Starting phenix.real_space_refine on Sat Jul 4 06:28:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pbu_13303/07_2026/7pbu_13303_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pbu_13303/07_2026/7pbu_13303.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7pbu_13303/07_2026/7pbu_13303_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pbu_13303/07_2026/7pbu_13303_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pbu_13303/07_2026/7pbu_13303.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pbu_13303/07_2026/7pbu_13303.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 68 5.49 5 S 40 5.16 5 C 6060 2.51 5 N 1666 2.21 5 O 1902 1.98 5 H 9507 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 19243 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2137 Classifications: {'peptide': 133} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 126} Chain: "B" Number of atoms: 2137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2137 Classifications: {'peptide': 133} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 126} Chain: "C" Number of atoms: 2137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2137 Classifications: {'peptide': 133} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 126} Chain: "D" Number of atoms: 2137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2137 Classifications: {'peptide': 133} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 126} Chain: "E" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 544 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "F" Number of atoms: 2137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2137 Classifications: {'peptide': 133} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 126} Chain: "G" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 544 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "H" Number of atoms: 2114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 2114 Classifications: {'peptide': 132} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 125} Chain: "I" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 541 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "J" Number of atoms: 2137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2137 Classifications: {'peptide': 133} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 126} Chain: "K" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 541 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "L" Number of atoms: 2137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2137 Classifications: {'peptide': 133} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 126} Time building chain proxies: 4.04, per 1000 atoms: 0.21 Number of scatterers: 19243 At special positions: 0 Unit cell: (88.29, 104.64, 101.37, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 40 16.00 P 68 15.00 O 1902 8.00 N 1666 7.00 C 6060 6.00 H 9507 1.00 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: 1.91 Conformation dependent library (CDL) restraints added in 780.3 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: 1918 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 2 sheets defined 49.6% alpha, 13.4% beta 15 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 3.24 Creating SS restraints... Processing helix chain 'A' and resid 34 through 38 Processing helix chain 'A' and resid 65 through 77 removed outlier: 3.676A pdb=" N LYS A 77 " --> pdb=" O LYS A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 93 Processing helix chain 'A' and resid 94 through 105 Processing helix chain 'A' and resid 106 through 112 removed outlier: 3.632A pdb=" N LEU A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 133 removed outlier: 4.631A pdb=" N ASP A 130 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ARG A 131 " --> pdb=" O GLU A 127 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE A 132 " --> pdb=" O MET A 128 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LYS A 133 " --> pdb=" O LYS A 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 38 Processing helix chain 'B' and resid 65 through 77 removed outlier: 3.646A pdb=" N LYS B 77 " --> pdb=" O LYS B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'B' and resid 94 through 105 Processing helix chain 'B' and resid 106 through 112 removed outlier: 3.582A pdb=" N LEU B 110 " --> pdb=" O GLU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 133 removed outlier: 4.598A pdb=" N ASP B 130 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ARG B 131 " --> pdb=" O GLU B 127 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE B 132 " --> pdb=" O MET B 128 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LYS B 133 " --> pdb=" O LYS B 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 38 removed outlier: 3.753A pdb=" N TYR C 36 " --> pdb=" O THR C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 77 removed outlier: 3.623A pdb=" N LYS C 77 " --> pdb=" O LYS C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 93 Processing helix chain 'C' and resid 94 through 105 Processing helix chain 'C' and resid 106 through 112 removed outlier: 3.651A pdb=" N LEU C 110 " --> pdb=" O GLU C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 133 removed outlier: 4.582A pdb=" N ASP C 130 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ARG C 131 " --> pdb=" O GLU C 127 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE C 132 " --> pdb=" O MET C 128 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LYS C 133 " --> pdb=" O LYS C 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 38 Processing helix chain 'D' and resid 65 through 77 removed outlier: 3.673A pdb=" N LYS D 77 " --> pdb=" O LYS D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 93 Processing helix chain 'D' and resid 94 through 105 Processing helix chain 'D' and resid 106 through 112 removed outlier: 3.628A pdb=" N LEU D 110 " --> pdb=" O GLU D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 133 removed outlier: 4.626A pdb=" N ASP D 130 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ARG