Starting phenix.real_space_refine on Thu Sep 18 17:29:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vwh_43586/09_2025/8vwh_43586.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vwh_43586/09_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_43586/09_2025/8vwh_43586.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vwh_43586/09_2025/8vwh_43586.map" model { file = "/net/cci-nas-00/data/ceres_data/8vwh_43586/09_2025/8vwh_43586.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vwh_43586/09_2025/8vwh_43586.cif" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 4.48, per 1000 atoms: 0.24 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: 1.53 Conformation dependent library (CDL) restraints added in 713.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.61 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: 2.76 Time building geometry restraints manager: 2.05 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: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 18.880 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.300 ------------------------------------------------------------------------------- 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 : 10.61 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (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 ARG 0.003 0.000 ARG E 80 TYR 0.012 0.001 TYR E 301 PHE 0.016 0.001 PHE K 168 TRP 0.008 0.002 TRP C 46 HIS 0.005 0.001 HIS K 81 Details of bonding type rmsd covalent geometry : bond 0.00228 (19269) covalent geometry : angle 0.43815 (26103) SS BOND : bond 0.00269 ( 9) SS BOND : angle 0.97198 ( 18) hydrogen bonds : bond 0.20993 ( 649) hydrogen bonds : angle 8.29710 ( 1731) metal coordination : bond 0.02433 ( 28) metal coordination : angle 4.68604 ( 21) *********************** 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 : 0.794 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: 0.8443 (m) REVERT: C 112 GLN cc_start: 0.7402 (mt0) cc_final: 0.7195 (mt0) REVERT: C 171 ARG cc_start: 0.7434 (mtm-85) cc_final: 0.5539 (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: 0.7150 (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: 0.7886 (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: 0.8626 (mt) REVERT: I 150 HIS cc_start: 0.7877 (t70) cc_final: 0.6905 (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: 0.8116 (tt) REVERT: K 215 GLU cc_start: 0.7642 (tt0) cc_final: 0.7280 (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: 0.8003 (t80) 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: 0.1538 time to fit residues: 115.3301 Evaluate side-chains 440 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 440 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.0020 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 3.9990 overall best weight: 1.9794 ------------------------------------------------------------------------------- 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 262 GLN C 320 ASN E 134 ASN E 305 ASN G 195 GLN I 16 ASN K 50 ASN K 195 GLN K 267 GLN ** M 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 124 ASN O 134 ASN O 195 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.210208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.185561 restraints weight = 20210.636| |-----------------------------------------------------------------------------| r_work (start): 0.4066 rms_B_bonded: 1.82 r_work: 0.3973 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3837 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.143 19306 Z= 0.215 Angle : 0.621 18.973 26142 Z= 0.331 Chirality : 0.046 0.191 2873 Planarity : 0.005 0.074 3460 Dihedral : 4.976 21.463 2572 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 4.71 % Allowed : 22.23 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.17), residues: 2285 helix: 0.66 (0.19), residues: 712 sheet: -1.26 (0.35), residues: 217 loop : -1.00 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 189 TYR 0.019 0.002 TYR M 216 PHE 0.027 0.002 PHE G 315 TRP 0.011 0.002 TRP C 46 HIS 0.009 0.002 HIS G 81 Details of bonding type rmsd covalent geometry : bond 0.00505 (19269) covalent geometry : angle 0.59732 (26103) SS BOND : bond 0.00747 ( 9) SS BOND : angle 2.49794 ( 18) hydrogen bonds : bond 0.04599 ( 649) hydrogen bonds : angle 6.12092 ( 1731) metal coordination : bond 0.03757 ( 28) metal coordination : angle 5.58897 ( 21) *********************** 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 538 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 439 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.8244 (mtt90) cc_final: 0.8011 (mtt90) REVERT: A 43 ASP cc_start: 0.8107 (t70) cc_final: 0.7792 (t70) REVERT: A 101 TYR cc_start: 0.8407 (p90) cc_final: 0.8147 (p90) REVERT: A 194 ASP cc_start: 0.7162 (t0) cc_final: 0.6810 (t0) REVERT: A 265 ARG cc_start: 0.7128 (ttm170) cc_final: 0.6644 (tpm170) REVERT: C 60 SER cc_start: 0.8732 (t) cc_final: 0.8413 (m) REVERT: C 112 GLN cc_start: 0.7707 (mt0) cc_final: 0.7506 (mp10) REVERT: C 171 ARG cc_start: 0.7740 (mtm-85) cc_final: 0.5843 (mmt180) REVERT: C 174 ARG cc_start: 0.7631 (mmm-85) cc_final: 0.7420 (mmm-85) REVERT: C 200 TYR cc_start: 0.7940 (m-80) cc_final: 0.7376 (m-80) REVERT: C 310 PHE cc_start: 0.8529 (t80) cc_final: 0.8261 (t80) REVERT: E 59 MET cc_start: 0.7269 (mtt) cc_final: 0.7054 (mtt) REVERT: E 68 ASP cc_start: 0.7405 (p0) cc_final: 0.7095 (p0) REVERT: G 16 ASN cc_start: 0.7225 (t0) cc_final: 0.6906 (t0) REVERT: G 67 PHE cc_start: 0.7987 (m-10) cc_final: 0.7642 (m-80) REVERT: G 174 ARG cc_start: 0.7387 (mpt90) cc_final: 0.6855 (tpt-90) REVERT: G 184 ASN cc_start: 0.7659 (OUTLIER) cc_final: 0.7445 (m-40) REVERT: G 248 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7850 (mm-30) REVERT: I 102 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.6415 (mm-40) REVERT: I 150 HIS cc_start: 0.8062 (t70) cc_final: 0.6892 (m-70) REVERT: I 171 ARG cc_start: 0.6873 (ptt180) cc_final: 0.5658 (mtt90) REVERT: K 67 PHE cc_start: 0.7896 (OUTLIER) cc_final: 0.7365 (t80) REVERT: K 110 MET cc_start: 0.8208 (mtt) cc_final: 0.7969 (mtt) REVERT: K 120 LEU cc_start: 0.8235 (mt) cc_final: 0.7925 (mt) REVERT: K 149 ILE cc_start: 0.8683 (tt) cc_final: 0.8467 (tt) REVERT: K 253 ILE cc_start: 0.6724 (OUTLIER) cc_final: 0.6222 (pp) REVERT: K 269 ARG cc_start: 0.8054 (ptt180) cc_final: 0.7577 (ptt-90) REVERT: K 307 GLU cc_start: 0.7859 (pm20) cc_final: 0.7643 (pm20) REVERT: K 312 ARG cc_start: 0.7939 (ptm160) cc_final: 0.7362 (ttp80) REVERT: M 107 LEU cc_start: 0.8195 (mt) cc_final: 0.7942 (mt) REVERT: M 122 TYR cc_start: 0.8390 (m-80) cc_final: 0.7668 (m-80) REVERT: M 141 PHE cc_start: 0.8507 (t80) cc_final: 0.8086 (t80) REVERT: O 51 ASN cc_start: 0.7007 (OUTLIER) cc_final: 0.6612 (t0) REVERT: O 109 SER cc_start: 0.6822 (p) cc_final: 0.6616 (m) REVERT: O 112 GLN cc_start: 0.7228 (pm20) cc_final: 0.6950 (pm20) REVERT: O 171 ARG cc_start: 0.7481 (mtm-85) cc_final: 0.6848 (mtt-85) REVERT: O 173 SER cc_start: 0.7246 (m) cc_final: 0.6915 (p) REVERT: O 176 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6959 (pt0) REVERT: O 198 ASN cc_start: 0.7263 (m-40) cc_final: 0.6865 (p0) REVERT: O 270 ASN cc_start: 0.7473 (t0) cc_final: 0.7033 (m-40) REVERT: O 301 TYR cc_start: 0.8129 (t80) cc_final: 0.7638 (t80) outliers start: 99 outliers final: 48 residues processed: 511 average time/residue: 0.1656 time to fit residues: 125.2504 Evaluate side-chains 456 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 402 time to evaluate : 0.800 ------------------------------------------------------------------------------- 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 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 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 E residue 316 ILE Chi-restraints excluded: chain G residue 184 ASN Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain G residue 270 ASN 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 77 THR 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 234 ILE Chi-restraints excluded: chain I residue 253 ILE Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 253 ILE Chi-restraints excluded: chain M residue 23 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 182 VAL Chi-restraints excluded: chain M residue 240 VAL Chi-restraints excluded: chain M residue 242 SER Chi-restraints excluded: chain M residue 268 ILE Chi-restraints excluded: chain M residue 