Starting phenix.real_space_refine on Sat Sep 12 22:44:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pbu_13303/09_2026/7pbu_13303_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pbu_13303/09_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_13303/09_2026/7pbu_13303_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pbu_13303/09_2026/7pbu_13303_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pbu_13303/09_2026/7pbu_13303.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pbu_13303/09_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-2.2.1-6174/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: 3.58, per 1000 atoms: 0.19 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: 1.70 Conformation dependent library (CDL) restraints added in 653.0 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: 3.26 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: 4.03 Time building geometry restraints manager: 2.40 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: 32041 1.16 - 2.33: 3154 2.33 - 3.49: 331 3.49 - 4.65: 69 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: 3.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.130 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 21.340 Find NCS groups from input model: 0.310 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: 27.190 ------------------------------------------------------------------------------- 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= 0.357 Angle : 0.873 5.815 13809 Z= 0.616 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 0.87338 / 0.62 (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 : 0.508 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: 0.8468 (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: 0.7104 (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: 0.6815 (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: 0.2758 time to fit residues: 150.8380 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 : 0.534 ------------------------------------------------------------------------------- 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 C 65 ASN D 65 ASN D 97 GLN H 65 ASN J 65 ASN J 97 GLN L 65 ASN L 97 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.165621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.110666 restraints weight = 32598.441| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.87 r_work: 0.3030 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 10038 Z= 0.214 Angle : 0.718 8.422 13809 Z= 0.412 Chirality : 0.047 0.196 1575 Planarity : 0.006 0.034 1538 Dihedral : 19.525 89.850 1922 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 2.25 % Allowed : 11.72 % Favored : 86.02 % 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: 1.48 (0.27), residues: 1047 helix: 0.74 (0.24), residues: 480 sheet: 0.27 (0.25), residues: 336 loop : 3.36 (0.50), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 54 TYR 0.007 0.002 TYR D 36 PHE 0.009 0.001 PHE H 98 HIS 0.003 0.001 HIS D 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.21 (10038) covalent geometry : angle 0.71769 / 0.41 (13809) hydrogen bonds : bond 0.07574 / 5.52 ( 382) hydrogen bonds : angle 4.23858 / 2.88 ( 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 343 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 323 time to evaluate : 0.371 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: 0.8265 (OUTLIER) cc_final: 0.7862 (m-80) REVERT: A 68 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7594 (mt-10) REVERT: A 84 LYS cc_start: 0.8723 (tptt) cc_final: 0.8431 (tttt) REVERT: B 35 PHE cc_start: 0.8340 (OUTLIER) cc_final: 0.7904 (m-80) REVERT: B 40 GLU cc_start: 0.7537 (mp0) cc_final: 0.7197 (pm20) REVERT: B 74 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8495 (mm-30) REVERT: C 35 PHE cc_start: 0.8299 (OUTLIER) cc_final: 0.7874 (m-80) REVERT: C 67 GLN cc_start: 0.8276 (mt0) cc_final: 0.8022 (mt0) REVERT: C 77 LYS cc_start: 0.8418 (mtmm) cc_final: 0.8136 (mtmm) REVERT: C 116 ILE cc_start: 0.8822 (mt) cc_final: 0.8483 (mp) REVERT: D 35 PHE cc_start: 0.8211 (OUTLIER) cc_final: 0.7827 (m-80) REVERT: D 67 GLN cc_start: 0.8365 (mt0) cc_final: 0.8135 (mt0) REVERT: D 77 LYS cc_start: 0.8464 (mtmt) cc_final: 0.8175 (mtmm) REVERT: F 35 PHE cc_start: 0.8412 (OUTLIER) cc_final: 0.7915 (m-80) REVERT: H 35 PHE cc_start: 0.8243 (OUTLIER) cc_final: 0.7893 (m-80) REVERT: J 35 PHE cc_start: 0.8466 (OUTLIER) cc_final: 0.8095 (m-80) REVERT: L 35 PHE cc_start: 0.8215 (OUTLIER) cc_final: 0.7821 (m-80) outliers start: 20 outliers final: 10 residues processed: 328 average time/residue: 