D 131 " --> pdb=" O GLU D 127 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE D 132 " --> pdb=" O MET D 128 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LYS D 133 " --> pdb=" O LYS D 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 38 Processing helix chain 'F' and resid 65 through 77 removed outlier: 3.612A pdb=" N LYS F 77 " --> pdb=" O LYS F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'F' and resid 94 through 105 Processing helix chain 'F' and resid 106 through 112 removed outlier: 3.646A pdb=" N LEU F 110 " --> pdb=" O GLU F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 133 removed outlier: 4.586A pdb=" N ASP F 130 " --> pdb=" O VAL F 126 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ARG F 131 " --> pdb=" O GLU F 127 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE F 132 " --> pdb=" O MET F 128 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LYS F 133 " --> pdb=" O LYS F 129 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 38 Processing helix chain 'H' and resid 65 through 77 removed outlier: 3.631A pdb=" N LYS H 77 " --> pdb=" O LYS H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 93 Processing helix chain 'H' and resid 94 through 105 Processing helix chain 'H' and resid 106 through 112 removed outlier: 3.681A pdb=" N LEU H 110 " --> pdb=" O GLU H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 129 Processing helix chain 'J' and resid 34 through 38 Processing helix chain 'J' and resid 65 through 78 removed outlier: 3.574A pdb=" N LYS J 77 " --> pdb=" O LYS J 73 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR J 78 " --> pdb=" O GLU J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 93 Processing helix chain 'J' and resid 94 through 105 Processing helix chain 'J' and resid 106 through 112 removed outlier: 3.638A pdb=" N LEU J 110 " --> pdb=" O GLU J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 117 through 133 removed outlier: 4.592A pdb=" N ASP J 130 " --> pdb=" O VAL J 126 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ARG J 131 " --> pdb=" O GLU J 127 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE J 132 " --> pdb=" O MET J 128 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LYS J 133 " --> pdb=" O LYS J 129 " (cutoff:3.500A) Processing helix chain 'L' and resid 33 through 38 removed outlier: 3.646A pdb=" N TYR L 36 " --> pdb=" O THR L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 65 through 77 removed outlier: 3.661A pdb=" N LYS L 77 " --> pdb=" O LYS L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 93 Processing helix chain 'L' and resid 94 through 105 Processing helix chain 'L' and resid 106 through 112 removed outlier: 3.640A pdb=" N LEU L 110 " --> pdb=" O GLU L 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 117 through 133 removed outlier: 4.584A pdb=" N ASP L 130 " --> pdb=" O VAL L 126 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARG L 131 " --> pdb=" O GLU L 127 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE L 132 " --> pdb=" O MET L 128 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LYS L 133 " --> pdb=" O LYS L 129 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 13 removed outlier: 6.820A pdb=" N LEU A 18 " --> pdb=" O LEU A 10 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LYS A 12 " --> pdb=" O ILE A 16 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ILE A 16 " --> pdb=" O LYS A 12 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 24 through 29 current: chain 'A' and resid 58 through 63 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 58 through 63 current: chain 'B' and resid 16 through 21 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 24 through 29 current: chain 'B' and resid 58 through 63 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 58 through 63 current: chain 'C' and resid 16 through 21 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 24 through 29 current: chain 'C' and resid 58 through 63 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 58 through 63 current: chain 'D' and resid 16 through 21 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 24 through 29 current: chain 'D' and resid 58 through 63 Processing sheet with id=AA2, first strand: chain 'F' and resid 2 through 13 removed outlier: 6.788A pdb=" N LEU F 18 " --> pdb=" O LEU F 10 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N LYS F 12 " --> pdb=" O ILE F 16 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ILE F 16 " --> pdb=" O LYS F 12 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 24 through 29 current: chain 'F' and resid 58 through 63 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 58 through 63 current: chain 'H' and resid 16 through 21 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 24 through 29 current: chain 'H' and resid 58 through 63 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 58 through 63 current: chain 'J' and resid 16 through 21 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 24 through 29 current: chain 'J' and resid 58 through 63 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 58 through 63 current: chain 'L' and resid 16 through 21 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 24 through 29 current: chain 'L' and resid 58 through 63 350 hydrogen bonds defined for protein. 