Starting phenix.real_space_refine on Wed May 14 15:18:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8khf_37243/05_2025/8khf_37243.cif Found real_map, /net/cci-nas-00/data/ceres_data/8khf_37243/05_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_37243/05_2025/8khf_37243.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8khf_37243/05_2025/8khf_37243.map" model { file = "/net/cci-nas-00/data/ceres_data/8khf_37243/05_2025/8khf_37243.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8khf_37243/05_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-5687/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: 8.36, per 1000 atoms: 0.69 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: 2.86 Conformation dependent library (CDL) restraints added in 1.6 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: 1.01 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: 3.28 Time building geometry restraints manager: 3.30 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: 5.960 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: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 28.340 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.970 ------------------------------------------------------------------------------- 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 : 1.361 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: 0.2749 time to fit residues: 109.0057 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 : 1.199 ------------------------------------------------------------------------------- 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: 0.6980 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: 3.9990 chunk 137 optimal weight: 2.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- 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 = 0.147889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.103471 restraints weight = 18814.319| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.42 r_work: 0.3087 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3093 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 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 = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3093 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12374 Z= 0.158 Angle : 0.577 8.157 16761 Z= 0.304 Chirality : 0.041 0.139 1974 Planarity : 0.004 0.044 2071 Dihedral : 5.913 69.332 1716 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.36 % Allowed : 8.93 % Favored : 89.71 % 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: -0.41 (0.20), residues: 1559 helix: 0.29 (0.15), residues: 1140 sheet: -1.88 (0.50), residues: 90 loop : -1.38 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 28 HIS 0.003 0.001 HIS H 51 PHE 0.017 0.001 PHE H 45 TYR 0.012 0.001 TYR G 44 ARG 0.003 0.000 ARG G 166 Details of bonding type rmsd hydrogen bonds : bond 0.05681 ( 933) hydrogen bonds : angle 4.70107 ( 2747) covalent geometry : bond 0.00330 (12374) covalent geometry : angle 0.57674 (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 269 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 252 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 31 SER cc_start: 0.8673 (m) cc_final: 0.8164 (p) REVERT: 4 75 MET cc_start: 0.7172 (mpp) cc_final: 0.6648 (mpp) REVERT: 5 69 PHE cc_start: 0.7807 (m-10) cc_final: 0.7144 (t80) REVERT: 7 7 LYS cc_start: 0.8421 (mtmt) cc_final: 0.8221 (mttt) REVERT: 7 69 PHE cc_start: 0.8157 (m-10) cc_final: 0.7237 (t80) REVERT: 8 7 LYS cc_start: 0.8001 (mtmt) cc_final: 0.7556 (mtpp) REVERT: G 81 ILE cc_start: 0.8244 (mm) cc_final: 0.7994 (mm) REVERT: G 188 ASP cc_start: 0.8362 (m-30) cc_final: 0.8130 (m-30) REVERT: I 7 GLN cc_start: 0.8303 (mm-40) cc_final: 0.7800 (mt0) REVERT: I 21 LYS cc_start: 0.8689 (tttm) cc_final: 0.8410 (tttp) REVERT: I 25 ASP cc_start: 0.9008 (m-30) cc_final: 0.8707 (m-30) REVERT: I 44 LYS cc_start: 0.8406 (mttm) cc_final: 0.7864 (mttt) REVERT: K 7 GLU cc_start: 0.8682 (tt0) cc_final: 0.8388 (tp30) REVERT: K 14 TYR cc_start: 0.8723 (m-80) cc_final: 0.8369 (m-80) REVERT: K 19 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7619 (mt-10) REVERT: K 26 TYR cc_start: 0.8048 (t80) cc_final: 0.7762 (t80) REVERT: K 48 LYS cc_start: 0.7225 (tttt) cc_final: 0.6132 (tmtt) REVERT: K 72 LYS cc_start: 0.8110 (mttt) cc_final: 0.7397 (mmtt) REVERT: K 84 LYS cc_start: 0.7861 (mttp) cc_final: 0.7370 (pttp) REVERT: N 181 MET cc_start: 0.7814 (tpp) cc_final: 0.7527 (tpp) REVERT: R 49 ARG cc_start: 0.7640 (ttm170) cc_final: 0.6401 (tmt170) REVERT: R 63 SER cc_start: 0.7790 (m) cc_final: 0.7509 (t) REVERT: R 85 LYS cc_start: 0.7808 (ptmt) cc_final: 0.7303 (pttm) REVERT: S 90 GLU cc_start: 0.7725 (tt0) cc_final: 0.7502 (tt0) outliers start: 17 outliers final: 10 residues processed: 261 average time/residue: 0.2732 