Starting phenix.real_space_refine on Mon May 19 16:06:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vwh_43586/05_2025/8vwh_43586.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vwh_43586/05_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_43586/05_2025/8vwh_43586.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vwh_43586/05_2025/8vwh_43586.map" model { file = "/net/cci-nas-00/data/ceres_data/8vwh_43586/05_2025/8vwh_43586.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vwh_43586/05_2025/8vwh_43586.cif" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.066 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 7 6.06 5 S 98 5.16 5 C 11917 2.51 5 N 3309 2.21 5 O 3558 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 18889 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2353 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 13, 'TRANS': 276} Chain breaks: 2 Chain: "C" Number of atoms: 2353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2353 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 13, 'TRANS': 276} Chain breaks: 2 Chain: "E" Number of atoms: 2293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2293 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 12, 'TRANS': 270} Chain breaks: 2 Chain: "G" Number of atoms: 2412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2412 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 284} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 2353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2353 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 13, 'TRANS': 276} Chain breaks: 2 Chain: "K" Number of atoms: 2353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2353 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 13, 'TRANS': 276} Chain breaks: 2 Chain: "M" Number of atoms: 2412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2412 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 284} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 2353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2353 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 13, 'TRANS': 276} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 32 SG CYS A 18 46.844 97.936 45.089 1.00 59.84 S ATOM 107 SG CYS A 36 50.259 97.420 43.372 1.00 79.76 S ATOM 214 SG CYS A 49 47.785 100.009 41.949 1.00 64.23 S ATOM 2385 SG CYS C 18 38.149 145.254 30.922 1.00 65.17 S ATOM 2460 SG CYS C 36 41.461 146.740 32.328 1.00 64.21 S ATOM 2567 SG CYS C 49 40.150 143.383 33.696 1.00 68.46 S ATOM 4738 SG CYS E 18 77.894 37.691 87.683 1.00 39.87 S ATOM 4813 SG CYS E 36 80.807 39.775 85.927 1.00 62.50 S ATOM 4920 SG CYS E 49 78.106 41.242 87.645 1.00 57.10 S ATOM 7031 SG CYS G 18 54.041 79.691 74.311 1.00 80.91 S ATOM 7165 SG CYS G 36 56.989 81.484 76.182 1.00 69.88 S ATOM 7272 SG CYS G 49 57.026 77.847 75.592 1.00 86.05 S ATOM 9443 SG CYS I 18 63.228 58.881 130.787 1.00 46.90 S ATOM 9518 SG CYS I 36 66.793 60.231 130.037 1.00 65.01 S ATOM 9625 SG CYS I 49 63.843 61.575 128.047 1.00 65.59 S ATOM 11796 SG CYS K 18 45.223 103.721 116.850 1.00 67.35 S ATOM 11871 SG CYS K 36 47.832 105.829 118.809 1.00 89.66 S ATOM 11978 SG CYS K 49 47.128 102.218 119.897 1.00 77.59 S ATOM 14149 SG CYS M 18 40.969 123.520 87.866 1.00 56.94 S ATOM 14283 SG CYS M 36 44.608 123.646 86.622 1.00 83.64 S ATOM 14390 SG CYS M 49 41.872 125.376 84.549 1.00 67.57 S Time building chain proxies: 10.75, per 1000 atoms: 0.57 Number of scatterers: 18889 At special positions: 0 Unit cell: (103.74, 208.81, 163.59, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 7 29.99 S 98 16.00 O 3558 8.00 N 3309 7.00 C 11917 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 132 " - pdb=" SG CYS G 169 " distance=2.03 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS G 132 " distance=2.03 Simple disulfide: pdb=" SG CYS A 229 " - pdb=" SG CYS C 229 " distance=2.03 Simple disulfide: pdb=" SG CYS E 229 " - pdb=" SG CYS G 229 " distance=2.03 Simple disulfide: pdb=" SG CYS G 29 " - pdb=" SG CYS M 29 " distance=2.03 Simple disulfide: pdb=" SG CYS I 229 " - pdb=" SG CYS K 229 " distance=2.04 Simple disulfide: pdb=" SG CYS K 132 " - pdb=" SG CYS M 169 " distance=2.03 Simple disulfide: pdb=" SG CYS K 169 " - pdb=" SG CYS M 132 " distance=2.04 Simple disulfide: pdb=" SG CYS M 229 " - pdb=" SG CYS O 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.51 Conformation dependent library (CDL) restraints added in 2.