978 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 32 hydrogen bonds 64 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 3.80 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9499 1.03 - 1.22: 36 1.22 - 1.42: 3958 1.42 - 1.61: 5939 1.61 - 1.80: 113 Bond restraints: 19545 Sorted by residual: bond pdb=" C5' DT K 7 " pdb=" C4' DT K 7 " ideal model delta sigma weight residual 1.512 1.536 -0.024 7.00e-03 2.04e+04 1.16e+01 bond pdb=" C1' DT E 32 " pdb=" N1 DT E 32 " ideal model delta sigma weight residual 1.468 1.512 -0.044 1.40e-02 5.10e+03 9.74e+00 bond pdb=" C5' DA E 35 " pdb=" C4' DA E 35 " ideal model delta sigma weight residual 1.512 1.533 -0.021 7.00e-03 2.04e+04 8.80e+00 bond pdb=" C1' DT G 32 " pdb=" N1 DT G 32 " ideal model delta sigma weight residual 1.468 1.509 -0.041 1.40e-02 5.10e+03 8.44e+00 bond pdb=" C3' DT E 25 " pdb=" C2' DT E 25 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.30e+00 ... (remaining 19540 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 32049 1.16 - 2.33: 3153 2.33 - 3.49: 326 3.49 - 4.65: 67 4.65 - 5.82: 27 Bond angle restraints: 35622 Sorted by residual: angle pdb=" O5' DA E 34 " pdb=" C5' DA E 34 " pdb=" C4' DA E 34 " ideal model delta sigma weight residual 109.40 113.42 -4.02 8.00e-01 1.56e+00 2.52e+01 angle pdb=" O4' DG G 41 " pdb=" C4' DG G 41 " pdb=" C3' DG G 41 " ideal model delta sigma weight residual 106.00 103.03 2.97 6.00e-01 2.78e+00 2.44e+01 angle pdb=" O4' DG E 41 " pdb=" C4' DG E 41 " pdb=" C3' DG E 41 " ideal model delta sigma weight residual 106.00 103.05 2.95 6.00e-01 2.78e+00 2.42e+01 angle pdb=" O5' DT K 9 " pdb=" C5' DT K 9 " pdb=" C4' DT K 9 " ideal model delta sigma weight residual 109.40 113.23 -3.83 8.00e-01 1.56e+00 2.29e+01 angle pdb=" C4' DT E 25 " pdb=" O4' DT E 25 " pdb=" C1' DT E 25 " ideal model delta sigma weight residual 110.10 105.71 4.39 1.00e+00 1.00e+00 1.93e+01 ... (remaining 35617 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 7840 17.86 - 35.73: 551 35.73 - 53.59: 280 53.59 - 71.45: 132 71.45 - 89.31: 11 Dihedral angle restraints: 8814 sinusoidal: 5393 harmonic: 3421 Sorted by residual: dihedral pdb=" CA LYS D 84 " pdb=" CB LYS D 84 " pdb=" CG LYS D 84 " pdb=" CD LYS D 84 " ideal model delta sinusoidal sigma weight residual 180.00 126.48 53.52 3 1.50e+01 4.44e-03 9.21e+00 dihedral pdb=" CB GLU A 106 " pdb=" CG GLU A 106 " pdb=" CD GLU A 106 " pdb=" OE1 GLU A 106 " ideal model delta sinusoidal sigma weight residual 0.00 73.71 -73.71 1 3.00e+01 1.11e-03 7.68e+00 dihedral pdb=" CG ARG J 54 " pdb=" CD ARG J 54 " pdb=" NE ARG J 54 " pdb=" CZ ARG J 54 " ideal model delta sinusoidal sigma weight residual -90.00 -124.88 34.88 2 1.50e+01 4.44e-03 6.98e+00 ... (remaining 8811 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1221 0.060 - 0.120: 293 0.120 - 0.181: 36 0.181 - 0.241: 19 0.241 - 0.301: 6 Chirality restraints: 1575 Sorted by residual: chirality pdb=" C3' DT E 30 " pdb=" C4' DT E 30 " pdb=" O3' DT E 30 " pdb=" C2' DT E 30 " both_signs ideal model delta sigma weight residual False -2.73 -2.43 -0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" C3' DT G 30 " pdb=" C4' DT G 30 " pdb=" O3' DT G 30 " pdb=" C2' DT G 30 " both_signs ideal model delta sigma weight residual False -2.73 -2.44 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" C3' DT G 28 " pdb=" C4' DT G 28 " pdb=" O3' DT G 28 " pdb=" C2' DT G 28 " both_signs ideal model delta sigma weight residual False -2.73 -2.47 -0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 1572 not shown) Planarity restraints: 2585 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 64 " 0.015 2.00e-02 2.50e+03 2.68e-02 1.08e+01 pdb=" CG ASN A 64 " -0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN A 64 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN A 64 " 0.047 2.00e-02 2.50e+03 pdb="HD21 ASN A 64 " 0.000 2.00e-02 2.50e+03 pdb="HD22 ASN A 64 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 64 " -0.015 2.00e-02 2.50e+03 2.68e-02 1.08e+01 pdb=" CG ASN F 64 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN F 64 " 0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN F 64 " -0.047 2.00e-02 2.50e+03 pdb="HD21 ASN F 64 " -0.001 2.00e-02 2.50e+03 pdb="HD22 ASN F 64 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 64 " 0.015 2.00e-02 2.50e+03 2.56e-02 9.86e+00 pdb=" CG ASN D 64 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN D 64 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN D 64 " 0.045 2.00e-02 2.50e+03 pdb="HD21 ASN D 64 " 0.000 2.00e-02 2.50e+03 pdb="HD22 ASN D 64 " -0.029 2.00e-02 2.50e+03 ... (remaining 2582 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 1445 2.24 - 2.83: 41587 2.83 - 3.42: 45307 3.42 - 4.01: 63119 4.01 - 4.60: 98727 Nonbonded interactions: 250185 Sorted by model distance: nonbonded pdb=" OE1 GLU A 74 " pdb=" HE ARG A 131 " model vdw 1.649 2.450 nonbonded pdb=" OE1 GLU C 74 " pdb=" HE ARG C 131 " model vdw 1.684 2.450 nonbonded pdb=" OE1 GLU L 74 " pdb=" HE ARG L 131 " model vdw 1.714 2.450 nonbonded pdb=" OE1 GLU D 74 " pdb=" HE ARG D 131 " model vdw 1.732 2.450 nonbonded pdb=" OE2 GLU D 127 " pdb="HH11 ARG F 123 " model vdw 1.742 2.450 ... (remaining 250180 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 132) selection = (chain 'B' and resid 1 through 132) selection = (chain 'C' and resid 1 through 132) selection = (chain 'D' and resid 1 through 132) selection = (chain 'F' and resid 1 through 132) selection = chain 'H' selection = (chain 'J' and resid 1 through 132) selection = (chain 'L' and resid 1 through 132) } ncs_group { reference = (chain 'E' and resid 25 through 40) selection = (chain 'G' and resid 25 through 40) selection = (chain 'I' and resid 2 through 17) selection = (chain 'K' and resid 2 through 17) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.610 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: 0.130 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 22.220 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 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 : 0.006 0.044 10038 Z= 0.356 Angle : 0.871 5.815 13809 Z= 0.612 Chirality : 0.056 0.301 1575 Planarity : 0.007 0.054 1538 Dihedral : 16.547 89.314 4038 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.22 (0.25), residues: 1047 helix: -0.89 (0.20), residues: 472 sheet: 0.77 (0.25), residues: 336 loop : 2.15 (0.46), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.002 ARG L 4 TYR 0.011 0.003 TYR D 36 PHE 0.012 0.002 PHE L 48 HIS 0.013 0.005 HIS J 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.36 (10038) covalent geometry : angle 0.87055 / 0.61 (13809) hydrogen bonds : bond 0.21306 / 14.40 ( 382) hydrogen bonds : angle 6.31309 / 4.39 ( 1042) *********************** 