Starting phenix.real_space_refine on Mon Jun 16 13:56:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vwh_43586/06_2025/8vwh_43586.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vwh_43586/06_2025/8vwh_43586.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vwh_43586/06_2025/8vwh_43586.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vwh_43586/06_2025/8vwh_43586.map" model { file = "/net/cci-nas-00/data/ceres_data/8vwh_43586/06_2025/8vwh_43586.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vwh_43586/06_2025/8vwh_43586.cif" } resolution = 3.06 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= 0.005 sd= 0.066 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 Zn 7 6.06 5 S 98 5.16 5 C 11917 2.51 5 N 3309 2.21 5 O 3558 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18889 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2353 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 13, 'TRANS': 276} Chain breaks: 2 Chain: "C" Number of atoms: 2353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2353 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 13, 'TRANS': 276} Chain breaks: 2 Chain: "E" Number of atoms: 2293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2293 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 12, 'TRANS': 270} Chain breaks: 2 Chain: "G" Number of atoms: 2412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2412 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 284} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 2353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2353 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 13, 'TRANS': 276} Chain breaks: 2 Chain: "K" Number of atoms: 2353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2353 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 13, 'TRANS': 276} Chain breaks: 2 Chain: "M" Number of atoms: 2412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2412 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 284} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 2353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2353 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 13, 'TRANS': 276} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 32 SG CYS A 18 46.844 97.936 45.089 1.00 59.84 S ATOM 107 SG CYS A 36 50.259 97.420 43.372 1.00 79.76 S ATOM 214 SG CYS A 49 47.785 100.009 41.949 1.00 64.23 S ATOM 2385 SG CYS C 18 38.149 145.254 30.922 1.00 65.17 S ATOM 2460 SG CYS C 36 41.461 146.740 32.328 1.00 64.21 S ATOM 2567 SG CYS C 49 40.150 143.383 33.696 1.00 68.46 S ATOM 4738 SG CYS E 18 77.894 37.691 87.683 1.00 39.87 S ATOM 4813 SG CYS E 36 80.807 39.775 85.927 1.00 62.50 S ATOM 4920 SG CYS E 49 78.106 41.242 87.645 1.00 57.10 S ATOM 7031 SG CYS G 18 54.041 79.691 74.311 1.00 80.91 S ATOM 7165 SG CYS G 36 56.989 81.484 76.182 1.00 69.88 S ATOM 7272 SG CYS G 49 57.026 77.847 75.592 1.00 86.05 S ATOM 9443 SG CYS I 18 63.228 58.881 130.787 1.00 46.90 S ATOM 9518 SG CYS I 36 66.793 60.231 130.037 1.00 65.01 S ATOM 9625 SG CYS I 49 63.843 61.575 128.047 1.00 65.59 S ATOM 11796 SG CYS K 18 45.223 103.721 116.850 1.00 67.35 S ATOM 11871 SG CYS K 36 47.832 105.829 118.809 1.00 89.66 S ATOM 11978 SG CYS K 49 47.128 102.218 119.897 1.00 77.59 S ATOM 14149 SG CYS M 18 40.969 123.520 87.866 1.00 56.94 S ATOM 14283 SG CYS M 36 44.608 123.646 86.622 1.00 83.64 S ATOM 14390 SG CYS M 49 41.872 125.376 84.549 1.00 67.57 S Time building chain proxies: 10.60, per 1000 atoms: 0.56 Number of scatterers: 18889 At special positions: 0 Unit cell: (103.74, 208.81, 163.59, 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) Zn 7 29.99 S 98 16.00 O 3558 8.00 N 3309 7.00 C 11917 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 132 " - pdb=" SG CYS G 169 " distance=2.03 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS G 132 " distance=2.03 Simple disulfide: pdb=" SG CYS A 229 " - pdb=" SG CYS C 229 " distance=2.03 Simple disulfide: pdb=" SG CYS E 229 " - pdb=" SG CYS G 229 " distance=2.03 Simple disulfide: pdb=" SG CYS G 29 " - pdb=" SG CYS M 29 " distance=2.03 Simple disulfide: pdb=" SG CYS I 229 " - pdb=" SG CYS K 229 " distance=2.04 Simple disulfide: pdb=" SG CYS K 132 " - pdb=" SG CYS M 169 " distance=2.03 Simple disulfide: pdb=" SG CYS K 169 " - pdb=" SG CYS M 132 " distance=2.04 Simple disulfide: pdb=" SG CYS M 229 " - pdb=" SG CYS O 229 " distance=2.03 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: 4.19 Conformation dependent library (CDL) restraints added in 2.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" ND1 HIS A 52 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 18 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 36 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 49 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" ND1 HIS C 52 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 36 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 18 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 49 " pdb=" ZN E 401 " pdb="ZN ZN E 401 " - pdb=" ND1 HIS E 52 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 49 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 18 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 36 " pdb=" ZN G 401 " pdb="ZN ZN G 401 " - pdb=" ND1 HIS G 52 " pdb="ZN ZN G 401 " - pdb=" SG CYS G 49 " pdb="ZN ZN G 401 " - pdb=" SG CYS G 18 " pdb="ZN ZN G 401 " - pdb=" SG CYS G 36 " pdb=" ZN I 401 " pdb="ZN ZN I 401 " - pdb=" ND1 HIS I 52 " pdb="ZN ZN I 401 " - pdb=" SG CYS I 49 " pdb="ZN ZN I 401 " - pdb=" SG CYS I 36 " pdb="ZN ZN I 401 " - pdb=" SG CYS I 18 " pdb=" ZN K 401 " pdb="ZN ZN K 401 " - pdb=" ND1 HIS K 52 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 49 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 36 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 18 " pdb=" ZN M 401 " pdb="ZN ZN M 401 " - pdb=" ND1 HIS M 52 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 36 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 18 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 49 " Number of angles added : 21 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4450 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 28 sheets defined 37.7% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'A' and resid 18 through 23 removed outlier: 4.083A pdb=" N SER A 22 " --> pdb=" O ILE A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 41 Processing helix chain 'A' and resid 49 through 58 removed outlier: 3.737A pdb=" N LYS A 58 " --> pdb=" O ILE A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 91 removed outlier: 3.716A pdb=" N LYS A 91 " --> pdb=" O ARG A 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 88 through 91' Processing helix chain 'A' and resid 100 through 106 removed outlier: 3.517A pdb=" N ASN A 106 " --> pdb=" O GLN A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 122 Processing helix chain 'A' and resid 124 through 135 Processing helix chain 'A' and resid 145 through 164 Processing helix chain 'A' and resid 184 through 188 Processing helix chain 'A' and resid 191 through 199 removed outlier: 3.973A pdb=" N ASN A 199 " --> pdb=" O GLN A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 212 Processing helix chain 'A' and resid 278 through 285 Processing helix chain 'C' and resid 37 through 41 Processing helix chain 'C' and resid 49 through 58 removed outlier: 3.674A pdb=" N LYS C 58 " --> pdb=" O ILE C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 91 removed outlier: 3.694A pdb=" N LYS C 91 " --> pdb=" O ARG C 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 88 through 91' Processing helix chain 'C' and resid 100 through 106 removed outlier: 3.520A pdb=" N VAL C 104 " --> pdb=" O ASN C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 110 Processing helix chain 'C' and resid 111 through 122 Processing helix chain 'C' and resid 124 through 137 removed outlier: 3.581A pdb=" N LEU C 135 " --> pdb=" O ILE C 131 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TYR C 137 " --> pdb=" O ASP C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 163 Processing helix chain 'C' and resid 184 through 188 Processing helix chain 'C' and resid 191 through 199 removed outlier: 3.696A pdb=" N ASN C 199 " --> pdb=" O GLN C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 212 Processing helix chain 'C' and resid 278 through 285 Processing helix chain 'E' and resid 18 through 22 removed outlier: 4.358A pdb=" N SER E 22 " --> pdb=" O ILE E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 58 removed outlier: 3.563A pdb=" N LYS E 58 " --> pdb=" O ILE E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 91 Processing helix chain 'E' and resid 101 through 106 removed outlier: 3.893A pdb=" N ASN E 106 " --> pdb=" O GLN E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 110 Processing helix chain 'E' and resid 111 through 122 removed outlier: 4.142A pdb=" N HIS E 119 " --> pdb=" O GLN E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 137 removed outlier: 3.916A pdb=" N TYR E 137 " --> pdb=" O ASP E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 164 removed outlier: 3.698A pdb=" N THR E 155 " --> pdb=" O SER E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 188 Processing helix chain 'E' and resid 191 through 199 removed outlier: 3.575A pdb=" N ASN E 199 " --> pdb=" O GLN E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 212 Processing helix chain 'E' and resid 279 through 285 Processing helix chain 'G' and resid 37 through 41 Processing helix chain 'G' and resid 49 through 56 Processing helix chain 'G' and resid 88 through 91 Processing helix chain 'G' and resid 100 through 106 Processing helix chain 'G' and resid 107 through 110 Processing helix chain 'G' and resid 111 through 122 Processing helix chain 'G' and resid 124 through 135 removed outlier: 3.549A pdb=" N LEU G 135 " --> pdb=" O ILE G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 144 removed outlier: 4.383A pdb=" N SER G 143 " --> pdb=" O GLU G 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 164 Processing helix chain 'G' and resid 184 through 188 Processing helix chain 'G' and resid 191 through 200 removed outlier: 3.675A pdb=" N ASN G 199 " --> pdb=" O GLN G 195 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TYR G 200 " --> pdb=" O LEU G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 201 through 212 Processing helix chain 'G' and resid 279 through 285 removed outlier: 3.536A pdb=" N LEU G 285 " --> pdb=" O LEU G 281 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 23 removed outlier: 4.247A pdb=" N SER I 22 " --> pdb=" O ILE I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 41 Processing helix chain 'I' and resid 49 through 58 removed outlier: 3.561A pdb=" N LYS I 58 " --> pdb=" O ILE I 54 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 91 Processing helix chain 'I' and resid 100 through 106 removed outlier: 3.548A pdb=" N VAL I 104 " --> pdb=" O ASN I 100 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 122 Processing helix chain 'I' and resid 124 through 137 removed outlier: 3.955A pdb=" N TYR I 137 " --> pdb=" O ASP I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 145 Processing helix chain 'I' and resid 145 through 164 Processing helix chain 'I' and resid 184 through 188 Processing helix chain 'I' and resid 191 through 199 removed outlier: 3.663A pdb=" N ASN I 199 " --> pdb=" O GLN I 195 " (cutoff:3.500A) Processing helix