Starting phenix.real_space_refine on Wed Jul 30 03:23:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8khf_37243/07_2025/8khf_37243.cif Found real_map, /net/cci-nas-00/data/ceres_data/8khf_37243/07_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_37243/07_2025/8khf_37243.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8khf_37243/07_2025/8khf_37243.map" model { file = "/net/cci-nas-00/data/ceres_data/8khf_37243/07_2025/8khf_37243.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8khf_37243/07_2025/8khf_37243.cif" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 11.36, per 1000 atoms: 0.94 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: 3.53 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.17 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: 3.96 Time building geometry restraints manager: 3.99 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: 8.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 35.110 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.150 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.008 0.001 TRP N 109 HIS 0.005 0.001 HIS H 51 PHE 0.021 0.002 PHE 7 29 TYR 0.015 0.001 TYR G 44 ARG 0.005 0.001 ARG I 24 Details of bonding type rmsd hydrogen bonds : bond 0.14905 ( 933) hydrogen bonds : angle 7.07081 ( 2747) covalent geometry : bond 0.00587 (12374) covalent geometry : angle 0.67089 (16761) *********************** 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 : 1.204 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: 0.2687 time to fit residues: 106.9137 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 : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 127 optimal weight: 0.6980 chunk 114 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 71 optimal weight: 0.0870 chunk 88 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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 = 0.3780 r_free = 0.3780 target = 0.147962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.103572 restraints weight = 18810.481| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.41 r_work: 0.3088 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3094 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3095 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1389 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 : 0.574 8.133 16761 Z= 0.303 Chirality : 0.041 0.139 1974 Planarity : 0.004 0.045 2071 Dihedral : 5.907 69.416 1716 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.36 % Allowed : 8.85 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.20), residues: 1559 helix: 0.28 (0.15), residues: 1140 sheet: -1.87 (0.50), residues: 90 loop : -1.39 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 28 HIS 0.003 0.001 HIS H 51 PHE 0.016 0.001 PHE H 45 TYR 0.012 0.001 TYR G 44 ARG 0.004 0.000 ARG N 159 Details of bonding type rmsd hydrogen bonds : bond 0.05665 ( 933) hydrogen bonds : angle 4.70716 ( 2747) covalent geometry : bond 0.00326 (12374) covalent geometry : angle 0.57415 (16761) *********************** 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 270 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 253 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 31 SER cc_start: 0.8673 (m) cc_final: 0.8165 (p) REVERT: 4 75 MET cc_start: 0.7168 (mpp) cc_final: 0.6640 (mpp) REVERT: 5 69 PHE cc_start: 0.7809 (m-10) cc_final: 0.7146 (t80) REVERT: 7 69 PHE cc_start: 0.8153 (m-10) cc_final: 0.7232 (t80) REVERT: 8 7 LYS cc_start: 0.8003 (mtmt) cc_final: 0.7558 (mtpp) REVERT: G 81 ILE cc_start: 0.8245 (mm) cc_final: 0.7993 (mm) REVERT: G 188 ASP cc_start: 0.8362 (m-30) cc_final: 0.8129 (m-30) REVERT: I 7 GLN cc_start: 0.8293 (mm-40) cc_final: 0.7791 (mt0) REVERT: I 21 LYS cc_start: 0.8697 (tttm) cc_final: 0.8418 (tttp) REVERT: I 25 ASP cc_start: 0.9009 (m-30) cc_final: 0.8709 (m-30) REVERT: I 44 LYS cc_start: 0.8406 (mttm) cc_final: 0.7864 (mttt) REVERT: K 7 GLU cc_start: 0.8680 (tt0) cc_final: 0.8387 (tp30) REVERT: K 14 TYR cc_start: 0.8721 (m-80) cc_final: 0.8367 (m-80) REVERT: K 19 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7620 (mt-10) REVERT: K 26 TYR cc_start: 0.8045 (t80) cc_final: 0.7761 (t80) REVERT: K 48 LYS cc_start: 0.7225 (tttt) cc_final: 0.6131 (tmtt) REVERT: K 72 LYS cc_start: 0.8109 (mttt) cc_final: 0.7396 (mmtt) REVERT: K 84 LYS cc_start: 0.7861 (mttp) cc_final: 0.7370 (pttp) REVERT: N 57 MET cc_start: 0.8352 (mmm) cc_final: 0.7801 (mmt) REVERT: N 181 MET cc_start: 0.7818 (tpp) cc_final: 0.7530 (tpp) REVERT: R 49 ARG cc_start: 0.7636 (ttm170) cc_final: 0.6397 (tmt170) REVERT: R 63 SER cc_start: 0.7793 (m) cc_final: 0.7514 (t) REVERT: R 85 LYS cc_start: 0.7803 (ptmt) cc_final: 0.7298 (pttm) REVERT: S 90 GLU cc_start: 0.7730 (tt0) cc_final: 0.7504 (tt0) outliers start: 17 outliers final: 10 residues processed: 262 average time/residue: 0.2719 time to fit residues: 98.6187 Evaluate side-chains 244 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 234 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 41 SER Chi-restraints excluded: chain 6 residue 70 LEU Chi-restraints excluded: chain 7 residue 72 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 18 optimal weight: 0.1980 chunk 39 optimal weight: 3.9990 chunk 148 optimal weight: 7.9990 chunk 90 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 117 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 86 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.3798 r_free = 0.3798 target = 0.149572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.105599 restraints weight = 23834.874| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 3.03 r_work: 0.3046 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 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 = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1817 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= 0.144 Angle : 0.550 8.133 16761 Z= 0.287 Chirality : 0.040 0.140 1974 Planarity : 0.004 0.043 2071 Dihedral : 5.497 66.335 1716 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.44 % Allowed : 11.56 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.21), residues: 1559 helix: 1.15 (0.15), residues: 1154 sheet: -1.45 (0.53), residues: 87 loop : -1.01 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 28 HIS 0.003 0.001 HIS H 51 PHE 0.019 0.001 PHE K 24 TYR 0.028 0.001 TYR S 100 ARG 0.004 0.000 ARG H 134 Details of bonding type rmsd hydrogen bonds : bond 0.05213 ( 933) hydrogen bonds : angle 4.37786 ( 2747) covalent geometry : bond 0.00305 (12374) covalent geometry : angle 0.55050 (16761) *********************** 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 264 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 246 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 66 MET cc_start: 0.7755 (ppp) cc_final: 0.7353 (ppp) REVERT: 5 69 PHE cc_start: 0.7951 (m-10) cc_final: 0.7156 (t80) REVERT: 7 58 GLU cc_start: 0.7582 (tt0) cc_final: 0.7211 (tt0) REVERT: 7 69 PHE cc_start: 0.8102 (m-10) cc_final: 0.7205 (t80) REVERT: 8 7 LYS cc_start: 0.7937 (mtmt) cc_final: 0.7526 (mtpp) REVERT: G 166 ARG cc_start: 0.8612 (ttp-110) cc_final: 0.8164 (mtm110) REVERT: G 188 ASP cc_start: 0.8369 (m-30) cc_final: 0.8146 (m-30) REVERT: I 7 GLN cc_start: 0.8358 (mm-40) cc_final: 0.7851 (mt0) REVERT: I 21 LYS cc_start: 0.8706 (tttm) cc_final: 0.8448 (tttp) REVERT: I 25 ASP cc_start: 0.9026 (m-30) cc_final: 0.8752 (m-30) REVERT: I 44 LYS cc_start: 0.8398 (mttm) cc_final: 0.7865 (mttt) REVERT: K 14 TYR cc_start: 0.8787 (m-80) cc_final: 0.8468 (m-80) REVERT: K 19 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7501 (mt-10) REVERT: K 26 TYR cc_start: 0.8066 (t80) cc_final: 0.7763 (t80) REVERT: K 48 LYS cc_start: 0.7234 (tttt) cc_final: 0.6177 (tmtt) REVERT: K 72 LYS cc_start: 0.8160 (mttt) cc_final: 0.7457 (mmtt) REVERT: K 84 LYS cc_start: 0.7878 (mttp) cc_final: 0.7375 (pttp) REVERT: N 57 MET cc_start: 0.8389 (mmm) cc_final: 0.8024 (mmt) REVERT: N 181 MET cc_start: 0.7937 (tpp) cc_final: 0.7583 (tpp) REVERT: R 49 ARG cc_start: 0.7661 (ttm170) cc_final: 0.6370 (tmt170) REVERT: R 63 SER cc_start: 0.7791 (m) cc_final: 0.7541 (t) REVERT: R 85 LYS cc_start: 0.7743 (ptmt) cc_final: 0.7253 (pttm) outliers start: 18 outliers final: 10 residues processed: 254 average time/residue: 0.2525 time to fit residues: 91.2543 Evaluate side-chains 247 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 237 time to evaluate : 1.363 ------------------------------------------------------------------------------- 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 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 149 LEU Chi-restraints excluded: chain R residue 24 GLU 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 78 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 141 optimal weight: 20.0000 chunk 50 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 chunk 56 optimal weight: 0.2980 chunk 144 optimal weight: 7.9990 chunk 135 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3789 r_free = 0.3789 target = 0.148695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.104804 restraints weight = 22211.256| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.86 r_work: 0.3047 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3057 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 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 = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3057 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12374 