Starting phenix.real_space_refine on Sun Aug 9 14:30:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8c97_16504/08_2026/8c97_16504.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c97_16504/08_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_16504/08_2026/8c97_16504.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c97_16504/08_2026/8c97_16504.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8c97_16504/08_2026/8c97_16504.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c97_16504/08_2026/8c97_16504.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8c97_16504/08_2026/8c97_16504.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8c97_16504/08_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-2.2rc3-6140/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: {'RNAv2': 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: 7.05, per 1000 atoms: 0.19 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: 3.20 Conformation dependent library (CDL) restraints added in 603.7 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: 5.08 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: 14.40 Time building geometry restraints manager: 4.37 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 1.478 1.573 -0.095 2.00e-02 2.50e+03 2.25e+01 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=" N MET N 1 " pdb=" CA MET N 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.05e+00 bond pdb=" N ALA U 1 " pdb=" CA ALA U 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.04e+00 ... (remaining 39573 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 58350 2.73 - 5.46: 1506 5.46 - 8.19: 10 8.19 - 10.92: 0 10.92 - 13.65: 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 119.70 106.05 13.65 1.20e+00 6.94e-01 1.29e+02 angle pdb=" C3' G A2732 " pdb=" O3' G A2732 " pdb=" P A A2733 " ideal model delta sigma weight residual 119.70 112.76 6.94 1.20e+00 6.94e-01 3.35e+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=" 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=" C3' G A2731 " pdb=" O3' G A2731 " pdb=" P G A2732 " ideal model delta sigma weight residual 119.70 114.45 5.25 1.20e+00 6.94e-01 1.91e+01 ... (remaining 59862 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 18504 35.91 - 71.82: 2169 71.82 - 107.73: 102 107.73 - 143.64: 4 143.64 - 179.54: 3 Dihedral angle restraints: 20782 sinusoidal: 17702 harmonic: 3080 Sorted by residual: dihedral pdb=" C4' U A 395 " pdb=" C3' U A 395 " pdb=" C2' U A 395 " pdb=" C1' U A 395 " ideal model delta sinusoidal sigma weight residual 36.34 -38.14 74.49 1 3.10e+00 1.04e-01 7.32e+02 dihedral pdb=" C4' G A 215 " pdb=" C3' G A 215 " pdb=" C2' G A 215 " pdb=" C1' G A 215 " ideal model delta sinusoidal sigma weight residual 36.34 -37.33 73.67 1 3.10e+00 1.04e-01 7.18e+02 dihedral pdb=" C4' G A 512 " pdb=" C3' G A 512 " pdb=" C2' G A 512 " pdb=" C1' G A 512 " ideal model delta sinusoidal sigma weight residual 36.35 -37.11 73.45 1 3.10e+00 1.04e-01 7.14e+02 ... (remaining 20779 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.139: 6117 0.139 - 0.279: 1606 0.279 - 0.418: 64 0.418 - 0.558: 0 0.558 - 0.697: 3 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 2.17 -2.87 -0.70 2.00e-01 2.50e+01 1.21e+01 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 2.17 -2.87 -0.69 2.00e-01 2.50e+01 1.20e+01 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 2.17 -2.75 -0.58 2.00e-01 2.50e+01 8.38e+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: 2.580 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: 0.030 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 41.820 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.620 ------------------------------------------------------------------------------- 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 : 0.003 0.095 39578 Z= 0.133 Angle : 0.871 13.646 59867 Z= 0.357 Chirality : 0.117 0.697 7790 Planarity : 0.002 0.025 2745 Dihedral : 20.945 179.544 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 0.00264 / 0.13 (39578) covalent geometry : angle 0.87113 / 0.36 (59867) hydrogen bonds : bond 0.09439 / 5.56 ( 1340) hydrogen bonds : angle 4.76139 / 2.97 ( 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 : 0.667 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: 0.2195 time to fit residues: 22.2617 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 : 0.634 ------------------------------------------------------------------------------- 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: 20.0000 chunk 194 optimal weight: 20.0000 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 30.0000 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 40.0000 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 40.0000 chunk 103 optimal weight: 9.9990 chunk 200 optimal weight: 9.9990 overall best weight: 9.