time to fit residues: 98.5814 Evaluate side-chains 246 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 236 time to evaluate : 1.275 ------------------------------------------------------------------------------- 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: 0.7980 chunk 39 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 chunk 90 optimal weight: 0.7980 chunk 118 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 chunk 83 optimal weight: 0.9980 chunk 123 optimal weight: 0.4980 chunk 86 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3796 r_free = 0.3796 target = 0.149271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.102408 restraints weight = 23835.068| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.76 r_work: 0.3079 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3089 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 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 = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3089 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12374 Z= 0.148 Angle : 0.552 7.862 16761 Z= 0.288 Chirality : 0.040 0.145 1974 Planarity : 0.004 0.043 2071 Dihedral : 5.468 65.658 1716 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.52 % Allowed : 11.72 % Favored : 86.76 % 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: 0.78 (0.21), residues: 1559 helix: 1.15 (0.15), residues: 1154 sheet: -1.46 (0.53), residues: 87 loop : -1.02 (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 0.018 0.001 PHE K 24 TYR 0.020 0.001 TYR S 100 ARG 0.002 0.000 ARG G 166 Details of bonding type rmsd hydrogen bonds : bond 0.05196 ( 933) hydrogen bonds : angle 4.37509 ( 2747) covalent geometry : bond 0.00320 (12374) covalent geometry : angle 0.55176 (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 266 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 247 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 66 MET cc_start: 0.7741 (ppp) cc_final: 0.7355 (ppp) REVERT: 5 69 PHE cc_start: 0.7904 (m-10) cc_final: 0.7114 (t80) REVERT: 7 7 LYS cc_start: 0.8346 (mtmt) cc_final: 0.8125 (mttt) REVERT: 7 58 GLU cc_start: 0.7507 (tt0) cc_final: 0.7147 (tt0) REVERT: 7 69 PHE cc_start: 0.8043 (m-10) cc_final: 0.7178 (t80) REVERT: 8 7 LYS cc_start: 0.7837 (mtmt) cc_final: 0.7430 (mtpp) REVERT: G 166 ARG cc_start: 0.8581 (ttp-110) cc_final: 0.8108 (mtm110) REVERT: G 188 ASP cc_start: 0.8371 (m-30) cc_final: 0.8153 (m-30) REVERT: I 7 GLN cc_start: 0.8321 (mm-40) cc_final: 0.7811 (mt0) REVERT: I 21 LYS cc_start: 0.8660 (tttm) cc_final: 0.8392 (tttp) REVERT: I 25 ASP cc_start: 0.9005 (m-30) cc_final: 0.8726 (m-30) REVERT: I 44 LYS cc_start: 0.8350 (mttm) cc_final: 0.7810 (mttt) REVERT: K 14 TYR cc_start: 0.8756 (m-80) cc_final: 0.8427 (m-80) REVERT: K 19 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7505 (mt-10) REVERT: K 26 TYR cc_start: 0.8063 (t80) cc_final: 0.7751 (t80) REVERT: K 48 LYS cc_start: 0.7174 (tttt) cc_final: 0.6130 (tmtt) REVERT: K 72 LYS cc_start: 0.8078 (mttt) cc_final: 0.7378 (mmtt) REVERT: K 84 LYS cc_start: 0.7806 (mttp) cc_final: 0.7308 (pttp) REVERT: N 181 MET cc_start: 0.7902 (tpp) cc_final: 0.7552 (tpp) REVERT: R 49 ARG cc_start: 0.7574 (ttm170) cc_final: 0.6295 (tmt170) REVERT: R 63 SER cc_start: 0.7673 (m) cc_final: 0.7415 (t) REVERT: R 85 LYS cc_start: 0.7720 (ptmt) cc_final: 0.7221 (pttm) REVERT: S 98 ILE cc_start: 0.8059 (mt) cc_final: 0.7850 (mt) outliers start: 19 outliers final: 11 residues processed: 255 average time/residue: 0.2469 time to fit residues: 89.4372 Evaluate side-chains 249 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 238 time to evaluate : 1.171 ------------------------------------------------------------------------------- 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 Q residue 6 THR Chi-restraints excluded: chain R residue 24 GLU Chi-restraints excluded: chain R residue 74 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 78 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 141 optimal weight: 20.0000 chunk 50 optimal weight: 0.3980 chunk 96 optimal weight: 0.9980 chunk 56 optimal weight: 0.0270 chunk 144 optimal weight: 7.9990 chunk 135 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 overall best weight: 0.6842 ------------------------------------------------------------------------------- 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 = 0.3806 r_free = 0.3806 target = 0.150064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.106553 restraints weight = 22082.045| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.80 r_work: 0.3076 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2077 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= 0.139 Angle : 0.537 7.264 16761 Z= 0.279 Chirality : 0.040 0.140 1974 Planarity : 0.004 0.038 2071 Dihedral : 5.278 