Z= 0.158 Angle : 0.554 7.305 16761 Z= 0.287 Chirality : 0.041 0.141 1974 Planarity : 0.004 0.040 2071 Dihedral : 5.342 62.348 1716 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.59 % Allowed : 13.40 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.21), residues: 1559 helix: 1.47 (0.15), residues: 1155 sheet: -0.94 (0.57), residues: 83 loop : -0.80 (0.36), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 28 HIS 0.004 0.001 HIS H 51 PHE 0.020 0.001 PHE K 24 TYR 0.014 0.001 TYR S 100 ARG 0.004 0.000 ARG 2 38 Details of bonding type rmsd hydrogen bonds : bond 0.05138 ( 933) hydrogen bonds : angle 4.27414 ( 2747) covalent geometry : bond 0.00354 (12374) covalent geometry : angle 0.55404 (16761) *********************** 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 258 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 238 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 66 MET cc_start: 0.7758 (ppp) cc_final: 0.7395 (ppp) REVERT: 2 31 SER cc_start: 0.8697 (m) cc_final: 0.8209 (p) REVERT: 2 39 ASN cc_start: 0.8475 (t0) cc_final: 0.8260 (t0) REVERT: 3 39 ASN cc_start: 0.8287 (t0) cc_final: 0.7862 (t0) REVERT: 4 60 MET cc_start: 0.7909 (tpt) cc_final: 0.7655 (tpt) REVERT: 5 69 PHE cc_start: 0.7950 (m-10) cc_final: 0.7138 (t80) REVERT: 6 75 MET cc_start: 0.7084 (mmp) cc_final: 0.6731 (ptt) REVERT: 7 58 GLU cc_start: 0.7615 (tt0) cc_final: 0.7277 (tt0) REVERT: 7 69 PHE cc_start: 0.8038 (m-10) cc_final: 0.7199 (t80) REVERT: 8 7 LYS cc_start: 0.7906 (mtmt) cc_final: 0.7489 (mtpp) REVERT: G 87 LYS cc_start: 0.8397 (ptmt) cc_final: 0.8023 (pptt) REVERT: G 113 ARG cc_start: 0.8752 (ttp80) cc_final: 0.8376 (ttp80) REVERT: G 166 ARG cc_start: 0.8604 (ttp-110) cc_final: 0.8157 (mtm110) REVERT: G 188 ASP cc_start: 0.8380 (m-30) cc_final: 0.8155 (m-30) REVERT: I 7 GLN cc_start: 0.8347 (mm-40) cc_final: 0.7841 (mt0) REVERT: I 21 LYS cc_start: 0.8704 (tttm) cc_final: 0.8468 (tttp) REVERT: I 25 ASP cc_start: 0.9026 (m-30) cc_final: 0.8768 (m-30) REVERT: I 44 LYS cc_start: 0.8385 (mttm) cc_final: 0.7846 (mttt) REVERT: K 14 TYR cc_start: 0.8787 (m-80) cc_final: 0.8422 (m-80) REVERT: K 19 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7528 (mt-10) REVERT: K 48 LYS cc_start: 0.7232 (tttt) cc_final: 0.6187 (tmtt) REVERT: K 72 LYS cc_start: 0.8152 (mttt) cc_final: 0.7445 (mmtt) REVERT: K 84 LYS cc_start: 0.7863 (mttp) cc_final: 0.7362 (pttp) REVERT: N 57 MET cc_start: 0.8393 (mmm) cc_final: 0.8116 (mmt) REVERT: N 181 MET cc_start: 0.8039 (tpp) cc_final: 0.7683 (tpp) REVERT: P 39 ARG cc_start: 0.8474 (mtm180) cc_final: 0.8154 (mmm-85) REVERT: R 49 ARG cc_start: 0.7658 (ttm170) cc_final: 0.6361 (tmt170) REVERT: R 63 SER cc_start: 0.7826 (m) cc_final: 0.7542 (t) REVERT: R 85 LYS cc_start: 0.7746 (ptmt) cc_final: 0.7252 (pttm) outliers start: 20 outliers final: 12 residues processed: 246 average time/residue: 0.2464 time to fit residues: 86.5651 Evaluate side-chains 249 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 237 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 41 SER Chi-restraints excluded: chain 4 residue 66 MET Chi-restraints excluded: chain 8 residue 67 VAL Chi-restraints excluded: chain 8 residue 71 ILE 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 149 LEU 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 49 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 64 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 56 optimal weight: 0.3980 chunk 139 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3804 r_free = 0.3804 target = 0.149972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.106425 restraints weight = 17199.180| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.42 r_work: 0.3115 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3123 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3123 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12374 Z= 0.142 Angle : 0.536 7.545 16761 Z= 0.276 Chirality : 0.040 0.138 1974 Planarity : 0.003 0.035 2071 Dihedral : 5.199 57.881 1716 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.99 % Allowed : 13.96 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.22), residues: 1559 helix: 1.73 (0.15), residues: 1151 sheet: -0.86 (0.58), residues: 83 loop : -0.64 (0.36), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 28 HIS 0.003 0.001 HIS H 51 PHE 0.021 0.001 PHE K 24 TYR 0.012 0.001 TYR R 92 ARG 0.003 0.000 ARG T 29 Details of bonding type rmsd hydrogen bonds : bond 0.04890 ( 933) hydrogen bonds : angle 4.15811 ( 2747) covalent geometry : bond 0.00310 (12374) covalent geometry : angle 0.53621 (16761) *********************** 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 272 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 