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 416 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 416 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLN cc_start: 0.8017 (mt0) cc_final: 0.7776 (mp10) REVERT: A 84 LYS cc_start: 0.8694 (tptt) cc_final: 0.8442 (tttt) REVERT: A 100 ASN cc_start: 0.7390 (m-40) cc_final: 0.7182 (m110) REVERT: B 13 GLN cc_start: 0.7059 (mt0) cc_final: 0.6773 (mt0) REVERT: B 100 ASN cc_start: 0.7356 (m-40) cc_final: 0.7103 (m110) REVERT: C 67 GLN cc_start: 0.8036 (mt0) cc_final: 0.7666 (mp10) REVERT: C 100 ASN cc_start: 0.7338 (m-40) cc_final: 0.7110 (m110) REVERT: D 13 GLN cc_start: 0.7163 (mt0) cc_final: 0.6919 (mt0) REVERT: D 67 GLN cc_start: 0.8055 (mt0) cc_final: 0.7736 (mp10) REVERT: D 100 ASN cc_start: 0.7327 (m-40) cc_final: 0.7082 (m110) REVERT: F 100 ASN cc_start: 0.7284 (m-40) cc_final: 0.6925 (m-40) REVERT: H 67 GLN cc_start: 0.8165 (mt0) cc_final: 0.7799 (mp10) REVERT: H 100 ASN cc_start: 0.7322 (m-40) cc_final: 0.7050 (m110) REVERT: J 67 GLN cc_start: 0.8097 (mt0) cc_final: 0.7852 (mp10) REVERT: J 100 ASN cc_start: 0.7415 (m-40) cc_final: 0.7133 (m110) REVERT: L 13 GLN cc_start: 0.7068 (mt0) cc_final: 0.6816 (mt0) REVERT: L 59 LEU cc_start: 0.9092 (mt) cc_final: 0.8892 (mp) REVERT: L 67 GLN cc_start: 0.8017 (mt0) cc_final: 0.7725 (mp10) REVERT: L 100 ASN cc_start: 0.7376 (m-40) cc_final: 0.7144 (m110) outliers start: 0 outliers final: 0 residues processed: 416 average time/residue: 0.2627 time to fit residues: 142.6816 Evaluate side-chains 319 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 0.2980 chunk 38 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 65 ASN B 13 GLN C 65 ASN D 65 ASN D 97 GLN H 65 ASN H 97 GLN J 65 ASN J 97 GLN L 65 ASN L 97 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.166227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.111388 restraints weight = 32522.395| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.86 r_work: 0.3119 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 10038 Z= 0.214 Angle : 0.690 7.591 13809 Z= 0.406 Chirality : 0.046 0.196 1575 Planarity : 0.006 0.033 1538 Dihedral : 19.441 89.495 1922 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 2.14 % Allowed : 11.50 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.43 (0.27), residues: 1047 helix: 0.62 (0.24), residues: 480 sheet: 0.38 (0.25), residues: 336 loop : 3.26 (0.50), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 54 TYR 0.008 0.002 TYR D 36 PHE 0.008 0.001 PHE A 63 HIS 0.003 0.001 HIS B 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.21 (10038) covalent geometry : angle 0.68983 / 0.41 (13809) hydrogen bonds : bond 0.08072 / 5.74 ( 382) hydrogen bonds : angle 4.41660 / 3.01 ( 1042) *********************** 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 337 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 318 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.7727 (m-80) REVERT: A 67 GLN cc_start: 0.8331 (mt0) cc_final: 0.8128 (mt0) REVERT: A 84 LYS cc_start: 0.8755 (tptt) cc_final: 0.8450 (tttt) REVERT: B 35 PHE cc_start: 0.8312 (OUTLIER) cc_final: 0.7880 (m-80) REVERT: B 74 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8457 (mm-30) REVERT: C 35 PHE cc_start: 0.8238 (OUTLIER) cc_final: 0.7793 (m-80) REVERT: C 67 GLN cc_start: 0.8280 (mt0) cc_final: 0.8021 (mt0) REVERT: C 116 ILE cc_start: 0.8763 (mt) cc_final: 0.8442 (mp) REVERT: D 35 PHE cc_start: 0.8212 (OUTLIER) cc_final: 0.7796 (m-80) REVERT: D 67 GLN cc_start: 0.8374 (mt0) cc_final: 0.8138 (mt0) REVERT: D 77 LYS cc_start: 0.8414 (mtmt) cc_final: 0.8160 (mtmm) REVERT: F 35 PHE cc_start: 0.8384 (OUTLIER) cc_final: 0.7870 (m-80) REVERT: H 35 PHE cc_start: 0.8199 (OUTLIER) cc_final: 0.7822 (m-80) REVERT: H 67 GLN cc_start: 0.8484 (mt0) cc_final: 0.8278 (mt0) REVERT: J 35 PHE cc_start: 0.8441 (OUTLIER) cc_final: 0.8015 (m-80) REVERT: L 35 PHE cc_start: 0.8139 (OUTLIER) cc_final: 0.7776 (m-80) outliers start: 19 outliers final: 9 residues processed: 325 average time/residue: 0.2850 time to fit residues: 118.7350 Evaluate side-chains 313 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 296 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain C residue 35 PHE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain D residue 35 PHE Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain F residue 35 PHE Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain H residue 35 PHE Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain J residue 35 PHE Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain L residue 35 PHE Chi-restraints excluded: chain L residue 102 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 68 optimal weight: 0.2980 chunk 15 optimal weight: 0.2980 chunk 90 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 45 optimal weight: 0.1980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 ASN B 100 ASN C 100 ASN D 100 ASN H 100 ASN L 100 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.165759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.110930 restraints weight = 32605.228| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.85 r_work: 0.3114 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10038 Z= 0.145 Angle : 0.614 5.931 13809 Z= 0.360 Chirality : 0.044 0.216 1575 Planarity : 0.004 0.031 1538 Dihedral : 19.725 89.381 1922 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 3.83 % Allowed : 13.08 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.27), residues: 1047 helix: 1.30 (0.25), residues: 480 sheet: -0.03 (0.29), residues: 240 loop : 2.09 (0.40), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 123 TYR 0.005 0.001 TYR H 61 PHE 0.006 0.001 PHE D 98 HIS 0.003 0.001 HIS L 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.15 (10038) covalent geometry : angle 0.61376 / 0.36 (13809) hydrogen bonds : bond 0.06872 / 5.11 ( 382) hydrogen bonds : angle 3.88747 / 2.63 ( 1042) *********************** 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 359 