Starting phenix.real_space_refine on Thu Mar 5 03:51:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pbu_13303/03_2026/7pbu_13303_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pbu_13303/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7pbu_13303/03_2026/7pbu_13303.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pbu_13303/03_2026/7pbu_13303.map" model { file = "/net/cci-nas-00/data/ceres_data/7pbu_13303/03_2026/7pbu_13303_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pbu_13303/03_2026/7pbu_13303_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 68 5.49 5 S 40 5.16 5 C 6060 2.51 5 N 1666 2.21 5 O 1902 1.98 5 H 9507 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 3.33, per 1000 atoms: 0.17 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: 1.69 Conformation dependent library (CDL) restraints added in 486.5 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: 2.67 Creating SS restraints... Processing helix chain 'A' and resid 34 through 38 Processing helix chain 'A' and resid 65 through 77 removed outlier: 3.676A pdb=" N LYS A 77 " --> pdb=" O LYS A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 93 Processing helix chain 'A' and resid 94 through 105 Processing helix chain 'A' and resid 106 through 112 removed outlier: 3.632A pdb=" N LEU A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 133 removed outlier: 4.631A pdb=" N ASP A 130 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ARG A 131 " --> pdb=" O GLU A 127 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE A 132 " --> pdb=" O MET A 128 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LYS A 133 " --> pdb=" O LYS A 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 38 Processing helix chain 'B' and resid 65 through 77 removed outlier: 3.646A pdb=" N LYS B 77 " --> pdb=" O LYS B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'B' and resid 94 through 105 Processing helix chain 'B' and resid 106 through 112 removed outlier: 3.582A pdb=" N LEU B 110 " --> pdb=" O GLU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 133 removed outlier: 4.598A pdb=" N ASP B 130 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ARG B 131 " --> pdb=" O GLU B 127 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE B 132 " --> pdb=" O MET B 128 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LYS B 133 " --> pdb=" O LYS B 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 38 removed outlier: 3.753A pdb=" N TYR C 36 " --> pdb=" O THR C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 77 removed outlier: 3.623A pdb=" N LYS C 77 " --> pdb=" O LYS C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 93 Processing helix chain 'C' and resid 94 through 105 Processing helix chain 'C' and resid 106 through 112 removed outlier: 3.651A pdb=" N LEU C 110 " --> pdb=" O GLU C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 133 removed outlier: 4.582A pdb=" N ASP C 130 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ARG C 131 " --> pdb=" O GLU C 127 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE C 132 " --> pdb=" O MET C 128 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LYS C 133 " --> pdb=" O LYS C 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 38 Processing helix chain 'D' and resid 65 through 77 removed outlier: 3.673A pdb=" N LYS D 77 " --> pdb=" O LYS D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 93 Processing helix chain 'D' and resid 94 through 105 Processing helix chain 'D' and resid 106 through 112 removed outlier: 3.628A pdb=" N LEU D 110 " --> pdb=" O GLU D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 133 removed outlier: 4.626A pdb=" N ASP D 130 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ARG D 131 " --> pdb=" O GLU D 127 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE D 132 " --> pdb=" O MET D 128 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LYS D 133 " --> pdb=" O LYS D 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 38 Processing helix chain 'F' and resid 65 through 77 removed outlier: 3.612A pdb=" N LYS F 77 " --> pdb=" O LYS F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'F' and resid 94 through 105 Processing helix chain 'F' and resid 106 through 112 removed outlier: 3.646A pdb=" N LEU F 110 " --> pdb=" O GLU F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 133 removed outlier: 4.586A pdb=" N ASP F 130 " --> pdb=" O VAL F 126 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ARG F 131 " --> pdb=" O GLU F 127 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE F 132 " --> pdb=" O MET F 128 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LYS F 133 " --> pdb=" O LYS F 129 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 38 Processing helix chain 'H' and resid 65 through 77 removed outlier: 3.631A pdb=" N LYS H 77 " --> pdb=" O LYS H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 93 Processing helix chain 'H' and resid 94 through 105 Processing helix chain 'H' and resid 106 through 112 removed outlier: 3.681A pdb=" N LEU H 110 " --> pdb=" O GLU H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 129 Processing helix chain 'J' and resid 34 through 38 Processing helix chain 'J' and resid 65 through 78 removed outlier: 3.574A pdb=" N LYS J 77 " --> pdb=" O LYS