61.458 1716 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.91 % Allowed : 12.92 % Favored : 85.17 % 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: 1.38 (0.22), residues: 1559 helix: 1.55 (0.15), residues: 1151 sheet: -0.96 (0.57), residues: 85 loop : -0.73 (0.36), residues: 323 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 0.012 0.001 TYR S 100 ARG 0.005 0.000 ARG T 29 Details of bonding type rmsd hydrogen bonds : bond 0.04941 ( 933) hydrogen bonds : angle 4.21542 ( 2747) covalent geometry : bond 0.00298 (12374) covalent geometry : angle 0.53656 (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 266 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 242 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 66 MET cc_start: 0.7806 (ppp) cc_final: 0.7395 (ppp) REVERT: 2 38 ARG cc_start: 0.7749 (mtt180) cc_final: 0.7505 (mpt-90) REVERT: 3 39 ASN cc_start: 0.8189 (t0) cc_final: 0.7806 (t0) REVERT: 4 63 PHE cc_start: 0.7942 (OUTLIER) cc_final: 0.7707 (m-10) REVERT: 4 75 MET cc_start: 0.7323 (mpp) cc_final: 0.6729 (mpp) REVERT: 5 69 PHE cc_start: 0.7947 (m-10) cc_final: 0.7147 (t80) REVERT: 6 75 MET cc_start: 0.7087 (mmp) cc_final: 0.6717 (ptt) REVERT: 7 7 LYS cc_start: 0.8378 (mtmt) cc_final: 0.8170 (mttt) REVERT: 7 58 GLU cc_start: 0.7613 (tt0) cc_final: 0.7277 (tt0) REVERT: 7 69 PHE cc_start: 0.8014 (m-10) cc_final: 0.7191 (t80) REVERT: 8 7 LYS cc_start: 0.7847 (mtmt) cc_final: 0.7419 (mtpp) REVERT: G 87 LYS cc_start: 0.8346 (ptmt) cc_final: 0.7992 (pptt) REVERT: G 113 ARG cc_start: 0.8763 (ttp80) cc_final: 0.8415 (ttp80) REVERT: G 166 ARG cc_start: 0.8593 (ttp-110) cc_final: 0.8176 (mtm110) REVERT: G 188 ASP cc_start: 0.8351 (m-30) cc_final: 0.8127 (m-30) REVERT: I 7 GLN cc_start: 0.8356 (mm-40) cc_final: 0.7850 (mt0) REVERT: I 21 LYS cc_start: 0.8682 (tttm) cc_final: 0.8444 (tttp) REVERT: I 25 ASP cc_start: 0.9008 (m-30) cc_final: 0.8740 (m-30) REVERT: I 44 LYS cc_start: 0.8378 (mttm) cc_final: 0.7837 (mttt) REVERT: K 14 TYR cc_start: 0.8775 (m-80) cc_final: 0.8428 (m-80) REVERT: K 19 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7524 (mt-10) REVERT: K 48 LYS cc_start: 0.7204 (tttt) cc_final: 0.6169 (tmtt) REVERT: K 72 LYS cc_start: 0.8128 (mttt) cc_final: 0.7394 (mmtt) REVERT: K 84 LYS cc_start: 0.7864 (mttp) cc_final: 0.7367 (pttp) REVERT: N 181 MET cc_start: 0.8009 (tpp) cc_final: 0.7668 (tpp) REVERT: P 39 ARG cc_start: 0.8487 (mtm180) cc_final: 0.8181 (mmm-85) REVERT: R 49 ARG cc_start: 0.7622 (ttm170) cc_final: 0.6378 (tmt170) REVERT: R 63 SER cc_start: 0.7794 (m) cc_final: 0.7516 (t) REVERT: R 85 LYS cc_start: 0.7763 (ptmt) cc_final: 0.7263 (pttm) outliers start: 24 outliers final: 15 residues processed: 252 average time/residue: 0.2435 time to fit residues: 87.2408 Evaluate side-chains 252 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 236 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 63 PHE 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 G residue 123 GLN Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain I residue 41 SER Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain N residue 140 MET Chi-restraints excluded: chain N residue 150 LEU Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain R residue 24 GLU Chi-restraints excluded: chain R residue 74 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 49 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 139 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.149079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.104768 restraints weight = 17177.497| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.39 r_work: 0.3115 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12374 Z= 0.154 Angle : 0.542 7.717 16761 Z= 0.281 Chirality : 0.040 0.139 1974 Planarity : 0.004 0.035 2071 Dihedral : 5.218 57.579 1716 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.15 % Allowed : 13.88 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.58 (0.22), residues: 1559 helix: 1.69 (0.15), residues: 1155 sheet: -0.84 (0.58), residues: 83 loop : -0.68 (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 0.021 0.001 PHE K 24 TYR 0.013 0.001 TYR G 44 ARG 0.002 0.000 ARG G 166 Details of bonding type rmsd hydrogen bonds : bond 0.04982 ( 933) hydrogen bonds : angle 4.17949 ( 2747) covalent geometry : bond 0.00346 (12374) covalent geometry : angle 0.54195 (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 269 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 242 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 66 MET cc_start: 0.7845 (ppp) cc_final: 0.7395 (ppp) REVERT: 2 31 SER cc_start: 0.8663 (m) cc_final: 0.8166 (p) REVERT: 3 39 ASN cc_start: 0.8222 (t0) cc_final: 0.7816 (t0) REVERT: 5 69 PHE cc_start: 0.7927 (m-10) cc_final: 0.7131 (t80) REVERT: 6 75 MET cc_start: 0.7062 (mmp) cc_final: 0.6817 (ptt) REVERT: 7 7 LYS cc_start: 0.8394 (mtmt) cc_final: 0.8181 (mttt) REVERT: 7 58 GLU cc_start: 0.7578 (tt0) cc_final: 0.7255 (tt0) REVERT: 7 69 PHE cc_start: 0.7983 (m-10) cc_final: 0.7184 (t80) REVERT: 8 7 LYS cc_start: 0.7871 (mtmt) cc_final: 0.7430 (mtpp) REVERT: G 87 LYS cc_start: 0.8388 (ptmt) cc_final: 0.8007 (pptt) REVERT: G 113 ARG cc_start: 0.8760 (ttp80) cc_final: 0.8481 (ttp80) REVERT: G 153 TYR cc_start: 0.7046 (t80) cc_final: 0.6821 (t80) REVERT: G 166 ARG cc_start: 0.8577 (ttp-110) cc_final: 0.8156 (mtm110) REVERT: G 188 ASP cc_start: 0.8357 (m-30) cc_final: 0.8151 (m-30) REVERT: I 7 GLN cc_start: 0.8336 (mm-40) cc_final: 0.7826 (mt0) REVERT: I 21 LYS cc_start: 0.8676 (tttm) cc_final: 0.8438 (tttp) REVERT: I 25 ASP cc_start: 0.9004 (m-30) cc_final: 0.8659 (m-30) REVERT: I 36 GLU cc_start: 0.8385 (mt-10) cc_final: 0.7964 (tm-30) REVERT: I 44 LYS cc_start: 0.8404 (mttm) cc_final: 0.7863 (mttt) REVERT: K 14 TYR cc_start: 0.8753 (m-80) cc_final: 0.8425 (m-80) REVERT: K 19 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7592 (mt-10) REVERT: K 48 LYS cc_start: 0.7242 (tttt) cc_final: 0.6207 (tmtt) REVERT: K 72 LYS cc_start: 0.8067 (mttt) cc_final: 0.7367 (mmtt) REVERT: K 84 LYS cc_start: 0.7851 (mttp) cc_final: 0.7358 (pttp) REVERT: N 181 MET cc_start: 0.8139 (tpp) cc_final: 0.7806 (tpp) REVERT: P 39 ARG cc_start: 0.8517 (mtm180) cc_final: 0.8280 (mmm-85) REVERT: R 49 ARG cc_start: 0.7621 (ttm170) cc_final: 0.6379 (tmt170) REVERT: R 63 SER cc_start: 0.7804 (m) cc_final: 0.7520 (t) REVERT: R 85 LYS cc_start: 0.7822 (ptmt) cc_final: 0.7317 (pttm) outliers start: 27 outliers final: 17 residues processed: 254 average time/residue: 0.2440 time to fit residues: 87.9770 Evaluate side-chains 262 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 245 time to evaluate : 1.349 ------------------------------------------------------------------------------- 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 123 GLN Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain I residue 41 SER Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain N residue 140 MET Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain R residue 24 GLU Chi-restraints excluded: chain R residue 74 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 95 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 138 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 58 optimal weight: 0.2980 chunk 60 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3774 r_free = 0.3774 target = 0.148094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.106416 restraints weight = 22576.958| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.71 r_work: 0.3058 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3057 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.090 | | 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) = 0.090 | | 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: 0.8147 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12374 Z= 0.140 Angle : 0.534 8.097 16761 Z= 0.275 Chirality : 0.040 0.150 1974 Planarity : 0.004 0.104 2071 Dihedral : 5.142 53.830 1716 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.39 % Allowed : 14.99 % 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: 1.70 (0.22), residues: 1559 helix: 1.96 (0.15), residues: 1113 sheet: -0.96 (0.57), residues: 85 loop : -0.96 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 28 HIS 0.003 0.001 HIS H 51 PHE 0.023 0.001 PHE K 24 TYR 0.012 0.001 TYR R 51 ARG 0.005 0.000 ARG N 41 Details of bonding type rmsd hydrogen bonds : bond 0.04818 ( 933) hydrogen bonds : angle 4.12152 ( 2747) covalent geometry : bond 0.00309 (12374) covalent geometry : angle 0.53436 (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 282 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 252 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 66 MET cc_start: 0.7983 (ppp) cc_final: 0.7417 (ppp) REVERT: 2 31 SER cc_start: 0.8785 (m) cc_final: 0.8399 (p) REVERT: 2 38 ARG cc_start: 0.7912 (mtt180) cc_final: 0.7677 (mpt-90) REVERT: 3 39 ASN cc_start: 0.8239 (t0) cc_final: 0.7898 (t0) REVERT: 4 75 MET cc_start: 0.7247 (mpp) cc_final: 0.6565 (mpp) REVERT: 5 69 PHE cc_start: 0.8006 (m-10) cc_final: 0.7251 (t80) REVERT: 5 75 MET cc_start: 0.5085 (ptt) cc_final: 0.4401 (ptp) REVERT: 6 75 MET cc_start: 0.7029 (mmp) cc_final: 0.6776 (ptt) REVERT: 7 7 LYS cc_start: 0.8530 (mtmt) cc_final: 0.8304 (mttt) REVERT: 7 69 PHE cc_start: 0.8041 (m-10) cc_final: 0.7280 (t80) REVERT: 8 7 LYS cc_start: 0.8052 (mtmt) cc_final: 0.7602 (mtpp) REVERT: G 87 LYS cc_start: 0.8337 (ptmt) cc_final: 0.7992 (pptt) REVERT: G 166 ARG cc_start: 0.8562 (ttp-110) cc_final: 0.8227 (mtm110) REVERT: I 7 GLN cc_start: 0.8401 (mm-40) cc_final: 0.7893 (mt0) REVERT: I 21 LYS cc_start: 