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" ND1 HIS A 52 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 18 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 36 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 49 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" ND1 HIS C 52 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 36 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 18 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 49 " pdb=" ZN E 401 " pdb="ZN ZN E 401 " - pdb=" ND1 HIS E 52 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 49 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 18 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 36 " pdb=" ZN G 401 " pdb="ZN ZN G 401 " - pdb=" ND1 HIS G 52 " pdb="ZN ZN G 401 " - pdb=" SG CYS G 49 " pdb="ZN ZN G 401 " - pdb=" SG CYS G 18 " pdb="ZN ZN G 401 " - pdb=" SG CYS G 36 " pdb=" ZN I 401 " pdb="ZN ZN I 401 " - pdb=" ND1 HIS I 52 " pdb="ZN ZN I 401 " - pdb=" SG CYS I 49 " pdb="ZN ZN I 401 " - pdb=" SG CYS I 36 " pdb="ZN ZN I 401 " - pdb=" SG CYS I 18 " pdb=" ZN K 401 " pdb="ZN ZN K 401 " - pdb=" ND1 HIS K 52 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 49 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 36 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 18 " pdb=" ZN M 401 " pdb="ZN ZN M 401 " - pdb=" ND1 HIS M 52 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 36 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 18 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 49 " Number of angles added : 21 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4450 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 28 sheets defined 37.7% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.08 Creating SS restraints... Processing helix chain 'A' and resid 18 through 23 removed outlier: 4.083A pdb=" N SER A 22 " --> pdb=" O ILE A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 41 Processing helix chain 'A' and resid 49 through 58 removed outlier: 3.737A pdb=" N LYS A 58 " --> pdb=" O ILE A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 91 removed outlier: 3.716A pdb=" N LYS A 91 " --> pdb=" O ARG A 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 88 through 91' Processing helix chain 'A' and resid 100 through 106 removed outlier: 3.517A pdb=" N ASN A 106 " --> pdb=" O GLN A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 122 Processing helix chain 'A' and resid 124 through 135 Processing helix chain 'A' and resid 145 through 164 Processing helix chain 'A' and resid 184 through 188 Processing helix chain 'A' and resid 191 through 199 removed outlier: 3.973A pdb=" N ASN A 199 " --> pdb=" O GLN A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 212 Processing helix chain 'A' and resid 278 through 285 Processing helix chain 'C' and resid 37 through 41 Processing helix chain 'C' and resid 49 through 58 removed outlier: 3.674A pdb=" N LYS C 58 " --> pdb=" O ILE C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 91 removed outlier: 3.694A pdb=" N LYS C 91 " --> pdb=" O ARG C 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 88 through 91' Processing helix chain 'C' and resid 100 through 106 removed outlier: 3.520A pdb=" N VAL C 104 " --> pdb=" O ASN C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 110 Processing helix chain 'C' and resid 111 through 122 Processing helix chain 'C' and resid 124 through 137 removed outlier: 3.581A pdb=" N LEU C 135 " --> pdb=" O ILE C 131 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TYR C 137 " --> pdb=" O ASP C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 163 Processing