1340) hydrogen bonds : angle 3.92843 / 2.63 ( 2506) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.768 Fit side-chains revert: symmetry clash REVERT: E 1 MET cc_start: 0.9101 (tmm) cc_final: 0.8660 (tmm) REVERT: K 20 MET cc_start: 0.8136 (ttt) cc_final: 0.7562 (tpp) REVERT: N 1 MET cc_start: 0.2407 (ttt) cc_final: 0.1816 (ttp) REVERT: N 20 MET cc_start: 0.9533 (tmm) cc_final: 0.9223 (tmm) REVERT: Y 30 MET cc_start: 0.8961 (mmp) cc_final: 0.8267 (mmp) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.2243 time to fit residues: 13.5158 Evaluate side-chains 32 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 70 optimal weight: 20.0000 chunk 2 optimal weight: 3.9990 chunk 30 optimal weight: 50.0000 chunk 43 optimal weight: 50.0000 chunk 108 optimal weight: 30.0000 chunk 24 optimal weight: 20.0000 chunk 9 optimal weight: 20.0000 chunk 154 optimal weight: 30.0000 chunk 92 optimal weight: 20.0000 chunk 190 optimal weight: 2.9990 chunk 216 optimal weight: 9.9990 overall best weight: 11.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN S 31 GLN ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.044043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.031298 restraints weight = 478930.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.031353 restraints weight = 219860.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.031594 restraints weight = 152051.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.031666 restraints weight = 128395.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.031706 restraints weight = 119946.146| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.6578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 39578 Z= 0.351 Angle : 0.786 9.275 59867 Z= 0.391 Chirality : 0.041 0.300 7790 Planarity : 0.006 0.057 2745 Dihedral : 17.245 179.226 16658 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 25.80 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.88 % Favored : 90.83 % Rotamer: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.96 (0.25), residues: 1047 helix: -0.94 (0.28), residues: 310 sheet: -1.31 (0.32), residues: 236 loop : -1.43 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 0 39 TYR 0.017 0.002 TYR N 112 PHE 0.031 0.002 PHE U 86 TRP 0.007 0.001 TRP D 80 HIS 0.007 0.002 HIS 0 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00669 / 0.35 (39578) covalent geometry : angle 0.78585 / 0.39 (59867) hydrogen bonds : bond 0.11461 / 7.29 ( 1340) hydrogen bonds : angle 4.43001 / 2.94 ( 2506) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.667 Fit side-chains revert: symmetry clash REVERT: E 1 MET cc_start: 0.9042 (tmm) cc_final: 0.8623 (tmm) REVERT: K 20 MET cc_start: 0.7917 (ttt) cc_final: 0.7416 (tpp) REVERT: N 1 MET cc_start: 0.2891 (ttt) cc_final: 0.2352 (ttp) REVERT: Y 30 MET cc_start: 0.9038 (mmp) cc_final: 0.8540 (mmp) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.2265 time to fit residues: 13.1479 Evaluate side-chains 31 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 3 optimal weight: 20.0000 chunk 229 optimal weight: 4.9990 chunk 165 optimal weight: 40.0000 chunk 227 optimal weight: 0.8980 chunk 127 optimal weight: 10.0000 chunk 230 optimal weight: 6.9990 chunk 221 optimal weight: 10.0000 chunk 6 optimal weight: 50.0000 chunk 199 optimal weight: 5.9990 chunk 60 optimal weight: 50.0000 chunk 65 optimal weight: 50.0000 overall best weight: 5.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 195 GLN S 31 GLN ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.044170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.031382 restraints weight = 476775.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.031472 restraints weight = 205326.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.031770 restraints weight = 137505.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.031822 restraints weight = 114979.