0.2901 time to fit residues: 122.4232 Evaluate side-chains 313 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 295 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 H residue 112 LYS 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: 0.3980 chunk 15 optimal weight: 0.3980 chunk 90 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 18 optimal weight: 0.0030 chunk 22 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.4390 ------------------------------------------------------------------------------- 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 = 0.3951 r_free = 0.3951 target = 0.166865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.111836 restraints weight = 32611.643| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.90 r_work: 0.3063 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10038 Z= 0.142 Angle : 0.604 5.466 13809 Z= 0.355 Chirality : 0.043 0.231 1575 Planarity : 0.004 0.028 1538 Dihedral : 19.787 89.007 1922 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 3.61 % Allowed : 13.08 % Favored : 83.31 % 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: 1.66 (0.27), residues: 1047 helix: 1.28 (0.25), residues: 480 sheet: 0.12 (0.29), residues: 233 loop : 1.98 (0.39), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 123 TYR 0.005 0.001 TYR J 26 PHE 0.006 0.001 PHE D 98 HIS 0.003 0.001 HIS D 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (10038) covalent geometry : angle 0.60381 / 0.35 (13809) hydrogen bonds : bond 0.06832 / 5.11 ( 382) hydrogen bonds : angle 3.83901 / 2.60 ( 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 352 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 320 time to evaluate : 0.502 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: A 35 PHE cc_start: 0.8330 (OUTLIER) cc_final: 0.7841 (m-80) REVERT: A 84 LYS cc_start: 0.8712 (tptt) cc_final: 0.8397 (tttt) REVERT: B 35 PHE cc_start: 0.8370 (OUTLIER) cc_final: 0.7867 (m-80) REVERT: C 35 PHE cc_start: 0.8330 (OUTLIER) cc_final: 0.7837 (m-80) REVERT: C 67 GLN cc_start: 0.8300 (mt0) cc_final: 0.8047 (mt0) REVERT: C 116 ILE cc_start: 0.8724 (mt) cc_final: 0.8470 (mp) REVERT: D 35 PHE cc_start: 0.8277 (OUTLIER) cc_final: 0.7928 (m-80) REVERT: D 67 GLN cc_start: 0.8374 (mt0) cc_final: 0.8166 (mt0) REVERT: F 35 PHE cc_start: 0.8390 (OUTLIER) cc_final: 0.7865 (m-80) REVERT: H 35 PHE cc_start: 0.8296 (OUTLIER) cc_final: 0.7835 (m-80) REVERT: J 35 PHE cc_start: 0.8484 (OUTLIER) cc_final: 0.8108 (m-80) REVERT: L 35 PHE cc_start: 0.8283 (OUTLIER) cc_final: 0.7895 (m-80) outliers start: 32 outliers final: 17 residues processed: 322 average time/residue: 0.3076 time to fit residues: 127.9772 Evaluate side-chains 316 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 291 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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 D residue 35 PHE 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 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 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: 0.8980 chunk 3 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- 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 = 0.3920 r_free = 0.3920 target = 0.163919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.108389 restraints weight = 32634.125| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.90 r_work: 0.2994 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 10038 Z= 0.218 Angle : 0.625 4.902 13809 Z= 0.367 Chirality : 0.044 0.193 1575 Planarity : 0.005 0.035 1538 Dihedral : 19.965 89.474 1922 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 4.85 % Allowed : 13.42 % Favored : 81.74 % 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: 1.07 (0.25), residues: 480 sheet: -0.47 (0.29), residues: 240 loop : 1.78 (0.39), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 123 TYR 0.006 0.002 TYR J 26 PHE 0.008 0.002 PHE F 35 HIS 0.004 0.002 HIS L 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.22 (10038) covalent geometry : angle 0.62495 / 0.37 (13809) hydrogen bonds : bond 0.06394 / 4.82 ( 382) hydrogen bonds : angle 3.72463 / 2.51 ( 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 333 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 290 time to evaluate : 0.504 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: A 35 PHE cc_start: 0.8486 (OUTLIER) cc_final: 0.8141 (m-80) REVERT: A 77 LYS cc_start: 0.8262 (mtmm) cc_final: 0.8054 (mtmm) REVERT: A 84 LYS cc_start: 0.8710 (tptt) cc_final: 0.8404 (tttt) REVERT: B 35 PHE cc_start: 0.8308 (OUTLIER) cc_final: 0.8020 (m-80) REVERT: C 35 PHE cc_start: 