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 325 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 PHE cc_start: 0.8306 (OUTLIER) cc_final: 0.7801 (m-80) REVERT: A 84 LYS cc_start: 0.8709 (tptt) cc_final: 0.8397 (tttt) REVERT: B 35 PHE cc_start: 0.8341 (OUTLIER) cc_final: 0.7847 (m-80) REVERT: C 35 PHE cc_start: 0.8322 (OUTLIER) cc_final: 0.7859 (m-80) REVERT: C 67 GLN cc_start: 0.8279 (mt0) cc_final: 0.8026 (mt0) REVERT: C 116 ILE cc_start: 0.8738 (mt) cc_final: 0.8452 (mp) REVERT: D 32 MET cc_start: 0.8254 (mmm) cc_final: 0.8037 (mmm) REVERT: D 35 PHE cc_start: 0.8263 (OUTLIER) cc_final: 0.7912 (m-80) REVERT: D 67 GLN cc_start: 0.8340 (mt0) cc_final: 0.8136 (mt0) REVERT: F 35 PHE cc_start: 0.8391 (OUTLIER) cc_final: 0.7879 (m-80) REVERT: H 35 PHE cc_start: 0.8294 (OUTLIER) cc_final: 0.7843 (m-80) REVERT: J 35 PHE cc_start: 0.8492 (OUTLIER) cc_final: 0.8122 (m-80) REVERT: L 35 PHE cc_start: 0.8268 (OUTLIER) cc_final: 0.7842 (m-80) outliers start: 34 outliers final: 18 residues processed: 327 average time/residue: 0.3076 time to fit residues: 129.5183 Evaluate side-chains 321 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 295 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain B residue 1 VAL Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain C residue 35 PHE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain D residue 35 PHE Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain F residue 1 VAL Chi-restraints excluded: chain F residue 35 PHE Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain H residue 1 VAL Chi-restraints excluded: chain H residue 35 PHE Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 112 LYS Chi-restraints excluded: chain J residue 35 PHE Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain L residue 35 PHE Chi-restraints excluded: chain L residue 102 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 6 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 ASN C 100 ASN D 100 ASN H 100 ASN L 100 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.164053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.108810 restraints weight = 32674.611| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.87 r_work: 0.3072 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 10038 Z= 0.208 Angle : 0.626 5.791 13809 Z= 0.366 Chirality : 0.043 0.189 1575 Planarity : 0.005 0.034 1538 Dihedral : 19.999 89.363 1922 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 4.96 % Allowed : 13.08 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.18 (0.27), residues: 1047 helix: 1.09 (0.25), residues: 480 sheet: -0.49 (0.29), residues: 240 loop : 1.75 (0.39), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 123 TYR 0.008 0.002 TYR J 26 PHE 0.009 0.002 PHE F 35 HIS 0.004 0.002 HIS D 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.21 (10038) covalent geometry : angle 0.62600 / 0.37 (13809) hydrogen bonds : bond 0.06390 / 4.86 ( 382) hydrogen bonds : angle 3.71223 / 2.50 ( 1042) *********************** 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 340 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 296 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 PHE cc_start: 0.8484 (OUTLIER) cc_final: 0.8133 (m-80) REVERT: A 84 LYS cc_start: 0.8708 (tptt) cc_final: 0.8394 (tttt) REVERT: B 35 PHE cc_start: 0.8313 (OUTLIER) cc_final: 0.8018 (m-80) REVERT: C 35 PHE cc_start: 0.8469 (OUTLIER) cc_final: 0.8065 (m-80) REVERT: C 67 GLN cc_start: 0.8265 (mt0) cc_final: 0.8004 (mt0) REVERT: C 116 ILE cc_start: 0.8728 (mt) cc_final: 0.8481 (mp) REVERT: C 122 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7312 (mp0) REVERT: D 35 PHE cc_start: 0.8442 (OUTLIER) cc_final: 0.8184 (m-80) REVERT: D 67 GLN cc_start: 0.8347 (mt0) cc_final: 0.8145 (mt0) REVERT: F 35 PHE cc_start: 0.8524 (OUTLIER) cc_final: 0.8049 (m-80) REVERT: H 35 PHE cc_start: 0.8438 (OUTLIER) cc_final: 0.8159 (m-80) REVERT: J 68 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7539 (mt-10) REVERT: L 35 PHE cc_start: 0.8421 (OUTLIER) cc_final: 0.8095 (m-80) REVERT: L 68 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7536 (mt-10) outliers start: 44 outliers final: 21 residues processed: 309 average time/residue: 0.3080 time to fit residues: 122.0161 Evaluate side-chains 300 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 271 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain C residue 35 PHE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain D residue 35 PHE Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain F residue 35 PHE Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain H residue 35 PHE Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 112 LYS Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain L residue 35 PHE Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 102 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 73 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 100 ASN D 100 ASN H 100 ASN L 100 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.164045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.109055 restraints weight = 32473.671| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.83 r_work: 0.3010 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.4475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 10038 Z= 0.167 Angle : 0.609 5.916 13809 Z= 0.351 Chirality : 0.043 0.185 1575 Planarity : 0.004 0.033 1538 Dihedral : 20.040 88.662 1922 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 5.52 % Allowed : 12.97 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.27), residues: 1047 helix: 1.07 (0.25), residues: 480 sheet: -0.63 (0.29), residues: 240 loop : 1.60 (0.39), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 123 TYR 0.005 0.001 TYR J 26 PHE 0.008 0.001 PHE C 35 HIS 0.004 0.002 HIS D 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 (10038) covalent geometry : angle 0.60898 / 0.35 (13809) hydrogen bonds : bond 0.06011 / 4.46 ( 382) hydrogen bonds : angle 3.62864 / 2.44 ( 1042) *********************** 