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.031942 restraints weight = 110066.423| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.6272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 39578 Z= 0.192 Angle : 0.602 14.543 59867 Z= 0.303 Chirality : 0.033 0.240 7790 Planarity : 0.004 0.043 2745 Dihedral : 16.687 178.193 16658 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.02 % Favored : 91.69 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.61 (0.25), residues: 1047 helix: -0.45 (0.29), residues: 312 sheet: -1.13 (0.33), residues: 242 loop : -1.35 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 0 39 TYR 0.010 0.001 TYR S 38 PHE 0.009 0.001 PHE Y 26 TRP 0.006 0.001 TRP D 80 HIS 0.005 0.001 HIS S 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.19 (39578) covalent geometry : angle 0.60185 / 0.30 (59867) hydrogen bonds : bond 0.08164 / 5.19 ( 1340) hydrogen bonds : angle 4.00964 / 2.68 ( 2506) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.743 Fit side-chains revert: symmetry clash REVERT: E 1 MET cc_start: 0.9046 (tmm) cc_final: 0.8629 (tmm) REVERT: K 20 MET cc_start: 0.8099 (ttt) cc_final: 0.7555 (tpp) REVERT: N 1 MET cc_start: 0.2624 (ttt) cc_final: 0.2051 (ttp) REVERT: N 20 MET cc_start: 0.9541 (tmm) cc_final: 0.9208 (tmm) REVERT: Y 30 MET cc_start: 0.8973 (mmp) cc_final: 0.8253 (mmp) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.2279 time to fit residues: 14.0341 Evaluate side-chains 32 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 9.9990 chunk 141 optimal weight: 0.0980 chunk 32 optimal weight: 30.0000 chunk 90 optimal weight: 40.0000 chunk 12 optimal weight: 20.0000 chunk 122 optimal weight: 40.0000 chunk 91 optimal weight: 20.0000 chunk 200 optimal weight: 9.9990 chunk 83 optimal weight: 20.0000 chunk 165 optimal weight: 50.0000 chunk 233 optimal weight: 9.9990 overall best weight: 10.0190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... T 72 GLN ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.044047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.031445 restraints weight = 478248.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.031330 restraints weight = 215852.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.031598 restraints weight = 147854.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.031663 restraints weight = 126200.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.031663 restraints weight = 120084.922| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.6718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 39578 Z= 0.301 Angle : 0.709 13.653 59867 Z= 0.354 Chirality : 0.038 0.270 7790 Planarity : 0.005 0.043 2745 Dihedral : 17.075 178.753 16658 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 22.81 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.79 % Favored : 90.93 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.97 (0.25), residues: 1047 helix: -0.82 (0.28), residues: 311 sheet: -1.39 (0.32), residues: 232 loop : -1.49 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG S 18 TYR 0.013 0.002 TYR N 112 PHE 0.013 0.002 PHE U 86 TRP 0.006 0.001 TRP D 80 HIS 0.007 0.002 HIS 0 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.30 (39578) covalent geometry : angle 0.70876 / 0.35 (59867) hydrogen bonds : bond 0.09999 / 6.34 ( 1340) hydrogen bonds : angle 4.24125 / 2.83 ( 2506) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.672 Fit side-chains revert: symmetry clash REVERT: D 165 MET cc_start: 0.6722 (tmm) cc_final: 0.6283 (tmm) REVERT: E 1 MET cc_start: 0.9041 (tmm) cc_final: 0.8619 (tmm) REVERT: K 20 MET cc_start: 0.7884 (ttt) cc_final: 0.7446 (tpp) REVERT: N 1 MET cc_start: 0.2807 (ttt) cc_final: 0.2212 (ttp) REVERT: T 24 MET cc_start: 0.9302 (tmm) cc_final: 0.8888 (tmm) REVERT: Y 30 MET cc_start: 0.9036 (mmp) cc_final: 0.8387 (mmp) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.2268 time to fit residues: 13.5370 Evaluate side-chains 32 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 19 optimal weight: 30.0000 chunk 30 optimal weight: 50.0000 chunk 12 optimal weight: 10.0000 chunk 193 optimal weight: 10.0000 chunk 107 optimal weight: 30.0000 chunk 69 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 52 optimal weight: 20.0000 chunk 188 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 chunk 145 optimal weight: 7.9990 overall best weight: 7.