J 73 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR J 78 " --> pdb=" O GLU J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 93 Processing helix chain 'J' and resid 94 through 105 Processing helix chain 'J' and resid 106 through 112 removed outlier: 3.638A pdb=" N LEU J 110 " --> pdb=" O GLU J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 117 through 133 removed outlier: 4.592A pdb=" N ASP J 130 " --> pdb=" O VAL J 126 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ARG J 131 " --> pdb=" O GLU J 127 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE J 132 " --> pdb=" O MET J 128 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LYS J 133 " --> pdb=" O LYS J 129 " (cutoff:3.500A) Processing helix chain 'L' and resid 33 through 38 removed outlier: 3.646A pdb=" N TYR L 36 " --> pdb=" O THR L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 65 through 77 removed outlier: 3.661A pdb=" N LYS L 77 " --> pdb=" O LYS L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 93 Processing helix chain 'L' and resid 94 through 105 Processing helix chain 'L' and resid 106 through 112 removed outlier: 3.640A pdb=" N LEU L 110 " --> pdb=" O GLU L 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 117 through 133 removed outlier: 4.584A pdb=" N ASP L 130 " --> pdb=" O VAL L 126 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARG L 131 " --> pdb=" O GLU L 127 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE L 132 " --> pdb=" O MET L 128 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LYS L 133 " --> pdb=" O LYS L 129 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 13 removed outlier: 6.820A pdb=" N LEU A 18 " --> pdb=" O LEU A 10 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LYS A 12 " --> pdb=" O ILE A 16 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ILE A 16 " --> pdb=" O LYS A 12 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 24 through 29 current: chain 'A' and resid 58 through 63 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 58 through 63 current: chain 'B' and resid 16 through 21 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 24 through 29 current: chain 'B' and resid 58 through 63 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 58 through 63 current: chain 'C' and resid 16 through 21 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 24 through 29 current: chain 'C' and resid 58 through 63 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 58 through 63 current: chain 'D' and resid 16 through 21 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 24 through 29 current: chain 'D' and resid 58 through 63 Processing sheet with id=AA2, first strand: chain 'F' and resid 2 through 13 removed outlier: 6.788A pdb=" N LEU F 18 " --> pdb=" O LEU F 10 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N LYS F 12 " --> pdb=" O ILE F 16 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ILE F 16 " --> pdb=" O LYS F 12 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 24 through 29 current: chain 'F' and resid 58 through 63 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 58 through 63 current: chain 'H' and resid 16 through 21 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 24 through 29 current: chain 'H' and resid 58 through 63 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 58 through 63 current: chain 'J' and resid 16 through 21 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 24 through 29 current: chain 'J' and resid 58 through 63 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 58 through 63 current: chain 'L' and resid 16 through 21 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 24 through 29 current: chain 'L' and resid 58 through 63 350 hydrogen bonds defined for protein. 978 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 32 hydrogen bonds 64 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 3.26 Time building geometry restraints manager: 2.36 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=" C4' DT E 27 " pdb=" C3' DT E 27 " ideal model delta sigma weight residual 1.523 1.502 0.021 2.00e-02 2.50e+03 1.10e+00 bond pdb=" C4' DT G 27 " pdb=" C3' DT G 27 " ideal model delta sigma weight residual 1.523 1.504 0.019 2.00e-02 2.50e+03 8.63e-01 bond pdb=" C3' DA E 33 " pdb=" O3' DA E 33 " ideal model delta sigma weight residual 1.422 1.450 -0.028 3.00e-02 1.11e+03 8.48e-01 bond pdb=" CB LEU C 60 " pdb=" CG LEU C 60 " ideal model delta sigma weight residual 1.530 1.512 0.018 2.00e-02 2.50e+03 8.32e-01 bond pdb=" CB LEU D 60 " pdb=" CG LEU D 60 " ideal model delta sigma weight residual 1.530 1.512 0.018 2.00e-02 2.50e+03 8.24e-01 ... (remaining 19540 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 31711 1.11 - 2.21: 3488 2.21 - 3.32: 339 3.32 - 4.42: 72 4.42 - 5.53: 12 Bond angle restraints: 35622 Sorted by residual: angle pdb=" C5' DT K 7 " pdb=" C4' DT K 7 " pdb=" O4' DT K 7 " ideal model delta sigma weight residual 109.40 113.89 -4.49 1.50e+00 4.44e-01 8.97e+00 angle pdb=" C3' DA G 33 " pdb=" C2' DA G 33 " pdb=" C1' DA G 33 " ideal model delta sigma weight residual 101.60 105.98 -4.38 1.50e+00 4.44e-01 8.53e+00 angle pdb=" C4' DT E 25 " pdb=" O4' DT E 25 " pdb=" C1' DT E 25 " ideal model delta sigma weight residual 109.70 105.71 3.99 1.50e+00 