chain 'I' and resid 201 through 212 Processing helix chain 'I' and resid 278 through 285 Processing helix chain 'K' and resid 37 through 41 Processing helix chain 'K' and resid 49 through 58 removed outlier: 3.782A pdb=" N LYS K 58 " --> pdb=" O ILE K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 91 Processing helix chain 'K' and resid 100 through 106 Processing helix chain 'K' and resid 111 through 122 Processing helix chain 'K' and resid 124 through 137 removed outlier: 4.031A pdb=" N TYR K 137 " --> pdb=" O ASP K 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 144 through 164 Processing helix chain 'K' and resid 191 through 199 removed outlier: 3.816A pdb=" N ASN K 199 " --> pdb=" O GLN K 195 " (cutoff:3.500A) Processing helix chain 'K' and resid 201 through 212 Processing helix chain 'K' and resid 279 through 285 Processing helix chain 'M' and resid 37 through 42 removed outlier: 3.790A pdb=" N TYR M 41 " --> pdb=" O PRO M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 56 Processing helix chain 'M' and resid 88 through 91 removed outlier: 3.783A pdb=" N LYS M 91 " --> pdb=" O ARG M 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 88 through 91' Processing helix chain 'M' and resid 100 through 106 Processing helix chain 'M' and resid 111 through 122 Processing helix chain 'M' and resid 124 through 136 Processing helix chain 'M' and resid 138 through 142 removed outlier: 3.655A pdb=" N THR M 142 " --> pdb=" O GLU M 139 " (cutoff:3.500A) Processing helix chain 'M' and resid 145 through 164 Processing helix chain 'M' and resid 184 through 188 removed outlier: 3.507A pdb=" N ALA M 187 " --> pdb=" O ASN M 184 " (cutoff:3.500A) Processing helix chain 'M' and resid 191 through 200 removed outlier: 3.565A pdb=" N ASN M 199 " --> pdb=" O GLN M 195 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TYR M 200 " --> pdb=" O LEU M 196 " (cutoff:3.500A) Processing helix chain 'M' and resid 201 through 211 Processing helix chain 'M' and resid 278 through 285 removed outlier: 3.634A pdb=" N LEU M 285 " --> pdb=" O LEU M 281 " (cutoff:3.500A) Processing helix chain 'O' and resid 18 through 22 removed outlier: 3.616A pdb=" N ALA O 21 " --> pdb=" O CYS O 18 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N SER O 22 " --> pdb=" O ILE O 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 18 through 22' Processing helix chain 'O' and resid 49 through 58 Processing helix chain 'O' and resid 88 through 91 Processing helix chain 'O' and resid 100 through 106 Processing helix chain 'O' and resid 107 through 110 Processing helix chain 'O' and resid 111 through 122 Processing helix chain 'O' and resid 124 through 137 removed outlier: 3.858A pdb=" N TYR O 137 " --> pdb=" O ASP O 133 " (cutoff:3.500A) Processing helix chain 'O' and resid 145 through 164 removed outlier: 3.610A pdb=" N SER O 151 " --> pdb=" O ARG O 147 " (cutoff:3.500A) Processing helix chain 'O' and resid 184 through 188 Processing helix chain 'O' and resid 191 through 199 removed outlier: 3.997A pdb=" N ASN O 199 " --> pdb=" O GLN O 195 " (cutoff:3.500A) Processing helix chain 'O' and resid 201 through 212 Processing helix chain 'O' and resid 280 through 285 Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 67 Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 96 removed outlier: 6.381A pdb=" N LEU A 239 " --> pdb=" O LEU A 94 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 179 Processing sheet with id=AA4, first strand: chain 'C' and resid 59 through 67 removed outlier: 3.607A pdb=" N PHE C 74 " --> pdb=" O ILE C 66 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 93 through 95 removed outlier: 6.684A pdb=" N LEU C 239 " --> pdb=" O LEU C 94 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 176 through 179 Processing sheet with id=AA7, first strand: chain 'C' and resid 268 through 271 Processing sheet with id=AA8, first strand: chain 'E' and resid 62 through 67 removed outlier: 3.600A pdb=" N MET E 76 " --> pdb=" O LEU E 64 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 93 through 96 removed outlier: 6.946A pdb=" N LEU E 239 " --> pdb=" O LEU E 94 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP E 235 " --> pdb=" O GLY E 238 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 176 through 179 removed outlier: 6.224A pdb=" N TYR E 216 " --> pdb=" O GLN E 302 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ILE E 304 " --> pdb=" O TYR E 216 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLN E 218 " --> pdb=" O ILE E 304 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 289 through 290 removed outlier: 5.839A pdb=" N GLU E 289 " --> pdb=" O VAL G 63 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 93 through 96 removed outlier: 3.743A pdb=" N ILE G 95 " --> pdb=" O LEU G 239 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 176 through 179 Processing sheet with id=AB5, first strand: chain 'G' and resid 216 through 219 Processing sheet with id=AB6, first strand: chain 'G' and resid 267 through 268 removed outlier: 3.763A pdb=" N GLN G 267 " --> pdb=" O GLU I 275 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 59 through 67 Processing sheet with id=AB8, first strand: chain 'I' and resid 93 through 95 Processing sheet with id=AB9, first strand: chain 'I' and resid 176 through 179 removed outlier: 5.960A pdb=" N TYR I 216 " --> pdb=" O GLN I 302 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ILE I 304 " --> pdb=" O TYR I 216 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLN I 218 " --> pdb=" O ILE I 304 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 59 through 67 Processing sheet with id=AC2, first strand: chain 'K' and resid 93 through 95 removed outlier: 3.836A pdb=" N ASP K 235 " --> pdb=" O GLY K 238 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 176 through 179 removed outlier: 6.623A pdb=" N TYR K 216 " --> pdb=" O GLN K 302 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ILE K 304 " --> pdb=" O TYR K 216 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLN K 218 " --> pdb=" O ILE K 304 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'M' and resid 73 through 81 removed outlier: 4.632A pdb=" N GLU O 289 " --> pdb=" O LYS M 61 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 93 through 96 removed outlier: 3.628A pdb=" N ILE M 95 " --> pdb=" O LEU M 239 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 176 through 179 removed outlier: 3.589A pdb=" N GLN M 302 " --> pdb=" O TYR M 216 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE M 304 " --> pdb=" O GLN M 218 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 212 through 213 Processing sheet with id=AC8, first strand: chain 'O' and resid 62 through 67 removed outlier: 3.645A pdb=" N ILE O 66 " --> pdb=" O PHE O 74 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'O' and resid 93 through 96 removed outlier: 6.708A pdb=" N LEU O 239 " --> pdb=" O LEU O 94 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'O' and resid 176 through 179 removed outlier: 6.236A pdb=" N TYR O 216 " --> pdb=" O GLN O 302 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ILE O 304 " --> pdb=" O TYR O 216 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N GLN O 218 " --> pdb=" O ILE O 304 " (cutoff:3.500A) 649 hydrogen bonds defined for protein. 1731 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: 5.39 Time building geometry restraints manager: 5.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6399 1.35 - 1.47: 4512 1.47 - 1.59: 8220 1.59 - 1.71: 0 1.71 - 1.83: 138 Bond restraints: 19269 Sorted by residual: bond pdb=" CB CYS O 49 " pdb=" SG CYS O 49 " ideal model delta sigma weight residual 1.808 1.777 0.031 3.30e-02 9.18e+02 8.75e-01 bond pdb=" CB CYS G 49 " pdb=" SG CYS G 49 " ideal model delta sigma weight residual 1.808 1.778 0.030 3.30e-02 9.18e+02 8.43e-01 bond pdb=" N VAL K 243 " pdb=" CA VAL K 243 " ideal model delta sigma weight residual 1.468 1.459 0.009 1.05e-02 9.07e+03 7.31e-01 bond pdb=" CA VAL K 212 " pdb=" CB VAL K 212 " ideal model delta sigma weight residual 1.530 1.539 -0.009 1.05e-02 9.07e+03 7.30e-01 bond pdb=" C THR E 145 " pdb=" O THR E 145 " ideal model delta sigma weight residual 1.234 1.245 -0.012 1.46e-02 4.69e+03 6.60e-01 ... (remaining 19264 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.90: 24872 0.90 - 1.79: 999 1.79 - 2.69: 150 2.69 - 3.59: 76 3.59 - 4.48: 6 Bond angle restraints: 26103 Sorted by residual: angle pdb=" N ASN C 144 " pdb=" CA ASN C 144 " pdb=" CB ASN C 144 " ideal model delta sigma weight residual 113.65 110.82 2.83 1.47e+00 4.63e-01 3.70e+00 angle pdb=" C SER E 37 " pdb=" N PRO E 38 " pdb=" CA PRO E 38 " ideal model delta sigma weight residual 121.91 119.41 2.50 1.35e+00 5.49e-01 3.44e+00 angle pdb=" CA CYS K 169 " pdb=" CB CYS K 169 " pdb=" SG CYS K 169 " ideal model delta sigma weight residual 114.40 118.64 -4.24 2.30e+00 1.89e-01 3.40e+00 angle pdb=" C ILE M 131 " pdb=" N CYS M 132 " pdb=" CA CYS M 132 " ideal model delta sigma weight residual 121.14 117.94 3.20 1.75e+00 3.27e-01 3.34e+00 angle pdb=" N PHE K 168 " pdb=" CA PHE K 168 " pdb=" CB PHE K 168 " ideal model delta sigma weight residual 110.49 107.46 3.03 1.69e+00 3.50e-01 3.21e+00 ... (remaining 26098 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 10046 17.92 - 35.83: 1287 35.83 - 53.75: 226 53.75 - 71.67: 77 71.67 - 89.58: 10 Dihedral angle restraints: 11646 sinusoidal: 4791 harmonic: 6855 Sorted by residual: dihedral pdb=" CB CYS I 229 " pdb=" SG CYS I 229 " pdb=" SG CYS K 229 " pdb=" CB CYS K 229 " ideal model delta sinusoidal sigma weight residual -86.00 -0.95 -85.05 1 1.00e+01 1.00e-02 8.77e+01 dihedral pdb=" CB CYS K 169 " pdb=" SG CYS K 169 " pdb=" SG CYS M 132 " pdb=" CB CYS M 132 " ideal model delta sinusoidal sigma weight residual -86.00 -17.26 -68.74 1 1.00e+01 1.00e-02 6.12e+01 dihedral pdb=" CB CYS K 132 " pdb=" SG CYS K 132 " pdb=" SG CYS M 169 " pdb=" CB CYS M 169 " ideal model delta sinusoidal sigma weight residual 93.00 156.71 -63.71 1 1.00e+01 1.00e-02 5.35e+01 ... (remaining 11643 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2147 0.042 - 0.084: 543 0.084 - 0.126: 175 0.126 - 0.169: 7 0.169 - 0.211: 1 Chirality restraints: 2873 Sorted by residual: chirality pdb=" CB ILE E 48 " pdb=" CA ILE E 48 " pdb=" CG1 ILE E 48 " pdb=" CG2 ILE E 48 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA ILE K 78 " pdb=" N ILE K 78 " pdb=" C ILE K 78 " pdb=" CB ILE K 78 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.18e-01 chirality pdb=" CA VAL E 24 " pdb=" N VAL E 24 " pdb=" C VAL E 24 " pdb=" CB VAL E 24 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.04e-01 ... (remaining 2870 not shown) Planarity restraints: 3460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE O 316 " 0.043 5.00e-02 4.00e+02 6.56e-02 6.89e+00 pdb=" N PRO O 317 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO O 317 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO O 317 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE I 316 " 0.035 5.00e-02 4.00e+02 5.34e-02 4.57e+00 pdb=" N PRO I 317 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO I 317 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO I 317 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER G 37 " 0.032 5.00e-02 4.00e+02 4.84e-02 3.75e+00 pdb=" N PRO G 38 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO G 38 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO G 38 " 0.027 