helix chain 'C' and resid 184 through 188 Processing helix chain 'C' and resid 191 through 199 removed outlier: 3.696A pdb=" N ASN C 199 " --> pdb=" O GLN C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 212 Processing helix chain 'C' and resid 278 through 285 Processing helix chain 'E' and resid 18 through 22 removed outlier: 4.358A pdb=" N SER E 22 " --> pdb=" O ILE E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 58 removed outlier: 3.563A pdb=" N LYS E 58 " --> pdb=" O ILE E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 91 Processing helix chain 'E' and resid 101 through 106 removed outlier: 3.893A pdb=" N ASN E 106 " --> pdb=" O GLN E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 110 Processing helix chain 'E' and resid 111 through 122 removed outlier: 4.142A pdb=" N HIS E 119 " --> pdb=" O GLN E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 137 removed outlier: 3.916A pdb=" N TYR E 137 " --> pdb=" O ASP E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 164 removed outlier: 3.698A pdb=" N THR E 155 " --> pdb=" O SER E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 188 Processing helix chain 'E' and resid 191 through 199 removed outlier: 3.575A pdb=" N ASN E 199 " --> pdb=" O GLN E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 212 Processing helix chain 'E' and resid 279 through 285 Processing helix chain 'G' and resid 37 through 41 Processing helix chain 'G' and resid 49 through 56 Processing helix chain 'G' and resid 88 through 91 Processing helix chain 'G' and resid 100 through 106 Processing helix chain 'G' and resid 107 through 110 Processing helix chain 'G' and resid 111 through 122 Processing helix chain 'G' and resid 124 through 135 removed outlier: 3.549A pdb=" N LEU G 135 " --> pdb=" O ILE G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 144 removed outlier: 4.383A pdb=" N SER G 143 " --> pdb=" O GLU G 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 164 Processing helix chain 'G' and resid 184 through 188 Processing helix chain 'G' and resid 191 through 200 removed outlier: 3.675A pdb=" N ASN G 199 " --> pdb=" O GLN G 195 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TYR G 200 " --> pdb=" O LEU G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 201 through 212 Processing helix chain 'G' and resid 279 through 285 removed outlier: 3.536A pdb=" N LEU G 285 " --> pdb=" O LEU G 281 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 23 removed outlier: 4.247A pdb=" N SER I 22 " --> pdb=" O ILE I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 41 Processing helix chain 'I' and resid 49 through 58 removed outlier: 3.561A pdb=" N LYS I 58 " --> pdb=" O ILE I 54 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 91 Processing helix chain 'I' and resid 100 through 106 removed outlier: 3.548A pdb=" N VAL I 104 " --> pdb=" O ASN I 100 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 122 Processing helix chain 'I' and resid 124 through 137 removed outlier: 3.955A pdb=" N TYR I 137 " --> pdb=" O ASP I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 145 Processing helix chain 'I' and resid 145 through 164 Processing helix chain 'I' and resid 184 through 188 Processing helix chain 'I' and resid 191 through 199 removed outlier: 3.663A pdb=" N ASN I 199 " --> pdb=" O GLN I 195 " (cutoff:3.500A) Processing helix chain 'I' and resid 201 through 212 Processing helix chain 'I' and resid 278 through 285 Processing helix chain 'K' and resid 37 through 41 Processing helix chain 'K' and resid 49 through 58 removed outlier: 3.782A pdb=" N LYS K 58 " --> pdb=" O ILE K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 91 Processing helix chain 'K' and resid 100 through 106 Processing helix chain 'K' and resid 111 through 122 Processing helix chain 'K' and resid 124 through 137 removed outlier: 4.031A pdb=" N TYR K 137 " --> pdb=" O ASP K 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 144 through 164 Processing helix chain 'K' and resid 191 through 199 removed outlier: 