4.44e-01 7.09e+00 angle pdb=" C3' DA E 34 " pdb=" C2' DA E 34 " pdb=" C1' DA E 34 " ideal model delta sigma weight residual 101.60 105.57 -3.97 1.50e+00 4.44e-01 7.00e+00 angle pdb=" C4' DT G 25 " pdb=" O4' DT G 25 " pdb=" C1' DT G 25 " ideal model delta sigma weight residual 109.70 105.74 3.96 1.50e+00 4.44e-01 6.97e+00 ... (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 - 0.046: 1125 0.046 - 0.092: 326 0.092 - 0.138: 110 0.138 - 0.185: 10 0.185 - 0.231: 4 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 -2.66 -2.43 -0.23 2.00e-01 2.50e+01 1.33e+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 -2.66 -2.44 -0.22 2.00e-01 2.50e+01 1.17e+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 -2.66 -2.47 -0.19 2.00e-01 2.50e+01 9.13e-01 ... (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: 3.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.100 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.060 Find NCS groups from input model: 0.270 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 10038 Z= 0.216 Angle : 0.819 5.529 13809 Z= 0.494 Chirality : 0.049 0.231 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 covalent geometry : bond 0.00519 (10038) covalent geometry : angle 0.81852 (13809) hydrogen bonds : bond 0.21306 ( 382) hydrogen bonds : angle 6.31309 ( 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 : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLN cc_start: 0.8017 (mt0) cc_final: 0.7776 (mp10) REVERT: A 84 LYS cc_start: 0.8694 (tptt) cc_final: 0.8442 (tttt) REVERT: A 100 ASN cc_start: 0.7390 (m-40) cc_final: 0.7182 (m110) REVERT: B 13 GLN cc_start: 0.7059 (mt0) cc_final: 0.6773 (mt0) REVERT: B 100 ASN cc_start: 0.7356 (m-40) cc_final: 0.7103 (m110) REVERT: C 67 GLN cc_start: 0.8036 (mt0) cc_final: 0.7666 (mp10) REVERT: C 100 ASN cc_start: 0.7338 (m-40) cc_final: 0.7110 (m110) REVERT: D 13 GLN cc_start: 0.7163 (mt0) cc_final: 0.6919 (mt0) REVERT: D 67 GLN cc_start: 0.8055 (mt0) cc_final: 0.7736 (mp10) REVERT: D 100 ASN cc_start: 0.7327 (m-40) cc_final: 0.7082 (m110) REVERT: F 100 ASN cc_start: 0.7284 (m-40) cc_final: 0.6925 (m-40) REVERT: H 67 GLN cc_start: 0.8165 (mt0) cc_final: 0.7799 (mp10) REVERT: H 100 ASN cc_start: 0.7322 (m-40) cc_final: 0.7050 (m110) REVERT: J 67 GLN cc_start: 0.8097 (mt0) cc_final: 0.7852 (mp10) REVERT: J 100 ASN cc_start: 0.7415 (m-40) cc_final: 0.7133 (m110) REVERT: L 13 GLN cc_start: 0.7068 (mt0) cc_final: 0.6816 (mt0) REVERT: L 59 LEU cc_start: 0.9092 (mt) cc_final: 0.8892 (mp) REVERT: L 67 GLN cc_start: 0.8017 (mt0) cc_final: 0.7725 (mp10) REVERT: L 100 ASN cc_start: 0.7376 (m-40) cc_final: 0.7144 (m110) outliers start: 0 outliers final: 0 residues processed: 416 average time/residue: 0.2915 time to fit residues: 155.8399 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 : 0.533 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 65 ASN B 97 GLN C 65 ASN C 97 GLN D 65 ASN D 97 GLN F 97 GLN H 65 ASN H 97 GLN J 65 ASN J 97 GLN L 65 ASN L 97 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.166114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.111255 restraints weight = 32586.250| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.87 r_work: 0.3066 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.3744 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= 0.208 Angle : 0.663 5.588 13809 Z= 0.381 Chirality : 0.044 0.164 1575 Planarity : 0.005 0.033 1538 Dihedral : 19.496 89.257 1922 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 2.48 % Allowed : 12.18 % Favored : 85.34 % 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: 1.54 (0.27), residues: 1047 helix: 0.80 (0.24), residues: 480 sheet: 0.29 (0.25), residues: 336 loop : 3.37 (0.50), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 4 TYR 0.007 0.001 TYR H 61 PHE 0.009 0.002 PHE B 63 HIS 0.005 0.002 HIS H 29 Details of bonding type rmsd covalent geometry : bond 0.00475 (10038) covalent geometry : angle 0.66328 (13809) hydrogen bonds : bond 0.06845 ( 382) hydrogen bonds : angle 4.09238 ( 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: 22 poor density : 321 time to evaluate : 0.444 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: 0.8343 (OUTLIER) cc_final: 0.7880 (m-80) REVERT: A 68 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7565 (mt-10) REVERT: A 84 LYS cc_start: 0.8758 (tptt) cc_final: 0.8467 (tttt) REVERT: A 100 ASN cc_start: 0.7190 (m-40) cc_final: 0.6988 (m110) REVERT: B 35 PHE cc_start: 0.8370 (OUTLIER) cc_final: 0.7952 (m-80) REVERT: B 40 GLU cc_start: 0.7570 (mp0) cc_final: 0.7263 (pm20) REVERT: B 74 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8506 (mm-30) REVERT: C 35 PHE cc_start: 0.8339 (OUTLIER) cc_final: 0.7856 (m-80) REVERT: C 67 GLN cc_start: 0.8265 (mt0) cc_final: 0.8018 (mt0) REVERT: C 116 ILE cc_start: 0.8739 (mt) cc_final: 0.8421 (mp) REVERT: D 35 PHE cc_start: 0.8297 (OUTLIER) cc_final: 0.7990 (m-80) REVERT: D 67 GLN cc_start: 0.8355 (mt0) cc_final: 0.8142 (mt0) REVERT: D 77 LYS cc_start: 0.8449 (mtmt) cc_final: 0.8188 (mtmm) REVERT: F 35 PHE cc_start: 0.8422 (OUTLIER) cc_final: 0.7896 (m-80) REVERT: F 100 ASN cc_start: 0.7194 (m-40) cc_final: 0.6860 (m-40) REVERT: F 103 GLU cc_start: 0.6727 (tm-30) cc_final: 0.6469 (tm-30) REVERT: H 35 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.7919 (m-80) REVERT: J 35 PHE cc_start: 0.8499 (OUTLIER) cc_final: 0.8158 (m-80) REVERT: L 35 PHE cc_start: 0.8301 (OUTLIER) cc_final: 0.7948 (m-80) REVERT: L 68 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7569 (mt-10) outliers start: 22 outliers final: 12 residues processed: 331 average time/residue: 0.3111 time to fit residues: 130.1214 Evaluate side-chains 312 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 292 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 C residue 124 LEU 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 85 LEU 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: 0.9980 chunk 15 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 ASN C 100 ASN D 100 ASN H 100 ASN L 100 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.164230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.109483 restraints weight = 32732.286| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.88 r_work: 0.3034 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 10038 Z= 0.183 Angle : 0.611 6.634 13809 Z= 0.349 Chirality : 0.043 0.145 1575 Planarity : 0.004 0.028 1538 Dihedral : 19.915 88.803 1922 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 4.51 % Allowed : 13.08 % Favored : 82.41 % 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: 1.17 (0.27), residues: 1047 helix: 0.96 (0.25), residues: 480 sheet: -0.45 (0.29), residues: 240 loop : 1.93 (0.39), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 123 TYR 0.008 0.002 TYR J 26 PHE 0.008 0.002 PHE C 35 HIS 0.004 0.002 HIS L 29 Details of bonding type rmsd covalent geometry : bond 0.00431 (10038) covalent geometry : angle 0.61150 (13809) hydrogen bonds : bond 0.06127 ( 382) hydrogen bonds : angle 3.70658 ( 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 343 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 303 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 PHE cc_start: 0.8498 (OUTLIER) cc_final: 0.8279 (m-80) REVERT: A 84 LYS cc_start: 0.8718 (tptt) cc_final: 0.8406 (tttt) REVERT: B 35 PHE cc_start: 0.8406 (OUTLIER) cc_final: 0.8125 (m-80) REVERT: C 35 PHE cc_start: 0.8512 (OUTLIER) cc_final: 0.8227 (m-80) REVERT: C 67 GLN cc_start: 0.8249 (mt0) cc_final: 0.7992 (mt0) REVERT: C 68 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7590 (mt-10) REVERT: C 122 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7292 (mp0) REVERT: D 67 GLN cc_start: 0.8369 (mt0) cc_final: 0.8158 (mt0) REVERT: D 77 LYS cc_start: 0.8370 (mtmt) cc_final: 0.8135 (mtmm) REVERT: F 35 PHE cc_start: 0.8498 (OUTLIER) cc_final: 0.8096 (m-80) REVERT: F 100 ASN cc_start: 0.7153 (m-40) cc_final: 0.6875 (m-40) REVERT: H 35 PHE cc_start: 0.8447 (OUTLIER) cc_final: 0.8219 (m-80) REVERT: J 68 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7549 (mt-10) REVERT: L 122 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7371 (mp0) outliers start: 40 outliers final: 19 residues processed: 311 average time/residue: 0.3150 time to fit residues: 123.1926 Evaluate side-chains 302 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 276 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain B residue 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 93 MET 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 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 85 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 112 LYS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 6 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 106 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 101 optimal weight: 0.4980 chunk 66 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN C 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.162684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.108160 restraints weight = 32470.417| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.82 r_work: 0.2983 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10038 Z= 0.187 Angle : 0.616 5.507 13809 Z= 0.346 Chirality : 0.043 0.129 1575 Planarity : 0.004 0.031 1538 Dihedral : 19.969 89.855 1922 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 4.51 % Allowed : 14.88 % Favored : 80.61 % 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: 0.81 (0.27), residues: 1047 helix: 0.87 (0.25), residues: 480 sheet: -0.86 (0.29), residues: 240 loop : 1.60 (0.39), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG F 104 TYR 0.007 0.002 TYR H 61 PHE 0.010 0.001 PHE H 35 HIS 0.004 0.002 HIS H 29 Details of bonding type rmsd covalent geometry : bond 0.00442 (10038) covalent geometry : angle 0.61560 (13809) hydrogen bonds : bond 0.05474 ( 382) hydrogen bonds : angle 3.64598 ( 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 328 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 288 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LYS cc_start: 0.8704 (tptt) cc_final: 0.8442 (ttmt) REVERT: B 106 GLU cc_start: 0.7831 (tp30) cc_final: 0.7382 (tp30) REVERT: C 67 GLN cc_start: 0.8257 (mt0) cc_final: 0.7972 (mt0) REVERT: C 122 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7330 (mp0) REVERT: D 67 GLN cc_start: 0.8329 (mt0) cc_final: 0.8115 (mt0) REVERT: D 77 LYS cc_start: 0.8393 (mtmt) cc_final: 0.8184 (mtmm) REVERT: F 35 PHE cc_start: 0.8544 (OUTLIER) cc_final: 0.8171 (m-80) REVERT: F 106 GLU cc_start: 