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 0 41 HIS D 36 GLN E 115 GLN E 163 ASN K 29 HIS S 61 ASN ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.045922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.033581 restraints weight = 475582.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.033443 restraints weight = 214684.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.033705 restraints weight = 146215.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.033849 restraints weight = 124737.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.033895 restraints weight = 117161.933| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 39578 Z= 0.350 Angle : 1.378 19.333 59867 Z= 0.542 Chirality : 0.102 1.515 7790 Planarity : 0.005 0.052 2745 Dihedral : 20.865 179.329 16658 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.78 % Favored : 93.03 % Rotamer: Outliers : 0.22 % Allowed : 2.89 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.17 (0.26), residues: 1047 helix: 0.73 (0.31), residues: 311 sheet: 0.23 (0.35), residues: 228 loop : -0.75 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 2 34 TYR 0.010 0.002 TYR E 101 PHE 0.026 0.002 PHE N 87 TRP 0.009 0.002 TRP P 30 HIS 0.007 0.002 HIS K 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00703 / 0.35 (39578) covalent geometry : angle 1.37751 / 0.54 (59867) hydrogen bonds : bond 0.10712 / 6.66 ( 1340) hydrogen bonds : angle 4.11314 / 2.53 ( 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 43 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.638 Fit side-chains REVERT: E 1 MET cc_start: 0.9129 (tmm) cc_final: 0.8676 (tmm) REVERT: K 20 MET cc_start: 0.8009 (ttt) cc_final: 0.7288 (tpp) REVERT: K 113 MET cc_start: 0.8666 (mmp) cc_final: 0.8389 (mmm) REVERT: N 20 MET cc_start: 0.9256 (tmm) cc_final: 0.9024 (tmm) REVERT: N 24 MET cc_start: 0.8814 (tpt) cc_final: 0.8557 (tpt) REVERT: P 12 MET cc_start: 0.7501 (mmt) cc_final: 0.6831 (mmt) REVERT: S 68 ASP cc_start: 0.9031 (t0) cc_final: 0.8641 (t0) REVERT: Y 30 MET cc_start: 0.8827 (mmp) cc_final: 0.8042 (mmp) outliers start: 2 outliers final: 1 residues processed: 43 average time/residue: 0.2237 time to fit residues: 16.5644 Evaluate side-chains 34 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.635 ------------------------------------------------------------------------------- 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: 20.0000 chunk 184 optimal weight: 5.9990 chunk 60 optimal weight: 40.0000 chunk 34 optimal weight: 20.0000 chunk 133 optimal weight: 10.0000 chunk 192 optimal weight: 20.0000 chunk 96 optimal weight: 20.0000 chunk 111 optimal weight: 20.0000 chunk 81 optimal weight: 20.0000 chunk 119 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 overall best weight: 11.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 40 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 = 0.3495 r_free = 0.3495 target = 0.044474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.032135 restraints weight = 483868.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.032036 restraints weight = 218612.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.032285 restraints weight = 151279.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.032418 restraints weight = 128897.