Starting phenix.real_space_refine on Sat Aug 23 12:04:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8khf_37243/08_2025/8khf_37243.cif Found real_map, /net/cci-nas-00/data/ceres_data/8khf_37243/08_2025/8khf_37243.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8khf_37243/08_2025/8khf_37243.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8khf_37243/08_2025/8khf_37243.map" model { file = "/net/cci-nas-00/data/ceres_data/8khf_37243/08_2025/8khf_37243.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8khf_37243/08_2025/8khf_37243.cif" } resolution = 3.13 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= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Br 1 7.06 5 S 63 5.16 5 C 7967 2.51 5 N 1937 2.21 5 O 2160 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 75 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12128 Number of models: 1 Model: "" Number of chains: 20 Chain: "1" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "2" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "3" Number of atoms: 542 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Conformer: "B" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} bond proxies already assigned to first conformer: 534 Chain: "4" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "5" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "6" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "7" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "8" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "G" Number of atoms: 1485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1485 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 5, 'TRANS': 185} Chain: "H" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 975 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "I" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 354 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "K" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 6, 'TRANS': 88} Chain: "M" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 311 Classifications: {'peptide': 36} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 30} Chain: "N" Number of atoms: 1718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1718 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 208} Chain: "P" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 344 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "Q" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 307 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 5, 'TRANS': 32} Chain: "R" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 621 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 605 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 72} Chain: "T" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 346 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 39} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "4" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'BQ1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.45, per 1000 atoms: 0.20 Number of scatterers: 12128 At special positions: 0 Unit cell: (121.18, 89.79, 135.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Br 1 34.99 S 63 16.00 O 2160 8.00 N 1937 7.00 C 7967 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 482.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2898 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 4 sheets defined 76.6% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain '1' and resid 2 through 15 Processing helix chain '1' and resid 17 through 39 removed outlier: 4.057A pdb=" N SER 1 21 " --> pdb=" O GLY 1 17 " (cutoff:3.500A) Processing helix chain '1' and resid 42 through 73 removed outlier: 3.860A pdb=" N ALA 1 59 " --> pdb=" O ALA 1 55 " (cutoff:3.500A) Processing helix chain '2' and resid 2 through 16 Processing helix chain '2' and resid 18 through 39 Processing helix chain '2' and resid 42 through 73 removed outlier: 3.674A pdb=" N ALA 2 59 " --> pdb=" O ALA 2 55 " (cutoff:3.500A) Processing helix chain '3' and resid 2 through 16 Processing helix chain '3' and resid 18 through 39 Processing helix chain '3' and resid 42 through 73 removed outlier: 3.572A pdb=" N ALA 3 59 " --> pdb=" O ALA 3 55 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY 3 61 " --> pdb=" O SER 3 57 " (cutoff:3.500A) Processing helix chain '4' and resid 2 through 16 Processing helix chain '4' and resid 18 through 39 Processing helix chain '4' and resid 42 through 73 removed outlier: 3.803A pdb=" N CYS 4 64 " --> pdb=" O MET 4 60 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL 4 67 " --> pdb=" O PHE 4 63 " (cutoff:3.500A) Processing helix chain '5' and resid 2 through 16 Processing helix chain '5' and resid 18 through 39 Processing helix chain '5' and resid 42 through 73 removed outlier: 3.513A pdb=" N GLU 5 58 " --> pdb=" O PHE 5 54 " (cutoff:3.500A) Processing helix chain '6' and resid 2 through 17 removed outlier: 4.050A pdb=" N GLY 6 17 " --> pdb=" O ALA 6 13 " (cutoff:3.500A) Processing helix chain '6' and resid 17 through 39 removed outlier: 4.399A pdb=" N SER 6 21 " --> pdb=" O GLY 6 17 " (cutoff:3.500A) Processing helix chain '6' and resid 42 through 73 Processing helix chain '7' and resid 2 through 16 Processing helix chain '7' and resid 17 through 39 removed outlier: 4.446A pdb=" N SER 7 21 " --> pdb=" O GLY 7 17 " (cutoff:3.500A) Processing helix chain '7' and resid 42 through 73 removed outlier: 3.894A pdb=" N ALA 7 59 " --> pdb=" O ALA 7 55 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE 7 73 " --> pdb=" O PHE 7 69 " (cutoff:3.500A) Processing helix chain '8' and resid 2 through 16 Processing helix chain '8' and resid 17 through 39 removed outlier: 4.390A pdb=" N SER 8 21 " --> pdb=" O GLY 8 17 " (cutoff:3.500A) Processing helix chain '8' and resid 42 through 72 removed outlier: 3.672A pdb=" N ALA 8 59 " --> pdb=" O ALA 8 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 48 removed outlier: 3.920A pdb=" N LYS G 39 " --> pdb=" O GLU G 35 " (cutoff:3.500A) Proline residue: G 40 - end of helix Processing helix chain 'G' and resid 49 through 55 removed outlier: 3.548A pdb=" N GLU G 53 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 98 Processing helix chain 'G' and resid 109 through 117 removed outlier: 3.509A pdb=" N ARG G 113 " --> pdb=" O GLY G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 150 Processing helix chain 'G' and resid 180 through 187 removed outlier: 3.548A pdb=" N VAL G 184 " --> pdb=" O SER G 180 " (cutoff:3.500A) Processing helix chain 'G' and resid 188 through 193 removed outlier: 3.622A pdb=" N SER G 191 " --> pdb=" O ASP G 188 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ILE G 192 " --> pdb=" O SER G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 221 removed outlier: 3.626A pdb=" N THR G 221 " --> pdb=" O LEU G 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 103 No H-bonds generated for 'chain 'H' and resid 101 through 103' Processing helix chain 'H' and resid 104 through 122 removed outlier: 3.862A pdb=" N ALA H 108 " --> pdb=" O ASP H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 146 Processing helix chain 'I' and resid 3 through 8 Processing helix chain 'I' and resid 11 through 26 Processing helix chain 'I' and resid 28 through 40 removed outlier: 4.536A pdb=" N ALA I 33 " --> pdb=" O THR I 29 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ASN I 34 " --> pdb=" O GLU I 