5.00e-02 4.00e+02 ... (remaining 3457 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 332 2.67 - 3.23: 18604 3.23 - 3.79: 29337 3.79 - 4.34: 41051 4.34 - 4.90: 68046 Nonbonded interactions: 157370 Sorted by model distance: nonbonded pdb=" OG SER G 37 " pdb=" OD1 ASN G 51 " model vdw 2.115 3.040 nonbonded pdb=" O ASN K 164 " pdb=" OG1 THR K 167 " model vdw 2.127 3.040 nonbonded pdb=" OG SER O 173 " pdb=" OD2 ASP O 175 " model vdw 2.200 3.040 nonbonded pdb=" OH TYR M 250 " pdb=" O PHE O 67 " model vdw 2.203 3.040 nonbonded pdb=" OH TYR I 288 " pdb=" OD2 ASP K 44 " model vdw 2.216 3.040 ... (remaining 157365 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 253 or resid 269 through 320)) selection = (chain 'C' and (resid 15 through 253 or resid 269 through 320)) selection = (chain 'E' and resid 15 through 320) selection = (chain 'G' and (resid 15 through 26 or resid 35 through 253 or resid 269 through \ 320)) selection = (chain 'I' and (resid 15 through 253 or resid 269 through 320)) selection = (chain 'K' and (resid 15 through 253 or resid 269 through 320)) selection = (chain 'M' and (resid 15 through 26 or resid 35 through 253 or resid 269 through \ 320)) selection = (chain 'O' and (resid 15 through 253 or resid 269 through 320)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 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: 0.030 Extract box with map and model: 0.860 Check model and map are aligned: 0.150 Set scattering table: 0.210 Process input model: 43.860 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.090 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 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 : 0.002 0.109 19306 Z= 0.100 Angle : 0.458 13.029 26142 Z= 0.242 Chirality : 0.041 0.211 2873 Planarity : 0.003 0.066 3460 Dihedral : 16.102 89.584 7169 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.10 % Allowed : 22.08 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.56 (0.17), residues: 2285 helix: 0.91 (0.19), residues: 729 sheet: -1.50 (0.39), residues: 167 loop : -0.93 (0.16), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 46 HIS 0.005 0.001 HIS K 81 PHE 0.016 0.001 PHE K 168 TYR 0.012 0.001 TYR E 301 ARG 0.003 0.000 ARG E 80 Details of bonding type rmsd hydrogen bonds : bond 0.20993 ( 649) hydrogen bonds : angle 8.29710 ( 1731) metal coordination : bond 0.02433 ( 28) metal coordination : angle 4.68604 ( 21) SS BOND : bond 0.00269 ( 9) SS BOND : angle 0.97198 ( 18) covalent geometry : bond 0.00228 (19269) covalent geometry : angle 0.43815 (26103) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 506 time to evaluate : 2.029 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.7900 (t70) cc_final: 0.7631 (t70) REVERT: A 111 MET cc_start: 0.7720 (mtt) cc_final: 0.7510 (mtm) REVERT: A 265 ARG cc_start: 0.7153 (ttm170) cc_final: 0.6857 (tpm170) REVERT: C 60 SER cc_start: 0.8679 (t) cc_final: 0.8442 (m) REVERT: C 112 GLN cc_start: 0.7402 (mt0) cc_final: 0.7193 (mt0) REVERT: C 171 ARG cc_start: 0.7434 (mtm-85) cc_final: 0.5538 (mmt180) REVERT: C 174 ARG cc_start: 0.7589 (mmm-85) cc_final: 0.7307 (mmm-85) REVERT: C 200 TYR cc_start: 0.7723 (m-80) cc_final: 0.7149 (m-80) REVERT: C 310 PHE cc_start: 0.8541 (t80) cc_final: 0.8235 (t80) REVERT: E 68 ASP cc_start: 0.6988 (p0) cc_final: 0.6745 (p0) REVERT: E 78 ILE cc_start: 0.7680 (tt) cc_final: 0.7372 (tt) REVERT: E 86 LYS cc_start: 0.8047 (mmmm) cc_final: 0.7606 (mttp) REVERT: E 92 ARG cc_start: 0.6428 (mtp85) cc_final: 0.6223 (mtp85) REVERT: E 223 GLU cc_start: 0.8206 (tt0) cc_final: 0.7885 (tt0) REVERT: G 16 ASN cc_start: 0.6930 (t0) cc_final: 0.6635 (t0) REVERT: G 67 PHE cc_start: 0.7523 (m-10) cc_final: 0.7275 (m-80) REVERT: G 122 TYR cc_start: 0.8458 (m-80) cc_final: 0.8232 (m-80) REVERT: G 174 ARG cc_start: 0.7227 (mpt90) cc_final: 0.6802 (tpt-90) REVERT: G 248 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8257 (mm-30) REVERT: I 54 ILE cc_start: 0.8829 (mt) cc_final: 0.8628 (mt) REVERT: I 150 HIS cc_start: 0.7877 (t70) cc_final: 0.6906 (m-70) REVERT: I 171 ARG cc_start: 0.6523 (ptt180) cc_final: 0.5458 (mtt90) REVERT: K 110 MET cc_start: 0.8042 (mtt) cc_final: 0.7788 (mtt) REVERT: K 111 MET cc_start: 0.7224 (mtt) cc_final: 0.7015 (mtm) REVERT: K 115 GLN cc_start: 0.7242 (mt0) cc_final: 0.6997 (mt0) REVERT: K 120 LEU cc_start: 0.8021 (mt) cc_final: 0.7708 (mt) REVERT: K 149 ILE cc_start: 0.8446 (tt) cc_final: 0.8115 (tt) REVERT: K 215 GLU cc_start: 0.7642 (tt0) cc_final: 0.7281 (tt0) REVERT: K 222 GLU cc_start: 0.6592 (mm-30) cc_final: 0.6368 (mm-30) REVERT: K 269 ARG cc_start: 0.7868 (ptt180) cc_final: 0.7380 (ptt-90) REVERT: K 312 ARG cc_start: 0.7889 (ptm160) cc_final: 0.7340 (ttp80) REVERT: M 25 SER cc_start: 0.8201 (t) cc_final: 0.7309 (t) REVERT: M 111 MET cc_start: 0.7936 (mtm) cc_final: 0.7650 (mtm) REVERT: M 115 GLN cc_start: 0.8481 (mt0) cc_final: 0.8195 (mt0) REVERT: M 141 PHE cc_start: 0.8307 (t80) cc_final: 0.8004 (t80) REVERT: M 188 LEU cc_start: 0.8243 (mp) cc_final: 0.8032 (mt) REVERT: O 59 MET cc_start: 0.7361 (mtm) cc_final: 0.6855 (mtp) REVERT: O 109 SER cc_start: 0.6797 (p) cc_final: 0.6590 (m) REVERT: O 111 MET cc_start: 0.6415 (tpp) cc_final: 0.6169 (tpp) REVERT: O 112 GLN cc_start: 0.7032 (pm20) cc_final: 0.6582 (pm20) REVERT: O 171 ARG cc_start: 0.7305 (mtm-85) cc_final: 0.6739 (mtt-85) REVERT: O 220 ASP cc_start: 0.6534 (m-30) cc_final: 0.6081 (m-30) outliers start: 2 outliers final: 0 residues processed: 507 average time/residue: 0.3478 time to fit residues: 259.5764 Evaluate side-chains 438 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 438 time to evaluate : 2.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 0.1980 chunk 175 optimal weight: 8.9990 chunk 97 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 181 optimal weight: 0.9980 chunk 70 optimal weight: 0.0470 chunk 110 optimal weight: 0.8980 chunk 134 optimal weight: 3.9990 chunk 209 optimal weight: 0.7980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 ASN A 262 GLN C 320 ASN E 134 ASN ** E 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 305 ASN G 195 GLN I 16 ASN I 106 ASN ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 195 GLN K 267 GLN M 251 ASN ** O 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 134 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.213087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.188358 restraints weight = 20356.355| |-----------------------------------------------------------------------------| r_work (start): 0.4135 rms_B_bonded: 1.89 r_work: 0.4042 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3905 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 19306 Z= 0.119 Angle : 0.521 8.613 26142 Z= 0.282 Chirality : 0.043 0.148 2873 Planarity : 0.004 0.066 3460 Dihedral : 4.605 20.757 2572 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.57 % Allowed : 21.66 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.17), residues: 2285 helix: 1.04 (0.19), residues: 744 sheet: -1.76 (0.39), residues: 158 loop : -0.85 (0.16), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP O 46 HIS 0.005 0.001 HIS G 81 PHE 0.021 0.002 PHE G 315 TYR 0.016 0.001 TYR E 301 ARG 0.007 0.000 ARG E 189 Details of bonding type rmsd hydrogen bonds : bond 0.04076 ( 649) hydrogen bonds : angle 5.82251 ( 1731) metal coordination : bond 0.02128 ( 28) metal coordination : angle 3.40677 ( 21) SS BOND : bond 0.00674 ( 9) SS BOND : angle 2.10227 ( 18) covalent geometry : bond 0.00268 (19269) covalent geometry : angle 0.50888 (26103) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 438 time to evaluate : 2.042 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8100 (t70) cc_final: 0.7764 (t70) REVERT: A 194 ASP cc_start: 0.7112 (t0) cc_final: 0.6814 (t0) REVERT: A 265 ARG cc_start: 0.7028 (ttm170) cc_final: 0.6560 (tpm170) REVERT: A 269 ARG cc_start: 0.4114 (mtm-85) cc_final: 0.3393 (mtm-85) REVERT: C 60 SER cc_start: 0.8638 (t) cc_final: 0.8365 (m) REVERT: C 112 GLN cc_start: 0.7714 (mt0) cc_final: 0.7506 (mp10) REVERT: C 171 ARG cc_start: 0.7588 (mtm-85) cc_final: 0.5754 (mmt180) REVERT: C 174 ARG cc_start: 0.7556 (mmm-85) cc_final: 0.7303 (mmm-85) REVERT: C 200 TYR cc_start: 0.7424 (m-80) cc_final: 0.6861 (m-80) REVERT: C 310 PHE cc_start: 0.8402 (t80) cc_final: 0.8108 (t80) REVERT: E 68 ASP cc_start: 0.7189 (p0) cc_final: 0.6857 (p0) REVERT: E 86 LYS cc_start: 0.8124 (mmmm) cc_final: 0.7515 (mtmm) REVERT: G 16 ASN cc_start: 0.7011 (t0) cc_final: 0.6654 (t0) REVERT: G 67 PHE cc_start: 0.7841 (m-10) cc_final: 0.7484 (m-80) REVERT: G 146 GLN cc_start: 0.7769 (tm-30) cc_final: 0.7405 (tp40) REVERT: G 174 ARG cc_start: 0.7420 (mpt90) cc_final: 0.6750 (tpt-90) REVERT: I 54 ILE cc_start: 0.8745 (mt) cc_final: 0.8533 (mt) REVERT: I 102 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.6362 (mm-40) REVERT: I 150 HIS cc_start: 0.7941 (t70) cc_final: 0.6859 (m-70) REVERT: I 171 ARG cc_start: 0.6736 (ptt180) cc_final: 0.5586 (mtt90) REVERT: I 267 GLN cc_start: 0.6253 (mm-40) cc_final: 0.5994 (mm-40) REVERT: K 67 PHE cc_start: 0.7597 (OUTLIER) cc_final: 0.7149 (t80) REVERT: K 103 ASP cc_start: 0.8389 (m-30) cc_final: 0.8158 (m-30) REVERT: K 120 LEU cc_start: 0.8151 (mt) cc_final: 0.7834 (mt) REVERT: K 253 ILE cc_start: 0.6722 (OUTLIER) cc_final: 0.6213 (pp) REVERT: K 269 ARG cc_start: 0.8045 (ptt180) cc_final: 0.7622 (ptt-90) REVERT: K 307 GLU cc_start: 0.7871 (pm20) cc_final: 0.7665 (pm20) REVERT: K 312 ARG cc_start: 0.7879 (ptm160) cc_final: 0.7336 (ttp80) REVERT: M 16 ASN cc_start: 0.7660 (t0) cc_final: 0.7198 (t0) REVERT: M 25 SER cc_start: 0.8059 (t) cc_final: 0.7847 (t) REVERT: M 107 LEU cc_start: 0.7993 (mt) cc_final: 0.7269 (mm) REVERT: M 115 GLN cc_start: 0.8585 (mt0) cc_final: 0.8218 (mt0) REVERT: M 122 TYR cc_start: 0.8196 (m-80) cc_final: 0.7456 (m-80) REVERT: M 141 PHE cc_start: 0.8455 (t80) cc_final: 0.8014 (t80) REVERT: M 188 LEU cc_start: 0.8371 (mp) cc_final: 0.8130 (mm) REVERT: M 204 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8250 (mt) REVERT: O 88 ARG cc_start: 0.7067 (ttm110) cc_final: 0.6785 (ttm110) REVERT: O 112 GLN cc_start: 0.7235 (pm20) cc_final: 0.6751 (pm20) REVERT: O 171 ARG cc_start: 0.7360 (mtm-85) cc_final: 0.6696 (mtt-85) REVERT: O 198 ASN cc_start: 0.7006 (m-40) cc_final: 0.6645 (p0) REVERT: O 269 ARG cc_start: 0.4679 (OUTLIER) cc_final: 0.4153 (pmt-80) REVERT: O 270 ASN cc_start: 0.7444 (t0) cc_final: 0.7039 (m-40) outliers start: 75 outliers final: 32 residues processed: 491 average time/residue: 0.3481 time to fit residues: 253.6038 Evaluate side-chains 434 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 397 time to evaluate : 2.