0.8489 (OUTLIER) cc_final: 0.8099 (m-80) REVERT: C 67 GLN cc_start: 0.8272 (mt0) cc_final: 0.8011 (mt0) REVERT: C 116 ILE cc_start: 0.8727 (mt) cc_final: 0.8479 (mp) REVERT: C 122 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7322 (mp0) REVERT: D 35 PHE cc_start: 0.8447 (OUTLIER) cc_final: 0.8226 (m-80) REVERT: D 67 GLN cc_start: 0.8360 (mt0) cc_final: 0.8158 (mt0) REVERT: F 35 PHE cc_start: 0.8479 (OUTLIER) cc_final: 0.8007 (m-80) REVERT: H 35 PHE cc_start: 0.8435 (OUTLIER) cc_final: 0.8153 (m-80) REVERT: L 35 PHE cc_start: 0.8423 (OUTLIER) cc_final: 0.8105 (m-80) outliers start: 43 outliers final: 22 residues processed: 301 average time/residue: 0.3016 time to fit residues: 117.0600 Evaluate side-chains 303 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 273 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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 A residue 112 LYS 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 102 VAL Chi-restraints excluded: chain L residue 122 GLU 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: 0.4980 chunk 32 optimal weight: 0.1980 chunk 29 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 77 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 100 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.164651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.109400 restraints weight = 32418.169| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.86 r_work: 0.3033 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.4448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10038 Z= 0.141 Angle : 0.594 5.765 13809 Z= 0.344 Chirality : 0.043 0.189 1575 Planarity : 0.004 0.032 1538 Dihedral : 20.025 89.064 1922 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 5.52 % Allowed : 13.19 % Favored : 81.29 % 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: 1.15 (0.27), residues: 1047 helix: 1.11 (0.25), residues: 480 sheet: -0.53 (0.28), residues: 240 loop : 1.69 (0.39), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 123 TYR 0.005 0.001 TYR B 61 PHE 0.008 0.001 PHE C 35 HIS 0.003 0.001 HIS L 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (10038) covalent geometry : angle 0.59388 / 0.34 (13809) hydrogen bonds : bond 0.05867 / 4.36 ( 382) hydrogen bonds : angle 3.56563 / 2.40 ( 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 346 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 297 time to evaluate : 0.513 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: A 84 LYS cc_start: 0.8711 (tptt) cc_final: 0.8432 (tttt) REVERT: B 35 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.8036 (m-80) REVERT: C 35 PHE cc_start: 0.8464 (OUTLIER) cc_final: 0.8192 (m-80) REVERT: C 67 GLN cc_start: 0.8235 (mt0) cc_final: 0.7978 (mt0) REVERT: D 35 PHE cc_start: 0.8380 (OUTLIER) cc_final: 0.8167 (m-80) REVERT: F 35 PHE cc_start: 0.8440 (OUTLIER) cc_final: 0.8007 (m-80) REVERT: L 35 PHE cc_start: 0.8423 (OUTLIER) cc_final: 0.8143 (m-80) outliers start: 49 outliers final: 30 residues processed: 306 average time/residue: 0.2978 time to fit residues: 118.0689 Evaluate side-chains 314 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 279 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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 85 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain C residue 1 VAL Chi-restraints excluded: chain C residue 35 PHE 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 D residue 1 VAL 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 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 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 91 SER Chi-restraints excluded: chain L residue 102 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 18 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.163185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.107524 restraints weight = 32422.425| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.87 r_work: 0.2976 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.4664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10038 Z= 0.204 Angle : 0.619 5.736 13809 Z= 0.357 Chirality : 0.043 0.168 1575 Planarity : 0.004 0.034 1538 Dihedral : 20.051 88.380 1922 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 5.19 % Allowed : 14.43 % Favored : 80.38 % 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: 0.78 (0.27), residues: 1047 helix: 0.95 (0.25), residues: 480 sheet: -0.94 (0.28), residues: 240 loop : 1.46 (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 0.009 0.001 PHE F 35 HIS 0.004 0.002 HIS D 