284 THR Chi-restraints excluded: chain M residue 294 TYR 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 176 GLU Chi-restraints excluded: chain O residue 195 GLN Chi-restraints excluded: chain O residue 224 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 11 optimal weight: 6.9990 chunk 219 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 194 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 176 optimal weight: 0.5980 chunk 17 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 225 optimal weight: 6.9990 chunk 161 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 199 ASN G 42 HIS ** G 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 267 GLN ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 267 GLN M 100 ASN ** M 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.205278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.179506 restraints weight = 20526.655| |-----------------------------------------------------------------------------| r_work (start): 0.4050 rms_B_bonded: 1.89 r_work: 0.3955 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3819 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.1721 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= 0.207 Angle : 0.610 17.133 26142 Z= 0.324 Chirality : 0.046 0.161 2873 Planarity : 0.005 0.076 3460 Dihedral : 5.067 20.515 2572 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 5.90 % Allowed : 21.66 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.17), residues: 2285 helix: 0.56 (0.19), residues: 710 sheet: -1.32 (0.34), residues: 219 loop : -1.10 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 189 TYR 0.023 0.002 TYR E 301 PHE 0.039 0.002 PHE G 315 TRP 0.012 0.002 TRP C 46 HIS 0.008 0.002 HIS O 81 Details of bonding type rmsd covalent geometry : bond 0.00489 (19269) covalent geometry : angle 0.58758 (26103) SS BOND : bond 0.00735 ( 9) SS BOND : angle 2.37463 ( 18) hydrogen bonds : bond 0.04227 ( 649) hydrogen bonds : angle 5.90017 ( 1731) metal coordination : bond 0.03721 ( 28) metal coordination : angle 5.34087 ( 21) *********************** 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 528 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 404 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 SER cc_start: 0.8676 (t) cc_final: 0.8312 (p) REVERT: A 43 ASP cc_start: 0.8106 (t70) cc_final: 0.7803 (t70) REVERT: A 101 TYR cc_start: 0.8418 (p90) cc_final: 0.8117 (p90) REVERT: A 194 ASP cc_start: 0.7243 (t0) cc_final: 0.6808 (t0) REVERT: A 265 ARG cc_start: 0.7129 (ttm170) cc_final: 0.6611 (tpm170) REVERT: A 269 ARG cc_start: 0.4230 (mtm-85) cc_final: 0.3538 (mtm-85) REVERT: C 102 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.6696 (mm-40) REVERT: C 112 GLN cc_start: 0.7688 (mt0) cc_final: 0.7466 (mp10) REVERT: C 131 ILE cc_start: 0.7826 (OUTLIER) cc_final: 0.7602 (tt) REVERT: C 171 ARG cc_start: 0.7682 (mtm-85) cc_final: 0.5784 (mmt180) REVERT: C 174 ARG cc_start: 0.7654 (mmm-85) cc_final: 0.7445 (mmm-85) REVERT: C 200 TYR cc_start: 0.7982 (m-80) cc_final: 0.7360 (m-80) REVERT: C 310 PHE cc_start: 0.8556 (t80) cc_final: 0.8297 (t80) REVERT: E 59 MET cc_start: 0.7655 (mtt) cc_final: 0.7328 (mtt) REVERT: E 68 ASP cc_start: 0.7296 (p0) cc_final: 0.6946 (p0) REVERT: E 92 ARG cc_start: 0.6501 (mtp85) cc_final: 0.6299 (mtp85) REVERT: G 16 ASN cc_start: 0.7093 (t0) cc_final: 0.6746 (t0) REVERT: G 67 PHE cc_start: 0.7937 (m-10) cc_final: 0.7695 (m-80) REVERT: G 68 ASP cc_start: 0.6249 (OUTLIER) cc_final: 0.5876 (m-30) REVERT: G 174 ARG cc_start: 0.7452 (mpt90) cc_final: 0.6846 (tpt-90) REVERT: G 248 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7839 (mm-30) REVERT: I 17 ARG cc_start: 0.8765 (ttm-80) cc_final: 0.8539 (ttm110) REVERT: I 19 ILE cc_start: 0.7835 (OUTLIER) cc_final: 0.7511 (tp) REVERT: I 102 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.6346 (mm-40) REVERT: I 150 HIS cc_start: 0.8273 (t70) cc_final: 0.6922 (m-70) REVERT: I 171 ARG cc_start: 0.6858 (ptt180) cc_final: 0.5637 (mtt90) REVERT: K 67 PHE cc_start: 0.8084 (OUTLIER) cc_final: 0.7394 (t80) REVERT: K 115 GLN cc_start: 0.7704 (mt0) cc_final: 0.7425 (mt0) REVERT: K 120 LEU cc_start: 0.8165 (mt) cc_final: 0.7817 (mt) REVERT: K 224 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8129 (mt) REVERT: K 253 ILE cc_start: 0.6680 (OUTLIER) cc_final: 0.6192 (pp) REVERT: K 269 ARG cc_start: 0.8047 (ptt180) cc_final: 0.7592 (ptt-90) REVERT: K 312 ARG cc_start: 0.7912 (ptm160) cc_final: 0.7318 (ttp80) REVERT: M 122 TYR cc_start: 0.8355 (m-80) cc_final: 0.7597 (m-80) REVERT: M 141 PHE cc_start: 0.8543 (t80) cc_final: 0.8037 (t80) REVERT: O 51 ASN cc_start: 0.7168 (OUTLIER) cc_final: 0.6824 (t0) REVERT: O 134 ASN cc_start: 0.6410 (OUTLIER) cc_final: 0.5847 (p0) REVERT: O 171 ARG cc_start: 0.7569 (mtm-85) cc_final: 0.6872 (mtt-85) REVERT: O 173 SER cc_start: 0.7150 (m) cc_final: 0.6950 (p) REVERT: O 198 ASN cc_start: 0.7141 (m-40) cc_final: 0.6757 (p0) REVERT: O 270 ASN cc_start: 0.7376 (t0) cc_final: 0.6906 (m-40) REVERT: O 301 TYR cc_start: 0.8166 (t80) cc_final: 0.7685 (t80) outliers start: 124 outliers final: 77 residues processed: 502 average time/residue: 0.1506 time to fit residues: 113.5379 Evaluate side-chains 472 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 385 time to evaluate : 0.672 ------------------------------------------------------------------------------- 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 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 77 THR Chi-restraints excluded: chain C residue 102 GLN Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 131 ILE 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 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 90 ILE 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 195 GLN Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain G residue 59 MET Chi-restraints excluded: chain G residue 68 ASP Chi-restraints excluded: chain G residue 135 LEU 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 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 77 THR Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 102 GLN Chi-restraints excluded: chain I residue 103 ASP Chi-restraints excluded: chain I residue 167 THR Chi-restraints excluded: chain I residue 169 CYS Chi-restraints excluded: chain I residue 234 ILE 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 63 VAL Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 195 GLN Chi-restraints excluded: chain K residue 224 LEU Chi-restraints excluded: chain K residue 253 ILE Chi-restraints excluded: chain M residue 23 ILE Chi-restraints excluded: chain M residue 57 PHE 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 195 GLN 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 268 ILE 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 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 149 ILE Chi-restraints excluded: chain O residue 150 HIS Chi-restraints excluded: chain O residue 152 VAL Chi-restraints excluded: chain O residue 169 CYS Chi-restraints excluded: chain O residue 204 LEU Chi-restraints excluded: chain O residue 224 LEU Chi-restraints excluded: chain O residue 234 ILE Chi-restraints excluded: chain O residue 239 LEU Chi-restraints excluded: chain O residue 293 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 227 optimal weight: 2.9990 chunk 229 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 230 optimal weight: 3.9990 chunk 194 optimal weight: 0.5980 chunk 189 optimal weight: 0.1980 chunk 56 optimal weight: 0.0020 chunk 201 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 123 optimal weight: 6.9990 chunk 121 optimal weight: 2.9990 overall best weight: 0.9590 ------------------------------------------------------------------------------- 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** E 199 ASN G 42 HIS G 270 ASN I 16 ASN I 267 GLN ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 267 GLN M 100 ASN M 251 ASN O 106 ASN ** O 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 195 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.209313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.184124 restraints weight = 20356.765| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 1.87 r_work: 0.4005 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3869 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 19306 Z= 0.138 Angle : 0.545 10.358 26142 Z= 0.292 Chirality : 0.043 0.161 2873 Planarity : 0.004 0.072 3460 Dihedral : 4.874 19.650 2572 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 5.52 % Allowed : 22.56 % Favored : 71.