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 30 Proline residue: K 27 - end of helix Processing helix chain 'K' and resid 32 through 48 Processing helix chain 'K' and resid 54 through 96 removed outlier: 3.830A pdb=" N PHE K 58 " --> pdb=" O SER K 54 " (cutoff:3.500A) Proline residue: K 76 - end of helix Processing helix chain 'M' and resid 126 through 130 removed outlier: 3.547A pdb=" N MET M 130 " --> pdb=" O PHE M 127 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 139 Processing helix chain 'N' and resid 6 through 10 Processing helix chain 'N' and resid 19 through 26 Processing helix chain 'N' and resid 27 through 31 Processing helix chain 'N' and resid 40 through 59 removed outlier: 3.613A pdb=" N THR N 59 " --> pdb=" O LYS N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 64 through 67 Processing helix chain 'N' and resid 68 through 86 Processing helix chain 'N' and resid 93 through 96 Processing helix chain 'N' and resid 97 through 119 Proline residue: N 107 - end of helix removed outlier: 3.751A pdb=" N SER N 119 " --> pdb=" O MET N 115 " (cutoff:3.500A) Processing helix chain 'N' and resid 120 through 128 removed outlier: 3.834A pdb=" N PHE N 128 " --> pdb=" O ALA N 124 " (cutoff:3.500A) Processing helix chain 'N' and resid 137 through 181 removed outlier: 3.816A pdb=" N LEU N 141 " --> pdb=" O LEU N 137 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU N 145 " --> pdb=" O LEU N 141 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR N 146 " --> pdb=" O VAL N 142 " (cutoff:3.500A) Proline residue: N 153 - end of helix removed outlier: 3.801A pdb=" N ASN N 163 " --> pdb=" O ARG N 159 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA N 166 " --> pdb=" O ALA N 162 " (cutoff:3.500A) Processing helix chain 'N' and resid 185 through 224 Processing helix chain 'P' and resid 13 through 19 Processing helix chain 'P' and resid 21 through 41 Processing helix chain 'Q' and resid 1 through 8 removed outlier: 5.337A pdb=" N THR Q 6 " --> pdb=" O GLN Q 3 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N THR Q 7 " --> pdb=" O LEU Q 4 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL Q 8 " --> pdb=" O ASN Q 5 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 21 Proline residue: Q 15 - end of helix Processing helix chain 'Q' and resid 22 through 30 Processing helix chain 'R' and resid 26 through 32 removed outlier: 3.937A pdb=" N LEU R 30 " --> pdb=" O PRO R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 35 through 55 Processing helix chain 'R' and resid 62 through 79 removed outlier: 4.415A pdb=" N VAL R 68 " --> pdb=" O GLY R 64 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE R 79 " --> pdb=" O PHE R 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 80 through 85 Processing helix chain 'R' and resid 86 through 88 No H-bonds generated for 'chain 'R' and resid 86 through 88' Processing helix chain 'S' and resid 27 through 37 removed outlier: 4.789A pdb=" N VAL S 35 " --> pdb=" O TYR S 31 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU S 36 " --> pdb=" O TYR S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 43 No H-bonds generated for 'chain 'S' and resid 41 through 43' Processing helix chain 'S' and resid 44 through 62 Processing helix chain 'S' and resid 63 through 67 Processing helix chain 'S' and resid 68 through 94 Processing helix chain 'T' and resid 8 through 45 Proline residue: T 35 - end of helix removed outlier: 3.867A pdb=" N ALA T 45 " --> pdb=" O ARG T 41 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 171 through 179 removed outlier: 5.258A pdb=" N ASN G 163 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N HIS G 66 " --> pdb=" O MET G 104 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N VAL G 106 " --> pdb=" O HIS G 66 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU G 68 " --> pdb=" O VAL G 106 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ILE G 108 " --> pdb=" O LEU G 68 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLY G 70 " --> pdb=" O ILE G 108 " (cutoff:3.500A) removed outlier: 10.143A pdb=" N VAL G 126 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU G 105 " --> pdb=" O VAL G 126 " (cutoff:3.500A) removed outlier: 8.883A pdb=" N PHE G 128 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N GLY G 107 " --> pdb=" O PHE G 128 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS I 44 " --> pdb=" O LYS G 129 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 26 through 31 removed outlier: 5.304A pdb=" N ASN H 29 " --> pdb=" O PHE H 20 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N PHE H 20 " --> pdb=" O ASN H 29 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N SER H 17 " --> pdb=" O VAL H 90 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LEU H 92 " --> pdb=" O SER H 17 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N THR H 19 " --> pdb=" O LEU H 92 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ALA H 94 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ALA H 21 " --> pdb=" O ALA H 94 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 43 through 47 removed outlier: 7.319A pdb=" N LEU H 62 " --> pdb=" O PRO H 39 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 12 through 13 933 hydrogen bonds defined for protein. 2747 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.73 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 3767 1.37 - 1.51: 3896 1.51 - 1.65: 4595 1.65 - 1.79: 58 1.79 - 1.93: 58 Bond restraints: 12374 Sorted by residual: bond pdb=" C10 BQ1 4 101 " pdb=" C17 BQ1 4 101 " ideal model delta sigma weight residual 1.437 1.369 0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" C17 BQ1 4 101 " pdb=" O03 BQ1 4 101 " ideal model delta sigma weight residual 1.330 1.395 -0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" C ILE S 45 " pdb=" N PRO S 46 " ideal model delta sigma weight residual 1.335 1.376 -0.041 1.30e-02 5.92e+03 9.88e+00 bond pdb=" C15 BQ1 4 101 " pdb=" C22 BQ1 4 101 " ideal model delta sigma weight residual 1.417 1.366 0.051 2.00e-02 2.50e+03 6.55e+00 bond pdb=" N SER 4 57 " pdb=" CA SER 4 57 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.17e-02 7.31e+03 5.72e+00 ... (remaining 12369 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 15960 1.38 - 2.77: 648 2.77 - 4.15: 117 4.15 - 5.53: 29 5.53 - 6.91: 7 Bond angle restraints: 16761 Sorted by residual: angle pdb=" N LYS R 91 " pdb=" CA LYS R 91 " pdb=" C LYS R 91 " ideal model delta sigma weight residual 114.64 108.40 6.24 1.52e+00 4.33e-01 1.69e+01 angle pdb=" N PHE N 26 " pdb=" CA PHE N 26 " pdb=" C PHE N 26 " ideal model delta sigma weight residual 109.81 116.66 -6.85 2.21e+00 2.05e-01 9.60e+00 angle pdb=" CA ALA 4 59 " pdb=" C ALA 4 59 " pdb=" O ALA 4 59 " ideal model delta sigma weight residual 120.90 118.13 2.77 1.03e+00 9.43e-01 7.24e+00 angle pdb=" CA SER 4 57 " pdb=" C SER 4 57 " pdb=" O SER 4 57 " ideal model delta sigma weight residual 121.00 118.28 2.72 1.05e+00 9.07e-01 6.73e+00 angle pdb=" C ALA 2 74 " pdb=" N MET 2 75 " pdb=" CA MET 2 75 " ideal model delta sigma weight residual 121.70 126.27 -4.57 1.80e+00 3.09e-01 6.46e+00 ... (remaining 16756 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 6676 17.64 - 35.29: 513 35.29 - 52.93: 73 52.93 - 70.57: 11 70.57 - 88.21: 12 Dihedral angle restraints: 7285 sinusoidal: 2743 harmonic: 4542 Sorted by residual: dihedral pdb=" CA THR N 135 " pdb=" C THR N 135 " pdb=" N PRO N 136 " pdb=" CA PRO N 136 " ideal model