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.20 (10038) covalent geometry : angle 0.61923 / 0.36 (13809) hydrogen bonds : bond 0.05903 / 4.31 ( 382) hydrogen bonds : angle 3.59961 / 2.42 ( 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: 46 poor density : 284 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LYS cc_start: 0.8709 (tptt) cc_final: 0.8416 (tttt) REVERT: B 35 PHE cc_start: 0.8387 (OUTLIER) cc_final: 0.8180 (m-80) REVERT: B 106 GLU cc_start: 0.7792 (tp30) cc_final: 0.7329 (tp30) REVERT: C 67 GLN cc_start: 0.8228 (mt0) cc_final: 0.7947 (mt0) REVERT: C 122 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7374 (mp0) REVERT: D 106 GLU cc_start: 0.8039 (tp30) cc_final: 0.7564 (tp30) REVERT: F 35 PHE cc_start: 0.8556 (OUTLIER) cc_final: 0.8161 (m-80) REVERT: H 68 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7572 (mt-10) REVERT: J 103 GLU cc_start: 0.6670 (tm-30) cc_final: 0.6428 (tm-30) REVERT: L 106 GLU cc_start: 0.7928 (tp30) cc_final: 0.7676 (tp30) outliers start: 46 outliers final: 28 residues processed: 294 average time/residue: 0.3045 time to fit residues: 115.7343 Evaluate side-chains 306 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 274 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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 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 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 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 H residue 1 VAL Chi-restraints excluded: chain H residue 68 GLU 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 85 LEU Chi-restraints excluded: chain J residue 102 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: 0.7980 chunk 18 optimal weight: 0.2980 chunk 94 optimal weight: 7.9990 chunk 19 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 81 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 27 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.164041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.108651 restraints weight = 32475.273| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.86 r_work: 0.2987 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.4810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10038 Z= 0.139 Angle : 0.586 5.433 13809 Z= 0.339 Chirality : 0.042 0.170 1575 Planarity : 0.004 0.032 1538 Dihedral : 19.955 89.210 1922 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 4.40 % Allowed : 15.90 % Favored : 79.71 % 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: 1.00 (0.25), residues: 480 sheet: -0.99 (0.28), residues: 240 loop : 1.57 (0.40), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 123 TYR 0.005 0.001 TYR J 26 PHE 0.007 0.001 PHE B 35 HIS 0.003 0.001 HIS D 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (10038) covalent geometry : angle 0.58605 / 0.34 (13809) hydrogen bonds : bond 0.05473 / 3.96 ( 382) hydrogen bonds : angle 3.47518 / 2.33 ( 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 314 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 275 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 LYS cc_start: 0.8697 (tptt) cc_final: 0.8382 (tttt) REVERT: C 67 GLN cc_start: 0.8230 (mt0) cc_final: 0.7969 (mt0) REVERT: C 116 ILE cc_start: 0.8768 (mt) cc_final: 0.8478 (mp) REVERT: C 122 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7350 (mp0) REVERT: D 106 GLU cc_start: 0.7833 (tp30) cc_final: 0.7413 (tp30) REVERT: F 35 PHE cc_start: 0.8478 (OUTLIER) cc_final: 0.8058 (m-80) REVERT: J 119 LYS cc_start: 0.7430 (tttm) cc_final: 0.7214 (tttt) REVERT: L 106 GLU cc_start: 0.7910 (tp30) cc_final: 0.7481 (tp30) outliers start: 39 outliers final: 31 residues processed: 282 average time/residue: 0.2935 time to fit residues: 108.2084 Evaluate side-chains 307 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 274 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain B residue 1 VAL 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 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 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 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 Chi-restraints excluded: chain L residue 112 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 0.2980 chunk 15 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 44 optimal weight: 0.0470 chunk 98 optimal weight: 0.0980 chunk 74 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.164470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.109095 restraints weight = 32271.795| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.85 r_work: 0.2997 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.4931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 