3.816A pdb=" N ASN K 199 " --> pdb=" O GLN K 195 " (cutoff:3.500A) Processing helix chain 'K' and resid 201 through 212 Processing helix chain 'K' and resid 279 through 285 Processing helix chain 'M' and resid 37 through 42 removed outlier: 3.790A pdb=" N TYR M 41 " --> pdb=" O PRO M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 56 Processing helix chain 'M' and resid 88 through 91 removed outlier: 3.783A pdb=" N LYS M 91 " --> pdb=" O ARG M 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 88 through 91' Processing helix chain 'M' and resid 100 through 106 Processing helix chain 'M' and resid 111 through 122 Processing helix chain 'M' and resid 124 through 136 Processing helix chain 'M' and resid 138 through 142 removed outlier: 3.655A pdb=" N THR M 142 " --> pdb=" O GLU M 139 " (cutoff:3.500A) Processing helix chain 'M' and resid 145 through 164 Processing helix chain 'M' and resid 184 through 188 removed outlier: 3.507A pdb=" N ALA M 187 " --> pdb=" O ASN M 184 " (cutoff:3.500A) Processing helix chain 'M' and resid 191 through 200 removed outlier: 3.565A pdb=" N ASN M 199 " --> pdb=" O GLN M 195 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TYR M 200 " --> pdb=" O LEU M 196 " (cutoff:3.500A) Processing helix chain 'M' and resid 201 through 211 Processing helix chain 'M' and resid 278 through 285 removed outlier: 3.634A pdb=" N LEU M 285 " --> pdb=" O LEU M 281 " (cutoff:3.500A) Processing helix chain 'O' and resid 18 through 22 removed outlier: 3.616A pdb=" N ALA O 21 " --> pdb=" O CYS O 18 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N SER O 22 " --> pdb=" O ILE O 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 18 through 22' Processing helix chain 'O' and resid 49 through 58 Processing helix chain 'O' and resid 88 through 91 Processing helix chain 'O' and resid 100 through 106 Processing helix chain 'O' and resid 107 through 110 Processing helix chain 'O' and resid 111 through 122 Processing helix chain 'O' and resid 124 through 137 removed outlier: 3.858A pdb=" N TYR O 137 " --> pdb=" O ASP O 133 " (cutoff:3.500A) Processing helix chain 'O' and resid 145 through 164 removed outlier: 3.610A pdb=" N SER O 151 " --> pdb=" O ARG O 147 " (cutoff:3.500A) Processing helix chain 'O' and resid 184 through 188 Processing helix chain 'O' and resid 191 through 199 removed outlier: 3.997A pdb=" N ASN O 199 " --> pdb=" O GLN O 195 " (cutoff:3.500A) Processing helix chain 'O' and resid 201 through 212 Processing helix chain 'O' and resid 280 through 285 Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 67 Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 96 removed outlier: 6.381A pdb=" N LEU A 239 " --> pdb=" O LEU A 94 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 179 Processing sheet with id=AA4, first strand: chain 'C' and resid 59 through 67 removed outlier: 3.607A pdb=" N PHE C 74 " --> pdb=" O ILE C 66 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 93 through 95 removed outlier: 6.684A pdb=" N LEU C 239 " --> pdb=" O LEU C 94 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 176 through 179 Processing sheet with id=AA7, first strand: chain 'C' and resid 268 through 271 Processing sheet with id=AA8, first strand: chain 'E' and resid 62 through 67 removed outlier: 3.600A pdb=" N MET E 76 " --> pdb=" O LEU E 64 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 93 through 96 removed outlier: 6.946A pdb=" N LEU E 239 " --> pdb=" O LEU E 94 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP E 235 " --> pdb=" O GLY E 238 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 176 through 179 removed outlier: 6.224A pdb=" N TYR E 216 " --> pdb=" O GLN E 302 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ILE E 304 " --> pdb=" O TYR E 216 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLN E 218 " --> pdb=" O ILE E 304 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 289 through 290 removed outlier: 5.839A pdb=" N GLU E 289 " --> pdb=" O VAL G 63 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 