0.8767 (tttm) cc_final: 0.8553 (tttp) REVERT: I 25 ASP cc_start: 0.8999 (m-30) cc_final: 0.8682 (m-30) REVERT: I 36 GLU cc_start: 0.8354 (mt-10) cc_final: 0.8008 (tm-30) REVERT: I 44 LYS cc_start: 0.8570 (mttm) cc_final: 0.8066 (mttt) REVERT: K 14 TYR cc_start: 0.8811 (m-80) cc_final: 0.8550 (m-80) REVERT: K 19 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7756 (mt-10) REVERT: K 48 LYS cc_start: 0.7488 (tttt) cc_final: 0.6395 (tmtt) REVERT: K 72 LYS cc_start: 0.8299 (mttt) cc_final: 0.7606 (mmtt) REVERT: K 84 LYS cc_start: 0.8038 (mttp) cc_final: 0.7592 (pttp) REVERT: N 58 MET cc_start: 0.8846 (mmm) cc_final: 0.8624 (mmm) REVERT: P 39 ARG cc_start: 0.8590 (mtm180) cc_final: 0.8381 (mmm-85) REVERT: R 49 ARG cc_start: 0.7895 (ttm170) cc_final: 0.6656 (tmt170) REVERT: R 63 SER cc_start: 0.8104 (m) cc_final: 0.7858 (t) REVERT: R 85 LYS cc_start: 0.7912 (ptmt) cc_final: 0.7419 (pttm) outliers start: 30 outliers final: 19 residues processed: 266 average time/residue: 0.2393 time to fit residues: 90.4604 Evaluate side-chains 263 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 244 time to evaluate : 1.254 ------------------------------------------------------------------------------- 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 6 residue 58 GLU Chi-restraints excluded: chain 6 residue 70 LEU Chi-restraints excluded: chain 7 residue 18 VAL Chi-restraints excluded: chain 8 residue 67 VAL Chi-restraints excluded: chain 8 residue 71 ILE Chi-restraints excluded: chain G residue 123 GLN Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain I residue 41 SER Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain N residue 140 MET Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain R residue 24 GLU Chi-restraints excluded: chain R residue 74 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 79 optimal weight: 0.2980 chunk 18 optimal weight: 0.0060 chunk 101 optimal weight: 3.9990 chunk 112 optimal weight: 0.0030 chunk 10 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 90 optimal weight: 0.0980 chunk 109 optimal weight: 0.0010 chunk 61 optimal weight: 5.9990 chunk 137 optimal weight: 0.8980 overall best weight: 0.0812 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.152680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.109790 restraints weight = 14972.190| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.99 r_work: 0.3196 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3059 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3059 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12374 Z= 0.117 Angle : 0.522 9.767 16761 Z= 0.267 Chirality : 0.039 0.141 1974 Planarity : 0.004 0.064 2071 Dihedral : 5.017 51.816 1716 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.75 % Allowed : 16.35 % Favored : 81.90 % 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: 1.96 (0.22), residues: 1559 helix: 2.14 (0.15), residues: 1111 sheet: -0.65 (0.59), residues: 81 loop : -0.89 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 28 HIS 0.002 0.000 HIS G 66 PHE 0.021 0.001 PHE 1 69 TYR 0.011 0.001 TYR R 51 ARG 0.005 0.000 ARG T 29 Details of bonding type rmsd hydrogen bonds : bond 0.04378 ( 933) hydrogen bonds : angle 3.97970 ( 2747) covalent geometry : bond 0.00225 (12374) covalent geometry : angle 0.52225 (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 278 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 256 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 66 MET cc_start: 0.7868 (ppp) cc_final: 0.7409 (ppp) REVERT: 2 38 ARG cc_start: 0.7842 (mtt180) cc_final: 0.7625 (mpt-90) REVERT: 4 75 MET cc_start: 0.7289 (mpp) cc_final: 0.6704 (mpp) REVERT: 5 69 PHE cc_start: 0.8021 (m-10) cc_final: 0.7259 (t80) REVERT: 5 75 MET cc_start: 0.5154 (ptt) cc_final: 0.4474 (ptp) REVERT: 6 75 MET cc_start: 0.7080 (mmp) cc_final: 0.6766 (ptt) REVERT: 7 7 LYS cc_start: 0.8462 (mtmt) cc_final: 0.8258 (mttt) REVERT: 7 69 PHE cc_start: 0.8021 (m-10) cc_final: 0.7258 (t80) REVERT: 8 7 LYS cc_start: 0.8006 (mtmt) cc_final: 0.7609 (mtpp) REVERT: G 46 LEU cc_start: 0.8535 (mt) cc_final: 0.8268 (mt) REVERT: G 87 LYS cc_start: 0.8350 (ptmt) cc_final: 0.8049 (pptt) REVERT: G 166 ARG cc_start: 0.8566 (ttp-110) cc_final: 0.8274 (mtm110) REVERT: I 7 GLN cc_start: 0.8426 (mm-40) cc_final: 0.7913 (mt0) REVERT: I 44 LYS cc_start: 0.8557 (mttm) cc_final: 0.8046 (mttt) REVERT: K 14 TYR cc_start: 0.8789 (m-80) cc_final: 0.8523 (m-80) REVERT: K 19 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7763 (mt-10) REVERT: K 48 LYS cc_start: 0.7481 (tttt) cc_final: 0.6431 (tmtt) REVERT: K 72 LYS cc_start: 0.8293 (mttt) cc_final: 0.7614 (mmtt) REVERT: R 49 ARG cc_start: 0.7855 (ttm170) cc_final: 0.6621 (tmt170) REVERT: R 85 LYS cc_start: 0.7878 (ptmt) cc_final: 0.7403 (pttm) REVERT: S 71 