delta harmonic sigma weight residual -180.00 -155.44 -24.56 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA GLN S 66 " pdb=" C GLN S 66 " pdb=" N LEU S 67 " pdb=" CA LEU S 67 " ideal model delta harmonic sigma weight residual 180.00 -163.37 -16.63 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CG ARG R 45 " pdb=" CD ARG R 45 " pdb=" NE ARG R 45 " pdb=" CZ ARG R 45 " ideal model delta sinusoidal sigma weight residual 180.00 135.14 44.86 2 1.50e+01 4.44e-03 1.06e+01 ... (remaining 7282 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1519 0.049 - 0.098: 381 0.098 - 0.147: 71 0.147 - 0.196: 2 0.196 - 0.245: 1 Chirality restraints: 1974 Sorted by residual: chirality pdb=" C07 BQ1 4 101 " pdb=" C06 BQ1 4 101 " pdb=" C10 BQ1 4 101 " pdb=" C12 BQ1 4 101 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA THR N 135 " pdb=" N THR N 135 " pdb=" C THR N 135 " pdb=" CB THR N 135 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.48e-01 chirality pdb=" CA THR Q 14 " pdb=" N THR Q 14 " pdb=" C THR Q 14 " pdb=" CB THR Q 14 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.74e-01 ... (remaining 1971 not shown) Planarity restraints: 2071 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE 3 54 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.08e+00 pdb=" C PHE 3 54 " -0.030 2.00e-02 2.50e+03 pdb=" O PHE 3 54 " 0.011 2.00e-02 2.50e+03 pdb=" N ALA 3 55 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE 8 54 " -0.009 2.00e-02 2.50e+03 1.70e-02 2.90e+00 pdb=" C PHE 8 54 " 0.029 2.00e-02 2.50e+03 pdb=" O PHE 8 54 " -0.011 2.00e-02 2.50e+03 pdb=" N ALA 8 55 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE 1 54 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.76e+00 pdb=" C PHE 1 54 " 0.029 2.00e-02 2.50e+03 pdb=" O PHE 1 54 " -0.011 2.00e-02 2.50e+03 pdb=" N ALA 1 55 " -0.010 2.00e-02 2.50e+03 ... (remaining 2068 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 486 2.72 - 3.26: 13424 3.26 - 3.81: 20226 3.81 - 4.35: 24815 4.35 - 4.90: 42277 Nonbonded interactions: 101228 Sorted by model distance: nonbonded pdb=" O LYS N 55 " pdb=" OG1 THR N 59 " model vdw 2.169 3.040 nonbonded pdb=" OH TYR G 52 " pdb=" OE1 GLN G 205 " model vdw 2.203 3.040 nonbonded pdb=" O MET N 181 " pdb=" OG1 THR N 189 " model vdw 2.207 3.040 nonbonded pdb=" O ASN G 182 " pdb=" OG SER G 186 " model vdw 2.219 3.040 nonbonded pdb=" OH TYR R 50 " pdb=" O GLY R 64 " model vdw 2.231 3.040 ... (remaining 101223 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 '1' and (resid 1 through 37 or resid 39 through 75)) selection = (chain '2' and (resid 1 through 37 or resid 39 through 75)) selection = (chain '3' and (resid 1 through 37 or resid 39 through 75)) selection = (chain '4' and (resid 1 through 37 or resid 39 through 75)) selection = (chain '5' and (resid 1 through 37 or resid 39 through 75)) selection = (chain '6' and (resid 1 through 37 or resid 39 through 75)) selection = (chain '7' and (resid 1 through 37 or resid 39 through 75)) selection = (chain '8' and (resid 1 through 37 or resid 39 through 75)) } 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=0.50 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: 11.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 10.420 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 12374 Z= 0.262 Angle : 0.671 6.915 16761 Z= 0.385 Chirality : 0.043 0.245 1974 Planarity : 0.005 0.041 2071 Dihedral : 12.893 88.214 4387 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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 aren not related in a simple way. whole: -2.87 (0.18), residues: 1559 helix: -1.59 (0.13), residues: 1130 sheet: -2.01 (0.48), residues: 89 loop : -2.19 (0.30), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 24 TYR 0.015 0.001 TYR G 44 PHE 0.021 0.002 PHE 7 29 TRP 0.008 0.001 TRP N 109 HIS 0.005 0.001 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00587 (12374) covalent geometry : angle 0.67089 (16761) hydrogen bonds : bond 0.14905 ( 933) hydrogen bonds : angle 7.07081 ( 2747) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: 2 31 SER cc_start: 0.8761 (m) cc_final: 0.8533 (m) REVERT: 7 7 LYS cc_start: 0.8740 (mtmt) cc_final: 0.8487 (mtmt) REVERT: 7 69 PHE cc_start: 0.8195 (m-10) cc_final: 0.7428 (t80) REVERT: 8 7 LYS cc_start: 0.8368 (mtmt) cc_final: 0.7935 (mtpp) REVERT: G 65 LYS cc_start: 0.7900 (mtpt) cc_final: 0.7671 (mtmm) REVERT: G 81 ILE cc_start: 0.8336 (mm) cc_final: 0.8112 (mm) REVERT: G 188 ASP cc_start: 0.7783 (m-30) cc_final: 0.7552 (m-30) REVERT: I 7 GLN cc_start: 0.8450 (mm110) cc_final: 0.7998 (mt0) REVERT: I 21 LYS cc_start: 0.8725 (tttm) cc_final: 0.8377 (tttp) REVERT: I 25 ASP cc_start: 0.8731 (m-30) cc_final: 0.8477 (m-30) REVERT: K 14 TYR cc_start: 0.8557 (m-80) cc_final: 0.8252 (m-80) REVERT: K 19 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7659 (mt-10) REVERT: K 26 TYR cc_start: 0.8241 (t80) cc_final: 0.7931 (t80) REVERT: K 48 LYS cc_start: 0.7737 (tttt) cc_final: 0.6492 (tmtt) REVERT: K 72 LYS cc_start: 0.8203 (mttt) cc_final: 0.7577 (mmtt) REVERT: K 84 LYS cc_start: 0.8106 (mttp) cc_final: 0.7826 (pttp) REVERT: N 57 MET cc_start: 0.8110 (mmm) cc_final: 0.7381 (mmt) REVERT: R 33 ASP cc_start: 0.8513 (t0) cc_final: 0.8297 (t0) REVERT: R 49 ARG cc_start: 0.7741 (ttm170) cc_final: 0.6738 (tmt170) REVERT: R 85 LYS cc_start: 0.7968 (ptmt) cc_final: 0.7545 (pttm) REVERT: S 94 LYS cc_start: 0.7967 (pttt) cc_final: 0.7528 (mtpt) outliers start: 0 outliers final: 0 residues processed: 288 average time/residue: 0.1057 time to fit residues: 42.5086 Evaluate side-chains 235 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 120 HIS G 163 ASN H 85 ASN I 7 GLN K 88 GLN N 46 GLN N 47 GLN N 61 HIS R 83 HIS S 75 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.147789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.103862 restraints weight = 17166.535| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.53 r_work: 0.3094 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3101 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3101 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12374 Z= 0.157 Angle : 0.572 7.442 16761 Z= 0.302 Chirality : 0.041 0.145 1974 Planarity : 0.004 0.044 2071 Dihedral : 5.930 70.002 1716 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.36 % Allowed : 8.45 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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 aren not related in a simple way. whole: -0.40 (0.20), residues: 1559 helix: 0.30 (0.15), residues: 1140 sheet: -1.83 (0.50), residues: 89 loop : -1.41 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 166 TYR 0.012 0.001 TYR G 44 PHE 0.017 0.001 PHE G 155 TRP 0.011 0.001 TRP R 28 HIS 0.003 0.001 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00327 (12374) covalent geometry : angle 0.57194 (16761) hydrogen bonds : bond 0.05741 ( 933) hydrogen bonds : angle 4.70655 ( 2747) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 256 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 31 SER cc_start: 0.8618 (m) cc_final: 0.8092 (p) REVERT: 5 69 PHE cc_start: 0.7745 (m-10) cc_final: 0.7065 (t80) REVERT: 7 7 LYS cc_start: 0.8348 (mtmt) cc_final: 0.8140 (mttt) REVERT: 7 69 PHE cc_start: 0.8109 (m-10) cc_final: 0.7170 (t80) REVERT: 8 7 LYS cc_start: 0.7926 (mtmt) cc_final: 0.7452 (mtpp) REVERT: G 81 ILE cc_start: 0.8159 (mm) cc_final: 0.7911 (mm) REVERT: G 188 ASP cc_start: 0.8356 (m-30) cc_final: 