93 through 96 removed outlier: 3.743A pdb=" N ILE G 95 " --> pdb=" O LEU G 239 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 176 through 179 Processing sheet with id=AB5, first strand: chain 'G' and resid 216 through 219 Processing sheet with id=AB6, first strand: chain 'G' and resid 267 through 268 removed outlier: 3.763A pdb=" N GLN G 267 " --> pdb=" O GLU I 275 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 59 through 67 Processing sheet with id=AB8, first strand: chain 'I' and resid 93 through 95 Processing sheet with id=AB9, first strand: chain 'I' and resid 176 through 179 removed outlier: 5.960A pdb=" N TYR I 216 " --> pdb=" O GLN I 302 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ILE I 304 " --> pdb=" O TYR I 216 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLN I 218 " --> pdb=" O ILE I 304 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 59 through 67 Processing sheet with id=AC2, first strand: chain 'K' and resid 93 through 95 removed outlier: 3.836A pdb=" N ASP K 235 " --> pdb=" O GLY K 238 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 176 through 179 removed outlier: 6.623A pdb=" N TYR K 216 " --> pdb=" O GLN K 302 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ILE K 304 " --> pdb=" O TYR K 216 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLN K 218 " --> pdb=" O ILE K 304 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'M' and resid 73 through 81 removed outlier: 4.632A pdb=" N GLU O 289 " --> pdb=" O LYS M 61 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 93 through 96 removed outlier: 3.628A pdb=" N ILE M 95 " --> pdb=" O LEU M 239 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 176 through 179 removed outlier: 3.589A pdb=" N GLN M 302 " --> pdb=" O TYR M 216 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE M 304 " --> pdb=" O GLN M 218 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 212 through 213 Processing sheet with id=AC8, first strand: chain 'O' and resid 62 through 67 removed outlier: 3.645A pdb=" N ILE O 66 " --> pdb=" O PHE O 74 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'O' and resid 93 through 96 removed outlier: 6.708A pdb=" N LEU O 239 " --> pdb=" O LEU O 94 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'O' and resid 176 through 179 removed outlier: 6.236A pdb=" N TYR O 216 " --> pdb=" O GLN O 302 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ILE O 304 " --> pdb=" O TYR O 216 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N GLN O 218 " --> pdb=" O ILE O 304 " (cutoff:3.500A) 649 hydrogen bonds defined for protein. 1731 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.11 Time building geometry restraints manager: 5.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 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: 0.970 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: 0.660 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 43.460 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.109 19306 Z= 0.100 Angle : 0.458 13.029 26142 Z= 0.242 Chirality : 0.041 0.211 2873 Planarity : 0.003 0.066 3460 Dihedral : 16.102 89.584 7169 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.10 % Allowed : 22.08 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.17), residues: 2285 helix: 0.91 (0.19), residues: 729 sheet: -1.50 (0.39), residues: 167 loop : -0.93 (0.16), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 46 HIS 0.005 0.001 HIS K 81 PHE 0.016 0.001 PHE K 168 TYR 0.012 0.001 TYR E 301 ARG 0.003 0.000 ARG E 80 Details of bonding type rmsd hydrogen bonds : bond 0.20993 ( 649) hydrogen bonds : angle 8.29710 ( 1731) metal coordination : bond 0.02433 ( 28) metal coordination : angle 4.68604 ( 21) SS BOND : bond 0.00269 ( 9) SS BOND : angle 0.97198 ( 18) covalent geometry : bond 0.00228 (19269) covalent geometry : angle 0.43815 (26103) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 506 time to evaluate : 2.049 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.7900 (t70) cc_final: 