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7510 (pm20) outliers start: 22 outliers final: 14 residues processed: 267 average time/residue: 0.2477 time to fit residues: 93.0313 Evaluate side-chains 258 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 243 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 7 residue 18 VAL Chi-restraints excluded: chain 8 residue 67 VAL Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain N residue 140 MET Chi-restraints excluded: chain R residue 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: 1.9990 chunk 75 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 46 optimal weight: 0.0010 chunk 123 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 17 GLN N 163 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.150063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.109423 restraints weight = 23959.230| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.84 r_work: 0.3093 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2722 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= 0.133 Angle : 0.543 7.748 16761 Z= 0.276 Chirality : 0.040 0.208 1974 Planarity : 0.004 0.052 2071 Dihedral : 4.981 47.653 1716 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.99 % Allowed : 16.83 % Favored : 81.18 % 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: 2.02 (0.22), residues: 1559 helix: 2.19 (0.15), residues: 1112 sheet: -0.74 (0.59), residues: 85 loop : -0.82 (0.34), residues: 362 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 0.020 0.001 PHE K 24 TYR 0.012 0.001 TYR R 51 ARG 0.008 0.001 ARG P 39 Details of bonding type rmsd hydrogen bonds : bond 0.04560 ( 933) hydrogen bonds : angle 4.00307 ( 2747) covalent geometry : bond 0.00290 (12374) covalent geometry : angle 0.54343 (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 274 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 249 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 66 MET cc_start: 0.7962 (ppp) cc_final: 0.7450 (ppp) REVERT: 2 38 ARG cc_start: 0.7884 (mtt180) cc_final: 0.7620 (mpt-90) REVERT: 4 65 LEU cc_start: 0.7731 (mm) cc_final: 0.7525 (mt) REVERT: 4 75 MET cc_start: 0.7274 (mpp) cc_final: 0.6673 (mpp) REVERT: 5 69 PHE cc_start: 0.8036 (m-10) cc_final: 0.7260 (t80) REVERT: 5 75 MET cc_start: 0.5082 (ptt) cc_final: 0.4400 (ptp) REVERT: 6 75 MET cc_start: 0.7017 (mmp) cc_final: 0.6737 (ptt) REVERT: 7 69 PHE cc_start: 0.8025 (m-10) cc_final: 0.7277 (t80) REVERT: 8 7 LYS cc_start: 0.8031 (mtmt) cc_final: 0.7580 (mtpp) REVERT: G 46 LEU cc_start: 0.8556 (mt) cc_final: 0.8286 (mt) REVERT: G 87 LYS cc_start: 0.8344 (ptmt) cc_final: 0.8032 (pptt) REVERT: G 110 ASP cc_start: 0.8030 (t0) cc_final: 0.7278 (t0) REVERT: G 113 ARG cc_start: 0.8778 (ttp80) cc_final: 0.8542 (ttp80) REVERT: G 166 ARG cc_start: 0.8520 (ttp-110) cc_final: 0.8245 (mtm110) REVERT: I 7 GLN cc_start: 0.8403 (mm-40) cc_final: 0.7870 (mt0) REVERT: I 25 ASP cc_start: 0.8890 (m-30) cc_final: 0.8668 (m-30) REVERT: I 44 LYS cc_start: 0.8628 (mttm) cc_final: 0.8120 (mttt) REVERT: K 14 TYR cc_start: 0.8753 (m-80) cc_final: 0.8446 (m-80) REVERT: K 19 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7740 (mt-10) REVERT: K 48 LYS cc_start: 0.7490 (tttt) cc_final: 0.6410 (tmtt) REVERT: K 72 LYS cc_start: 0.8290 (mttt) cc_final: 0.7606 (mmtt) REVERT: P 39 ARG cc_start: 0.8385 (mmm-85) cc_final: 0.8120 (mmm-85) REVERT: R 31 MET cc_start: 0.6364 (ttt) cc_final: 0.6116 (tpp) REVERT: R 49 ARG cc_start: 0.7872 (ttm170) cc_final: 0.6642 (tmt170) REVERT: R 63 SER cc_start: 0.8111 (m) cc_final: 0.7868 (t) REVERT: R 85 LYS cc_start: 0.7954 (ptmt) cc_final: 0.7470 (pttm) REVERT: S 71 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7453 (pm20) outliers start: 25 outliers final: 16 residues processed: 261 average time/residue: 0.2508 time to fit residues: 92.3042 Evaluate side-chains 260 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 243 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 63 PHE Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 4 residue 66 MET Chi-restraints excluded: chain 5 residue 18 VAL Chi-restraints excluded: chain 5 residue 31 SER Chi-restraints excluded: chain 6 residue 58 GLU Chi-restraints excluded: chain 6 residue 70 LEU Chi-restraints excluded: chain 7 residue 18 VAL Chi-restraints excluded: chain 8 residue 67 VAL Chi-restraints excluded: chain 8 residue 71 ILE Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain N residue 140 MET Chi-restraints excluded: chain R residue 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: 0.9980 chunk 126 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 127 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3806 r_free = 0.3806 target = 0.149510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.108775 restraints weight = 