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.17), residues: 2285 helix: 0.77 (0.19), residues: 713 sheet: -1.61 (0.33), residues: 226 loop : -1.00 (0.16), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 17 TYR 0.022 0.002 TYR E 301 PHE 0.032 0.002 PHE G 315 TRP 0.008 0.002 TRP G 46 HIS 0.005 0.001 HIS K 119 Details of bonding type rmsd covalent geometry : bond 0.00321 (19269) covalent geometry : angle 0.53269 (26103) SS BOND : bond 0.00597 ( 9) SS BOND : angle 1.76264 ( 18) hydrogen bonds : bond 0.03629 ( 649) hydrogen bonds : angle 5.58749 ( 1731) metal coordination : bond 0.02648 ( 28) metal coordination : angle 3.77744 ( 21) *********************** 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 529 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 413 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.8398 (mtt90) cc_final: 0.8018 (mtt90) REVERT: A 25 SER cc_start: 0.8662 (t) cc_final: 0.8299 (p) REVERT: A 43 ASP cc_start: 0.8026 (t70) cc_final: 0.7714 (t70) REVERT: A 101 TYR cc_start: 0.8395 (p90) cc_final: 0.8101 (p90) REVERT: A 265 ARG cc_start: 0.7179 (ttm170) cc_final: 0.6608 (tpm170) REVERT: A 269 ARG cc_start: 0.4558 (mtm-85) cc_final: 0.3582 (mtm180) REVERT: C 102 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.6642 (mm-40) REVERT: C 112 GLN cc_start: 0.7704 (mt0) cc_final: 0.7501 (mp10) REVERT: C 171 ARG cc_start: 0.7648 (mtm-85) cc_final: 0.5789 (mmt180) REVERT: C 174 ARG cc_start: 0.7654 (mmm-85) cc_final: 0.7445 (mmm-85) REVERT: C 200 TYR cc_start: 0.7764 (m-80) cc_final: 0.7169 (m-80) REVERT: C 224 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8245 (mt) REVERT: C 310 PHE cc_start: 0.8484 (t80) cc_final: 0.8234 (t80) REVERT: E 68 ASP cc_start: 0.7296 (p0) cc_final: 0.6890 (p0) REVERT: E 105 PHE cc_start: 0.7664 (m-80) cc_final: 0.7434 (m-80) REVERT: G 16 ASN cc_start: 0.7038 (t0) cc_final: 0.6701 (t0) REVERT: G 42 HIS cc_start: 0.7835 (m90) cc_final: 0.6861 (m90) REVERT: G 62 MET cc_start: 0.7515 (mtm) cc_final: 0.7295 (mtp) REVERT: G 67 PHE cc_start: 0.7882 (m-10) cc_final: 0.7586 (m-80) REVERT: G 68 ASP cc_start: 0.6122 (OUTLIER) cc_final: 0.5723 (m-30) REVERT: G 174 ARG cc_start: 0.7588 (mpt90) cc_final: 0.6944 (tpt-90) REVERT: G 248 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7868 (mm-30) REVERT: G 273 LYS cc_start: 0.8149 (ptmt) cc_final: 0.7589 (pttm) REVERT: I 102 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.6318 (mm-40) REVERT: I 171 ARG cc_start: 0.6890 (ptt180) cc_final: 0.5682 (mtt90) REVERT: K 67 PHE cc_start: 0.8073 (OUTLIER) cc_final: 0.7374 (t80) REVERT: K 120 LEU cc_start: 0.8176 (mt) cc_final: 0.7837 (mt) REVERT: K 149 ILE cc_start: 0.8488 (tt) cc_final: 0.8228 (pt) REVERT: K 224 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8239 (mt) REVERT: K 253 ILE cc_start: 0.6679 (OUTLIER) cc_final: 0.6188 (pp) REVERT: K 267 GLN cc_start: 0.7446 (mt0) cc_final: 0.7172 (pm20) REVERT: K 269 ARG cc_start: 0.8041 (ptt180) cc_final: 0.7595 (ptt-90) REVERT: K 312 ARG cc_start: 0.7874 (ptm160) cc_final: 0.7309 (ttp80) REVERT: M 141 PHE cc_start: 0.8556 (t80) cc_final: 0.8066 (t80) REVERT: O 51 ASN cc_start: 0.6943 (OUTLIER) cc_final: 0.6615 (t0) REVERT: O 62 MET cc_start: 0.7131 (mtm) cc_final: 0.6918 (mtp) REVERT: O 76 MET cc_start: 0.7574 (ttm) cc_final: 0.6970 (ttt) REVERT: O 134 ASN cc_start: 0.6606 (OUTLIER) cc_final: 0.5901 (p0) REVERT: O 157 LYS cc_start: 0.7175 (mmmm) cc_final: 0.6829 (mmmt) REVERT: O 171 ARG cc_start: 0.7463 (mtm-85) cc_final: 0.6656 (mtt-85) REVERT: O 198 ASN cc_start: 0.6893 (m-40) cc_final: 0.6634 (p0) REVERT: O 270 ASN cc_start: 0.7266 (t0) cc_final: 0.6873 (m-40) REVERT: O 310 PHE cc_start: 0.8091 (OUTLIER) cc_final: 0.7746 (m-10) outliers start: 116 outliers final: 76 residues processed: 502 average time/residue: 0.1539 time to fit residues: 115.1932 Evaluate side-chains 475 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 389 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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 253 ILE 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 267 GLN Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 42 HIS 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 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 66 ILE Chi-restraints excluded: chain G residue 68 ASP Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 175 ASP Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain G residue 271 VAL 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 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 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 224 LEU Chi-restraints excluded: chain K residue 253 ILE Chi-restraints excluded: chain M residue 23 ILE Chi-restraints excluded: chain M residue 57 PHE Chi-restraints excluded: chain M residue 90 ILE Chi-restraints excluded: chain M residue 132 CYS 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 268 ILE Chi-restraints excluded: chain M residue 294 TYR Chi-restraints excluded: chain M residue 306 SER 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 108 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 152 VAL Chi-restraints excluded: chain O residue 169 CYS Chi-restraints excluded: chain O residue 195 GLN Chi-restraints excluded: chain O residue 204 LEU Chi-restraints excluded: chain O residue 224 LEU Chi-restraints excluded: chain O residue 234 ILE Chi-restraints excluded: chain O residue 239 LEU Chi-restraints excluded: chain O residue 293 THR Chi-restraints excluded: chain O residue 310 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 114 optimal weight: 6.9990 chunk 28 optimal weight: 0.1980 chunk 127 optimal weight: 0.9990 chunk 123 optimal weight: 0.4980 chunk 56 optimal weight: 0.0040 chunk 230 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 202 optimal weight: 3.9990 chunk 180 optimal weight: 7.9990 overall best weight: 1.1396 ------------------------------------------------------------------------------- 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** E 199 ASN ** E 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 228 ASN I 267 GLN ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 115 GLN M 100 ASN ** M 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 134 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.208742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.183495 restraints weight = 20339.442| |-----------------------------------------------------------------------------| r_work (start): 0.4091 rms_B_bonded: 1.87 r_work: 0.4000 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3866 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 19306 Z= 0.152 Angle : 0.562 10.816 26142 Z= 0.299 Chirality : 0.044 0.159 2873 Planarity : 0.004 0.073 3460 Dihedral : 4.881 21.235 2572 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 5.47 % Allowed : 23.04 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.17), residues: 2285 helix: 0.76 (0.19), residues: 718 sheet: -1.62 (0.33), residues: 226 loop : -0.98 (0.16), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 318 TYR 0.021 0.002 TYR E 301 PHE 0.025 0.002 PHE G 315 TRP 0.009 0.002 TRP C 46 HIS 0.006 0.001 HIS K 81 Details of bonding type rmsd covalent geometry : bond 0.00357 (19269) covalent geometry : angle 0.54861 (26103) SS BOND : bond 0.00509 ( 9) SS BOND : angle 1.90295 ( 18) hydrogen bonds : bond 0.03660 ( 649) hydrogen bonds : angle 5.51885 ( 1731) metal coordination : bond 0.02739 ( 28) metal coordination : angle 3.97951 ( 21) *********************** 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 515 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 400 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.8340 (mtt90) cc_final: 0.7847 (mtt90) REVERT: A 25 SER cc_start: 0.8640 (t) cc_final: 0.8292 (p) REVERT: A 43 ASP cc_start: 0.8055 (t70) cc_final: 0.7736 (t70) REVERT: A 101 TYR cc_start: 0.8378 (p90) cc_final: 0.8091 (p90) REVERT: A 265 ARG cc_start: 0.7205 (ttm170) cc_final: 0.6632 (tpm170) REVERT: A 269 ARG cc_start: 0.4386 (mtm-85) cc_final: 0.3128 (mtm180) REVERT: C 102 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.6664 (mm-40) REVERT: C 171 ARG cc_start: 0.7664 (mtm-85) cc_final: 0.5798 (mmt180) REVERT: C 174 ARG cc_start: 0.7671 (mmm-85) cc_final: 0.7459 (mmm-85) REVERT: C 200 TYR cc_start: 0.7712 (m-80) cc_final: 0.7124 (m-80) REVERT: C 224 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8253 (mt) REVERT: C 310 PHE cc_start: 0.8469 (t80) cc_final: 0.8219 (t80) REVERT: E 59 MET cc_start: 0.6969 (mtt) cc_final: 0.6757 (mtt) REVERT: E 68 ASP cc_start: 0.7292 (p0) cc_final: 0.6777 (p0) REVERT: E 70 ASP cc_start: 0.7503 (t70) cc_final: 0.7258 (t0) REVERT: E 105 PHE cc_start: 0.7656 (m-80) cc_final: 0.7397 (m-80) REVERT: E 184 ASN cc_start: 0.8565 (t0) cc_final: 0.8303 (t0) REVERT: E 248 GLU cc_start: 0.7005 (mm-30) cc_final: 0.6693 (mm-30) REVERT: G 16 ASN cc_start: 0.6986 (t0) cc_final: 0.6628 (t0) REVERT: G 42 HIS cc_start: 0.7786 (m90) cc_final: 0.6729 (m90) REVERT: G 62 MET cc_start: 0.7601 (mtm) cc_final: 0.7368 (mtp) REVERT: G 67 PHE cc_start: 0.7914 (m-10) cc_final: 0.7710 (m-80) REVERT: G 68 ASP cc_start: 0.6158 (OUTLIER) cc_final: 0.5740 (m-30) REVERT: G 171 ARG cc_start: 0.6267 (OUTLIER) cc_final: 0.5988 (ptm-80) REVERT: G 174 ARG cc_start: 0.7611 (mpt90) cc_final: 0.7047 (tpt-90) REVERT: G 248 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7875 (mm-30) REVERT: G 273 LYS cc_start: 0.8179 (ptmt) cc_final: 0.7623 (pttm) REVERT: I 19 ILE cc_start: 0.7752 (OUTLIER) cc_final: 0.7410 (tp) REVERT: I 102 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.6417 (mm-40) REVERT: I 171 ARG cc_start: 0.6956 (ptt180) cc_final: 0.5626 (mtt90) REVERT: K 67 PHE cc_start: 0.8153 (OUTLIER) cc_final: 0.7452 (t80) REVERT: K 120 LEU cc_start: 0.8112 (mt) cc_final: 0.7766 (mt) REVERT: K 224 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8227 (mt) REVERT: K 253 ILE cc_start: 0.6686 (OUTLIER) cc_final: 0.6196 (pp) REVERT: K 312 ARG cc_start: 0.7850 (ptm160) cc_final: 0.7311 (ttp80) REVERT: M 115 GLN cc_start: 0.8460 (mt0) cc_final: 0.8020 (mt0) REVERT: M 141 PHE cc_start: 0.8563 (t80) cc_final: 0.8025 (t80) REVERT: M 307 GLU cc_start: 0.7050 (mp0) cc_final: 0.6696 (mt-10) REVERT: O 51 ASN cc_start: 0.6942 (OUTLIER) cc_final: 0.6596 (t0) REVERT: O 76 MET cc_start: 0.7482 (ttm) cc_final: 0.7222 (ttt) REVERT: O 134 ASN cc_start: 0.6522 (OUTLIER) cc_final: 0.5843 (p0) REVERT: O 157 LYS cc_start: 0.7140 (mmmm) cc_final: 0.6752 (mmmt) REVERT: O 171 ARG cc_start: 0.7393 (mtm-85) cc_final: 0.6593 (mtt-85) REVERT: O 198 ASN cc_start: 0.6845 (m-40) cc_final: 0.6610 (p0) REVERT: O 270 ASN cc_start: 0.7281 (t0) cc_final: 0.6861 (m-40) outliers start: 115 outliers final: 81 residues processed: 494 average time/residue: 0.1535 time to fit residues: 114.6288 Evaluate side-chains 479 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 387 time to evaluate : 0.695 ------------------------------------------------------------------------------- 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 253 ILE 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 306 SER Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 36 CYS Chi-restraints excluded: chain C residue 60 SER 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 C residue 306 SER Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 51 ASN Chi-restraints excluded: chain E residue 63 VAL 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 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 66 ILE Chi-restraints excluded: chain G residue 68 ASP Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 171 ARG Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 294 TYR 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 103 ASP 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 67 PHE Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 150 HIS Chi-restraints excluded: chain K residue 224 LEU Chi-restraints excluded: chain K residue 253 ILE Chi-restraints excluded: chain M residue 23 ILE Chi-restraints excluded: chain M residue 57 PHE Chi-restraints excluded: chain M residue 90 ILE Chi-restraints excluded: chain M residue 132 CYS 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 204 LEU 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 268 ILE Chi-restraints excluded: chain M residue 271 VAL Chi-restraints excluded: chain M residue 294 TYR Chi-restraints excluded: chain M residue 306 SER 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 149 ILE Chi-restraints excluded: chain O residue 150 HIS Chi-restraints excluded: chain O residue 152 VAL Chi-restraints excluded: chain O residue 167 THR Chi-restraints excluded: chain O residue 169 CYS Chi-restraints excluded: chain O residue 204 LEU Chi-restraints excluded: chain O residue 224 LEU Chi-restraints excluded: chain O residue 234 ILE Chi-restraints excluded: chain O residue 239 LEU Chi-restraints excluded: chain O residue 293 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 20 optimal weight: 1.9990 chunk 209 optimal weight: 0.9990 chunk 98 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 108 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 147 optimal weight: 0.0270 overall best weight: 0.9444 ------------------------------------------------------------------------------- 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** E 199 ASN ** E 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 267 GLN ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 115 GLN M 100 ASN M 251 ASN M 270 ASN ** O 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 166 ASN O 195 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.214245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.189898 restraints weight = 20191.044| |-----------------------------------------------------------------------------| r_work (start): 0.4102 rms_B_bonded: 1.83 r_work: 0.4013 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3876 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 19306 Z= 0.138 Angle : 0.549 9.850 26142 Z= 0.292 Chirality : 0.043 0.155 2873 Planarity : 0.004 0.071 3460 Dihedral : 4.793 21.787 2572 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 5.71 % Allowed : 23.27 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.17), residues: 2285 helix: 0.79 (0.19), residues: 724 sheet: -1.67 (0.34), residues: 206 loop : -0.99 (0.16), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 269 TYR 0.018 0.001 TYR E 301 PHE 0.022 0.002 PHE G 315 TRP 0.009 0.002 TRP E 46 HIS 0.005 0.001 HIS C 81 Details of bonding type rmsd covalent geometry : bond 0.00322 (19269) covalent geometry : angle 0.53739 (26103) SS BOND : bond 0.00469 ( 9) SS BOND : angle 1.82509 ( 18) hydrogen bonds : bond 0.03509 ( 649) hydrogen bonds : angle 5.42649 ( 1731) metal coordination : bond 0.02500 ( 28) metal coordination : angle 3.74646 ( 21) *********************** 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 525 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 405 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.8322 (mtt90) cc_final: 0.7798 (mtt90) REVERT: A 25 SER cc_start: 0.8621 (t) cc_final: 0.8275 (p) REVERT: A 43 ASP cc_start: 0.8044 (t70) cc_final: 0.7717 (t70) REVERT: A 62 MET cc_start: 0.8427 (mtp) cc_final: 0.8100 (mtp) REVERT: A 101 TYR cc_start: 0.8344 (p90) cc_final: 0.8055 (p90) REVERT: A 265 ARG cc_start: 0.6793 (ttm170) cc_final: 0.6431 (tpm170) REVERT: A 269 ARG cc_start: 0.4953 (mtm-85) cc_final: 0.3500 (mtm180) REVERT: C 102 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.6661 (mm-40) REVERT: C 171 ARG cc_start: 0.7595 (mtm-85) cc_final: 0.5799 (mmt180) REVERT: C 174 ARG cc_start: 0.7659 (mmm-85) cc_final: 0.7449 (mmm-85) REVERT: C 200 TYR cc_start: 0.7621 (m-80) cc_final: 0.7036 (m-80) REVERT: C 310 PHE cc_start: 0.8451 (t80) cc_final: 0.8194 (t80) REVERT: E 59 MET cc_start: 0.6938 (mtt) cc_final: 0.6729 (mtt) REVERT: E 68 ASP cc_start: 0.7250 (p0) cc_final: 0.6600 (p0) REVERT: E 70 ASP cc_start: 0.7502 (t70) cc_final: 0.7264 (t0) REVERT: E 105 PHE cc_start: 0.7637 (m-80) cc_final: 0.7389 (m-80) REVERT: E 184 ASN cc_start: 0.8597 (t0) cc_final: 0.8040 (t0) REVERT: G 16 ASN cc_start: 0.6950 (t0) cc_final: 0.6606 (t0) REVERT: G 42 HIS cc_start: 0.7774 (m90) cc_final: 0.6761 (m90) REVERT: G 67 PHE cc_start: 0.7931 (m-10) cc_final: 0.7726 (m-80) REVERT: G 68 ASP cc_start: 0.6123 (OUTLIER) cc_final: 0.5654 (m-30) REVERT: G 171 ARG cc_start: 0.6234 (OUTLIER) cc_final: 0.5967 (ptm-80) REVERT: G 174 ARG cc_start: 0.7610 (mpt90) cc_final: 0.7040 (tpt-90) REVERT: G 248 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7829 (mm-30) REVERT: G 273 LYS cc_start: 0.8165 (ptmt) cc_final: 0.7608 (pttm) REVERT: I 19 ILE cc_start: 0.7731 (OUTLIER) cc_final: 0.7385 (tp) REVERT: I 102 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.6369 (mm-40) REVERT: I 171 ARG cc_start: 0.6962 (ptt180) cc_final: 0.5624 (mtt90) REVERT: K 67 PHE cc_start: 0.8138 (OUTLIER) cc_final: 0.7394 (t80) REVERT: K 120 LEU cc_start: 0.8097 (mt) cc_final: 0.7738 (mt) REVERT: K 149 ILE cc_start: 0.8461 (tt) cc_final: 0.8232 (pt) REVERT: K 195 GLN cc_start: 0.6933 (tm-30) cc_final: 0.6600 (pp30) REVERT: K 224 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8231 (mt) REVERT: K 253 ILE cc_start: 0.6769 (OUTLIER) cc_final: 0.6269 (pp) REVERT: K 312 ARG cc_start: 0.7832 (ptm160) cc_final: 0.7259 (ttp80) REVERT: M 141 PHE cc_start: 0.8568 (t80) cc_final: 0.8077 (t80) REVERT: O 51 ASN cc_start: 0.6917 (OUTLIER) cc_final: 0.6582 (t0) REVERT: O 76 MET cc_start: 0.7470 (ttm) cc_final: 0.7215 (ttt) REVERT: O 134 ASN cc_start: 0.6810 (OUTLIER) cc_final: 0.6594 (p0) REVERT: O 157 LYS cc_start: 0.7114 (mmmm) cc_final: 0.6713 (mmmt) REVERT: O 171 ARG cc_start: 0.7303 (mtm-85) cc_final: 0.6527 (mtt-85) REVERT: O 198 ASN cc_start: 0.6837 (m-40) cc_final: 0.6593 (p0) REVERT: O 206 ASN cc_start: 0.6860 (OUTLIER) cc_final: 0.6636 (t0) REVERT: O 270 ASN cc_start: 0.7275 (t0) cc_final: 0.6855 (m-40) REVERT: O 310 PHE cc_start: 0.8105 (OUTLIER) cc_final: 0.7784 (m-80) outliers start: 120 outliers final: 88 residues processed: 500 average time/residue: 0.1448 time to fit residues: 108.9867 Evaluate side-chains 487 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 387 time to evaluate : 0.673 ------------------------------------------------------------------------------- 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 83 VAL 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 253 ILE 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 306 SER 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 60 SER 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 253 ILE Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain E residue 15 VAL 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 90 ILE 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 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 66 ILE Chi-restraints excluded: chain G residue 68 ASP Chi-restraints excluded: chain G residue 80 ARG Chi-restraints excluded: chain G residue 171 ARG Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 294 TYR 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 233 ILE 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 224 LEU Chi-restraints excluded: chain K residue 253 ILE Chi-restraints excluded: chain M residue 23 ILE Chi-restraints excluded: chain M residue 90 ILE Chi-restraints excluded: chain M residue 132 CYS 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 204 LEU 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 245 ASP Chi-restraints excluded: chain M residue 294 TYR Chi-restraints excluded: chain M residue 306 SER 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 108 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 152 VAL Chi-restraints excluded: chain O residue 166 ASN Chi-restraints excluded: chain O residue 167 THR Chi-restraints excluded: chain O residue 169 CYS Chi-restraints excluded: chain O residue 195 GLN Chi-restraints excluded: chain O residue 204 LEU Chi-restraints excluded: chain O residue 206 ASN Chi-restraints excluded: chain O residue 224 LEU Chi-restraints excluded: chain O residue 234 ILE Chi-restraints excluded: chain O residue 239 LEU Chi-restraints excluded: chain O residue 293 THR Chi-restraints excluded: chain O residue 310 PHE 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 189 optimal weight: 0.6980 chunk 14 optimal weight: 6.9990 chunk 17 optimal weight: 0.6980 chunk 195 optimal weight: 8.9990 chunk 137 optimal weight: 4.9990 chunk 220 optimal weight: 0.9980 chunk 140 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 65 optimal weight: 0.0970 chunk 108 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 overall best weight: 1.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 199 ASN ** G 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 267 GLN ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 ASN M 115 GLN ** M 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 264 ASN O 134 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.209555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.186649 restraints weight = 20298.764| |-----------------------------------------------------------------------------| r_work (start): 0.4084 rms_B_bonded: 1.63 r_work: 0.3990 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3860 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 19306 Z= 0.175 Angle : 0.585 11.951 26142 Z= 0.309 Chirality : 0.044 0.160 2873 Planarity : 0.004 0.072 3460 Dihedral : 4.884 22.618 2572 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 6.24 % Allowed : 22.94 % Favored : 70.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.17), residues: 2285 helix: 0.77 (0.19), residues: 717 sheet: -1.39 (0.34), residues: 212 loop : -1.09 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 318 TYR 0.019 0.002 TYR E 301 PHE 0.024 0.002 PHE G 315 TRP 0.011 0.002 TRP C 46 HIS 0.007 0.002 HIS C 81 Details of bonding type rmsd covalent geometry : bond 0.00414 (19269) covalent geometry : angle 0.56867 (26103) SS BOND : bond 0.00600 ( 9) SS BOND : angle 1.98824 ( 18) hydrogen bonds : bond 0.03690 ( 649) hydrogen bonds : angle 5.53398 ( 1731) metal coordination : bond 0.03035 ( 28) metal coordination : angle 4.47268 ( 21) *********************** 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 523 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 392 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.8432 (mtt90) cc_final: 0.8035 (mtt90) REVERT: A 25 SER cc_start: 0.8567 (t) cc_final: 0.8256 (p) REVERT: A 43 ASP cc_start: 0.8059 (t70) cc_final: 0.7725 (t70) REVERT: A 62 MET cc_start: 0.8448 (mtp) cc_final: 0.8164 (mtp) REVERT: A 101 TYR cc_start: 0.8305 (p90) cc_final: 0.8051 (p90) REVERT: A 134 ASN cc_start: 0.6944 (m-40) cc_final: 0.6734 (m-40) REVERT: A 265 ARG cc_start: 0.6537 (ttm170) cc_final: 0.6305 (tpm170) REVERT: C 102 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.6702 (mm-40) REVERT: C 171 ARG cc_start: 0.7734 (mtm-85) cc_final: 0.5971 (mmt180) REVERT: C 200 TYR cc_start: 0.7874 (m-80) cc_final: 0.7360 (m-80) REVERT: C 224 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8093 (mt) REVERT: C 310 PHE cc_start: 0.8431 (t80) cc_final: 0.8170 (t80) REVERT: E 68 ASP cc_start: 0.7404 (p0) cc_final: 0.6812 (p0) REVERT: E 184 ASN cc_start: 0.8560 (t0) cc_final: 0.7890 (t0) REVERT: G 16 ASN cc_start: 0.7048 (t0) cc_final: 0.6757 (t0) REVERT: G 42 HIS cc_start: 0.7731 (m90) cc_final: 0.6832 (m90) REVERT: G 67 PHE cc_start: 0.8022 (m-10) cc_final: 0.7805 (m-80) REVERT: G 68 ASP cc_start: 0.6206 (OUTLIER) cc_final: 0.5782 (m-30) REVERT: G 171 ARG cc_start: 0.6490 (OUTLIER) cc_final: 0.6203 (ptm-80) REVERT: G 174 ARG cc_start: 0.7624 (mpt90) cc_final: 0.7120 (tpt-90) REVERT: G 248 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7982 (mm-30) REVERT: I 19 ILE cc_start: 0.7692 (OUTLIER) cc_final: 0.7338 (tp) REVERT: I 102 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.6378 (mm-40) REVERT: I 171 ARG cc_start: 0.7038 (ptt180) cc_final: 0.5738 (mtt90) REVERT: K 67 PHE cc_start: 0.8226 (OUTLIER) cc_final: 0.7515 (t80) REVERT: K 120 LEU cc_start: 0.8163 (mt) cc_final: 0.7806 (mt) REVERT: K 149 ILE cc_start: 0.8424 (tt) cc_final: 0.8177 (pt) REVERT: K 195 GLN cc_start: 0.7299 (tm-30) cc_final: 0.6970 (pp30) REVERT: K 224 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8222 (mt) REVERT: K 253 ILE cc_start: 0.6712 (OUTLIER) cc_final: 0.6196 (pp) REVERT: K 312 ARG cc_start: 0.7797 (ptm160) cc_final: 0.7269 (ttp80) REVERT: M 141 PHE cc_start: 0.8545 (t80) cc_final: 0.8160 (t80) REVERT: M 270 ASN cc_start: 0.7601 (OUTLIER) cc_final: 0.7326 (m110) REVERT: O 51 ASN cc_start: 0.7008 (OUTLIER) cc_final: 0.6668 (t0) REVERT: O 134 ASN cc_start: 0.6698 (OUTLIER) cc_final: 0.6078 (p0) REVERT: O 171 ARG cc_start: 0.7280 (mtm-85) cc_final: 0.6556 (mtt-85) REVERT: O 270 ASN cc_start: 0.7148 (t0) cc_final: 0.6921 (m-40) REVERT: O 301 TYR cc_start: 0.8027 (t80) cc_final: 0.7601 (t80) REVERT: O 