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 36 CYS Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 169 CYS Chi-restraints excluded: chain E residue 195 GLN Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain G residue 294 TYR Chi-restraints excluded: chain I residue 102 GLN Chi-restraints excluded: chain I residue 167 THR Chi-restraints excluded: chain I residue 169 CYS Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 150 HIS Chi-restraints excluded: chain K residue 253 ILE Chi-restraints excluded: chain M residue 90 ILE Chi-restraints excluded: chain M residue 195 GLN Chi-restraints excluded: chain M residue 204 LEU Chi-restraints excluded: chain M residue 240 VAL Chi-restraints excluded: chain M residue 284 THR Chi-restraints excluded: chain M residue 294 TYR Chi-restraints excluded: chain M residue 306 SER Chi-restraints excluded: chain O residue 60 SER Chi-restraints excluded: chain O residue 134 ASN Chi-restraints excluded: chain O residue 149 ILE Chi-restraints excluded: chain O residue 150 HIS Chi-restraints excluded: chain O residue 169 CYS Chi-restraints excluded: chain O residue 224 LEU Chi-restraints excluded: chain O residue 269 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 2 optimal weight: 5.9990 chunk 129 optimal weight: 0.0170 chunk 65 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 112 optimal weight: 0.0670 chunk 9 optimal weight: 0.0020 chunk 230 optimal weight: 5.9990 chunk 178 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 213 optimal weight: 4.9990 chunk 136 optimal weight: 0.7980 overall best weight: 0.5766 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 199 ASN E 305 ASN I 106 ASN I 164 ASN ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 195 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.214043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.189839 restraints weight = 20280.547| |-----------------------------------------------------------------------------| r_work (start): 0.4151 rms_B_bonded: 1.85 r_work: 0.4058 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3925 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 19306 Z= 0.115 Angle : 0.508 8.579 26142 Z= 0.272 Chirality : 0.042 0.149 2873 Planarity : 0.004 0.067 3460 Dihedral : 4.546 19.030 2572 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.52 % Allowed : 22.47 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.38 (0.17), residues: 2285 helix: 1.18 (0.19), residues: 719 sheet: -1.80 (0.36), residues: 176 loop : -0.82 (0.16), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 46 HIS 0.004 0.001 HIS C 81 PHE 0.030 0.002 PHE G 315 TYR 0.022 0.001 TYR E 301 ARG 0.008 0.000 ARG E 189 Details of bonding type rmsd hydrogen bonds : bond 0.03523 ( 649) hydrogen bonds : angle 5.41893 ( 1731) metal coordination : bond 0.02006 ( 28) metal coordination : angle 3.29764 ( 21) SS BOND : bond 0.00434 ( 9) SS BOND : angle 1.85857 ( 18) covalent geometry : bond 0.00261 (19269) covalent geometry : angle 0.49684 (26103) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 440 time to evaluate : 1.978 Fit side-chains revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8063 (t70) cc_final: 0.7744 (t70) REVERT: A 265 ARG cc_start: 0.7090 (ttm170) cc_final: 0.6584 (tpm170) REVERT: A 269 ARG cc_start: 0.4416 (mtm-85) cc_final: 0.3483 (mtm-85) REVERT: C 43 ASP cc_start: 0.7609 (t0) cc_final: 0.7387 (t0) REVERT: C 60 SER cc_start: 0.8640 (t) cc_final: 0.8349 (m) REVERT: C 171 ARG cc_start: 0.7568 (mtm-85) cc_final: 0.5781 (mmt180) REVERT: C 174 ARG cc_start: 0.7605 (mmm-85) cc_final: 0.7338 (mmm-85) REVERT: C 200 TYR cc_start: 0.7436 (m-80) cc_final: 0.6860 (m-80) REVERT: C 310 PHE cc_start: 0.8362 (t80) cc_final: 0.8069 (t80) REVERT: E 68 ASP cc_start: 0.7208 (p0) cc_final: 0.6808 (p0) REVERT: G 16 ASN cc_start: 0.6843 (t0) cc_final: 0.6498 (t0) REVERT: G 42 HIS cc_start: 0.7670 (m90) cc_final: 0.6703 (m90) REVERT: G 67 PHE cc_start: 0.7712 (m-10) cc_final: 0.7263 (m-80) REVERT: G 174 ARG cc_start: 0.7545 (mpt90) cc_final: 0.6922 (tpt-90) REVERT: G 248 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7758 (mm-30) REVERT: I 150 HIS cc_start: 0.7923 (t70) cc_final: 0.6891 (m-70) REVERT: I 171 ARG cc_start: 0.6821 (ptt180) cc_final: 0.5623 (mtt90) REVERT: K 67 PHE cc_start: 0.7669 (OUTLIER) cc_final: 0.7134 (t80) REVERT: K 120 LEU cc_start: 0.8159 (mt) cc_final: 0.7838 (mt) REVERT: K 133 ASP cc_start: 0.7426 (t0) cc_final: 0.6798 (m-30) REVERT: K 150 HIS cc_start: 0.6844 (OUTLIER) cc_final: 0.6135 (m-70) REVERT: K 253 ILE cc_start: 0.6693 (OUTLIER) cc_final: 0.6179 (pp) REVERT: K 269 ARG cc_start: 0.8014 (ptt180) cc_final: 0.7556 (ptt-90) REVERT: K 307 GLU cc_start: 0.7496 (pm20) cc_final: 0.7287 (pm20) REVERT: K 312 ARG cc_start: 0.7869 (ptm160) cc_final: 0.7356 (ttp80) REVERT: M 16 ASN cc_start: 0.7710 (t0) cc_final: 0.7351 (t0) REVERT: M 68 ASP cc_start: 0.4900 (t0) cc_final: 0.4673 (t0) REVERT: M 122 TYR cc_start: 0.8214 (m-80) cc_final: 0.7504 (m-80) REVERT: M 141 PHE cc_start: 0.8462 (t80) cc_final: 0.7989 (t80) REVERT: M 188 LEU cc_start: 0.8367 (mp) cc_final: 0.8137 (mm) REVERT: O 35 PRO cc_start: 0.6922 (Cg_exo) cc_final: 0.6633 (Cg_endo) REVERT: O 51 ASN cc_start: 0.6780 (OUTLIER) cc_final: 0.6396 (t0) REVERT: O 88 ARG cc_start: 0.7001 (ttm110) cc_final: 0.6739 (ttm110) REVERT: O 112 GLN cc_start: 0.7163 (pm20) cc_final: 0.6780 (pm20) REVERT: O 134 ASN cc_start: 0.6691 (OUTLIER) cc_final: 0.6100 (p0) REVERT: O 171 ARG cc_start: 0.7258 (mtm-85) cc_final: 0.6588 (mtt-85) REVERT: O 198 ASN cc_start: 0.6882 (m-40) cc_final: 0.6581 (p0) REVERT: O 269 ARG cc_start: 0.4675 (OUTLIER) cc_final: 0.4164 (pmt-80) REVERT: O 270 ASN cc_start: 0.7477 (t0) cc_final: 0.7076 (m-40) outliers start: 74 outliers final: 46 residues processed: 491 average time/residue: 0.3647 time to fit residues: 268.0112 Evaluate side-chains 459 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 407 time to evaluate : 3.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 150 HIS Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 36 CYS Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain E residue 51 ASN Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 169 CYS Chi-restraints excluded: chain E residue 195 GLN Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain G residue 294 TYR Chi-restraints excluded: chain I residue 62 MET Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 167 THR Chi-restraints excluded: chain I residue 169 CYS Chi-restraints excluded: chain I residue 229 CYS Chi-restraints excluded: chain I residue 253 ILE Chi-restraints excluded: chain I residue 293 THR Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 150 HIS Chi-restraints excluded: chain K residue 253 ILE Chi-restraints excluded: chain M residue 57 PHE Chi-restraints excluded: chain M residue 132 CYS Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 195 GLN Chi-restraints excluded: chain M residue 221 THR Chi-restraints excluded: chain M residue 240 VAL Chi-restraints excluded: chain M residue 242 SER Chi-restraints excluded: chain M residue 284 THR Chi-restraints excluded: chain M residue 294 TYR Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 51 ASN Chi-restraints excluded: chain O residue 60 SER Chi-restraints excluded: chain O residue 120 LEU Chi-restraints excluded: chain O residue 134 ASN Chi-restraints excluded: chain O residue 142 THR Chi-restraints excluded: chain O residue 149 ILE Chi-restraints excluded: chain O residue 150 HIS Chi-restraints excluded: chain O residue 169 CYS Chi-restraints excluded: chain O residue 195 GLN Chi-restraints excluded: chain O residue 224 LEU Chi-restraints excluded: chain O residue 269 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 187 optimal weight: 2.9990 chunk 91 optimal weight: 0.0470 chunk 83 optimal weight: 0.6980 chunk 166 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 chunk 86 optimal weight: 0.7980 chunk 14 optimal weight: 10.0000 chunk 170 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 199 ASN G 270 ASN I 16 ASN ** M 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 251 ASN ** O 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.216172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.191640 restraints weight = 20276.453| |-----------------------------------------------------------------------------| r_work (start): 0.4135 rms_B_bonded: 1.87 r_work: 0.4042 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3907 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 19306 Z= 0.117 Angle : 0.511 8.922 26142 Z= 0.273 Chirality : 0.042 0.190 2873 Planarity : 0.004 0.070 3460 Dihedral : 4.521 18.950 2572 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 4.14 % Allowed : 23.08 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.38 (0.17), residues: 2285 helix: 1.07 (0.19), residues: 749 sheet: -1.50 (0.37), residues: 189 loop : -0.82 (0.16), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 46 HIS 0.005 0.001 HIS K 81 PHE 0.023 0.001 PHE G 315 TYR 0.019 0.001 TYR E 301 ARG 0.009 0.000 ARG E 189 Details of bonding type rmsd hydrogen bonds : bond 0.03391 ( 649) hydrogen bonds : angle 5.24480 ( 1731) metal coordination : bond 0.02065 ( 28) metal coordination : angle 3.27207 ( 21) SS BOND : bond 0.00402 ( 9) SS BOND : angle 1.64935 ( 18) covalent geometry : bond 0.00270 (19269) covalent geometry : angle 0.50126 (26103) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 410 time to evaluate : 1.986 Fit side-chains revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8131 (t70) cc_final: 0.7826 (t70) REVERT: A 265 ARG cc_start: 0.7029 (ttm170) cc_final: 0.6692 (tpm170) REVERT: C 60 SER cc_start: 0.8641 (t) cc_final: 0.8337 (m) REVERT: C 102 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.6553 (mm-40) REVERT: C 171 ARG cc_start: 0.7567 (mtm-85) cc_final: 0.5712 (mmt180) REVERT: C 174 ARG cc_start: 0.7611 (mmm-85) cc_final: 0.7317 (mmm-85) REVERT: C 200 TYR cc_start: 0.7459 (m-80) cc_final: 0.6878 (m-80) REVERT: C 267 GLN cc_start: 0.6544 (mt0) cc_final: 0.6058 (mm-40) REVERT: C 310 PHE cc_start: 0.8389 (t80) cc_final: 0.8108 (t80) REVERT: E 68 ASP cc_start: 0.7064 (p0) cc_final: 0.6576 (p0) REVERT: G 16 ASN cc_start: 0.6827 (t0) cc_final: 0.6497 (t0) REVERT: G 39 ASP cc_start: 0.7539 (OUTLIER) cc_final: 0.7274 (p0) REVERT: G 42 HIS cc_start: 0.7703 (m90) cc_final: 0.6685 (m90) REVERT: G 67 PHE cc_start: 0.7796 (m-10) cc_final: 0.7439 (m-80) REVERT: G 174 ARG cc_start: 0.7576 (mpt90) cc_final: 0.6995 (tpt-90) REVERT: G 248 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7781 (mm-30) REVERT: I 102 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.6294 (mm-40) REVERT: I 150 HIS cc_start: 0.7744 (t70) cc_final: 0.6970 (m-70) REVERT: I 171 ARG cc_start: 0.6847 (ptt180) cc_final: 0.5539 (mpt180) REVERT: I 189 ARG cc_start: 0.8092 (mtm110) cc_final: 0.7888 (ttp-110) REVERT: I 305 ASN cc_start: 0.8296 (m-40) cc_final: 0.8091 (m-40) REVERT: K 67 PHE cc_start: 0.7817 (OUTLIER) cc_final: 0.7245 (t80) REVERT: K 120 LEU cc_start: 0.8134 (mt) cc_final: 0.7787 (mt) REVERT: K 133 ASP cc_start: 0.7214 (t0) cc_final: 0.6770 (m-30) REVERT: K 149 ILE cc_start: 0.8319 (tt) cc_final: 0.8090 (pt) REVERT: K 195 GLN cc_start: 0.7049 (tm-30) cc_final: 0.6665 (pp30) REVERT: K 253 ILE cc_start: 0.6700 (OUTLIER) cc_final: 0.6171 (pp) REVERT: K 312 ARG cc_start: 0.7869 (ptm160) cc_final: 0.7330 (ttp80) REVERT: M 16 ASN cc_start: 0.7792 (t0) cc_final: 0.7416 (t0) REVERT: M 68 ASP cc_start: 0.5388 (t0) cc_final: 0.5138 (t0) REVERT: M 122 TYR cc_start: 0.8225 (m-80) cc_final: 0.7480 (m-80) REVERT: M 141 PHE cc_start: 0.8458 (t80) cc_final: 0.8029 (t80) REVERT: M 188 LEU cc_start: 0.8467 (mp) cc_final: 0.8232 (mm) REVERT: O 51 ASN cc_start: 0.6781 (OUTLIER) cc_final: 0.6398 (t0) REVERT: O 112 GLN cc_start: 0.7227 (pm20) cc_final: 0.6751 (pm20) REVERT: O 134 ASN cc_start: 0.6700 (OUTLIER) cc_final: 0.6143 (p0) REVERT: O 171 ARG cc_start: 0.7148 (mtm-85) cc_final: 0.6500 (mtt-85) REVERT: O 269 ARG cc_start: 0.4718 (OUTLIER) cc_final: 0.4214 (pmt-80) REVERT: O 270 ASN cc_start: 0.7374 (t0) cc_final: 0.6949 (m-40) outliers start: 87 outliers final: 58 residues processed: 475 average time/residue: 0.3575 time to fit residues: 254.6492 Evaluate side-chains 457 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 391 time to evaluate : 1.