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.032418 restraints weight = 121251.895| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.5548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.106 39578 Z= 0.376 Angle : 1.354 16.047 59867 Z= 0.539 Chirality : 0.097 1.108 7790 Planarity : 0.006 0.066 2745 Dihedral : 21.527 179.965 16658 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 26.70 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.45 % Favored : 92.07 % Rotamer: Outliers : 0.33 % Allowed : 5.33 % Favored : 94.34 % 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: -1.39 (0.25), residues: 1047 helix: -0.57 (0.28), residues: 322 sheet: -0.69 (0.31), residues: 250 loop : -1.18 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 0 39 TYR 0.012 0.002 TYR E 101 PHE 0.024 0.003 PHE N 87 TRP 0.009 0.002 TRP D 80 HIS 0.007 0.002 HIS 2 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00759 / 0.38 (39578) covalent geometry : angle 1.35396 / 0.54 (59867) hydrogen bonds : bond 0.11848 / 7.15 ( 1340) hydrogen bonds : angle 4.45660 / 2.70 ( 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 40 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.642 Fit side-chains revert: symmetry clash REVERT: E 1 MET cc_start: 0.9084 (tmm) cc_final: 0.8666 (tmm) REVERT: E 100 MET cc_start: 0.9284 (ptt) cc_final: 0.8995 (ppp) REVERT: K 20 MET cc_start: 0.8169 (ttt) cc_final: 0.7601 (tpp) REVERT: N 1 MET cc_start: 0.3015 (ttt) cc_final: 0.2645 (ttp) REVERT: N 24 MET cc_start: 0.8940 (tpt) cc_final: 0.8651 (tpp) REVERT: Y 30 MET cc_start: 0.9035 (mmp) cc_final: 0.8540 (mmp) outliers start: 3 outliers final: 3 residues processed: 40 average time/residue: 0.2094 time to fit residues: 14.6065 Evaluate side-chains 34 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.610 ------------------------------------------------------------------------------- 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: 30.0000 chunk 47 optimal weight: 30.0000 chunk 31 optimal weight: 30.0000 chunk 158 optimal weight: 10.0000 chunk 138 optimal weight: 20.0000 chunk 171 optimal weight: 30.0000 chunk 40 optimal weight: 10.0000 chunk 225 optimal weight: 6.9990 chunk 96 optimal weight: 20.0000 chunk 163 optimal weight: 8.9990 chunk 75 optimal weight: 20.0000 overall best weight: 11.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 26 ASN 2 29 GLN S 31 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.044187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.031872 restraints weight = 486588.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.031799 restraints weight = 217132.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.032017 restraints weight = 148098.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.032184 restraints weight = 127856.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.032228 restraints weight = 119645.032| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.6129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 39578 Z= 0.368 Angle : 1.311 16.441 59867 Z= 0.519 Chirality : 0.093 1.116 7790 Planarity : 0.006 0.057 2745 Dihedral : 21.446 176.018 16658 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 25.19 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.02 % Favored : 91.69 % Rotamer: Outliers : 0.11 % Allowed : 3.88 % Favored : 96.00 % 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: -1.69 (0.25), residues: 1047 helix: -0.82 (0.28), residues: 324 sheet: -1.01 (0.32), residues: 236 loop : -1.27 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG 2 34 TYR 0.017 0.002 TYR N 112 PHE 0.012 0.002 PHE N 87 TRP 0.009 0.001 TRP D 80 HIS 0.007 0.002 HIS 0 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00743 / 0.37 (39578) covalent geometry : angle 1.31106 / 0.52 (59867) hydrogen bonds : bond 0.11202 / 6.85 ( 1340) hydrogen bonds : angle 4.45094 / 2.72 ( 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 36 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.659 Fit side-chains revert: symmetry clash REVERT: E 1 MET cc_start: 0.9028 (tmm) cc_final: 0.8605 (tmm) REVERT: K 20 MET cc_start: 0.8196 (ttt) cc_final: 0.7619 (tpp) REVERT: N 1 MET cc_start: 0.3175 (ttt) cc_final: 0.2809 (ttp) REVERT: N 24 MET cc_start: 0.8783 (tpt) cc_final: 0.8499 (tpt) REVERT: Y 30 MET cc_start: 0.8958 (mmp) cc_final: 0.8420 (mmp) outliers start: 1 outliers final: 1 residues processed: 36 average time/residue: 0.2096 time to fit residues: 13.3013 Evaluate side-chains 32 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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: 9.9990 chunk 224 optimal weight: 8.9990 chunk 214 optimal weight: 8.9990 chunk 20 optimal weight: 20.0000 chunk 103 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 233 optimal weight: 5.9990 chunk 187 optimal weight: 6.9990 chunk 49 optimal weight: 20.0000 chunk 89 optimal weight: 20.0000 chunk 223 optimal weight: 30.