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.044119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.031552 restraints weight = 477300.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.031432 restraints weight = 216488.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.031682 restraints weight = 150101.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.031731 restraints weight = 127489.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.031731 restraints weight = 121430.005| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.6723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 39578 Z= 0.251 Angle : 0.651 15.481 59867 Z= 0.327 Chirality : 0.035 0.250 7790 Planarity : 0.005 0.042 2745 Dihedral : 16.963 178.401 16658 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 20.04 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.60 % Favored : 91.12 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.25), residues: 1047 helix: -0.72 (0.28), residues: 312 sheet: -1.45 (0.34), residues: 218 loop : -1.40 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG S 18 TYR 0.011 0.002 TYR N 112 PHE 0.011 0.002 PHE U 86 TRP 0.006 0.001 TRP D 80 HIS 0.005 0.001 HIS 2 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.25 (39578) covalent geometry : angle 0.65097 / 0.33 (59867) hydrogen bonds : bond 0.08899 / 5.64 ( 1340) hydrogen bonds : angle 4.11435 / 2.76 ( 2506) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.682 Fit side-chains revert: symmetry clash REVERT: D 165 MET cc_start: 0.6727 (tmm) cc_final: 0.6411 (tmm) REVERT: E 1 MET cc_start: 0.9072 (tmm) cc_final: 0.8645 (tmm) REVERT: K 20 MET cc_start: 0.7878 (ttt) cc_final: 0.7441 (tpp) REVERT: K 32 TYR cc_start: 0.5419 (m-10) cc_final: 0.5191 (m-10) REVERT: N 1 MET cc_start: 0.2785 (ttt) cc_final: 0.2173 (ttp) REVERT: T 24 MET cc_start: 0.9302 (tmm) cc_final: 0.8883 (tmm) REVERT: Y 30 MET cc_start: 0.9002 (mmp) cc_final: 0.8340 (mmp) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.2229 time to fit residues: 13.3493 Evaluate side-chains 32 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 145 optimal weight: 8.9990 chunk 64 optimal weight: 50.0000 chunk 231 optimal weight: 20.0000 chunk 116 optimal weight: 10.0000 chunk 233 optimal weight: 0.9980 chunk 105 optimal weight: 30.0000 chunk 222 optimal weight: 6.9990 chunk 154 optimal weight: 6.9990 chunk 115 optimal weight: 20.0000 chunk 182 optimal weight: 0.8980 chunk 3 optimal weight: 30.0000 overall best weight: 4.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.044493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.031967 restraints weight = 470831.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.031844 restraints weight = 210257.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.032110 restraints weight = 145520.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.032242 restraints weight = 122934.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.032271 restraints weight = 116888.192| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.6522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 39578 Z= 0.170 Angle : 0.570 14.354 59867 Z= 0.287 Chirality : 0.032 0.236 7790 Planarity : 0.004 0.043 2745 Dihedral : 16.556 177.937 16658 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.16 % Favored : 92.55 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.56 (0.25), residues: 1047 helix: -0.28 (0.29), residues: 313 sheet: -1.30 (0.34), residues: 218 loop : -1.32 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 18 TYR 0.010 0.001 TYR S 38 PHE 0.007 0.001 PHE E 183 TRP 0.004 0.001 TRP D 80 HIS 0.004 0.001 HIS S 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.17 (39578) covalent geometry : angle 0.56999 / 0.29 (59867) hydrogen bonds : bond 0.07569 / 4.81 ( 1340) hydrogen bonds : angle 3.88922 / 2.61 ( 2506) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5522.42 seconds wall clock time: 97 minutes 9.40 seconds (5829.40 seconds total)