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 333 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 284 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 LYS cc_start: 0.8700 (tptt) cc_final: 0.8405 (tttt) REVERT: B 35 PHE cc_start: 0.8334 (OUTLIER) cc_final: 0.8057 (m-80) REVERT: B 106 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7136 (tp30) REVERT: C 35 PHE cc_start: 0.8499 (OUTLIER) cc_final: 0.8236 (m-80) REVERT: C 67 GLN cc_start: 0.8236 (mt0) cc_final: 0.7966 (mt0) REVERT: C 116 ILE cc_start: 0.8731 (mt) cc_final: 0.8496 (mp) REVERT: C 122 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7303 (mp0) REVERT: D 68 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7539 (mt-10) REVERT: F 35 PHE cc_start: 0.8466 (OUTLIER) cc_final: 0.8026 (m-80) REVERT: L 35 PHE cc_start: 0.8441 (OUTLIER) cc_final: 0.8211 (m-80) REVERT: L 106 GLU cc_start: 0.7783 (tp30) cc_final: 0.7262 (tp30) outliers start: 49 outliers final: 28 residues processed: 298 average time/residue: 0.2938 time to fit residues: 112.2277 Evaluate side-chains 308 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 275 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain B residue 1 VAL Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain C residue 1 VAL Chi-restraints excluded: chain C residue 35 PHE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain D residue 1 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain F residue 1 VAL Chi-restraints excluded: chain F residue 35 PHE Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain H residue 1 VAL Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 112 LYS Chi-restraints excluded: chain J residue 1 VAL Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain L residue 1 VAL Chi-restraints excluded: chain L residue 35 PHE Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 122 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 18 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 58 optimal weight: 0.0770 chunk 77 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 92 optimal weight: 0.4980 chunk 64 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 100 ASN H 100 ASN L 100 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.164098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.108978 restraints weight = 32379.524| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.85 r_work: 0.2981 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.4677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10038 Z= 0.158 Angle : 0.587 5.878 13809 Z= 0.341 Chirality : 0.043 0.163 1575 Planarity : 0.004 0.031 1538 Dihedral : 20.076 87.886 1922 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 5.07 % Allowed : 14.43 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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 (0.27), residues: 1047 helix: 1.08 (0.25), residues: 480 sheet: -0.71 (0.29), residues: 240 loop : 1.55 (0.40), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 123 TYR 0.007 0.001 TYR B 61 PHE 0.006 0.001 PHE F 35 HIS 0.003 0.001 HIS H 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 (10038) covalent geometry : angle 0.58741 / 0.34 (13809) hydrogen bonds : bond 0.05629 / 4.13 ( 382) hydrogen bonds : angle 3.52465 / 2.37 ( 1042) *********************** 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 330 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 285 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LYS cc_start: 0.8688 (tptt) cc_final: 0.8360 (tttt) REVERT: B 35 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.8132 (m-80) REVERT: B 106 GLU cc_start: 0.7540 (mm-30) cc_final: 0.7154 (tp30) REVERT: C 67 GLN cc_start: 0.8255 (mt0) cc_final: 0.7995 (mt0) REVERT: C 122 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7335 (mp0) REVERT: F 35 PHE cc_start: 0.8466 (OUTLIER) cc_final: 0.8075 (m-80) outliers start: 45 outliers final: 26 residues processed: 291 average time/residue: 0.3049 time to fit residues: 114.1800 Evaluate side-chains 298 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 269 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain B residue 1 VAL Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain C residue 1 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain D residue 1 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain F residue 1 VAL Chi-restraints excluded: chain F residue 35 PHE Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain H residue 1 VAL Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain J residue 1 VAL Chi-restraints excluded: chain J residue 68 GLU Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain L residue 1 VAL Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 102 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 60 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 94 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 81 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 27 optimal weight: 0.4980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 100 ASN H 100 ASN L 100 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.162946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.107392 restraints weight = 32740.461| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.88 r_work: 0.2962 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.4782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 10038 Z= 0.193 Angle : 0.603 4.778 13809 Z= 0.348 Chirality : 0.043 0.173 1575 Planarity : 0.004 0.032 1538 Dihedral : 20.003 89.299 1922 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 4.51 % Allowed : 16.01 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.76 (0.27), residues: 1047 helix: 0.98 (0.25), residues: 480 sheet: -1.00 (0.28), residues: 240 loop : 1.42 (0.39), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 123 TYR 0.008 0.001 TYR J 26 PHE 0.007 0.001 PHE F 35 HIS 0.004 0.002 HIS L 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 (10038) covalent geometry : angle 0.60292 / 0.35 (13809) hydrogen bonds : bond 