0.8124 (m-30) REVERT: I 7 GLN cc_start: 0.8271 (mm-40) cc_final: 0.7767 (mt0) REVERT: I 21 LYS cc_start: 0.8640 (tttm) cc_final: 0.8353 (tttp) REVERT: I 25 ASP cc_start: 0.9001 (m-30) cc_final: 0.8687 (m-30) REVERT: I 44 LYS cc_start: 0.8339 (mttm) cc_final: 0.7800 (mttt) REVERT: K 7 GLU cc_start: 0.8677 (tt0) cc_final: 0.8367 (tp30) REVERT: K 14 TYR cc_start: 0.8721 (m-80) cc_final: 0.8307 (m-80) REVERT: K 19 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7555 (mt-10) REVERT: K 26 TYR cc_start: 0.7992 (t80) cc_final: 0.7698 (t80) REVERT: K 48 LYS cc_start: 0.7137 (tttt) cc_final: 0.6045 (tmtt) REVERT: K 72 LYS cc_start: 0.8034 (mttt) cc_final: 0.7327 (mmtt) REVERT: K 84 LYS cc_start: 0.7800 (mttp) cc_final: 0.7310 (pttp) REVERT: N 57 MET cc_start: 0.8337 (mmm) cc_final: 0.7801 (mmt) REVERT: N 181 MET cc_start: 0.7752 (tpp) cc_final: 0.7454 (tpp) REVERT: R 49 ARG cc_start: 0.7561 (ttm170) cc_final: 0.6322 (tmt170) REVERT: R 85 LYS cc_start: 0.7762 (ptmt) cc_final: 0.7250 (pttm) REVERT: S 94 LYS cc_start: 0.7464 (pttt) cc_final: 0.7201 (mtpt) outliers start: 17 outliers final: 9 residues processed: 264 average time/residue: 0.1036 time to fit residues: 38.3898 Evaluate side-chains 249 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 240 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 41 SER Chi-restraints excluded: chain 6 residue 70 LEU Chi-restraints excluded: chain 8 residue 67 VAL Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain N residue 10 ILE Chi-restraints excluded: chain N residue 149 LEU Chi-restraints excluded: chain R residue 74 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 60 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 146 optimal weight: 4.9990 chunk 149 optimal weight: 0.9990 chunk 7 optimal weight: 0.1980 chunk 10 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.147757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.104205 restraints weight = 23928.455| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.98 r_work: 0.3036 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3037 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3037 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12374 Z= 0.163 Angle : 0.565 7.911 16761 Z= 0.294 Chirality : 0.041 0.143 1974 Planarity : 0.004 0.044 2071 Dihedral : 5.539 66.156 1716 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.91 % Allowed : 11.16 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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 aren not related in a simple way. whole: 0.70 (0.21), residues: 1559 helix: 1.08 (0.15), residues: 1154 sheet: -1.44 (0.53), residues: 89 loop : -1.04 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 6 TYR 0.013 0.001 TYR G 44 PHE 0.019 0.001 PHE K 24 TRP 0.010 0.001 TRP R 28 HIS 0.003 0.001 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00364 (12374) covalent geometry : angle 0.56478 (16761) hydrogen bonds : bond 0.05384 ( 933) hydrogen bonds : angle 4.40581 ( 2747) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 248 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 31 SER cc_start: 0.8736 (m) cc_final: 0.8227 (p) REVERT: 3 39 ASN cc_start: 0.8352 (t0) cc_final: 0.7960 (t0) REVERT: 5 69 PHE cc_start: 0.7964 (m-10) cc_final: 0.7167 (t80) REVERT: 6 65 LEU cc_start: 0.8539 (tp) cc_final: 0.8277 (mp) REVERT: 7 7 LYS cc_start: 0.8406 (mtmt) cc_final: 0.8178 (mttt) REVERT: 7 58 GLU cc_start: 0.7543 (tt0) cc_final: 0.7198 (tt0) REVERT: 7 69 PHE cc_start: 0.8088 (m-10) cc_final: 0.7209 (t80) REVERT: 8 7 LYS cc_start: 0.7925 (mtmt) cc_final: 0.7483 (mtpp) REVERT: G 166 ARG cc_start: 0.8626 (ttp-110) cc_final: 0.8173 (mtm110) REVERT: G 188 ASP cc_start: 0.8417 (m-30) cc_final: 0.8199 (m-30) REVERT: I 7 GLN cc_start: 0.8344 (mm-40) cc_final: 0.7826 (mt0) REVERT: I 21 LYS cc_start: 0.8712 (tttm) cc_final: 0.8460 (tttp) REVERT: I 25 ASP cc_start: 0.9036 (m-30) cc_final: 0.8760 (m-30) REVERT: I 44 LYS cc_start: 0.8414 (mttm) cc_final: 0.7881 (mttt) REVERT: K 14 TYR cc_start: 0.8766 (m-80) cc_final: 0.8441 (m-80) REVERT: K 19 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7560 (mt-10) REVERT: K 48 LYS cc_start: 0.7260 (tttt) cc_final: 0.6189 (tmtt) REVERT: K 72 LYS cc_start: 0.8184 (mttt) cc_final: 0.7439 (mmtt) REVERT: K 84 LYS cc_start: 0.7883 (mttp) cc_final: 0.7380 (pttp) REVERT: N 56 GLN cc_start: 0.8461 (tp40) cc_final: 0.8238 (tp40) REVERT: N 57 MET cc_start: 0.8423 (mmm) cc_final: 0.8038 (mmt) REVERT: N 181 MET cc_start: 0.7989 (tpp) cc_final: 0.7643 (tpp) REVERT: R 49 ARG cc_start: 0.7690 (ttm170) cc_final: 0.6374 (tmt170) REVERT: R 63 SER cc_start: 0.7854 (m) cc_final: 0.7594 (t) REVERT: R 85 LYS cc_start: 0.7781 (ptmt) cc_final: 0.7286 (pttm) REVERT: R 91 LYS cc_start: 0.8364 (tmmt) cc_final: 0.7804 (tmmt) REVERT: R 92 TYR cc_start: 0.4919 (m-80) cc_final: 0.4718 (m-80) outliers start: 24 outliers final: 17 residues processed: 257 average time/residue: 0.1002 time to fit residues: 36.7463 Evaluate side-chains 260 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 243 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 41 SER Chi-restraints excluded: chain 4 residue 66 MET Chi-restraints excluded: chain 6 residue 70 LEU Chi-restraints excluded: chain 7 residue 41 SER Chi-restraints excluded: chain 7 residue 72 LEU Chi-restraints excluded: chain 8 residue 67 VAL Chi-restraints excluded: chain G residue 123 GLN Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain I residue 41 SER Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain N residue 149 LEU Chi-restraints excluded: chain R residue 24 GLU Chi-restraints excluded: chain R residue 37 SER Chi-restraints excluded: chain R residue 74 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 135 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 141 optimal weight: 0.1980 chunk 54 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 39 ASN I 17 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.149756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.103638 restraints weight = 27634.938| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 3.21 r_work: 0.3059 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3067 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3067 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12374 Z= 0.143 Angle : 0.542 7.267 16761 Z= 0.281 Chirality : 0.040 0.139 1974 Planarity : 0.004 0.040 2071 Dihedral : 5.269 61.765 1716 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.15 % Allowed : 13.24 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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 aren not related in a simple way. whole: 1.36 (0.21), residues: 1559 helix: 1.54 (0.15), residues: 1151 sheet: -0.99 (0.56), residues: 85 loop : -0.76 (0.36), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 159 TYR 0.011 0.001 TYR G 44 PHE 0.020 0.001 PHE K 24 TRP 0.010 0.001 TRP R 28 HIS 0.003 0.001 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00310 (12374) covalent geometry : angle 0.54243 (16761) hydrogen bonds : bond 0.04993 ( 933) hydrogen bonds : angle 4.23902 ( 2747) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 246 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 66 MET cc_start: 0.7760 (ppp) cc_final: 0.7350 (ppp) REVERT: 2 31 SER cc_start: 0.8647 (m) cc_final: 0.8158 (p) REVERT: 2 39 ASN cc_start: 0.8383 (t0) cc_final: 0.8163 (t0) REVERT: 4 60 MET cc_start: 0.7824 (tpt) cc_final: 0.7575 (tpt) REVERT: 4 63 PHE cc_start: 0.7882 (OUTLIER) cc_final: 0.7646 (m-10) REVERT: 5 69 PHE cc_start: 0.7900 (m-10) cc_final: 0.7092 (t80) REVERT: 6 75 MET cc_start: 0.7101 (mmp) cc_final: 0.6720 (ptt) REVERT: 7 58 GLU cc_start: 0.7618 (tt0) cc_final: 0.7271 (tt0) REVERT: 7 69 PHE cc_start: 0.8010 (m-10) cc_final: 0.7162 (t80) REVERT: 8 7 LYS cc_start: 0.7829 (mtmt) cc_final: 0.7412 (mtpp) REVERT: G 113 ARG cc_start: 0.8734 (ttp80) cc_final: 0.8393 (ttp80) REVERT: G 166 ARG cc_start: 0.8616 (ttp-110) cc_final: 0.8144 (mtm110) REVERT: G 188 ASP cc_start: 0.8366 (m-30) cc_final: 0.8140 (m-30) REVERT: I 7 GLN cc_start: 0.8326 (mm-40) cc_final: 0.7827 (mt0) REVERT: I 21 LYS cc_start: 0.8655 (tttm) cc_final: 0.8406 (tttp) REVERT: I 25 ASP cc_start: 0.9020 (m-30) cc_final: 0.8753 (m-30) REVERT: I 44 LYS cc_start: 0.8309 (mttm) cc_final: 0.7764 (mttt) REVERT: K 14 TYR cc_start: 0.8733 (m-80) cc_final: 0.8402 (m-80) REVERT: K 19 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7502 (mt-10) REVERT: K 48 LYS cc_start: 0.7176 (tttt) cc_final: 0.6152 (tmtt) REVERT: K 72 LYS cc_start: 0.8083 (mttt) cc_final: 0.7383 (mmtt) REVERT: K 84 LYS cc_start: 0.7805 (mttp) cc_final: 0.7305 (pttp) REVERT: N 57 MET cc_start: 0.8363 (mmm) cc_final: 0.8118 (mmt) REVERT: N 181 MET cc_start: 0.7967 (tpp) cc_final: 0.7621 (tpp) REVERT: P 39 ARG cc_start: 0.8445 (mtm180) cc_final: 0.8143 (mmm-85) REVERT: R 49 ARG cc_start: 0.7572 (ttm170) cc_final: 0.6315 (tmt170) REVERT: R 63 SER cc_start: 0.7730 (m) cc_final: 0.7449 (t) REVERT: R 85 LYS cc_start: 0.7720 (ptmt) cc_final: 0.7211 (pttm) outliers start: 27 outliers final: 16 residues processed: 260 average time/residue: 0.0918 time to fit residues: 34.1580 Evaluate side-chains 257 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 240 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 41 SER Chi-restraints excluded: chain 4 residue 63 PHE Chi-restraints excluded: chain 4 residue 66 MET Chi-restraints excluded: chain 6 residue 58 GLU Chi-restraints excluded: chain 7 residue 18 VAL Chi-restraints excluded: chain 8 residue 71 ILE Chi-restraints excluded: chain G residue 123 GLN Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain I residue 41 SER Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain N residue 140 MET Chi-restraints excluded: chain N residue 150 LEU Chi-restraints excluded: chain R residue 24 GLU Chi-restraints excluded: chain R residue 74 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 25 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 106 optimal weight: 0.0970 chunk 92 optimal weight: 0.0870 chunk 17 optimal weight: 0.9980 overall best weight: 0.4356 ------------------------------------------------------------------------------- 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 = 0.3824 r_free = 0.3824 target = 0.151750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.109389 restraints weight = 18638.058| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.48 r_work: 0.3131 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3140 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3140 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12374 Z= 0.127 Angle : 0.524 7.193 16761 Z= 0.271 Chirality : 0.039 0.137 1974 Planarity : 0.004 0.091 2071 Dihedral : 5.123 57.572 1716 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.07 % Allowed : 13.96 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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 aren not related in a simple way. whole: 1.74 (0.22), residues: 1559 helix: 1.81 (0.15), residues: 1151 sheet: -0.85 (0.58), residues: 85 loop : -0.57 (0.36), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 41 TYR 0.012 0.001 TYR R 51 PHE 0.021 0.001 PHE K 24 TRP 0.009 0.001 TRP R 28 HIS 0.002 0.000 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00261 (12374) covalent geometry : angle 0.52401 (16761) hydrogen bonds : bond 0.04688 ( 933) hydrogen bonds : angle 4.09838 ( 2747) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 251 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 66 MET cc_start: 0.7807 (ppp) cc_final: 0.7264 (ppp) REVERT: 2 38 ARG cc_start: 0.7628 (mtt180) cc_final: 0.7407 (mpt-90) REVERT: 3 39 ASN cc_start: 0.8027 (t0) cc_final: 0.7671 (t0) REVERT: 4 60 MET cc_start: 0.7829 (tpt) cc_final: 0.7543 (tpt) REVERT: 4 63 PHE cc_start: 0.7789 (OUTLIER) cc_final: 0.7549 (m-10) REVERT: 4 75 MET cc_start: 0.7127 (mpp) cc_final: 0.6485 (mpp) REVERT: 5 69 PHE cc_start: 0.7870 (m-10) cc_final: 0.7065 (t80) REVERT: 6 75 MET cc_start: 0.7039 (mmp) cc_final: 0.6787 (ptt) REVERT: 7 58 GLU cc_start: 0.7566 (tt0) cc_final: 0.7276 (tt0) REVERT: 7 69 PHE cc_start: 0.7911 (m-10) cc_final: 0.7096 (t80) REVERT: 8 7 LYS cc_start: 0.7807 (mtmt) cc_final: 0.7379 (mtpp) REVERT: G 113 ARG cc_start: 0.8726 (ttp80) cc_final: 0.8388 (ttp80) REVERT: G 166 ARG cc_start: 0.8580 (ttp-110) cc_final: 0.8147 (mtm110) REVERT: G 188 ASP cc_start: 0.8328 (m-30) cc_final: 0.8123 (m-30) REVERT: H 111 ASN cc_start: 0.7612 (t0) cc_final: 0.7139 (m110) REVERT: I 7 GLN cc_start: 0.8337 (mm-40) cc_final: 0.7811 (mt0) REVERT: I 21 LYS cc_start: 0.8648 (tttm) cc_final: 0.8416 (tttp) REVERT: I 25 ASP cc_start: 0.8964 (m-30) cc_final: 0.8624 (m-30) REVERT: I 36 GLU cc_start: 0.8350 (mt-10) cc_final: 0.7932 (tm-30) REVERT: I 44 LYS cc_start: 0.8349 (mttm) cc_final: 0.7811 (mttt) REVERT: K 14 TYR cc_start: 0.8720 (m-80) cc_final: 0.8423 (m-80) REVERT: K 19 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7534 (mt-10) REVERT: K 48 LYS cc_start: 0.7137 (tttt) cc_final: 0.6135 (tmtt) REVERT: K 72 LYS cc_start: 0.8026 (mttt) cc_final: 0.7301 (mmtt) REVERT: K 84 LYS cc_start: 0.7816 (mttp) cc_final: 0.7340 (pttp) REVERT: N 181 MET cc_start: 0.8042 (tpp) cc_final: 0.7706 (tpp) REVERT: P 39 ARG cc_start: 0.8495 (mtm180) cc_final: 0.8246 (mmm-85) REVERT: R 49 ARG cc_start: 0.7538 (ttm170) cc_final: 0.6314 (tmt170) REVERT: R 63 SER cc_start: 0.7720 (m) cc_final: 0.7443 (t) REVERT: R 85 LYS cc_start: 0.7798 (ptmt) cc_final: 0.7286 (pttm) outliers start: 26 outliers final: 17 residues processed: 262 average time/residue: 0.1160 time to fit residues: 43.6544 Evaluate side-chains 260 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 242 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 63 PHE Chi-restraints excluded: chain 4 residue 66 MET Chi-restraints excluded: chain 5 residue 18 VAL Chi-restraints excluded: chain 6 residue 58 GLU Chi-restraints excluded: chain 6 residue 70 LEU Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 18 VAL Chi-restraints excluded: chain 7 residue 72 LEU Chi-restraints excluded: chain 8 residue 67 VAL Chi-restraints excluded: chain 8 residue 71 ILE Chi-restraints excluded: chain G residue 123 GLN Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain N residue 140 MET Chi-restraints excluded: chain R residue 24 GLU Chi-restraints excluded: chain R residue 74 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 6 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 145 optimal weight: 0.9990 chunk 126 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- 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 = 0.3786 r_free = 0.3786 target = 0.148116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.105457 restraints weight = 19465.026| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.49 r_work: 0.3072 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3079 