24912.657| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 3.20 r_work: 0.3071 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3077 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 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 = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3077 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12374 Z= 0.149 Angle : 0.554 8.920 16761 Z= 0.282 Chirality : 0.040 0.183 1974 Planarity : 0.004 0.049 2071 Dihedral : 5.007 45.290 1716 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.99 % Allowed : 17.07 % 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: 1.99 (0.22), residues: 1559 helix: 2.16 (0.15), residues: 1113 sheet: -0.92 (0.58), residues: 86 loop : -0.78 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 28 HIS 0.004 0.001 HIS H 51 PHE 0.020 0.001 PHE K 24 TYR 0.013 0.001 TYR G 44 ARG 0.008 0.001 ARG G 36 Details of bonding type rmsd hydrogen bonds : bond 0.04735 ( 933) hydrogen bonds : angle 4.02230 ( 2747) covalent geometry : bond 0.00337 (12374) covalent geometry : angle 0.55432 (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 269 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 244 time to evaluate : 1.682 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 66 MET cc_start: 0.8009 (ppp) cc_final: 0.7485 (ppp) REVERT: 2 31 SER cc_start: 0.8913 (m) cc_final: 0.8551 (p) REVERT: 2 38 ARG cc_start: 0.7995 (mtt180) cc_final: 0.7707 (mpt-90) REVERT: 3 39 ASN cc_start: 0.8224 (t0) cc_final: 0.7934 (t0) REVERT: 4 65 LEU cc_start: 0.7918 (mm) cc_final: 0.7689 (mt) REVERT: 4 75 MET cc_start: 0.7353 (mpp) cc_final: 0.6765 (mpp) REVERT: 5 69 PHE cc_start: 0.8089 (m-10) cc_final: 0.7330 (t80) REVERT: 5 75 MET cc_start: 0.5132 (ptt) cc_final: 0.4572 (ptp) REVERT: 6 75 MET cc_start: 0.7070 (mmp) cc_final: 0.6804 (ptt) REVERT: 7 69 PHE cc_start: 0.8063 (m-10) cc_final: 0.7274 (t80) REVERT: 8 7 LYS cc_start: 0.8133 (mtmt) cc_final: 0.7678 (mtpp) REVERT: G 36 ARG cc_start: 0.9007 (mtm110) cc_final: 0.8711 (ptm160) REVERT: G 87 LYS cc_start: 0.8370 (ptmt) cc_final: 0.8059 (pptt) REVERT: G 110 ASP cc_start: 0.8032 (t0) cc_final: 0.7449 (t0) REVERT: G 113 ARG cc_start: 0.8789 (ttp80) cc_final: 0.8546 (ttp80) REVERT: G 166 ARG cc_start: 0.8540 (ttp-110) cc_final: 0.8283 (mtm110) REVERT: G 188 ASP cc_start: 0.8168 (m-30) cc_final: 0.7523 (t0) REVERT: H 111 ASN cc_start: 0.7636 (t0) cc_final: 0.7155 (m110) REVERT: I 7 GLN cc_start: 0.8427 (mm-40) cc_final: 0.7889 (mt0) REVERT: I 25 ASP cc_start: 0.8928 (m-30) cc_final: 0.8718 (m-30) REVERT: I 44 LYS cc_start: 0.8700 (mttm) cc_final: 0.8202 (mttt) REVERT: K 14 TYR cc_start: 0.8811 (m-80) cc_final: 0.8495 (m-80) REVERT: K 19 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7814 (mt-10) REVERT: K 48 LYS cc_start: 0.7626 (tttt) cc_final: 0.6496 (tmtt) REVERT: K 72 LYS cc_start: 0.8362 (mttt) cc_final: 0.7655 (mmtt) REVERT: P 39 ARG cc_start: 0.8443 (mmm-85) cc_final: 0.8240 (mmm-85) REVERT: R 32 ARG cc_start: 0.6084 (mmp-170) cc_final: 0.5787 (mmm-85) REVERT: R 49 ARG cc_start: 0.7990 (ttm170) cc_final: 0.6773 (tmt170) REVERT: R 63 SER cc_start: 0.8228 (m) cc_final: 0.8013 (t) REVERT: R 85 LYS cc_start: 0.7963 (ptmt) cc_final: 0.7470 (pttm) outliers start: 25 outliers final: 17 residues processed: 256 average time/residue: 0.2551 time to fit residues: 93.1970 Evaluate side-chains 257 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 240 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 63 PHE Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 4 residue 66 MET Chi-restraints excluded: chain 5 residue 18 VAL Chi-restraints excluded: chain 5 residue 31 SER Chi-restraints excluded: chain 6 residue 58 GLU Chi-restraints excluded: chain 6 residue 70 LEU Chi-restraints excluded: chain 8 residue 67 VAL Chi-restraints excluded: chain 8 residue 71 ILE Chi-restraints excluded: chain G residue 123 GLN Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain I residue 41 SER Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain N residue 140 MET Chi-restraints excluded: chain R residue 74 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 41 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 56 optimal weight: 0.0030 chunk 146 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 overall best weight: 0.7190 ------------------------------------------------------------------------------- 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 = 0.3815 r_free = 0.3815 target = 0.150271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.107662 restraints weight = 20101.601| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.51 r_work: 0.3154 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3167 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12374 Z= 0.139 Angle : 0.551 10.223 16761 Z= 0.279 Chirality : 