10038 Z= 0.142 Angle : 0.569 4.151 13809 Z= 0.331 Chirality : 0.042 0.174 1575 Planarity : 0.004 0.033 1538 Dihedral : 19.708 89.313 1922 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 4.28 % Allowed : 16.23 % 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: 0.91 (0.27), residues: 1047 helix: 1.07 (0.25), residues: 480 sheet: -0.98 (0.28), residues: 240 loop : 1.60 (0.40), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 123 TYR 0.007 0.001 TYR J 26 PHE 0.008 0.001 PHE F 35 HIS 0.003 0.001 HIS L 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (10038) covalent geometry : angle 0.56880 / 0.33 (13809) hydrogen bonds : bond 0.05214 / 3.78 ( 382) hydrogen bonds : angle 3.38697 / 2.26 ( 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 329 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 291 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LYS cc_start: 0.8697 (tptt) cc_final: 0.8386 (tttt) REVERT: B 106 GLU cc_start: 0.8022 (tp30) cc_final: 0.7527 (tp30) REVERT: C 67 GLN cc_start: 0.8242 (mt0) cc_final: 0.7939 (mt0) REVERT: C 116 ILE cc_start: 0.8802 (mt) cc_final: 0.8530 (mp) REVERT: C 122 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7348 (mp0) REVERT: D 106 GLU cc_start: 0.7871 (tp30) cc_final: 0.7455 (tp30) REVERT: F 35 PHE cc_start: 0.8525 (OUTLIER) cc_final: 0.8156 (m-80) REVERT: F 106 GLU cc_start: 0.7947 (tp30) cc_final: 0.7455 (tp30) REVERT: J 103 GLU cc_start: 0.6677 (tm-30) cc_final: 0.6320 (tm-30) REVERT: L 103 GLU cc_start: 0.6802 (tm-30) cc_final: 0.6549 (tm-30) REVERT: L 106 GLU cc_start: 0.7924 (tp30) cc_final: 0.7502 (tp30) REVERT: L 122 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7383 (mp0) outliers start: 38 outliers final: 29 residues processed: 294 average time/residue: 0.2846 time to fit residues: 109.6555 Evaluate side-chains 318 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 286 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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 85 LEU Chi-restraints excluded: chain B residue 102 VAL 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 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 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 85 LEU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 122 GLU 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: 0.9990 chunk 83 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 92 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 106 optimal weight: 0.4980 chunk 45 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 3 optimal weight: 0.0670 chunk 55 optimal weight: 0.9980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.163785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.108487 restraints weight = 32181.206| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.86 r_work: 0.2971 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.5012 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= 0.155 Angle : 0.568 4.157 13809 Z= 0.331 Chirality : 0.042 0.171 1575 Planarity : 0.004 0.031 1538 Dihedral : 19.564 87.595 1922 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 4.40 % Allowed : 16.12 % 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: 1.08 (0.25), residues: 480 sheet: -1.09 (0.28), residues: 240 loop : 1.53 (0.39), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 123 TYR 0.006 0.001 TYR J 26 PHE 0.006 0.001 PHE F 35 HIS 0.004 0.001 HIS L 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (10038) covalent geometry : angle 0.56778 / 0.33 (13809) hydrogen bonds : bond 0.05268 / 3.79 ( 382) hydrogen bonds : angle 3.40568 / 2.28 ( 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 331 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 292 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LYS cc_start: 0.8697 (tptt) cc_final: 0.8432 (tttt) REVERT: B 106 GLU cc_start: 0.7836 (tp30) cc_final: 0.7392 (tp30) REVERT: C 67 GLN cc_start: 0.8265 (mt0) cc_final: 0.7956 (mt0) REVERT: C 116 ILE cc_start: 0.8768 (mt) cc_final: 0.8502 (mp) REVERT: C 122 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7356 (mp0) REVERT: D 106 GLU cc_start: 0.7858 (tp30) cc_final: 0.7433 (tp30) REVERT: F 35 PHE cc_start: 0.8530 (OUTLIER) cc_final: 0.8213 (m-80) REVERT: F 106 GLU cc_start: 0.7775 (tp30) cc_final: 0.7345 (tp30) REVERT: H 103 GLU cc_start: 0.6766 (tm-30) cc_final: 0.6519 (tm-30) REVERT: L 33 THR cc_start: 0.8927 (t) cc_final: 0.8579 (m) REVERT: L 106 GLU cc_start: 0.7891 (tp30) cc_final: 0.7451 (tp30) outliers start: 39 outliers final: 28 residues