0.7831 (tp30) cc_final: 0.7379 (tp30) REVERT: H 122 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7255 (mp0) REVERT: L 106 GLU cc_start: 0.8321 (tp30) cc_final: 0.7917 (tp30) outliers start: 40 outliers final: 24 residues processed: 296 average time/residue: 0.3096 time to fit residues: 115.4572 Evaluate side-chains 299 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 272 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL 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 85 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain D residue 1 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain F residue 1 VAL Chi-restraints excluded: chain F residue 35 PHE Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain H residue 1 VAL Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 112 LYS Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain J residue 1 VAL Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain L residue 1 VAL Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 102 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 73 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 29 optimal weight: 0.0980 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 58 optimal weight: 0.2980 chunk 17 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.162721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.110583 restraints weight = 32622.036| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.74 r_work: 0.3122 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.4887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10038 Z= 0.148 Angle : 0.570 4.470 13809 Z= 0.323 Chirality : 0.042 0.128 1575 Planarity : 0.004 0.028 1538 Dihedral : 19.883 87.869 1922 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 3.72 % Allowed : 16.12 % Favored : 80.16 % 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: 0.86 (0.27), residues: 1047 helix: 0.99 (0.25), residues: 480 sheet: -0.96 (0.28), residues: 240 loop : 1.58 (0.39), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 123 TYR 0.006 0.001 TYR J 61 PHE 0.006 0.001 PHE F 35 HIS 0.003 0.001 HIS L 29 Details of bonding type rmsd covalent geometry : bond 0.00349 (10038) covalent geometry : angle 0.56971 (13809) hydrogen bonds : bond 0.04953 ( 382) hydrogen bonds : angle 3.44648 ( 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 315 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 282 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LYS cc_start: 0.8690 (tptt) cc_final: 0.8435 (tttt) REVERT: C 67 GLN cc_start: 0.8293 (mt0) cc_final: 0.7989 (mt0) REVERT: C 122 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7366 (mp0) REVERT: D 67 GLN cc_start: 0.8297 (mt0) cc_final: 0.8091 (mt0) REVERT: D 77 LYS cc_start: 0.8350 (mtmt) cc_final: 0.8148 (mtmm) REVERT: D 106 GLU cc_start: 0.7834 (tp30) cc_final: 0.7627 (tp30) REVERT: F 35 PHE cc_start: 0.8559 (OUTLIER) cc_final: 0.8256 (m-80) REVERT: H 122 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7308 (mp0) REVERT: L 106 GLU cc_start: 0.8239 (tp30) cc_final: 0.7953 (tp30) outliers start: 33 outliers final: 24 residues processed: 283 average time/residue: 0.2856 time to fit residues: 104.4074 Evaluate side-chains 304 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 277 time to evaluate : 0.486 ------------------------------------------------------------------------------- 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 85 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain D residue 1 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain F residue 1 VAL Chi-restraints excluded: chain F residue 35 PHE Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain H residue 1 VAL Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain J residue 1 VAL Chi-restraints excluded: chain J residue 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 18 optimal weight: 0.9990 chunk 68 optimal weight: 0.4980 chunk 58 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.161325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.109150 restraints weight = 32587.255| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.73 r_work: 0.3102 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.5028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 10038 Z= 0.189 Angle : 0.590 4.452 13809 Z= 0.332 Chirality : 0.043 0.127 1575 Planarity : 0.004 0.029 1538 Dihedral : 19.729 84.214 1922 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 4.17 % Allowed : 15.45 % 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: 0.55 (0.27), residues: 1047 helix: 0.91 (0.25), residues: 480 sheet: -1.38 (0.28), residues: 240 loop : 1.38 (0.39), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 54 TYR 0.008 0.001 TYR J 26 PHE 0.007 0.001 PHE F 35 HIS 0.004 0.002 HIS L 29 Details of bonding type rmsd covalent geometry : bond 0.00447 (10038) covalent geometry : angle 0.58950 (13809) hydrogen bonds : bond 0.05195 ( 382) hydrogen bonds : angle 3.63086 ( 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 325 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 288 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LYS cc_start: 0.8718 (tptt) cc_final: 0.8453 (tttt) REVERT: B 106 GLU cc_start: 0.7889 (tp30) cc_final: 0.7640 (tp30) REVERT: C 67 GLN cc_start: 