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- 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 = 0.3493 r_free = 0.3493 target = 0.044305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.031939 restraints weight = 484098.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.031901 restraints weight = 215532.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.032161 restraints weight = 149064.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.032320 restraints weight = 125451.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.032313 restraints weight = 118136.716| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.6337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 39578 Z= 0.293 Angle : 1.203 14.740 59867 Z= 0.476 Chirality : 0.087 0.984 7790 Planarity : 0.005 0.047 2745 Dihedral : 21.320 179.332 16658 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 22.45 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.93 % Favored : 91.79 % Rotamer: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % 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: -1.59 (0.25), residues: 1047 helix: -0.65 (0.28), residues: 319 sheet: -0.89 (0.33), residues: 224 loop : -1.31 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG 2 34 TYR 0.012 0.002 TYR N 112 PHE 0.019 0.002 PHE Y 26 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 0.00590 / 0.29 (39578) covalent geometry : angle 1.20260 / 0.48 (59867) hydrogen bonds : bond 0.10010 / 6.16 ( 1340) hydrogen bonds : angle 4.23980 / 2.59 ( 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 35 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.542 Fit side-chains revert: symmetry clash REVERT: E 1 MET cc_start: 0.9156 (tmm) cc_final: 0.8709 (tmm) REVERT: K 20 MET cc_start: 0.8148 (ttt) cc_final: 0.7611 (tpp) REVERT: N 1 MET cc_start: 0.2303 (ttt) cc_final: 0.1966 (ttp) REVERT: S 1 MET cc_start: 0.6950 (ptt) cc_final: 0.6712 (ptt) REVERT: Y 30 MET cc_start: 0.8975 (mmp) cc_final: 0.8286 (mmp) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1937 time to fit residues: 12.0836 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 : 0.617 ------------------------------------------------------------------------------- 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: 10.0000 chunk 211 optimal weight: 7.9990 chunk 205 optimal weight: 0.7980 chunk 41 optimal weight: 20.0000 chunk 225 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 chunk 143 optimal weight: 4.9990 chunk 147 optimal weight: 20.0000 chunk 196 optimal weight: 10.0000 chunk 179 optimal weight: 1.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 40 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 = 0.3524 r_free = 0.3524 target = 0.045086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.032027 restraints weight = 480411.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.032589 restraints weight = 213176.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.032909 restraints weight = 147498.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.033017 restraints weight = 125238.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.033111 restraints weight = 117896.639| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.6132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 39578 Z= 0.182 Angle : 1.060 13.764 59867 Z= 0.420 Chirality : 0.081 0.866 7790 Planarity : 0.004 0.044 2745 Dihedral : 20.967 179.411 16658 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.78 % Favored : 93.03 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % 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: -1.22 (0.25), residues: 1047 helix: 0.06 (0.30), residues: 298 sheet: -0.71 (0.33), residues: 226 loop : -1.33 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 0 39 TYR 0.008 0.001 TYR S 38 PHE 0.011 0.001 PHE P 73 TRP 0.004 0.001 TRP D 80 HIS 0.005 0.001 HIS S 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.18 (39578) covalent geometry : angle 1.06000 / 0.42 (59867) hydrogen bonds : bond 0.08395 / 5.28 ( 1340) hydrogen bonds : angle 3.92675 / 2.42 ( 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 36 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.634 Fit side-chains revert: symmetry clash REVERT: E 1 MET cc_start: 0.9178 (tmm) cc_final: 0.8743 (tmm) REVERT: K 20 MET cc_start: 0.8149 (ttt) cc_final: 0.7564 (tpp) REVERT: N 1 MET cc_start: 0.1753 (ttt) cc_final: 0.1337 (ttp) REVERT: N 20 MET cc_start: 0.9545 (tmm) cc_final: 0.9238 (tmm) REVERT: Y 30 MET cc_start: 0.8786 (mmp) cc_final: 0.8054 (mmp) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1930 time to fit residues: 12.4735 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 : 0.643 ------------------------------------------------------------------------------- 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: 10.0000 chunk 2 optimal weight: 6.9990 chunk 30 optimal weight: 30.0000 chunk 43 optimal weight: 40.0000 chunk 108 optimal weight: 30.0000 chunk 24 optimal weight: 20.0000 chunk 9 optimal weight: 9.9990 chunk 154 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 chunk 190 optimal weight: 0.6980 chunk 216 optimal weight: 20.0000 overall best weight: 7.5390 ------------------------------------------------------------------------------- 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 = 0.3501 r_free = 0.3501 target = 0.044626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.031444 restraints weight = 481350.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.032000 restraints weight = 215131.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 72)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.032285 restraints weight = 150307.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.032386 restraints weight = 128561.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.032470 restraints weight = 121316.640| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.6358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 39578 Z= 0.267 Angle : 1.140 14.720 59867 Z= 0.451 Chirality : 0.083 0.861 7790 Planarity : 0.005 0.044 2745 Dihedral : 21.038 179.231 16658 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 19.94 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.35 % Favored : 92.36 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % 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: -0.20 (0.29), residues: 311 sheet: -0.81 (0.33), residues: 227 loop : -1.37 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 0 39 TYR 0.009 0.001 TYR N 112 PHE 0.010 0.002 PHE P 58 TRP 0.004 0.001 TRP D 80 HIS 0.005 0.001 HIS S 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.27 (39578) covalent geometry : angle 1.13986 / 0.45 (59867) hydrogen bonds : bond 0.09424 / 5.83 ( 1340) hydrogen bonds : angle 4.05722 / 2.48 ( 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 : 0.628 Fit side-chains revert: symmetry clash REVERT: D 165 MET cc_start: 0.6509 (tmm) cc_final: 0.6132 (tmm) REVERT: E 1 MET cc_start: 0.9140 (tmm) cc_final: 0.8678 (tmm) REVERT: K 20 MET cc_start: 0.8140 (ttt) cc_final: 0.7569 (tpp) REVERT: N 1 MET cc_start: 0.2027 (ttt) cc_final: 0.1665 (ttp) REVERT: Y 30 MET cc_start: 0.8875 (mmp) cc_final: 0.8139 (mmp) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1979 time to fit residues: 11.5686 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 : 0.537 ------------------------------------------------------------------------------- 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: 30.0000 chunk 229 optimal weight: 6.9990 chunk 165 optimal weight: 2.9990 chunk 227 optimal weight: 6.9990 chunk 127 optimal weight: 10.0000 chunk 230 optimal weight: 0.9990 chunk 221 optimal weight: 4.9990 chunk 6 optimal weight: 50.0000 chunk 199 optimal weight: 0.8980 chunk 60 optimal weight: 40.0000 chunk 65 optimal weight: 40.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 = 0.3531 r_free = 0.3531 target = 0.045195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.032989 restraints weight = 479683.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.032914 restraints weight = 214592.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.033207 restraints weight = 145614.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.033365 restraints weight = 121768.