0.05731 / 4.15 ( 382) hydrogen bonds : angle 3.61074 / 2.42 ( 1042) *********************** 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 315 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 275 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 LYS cc_start: 0.8707 (tptt) cc_final: 0.8376 (tttt) REVERT: B 106 GLU cc_start: 0.7519 (mm-30) cc_final: 0.7134 (tp30) REVERT: C 67 GLN cc_start: 0.8267 (mt0) cc_final: 0.7992 (mt0) REVERT: C 116 ILE cc_start: 0.8712 (mt) cc_final: 0.8419 (mp) REVERT: C 122 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7360 (mp0) REVERT: D 106 GLU cc_start: 0.7978 (tp30) cc_final: 0.7508 (tp30) REVERT: F 35 PHE cc_start: 0.8553 (OUTLIER) cc_final: 0.8160 (m-80) REVERT: F 106 GLU cc_start: 0.7993 (tp30) cc_final: 0.7489 (tp30) REVERT: L 13 GLN cc_start: 0.7642 (mt0) cc_final: 0.7374 (mp10) outliers start: 40 outliers final: 32 residues processed: 285 average time/residue: 0.3052 time to fit residues: 112.0149 Evaluate side-chains 306 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 272 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain B residue 1 VAL Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain C residue 1 VAL Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain D residue 1 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 112 LYS Chi-restraints excluded: chain F residue 1 VAL Chi-restraints excluded: chain F residue 35 PHE Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 112 LYS Chi-restraints excluded: chain F residue 122 GLU Chi-restraints excluded: chain H residue 1 VAL Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain J residue 1 VAL Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 112 LYS Chi-restraints excluded: chain L residue 1 VAL Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 102 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 0.7980 chunk 15 optimal weight: 0.4980 chunk 2 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 98 optimal weight: 0.0270 chunk 74 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 100 ASN H 100 ASN L 100 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.163852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.108596 restraints weight = 32350.992| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.86 r_work: 0.3082 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.4916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 10038 Z= 0.147 Angle : 0.576 4.165 13809 Z= 0.335 Chirality : 0.042 0.178 1575 Planarity : 0.004 0.032 1538 Dihedral : 19.799 89.067 1922 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 4.62 % Allowed : 15.78 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.76 (0.27), residues: 1047 helix: 1.01 (0.25), residues: 480 sheet: -1.12 (0.28), residues: 240 loop : 1.45 (0.40), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 123 TYR 0.006 0.001 TYR J 26 PHE 0.006 0.001 PHE F 35 HIS 0.003 0.001 HIS B 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 (10038) covalent geometry : angle 0.57562 / 0.34 (13809) hydrogen bonds : bond 0.05334 / 3.86 ( 382) hydrogen bonds : angle 3.47939 / 2.33 ( 1042) *********************** 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 321 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 280 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LYS cc_start: 0.8708 (tptt) cc_final: 0.8402 (tttt) REVERT: B 106 GLU cc_start: 0.7506 (mm-30) cc_final: 0.7104 (tp30) REVERT: C 67 GLN cc_start: 0.8250 (mt0) cc_final: 0.7947 (mt0) REVERT: C 116 ILE cc_start: 0.8724 (mt) cc_final: 0.8439 (mp) REVERT: C 122 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7357 (mp0) REVERT: D 106 GLU cc_start: 0.7839 (tp30) cc_final: 0.7407 (tp30) REVERT: F 35 PHE cc_start: 0.8541 (OUTLIER) cc_final: 0.8148 (m-80) REVERT: F 106 GLU cc_start: 0.7819 (tp30) cc_final: 0.7382 (tp30) REVERT: J 106 GLU cc_start: 0.7734 (tp30) cc_final: 0.7268 (tp30) REVERT: L 13 GLN cc_start: 0.7615 (mt0) cc_final: 0.7377 (mp10) outliers start: 41 outliers final: 25 residues processed: 286 average time/residue: 0.2952 time to fit residues: 109.4348 Evaluate side-chains 300 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 273 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain B residue 1 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain C residue 1 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain D residue 1 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain F residue 1 VAL Chi-restraints excluded: chain F residue 35 PHE Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain H residue 1 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain J residue 1 VAL Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain L residue 1 VAL Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 102 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 88 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 106 optimal weight: 0.4980 chunk 45 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 55 optimal weight: 0.0670 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 100 ASN H 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.163051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.107747 restraints weight = 32221.515| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.85 r_work: 0.3034 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.4997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10038 Z= 0.159 Angle : 0.574 4.318 13809 Z= 0.335 Chirality : 0.042 0.177 1575 Planarity : 0.004 0.030 1538 Dihedral : 19.659 87.524 1922 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 4.40 % Allowed : 16.01 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.73 (0.27), residues: 1047 helix: 1.03 (0.25), residues: 480 sheet: -1.17 (0.28), residues: 240 loop : 1.39 (0.39), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 104 TYR 0.006 0.001 TYR J 26 PHE 0.007 0.001 PHE F 35 HIS 0.003 0.001 HIS L 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (10038) covalent geometry : angle 0.57363 / 0.34 (13809) hydrogen