processed: 297 average time/residue: 0.2853 time to fit residues: 111.1638 Evaluate side-chains 308 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 278 time to evaluate : 0.525 ------------------------------------------------------------------------------- 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 85 LEU Chi-restraints excluded: chain B residue 102 VAL 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 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 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 83 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 64 optimal weight: 0.2980 chunk 11 optimal weight: 0.9980 chunk 56 optimal weight: 0.0970 chunk 17 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.163716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.108217 restraints weight = 32282.925| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.86 r_work: 0.2971 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.5096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 10038 Z= 0.151 Angle : 0.571 4.145 13809 Z= 0.332 Chirality : 0.042 0.173 1575 Planarity : 0.004 0.036 1538 Dihedral : 19.456 84.973 1922 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 4.17 % Allowed : 16.57 % Favored : 79.26 % 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: 0.82 (0.27), residues: 1047 helix: 1.05 (0.24), residues: 480 sheet: -1.15 (0.28), residues: 240 loop : 1.56 (0.40), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 104 TYR 0.006 0.001 TYR B 61 PHE 0.008 0.001 PHE F 35 HIS 0.003 0.001 HIS L 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (10038) covalent geometry : angle 0.57077 / 0.33 (13809) hydrogen bonds : bond 0.05208 / 3.78 ( 382) hydrogen bonds : angle 3.38381 / 2.27 ( 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 321 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 284 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LYS cc_start: 0.8706 (tptt) cc_final: 0.8441 (tttt) REVERT: B 11 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7804 (mt-10) REVERT: B 106 GLU cc_start: 0.7858 (tp30) cc_final: 0.7408 (tp30) REVERT: C 67 GLN cc_start: 0.8267 (mt0) cc_final: 0.7953 (mt0) REVERT: C 116 ILE cc_start: 0.8704 (mt) cc_final: 0.8452 (mp) REVERT: C 122 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7347 (mp0) REVERT: D 106 GLU cc_start: 0.7892 (tp30) cc_final: 0.7435 (tp30) REVERT: F 35 PHE cc_start: 0.8541 (OUTLIER) cc_final: 0.8265 (m-80) REVERT: F 106 GLU cc_start: 0.7814 (tp30) cc_final: 0.7362 (tp30) REVERT: H 103 GLU cc_start: 0.6681 (tm-30) cc_final: 0.6469 (tm-30) REVERT: L 103 GLU cc_start: 0.6735 (tm-30) cc_final: 0.6473 (tm-30) REVERT: L 106 GLU cc_start: 0.7942 (tp30) cc_final: 0.7493 (tp30) REVERT: L 122 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7262 (mp0) outliers start: 37 outliers final: 26 residues processed: 289 average time/residue: 0.2933 time to fit residues: 111.7908 Evaluate side-chains 309 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 280 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain L residue 122 GLU 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: 0.9980 chunk 60 optimal weight: 0.9980 chunk 52 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 97 optimal weight: 0.0570 chunk 29 optimal weight: 0.0270 chunk 93 optimal weight: 1.9990 chunk 3 optimal weight: 0.2980 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 64 ASN J 64 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.164045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.108716 restraints weight = 32440.187| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.87 r_work: 0.2974 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.5154 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= 0.135 Angle : 0.558 4.129 13809 Z= 0.326 Chirality : 0.042 0.172 1575 Planarity : 0.004 0.031 1538 Dihedral : 19.431 83.266 1922 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 3.95 % Allowed : 16.69 % 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: 0.92 (0.27), residues: 1047 helix: 1.13 (0.24), residues: 480 sheet: -1.08 (0.28), residues: 240 loop : 1.59 (0.40), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 123 TYR 0.005 0.001 TYR J 26 PHE 0.006 0.001 PHE F 35 HIS 0.003 0.001 HIS L 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (10038) covalent geometry : angle 0.55788 / 0.33 (13809) hydrogen bonds : bond 0.05028 / 3.64 ( 382) hydrogen bonds : angle 3.31914 / 2.23 ( 1042) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4821.26 seconds wall clock time: 82 minutes 21.52 seconds (4941.52 seconds total)