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.033377 restraints weight = 114212.791| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.6255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 39578 Z= 0.173 Angle : 1.039 14.384 59867 Z= 0.412 Chirality : 0.078 0.855 7790 Planarity : 0.004 0.049 2745 Dihedral : 20.854 179.789 16658 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.21 % Favored : 93.51 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % 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: -1.08 (0.26), residues: 1047 helix: 0.19 (0.30), residues: 305 sheet: -0.77 (0.33), residues: 240 loop : -1.20 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG T 73 TYR 0.009 0.001 TYR S 38 PHE 0.012 0.001 PHE P 73 TRP 0.004 0.001 TRP D 80 HIS 0.006 0.001 HIS S 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.17 (39578) covalent geometry : angle 1.03872 / 0.41 (59867) hydrogen bonds : bond 0.08268 / 5.20 ( 1340) hydrogen bonds : angle 3.84184 / 2.37 ( 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 37 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.626 Fit side-chains revert: symmetry clash REVERT: D 186 LEU cc_start: 0.8865 (tt) cc_final: 0.8585 (mt) REVERT: E 1 MET cc_start: 0.9188 (tmm) cc_final: 0.8743 (tmm) REVERT: K 20 MET cc_start: 0.8152 (ttt) cc_final: 0.7572 (tpp) REVERT: N 1 MET cc_start: 0.1913 (ttt) cc_final: 0.1550 (ttp) REVERT: N 20 MET cc_start: 0.9534 (tmm) cc_final: 0.9214 (tmm) REVERT: S 1 MET cc_start: 0.6701 (ptt) cc_final: 0.6499 (ptt) REVERT: Y 30 MET cc_start: 0.8788 (mmp) cc_final: 0.8123 (mmp) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.2029 time to fit residues: 13.4331 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 : 0.644 ------------------------------------------------------------------------------- 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: 6.9990 chunk 141 optimal weight: 0.0030 chunk 32 optimal weight: 20.0000 chunk 90 optimal weight: 30.0000 chunk 12 optimal weight: 9.9990 chunk 122 optimal weight: 30.0000 chunk 91 optimal weight: 10.0000 chunk 200 optimal weight: 20.0000 chunk 83 optimal weight: 10.0000 chunk 165 optimal weight: 0.9980 chunk 233 optimal weight: 9.9990 overall best weight: 5.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** S 57 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 = 0.3522 r_free = 0.3522 target = 0.045000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.032756 restraints weight = 480855.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.032687 restraints weight = 216325.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.032962 restraints weight = 146578.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.033137 restraints weight = 123637.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.033139 restraints weight = 114778.038| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.6299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 39578 Z= 0.215 Angle : 1.066 13.446 59867 Z= 0.422 Chirality : 0.079 0.839 7790 Planarity : 0.004 0.045 2745 Dihedral : 20.876 179.738 16658 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.21 % Favored : 93.51 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % 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: -1.09 (0.26), residues: 1047 helix: 0.21 (0.30), residues: 305 sheet: -0.82 (0.32), residues: 240 loop : -1.20 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 0 39 TYR 0.013 0.002 TYR S 38 PHE 0.011 0.001 PHE Y 26 TRP 0.004 0.001 TRP D 80 HIS 0.005 0.001 HIS S 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.22 (39578) covalent geometry : angle 1.06644 / 0.42 (59867) hydrogen bonds : bond 0.08464 / 5.30 ( 1340) hydrogen bonds : angle 3.85660 / 2.37 ( 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 33 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.624 Fit side-chains revert: symmetry clash REVERT: D 11 MET cc_start: 0.8606 (ptm) cc_final: 0.8018 (ppp) REVERT: D 186 LEU cc_start: 0.8892 (tt) cc_final: 0.8602 (mt) REVERT: E 1 MET cc_start: 0.9153 (tmm) cc_final: 0.8700 (tmm) REVERT: K 20 MET cc_start: 0.8140 (ttt) cc_final: 0.7573 (tpp) REVERT: N 1 MET cc_start: 0.1966 (ttt) cc_final: 0.1600 (ttp) REVERT: Y 30 MET cc_start: 0.8831 (mmp) cc_final: 0.8139 (mmp) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1975 time to fit residues: 11.8402 Evaluate side-chains 30 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.446 ------------------------------------------------------------------------------- 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: 20.0000 chunk 30 optimal weight: 30.0000 chunk 12 optimal weight: 10.0000 chunk 193 optimal weight: 8.9990 chunk 107 optimal weight: 20.0000 chunk 69 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 188 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 chunk 145 optimal weight: 0.7980 overall best weight: 7.5592 ------------------------------------------------------------------------------- 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 = 0.3508 r_free = 0.3508 target = 0.044626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.032214 restraints weight = 481225.