247 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 66 MET cc_start: 0.7831 (ppp) cc_final: 0.7306 (ppp) REVERT: 2 31 SER cc_start: 0.8651 (m) cc_final: 0.8173 (p) REVERT: 2 38 ARG cc_start: 0.7740 (mtt180) cc_final: 0.7473 (mpt-90) REVERT: 3 39 ASN cc_start: 0.8189 (t0) cc_final: 0.7775 (t0) REVERT: 4 60 MET cc_start: 0.7929 (tpt) cc_final: 0.7599 (tpt) REVERT: 4 75 MET cc_start: 0.7093 (mpp) cc_final: 0.6444 (mpp) REVERT: 5 69 PHE cc_start: 0.7909 (m-10) cc_final: 0.7109 (t80) REVERT: 6 75 MET cc_start: 0.7029 (mmp) cc_final: 0.6788 (ptt) REVERT: 7 58 GLU cc_start: 0.7579 (tt0) cc_final: 0.7257 (tt0) REVERT: 7 69 PHE cc_start: 0.7962 (m-10) cc_final: 0.7164 (t80) REVERT: 8 7 LYS cc_start: 0.7924 (mtmt) cc_final: 0.7513 (mtpp) REVERT: G 87 LYS cc_start: 0.8434 (ptmt) cc_final: 0.8019 (pptt) REVERT: G 113 ARG cc_start: 0.8750 (ttp80) cc_final: 0.8405 (ttp80) REVERT: G 153 TYR cc_start: 0.7023 (t80) cc_final: 0.6796 (t80) REVERT: G 166 ARG cc_start: 0.8589 (ttp-110) cc_final: 0.8155 (mtm110) REVERT: G 188 ASP cc_start: 0.8345 (m-30) cc_final: 0.8135 (m-30) REVERT: I 7 GLN cc_start: 0.8351 (mm-40) cc_final: 0.7841 (mt0) REVERT: I 21 LYS cc_start: 0.8686 (tttm) cc_final: 0.8453 (tttp) REVERT: I 25 ASP cc_start: 0.8991 (m-30) cc_final: 0.8644 (m-30) REVERT: I 36 GLU cc_start: 0.8364 (mt-10) cc_final: 0.7960 (tm-30) REVERT: I 44 LYS cc_start: 0.8400 (mttm) cc_final: 0.7858 (mttt) REVERT: K 14 TYR cc_start: 0.8757 (m-80) cc_final: 0.8441 (m-80) REVERT: K 19 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7597 (mt-10) REVERT: K 48 LYS cc_start: 0.7224 (tttt) cc_final: 0.6205 (tmtt) REVERT: K 72 LYS cc_start: 0.8090 (mttt) cc_final: 0.7400 (mmtt) REVERT: K 84 LYS cc_start: 0.7855 (mttp) cc_final: 0.7360 (pttp) REVERT: N 57 MET cc_start: 0.8372 (mmm) cc_final: 0.8107 (mmt) REVERT: N 140 MET cc_start: 0.6012 (OUTLIER) cc_final: 0.5794 (tmm) REVERT: N 181 MET cc_start: 0.8141 (tpp) cc_final: 0.7812 (tpp) REVERT: P 39 ARG cc_start: 0.8542 (mtm180) cc_final: 0.8282 (mmm-85) REVERT: R 49 ARG cc_start: 0.7620 (ttm170) cc_final: 0.6377 (tmt170) REVERT: R 63 SER cc_start: 0.7770 (m) cc_final: 0.7485 (t) REVERT: R 85 LYS cc_start: 0.7817 (ptmt) cc_final: 0.7311 (pttm) outliers start: 25 outliers final: 14 residues processed: 257 average time/residue: 0.2402 time to fit residues: 88.1388 Evaluate side-chains 260 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 245 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 6 residue 71 ILE 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 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 N residue 149 LEU 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 95 optimal weight: 4.9990 chunk 146 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 138 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 60 optimal weight: 0.0970 chunk 2 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 = 0.3814 r_free = 0.3814 target = 0.150739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.107406 restraints weight = 22209.703| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.82 r_work: 0.3088 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3097 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3097 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2394 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= 0.132 Angle : 0.528 7.410 16761 Z= 0.272 Chirality : 0.040 0.137 1974 Planarity : 0.004 0.105 2071 Dihedral : 5.113 54.355 1716 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.07 % Allowed : 15.31 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.22), residues: 1559 helix: 1.97 (0.15), residues: 1113 sheet: -0.93 (0.57), residues: 85 loop : -0.94 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 28 HIS 0.003 0.001 HIS H 51 PHE 0.019 0.001 PHE 1 69 TYR 0.012 0.001 TYR R 51 ARG 0.006 0.000 ARG N 41 Details of bonding type rmsd hydrogen bonds : bond 0.04749 ( 933) hydrogen bonds : angle 4.10625 ( 2747) covalent geometry : bond 0.00282 (12374) covalent geometry : angle 0.52798 (16761) *********************** 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 280 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 254 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 66 MET cc_start: 0.7711 (ppp) cc_final: 0.7299 (ppp) REVERT: 2 31 SER cc_start: 0.8637 (m) cc_final: 0.8174 (p) REVERT: 2 38 ARG cc_start: 0.7717 (mtt180) cc_final: 0.7435 (mpt-90) REVERT: 2 39 ASN cc_start: 0.8296 (t0) cc_final: 0.8056 (t0) REVERT: 3 39 ASN cc_start: 0.8100 (t0) cc_final: 0.7735 (t0) REVERT: 4 60 MET cc_start: 0.7842 (tpt) cc_final: 0.7515 (tpt) REVERT: 4 75 MET cc_start: 0.7290 (mpp) cc_final: 0.6740 (mpp) REVERT: 5 69 PHE cc_start: 0.7843 (m-10) cc_final: 0.7045 (t80) REVERT: 5 