0.8259 (mt0) cc_final: 0.7942 (mt0) REVERT: C 122 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7336 (mp0) REVERT: D 67 GLN cc_start: 0.8308 (mt0) cc_final: 0.8102 (mt0) REVERT: D 77 LYS cc_start: 0.8391 (mtmt) cc_final: 0.8139 (mtmm) REVERT: F 35 PHE cc_start: 0.8612 (OUTLIER) cc_final: 0.8359 (m-80) REVERT: F 106 GLU cc_start: 0.8092 (tp30) cc_final: 0.7668 (tp30) REVERT: J 106 GLU cc_start: 0.7998 (tp30) cc_final: 0.7735 (tp30) REVERT: L 106 GLU cc_start: 0.8151 (tp30) cc_final: 0.7803 (tp30) outliers start: 37 outliers final: 27 residues processed: 293 average time/residue: 0.2877 time to fit residues: 108.2640 Evaluate side-chains 308 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 279 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain B residue 1 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain C residue 1 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain D residue 1 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain F residue 1 VAL Chi-restraints excluded: chain F residue 35 PHE Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain H residue 1 VAL 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 J residue 1 VAL Chi-restraints excluded: chain J residue 11 GLU Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain L residue 1 VAL Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 102 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 60 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 3 optimal weight: 0.0570 chunk 27 optimal weight: 0.2980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 64 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.162160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.109834 restraints weight = 32724.053| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.76 r_work: 0.3109 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.5148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10038 Z= 0.143 Angle : 0.562 4.440 13809 Z= 0.317 Chirality : 0.042 0.128 1575 Planarity : 0.004 0.027 1538 Dihedral : 19.574 81.210 1922 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 3.95 % Allowed : 16.12 % Favored : 79.93 % 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: 0.67 (0.27), residues: 1047 helix: 1.00 (0.25), residues: 480 sheet: -1.31 (0.29), residues: 240 loop : 1.43 (0.40), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 104 TYR 0.005 0.001 TYR H 61 PHE 0.006 0.001 PHE F 35 HIS 0.003 0.001 HIS B 29 Details of bonding type rmsd covalent geometry : bond 0.00335 (10038) covalent geometry : angle 0.56194 (13809) hydrogen bonds : bond 0.04693 ( 382) hydrogen bonds : angle 3.41868 ( 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 320 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 285 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LYS cc_start: 0.8709 (tptt) cc_final: 0.8444 (tttt) REVERT: C 67 GLN cc_start: 0.8298 (mt0) cc_final: 0.7992 (mt0) REVERT: C 106 GLU cc_start: 0.7923 (tp30) cc_final: 0.7655 (tp30) REVERT: C 122 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7368 (mp0) REVERT: D 67 GLN cc_start: 0.8294 (mt0) cc_final: 0.8091 (mt0) REVERT: D 77 LYS cc_start: 0.8378 (mtmt) cc_final: 0.8134 (mtmm) REVERT: D 106 GLU cc_start: 0.7873 (tp30) cc_final: 0.7660 (tp30) REVERT: F 33 THR cc_start: 0.8968 (t) cc_final: 0.8589 (m) REVERT: F 35 PHE cc_start: 0.8602 (OUTLIER) cc_final: 0.8379 (m-80) REVERT: F 106 GLU cc_start: 0.8138 (tp30) cc_final: 0.7896 (tp30) REVERT: H 122 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7188 (mp0) REVERT: J 106 GLU cc_start: 0.7930 (tp30) cc_final: 0.7678 (tp30) REVERT: L 106 GLU cc_start: 0.7924 (tp30) cc_final: 0.7609 (tp30) outliers start: 35 outliers final: 28 residues processed: 289 average time/residue: 0.2806 time to fit residues: 104.8544 Evaluate side-chains 311 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 280 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain B residue 1 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain C residue 1 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain D residue 1 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain F residue 1 VAL Chi-restraints excluded: chain F residue 35 PHE Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain H residue 1 VAL Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 119 LYS Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain J residue 1 VAL Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain L residue 1 VAL Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 102 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 98 optimal weight: 0.1980 chunk 74 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 60 optimal weight: 0.3980 chunk 13 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.161735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.110129 restraints weight = 32625.351| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.73 r_work: 0.3104 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.5269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 10038 Z= 0.156 Angle : 0.562 4.393 13809 Z= 0.317 Chirality : 0.042 0.128 1575 Planarity : 0.004 0.028 1538 Dihedral : 19.436 75.234 1922 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 4.17 % Allowed : 15.67 % Favored : 80.16 % 