310 PHE cc_start: 0.8110 (OUTLIER) cc_final: 0.7812 (m-80) outliers start: 131 outliers final: 100 residues processed: 495 average time/residue: 0.1428 time to fit residues: 107.1532 Evaluate side-chains 495 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 382 time to evaluate : 0.757 ------------------------------------------------------------------------------- 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 83 VAL 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 206 ASN Chi-restraints excluded: chain A residue 253 ILE 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 306 SER 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 60 SER 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 C residue 306 SER Chi-restraints excluded: chain E residue 15 VAL 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 90 ILE 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 176 GLU 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 E residue 316 ILE Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 68 ASP Chi-restraints excluded: chain G residue 80 ARG Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 171 ARG Chi-restraints excluded: chain G residue 175 ASP Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 284 THR Chi-restraints excluded: chain G residue 294 TYR 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 103 ASP 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 233 ILE Chi-restraints excluded: chain I residue 234 ILE 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 63 VAL Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 77 THR 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 224 LEU Chi-restraints excluded: chain K residue 253 ILE Chi-restraints excluded: chain M residue 23 ILE Chi-restraints excluded: chain M residue 57 PHE 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 204 LEU 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 270 ASN Chi-restraints excluded: chain M residue 294 TYR Chi-restraints excluded: chain M residue 306 SER 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 108 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 152 VAL Chi-restraints excluded: chain O residue 167 THR Chi-restraints excluded: chain O residue 169 CYS Chi-restraints excluded: chain O residue 204 LEU Chi-restraints excluded: chain O residue 224 LEU Chi-restraints excluded: chain O residue 229 CYS Chi-restraints excluded: chain O residue 234 ILE Chi-restraints excluded: chain O residue 239 LEU Chi-restraints excluded: chain O residue 293 THR Chi-restraints excluded: chain O residue 310 PHE 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 187 optimal weight: 4.9990 chunk 152 optimal weight: 0.7980 chunk 179 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 chunk 61 optimal weight: 0.0670 chunk 71 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 85 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.8120 ------------------------------------------------------------------------------- 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 305 ASN E 184 ASN E 199 ASN I 164 ASN ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 ASN M 251 ASN ** O 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 195 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.210064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.184786 restraints weight = 20334.060| |-----------------------------------------------------------------------------| r_work (start): 0.4093 rms_B_bonded: 1.90 r_work: 0.3998 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3861 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 19306 Z= 0.132 Angle : 0.560 11.012 26142 Z= 0.297 Chirality : 0.043 0.150 2873 Planarity : 0.004 0.071 3460 Dihedral : 4.793 22.579 2572 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 5.90 % Allowed : 23.32 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.17), residues: 2285 helix: 0.88 (0.19), residues: 723 sheet: -1.59 (0.34), residues: 206 loop : -1.00 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 189 TYR 0.017 0.001 TYR E 301 PHE 0.024 0.002 PHE A 315 TRP 0.016 0.002 TRP E 46 HIS 0.005 0.001 HIS G 52 Details of bonding type rmsd covalent geometry : bond 0.00307 (19269) covalent geometry : angle 0.54763 (26103) SS BOND : bond 0.00516 ( 9) SS BOND : angle 1.99633 ( 18) hydrogen bonds : bond 0.03426 ( 649) hydrogen bonds : angle 5.37508 ( 1731) metal coordination : bond 0.02401 ( 28) metal coordination : angle 3.74759 ( 21) *********************** 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 521 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 397 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.8469 (mtt90) cc_final: 0.8105 (mtt90) REVERT: A 25 SER cc_start: 0.8620 (t) cc_final: 0.8287 (p) REVERT: A 43 ASP cc_start: 0.8118 (t70) cc_final: 0.7785 (t70) REVERT: A 62 MET cc_start: 0.8500 (mtp) cc_final: 0.8206 (mtp) REVERT: A 101 TYR cc_start: 0.8117 (p90) cc_final: 0.7805 (p90) REVERT: A 265 ARG cc_start: 0.6529 (ttm170) cc_final: 0.6179 (tpm170) REVERT: A 269 ARG cc_start: 0.5054 (OUTLIER) cc_final: 0.3122 (mtm180) REVERT: C 102 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.6685 (mm-40) REVERT: C 171 ARG cc_start: 0.7657 (mtm-85) cc_final: 0.5808 (mmt180) REVERT: C 200 TYR cc_start: 0.7635 (m-80) cc_final: 0.7024 (m-80) REVERT: E 105 PHE cc_start: 0.7681 (m-80) cc_final: 0.7458 (m-80) REVERT: E 184 ASN cc_start: 0.8619 (OUTLIER) cc_final: 0.8307 (t0) REVERT: E 273 LYS cc_start: 0.5259 (OUTLIER) cc_final: 0.4131 (pttm) REVERT: G 16 ASN cc_start: 0.6938 (t0) cc_final: 0.6572 (t0) REVERT: G 42 HIS cc_start: 0.7810 (m90) cc_final: 0.6777 (m90) REVERT: G 67 PHE cc_start: 0.7992 (m-10) cc_final: 0.7780 (m-80) REVERT: G 68 ASP cc_start: 0.6148 (OUTLIER) cc_final: 0.5669 (m-30) REVERT: G 171 ARG cc_start: 0.6265 (OUTLIER) cc_final: 0.5990 (ptm-80) REVERT: G 174 ARG cc_start: 0.7653 (mpt90) cc_final: 0.7020 (tpt-90) REVERT: G 248 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7855 (mm-30) REVERT: G 273 LYS cc_start: 0.8288 (ptmt) cc_final: 0.7594 (pttm) REVERT: I 19 ILE cc_start: 0.7689 (OUTLIER) cc_final: 0.7332 (tp) REVERT: I 102 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.6449 (mm-40) REVERT: I 171 ARG cc_start: 0.6995 (ptt180) cc_final: 0.5653 (mtt90) REVERT: K 67 PHE cc_start: 0.8148 (OUTLIER) cc_final: 0.7366 (t80) REVERT: K 120 LEU cc_start: 0.8180 (mt) cc_final: 0.7841 (mt) REVERT: K 149 ILE cc_start: 0.8327 (tt) cc_final: 0.8059 (pt) REVERT: K 195 GLN cc_start: 0.7305 (tm-30) cc_final: 0.6946 (pp30) REVERT: K 224 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8236 (mt) REVERT: K 253 ILE cc_start: 0.6732 (OUTLIER) cc_final: 0.6220 (pp) REVERT: K 312 ARG cc_start: 0.7799 (ptm160) cc_final: 0.7272 (ttp80) REVERT: M 115 GLN cc_start: 0.8543 (mt0) cc_final: 0.8171 (mt0) REVERT: M 141 PHE cc_start: 0.8561 (t80) cc_final: 0.8072 (t80) REVERT: O 51 ASN cc_start: 0.6965 (OUTLIER) cc_final: 0.6709 (t0) REVERT: O 103 ASP cc_start: 0.7101 (OUTLIER) cc_final: 0.6425 (p0) REVERT: O 157 LYS cc_start: 0.7204 (mmmm) cc_final: 0.6856 (mmmt) REVERT: O 171 ARG cc_start: 0.7255 (mtm-85) cc_final: 0.6439 (mtt-85) REVERT: O 270 ASN cc_start: 0.7191 (t0) cc_final: 0.6704 (m-40) REVERT: O 310 PHE cc_start: 0.8127 (OUTLIER) cc_final: 0.7831 (m-80) outliers start: 124 outliers final: 92 residues processed: 493 average time/residue: 0.1484 time to fit residues: 111.1826 Evaluate side-chains 488 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 382 time to evaluate : 0.785 ------------------------------------------------------------------------------- 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 83 VAL Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 150 HIS Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 269 ARG 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 60 SER 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 253 ILE Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain E residue 15 VAL 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 169 CYS Chi-restraints excluded: chain E residue 176 GLU Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 189 ARG 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 E residue 273 LYS Chi-restraints excluded: chain E residue 316 ILE Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 68 ASP Chi-restraints excluded: chain G residue 80 ARG Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 