75 MET cc_start: 0.5022 (ptt) cc_final: 0.4345 (ptp) REVERT: 6 75 MET cc_start: 0.7026 (mmp) cc_final: 0.6720 (ptt) REVERT: 7 69 PHE cc_start: 0.7891 (m-10) cc_final: 0.7067 (t80) REVERT: 8 7 LYS cc_start: 0.7804 (mtmt) cc_final: 0.7374 (mtpp) REVERT: G 87 LYS cc_start: 0.8461 (ptmt) cc_final: 0.8068 (pptt) REVERT: G 153 TYR cc_start: 0.6970 (t80) cc_final: 0.6744 (t80) REVERT: G 166 ARG cc_start: 0.8589 (ttp-110) cc_final: 0.8155 (mtm110) REVERT: H 111 ASN cc_start: 0.7601 (t0) cc_final: 0.7124 (m110) REVERT: I 7 GLN cc_start: 0.8342 (mm-40) cc_final: 0.7840 (mt0) REVERT: I 21 LYS cc_start: 0.8662 (tttm) cc_final: 0.8434 (tttp) REVERT: I 25 ASP cc_start: 0.8998 (m-30) cc_final: 0.8664 (m-30) REVERT: I 36 GLU cc_start: 0.8379 (mt-10) cc_final: 0.7948 (tm-30) REVERT: I 44 LYS cc_start: 0.8345 (mttm) cc_final: 0.7836 (mttt) REVERT: K 14 TYR cc_start: 0.8742 (m-80) cc_final: 0.8412 (m-80) REVERT: K 19 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7577 (mt-10) REVERT: K 48 LYS cc_start: 0.7195 (tttt) cc_final: 0.6160 (tmtt) REVERT: K 72 LYS cc_start: 0.8051 (mttt) cc_final: 0.7365 (mmtt) REVERT: K 84 LYS cc_start: 0.7816 (mttp) cc_final: 0.7332 (pttp) REVERT: M 158 GLU cc_start: 0.9080 (mp0) cc_final: 0.8828 (mp0) REVERT: N 57 MET cc_start: 0.8345 (mmm) cc_final: 0.8140 (mmt) REVERT: N 140 MET cc_start: 0.5927 (OUTLIER) cc_final: 0.5711 (tmm) REVERT: N 181 MET cc_start: 0.8009 (tpp) cc_final: 0.7646 (tpp) REVERT: P 39 ARG cc_start: 0.8538 (mtm180) cc_final: 0.8308 (mmm-85) REVERT: R 49 ARG cc_start: 0.7574 (ttm170) cc_final: 0.6359 (tmt170) REVERT: R 63 SER cc_start: 0.7776 (m) cc_final: 0.7494 (t) REVERT: R 85 LYS cc_start: 0.7786 (ptmt) cc_final: 0.7271 (pttm) outliers start: 26 outliers final: 15 residues processed: 267 average time/residue: 0.2445 time to fit residues: 92.7795 Evaluate side-chains 262 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 246 time to evaluate : 1.279 ------------------------------------------------------------------------------- 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 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 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 N residue 149 LEU 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 79 optimal weight: 0.7980 chunk 18 optimal weight: 0.0980 chunk 101 optimal weight: 0.8980 chunk 112 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 118 optimal weight: 0.0670 chunk 51 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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 = 0.3820 r_free = 0.3820 target = 0.151240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.106702 restraints weight = 14846.982| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.16 r_work: 0.3164 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3035 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3035 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12374 Z= 0.129 Angle : 0.529 7.280 16761 Z= 0.271 Chirality : 0.040 0.136 1974 Planarity : 0.004 0.062 2071 Dihedral : 5.027 52.305 1716 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.23 % Allowed : 15.95 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.22), residues: 1559 helix: 2.06 (0.15), residues: 1112 sheet: -0.86 (0.58), residues: 85 loop : -0.89 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 28 HIS 0.002 0.000 HIS H 51 PHE 0.018 0.001 PHE 1 69 TYR 0.011 0.001 TYR R 51 ARG 0.003 0.000 ARG N 41 Details of bonding type rmsd hydrogen bonds : bond 0.04659 ( 933) hydrogen bonds : angle 4.05802 ( 2747) covalent geometry : bond 0.00273 (12374) covalent geometry : angle 0.52870 (16761) *********************** 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 277 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 249 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 66 MET cc_start: 0.7685 (ppp) cc_final: 0.7224 (ppp) REVERT: 2 38 ARG cc_start: 0.7766 (mtt180) cc_final: 0.7479 (mpt-90) REVERT: 2 39 ASN cc_start: 0.8258 (t0) cc_final: 0.7987 (t0) REVERT: 3 39 ASN cc_start: 0.8081 (t0) cc_final: 0.7726 (t0) REVERT: 4 60 MET cc_start: 0.7780 (tpt) cc_final: 0.7470 (tpt) REVERT: 4 75 MET cc_start: 0.7328 (mpp) cc_final: 0.6834 (mpp) REVERT: 5 69 PHE cc_start: 0.7853 (m-10) cc_final: 0.7043 (t80) REVERT: 5 75 MET cc_start: 0.5096 (ptt) cc_final: 0.4380 (ptp) REVERT: 6 75 MET cc_start: 0.7079 (mmp) cc_final: 0.6739 (ptt) REVERT: 7 69 PHE cc_start: 0.7934 (m-10) cc_final: 0.7092 (t80) REVERT: 8 7 LYS cc_start: 0.7837 (mtmt) cc_final: 0.7408 (mtpp) REVERT: G 87 LYS cc_start: 0.8450 (ptmt) cc_final: 0.8048 (pptt) REVERT: G 166 ARG cc_start: 0.8608 (ttp-110) cc_final: 0.8192 (mtm110) REVERT: G 188 ASP cc_start: 0.8366 (m-30) cc_final: 0.8155 (t0) REVERT: I 7 GLN cc_start: 0.8373 (mm-40) cc_final: 0.7865 (mt0) REVERT: I 21 LYS cc_start: 0.8662 (tttm) cc_final: 0.8431 (tttp) REVERT: I 25 ASP cc_start: 0.8992 (m-30) cc_final: 0.8739 (m-30) REVERT: I 44 LYS cc_start: 0.8341 (mttm) cc_final: 0.7816 (mttt) REVERT: K 14 TYR cc_start: 0.8762 (m-80) cc_final: 0.8380 (m-80) REVERT: K 19 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7628 (mt-10) REVERT: K 48 LYS cc_start: 0.7286 (tttt) cc_final: 0.6234 (tmtt) REVERT: K 72 LYS cc_start: 0.8092 (mttt) cc_final: 0.7406 (mmtt) REVERT: K 84 LYS cc_start: 0.7842 (mttp) cc_final: 0.7312 (pttp) REVERT: N 181 MET cc_start: 0.8016 (tpp) cc_final: 0.7633 (tpp) REVERT: P 39 ARG cc_start: 0.8502 (mtm180) cc_final: 0.8287 (mmm-85) REVERT: R 49 ARG cc_start: 0.7626 (ttm170) cc_final: 0.6397 (tmt170) REVERT: R 63 SER cc_start: 0.7825 (m) cc_final: 0.7547 (t) REVERT: R 85 LYS cc_start: 0.7778 (ptmt) cc_final: 0.7271 (pttm) REVERT: S 71 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7514 (pm20) outliers start: 28 outliers final: 17 residues processed: 264 average time/residue: 0.2546 time to fit residues: 95.0105 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 : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 64 CYS 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 N residue 149 LEU Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain S residue 71 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 45 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 63 optimal weight: 0.0570 chunk 26 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 chunk 103 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 123 optimal weight: 0.7980 chunk 140 optimal weight: 7.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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 = 0.3796 r_free = 0.3796 target = 0.150125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.107685 restraints weight = 23941.322| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.82 r_work: 0.3075 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12374 Z= 0.127 Angle : 0.530 8.942 16761 Z= 0.271 Chirality : 0.039 0.136 1974 Planarity : 0.004 0.054 2071 Dihedral : 4.966 49.199 1716 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.15 % Allowed : 16.19 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.22), residues: 1559 helix: 2.13 (0.15), residues: 1112 sheet: -0.77 (0.58), residues: 85 loop : -0.80 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 28 HIS 0.002 0.000 HIS H 51 PHE 0.019 0.001 PHE 1 69 TYR 0.012 0.001 TYR R 51 ARG 0.004 0.000 ARG T 29 Details of bonding type rmsd hydrogen bonds : bond 0.04566 ( 933) hydrogen bonds : angle 4.01956 ( 2747) covalent geometry : bond 0.00267 (12374) covalent geometry : angle 0.52977 (16761) *********************** 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 281 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 254 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 66 MET cc_start: 0.7924 (ppp) cc_final: 0.7432 (ppp) REVERT: 2 31 SER cc_start: 0.8775 (m) cc_final: 0.8428 (p) REVERT: 2 39 ASN cc_start: 0.8318 (t0) cc_final: 0.8093 (t0) REVERT: 4 60 MET cc_start: 0.7977 (tpt) cc_final: 0.7648 (tpt) REVERT: 4 75 MET cc_start: 0.7305 (mpp) cc_final: 0.6831 (mpp) REVERT: 5 69 PHE cc_start: 0.8009 (m-10) cc_final: 0.7233 (t80) REVERT: 5 75 MET cc_start: 0.5103 (ptt) cc_final: 0.4434 (ptp) REVERT: 6 75 MET cc_start: 0.7013 (mmp) cc_final: 0.6736 (ptt) REVERT: 7 16 VAL cc_start: 0.8652 (OUTLIER) cc_final: 0.8451 (p) REVERT: 7 69 PHE cc_start: 0.7980 (m-10) cc_final: 0.7212 (t80) REVERT: 8 7 LYS cc_start: 0.8008 (mtmt) cc_final: 0.7589 (mtpp) REVERT: G 46 LEU cc_start: 0.8558 (mt) cc_final: 0.8280 (mt) REVERT: G 87 LYS cc_start: 0.8378 (ptmt) cc_final: 0.8009 (pptt) REVERT: G 166 ARG cc_start: 0.8534 (ttp-110) cc_final: 0.8233 (mtm110) REVERT: H 111 ASN cc_start: 0.7624 (t0) cc_final: 0.7138 (m110) REVERT: I 7 GLN cc_start: 0.8411 (mm-40) cc_final: 0.7901 (mt0) REVERT: I 21 LYS cc_start: 0.8723 (tttm) cc_final: 0.8499 (tttp) REVERT: I 25 ASP cc_start: 0.8918 (m-30) cc_final: 0.8692 (m-30) REVERT: I 44 LYS cc_start: 0.8588 (mttm) cc_final: 0.8080 (mttt) REVERT: K 14 TYR cc_start: 0.8769 (m-80) cc_final: 0.8438 (m-80) REVERT: K 19 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7694 (mt-10) REVERT: K 48 LYS cc_start: 0.7449 (tttt) cc_final: 0.6377 (tmtt) REVERT: K 72 LYS cc_start: 0.8242 (mttt) cc_final: 0.7548 (mmtt) REVERT: K 84 LYS cc_start: 0.8007 (mttp) cc_final: 0.7528 (pttp) REVERT: R 31 MET cc_start: 0.6371 (ttt) cc_final: 0.6102 (tpp) REVERT: R 49 ARG cc_start: 0.7831 (ttm170) cc_final: 0.6594 (tmt170) REVERT: R 63 SER cc_start: 0.8050 (m) cc_final: 0.7797 (t) REVERT: R 85 LYS cc_start: 0.7894 (ptmt) cc_final: 0.7403 (pttm) REVERT: S 71 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7497 (pm20) outliers start: 27 outliers final: 18 residues processed: 270 average time/residue: 0.2554 time to fit residues: 97.8429 Evaluate side-chains 268 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 248 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 63 PHE Chi-restraints excluded: chain 2 residue 64 CYS 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 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 I residue 41 SER Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain S residue 71 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 39 optimal weight: 0.0870 chunk 126 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 86 optimal weight: 0.0040 chunk 127 optimal weight: 0.9980 overall best weight: 0.5370 ------------------------------------------------------------------------------- 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 = 0.150461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.108769 restraints weight = 24221.998| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 3.01 r_work: 0.3065 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3067 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 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 = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3067 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12374 Z= 0.128 Angle : 0.540 9.111 16761 Z= 0.275 Chirality : 0.040 0.183 1974 Planarity : 0.004 0.050 2071 Dihedral : 4.883 44.479 1716 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.75 % Allowed : 17.30 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.22), residues: 1559 helix: 2.18 (0.15), residues: 1113 sheet: -0.71 (0.59), residues: 85 loop : -0.77 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 28 HIS 0.002 0.000 HIS H 51 PHE 0.020 0.001 PHE 1 69 TYR 0.012 0.001 TYR R 92 ARG 0.007 0.000 ARG P 39 Details of bonding type rmsd hydrogen bonds : bond 0.04516 ( 933) hydrogen bonds : angle 3.98387 ( 2747) covalent geometry : bond 0.00273 (12374) covalent geometry : angle 0.54048 (16761) *********************** 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 271 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 249 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 66 MET cc_start: 0.7933 (ppp) cc_final: 0.7422 (ppp) REVERT: 2 31 SER cc_start: 0.8796 (m) cc_final: 0.8443 (p) REVERT: 2 39 ASN cc_start: 0.8364 (t0) cc_final: 0.8134 (t0) REVERT: 4 60 MET cc_start: 0.7969 (tpt) cc_final: 0.7612 (tpt) REVERT: 4 75 MET cc_start: 0.7349 (mpp) cc_final: 0.6886 (mpp) REVERT: 5 69 PHE cc_start: 0.8046 (m-10) cc_final: 0.7257 (t80) REVERT: 5 75 MET cc_start: 0.5012 (ptt) cc_final: 0.4472 (ptp) REVERT: 6 75 MET cc_start: 0.7048 (mmp) cc_final: 0.6785 (ptt) REVERT: 7 69 PHE cc_start: 0.7976 (m-10) cc_final: 0.7183 (t80) REVERT: 8 7 LYS cc_start: 0.8039 (mtmt) cc_final: 0.7641 (mtpp) REVERT: G 46 LEU cc_start: 0.8539 (mt) cc_final: 0.8273 (mt) REVERT: G 87 LYS cc_start: 0.8387 (ptmt) cc_final: 0.8059 (pptt) REVERT: G 113 ARG cc_start: 0.8777 (ttp80) cc_final: 0.8572 (ttp80) REVERT: G 166 ARG cc_start: 0.8539 (ttp-110) cc_final: 0.8254 (mtm110) REVERT: H 111 ASN cc_start: 0.7612 (t0) cc_final: 0.7131 (m110) REVERT: I 7 GLN cc_start: 0.8420 (mm-40) cc_final: 0.7918 (mt0) REVERT: I 44 LYS cc_start: 0.8595 (mttm) cc_final: 0.8083 (mttt) REVERT: K 14 TYR cc_start: 0.8780 (m-80) cc_final: 0.8432 (m-80) REVERT: K 19 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7730 (mt-10) REVERT: K 48 LYS cc_start: 0.7489 (tttt) cc_final: 0.6401 (tmtt) REVERT: K 72 LYS cc_start: 0.8269 (mttt) cc_final: 0.7570 (mmtt) REVERT: P 39 ARG cc_start: 0.8368 (mmm-85) cc_final: 0.8126 (mmm-85) REVERT: R 32 ARG cc_start: 0.6139 (mmp-170) cc_final: 0.5868 (mmm-85) REVERT: R 49 ARG cc_start: 0.7854 (ttm170) cc_final: 0.6617 (tmt170) REVERT: R 63 SER cc_start: 0.8104 (m) cc_final: 0.7860 (t) REVERT: R 85 LYS cc_start: 0.7948 (ptmt) cc_final: 0.7454 (pttm) outliers start: 22 outliers final: 16 residues processed: 261 average time/residue: 0.2483 time to fit residues: 91.5141 Evaluate side-chains 259 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 243 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 Q residue 6 THR 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 41 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 29 optimal weight: 0.0770 chunk 56 optimal weight: 0.9980 chunk 146 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 101 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 89 optimal weight: 0.5980 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 = 0.3826 r_free = 0.3826 target = 0.151408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.107035 