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 150 HIS Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 36 CYS Chi-restraints excluded: chain C residue 102 GLN Chi-restraints excluded: chain C residue 195 GLN Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 51 ASN Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 169 CYS Chi-restraints excluded: chain E residue 195 GLN Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain G residue 284 THR Chi-restraints excluded: chain G residue 294 TYR Chi-restraints excluded: chain I residue 36 CYS Chi-restraints excluded: chain I residue 62 MET Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 102 GLN Chi-restraints excluded: chain I residue 167 THR Chi-restraints excluded: chain I residue 169 CYS Chi-restraints excluded: chain I residue 229 CYS Chi-restraints excluded: chain I residue 253 ILE Chi-restraints excluded: chain I residue 293 THR Chi-restraints excluded: chain I residue 311 LEU Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 150 HIS Chi-restraints excluded: chain K residue 253 ILE Chi-restraints excluded: chain M residue 57 PHE Chi-restraints excluded: chain M residue 132 CYS Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 182 VAL Chi-restraints excluded: chain M residue 195 GLN Chi-restraints excluded: chain M residue 221 THR Chi-restraints excluded: chain M residue 240 VAL Chi-restraints excluded: chain M residue 242 SER Chi-restraints excluded: chain M residue 245 ASP Chi-restraints excluded: chain M residue 294 TYR Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 51 ASN Chi-restraints excluded: chain O residue 120 LEU Chi-restraints excluded: chain O residue 134 ASN Chi-restraints excluded: chain O residue 142 THR Chi-restraints excluded: chain O residue 149 ILE Chi-restraints excluded: chain O residue 150 HIS Chi-restraints excluded: chain O residue 166 ASN Chi-restraints excluded: chain O residue 169 CYS Chi-restraints excluded: chain O residue 224 LEU Chi-restraints excluded: chain O residue 269 ARG Chi-restraints excluded: chain O residue 293 THR Chi-restraints excluded: chain O residue 316 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 44 optimal weight: 5.9990 chunk 93 optimal weight: 0.0570 chunk 135 optimal weight: 3.9990 chunk 176 optimal weight: 0.3980 chunk 99 optimal weight: 3.9990 chunk 141 optimal weight: 0.7980 chunk 150 optimal weight: 0.5980 chunk 142 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 199 ASN M 100 ASN M 115 GLN ** O 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 195 GLN O 198 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.215708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.191271 restraints weight = 20309.597| |-----------------------------------------------------------------------------| r_work (start): 0.4129 rms_B_bonded: 1.87 r_work: 0.4035 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3898 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 19306 Z= 0.122 Angle : 0.516 9.320 26142 Z= 0.274 Chirality : 0.043 0.154 2873 Planarity : 0.004 0.071 3460 Dihedral : 4.501 19.350 2572 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 4.66 % Allowed : 22.75 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.38 (0.17), residues: 2285 helix: 1.07 (0.19), residues: 749 sheet: -1.46 (0.37), residues: 185 loop : -0.84 (0.16), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 46 HIS 0.005 0.001 HIS C 81 PHE 0.025 0.002 PHE K 315 TYR 0.018 0.001 TYR E 301 ARG 0.009 0.000 ARG E 189 Details of bonding type rmsd hydrogen bonds : bond 0.03396 ( 649) hydrogen bonds : angle 5.21336 ( 1731) metal coordination : bond 0.02140 ( 28) metal coordination : angle 3.35948 ( 21) SS BOND : bond 0.00366 ( 9) SS BOND : angle 1.63656 ( 18) covalent geometry : bond 0.00284 (19269) covalent geometry : angle 0.50603 (26103) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 409 time to evaluate : 2.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8145 (t70) cc_final: 0.7844 (t70) REVERT: A 194 ASP cc_start: 0.7283 (t0) cc_final: 0.6818 (t0) REVERT: A 265 ARG cc_start: 0.7011 (ttm170) cc_final: 0.6597 (tpm170) REVERT: A 269 ARG cc_start: 0.4136 (mtm-85) cc_final: 0.3800 (mtm180) REVERT: C 60 SER cc_start: 0.8649 (t) cc_final: 0.8339 (m) REVERT: C 102 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.6566 (mm-40) REVERT: C 171 ARG cc_start: 0.7585 (mtm-85) cc_final: 0.5707 (mmt180) REVERT: C 174 ARG cc_start: 0.7607 (mmm-85) cc_final: 0.7320 (mmm-85) REVERT: C 200 TYR cc_start: 0.7496 (m-80) cc_final: 0.6920 (m-80) REVERT: C 222 GLU cc_start: 0.5811 (OUTLIER) cc_final: 0.4848 (mp0) REVERT: C 310 PHE cc_start: 0.8405 (t80) cc_final: 0.8112 (t80) REVERT: E 59 MET cc_start: 0.6726 (mtt) cc_final: 0.6458 (mtm) REVERT: E 222 GLU cc_start: 0.6883 (pm20) cc_final: 0.6666 (pm20) REVERT: G 16 ASN cc_start: 0.6848 (t0) cc_final: 0.6516 (t0) REVERT: G 39 ASP cc_start: 0.7559 (OUTLIER) cc_final: 0.7265 (p0) REVERT: G 42 HIS cc_start: 0.7710 (m90) cc_final: 0.6667 (m90) REVERT: G 67 PHE cc_start: 0.7643 (m-10) cc_final: 0.7317 (m-80) REVERT: G 174 ARG cc_start: 0.7593 (mpt90) cc_final: 0.6989 (tpt-90) REVERT: G 248 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7823 (mm-30) REVERT: I 102 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.6244 (mm-40) REVERT: I 171 ARG cc_start: 0.6851 (ptt180) cc_final: 0.5549 (mpt180) REVERT: I 305 ASN cc_start: 0.8315 (m-40) cc_final: 0.8067 (m-40) REVERT: K 67 PHE cc_start: 0.7862 (OUTLIER) cc_final: 0.7201 (t80) REVERT: K 120 LEU cc_start: 0.8150 (mt) cc_final: 0.7820 (mt) REVERT: K 133 ASP cc_start: 0.7184 (t0) cc_final: 0.6779 (m-30) REVERT: K 149 ILE cc_start: 0.8334 (tt) cc_final: 0.8045 (pt) REVERT: K 253 ILE cc_start: 0.6689 (OUTLIER) cc_final: 0.6169 (pp) REVERT: K 312 ARG cc_start: 0.7779 (ptm160) cc_final: 0.7272 (ttp80) REVERT: M 16 ASN cc_start: 0.7849 (t0) cc_final: 0.7471 (t0) REVERT: M 115 GLN cc_start: 0.8482 (mt0) cc_final: 0.8043 (mt0) REVERT: M 141 PHE cc_start: 0.8476 (t80) cc_final: 0.8053 (t80) REVERT: M 188 LEU cc_start: 0.8432 (mp) cc_final: 0.8209 (mm) REVERT: O 51 ASN cc_start: 0.6817 (OUTLIER) cc_final: 0.6419 (t0) REVERT: O 62 MET cc_start: 0.7129 (mtm) cc_final: 0.6880 (mtp) REVERT: O 88 ARG cc_start: 0.7118 (ttm110) cc_final: 0.6776 (ttm110) REVERT: O 112 GLN cc_start: 0.7055 (pm20) cc_final: 0.6781 (pm20) REVERT: O 134 ASN cc_start: 0.6576 (OUTLIER) cc_final: 0.5856 (p0) REVERT: O 157 LYS cc_start: 0.6886 (mmmt) cc_final: 0.6640 (mmmt) REVERT: O 171 ARG cc_start: 0.7171 (mtm-85) cc_final: 0.6458 (mtt-85) REVERT: O 269 ARG cc_start: 0.4744 (OUTLIER) cc_final: 0.4231 (pmt-80) REVERT: O 270 ASN cc_start: 0.7369 (t0) cc_final: 0.6950 (m-40) outliers start: 98 outliers final: 69 residues processed: 482 average time/residue: 0.3217 time to fit residues: 232.7669 Evaluate side-chains 469 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 391 time to evaluate : 1.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 150 HIS Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 36 CYS Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 102 GLN Chi-restraints excluded: chain C residue 195 GLN Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 51 ASN Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 169 CYS Chi-restraints excluded: chain E residue 195 GLN Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain G residue 284 THR Chi-restraints excluded: chain G residue 285 LEU Chi-restraints excluded: chain G residue 294 TYR Chi-restraints excluded: chain I residue 36 CYS Chi-restraints excluded: chain I residue 62 MET Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 102 GLN Chi-restraints excluded: chain I residue 167 THR Chi-restraints excluded: chain I residue 169 CYS Chi-restraints excluded: chain I residue 229 CYS Chi-restraints excluded: chain I residue 253 ILE Chi-restraints excluded: chain I residue 293 THR Chi-restraints excluded: chain I residue 311 LEU Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 150 HIS Chi-restraints excluded: chain K residue 253 ILE Chi-restraints excluded: chain M residue 57 PHE Chi-restraints excluded: chain M residue 76 MET Chi-restraints excluded: chain M residue 90 ILE Chi-restraints excluded: chain M residue 132 CYS Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 168 PHE Chi-restraints excluded: chain M residue 182 VAL Chi-restraints excluded: chain M residue 195 GLN Chi-restraints excluded: chain M residue 221 THR Chi-restraints excluded: chain M residue 240 VAL Chi-restraints excluded: chain M residue 242 SER Chi-restraints excluded: chain M residue 284 THR Chi-restraints excluded: chain M residue 294 TYR Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 51 ASN Chi-restraints excluded: chain O residue 60 SER Chi-restraints excluded: chain O residue 134 ASN Chi-restraints excluded: chain O residue 142 THR Chi-restraints excluded: chain O residue 149 ILE Chi-restraints excluded: chain O residue 150 HIS Chi-restraints excluded: chain O residue 166 ASN Chi-restraints excluded: chain O residue 169 CYS Chi-restraints excluded: chain O residue 195 GLN Chi-restraints excluded: chain O residue 224 LEU Chi-restraints excluded: chain O residue 269 ARG Chi-restraints excluded: chain O residue 293 THR Chi-restraints excluded: chain O residue 316 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 211 optimal weight: 0.9980 chunk 28 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 229 optimal weight: 7.9990 chunk 169 optimal weight: 0.9990 chunk 110 optimal weight: 0.0060 chunk 87 optimal weight: 7.9990 chunk 104 optimal weight: 4.9990 chunk 165 optimal weight: 4.9990 chunk 227 optimal weight: 2.9990 chunk 147 optimal weight: 0.3980 overall best weight: 1.0800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 199 ASN G 228 ASN ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 124 ASN ** O 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.211655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.186551 restraints weight = 20347.403| |-----------------------------------------------------------------------------| r_work (start): 0.4111 rms_B_bonded: 1.89 r_work: 0.4017 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3881 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 19306 Z= 0.143 Angle : 0.541 9.795 26142 Z= 0.286 Chirality : 0.043 0.153 2873 Planarity : 0.004 0.072 3460 Dihedral : 4.595 19.800 2572 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 4.71 % Allowed : 23.51 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.46 (0.17), residues: 2285 helix: 1.01 (0.19), residues: 749 sheet: -1.33 (0.33), residues: 235 loop : -0.89 (0.16), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 46 HIS 0.006 0.001 HIS C 81 PHE 0.023 0.002 PHE E 74 TYR 0.018 0.001 TYR E 301 ARG 0.010 0.000 ARG E 189 Details of bonding type rmsd hydrogen bonds : bond 0.03456 ( 649) hydrogen bonds : angle 5.25353 ( 1731) metal coordination : bond 0.02384 ( 28) metal coordination : angle 3.75162 ( 21) SS BOND : bond 0.00459 ( 9) SS BOND : angle 1.85472 ( 18) covalent geometry : bond 0.00336 (19269) covalent geometry : angle 0.52834 (26103) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 393 time to evaluate : 2.