171 ARG Chi-restraints excluded: chain G residue 175 ASP Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 284 THR Chi-restraints excluded: chain G residue 294 TYR 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 135 LEU 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 224 LEU Chi-restraints excluded: chain K residue 253 ILE Chi-restraints excluded: chain M residue 23 ILE Chi-restraints excluded: chain M residue 57 PHE 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 204 LEU 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 294 TYR Chi-restraints excluded: chain M residue 306 SER Chi-restraints excluded: chain M residue 311 LEU 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 103 ASP Chi-restraints excluded: chain O residue 108 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 152 VAL Chi-restraints excluded: chain O residue 167 THR Chi-restraints excluded: chain O residue 169 CYS Chi-restraints excluded: chain O residue 195 GLN Chi-restraints excluded: chain O residue 204 LEU Chi-restraints excluded: chain O residue 224 LEU Chi-restraints excluded: chain O residue 229 CYS Chi-restraints excluded: chain O residue 234 ILE Chi-restraints excluded: chain O residue 293 THR Chi-restraints excluded: chain O residue 310 PHE 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 102 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 227 optimal weight: 5.9990 chunk 192 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 128 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN E 184 ASN E 199 ASN K 50 ASN ** K 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 ASN ** M 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 134 ASN O 195 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.208385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.184975 restraints weight = 20323.640| |-----------------------------------------------------------------------------| r_work (start): 0.4064 rms_B_bonded: 1.65 r_work: 0.3971 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3844 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.124 19306 Z= 0.216 Angle : 0.643 15.523 26142 Z= 0.339 Chirality : 0.046 0.175 2873 Planarity : 0.005 0.073 3460 Dihedral : 5.045 23.135 2572 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 5.52 % Allowed : 24.18 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.17), residues: 2285 helix: 0.62 (0.19), residues: 716 sheet: -1.26 (0.36), residues: 203 loop : -1.18 (0.16), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 189 TYR 0.020 0.002 TYR E 301 PHE 0.028 0.002 PHE G 315 TRP 0.017 0.002 TRP E 46 HIS 0.009 0.002 HIS M 81 Details of bonding type rmsd covalent geometry : bond 0.00514 (19269) covalent geometry : angle 0.62118 (26103) SS BOND : bond 0.00688 ( 9) SS BOND : angle 2.28209 ( 18) hydrogen bonds : bond 0.03913 ( 649) hydrogen bonds : angle 5.65453 ( 1731) metal coordination : bond 0.03727 ( 28) metal coordination : angle 5.47893 ( 21) *********************** 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 504 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 388 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.8345 (mtt90) cc_final: 0.7976 (mtt90) REVERT: A 25 SER cc_start: 0.8560 (t) cc_final: 0.8247 (p) REVERT: A 43 ASP cc_start: 0.8153 (t70) cc_final: 0.7850 (t70) REVERT: A 62 MET cc_start: 0.8527 (mtp) cc_final: 0.8287 (mtp) REVERT: A 265 ARG cc_start: 0.6364 (ttm170) cc_final: 0.6138 (tpm170) REVERT: A 269 ARG cc_start: 0.5640 (OUTLIER) cc_final: 0.2251 (mtm-85) REVERT: C 102 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.6839 (mm-40) REVERT: C 171 ARG cc_start: 0.7761 (mtm-85) cc_final: 0.5947 (mmt180) REVERT: C 200 TYR cc_start: 0.7971 (m-80) cc_final: 0.7434 (m-80) REVERT: E 176 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.6489 (pt0) REVERT: E 273 LYS cc_start: 0.5760 (OUTLIER) cc_final: 0.3923 (pttm) REVERT: G 16 ASN cc_start: 0.7118 (t0) cc_final: 0.6836 (t0) REVERT: G 42 HIS cc_start: 0.7723 (m90) cc_final: 0.6811 (m90) REVERT: G 67 PHE cc_start: 0.8055 (m-10) cc_final: 0.7780 (m-80) REVERT: G 68 ASP cc_start: 0.6265 (OUTLIER) cc_final: 0.5865 (m-30) REVERT: G 171 ARG cc_start: 0.6568 (OUTLIER) cc_final: 0.6274 (ptm-80) REVERT: G 174 ARG cc_start: 0.7627 (mpt90) cc_final: 0.7140 (tpt-90) REVERT: G 248 GLU cc_start: 0.8280 (mm-30) cc_final: 0.8038 (mm-30) REVERT: I 19 ILE cc_start: 0.7730 (OUTLIER) cc_final: 0.7350 (tp) REVERT: I 171 ARG cc_start: 0.7065 (ptt180) cc_final: 0.5755 (mtt90) REVERT: K 67 PHE cc_start: 0.8311 (OUTLIER) cc_final: 0.7556 (t80) REVERT: K 120 LEU cc_start: 0.8224 (mt) cc_final: 0.7872 (mt) REVERT: K 195 GLN cc_start: 0.7289 (tm-30) cc_final: 0.6972 (pp30) REVERT: K 224 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8166 (mt) REVERT: K 253 ILE cc_start: 0.6763 (OUTLIER) cc_final: 0.6238 (pp) REVERT: K 312 ARG cc_start: 0.7770 (ptm160) cc_final: 0.7287 (ttp80) REVERT: M 115 GLN cc_start: 0.8602 (mt0) cc_final: 0.8191 (mt0) REVERT: M 141 PHE cc_start: 0.8535 (t80) cc_final: 0.8100 (t80) REVERT: M 218 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.7611 (tt0) REVERT: M 307 GLU cc_start: 0.6917 (mp0) cc_final: 0.6524 (mt-10) REVERT: O 51 ASN cc_start: 0.7047 (OUTLIER) cc_final: 0.6691 (t0) REVERT: O 103 ASP cc_start: 0.6859 (OUTLIER) cc_final: 0.6282 (p0) REVERT: O 134 ASN cc_start: 0.6626 (OUTLIER) cc_final: 0.6063 (p0) REVERT: O 171 ARG cc_start: 0.7360 (mtm-85) cc_final: 0.6641 (mtt-85) REVERT: O 301 TYR cc_start: 0.8033 (t80) cc_final: 0.7638 (t80) REVERT: O 310 PHE cc_start: 0.8092 (OUTLIER) cc_final: 0.7792 (m-80) outliers start: 116 outliers final: 90 residues processed: 478 average time/residue: 0.1469 time to fit residues: 106.3948 Evaluate side-chains 486 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 381 time to evaluate : 0.844 ------------------------------------------------------------------------------- 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 83 VAL 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 206 ASN Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 269 ARG 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 60 SER 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 253 ILE Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain E residue 15 VAL 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 90 ILE Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 114 GLU Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 169 CYS Chi-restraints excluded: chain E residue 176 GLU Chi-restraints excluded: chain E residue 188 LEU 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 E residue 273 LYS Chi-restraints excluded: chain E residue 316 ILE Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 68 ASP Chi-restraints excluded: chain G residue 80 ARG Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 171 ARG Chi-restraints excluded: chain G residue 175 ASP Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 284 THR 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 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 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 224 LEU Chi-restraints excluded: chain K residue 253 ILE Chi-restraints excluded: chain M residue 23 ILE Chi-restraints excluded: chain M residue 57 PHE 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 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 294 TYR Chi-restraints excluded: chain M residue 306 SER Chi-restraints excluded: chain M residue 311 LEU 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 103 ASP Chi-restraints excluded: chain O residue 108 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 152 VAL Chi-restraints excluded: chain O residue 167 THR Chi-restraints excluded: chain O residue 169 CYS Chi-restraints excluded: chain O residue 195 GLN Chi-restraints excluded: chain O residue 204 LEU Chi-restraints excluded: chain O residue 224 LEU Chi-restraints excluded: chain O residue 229 CYS Chi-restraints excluded: chain O residue 234 ILE Chi-restraints excluded: chain O residue 293 THR Chi-restraints excluded: chain O residue 310 PHE 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 12 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 173 optimal weight: 5.9990 chunk 98 optimal weight: 9.9990 chunk 2 optimal weight: 0.3980 chunk 208 optimal weight: 0.0000 chunk 95 optimal weight: 0.6980 chunk 141 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 168 optimal weight: 3.