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.032187 restraints weight = 217244.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.032468 restraints weight = 148772.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.032635 restraints weight = 125506.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.032642 restraints weight = 116371.860| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.6434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 39578 Z= 0.262 Angle : 1.122 14.000 59867 Z= 0.444 Chirality : 0.081 0.835 7790 Planarity : 0.005 0.046 2745 Dihedral : 20.959 179.870 16658 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 20.31 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.55 % Favored : 92.17 % 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: -1.32 (0.25), residues: 1047 helix: -0.03 (0.30), residues: 311 sheet: -0.97 (0.32), residues: 234 loop : -1.31 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 2 34 TYR 0.007 0.001 TYR P 98 PHE 0.011 0.002 PHE U 86 TRP 0.006 0.001 TRP P 30 HIS 0.005 0.001 HIS 2 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.26 (39578) covalent geometry : angle 1.12167 / 0.44 (59867) hydrogen bonds : bond 0.09160 / 5.67 ( 1340) hydrogen bonds : angle 3.98006 / 2.44 ( 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 33 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.620 Fit side-chains revert: symmetry clash REVERT: E 1 MET cc_start: 0.9169 (tmm) cc_final: 0.8692 (tmm) REVERT: E 199 MET cc_start: 0.5851 (tpt) cc_final: 0.5066 (tpt) REVERT: K 20 MET cc_start: 0.8139 (ttt) cc_final: 0.7569 (tpp) REVERT: N 1 MET cc_start: 0.2012 (ttt) cc_final: 0.1660 (ttp) REVERT: Y 30 MET cc_start: 0.8869 (mmp) cc_final: 0.8180 (mmp) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.2076 time to fit residues: 12.1644 Evaluate side-chains 30 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.403 ------------------------------------------------------------------------------- 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: 6.9990 chunk 64 optimal weight: 50.0000 chunk 231 optimal weight: 8.9990 chunk 116 optimal weight: 10.0000 chunk 233 optimal weight: 0.8980 chunk 105 optimal weight: 20.0000 chunk 222 optimal weight: 0.9980 chunk 154 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 182 optimal weight: 1.9990 chunk 3 optimal weight: 20.0000 overall best weight: 3.9786 ------------------------------------------------------------------------------- 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 = 0.3530 r_free = 0.3530 target = 0.045049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.032891 restraints weight = 477667.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.032770 restraints weight = 213518.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.033039 restraints weight = 143779.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.033195 restraints weight = 122925.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.033230 restraints weight = 114946.836| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.6422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 39578 Z= 0.180 Angle : 1.044 13.662 59867 Z= 0.414 Chirality : 0.079 0.852 7790 Planarity : 0.004 0.047 2745 Dihedral : 20.873 179.696 16658 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.11 % Favored : 93.60 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.14 (0.25), residues: 1047 helix: 0.19 (0.30), residues: 305 sheet: -0.81 (0.33), residues: 221 loop : -1.27 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 0 39 TYR 0.009 0.001 TYR S 38 PHE 0.010 0.001 PHE P 73 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 0.00362 / 0.18 (39578) covalent geometry : angle 1.04351 / 0.41 (59867) hydrogen bonds : bond 0.08445 / 5.30 ( 1340) hydrogen bonds : angle 3.86571 / 2.38 ( 2506) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5454.61 seconds wall clock time: 95 minutes 51.79 seconds (5751.79 seconds total)