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 SER cc_start: 0.8653 (t) cc_final: 0.8303 (p) REVERT: A 43 ASP cc_start: 0.8144 (t70) cc_final: 0.7850 (t70) REVERT: A 194 ASP cc_start: 0.7274 (t0) cc_final: 0.6817 (t0) REVERT: A 265 ARG cc_start: 0.7058 (ttm170) cc_final: 0.6620 (tpm170) REVERT: A 269 ARG cc_start: 0.4313 (mtm-85) cc_final: 0.3763 (mtm180) REVERT: C 60 SER cc_start: 0.8647 (t) cc_final: 0.8313 (m) REVERT: C 102 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.6595 (mm-40) REVERT: C 171 ARG cc_start: 0.7618 (mtm-85) cc_final: 0.5721 (mmt180) REVERT: C 174 ARG cc_start: 0.7628 (mmm-85) cc_final: 0.7350 (mmm-85) REVERT: C 200 TYR cc_start: 0.7473 (m-80) cc_final: 0.6866 (m-80) REVERT: C 222 GLU cc_start: 0.5845 (OUTLIER) cc_final: 0.4844 (mp0) REVERT: C 224 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8106 (mt) REVERT: C 267 GLN cc_start: 0.6748 (mt0) cc_final: 0.6004 (mm-40) REVERT: C 310 PHE cc_start: 0.8426 (t80) cc_final: 0.8128 (t80) REVERT: E 59 MET cc_start: 0.6801 (mtt) cc_final: 0.6505 (mtm) REVERT: G 16 ASN cc_start: 0.6775 (t0) cc_final: 0.6454 (t0) REVERT: G 39 ASP cc_start: 0.7600 (OUTLIER) cc_final: 0.7295 (p0) REVERT: G 42 HIS cc_start: 0.7729 (m90) cc_final: 0.6688 (m90) REVERT: G 67 PHE cc_start: 0.7714 (m-10) cc_final: 0.7385 (m-80) REVERT: G 174 ARG cc_start: 0.7593 (mpt90) cc_final: 0.6994 (tpt-90) REVERT: G 248 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7884 (mm-30) REVERT: I 102 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.6224 (mm-40) REVERT: I 171 ARG cc_start: 0.6866 (ptt180) cc_final: 0.5561 (mpt180) REVERT: I 305 ASN cc_start: 0.8320 (m-40) cc_final: 0.8076 (m-40) REVERT: K 67 PHE cc_start: 0.7873 (OUTLIER) cc_final: 0.7230 (t80) REVERT: K 120 LEU cc_start: 0.8136 (mt) cc_final: 0.7792 (mt) REVERT: K 133 ASP cc_start: 0.6998 (t0) cc_final: 0.6664 (m-30) REVERT: K 149 ILE cc_start: 0.8272 (tt) cc_final: 0.8025 (pt) REVERT: K 195 GLN cc_start: 0.6998 (tm-30) cc_final: 0.6653 (pp30) REVERT: K 253 ILE cc_start: 0.6683 (OUTLIER) cc_final: 0.6165 (pp) REVERT: K 312 ARG cc_start: 0.7842 (ptm160) cc_final: 0.7321 (ttp80) REVERT: M 115 GLN cc_start: 0.8527 (mt0) cc_final: 0.8108 (mt0) REVERT: M 141 PHE cc_start: 0.8552 (t80) cc_final: 0.8073 (t80) REVERT: M 188 LEU cc_start: 0.8506 (mp) cc_final: 0.8292 (mm) REVERT: O 51 ASN cc_start: 0.6909 (OUTLIER) cc_final: 0.6502 (t0) REVERT: O 112 GLN cc_start: 0.7067 (pm20) cc_final: 0.6799 (pm20) REVERT: O 134 ASN cc_start: 0.6590 (OUTLIER) cc_final: 0.5869 (p0) REVERT: O 157 LYS cc_start: 0.6826 (mmmt) cc_final: 0.6583 (mmmt) REVERT: O 171 ARG cc_start: 0.7136 (mtm-85) cc_final: 0.6417 (mtt-85) REVERT: O 269 ARG cc_start: 0.4676 (OUTLIER) cc_final: 0.4170 (pmt-80) REVERT: O 270 ASN cc_start: 0.7377 (t0) cc_final: 0.6939 (m-40) outliers start: 99 outliers final: 72 residues processed: 468 average time/residue: 0.3138 time to fit residues: 221.1231 Evaluate side-chains 461 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 379 time to evaluate : 2.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 150 HIS Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 36 CYS Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 102 GLN Chi-restraints excluded: chain C residue 195 GLN Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 51 ASN Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 169 CYS Chi-restraints excluded: chain E residue 195 GLN Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain G residue 284 THR Chi-restraints excluded: chain G residue 285 LEU Chi-restraints excluded: chain I residue 36 CYS Chi-restraints excluded: chain I residue 62 MET Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 102 GLN Chi-restraints excluded: chain I residue 167 THR Chi-restraints excluded: chain I residue 169 CYS Chi-restraints excluded: chain I residue 229 CYS Chi-restraints excluded: chain I residue 253 ILE Chi-restraints excluded: chain I residue 293 THR Chi-restraints excluded: chain I residue 311 LEU Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 131 ILE Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 150 HIS Chi-restraints excluded: chain K residue 253 ILE Chi-restraints excluded: chain M residue 57 PHE Chi-restraints excluded: chain M residue 76 MET Chi-restraints excluded: chain M residue 90 ILE Chi-restraints excluded: chain M residue 132 CYS Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 168 PHE Chi-restraints excluded: chain M residue 182 VAL Chi-restraints excluded: chain M residue 195 GLN Chi-restraints excluded: chain M residue 218 GLN Chi-restraints excluded: chain M residue 221 THR Chi-restraints excluded: chain M residue 240 VAL Chi-restraints excluded: chain M residue 242 SER Chi-restraints excluded: chain M residue 245 ASP Chi-restraints excluded: chain M residue 284 THR Chi-restraints excluded: chain M residue 294 TYR Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 51 ASN Chi-restraints excluded: chain O residue 134 ASN Chi-restraints excluded: chain O residue 142 THR Chi-restraints excluded: chain O residue 149 ILE Chi-restraints excluded: chain O residue 150 HIS Chi-restraints excluded: chain O residue 166 ASN Chi-restraints excluded: chain O residue 169 CYS Chi-restraints excluded: chain O residue 195 GLN Chi-restraints excluded: chain O residue 224 LEU Chi-restraints excluded: chain O residue 269 ARG Chi-restraints excluded: chain O residue 293 THR Chi-restraints excluded: chain O residue 316 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 49 optimal weight: 4.9990 chunk 152 optimal weight: 0.7980 chunk 101 optimal weight: 6.9990 chunk 150 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 228 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 147 optimal weight: 0.5980 chunk 142 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 chunk 45 optimal weight: 0.0010 overall best weight: 1.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN E 199 ASN I 16 ASN ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 106 ASN O 134 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.215184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.192653 restraints weight = 20203.120| |-----------------------------------------------------------------------------| r_work (start): 0.4128 rms_B_bonded: 1.62 r_work: 0.4040 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3914 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 19306 Z= 0.144 Angle : 0.546 10.073 26142 Z= 0.290 Chirality : 0.043 0.177 2873 Planarity : 0.004 0.072 3460 Dihedral : 4.644 20.589 2572 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 4.66 % Allowed : 23.89 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.47 (0.17), residues: 2285 helix: 1.08 (0.19), residues: 721 sheet: -1.31 (0.33), residues: 235 loop : -0.91 (0.16), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 46 HIS 0.006 0.001 HIS C 81 PHE 0.023 0.002 PHE E 74 TYR 0.018 0.002 TYR E 301 ARG 0.012 0.000 ARG E 189 Details of bonding type rmsd hydrogen bonds : bond 0.03451 ( 649) hydrogen bonds : angle 5.28213 ( 1731) metal coordination : bond 0.02394 ( 28) metal coordination : angle 3.76875 ( 21) SS BOND : bond 0.00516 ( 9) SS BOND : angle 1.94041 ( 18) covalent geometry : bond 0.00339 (19269) covalent geometry : angle 0.53365 (26103) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 395 time to evaluate : 1.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 SER cc_start: 0.8585 (t) cc_final: 0.8255 (p) REVERT: A 43 ASP cc_start: 0.8056 (t70) cc_final: 0.7775 (t70) REVERT: A 194 ASP cc_start: 0.7042 (t0) cc_final: 0.6616 (t0) REVERT: A 265 ARG cc_start: 0.7055 (ttm170) cc_final: 0.6783 (tpm170) REVERT: A 269 ARG cc_start: 0.4745 (mtm-85) cc_final: 0.3812 (mtm180) REVERT: C 60 SER cc_start: 0.8593 (t) cc_final: 0.8253 (m) REVERT: C 102 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.6622 (mm-40) REVERT: C 171 ARG cc_start: 0.7669 (mtm-85) cc_final: 0.5875 (mmt180) REVERT: C 174 ARG cc_start: 0.7712 (mmm-85) cc_final: 0.7460 (mmm-85) REVERT: C 200 TYR cc_start: 0.7628 (m-80) cc_final: 0.7100 (m-80) REVERT: C 222 GLU cc_start: 0.6070 (OUTLIER) cc_final: 0.5052 (mp0) REVERT: C 224 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8025 (mt) REVERT: C 310 PHE cc_start: 0.8364 (t80) cc_final: 0.8085 (t80) REVERT: E 222 GLU cc_start: 0.7080 (pm20) cc_final: 0.6863 (pm20) REVERT: G 16 ASN cc_start: 0.6751 (t0) cc_final: 0.6484 (t0) REVERT: G 39 ASP cc_start: 0.7531 (OUTLIER) cc_final: 0.7248 (p0) REVERT: G 42 HIS cc_start: 0.7644 (m90) cc_final: 0.6717 (m90) REVERT: G 67 PHE cc_start: 0.7691 (m-10) cc_final: 0.7439 (m-80) REVERT: G 174 ARG cc_start: 0.7531 (mpt90) cc_final: 0.7095 (tpt-90) REVERT: G 248 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7776 (mm-30) REVERT: I 19 ILE cc_start: 0.7694 (OUTLIER) cc_final: 0.7314 (tp) REVERT: I 102 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.6417 (mm-40) REVERT: I 171 ARG cc_start: 0.6882 (ptt180) cc_final: 0.5630 (mpt180) REVERT: I 305 ASN cc_start: 0.8278 (m-40) cc_final: 0.8073 (m-40) REVERT: K 67 PHE cc_start: 0.7979 (OUTLIER) cc_final: 0.7304 (t80) REVERT: K 120 LEU cc_start: 0.8204 (mt) cc_final: 0.7863 (mt) REVERT: K 149 ILE cc_start: 0.8348 (tt) cc_final: 0.8126 (pt) REVERT: K 195 GLN cc_start: 0.7051 (tm-30) cc_final: 0.6718 (pp30) REVERT: K 253 ILE cc_start: 0.6669 (OUTLIER) cc_final: 0.6156 (pp) REVERT: K 312 ARG cc_start: 0.7774 (ptm160) cc_final: 0.7335 (ttp80) REVERT: M 115 GLN cc_start: 0.8540 (mt0) cc_final: 0.8173 (mt0) REVERT: M 141 PHE cc_start: 0.8513 (t80) cc_final: 0.8140 (t80) REVERT: O 51 ASN cc_start: 0.6865 (OUTLIER) cc_final: 0.6465 (t0) REVERT: O 112 GLN cc_start: 0.7005 (pm20) cc_final: 0.6783 (pm20) REVERT: O 134 ASN cc_start: 0.6550 (OUTLIER) cc_final: 0.5625 (p0) REVERT: O 171 ARG cc_start: 0.7104 (mtm-85) cc_final: 0.6488 (mtt-85) REVERT: O 270 ASN cc_start: 0.7196 (t0) cc_final: 0.6921 (m-40) outliers start: 98 outliers final: 75 residues processed: 470 average time/residue: 0.3192 time to fit residues: 225.1438 Evaluate side-chains 468 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 383 time to evaluate : 1.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 150 HIS Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 36 CYS Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 102 GLN Chi-restraints excluded: chain C residue 195 GLN Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 51 ASN Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 169 CYS Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 195 GLN Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 284 THR Chi-restraints excluded: chain G residue 285 LEU Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 36 CYS Chi-restraints excluded: chain I residue 62 MET Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 102 GLN Chi-restraints excluded: chain I residue 167 THR Chi-restraints excluded: chain I residue 169 CYS Chi-restraints excluded: chain I residue 229 CYS Chi-restraints excluded: chain I residue 253 ILE Chi-restraints excluded: chain I residue 293 THR Chi-restraints excluded: chain I residue 311 LEU Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 150 HIS Chi-restraints excluded: chain K residue 253 ILE Chi-restraints excluded: chain M residue 57 PHE Chi-restraints excluded: chain M residue 76 MET Chi-restraints excluded: chain M residue 90 ILE Chi-restraints excluded: chain M residue 132 CYS Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 168 PHE Chi-restraints excluded: chain M residue 182 VAL Chi-restraints excluded: chain M residue 195 GLN Chi-restraints excluded: chain M residue 218 GLN Chi-restraints excluded: chain M residue 221 THR Chi-restraints excluded: chain M residue 222 GLU Chi-restraints excluded: chain M residue 240 VAL Chi-restraints excluded: chain M residue 242 SER Chi-restraints excluded: chain M residue 245 ASP Chi-restraints excluded: chain M residue 284 THR Chi-restraints excluded: chain M residue 294 TYR Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 51 ASN Chi-restraints excluded: chain O residue 60 SER Chi-restraints excluded: chain O residue 134 ASN Chi-restraints excluded: chain O residue 142 THR Chi-restraints excluded: chain O residue 149 ILE Chi-restraints excluded: chain O residue 150 HIS Chi-restraints excluded: chain O residue 166 ASN Chi-restraints excluded: chain O residue 169 CYS Chi-restraints excluded: chain O residue 224 LEU Chi-restraints excluded: chain O residue 293 THR Chi-restraints excluded: chain O residue 297 LEU Chi-restraints excluded: chain O residue 316 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 221 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 160 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 161 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 chunk 3 optimal weight: 0.6980 chunk 230 optimal weight: 2.