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- 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** E 199 ASN ** E 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 ASN ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 ASN M 251 ASN ** 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 = 0.4366 r_free = 0.4366 target = 0.212717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.188332 restraints weight = 20420.996| |-----------------------------------------------------------------------------| r_work (start): 0.4171 rms_B_bonded: 1.87 r_work: 0.4058 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3925 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 19306 Z= 0.125 Angle : 0.568 11.193 26142 Z= 0.303 Chirality : 0.043 0.151 2873 Planarity : 0.004 0.072 3460 Dihedral : 4.802 22.181 2572 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 4.43 % Allowed : 25.42 % Favored : 70.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.17), residues: 2285 helix: 0.88 (0.19), residues: 724 sheet: -1.52 (0.35), residues: 200 loop : -1.04 (0.16), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 189 TYR 0.015 0.001 TYR E 301 PHE 0.017 0.001 PHE K 141 TRP 0.015 0.002 TRP E 46 HIS 0.005 0.001 HIS G 52 Details of bonding type rmsd covalent geometry : bond 0.00288 (19269) covalent geometry : angle 0.55794 (26103) SS BOND : bond 0.00315 ( 9) SS BOND : angle 1.64480 ( 18) hydrogen bonds : bond 0.03368 ( 649) hydrogen bonds : angle 5.35184 ( 1731) metal coordination : bond 0.02146 ( 28) metal coordination : angle 3.47321 ( 21) ********************** 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 492 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 399 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.8370 (mtt90) cc_final: 0.8066 (mtt90) REVERT: A 25 SER cc_start: 0.8589 (t) cc_final: 0.8270 (p) REVERT: A 43 ASP cc_start: 0.8126 (t70) cc_final: 0.7801 (t70) REVERT: A 62 MET cc_start: 0.8453 (mtp) cc_final: 0.8203 (mtp) REVERT: A 101 TYR cc_start: 0.8116 (p90) cc_final: 0.7834 (p90) REVERT: A 265 ARG cc_start: 0.6532 (ttm170) cc_final: 0.6219 (tpm170) REVERT: A 269 ARG cc_start: 0.5639 (OUTLIER) cc_final: 0.1924 (mtm-85) REVERT: C 102 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.6700 (mm-40) REVERT: C 171 ARG cc_start: 0.7674 (mtm-85) cc_final: 0.5773 (mmt180) REVERT: C 174 ARG cc_start: 0.7374 (mmm160) cc_final: 0.6919 (tpt90) REVERT: C 200 TYR cc_start: 0.7665 (m-80) cc_final: 0.7076 (m-80) REVERT: E 105 PHE cc_start: 0.7691 (m-80) cc_final: 0.7461 (m-80) REVERT: E 273 LYS cc_start: 0.5477 (OUTLIER) cc_final: 0.4301 (pttm) REVERT: G 16 ASN cc_start: 0.7010 (t0) cc_final: 0.6662 (t0) REVERT: G 42 HIS cc_start: 0.7637 (m90) cc_final: 0.6653 (m90) REVERT: G 67 PHE cc_start: 0.8112 (m-10) cc_final: 0.7843 (m-80) REVERT: G 91 LYS cc_start: 0.8506 (mtmt) cc_final: 0.8250 (mtmm) REVERT: G 171 ARG cc_start: 0.6186 (OUTLIER) cc_final: 0.5952 (ptm-80) REVERT: G 174 ARG cc_start: 0.7635 (mpt90) cc_final: 0.7022 (tpt-90) REVERT: G 248 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7863 (mm-30) REVERT: I 19 ILE cc_start: 0.7609 (OUTLIER) cc_final: 0.7254 (tp) REVERT: I 171 ARG cc_start: 0.7043 (ptt180) cc_final: 0.5696 (mtt90) REVERT: K 67 PHE cc_start: 0.8175 (OUTLIER) cc_final: 0.7392 (t80) REVERT: K 120 LEU cc_start: 0.8198 (mt) cc_final: 0.7832 (mt) REVERT: K 149 ILE cc_start: 0.8372 (tt) cc_final: 0.8136 (pt) REVERT: K 195 GLN cc_start: 0.7334 (tm-30) cc_final: 0.6984 (pp30) REVERT: K 224 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8226 (mt) REVERT: K 253 ILE cc_start: 0.6654 (OUTLIER) cc_final: 0.6151 (pp) REVERT: K 312 ARG cc_start: 0.7775 (ptm160) cc_final: 0.7291 (ttp80) REVERT: M 115 GLN cc_start: 0.8562 (mt0) cc_final: 0.8119 (mt0) REVERT: M 141 PHE cc_start: 0.8553 (t80) cc_final: 0.8048 (t80) REVERT: M 307 GLU cc_start: 0.6907 (mp0) cc_final: 0.6494 (mt-10) REVERT: O 103 ASP cc_start: 0.7094 (OUTLIER) cc_final: 0.6433 (p0) REVERT: O 110 MET cc_start: 0.4773 (mtt) cc_final: 0.3240 (tpp) REVERT: O 157 LYS cc_start: 0.7111 (mmmm) cc_final: 0.6772 (mmmt) REVERT: O 171 ARG cc_start: 0.7241 (mtm-85) cc_final: 0.6471 (mtt-85) REVERT: O 270 ASN cc_start: 0.7608 (t0) cc_final: 0.7030 (m-40) REVERT: O 310 PHE cc_start: 0.8097 (OUTLIER) cc_final: 0.7765 (m-80) outliers start: 93 outliers final: 73 residues processed: 469 average time/residue: 0.1422 time to fit residues: 100.6122 Evaluate side-chains 464 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 381 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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 206 ASN Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 278 THR 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 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 253 ILE Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 114 GLU Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 169 CYS Chi-restraints excluded: chain E residue 176 GLU 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 E residue 273 LYS Chi-restraints excluded: chain E residue 316 ILE Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 80 ARG Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 171 ARG Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 271 VAL 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 167 THR 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 224 LEU Chi-restraints excluded: chain K residue 253 ILE Chi-restraints excluded: chain M residue 23 ILE Chi-restraints excluded: chain M residue 57 PHE Chi-restraints excluded: chain M residue 90 ILE Chi-restraints excluded: chain M residue 132 CYS Chi-restraints excluded: chain M residue 168 PHE Chi-restraints excluded: chain M residue 195 GLN Chi-restraints excluded: chain M residue 218 GLN 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 294 TYR Chi-restraints excluded: chain M residue 306 SER Chi-restraints excluded: chain M residue 311 LEU Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 60 SER Chi-restraints excluded: chain O residue 103 ASP Chi-restraints excluded: chain O residue 108 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 152 VAL Chi-restraints excluded: chain O residue 167 THR Chi-restraints excluded: chain O residue 169 CYS Chi-restraints excluded: chain O residue 195 GLN Chi-restraints excluded: chain O residue 204 LEU Chi-restraints excluded: chain O residue 224 LEU Chi-restraints excluded: chain O residue 293 THR Chi-restraints excluded: chain O residue 310 PHE 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 32 optimal weight: 2.9990 chunk 118 optimal weight: 0.5980 chunk 169 optimal weight: 0.0980 chunk 8 optimal weight: 3.9990 chunk 205 optimal weight: 1.9990 chunk 174 optimal weight: 0.9990 chunk 115 optimal weight: 5.9990 chunk 55 optimal weight: 0.4980 chunk 188 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN C 267 GLN ** E 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 ASN M 251 ASN O 134 ASN O 195 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.211603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.186847 restraints weight = 20604.064| |-----------------------------------------------------------------------------| r_work (start): 0.4161 rms_B_bonded: 1.90 r_work: 0.4046 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3911 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 19306 Z= 0.135 Angle : 0.570 11.660 26142 Z= 0.303 Chirality : 0.043 0.151 2873 Planarity : 0.004 0.071 3460 Dihedral : 4.749 23.293 2572 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 4.57 % Allowed : 25.65 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.17), residues: 2285 helix: 0.93 (0.19), residues: 725 sheet: -1.48 (0.35), residues: 200 loop : -1.01 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG E 318 TYR 0.016 0.001 TYR E 301 PHE 0.043 0.002 PHE K 141 TRP 0.014 0.002 TRP E 46 HIS 0.005 0.001 HIS G 52 Details of bonding type rmsd covalent geometry : bond 0.00316 (19269) covalent geometry : angle 0.55764 (26103) SS BOND : bond 0.00413 ( 9) SS BOND : angle 1.67067 ( 18) hydrogen bonds : bond 0.03378 ( 649) hydrogen bonds : angle 5.32515 ( 1731) metal coordination : bond 0.02460 ( 28) metal coordination : angle 3.97423 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5843.77 seconds wall clock time: 100 minutes 25.43 seconds (6025.43 seconds total)