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3079 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12374 Z= 0.173 Angle : 0.555 7.173 16761 Z= 0.286 Chirality : 0.041 0.166 1974 Planarity : 0.004 0.057 2071 Dihedral : 5.083 51.478 1716 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.55 % Allowed : 15.07 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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 aren not related in a simple way. whole: 1.72 (0.22), residues: 1559 helix: 1.80 (0.15), residues: 1156 sheet: -1.03 (0.57), residues: 86 loop : -0.58 (0.37), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 166 TYR 0.015 0.001 TYR G 44 PHE 0.021 0.002 PHE H 45 TRP 0.014 0.001 TRP R 28 HIS 0.005 0.001 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00400 (12374) covalent geometry : angle 0.55505 (16761) hydrogen bonds : bond 0.05043 ( 933) hydrogen bonds : angle 4.16829 ( 2747) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 246 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 66 MET cc_start: 0.7776 (ppp) cc_final: 0.7334 (ppp) REVERT: 2 38 ARG cc_start: 0.7819 (mtt180) cc_final: 0.7549 (mpt-90) REVERT: 3 39 ASN cc_start: 0.8283 (t0) cc_final: 0.7911 (t0) REVERT: 4 60 MET cc_start: 0.8001 (tpt) cc_final: 0.7655 (tpt) REVERT: 4 75 MET cc_start: 0.7247 (mpp) cc_final: 0.6669 (mpp) REVERT: 5 69 PHE cc_start: 0.7881 (m-10) cc_final: 0.7091 (t80) REVERT: 5 75 MET cc_start: 0.4970 (ptt) cc_final: 0.4301 (ptp) REVERT: 7 69 PHE cc_start: 0.7967 (m-10) cc_final: 0.7168 (t80) REVERT: 8 7 LYS cc_start: 0.7868 (mtmt) cc_final: 0.7442 (mtpp) REVERT: G 87 LYS cc_start: 0.8376 (ptmt) cc_final: 0.7965 (pptt) REVERT: G 113 ARG cc_start: 0.8758 (ttp80) cc_final: 0.8507 (ttp80) REVERT: G 166 ARG cc_start: 0.8590 (ttp-110) cc_final: 0.8152 (mtm110) REVERT: I 7 GLN cc_start: 0.8350 (mm-40) cc_final: 0.7838 (mt0) REVERT: I 21 LYS cc_start: 0.8703 (tttm) cc_final: 0.8468 (tttp) REVERT: I 25 ASP cc_start: 0.9003 (m-30) cc_final: 0.8666 (m-30) REVERT: I 36 GLU cc_start: 0.8384 (mt-10) cc_final: 0.7985 (tm-30) REVERT: I 44 LYS cc_start: 0.8415 (mttm) cc_final: 0.7911 (mttt) REVERT: K 14 TYR cc_start: 0.8753 (m-80) cc_final: 0.8399 (m-80) REVERT: K 19 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7644 (mt-10) REVERT: K 48 LYS cc_start: 0.7275 (tttt) cc_final: 0.6206 (tmtt) REVERT: K 72 LYS cc_start: 0.8094 (mttt) cc_final: 0.7376 (mmtt) REVERT: K 84 LYS cc_start: 0.7878 (mttp) cc_final: 0.7386 (pttp) REVERT: N 181 MET cc_start: 0.8077 (tpp) cc_final: 0.7706 (tpp) REVERT: P 39 ARG cc_start: 0.8554 (mtm180) cc_final: 0.8328 (mmm-85) REVERT: R 49 ARG cc_start: 0.7722 (ttm170) cc_final: 0.6480 (tmt170) REVERT: R 63 SER cc_start: 0.7870 (m) cc_final: 0.7580 (t) REVERT: R 85 LYS cc_start: 0.7835 (ptmt) cc_final: 0.7316 (pttm) outliers start: 32 outliers final: 22 residues processed: 265 average time/residue: 0.1158 time to fit residues: 43.7967 Evaluate side-chains 269 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 247 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 66 MET Chi-restraints excluded: chain 5 residue 18 VAL Chi-restraints excluded: chain 5 residue 31 SER Chi-restraints excluded: chain 6 residue 58 GLU Chi-restraints excluded: chain 6 residue 70 LEU Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 18 VAL Chi-restraints excluded: chain 7 residue 72 LEU Chi-restraints excluded: chain 8 residue 67 VAL Chi-restraints excluded: chain 8 residue 71 ILE Chi-restraints excluded: chain G residue 123 GLN Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain I residue 41 SER Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain N residue 140 MET Chi-restraints excluded: chain P residue 42 ASP Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain R residue 24 GLU Chi-restraints excluded: chain R residue 74 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 142 optimal weight: 9.9990 chunk 137 optimal weight: 0.2980 chunk 133 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 29 optimal weight: 0.0970 chunk 125 optimal weight: 0.9980 chunk 143 optimal weight: 7.9990 chunk 54 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 = 0.3779 r_free = 0.3779 target = 0.148744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.105027 restraints weight = 15037.992| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.04 r_work: 0.3130 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2991 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2991 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12374 Z= 0.133 Angle : 0.534 8.388 16761 Z= 0.274 Chirality : 0.040 0.137 1974 Planarity : 0.004 0.045 2071 Dihedral : 4.994 48.151 1716 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.15 % Allowed : 16.11 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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 aren not related in a simple way. whole: 1.81 (0.22), residues: 1559 helix: 2.03 (0.15), residues: 1112 sheet: -0.83 (0.58), residues: 85 loop : -0.90 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 36 TYR 0.011 0.001 TYR G 44 PHE 0.018 0.001 PHE 1 69 TRP 0.012 0.001 TRP R 28 HIS 0.003 0.001 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00286 (12374) covalent geometry : angle 0.53435 (16761) hydrogen bonds : bond 0.04743 ( 933) hydrogen bonds : angle 4.07277 ( 2747) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 253 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 66 MET cc_start: 0.7939 (ppp) cc_final: 0.7448 (ppp) REVERT: 2 38 ARG cc_start: 0.7973 (mtt180) cc_final: 0.7762 (mpt-90) REVERT: 3 39 ASN cc_start: 0.8212 (t0) cc_final: 0.7977 (t0) REVERT: 4 60 MET cc_start: 0.8092 (tpt) cc_final: 0.7706 (tpt) REVERT: 4 65 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7649 (mt) REVERT: 4 75 MET cc_start: 0.7296 (mpp) cc_final: 0.6806 (mpp) REVERT: 5 69 PHE cc_start: 0.8101 (m-10) cc_final: 0.7308 (t80) REVERT: 5 75 MET cc_start: 0.5164 (ptt) cc_final: 0.4464 (ptp) REVERT: 6 75 MET cc_start: 0.7156 (mmp) cc_final: 0.6766 (ptt) REVERT: 7 69 PHE cc_start: 0.8123 (m-10) cc_final: 0.7352 (t80) REVERT: 8 7 LYS cc_start: 0.8156 (mtmt) cc_final: 0.7716 (mtpp) REVERT: G 87 LYS cc_start: 0.8393 (ptmt) cc_final: 0.8035 (pptt) REVERT: G 166 ARG cc_start: 0.8594 (ttp-110) cc_final: 0.8272 (mtm110) REVERT: H 111 ASN cc_start: 0.7680 (t0) cc_final: 0.7199 (m110) REVERT: I 7 GLN cc_start: 0.8465 (mm-40) cc_final: 0.7971 (mt0) REVERT: I 21 LYS cc_start: 0.8787 (tttm) cc_final: 0.8567 (tttp) REVERT: I 25 ASP cc_start: 0.9005 (m-30) cc_final: 0.8788 (m-30) REVERT: I 44 LYS cc_start: 0.8613 (mttm) cc_final: 0.8111 (mttt) REVERT: K 14 TYR cc_start: 0.8846 (m-80) cc_final: 0.8606 (m-80) REVERT: K 19 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7849 (mt-10) REVERT: K 48 LYS cc_start: 0.7613 (tttt) cc_final: 0.6527 (tmtt) REVERT: K 72 LYS cc_start: 0.8396 (mttt) cc_final: 0.7692 (mmtt) REVERT: K 84 LYS cc_start: 0.8113 (mttp) cc_final: 0.7629 (pttp) REVERT: P 39 ARG cc_start: 0.8603 (mtm180) cc_final: 0.8390 (mmm-85) REVERT: R 49 ARG cc_start: 0.7974 (ttm170) cc_final: 0.6751 (tmt170) REVERT: R 63 SER cc_start: 0.8209 (m) cc_final: 0.7982 (t) REVERT: R 85 LYS cc_start: 0.7947 (ptmt) cc_final: 0.7460 (pttm) outliers start: 27 outliers final: 18 residues processed: 268 average time/residue: 0.1141 time to fit residues: 43.4945 Evaluate side-chains 261 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 242 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 63 