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 199 ASN I 264 ASN K 50 ASN ** K 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 195 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.207456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.181771 restraints weight = 20297.520| |-----------------------------------------------------------------------------| r_work (start): 0.4062 rms_B_bonded: 1.90 r_work: 0.3966 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3828 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 19306 Z= 0.203 Angle : 0.610 12.755 26142 Z= 0.321 Chirality : 0.045 0.178 2873 Planarity : 0.005 0.074 3460 Dihedral : 4.882 22.086 2572 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 4.71 % Allowed : 24.13 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.66 (0.17), residues: 2285 helix: 0.87 (0.19), residues: 712 sheet: -1.31 (0.35), residues: 213 loop : -1.02 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 46 HIS 0.009 0.002 HIS O 81 PHE 0.026 0.002 PHE G 315 TYR 0.020 0.002 TYR M 216 ARG 0.013 0.001 ARG E 189 Details of bonding type rmsd hydrogen bonds : bond 0.03786 ( 649) hydrogen bonds : angle 5.49790 ( 1731) metal coordination : bond 0.03345 ( 28) metal coordination : angle 4.80556 ( 21) SS BOND : bond 0.00725 ( 9) SS BOND : angle 2.07749 ( 18) covalent geometry : bond 0.00482 (19269) covalent geometry : angle 0.59266 (26103) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 389 time to evaluate : 2.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 SER cc_start: 0.8626 (t) cc_final: 0.8284 (p) REVERT: A 43 ASP cc_start: 0.8162 (t70) cc_final: 0.7883 (t70) REVERT: A 62 MET cc_start: 0.8512 (mtp) cc_final: 0.8154 (mtp) REVERT: A 265 ARG cc_start: 0.7117 (ttm170) cc_final: 0.6632 (tpm170) REVERT: A 269 ARG cc_start: 0.4695 (mtm-85) cc_final: 0.3790 (mtm-85) REVERT: C 43 ASP cc_start: 0.7733 (t0) cc_final: 0.7474 (t0) REVERT: C 102 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.6801 (mm-40) REVERT: C 171 ARG cc_start: 0.7719 (mtm-85) cc_final: 0.5787 (mmt180) REVERT: C 174 ARG cc_start: 0.7672 (mmm-85) cc_final: 0.7413 (mmm-85) REVERT: C 200 TYR cc_start: 0.7923 (m-80) cc_final: 0.7361 (m-80) REVERT: C 224 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8101 (mt) REVERT: C 310 PHE cc_start: 0.8517 (t80) cc_final: 0.8249 (t80) REVERT: G 16 ASN cc_start: 0.6989 (t0) cc_final: 0.6639 (t0) REVERT: G 39 ASP cc_start: 0.7760 (OUTLIER) cc_final: 0.7452 (p0) REVERT: G 42 HIS cc_start: 0.7786 (m90) cc_final: 0.6739 (m90) REVERT: G 67 PHE cc_start: 0.7843 (m-10) cc_final: 0.7611 (m-80) REVERT: G 174 ARG cc_start: 0.7647 (mpt90) cc_final: 0.7034 (tpt-90) REVERT: I 19 ILE cc_start: 0.7832 (OUTLIER) cc_final: 0.7502 (tp) REVERT: I 102 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.6413 (mm-40) REVERT: I 171 ARG cc_start: 0.6899 (ptt180) cc_final: 0.5575 (mpt180) REVERT: K 50 ASN cc_start: 0.8351 (OUTLIER) cc_final: 0.8151 (t0) REVERT: K 67 PHE cc_start: 0.8122 (OUTLIER) cc_final: 0.7369 (t80) REVERT: K 102 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.7569 (mt0) REVERT: K 120 LEU cc_start: 0.8232 (mt) cc_final: 0.7887 (mt) REVERT: K 253 ILE cc_start: 0.6680 (OUTLIER) cc_final: 0.6176 (pp) REVERT: K 312 ARG cc_start: 0.7886 (ptm160) cc_final: 0.7381 (ttp80) REVERT: M 141 PHE cc_start: 0.8545 (t80) cc_final: 0.8108 (t80) REVERT: O 51 ASN cc_start: 0.7202 (OUTLIER) cc_final: 0.6870 (t0) REVERT: O 88 ARG cc_start: 0.7138 (ttm110) cc_final: 0.6756 (ttm110) REVERT: O 134 ASN cc_start: 0.6390 (OUTLIER) cc_final: 0.6061 (p0) REVERT: O 157 LYS cc_start: 0.7129 (mmmm) cc_final: 0.6815 (mmmt) REVERT: O 171 ARG cc_start: 0.7294 (mtm-85) cc_final: 0.6388 (mtt-85) REVERT: O 301 TYR cc_start: 0.8177 (t80) cc_final: 0.7699 (t80) outliers start: 99 outliers final: 73 residues processed: 466 average time/residue: 0.3192 time to fit residues: 222.5299 Evaluate side-chains 469 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 385 time to evaluate : 2.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 150 HIS Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 36 CYS Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 102 GLN Chi-restraints excluded: chain C residue 195 GLN Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 51 ASN Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 169 CYS Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 195 GLN Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 59 MET Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 284 THR Chi-restraints excluded: chain G residue 285 LEU Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 36 CYS Chi-restraints excluded: chain I residue 62 MET Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 102 GLN Chi-restraints excluded: chain I residue 167 THR Chi-restraints excluded: chain I residue 169 CYS Chi-restraints excluded: chain I residue 253 ILE Chi-restraints excluded: chain I residue 293 THR Chi-restraints excluded: chain I residue 311 LEU Chi-restraints excluded: chain K residue 50 ASN Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 102 GLN Chi-restraints excluded: chain K residue 131 ILE Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 150 HIS Chi-restraints excluded: chain K residue 253 ILE Chi-restraints excluded: chain M residue 23 ILE Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 57 PHE Chi-restraints excluded: chain M residue 90 ILE Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 168 PHE Chi-restraints excluded: chain M residue 182 VAL Chi-restraints excluded: chain M residue 222 GLU Chi-restraints excluded: chain M residue 240 VAL Chi-restraints excluded: chain M residue 242 SER Chi-restraints excluded: chain M residue 245 ASP Chi-restraints excluded: chain M residue 271 VAL Chi-restraints excluded: chain M residue 284 THR Chi-restraints excluded: chain M residue 294 TYR Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 51 ASN Chi-restraints excluded: chain O residue 60 SER Chi-restraints excluded: chain O residue 134 ASN Chi-restraints excluded: chain O residue 142 THR Chi-restraints excluded: chain O residue 149 ILE Chi-restraints excluded: chain O residue 150 HIS Chi-restraints excluded: chain O residue 169 CYS Chi-restraints excluded: chain O residue 195 GLN Chi-restraints excluded: chain O residue 224 LEU Chi-restraints excluded: chain O residue 229 CYS Chi-restraints excluded: chain O residue 293 THR Chi-restraints excluded: chain O residue 297 LEU Chi-restraints excluded: chain O residue 316 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 125 optimal weight: 0.7980 chunk 226 optimal weight: 5.9990 chunk 146 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 60 optimal weight: 0.3980 chunk 204 optimal weight: 0.8980 chunk 202 optimal weight: 0.9990 chunk 205 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 199 ASN I 264 ASN K 50 ASN ** M 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 115 GLN M 251 ASN M 270 ASN ** O 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.216237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.192921 restraints weight = 20258.486| |-----------------------------------------------------------------------------| r_work (start): 0.4131 rms_B_bonded: 1.72 r_work: 0.4037 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3908 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 19306 Z= 0.127 Angle : 0.553 10.511 26142 Z= 0.293 Chirality : 0.043 0.169 2873 Planarity : 0.004 0.073 3460 Dihedral : 4.704 21.462 2572 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 4.09 % Allowed : 24.94 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.58 (0.17), residues: 2285 helix: 0.97 (0.19), residues: 726 sheet: -1.50 (0.35), residues: 200 loop : -0.98 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 46 HIS 0.004 0.001 HIS C 81 PHE 0.023 0.001 PHE E 74 TYR 0.022 0.001 TYR E 301 ARG 0.013 0.001 ARG E 189 Details of bonding type rmsd hydrogen bonds : bond 0.03307 ( 649) hydrogen bonds : angle 5.28977 ( 1731) metal coordination : bond 0.02149 ( 28) metal coordination : angle 3.48109 ( 21) SS BOND : bond 0.00366 ( 9) SS BOND : angle 1.63229 ( 18) covalent geometry : bond 0.00295 (19269) covalent geometry : angle 0.54261 (26103) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 394 time to evaluate : 2.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 SER cc_start: 0.8577 (t) cc_final: 0.8254 (p) REVERT: A 43 ASP cc_start: 0.8082 (t70) cc_final: 0.7804 (t70) REVERT: A 101 TYR cc_start: 0.8114 (p90) cc_final: 0.7900 (p90) REVERT: A 265 ARG cc_start: 0.7110 (ttm170) cc_final: 0.6746 (tpm170) REVERT: A 269 ARG cc_start: 0.4342 (mtm-85) cc_final: 0.3139 (mtm180) REVERT: C 102 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.6754 (mm-40) REVERT: C 171 ARG cc_start: 0.7695 (mtm-85) cc_final: 0.5879 (mmt180) REVERT: C 174 ARG cc_start: 0.7705 (mmm-85) cc_final: 0.7464 (mmm-85) REVERT: C 200 TYR cc_start: 0.7466 (m-80) cc_final: 0.6930 (m-80) REVERT: C 224 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8004 (mt) REVERT: C 310 PHE cc_start: 0.8360 (t80) cc_final: 0.8102 (t80) REVERT: E 78 ILE cc_start: 0.7743 (tt) cc_final: 0.7506 (tt) REVERT: E 184 ASN cc_start: 0.8592 (t0) cc_final: 0.6938 (t0) REVERT: E 318 ARG cc_start: 0.7404 (ttm110) cc_final: 0.7057 (ttp-170) REVERT: G 16 ASN cc_start: 0.6807 (t0) cc_final: 0.6504 (t0) REVERT: G 39 ASP cc_start: 0.7620 (OUTLIER) cc_final: 0.7280 (p0) REVERT: G 42 HIS cc_start: 0.7718 (m90) cc_final: 0.6725 (m90) REVERT: G 67 PHE cc_start: 0.7749 (m-10) cc_final: 0.7519 (m-80) REVERT: G 91 LYS cc_start: 0.8498 (mtmt) cc_final: 0.8256 (mtmm) REVERT: G 171 ARG cc_start: 0.6332 (OUTLIER) cc_final: 0.6079 (ptm-80) REVERT: G 174 ARG cc_start: 0.7588 (mpt90) cc_final: 0.7081 (tpt-90) REVERT: I 19 ILE cc_start: 0.7639 (OUTLIER) cc_final: 0.7267 (tp) REVERT: I 102 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.6398 (mm-40) REVERT: I 171 ARG cc_start: 0.6898 (ptt180) cc_final: 0.5625 (mpt180) REVERT: I 305 ASN cc_start: 0.8323 (m-40) cc_final: 0.8119 (m-40) REVERT: K 67 PHE cc_start: 0.8096 (OUTLIER) cc_final: 0.7327 (t80) REVERT: K 120 LEU cc_start: 0.8193 (mt) cc_final: 0.7863 (mt) REVERT: K 195 GLN cc_start: 0.7026 (tm-30) cc_final: 0.6730 (pp30) REVERT: K 253 ILE cc_start: 0.6728 (OUTLIER) cc_final: 0.6217 (pp) REVERT: K 312 ARG cc_start: 0.7846 (ptm160) cc_final: 0.7405 (ttp80) REVERT: M 115 GLN cc_start: 0.8542 (mt0) cc_final: 0.8172 (mt0) REVERT: M 141 PHE cc_start: 0.8499 (t80) cc_final: 0.8106 (t80) REVERT: M 307 GLU cc_start: 0.6758 (mp0) cc_final: 0.6492 (mt-10) REVERT: O 51 ASN cc_start: 0.6991 (OUTLIER) cc_final: 0.6721 (t0) REVERT: O 112 GLN cc_start: 0.6803 (pm20) cc_final: 0.6542 (pt0) REVERT: O 134 ASN cc_start: 0.6754 (OUTLIER) cc_final: 0.6238 (p0) REVERT: O 157 LYS cc_start: 0.7156 (mmmm) cc_final: 0.6821 (mmmt) REVERT: O 171 ARG cc_start: 0.7040 (mtm-85) cc_final: 0.6240 (mtt-85) REVERT: O 223 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.8111 (tt0) REVERT: O 270 ASN cc_start: 0.7505 (t0) cc_final: 0.7106 (m-40) outliers start: 86 outliers final: 58 residues processed: 459 average time/residue: 0.3434 time to fit residues: 239.0412 Evaluate side-chains 447 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 378 time to evaluate : 2.