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: 0.62 (0.27), residues: 1047 helix: 1.04 (0.25), residues: 480 sheet: -1.44 (0.29), residues: 240 loop : 1.36 (0.40), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 104 TYR 0.007 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 covalent geometry : bond 0.00364 (10038) covalent geometry : angle 0.56230 (13809) hydrogen bonds : bond 0.04754 ( 382) hydrogen bonds : angle 3.41707 ( 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 322 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 285 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 33 THR cc_start: 0.9046 (t) cc_final: 0.8786 (m) REVERT: C 67 GLN cc_start: 0.8271 (mt0) cc_final: 0.7953 (mt0) REVERT: C 106 GLU cc_start: 0.7877 (tp30) cc_final: 0.7616 (tp30) REVERT: C 122 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7346 (mp0) REVERT: D 67 GLN cc_start: 0.8305 (mt0) cc_final: 0.8097 (mt0) REVERT: D 77 LYS cc_start: 0.8425 (mtmt) cc_final: 0.8166 (mtmm) REVERT: F 33 THR cc_start: 0.9014 (t) cc_final: 0.8766 (m) REVERT: F 106 GLU cc_start: 0.7968 (tp30) cc_final: 0.7716 (tp30) REVERT: H 33 THR cc_start: 0.9019 (t) cc_final: 0.8762 (m) REVERT: H 103 GLU cc_start: 0.6678 (tm-30) cc_final: 0.6465 (tm-30) REVERT: H 122 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7250 (mp0) REVERT: J 103 GLU cc_start: 0.6686 (tm-30) cc_final: 0.6443 (tm-30) REVERT: J 106 GLU cc_start: 0.7955 (tp30) cc_final: 0.7544 (tp30) REVERT: L 33 THR cc_start: 0.9101 (t) cc_final: 0.8888 (m) REVERT: L 106 GLU cc_start: 0.7965 (tp30) cc_final: 0.7606 (tp30) REVERT: L 122 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7175 (mp0) outliers start: 37 outliers final: 28 residues processed: 290 average time/residue: 0.2745 time to fit residues: 103.8590 Evaluate side-chains 310 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 279 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain B residue 1 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain C residue 1 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain D residue 1 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain F residue 1 VAL Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain H residue 1 VAL Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain J residue 1 VAL Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 88 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 3 optimal weight: 0.0980 chunk 55 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 64 ASN L 64 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.160931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.109251 restraints weight = 32640.132| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.72 r_work: 0.3100 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.5373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 10038 Z= 0.180 Angle : 0.580 4.314 13809 Z= 0.326 Chirality : 0.042 0.128 1575 Planarity : 0.004 0.032 1538 Dihedral : 19.425 70.171 1922 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 3.61 % Allowed : 15.90 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.27), residues: 1047 helix: 0.95 (0.25), residues: 480 sheet: -1.64 (0.28), residues: 240 loop : 1.17 (0.39), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 104 TYR 0.007 0.001 TYR J 26 PHE 0.006 0.001 PHE C 72 HIS 0.004 0.001 HIS B 29 Details of bonding type rmsd covalent geometry : bond 0.00425 (10038) covalent geometry : angle 0.57986 (13809) hydrogen bonds : bond 0.04900 ( 382) hydrogen bonds : angle 3.52141 ( 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 299 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 267 time to evaluate : 0.466 Fit side-chains revert: symmetry clash REVERT: A 84 LYS cc_start: 0.8732 (tptt) cc_final: 0.8497 (ttmt) REVERT: B 33 THR cc_start: 0.9032 (t) cc_final: 0.8826 (m) REVERT: B 106 GLU cc_start: 0.8072 (tp30) cc_final: 0.7633 (tp30) REVERT: B 122 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7200 (mp0) REVERT: C 33 THR cc_start: 0.9015 (t) cc_final: 0.8744 (m) REVERT: C 67 GLN cc_start: 0.8253 (mt0) cc_final: 0.7928 (mt0) REVERT: C 106 GLU cc_start: 0.7900 (tp30) cc_final: 0.7633 (tp30) REVERT: C 122 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7368 (mp0) REVERT: D 67 GLN cc_start: 0.8268 (mt0) cc_final: 0.8064 (mt0) REVERT: D 77 LYS cc_start: 0.8490 (mtmt) cc_final: 0.8230 (mtmm) REVERT: D 106 GLU cc_start: 0.7875 (tp30) cc_final: 0.7631 (tp30) REVERT: F 106 GLU cc_start: 0.7968 (tp30) cc_final: 0.7714 (tp30) REVERT: H 33 THR cc_start: 0.9020 (t) cc_final: 0.8799 (m) REVERT: H 103 GLU cc_start: 0.6701 (tm-30) cc_final: 0.6493 (tm-30) REVERT: H 122 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7174 (mp0) REVERT: J 103 GLU cc_start: 0.6725 (tm-30) cc_final: 0.6513 (tm-30) REVERT: J 106 GLU cc_start: 0.7978 (tp30) cc_final: 0.7572 (tp30) REVERT: L 106 GLU cc_start: 0.7975 (tp30) cc_final: 0.7614 (tp30) REVERT: L 122 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7205 (mp0) outliers start: 32 outliers final: 21 residues processed: 272 average time/residue: 0.2645 time to fit residues: 93.4421 Evaluate side-chains 289 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 264 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain B residue 1 VAL Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain C residue 1 VAL Chi-restraints excluded: chain C residue 85 LEU 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 85 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain H residue 1 VAL Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain J residue 1 VAL Chi-restraints excluded: chain L residue 1 VAL Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 91 SER 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 83 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 56 optimal weight: 0.0270 chunk 17 optimal weight: 0.9980 chunk 101 optimal weight: 0.0470 chunk 69 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.159776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.108118 restraints weight = 33703.087| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.84 r_work: 0.3078 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.5445 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= 0.135 Angle : 0.550 4.128 13809 Z= 0.310 Chirality : 0.041 0.128 1575 Planarity : 0.004 0.030 1538 Dihedral : 19.403 71.384 1922 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.93 % Allowed : 16.23 % Favored : 80.83 % 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: 0.65 (0.27), residues: 1047 helix: 1.11 (0.25), residues: 480 sheet: -1.45 (0.28), residues: 252 loop : 1.45 (0.40), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 104 TYR 0.005 0.001 TYR J 61 PHE 0.004 0.001 PHE F 51 HIS 0.003 0.001 HIS B 29 Details of bonding type rmsd covalent geometry : bond 0.00313 (10038) covalent geometry : angle 0.54992 (13809) hydrogen bonds : bond 0.04374 ( 382) hydrogen bonds : angle 3.30373 ( 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 305 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 279 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.9011 (t) cc_final: 0.8721 (m) REVERT: A 84 LYS cc_start: 0.8680 (tptt) cc_final: 0.8465 (ttmt) REVERT: B 106 GLU cc_start: 0.8039 (tp30) cc_final: 0.7598 (tp30) REVERT: B 122 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7259 (mp0) REVERT: C 33 THR cc_start: 0.8981 (t) cc_final: 0.8718 (m) REVERT: C 67 GLN cc_start: 0.8309 (mt0) cc_final: 0.7993 (mt0) REVERT: C 106 GLU cc_start: 0.7948 (tp30) cc_final: 0.7696 (tp30) REVERT: C 122 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7318 (mp0) REVERT: D 67 GLN cc_start: 0.8357 (mt0) cc_final: 0.8149 (mt0) REVERT: D 77 LYS cc_start: 0.8505 (mtmt) cc_final: 0.8258 (mtmm) REVERT: D 106 GLU cc_start: 0.7804 (tp30) cc_final: 0.7553 (tp30) REVERT: F 106 GLU cc_start: 0.7933 (tp30) cc_final: 0.7681 (tp30) REVERT: H 33 THR cc_start: 0.9002 (t) cc_final: 0.8802 (m) REVERT: H 103 GLU cc_start: 0.6621 (tm-30) cc_final: 0.6413 (tm-30) REVERT: H 122 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7240 (mp0) REVERT: J 103 GLU cc_start: 0.6543 (tm-30) cc_final: 0.6332 (tm-30) REVERT: J 106 GLU cc_start: 0.7932 (tp30) cc_final: 0.7527 (tp30) REVERT: L 106 GLU cc_start: 0.7913 (tp30) cc_final: 0.7547 (tp30) REVERT: L 122 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7292 (mp0) outliers start: 26 outliers final: 18 residues processed: 280 average time/residue: 0.2433 time to fit residues: 89.6073 Evaluate side-chains 297 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 275 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain B residue 1 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain C residue 1 VAL Chi-restraints excluded: chain C residue 85 LEU 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 85 LEU Chi-restraints excluded: chain H residue 1 VAL Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain J residue 1 VAL Chi-restraints excluded: chain L residue 1 VAL Chi-restraints excluded: chain L residue 85 LEU 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: 0.9980 chunk 48 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 89 optimal weight: 0.2980 chunk 69 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 97 optimal weight: 0.0170 chunk 29 optimal weight: 0.2980 chunk 93 optimal weight: 1.9990 chunk 3 optimal weight: 0.2980 overall best weight: 0.3818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.163151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.110900 restraints weight = 32684.784| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.75 r_work: 0.3119 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.5516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10038 Z= 0.125 Angle : 0.541 4.172 13809 Z= 0.305 Chirality : 0.041 0.128 1575 Planarity : 0.004 0.028 1538 Dihedral : 19.365 71.925 1922 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.59 % Allowed : 16.23 % Favored : 81.17 % 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: 0.95 (0.28), residues: 1047 helix: 1.26 (0.25), residues: 480 sheet: -0.94 (0.26), residues: 336 loop : 2.42 (0.51), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 104 TYR 0.004 0.001 TYR B 61 PHE 0.004 0.001 PHE A 72 HIS 0.003 0.001 HIS B 29 Details of bonding type rmsd covalent geometry : bond 0.00288 (10038) covalent geometry : angle 0.54068 (13809) hydrogen bonds : bond 0.04260 ( 382) hydrogen bonds : angle 3.24132 ( 1042) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4408.98 seconds wall clock time: 75 minutes 54.66 seconds (4554.66 seconds total)