PHE Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 4 residue 65 LEU Chi-restraints excluded: chain 4 residue 66 MET Chi-restraints excluded: chain 6 residue 58 GLU Chi-restraints excluded: chain 6 residue 70 LEU Chi-restraints excluded: chain 7 residue 18 VAL Chi-restraints excluded: chain 7 residue 72 LEU Chi-restraints excluded: chain 8 residue 67 VAL Chi-restraints excluded: chain 8 residue 71 ILE Chi-restraints excluded: chain G residue 123 GLN Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain I residue 41 SER Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain N residue 140 MET Chi-restraints excluded: chain R residue 24 GLU Chi-restraints excluded: chain R residue 74 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 113 optimal weight: 0.6980 chunk 131 optimal weight: 0.8980 chunk 134 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 71 optimal weight: 0.0770 chunk 48 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.6740 ------------------------------------------------------------------------------- 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 = 0.3782 r_free = 0.3782 target = 0.148936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.107678 restraints weight = 23953.942| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.76 r_work: 0.3066 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3066 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12374 Z= 0.136 Angle : 0.541 8.375 16761 Z= 0.276 Chirality : 0.040 0.137 1974 Planarity : 0.004 0.038 2071 Dihedral : 4.966 46.146 1716 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.15 % Allowed : 16.83 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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 aren not related in a simple way. whole: 1.95 (0.22), residues: 1559 helix: 2.12 (0.15), residues: 1106 sheet: -0.80 (0.58), residues: 85 loop : -0.75 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 134 TYR 0.012 0.001 TYR G 44 PHE 0.018 0.001 PHE 1 69 TRP 0.012 0.001 TRP R 28 HIS 0.003 0.001 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00297 (12374) covalent geometry : angle 0.54073 (16761) hydrogen bonds : bond 0.04694 ( 933) hydrogen bonds : angle 4.06841 ( 2747) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 249 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 66 MET cc_start: 0.7939 (ppp) cc_final: 0.7424 (ppp) REVERT: 2 38 ARG cc_start: 0.7868 (mtt180) cc_final: 0.7637 (mpt-90) REVERT: 3 39 ASN cc_start: 0.8154 (t0) cc_final: 0.7903 (t0) REVERT: 4 60 MET cc_start: 0.8040 (tpt) cc_final: 0.7658 (tpt) REVERT: 4 75 MET cc_start: 0.7318 (mpp) cc_final: 0.6838 (mpp) REVERT: 5 69 PHE cc_start: 0.8060 (m-10) cc_final: 0.7300 (t80) REVERT: 5 75 MET cc_start: 0.5091 (ptt) cc_final: 0.4415 (ptp) REVERT: 6 75 MET cc_start: 0.7045 (mmp) cc_final: 0.6706 (ptt) REVERT: 7 69 PHE cc_start: 0.8052 (m-10) cc_final: 0.7276 (t80) REVERT: 8 7 LYS cc_start: 0.8099 (mtmt) cc_final: 0.7654 (mtpp) REVERT: G 87 LYS cc_start: 0.8410 (ptmt) cc_final: 0.8044 (pptt) REVERT: G 166 ARG cc_start: 0.8525 (ttp-110) cc_final: 0.8223 (mtm110) REVERT: I 7 GLN cc_start: 0.8417 (mm-40) cc_final: 0.7919 (mt0) REVERT: I 21 LYS cc_start: 0.8745 (tttm) cc_final: 0.8508 (tttp) REVERT: I 25 ASP cc_start: 0.8936 (m-30) cc_final: 0.8703 (m-30) REVERT: I 44 LYS cc_start: 0.8620 (mttm) cc_final: 0.8107 (mttt) REVERT: K 14 TYR cc_start: 0.8785 (m-80) cc_final: 0.8528 (m-80) REVERT: K 19 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7766 (mt-10) REVERT: K 48 LYS cc_start: 0.7509 (tttt) cc_final: 0.6411 (tmtt) REVERT: K 72 LYS cc_start: 0.8297 (mttt) cc_final: 0.7602 (mmtt) REVERT: K 84 LYS cc_start: 0.8041 (mttp) cc_final: 0.7577 (pttp) REVERT: M 136 ASN cc_start: 0.8719 (m-40) cc_final: 0.8497 (m-40) REVERT: R 31 MET cc_start: 0.6299 (ttt) cc_final: 0.6056 (tpp) REVERT: R 49 ARG cc_start: 0.7890 (ttm170) cc_final: 0.6665 (tmt170) REVERT: R 63 SER cc_start: 0.8105 (m) cc_final: 0.7856 (t) REVERT: R 85 LYS cc_start: 0.7913 (ptmt) cc_final: 0.7421 (pttm) outliers start: 27 outliers final: 21 residues processed: 262 average time/residue: 0.1208 time to fit residues: 44.8508 Evaluate side-chains 265 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 244 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 63 PHE Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 4 residue 66 MET Chi-restraints excluded: chain 5 residue 18 VAL Chi-restraints excluded: chain 5 residue 31 SER Chi-restraints excluded: chain 6 residue 58 GLU Chi-restraints excluded: chain 6 residue 70 LEU Chi-restraints excluded: chain 7 residue 18 VAL Chi-restraints excluded: chain 8 residue 67 VAL Chi-restraints excluded: chain 8 residue 71 ILE Chi-restraints excluded: chain G residue 123 GLN Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain I residue 41 SER Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain N residue 140 MET Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain R residue 24 GLU Chi-restraints excluded: chain R residue 74 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 115 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 90 HIS N 163 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.148836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.107624 restraints weight = 24723.930| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 3.00 r_work: 0.3062 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3064 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3064 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12374 Z= 0.147 Angle : 0.549 9.531 16761 Z= 0.281 Chirality : 0.040 0.137 1974 Planarity : 0.004 0.037 2071 Dihedral : 4.966 43.553 1716 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.23 % Allowed : 16.91 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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 aren not related in a simple way. whole: 1.90 (0.22), residues: 1559 helix: 2.09 (0.15), residues: 1111 sheet: -0.86 (0.58), residues: 86 loop : -0.82 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P 39 TYR 0.013 0.001 TYR G 44 PHE 0.020 0.001 PHE 1 69 TRP 0.009 0.001 TRP R 28 HIS 0.004 0.001 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00331 (12374) covalent geometry : angle 0.54921 (16761) hydrogen bonds : bond 0.04773 ( 933) hydrogen bonds : angle 4.06649 ( 2747) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 244 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 66 MET cc_start: 0.7997 (ppp) cc_final: 0.7486 (ppp) REVERT: 3 39 ASN cc_start: 0.8217 (t0) cc_final: 0.7929 (t0) REVERT: 4 60 MET cc_start: 0.8114 (tpt) cc_final: 0.7703 (tpt) REVERT: 4 65 LEU cc_start: 0.7859 (mm) cc_final: 0.7627 (mt) REVERT: 5 69 PHE cc_start: 0.8106 (m-10) cc_final: 0.7370 (t80) REVERT: 5 75 MET cc_start: 0.5164 (ptt) cc_final: 0.4586 (ptp) REVERT: 6 75 MET cc_start: 0.7083 (mmp) cc_final: 0.6781 (ptt) REVERT: 7 16 VAL cc_start: 0.8717 (OUTLIER) cc_final: 0.8487 (p) REVERT: 7 69 PHE cc_start: 0.8071 (m-10) cc_final: 0.7363 (t80) REVERT: 8 7 LYS cc_start: 0.8145 (mtmt) cc_final: 0.7701 (mtpp) REVERT: G 87 LYS cc_start: 0.8418 (ptmt) cc_final: 0.8065 (pptt) REVERT: G 166 ARG cc_start: 0.8530 (ttp-110) cc_final: 0.8247 (mtm110) REVERT: I 7 GLN cc_start: 0.8444 (mm-40) cc_final: 0.7934 (mt0) REVERT: I 21 LYS cc_start: 0.8749 (tttm) cc_final: 0.8522 (tttp) REVERT: I 25 ASP cc_start: 0.8947 (m-30) cc_final: 0.8716 (m-30) REVERT: I 44 LYS cc_start: 0.8654 (mttm) cc_final: 0.8151 (mttt) REVERT: K 14 TYR