0.040 0.184 1974 Planarity : 0.004 0.047 2071 Dihedral : 5.016 43.587 1716 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.52 % Allowed : 17.38 % Favored : 81.10 % 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: 2.03 (0.22), residues: 1559 helix: 2.18 (0.15), residues: 1111 sheet: -0.86 (0.58), residues: 86 loop : -0.74 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 28 HIS 0.004 0.001 HIS N 61 PHE 0.019 0.001 PHE K 24 TYR 0.013 0.001 TYR G 44 ARG 0.007 0.001 ARG G 36 Details of bonding type rmsd hydrogen bonds : bond 0.04656 ( 933) hydrogen bonds : angle 4.01851 ( 2747) covalent geometry : bond 0.00307 (12374) covalent geometry : angle 0.55147 (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 258 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 239 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 66 MET cc_start: 0.7991 (ppp) cc_final: 0.7445 (ppp) REVERT: 2 31 SER cc_start: 0.8832 (m) cc_final: 0.8483 (p) REVERT: 3 39 ASN cc_start: 0.8160 (t0) cc_final: 0.7865 (t0) REVERT: 4 65 LEU cc_start: 0.7835 (mm) cc_final: 0.7618 (mt) REVERT: 4 75 MET cc_start: 0.7253 (mpp) cc_final: 0.6662 (mpp) REVERT: 5 69 PHE cc_start: 0.8057 (m-10) cc_final: 0.7320 (t80) REVERT: 5 75 MET cc_start: 0.5116 (ptt) cc_final: 0.4481 (ptp) REVERT: 6 75 MET cc_start: 0.6985 (mmp) cc_final: 0.6782 (ptt) REVERT: 7 69 PHE cc_start: 0.8035 (m-10) cc_final: 0.7258 (t80) REVERT: 8 7 LYS cc_start: 0.8109 (mtmt) cc_final: 0.7661 (mtpp) REVERT: G 36 ARG cc_start: 0.8943 (mtm110) cc_final: 0.8672 (ptm160) REVERT: G 87 LYS cc_start: 0.8350 (ptmt) cc_final: 0.8052 (pptt) REVERT: G 110 ASP cc_start: 0.7977 (t0) cc_final: 0.7393 (t0) REVERT: G 113 ARG cc_start: 0.8774 (ttp80) cc_final: 0.8543 (ttp80) REVERT: G 166 ARG cc_start: 0.8472 (ttp-110) cc_final: 0.8220 (mtm110) REVERT: G 188 ASP cc_start: 0.8049 (m-30) cc_final: 0.7457 (t0) REVERT: I 7 GLN cc_start: 0.8413 (mm-40) cc_final: 0.7893 (mt0) REVERT: I 25 ASP cc_start: 0.8856 (m-30) cc_final: 0.8629 (m-30) REVERT: I 44 LYS cc_start: 0.8699 (mttm) cc_final: 0.8196 (mttt) REVERT: K 14 TYR cc_start: 0.8756 (m-80) cc_final: 0.8399 (m-80) REVERT: K 19 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7775 (mt-10) REVERT: K 48 LYS cc_start: 0.7574 (tttt) cc_final: 0.6467 (tmtt) REVERT: K 72 LYS cc_start: 0.8303 (mttt) cc_final: 0.7608 (mmtt) REVERT: R 49 ARG cc_start: 0.7932 (ttm170) cc_final: 0.6718 (tmt170) REVERT: R 63 SER cc_start: 0.8159 (m) cc_final: 0.7934 (t) REVERT: R 85 LYS cc_start: 0.7949 (ptmt) cc_final: 0.7458 (pttm) outliers start: 19 outliers final: 16 residues processed: 248 average time/residue: 0.2663 time to fit residues: 94.6527 Evaluate side-chains 254 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 238 time to evaluate : 1.705 ------------------------------------------------------------------------------- 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 8 residue 71 ILE Chi-restraints excluded: chain G residue 123 GLN Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain I residue 41 SER Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain N residue 140 MET Chi-restraints excluded: chain R residue 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: 3.9990 chunk 64 optimal weight: 3.9990 chunk 134 optimal weight: 10.0000 chunk 42 optimal weight: 0.0270 chunk 126 optimal weight: 3.9990 chunk 135 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 overall best weight: 0.7438 ------------------------------------------------------------------------------- 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 = 0.3813 r_free = 0.3813 target = 0.149991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.107817 restraints weight = 19364.464| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.42 r_work: 0.3157 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3167 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2793 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= 0.140 Angle : 0.564 11.335 16761 Z= 0.283 Chirality : 0.040 0.185 1974 Planarity : 0.004 0.046 2071 Dihedral : 5.010 45.130 1716 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.59 % Allowed : 17.22 % Favored : 81.18 % 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: 2.10 (0.22), residues: 1559 helix: 2.10 (0.15), residues: 1135 sheet: -0.84 (0.58), residues: 86 loop : -0.41 (0.36), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 28 HIS 0.004 0.001 HIS N 61 PHE 0.020 0.001 PHE 1 69 TYR 0.013 0.001 TYR G 44 ARG 0.007 0.001 ARG P 39 Details of bonding type rmsd hydrogen bonds : bond 0.04656 ( 933) hydrogen bonds : angle 4.00925 ( 2747) covalent geometry : bond 0.00313 (12374) covalent geometry : angle 0.56441 (16761) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7405.97 seconds wall clock time: 128 minutes 49.34 seconds (7729.34 seconds total)