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 150 HIS Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 36 CYS Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 102 GLN Chi-restraints excluded: chain C residue 195 GLN Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 51 ASN Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 195 GLN Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 171 ARG Chi-restraints excluded: chain G residue 285 LEU Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 36 CYS Chi-restraints excluded: chain I residue 62 MET Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 102 GLN Chi-restraints excluded: chain I residue 167 THR Chi-restraints excluded: chain I residue 169 CYS Chi-restraints excluded: chain I residue 229 CYS Chi-restraints excluded: chain I residue 253 ILE Chi-restraints excluded: chain I residue 293 THR Chi-restraints excluded: chain I residue 311 LEU Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 150 HIS Chi-restraints excluded: chain K residue 253 ILE Chi-restraints excluded: chain M residue 57 PHE Chi-restraints excluded: chain M residue 90 ILE Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 151 SER Chi-restraints excluded: chain M residue 168 PHE Chi-restraints excluded: chain M residue 240 VAL Chi-restraints excluded: chain M residue 242 SER Chi-restraints excluded: chain M residue 294 TYR Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 51 ASN Chi-restraints excluded: chain O residue 134 ASN Chi-restraints excluded: chain O residue 142 THR Chi-restraints excluded: chain O residue 149 ILE Chi-restraints excluded: chain O residue 150 HIS Chi-restraints excluded: chain O residue 169 CYS Chi-restraints excluded: chain O residue 223 GLU Chi-restraints excluded: chain O residue 224 LEU Chi-restraints excluded: chain O residue 293 THR Chi-restraints excluded: chain O residue 297 LEU Chi-restraints excluded: chain O residue 316 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 207 optimal weight: 4.9990 chunk 111 optimal weight: 0.1980 chunk 151 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 170 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 152 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 64 optimal weight: 0.0980 chunk 79 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN ** M 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 195 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.216635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.194111 restraints weight = 20178.091| |-----------------------------------------------------------------------------| r_work (start): 0.4155 rms_B_bonded: 1.64 r_work: 0.4061 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3934 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 19306 Z= 0.120 Angle : 0.544 10.871 26142 Z= 0.288 Chirality : 0.043 0.192 2873 Planarity : 0.004 0.072 3460 Dihedral : 4.572 21.252 2572 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.47 % Allowed : 25.65 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.45 (0.17), residues: 2285 helix: 1.13 (0.20), residues: 726 sheet: -1.30 (0.34), residues: 213 loop : -0.94 (0.16), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 46 HIS 0.005 0.001 HIS M 81 PHE 0.023 0.001 PHE E 74 TYR 0.017 0.001 TYR E 301 ARG 0.008 0.000 ARG I 189 Details of bonding type rmsd hydrogen bonds : bond 0.03234 ( 649) hydrogen bonds : angle 5.17744 ( 1731) metal coordination : bond 0.02067 ( 28) metal coordination : angle 3.44567 ( 21) SS BOND : bond 0.00292 ( 9) SS BOND : angle 1.49512 ( 18) covalent geometry : bond 0.00277 (19269) covalent geometry : angle 0.53417 (26103) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 389 time to evaluate : 2.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 SER cc_start: 0.8565 (t) cc_final: 0.8248 (p) REVERT: A 43 ASP cc_start: 0.8100 (t70) cc_final: 0.7834 (t70) REVERT: A 265 ARG cc_start: 0.7106 (ttm170) cc_final: 0.6858 (tpm170) REVERT: A 269 ARG cc_start: 0.4390 (mtm-85) cc_final: 0.3111 (mtm180) REVERT: A 311 LEU cc_start: 0.8718 (mm) cc_final: 0.8505 (mm) REVERT: C 102 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.6629 (mm-40) REVERT: C 171 ARG cc_start: 0.7668 (mtm-85) cc_final: 0.5917 (mmt180) REVERT: C 174 ARG cc_start: 0.7749 (mmm-85) cc_final: 0.7248 (mmm-85) REVERT: C 200 TYR cc_start: 0.7538 (m-80) cc_final: 0.7042 (m-80) REVERT: C 224 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7992 (mt) REVERT: C 310 PHE cc_start: 0.8295 (t80) cc_final: 0.8052 (t80) REVERT: E 15 VAL cc_start: 0.7267 (OUTLIER) cc_final: 0.7060 (t) REVERT: E 105 PHE cc_start: 0.7514 (m-10) cc_final: 0.7148 (m-10) REVERT: E 184 ASN cc_start: 0.8547 (t0) cc_final: 0.8309 (t0) REVERT: G 16 ASN cc_start: 0.6745 (t0) cc_final: 0.6481 (t0) REVERT: G 39 ASP cc_start: 0.7449 (OUTLIER) cc_final: 0.7151 (p0) REVERT: G 42 HIS cc_start: 0.7520 (m90) cc_final: 0.6615 (m90) REVERT: G 67 PHE cc_start: 0.7728 (m-10) cc_final: 0.7488 (m-80) REVERT: G 91 LYS cc_start: 0.8554 (mtmt) cc_final: 0.8308 (mtmm) REVERT: G 171 ARG cc_start: 0.6400 (OUTLIER) cc_final: 0.6136 (ptm-80) REVERT: G 174 ARG cc_start: 0.7526 (mpt90) cc_final: 0.7124 (tpt-90) REVERT: G 189 ARG cc_start: 0.7568 (ttp-110) cc_final: 0.7194 (mtm110) REVERT: I 19 ILE cc_start: 0.7568 (OUTLIER) cc_final: 0.7186 (tp) REVERT: I 102 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.6271 (mm-40) REVERT: I 171 ARG cc_start: 0.6884 (ptt180) cc_final: 0.5647 (mpt180) REVERT: I 305 ASN cc_start: 0.8301 (m-40) cc_final: 0.8077 (m-40) REVERT: K 67 PHE cc_start: 0.8055 (OUTLIER) cc_final: 0.7321 (t80) REVERT: K 120 LEU cc_start: 0.8200 (mt) cc_final: 0.7873 (mt) REVERT: K 195 GLN cc_start: 0.7074 (tm-30) cc_final: 0.6795 (pp30) REVERT: K 253 ILE cc_start: 0.6520 (OUTLIER) cc_final: 0.6002 (pp) REVERT: K 312 ARG cc_start: 0.7763 (ptm160) cc_final: 0.7368 (ttp80) REVERT: M 115 GLN cc_start: 0.8530 (mt0) cc_final: 0.8193 (mt0) REVERT: M 141 PHE cc_start: 0.8440 (t80) cc_final: 0.8062 (t80) REVERT: M 307 GLU cc_start: 0.6642 (mp0) cc_final: 0.6424 (mt-10) REVERT: O 51 ASN cc_start: 0.6771 (OUTLIER) cc_final: 0.6396 (t0) REVERT: O 110 MET cc_start: 0.4662 (mtt) cc_final: 0.3293 (tpp) REVERT: O 134 ASN cc_start: 0.6597 (OUTLIER) cc_final: 0.6091 (p0) REVERT: O 157 LYS cc_start: 0.7121 (mmmm) cc_final: 0.6810 (mmmt) REVERT: O 171 ARG cc_start: 0.6877 (mtm-85) cc_final: 0.6225 (mtt-85) REVERT: O 223 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.8112 (tt0) REVERT: O 270 ASN cc_start: 0.7530 (t0) cc_final: 0.7096 (m-40) outliers start: 73 outliers final: 57 residues processed: 445 average time/residue: 0.3668 time to fit residues: 245.1497 Evaluate side-chains 437 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 368 time to evaluate : 1.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 150 HIS Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 36 CYS Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 102 GLN Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 51 ASN Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 195 GLN Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 171 ARG Chi-restraints excluded: chain G residue 285 LEU Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 36 CYS Chi-restraints excluded: chain I residue 62 MET Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 102 GLN Chi-restraints excluded: chain I residue 167 THR Chi-restraints excluded: chain I residue 169 CYS Chi-restraints excluded: chain I residue 229 CYS Chi-restraints excluded: chain I residue 253 ILE Chi-restraints excluded: chain I residue 293 THR Chi-restraints excluded: chain I residue 311 LEU Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 150 HIS Chi-restraints excluded: chain K residue 253 ILE Chi-restraints excluded: chain M residue 57 PHE Chi-restraints excluded: chain M residue 90 ILE Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 168 PHE Chi-restraints excluded: chain M residue 195 GLN Chi-restraints excluded: chain M residue 240 VAL Chi-restraints excluded: chain M residue 242 SER Chi-restraints excluded: chain M residue 245 ASP Chi-restraints excluded: chain M residue 294 TYR Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 51 ASN Chi-restraints excluded: chain O residue 134 ASN Chi-restraints excluded: chain O residue 142 THR Chi-restraints excluded: chain O residue 149 ILE Chi-restraints excluded: chain O residue 150 HIS Chi-restraints excluded: chain O residue 169 CYS Chi-restraints excluded: chain O residue 195 GLN Chi-restraints excluded: chain O residue 223 GLU Chi-restraints excluded: chain O residue 224 LEU Chi-restraints excluded: chain O residue 229 CYS Chi-restraints excluded: chain O residue 293 THR Chi-restraints excluded: chain O residue 316 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 74 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 126 optimal weight: 0.9980 chunk 160 optimal weight: 8.9990 chunk 196 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 ASN ** G 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 195 GLN ** O 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.215695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.192181 restraints weight = 20379.178| |-----------------------------------------------------------------------------| r_work (start): 0.4182 rms_B_bonded: 1.74 r_work: 0.4085 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3955 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.134 19306 Z= 0.211 Angle : 0.731 59.189 26142 Z= 0.421 Chirality : 0.047 0.468 2873 Planarity : 0.004 0.072 3460 Dihedral : 4.579 21.008 2572 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.00 % Allowed : 25.08 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.48 (0.17), residues: 2285 helix: 1.09 (0.19), residues: 726 sheet: -1.29 (0.34), residues: 213 loop : -0.96 (0.16), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 46 HIS 0.006 0.001 HIS C 81 PHE 0.027 0.002 PHE C 315 TYR 0.015 0.002 TYR E 301 ARG 0.019 0.001 ARG E 318 Details of bonding type rmsd hydrogen bonds : bond 0.03305 ( 649) hydrogen bonds : angle 5.18815 ( 1731) metal coordination : bond 0.02293 ( 28) metal coordination : angle 3.65563 ( 21) SS BOND : bond 0.00841 ( 9) SS BOND : angle 1.77804 ( 18) covalent geometry : bond 0.00498 (19269) covalent geometry : angle 0.72282 (26103) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12429.35 seconds wall clock time: 215 minutes 49.30 seconds (12949.30 seconds total)