restraints weight = 19970.114| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.44 r_work: 0.3181 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2802 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= 0.130 Angle : 0.551 11.546 16761 Z= 0.277 Chirality : 0.040 0.190 1974 Planarity : 0.004 0.049 2071 Dihedral : 4.890 42.015 1716 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.52 % Allowed : 17.22 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.22), residues: 1559 helix: 2.09 (0.15), residues: 1135 sheet: -0.70 (0.59), residues: 85 loop : -0.46 (0.36), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 28 HIS 0.003 0.000 HIS H 51 PHE 0.020 0.001 PHE 1 69 TYR 0.011 0.001 TYR G 44 ARG 0.008 0.000 ARG G 36 Details of bonding type rmsd hydrogen bonds : bond 0.04535 ( 933) hydrogen bonds : angle 3.97889 ( 2747) covalent geometry : bond 0.00280 (12374) covalent geometry : angle 0.55103 (16761) ********************** 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 269 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 250 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 66 MET cc_start: 0.7987 (ppp) cc_final: 0.7439 (ppp) REVERT: 2 31 SER cc_start: 0.8824 (m) cc_final: 0.8480 (p) REVERT: 2 39 ASN cc_start: 0.8437 (t0) cc_final: 0.8214 (t0) REVERT: 4 60 MET cc_start: 0.8069 (tpt) cc_final: 0.7721 (tpt) REVERT: 4 65 LEU cc_start: 0.7809 (mm) cc_final: 0.7585 (mt) REVERT: 4 75 MET cc_start: 0.7193 (mpp) cc_final: 0.6733 (mpp) REVERT: 5 69 PHE cc_start: 0.8078 (m-10) cc_final: 0.7353 (t80) REVERT: 5 75 MET cc_start: 0.5163 (ptt) cc_final: 0.4616 (ptp) REVERT: 7 69 PHE cc_start: 0.8055 (m-10) cc_final: 0.7269 (t80) REVERT: 8 7 LYS cc_start: 0.8117 (mtmt) cc_final: 0.7715 (mtpp) REVERT: G 36 ARG cc_start: 0.8922 (mtm110) cc_final: 0.8642 (ptm160) REVERT: G 46 LEU cc_start: 0.8556 (mt) cc_final: 0.8303 (mt) REVERT: G 87 LYS cc_start: 0.8348 (ptmt) cc_final: 0.8056 (pptt) REVERT: G 166 ARG cc_start: 0.8447 (ttp-110) cc_final: 0.8204 (mtm110) REVERT: H 111 ASN cc_start: 0.7626 (t0) cc_final: 0.7170 (m110) REVERT: I 7 GLN cc_start: 0.8411 (mm-40) cc_final: 0.7901 (mt0) REVERT: I 44 LYS cc_start: 0.8699 (mttm) cc_final: 0.8198 (mttt) REVERT: K 14 TYR cc_start: 0.8761 (m-80) cc_final: 0.8432 (m-80) REVERT: K 19 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7795 (mt-10) REVERT: K 48 LYS cc_start: 0.7667 (tttt) cc_final: 0.6570 (tmtt) REVERT: K 72 LYS cc_start: 0.8326 (mttt) cc_final: 0.7643 (mmtt) REVERT: R 49 ARG cc_start: 0.7951 (ttm170) cc_final: 0.6750 (tmt170) REVERT: R 63 SER cc_start: 0.8202 (m) cc_final: 0.7986 (t) REVERT: R 85 LYS cc_start: 0.7957 (ptmt) cc_final: 0.7484 (pttm) outliers start: 19 outliers final: 15 residues processed: 261 average time/residue: 0.2386 time to fit residues: 88.8757 Evaluate side-chains 264 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 249 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 I residue 41 SER Chi-restraints excluded: chain K residue 52 VAL 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 32 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 60 optimal weight: 0.0030 chunk 64 optimal weight: 5.9990 chunk 134 optimal weight: 7.9990 chunk 42 optimal weight: 0.7980 chunk 126 optimal weight: 5.9990 chunk 135 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 overall best weight: 0.6590 ------------------------------------------------------------------------------- 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 = 0.3832 r_free = 0.3832 target = 0.151720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.107719 restraints weight = 19259.926| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.40 r_work: 0.3185 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3187 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3187 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.131 12374 Z= 0.180 Angle : 0.827 59.190 16761 Z= 0.479 Chirality : 0.040 0.226 1974 Planarity : 0.004 0.045 2071 Dihedral : 4.891 42.039 1716 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.36 % Allowed : 17.54 % Favored : 81.10 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.22), residues: 1559 helix: 2.08 (0.15), residues: 1135 sheet: -0.70 (0.59), residues: 85 loop : -0.46 (0.36), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 28 HIS 0.003 0.000 HIS H 51 PHE 0.019 0.001 PHE 1 69 TYR 0.012 0.001 TYR G 44 ARG 0.010 0.001 ARG R 32 Details of bonding type rmsd hydrogen bonds : bond 0.04549 ( 933) hydrogen bonds : angle 3.97547 ( 2747) covalent geometry : bond 0.00360 (12374) covalent geometry : angle 0.82667 (16761) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7906.03 seconds wall clock time: 135 minutes 38.05 seconds (8138.05 seconds total)