cc_start: 0.8817 (m-80) cc_final: 0.8534 (m-80) REVERT: K 19 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7813 (mt-10) REVERT: K 48 LYS cc_start: 0.7630 (tttt) cc_final: 0.6484 (tmtt) REVERT: K 72 LYS cc_start: 0.8347 (mttt) cc_final: 0.7637 (mmtt) REVERT: K 84 LYS cc_start: 0.8071 (mttp) cc_final: 0.7592 (pttp) REVERT: R 32 ARG cc_start: 0.6074 (mmp-170) cc_final: 0.5778 (mmm-85) REVERT: R 49 ARG cc_start: 0.7977 (ttm170) cc_final: 0.6768 (tmt170) REVERT: R 63 SER cc_start: 0.8201 (m) cc_final: 0.7974 (t) REVERT: R 85 LYS cc_start: 0.7959 (ptmt) cc_final: 0.7464 (pttm) outliers start: 28 outliers final: 22 residues processed: 260 average time/residue: 0.1140 time to fit residues: 42.1451 Evaluate side-chains 264 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 241 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 63 PHE Chi-restraints excluded: chain 4 residue 18 VAL Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 4 residue 66 MET Chi-restraints excluded: chain 5 residue 18 VAL Chi-restraints excluded: chain 5 residue 31 SER Chi-restraints excluded: chain 6 residue 58 GLU Chi-restraints excluded: chain 6 residue 70 LEU Chi-restraints excluded: chain 7 residue 16 VAL Chi-restraints excluded: chain 7 residue 18 VAL Chi-restraints excluded: chain 7 residue 72 LEU Chi-restraints excluded: chain 8 residue 67 VAL Chi-restraints excluded: chain 8 residue 71 ILE Chi-restraints excluded: chain G residue 123 GLN Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain I residue 41 SER Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain N residue 140 MET Chi-restraints excluded: chain R residue 74 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 11 optimal weight: 0.9980 chunk 134 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 78 optimal weight: 0.5980 chunk 64 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.149161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.105009 restraints weight = 19693.901| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.39 r_work: 0.3136 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12374 Z= 0.148 Angle : 0.569 11.066 16761 Z= 0.287 Chirality : 0.040 0.179 1974 Planarity : 0.004 0.041 2071 Dihedral : 4.954 43.053 1716 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.23 % Allowed : 16.91 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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 aren not related in a simple way. whole: 1.91 (0.22), residues: 1559 helix: 2.10 (0.15), residues: 1111 sheet: -0.89 (0.58), residues: 86 loop : -0.82 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 36 TYR 0.012 0.001 TYR G 44 PHE 0.019 0.001 PHE 1 69 TRP 0.010 0.001 TRP R 28 HIS 0.003 0.001 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00332 (12374) covalent geometry : angle 0.56857 (16761) hydrogen bonds : bond 0.04767 ( 933) hydrogen bonds : angle 4.07015 ( 2747) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 248 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 66 MET cc_start: 0.7996 (ppp) cc_final: 0.7461 (ppp) REVERT: 2 38 ARG cc_start: 0.7910 (mtt180) cc_final: 0.7694 (mpt-90) REVERT: 3 39 ASN cc_start: 0.8222 (t0) cc_final: 0.7932 (t0) REVERT: 4 60 MET cc_start: 0.8115 (tpt) cc_final: 0.7717 (tpt) REVERT: 4 65 LEU cc_start: 0.7859 (mm) cc_final: 0.7625 (mt) REVERT: 4 75 MET cc_start: 0.7120 (mpp) cc_final: 0.6379 (mpp) REVERT: 5 69 PHE cc_start: 0.8087 (m-10) cc_final: 0.7373 (t80) REVERT: 5 75 MET cc_start: 0.5118 (ptt) cc_final: 0.4476 (ptp) REVERT: 6 75 MET cc_start: 0.7001 (mmp) cc_final: 0.6772 (ptt) REVERT: 7 16 VAL cc_start: 0.8695 (OUTLIER) cc_final: 0.8471 (p) REVERT: 7 69 PHE cc_start: 0.7999 (m-10) cc_final: 0.7320 (t80) REVERT: 8 7 LYS cc_start: 0.8134 (mtmt) cc_final: 0.7709 (mtpp) REVERT: G 36 ARG cc_start: 0.8932 (mtm110) cc_final: 0.8652 (ptm160) REVERT: G 87 LYS cc_start: 0.8360 (ptmt) cc_final: 0.8000 (pptt) REVERT: G 166 ARG cc_start: 0.8489 (ttp-110) cc_final: 0.8214 (mtm110) REVERT: G 188 ASP cc_start: 0.8226 (t70) cc_final: 0.7958 (t70) REVERT: I 7 GLN cc_start: 0.8405 (mm-40) cc_final: 0.7902 (mt0) REVERT: I 21 LYS cc_start: 0.8758 (tttm) cc_final: 0.8521 (tttp) REVERT: I 25 ASP cc_start: 0.8889 (m-30) cc_final: 0.8660 (m-30) REVERT: I 44 LYS cc_start: 0.8679 (mttm) cc_final: 0.8177 (mttt) REVERT: K 14 TYR cc_start: 0.8787 (m-80) cc_final: 0.8501 (m-80) REVERT: K 19 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7800 (mt-10) REVERT: K 48 LYS cc_start: 0.7587 (tttt) cc_final: 0.6394 (tmtt) REVERT: K 72 LYS cc_start: 0.8306 (mttt) cc_final: 0.7602 (mmtt) REVERT: K 84 LYS cc_start: 0.8048 (mttp) cc_final: 0.7588 (pttp) REVERT: P 39 ARG cc_start: 0.8458 (mmm-85) cc_final: 0.8242 (mmm-85) REVERT: R 49 ARG cc_start: 0.7942 (ttm170) cc_final: 0.6739 (tmt170) REVERT: R 63 SER cc_start: 0.8169 (m) cc_final: 0.7939 (t) REVERT: R 85 LYS cc_start: 0.7947 (ptmt) cc_final: 0.7449 (pttm) outliers start: 28 outliers final: 22 residues processed: 263 average time/residue: 0.1173 time to fit residues: 43.9117 Evaluate side-chains 268 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 245 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 18 VAL Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 4 residue 66 MET Chi-restraints excluded: chain 5 residue 18 VAL Chi-restraints excluded: chain 5 residue 31 SER Chi-restraints excluded: chain 6 residue 58 GLU Chi-restraints excluded: chain 6 residue 70 LEU Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 16 VAL Chi-restraints excluded: chain 7 residue 18 VAL Chi-restraints excluded: chain 7 residue 72 LEU Chi-restraints excluded: chain 8 residue 67 VAL Chi-restraints excluded: chain G residue 123 GLN Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain I residue 41 SER Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain N residue 140 MET Chi-restraints excluded: chain N residue 163 ASN Chi-restraints excluded: chain R residue 74 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 140 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 145 optimal weight: 7.9990 chunk 12 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3799 r_free = 0.3799 target = 0.149004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.103834 restraints weight = 24855.081| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.72 r_work: 0.3128 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3130 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3130 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 12374 Z= 0.184 Angle : 0.853 59.181 16761 Z= 0.496 Chirality : 0.040 0.187 1974 Planarity : 0.004 0.040 2071 Dihedral : 4.956 43.201 1716 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.15 % Allowed : 17.30 % Favored : 80.54 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 1.69 % 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 aren not related in a simple way. whole: 1.92 (0.22), residues: 1559 helix: 2.11 (0.15), residues: 1111 sheet: -0.89 (0.58), residues: 86 loop : -0.82 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG G 113 TYR 0.012 0.001 TYR G 44 PHE 0.018 0.001 PHE 1 69 TRP 0.010 0.001 TRP R 28 HIS 0.003 0.001 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00376 (12374) covalent geometry : angle 0.85300 (16761) hydrogen bonds : bond 0.04779 ( 933) hydrogen bonds : angle 4.06748 ( 2747) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3546.46 seconds wall clock time: 61 minutes 28.39 seconds (3688.39 seconds total)