bonds : bond 0.05357 / 3.86 ( 382) hydrogen bonds : angle 3.45535 / 2.31 ( 1042) *********************** 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 314 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 275 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LYS cc_start: 0.8707 (tptt) cc_final: 0.8414 (tttt) REVERT: B 106 GLU cc_start: 0.7524 (mm-30) cc_final: 0.7152 (tp30) REVERT: C 67 GLN cc_start: 0.8252 (mt0) cc_final: 0.7945 (mt0) REVERT: C 116 ILE cc_start: 0.8753 (mt) cc_final: 0.8484 (mp) REVERT: C 122 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7353 (mp0) REVERT: D 106 GLU cc_start: 0.7882 (tp30) cc_final: 0.7457 (tp30) REVERT: F 35 PHE cc_start: 0.8553 (OUTLIER) cc_final: 0.8232 (m-80) REVERT: F 106 GLU cc_start: 0.7855 (tp30) cc_final: 0.7416 (tp30) REVERT: L 13 GLN cc_start: 0.7661 (mt0) cc_final: 0.7407 (mp10) outliers start: 39 outliers final: 28 residues processed: 282 average time/residue: 0.2884 time to fit residues: 106.2874 Evaluate side-chains 306 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 276 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain B residue 1 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain C residue 1 VAL Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain D residue 1 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain F residue 1 VAL Chi-restraints excluded: chain F residue 35 PHE Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain H residue 1 VAL Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain J residue 1 VAL Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain L residue 1 VAL Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 102 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 83 optimal weight: 0.9990 chunk 15 optimal weight: 0.1980 chunk 4 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 56 optimal weight: 0.1980 chunk 17 optimal weight: 0.5980 chunk 101 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 100 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.163777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.108598 restraints weight = 32370.322| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.87 r_work: 0.2971 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.5070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10038 Z= 0.134 Angle : 0.559 4.152 13809 Z= 0.326 Chirality : 0.042 0.169 1575 Planarity : 0.004 0.049 1538 Dihedral : 19.520 85.643 1922 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 4.06 % Allowed : 16.46 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.85 (0.27), residues: 1047 helix: 1.10 (0.24), residues: 480 sheet: -1.08 (0.29), residues: 240 loop : 1.48 (0.40), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 104 TYR 0.005 0.001 TYR B 61 PHE 0.006 0.001 PHE F 35 HIS 0.003 0.001 HIS B 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (10038) covalent geometry : angle 0.55886 / 0.33 (13809) hydrogen bonds : bond 0.05088 / 3.68 ( 382) hydrogen bonds : angle 3.37437 / 2.26 ( 1042) ********************** 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 325 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 289 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LYS cc_start: 0.8697 (tptt) cc_final: 0.8434 (ttmt) REVERT: A 103 GLU cc_start: 0.6673 (tm-30) cc_final: 0.6444 (tm-30) REVERT: B 106 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7094 (tp30) REVERT: C 67 GLN cc_start: 0.8268 (mt0) cc_final: 0.7958 (mt0) REVERT: C 116 ILE cc_start: 0.8743 (mt) cc_final: 0.8465 (mp) REVERT: C 122 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7375 (mp0) REVERT: D 106 GLU cc_start: 0.7847 (tp30) cc_final: 0.7405 (tp30) REVERT: F 35 PHE cc_start: 0.8515 (OUTLIER) cc_final: 0.8220 (m-80) REVERT: F 106 GLU cc_start: 0.7834 (tp30) cc_final: 0.7374 (tp30) outliers start: 36 outliers final: 27 residues processed: 295 average time/residue: 0.2749 time to fit residues: 107.3384 Evaluate side-chains 311 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 282 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain B residue 1 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain C residue 1 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain D residue 1 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain F residue 1 VAL Chi-restraints excluded: chain F residue 35 PHE Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain H residue 1 VAL Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain J residue 1 VAL Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain L residue 1 VAL Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 102 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 15 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 52 optimal weight: 7.9990 chunk 89 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 64 ASN D 64 ASN H 100 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.162625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.107196 restraints weight = 32509.041| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.88 r_work: 0.3020 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.5129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 10038 Z= 0.179 Angle : 0.576 4.176 13809 Z= 0.336 Chirality : 0.042 0.171 1575 Planarity : 0.004 0.027 1538 Dihedral : 19.472 83.122 1922 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 4.28 % Allowed : 16.35 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.64 (0.27), residues: 1047 helix: 1.02 (0.24), residues: 480 sheet: -1.28 (0.29), residues: 240 loop : 1.31 (0.39), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 123 TYR 0.008 0.001 TYR J 26 PHE 0.008 0.001 PHE F 35 HIS 0.004 0.002 HIS D 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.18 (10038) covalent geometry : angle 0.57568 / 0.34 (13809) hydrogen bonds : bond 0.05370 / 3.87 ( 382) hydrogen bonds : angle 3.45646 / 2.31 ( 1042) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4615.75 seconds wall clock time: 78 minutes 55.01 seconds (4735.01 seconds total)