0.7631 (t70) REVERT: A 111 MET cc_start: 0.7720 (mtt) cc_final: 0.7510 (mtm) REVERT: A 265 ARG cc_start: 0.7153 (ttm170) cc_final: 0.6857 (tpm170) REVERT: C 60 SER cc_start: 0.8679 (t) cc_final: 0.8442 (m) REVERT: C 112 GLN cc_start: 0.7402 (mt0) cc_final: 0.7193 (mt0) REVERT: C 171 ARG cc_start: 0.7434 (mtm-85) cc_final: 0.5538 (mmt180) REVERT: C 174 ARG cc_start: 0.7589 (mmm-85) cc_final: 0.7307 (mmm-85) REVERT: C 200 TYR cc_start: 0.7723 (m-80) cc_final: 0.7149 (m-80) REVERT: C 310 PHE cc_start: 0.8541 (t80) cc_final: 0.8235 (t80) REVERT: E 68 ASP cc_start: 0.6988 (p0) cc_final: 0.6745 (p0) REVERT: E 78 ILE cc_start: 0.7680 (tt) cc_final: 0.7372 (tt) REVERT: E 86 LYS cc_start: 0.8047 (mmmm) cc_final: 0.7606 (mttp) REVERT: E 92 ARG cc_start: 0.6428 (mtp85) cc_final: 0.6223 (mtp85) REVERT: E 223 GLU cc_start: 0.8206 (tt0) cc_final: 0.7885 (tt0) REVERT: G 16 ASN cc_start: 0.6930 (t0) cc_final: 0.6635 (t0) REVERT: G 67 PHE cc_start: 0.7523 (m-10) cc_final: 0.7275 (m-80) REVERT: G 122 TYR cc_start: 0.8458 (m-80) cc_final: 0.8232 (m-80) REVERT: G 174 ARG cc_start: 0.7227 (mpt90) cc_final: 0.6802 (tpt-90) REVERT: G 248 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8257 (mm-30) REVERT: I 54 ILE cc_start: 0.8829 (mt) cc_final: 0.8628 (mt) REVERT: I 150 HIS cc_start: 0.7877 (t70) cc_final: 0.6906 (m-70) REVERT: I 171 ARG cc_start: 0.6523 (ptt180) cc_final: 0.5458 (mtt90) REVERT: K 110 MET cc_start: 0.8042 (mtt) cc_final: 0.7788 (mtt) REVERT: K 111 MET cc_start: 0.7224 (mtt) cc_final: 0.7015 (mtm) REVERT: K 115 GLN cc_start: 0.7242 (mt0) cc_final: 0.6997 (mt0) REVERT: K 120 LEU cc_start: 0.8021 (mt) cc_final: 0.7708 (mt) REVERT: K 149 ILE cc_start: 0.8446 (tt) cc_final: 0.8115 (tt) REVERT: K 215 GLU cc_start: 0.7642 (tt0) cc_final: 0.7281 (tt0) REVERT: K 222 GLU cc_start: 0.6592 (mm-30) cc_final: 0.6368 (mm-30) REVERT: K 269 ARG cc_start: 0.7868 (ptt180) cc_final: 0.7380 (ptt-90) REVERT: K 312 ARG cc_start: 0.7889 (ptm160) cc_final: 0.7340 (ttp80) REVERT: M 25 SER cc_start: 0.8201 (t) cc_final: 0.7309 (t) REVERT: M 111 MET cc_start: 0.7936 (mtm) cc_final: 0.7650 (mtm) REVERT: M 115 GLN cc_start: 0.8481 (mt0) cc_final: 0.8195 (mt0) REVERT: M 141 PHE cc_start: 0.8307 (t80) cc_final: 0.8004 (t80) REVERT: M 188 LEU cc_start: 0.8243 (mp) cc_final: 0.8032 (mt) REVERT: O 59 MET cc_start: 0.7361 (mtm) cc_final: 0.6855 (mtp) REVERT: O 109 SER cc_start: 0.6797 (p) cc_final: 0.6590 (m) REVERT: O 111 MET cc_start: 0.6415 (tpp) cc_final: 0.6169 (tpp) REVERT: O 112 GLN cc_start: 0.7032 (pm20) cc_final: 0.6582 (pm20) REVERT: O 171 ARG cc_start: 0.7305 (mtm-85) cc_final: 0.6739 (mtt-85) REVERT: O 220 ASP cc_start: 0.6534 (m-30) cc_final: 0.6081 (m-30) outliers start: 2 outliers final: 0 residues processed: 507 average time/residue: 0.3281 time to fit residues: 244.0193 Evaluate side-chains 438 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 438 time to evaluate : 1.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 0.1980 chunk 175 optimal weight: 8.9990 chunk 97 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 181 optimal weight: 0.9980 chunk 70 optimal weight: 0.0470 chunk 110 optimal weight: 0.8980 chunk 134 optimal weight: 3.9990 chunk 209 optimal weight: 0.7980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 ASN A 262 GLN C 320 ASN E 134 ASN ** E 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 305 ASN G 195 GLN I 16 ASN I 106 ASN ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 195 GLN K 267 GLN M 251 ASN ** O 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 134 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.212918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.188267 restraints weight = 20372.050| |-----------------------------------------------------------------------------| r_work (start): 0.4135 rms_B_bonded: 1.88 r_work: 0.4041 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3906 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 19306 Z= 0.119 Angle : 0.521 8.613 26142 Z= 0.282 Chirality : 0.043 0.148 2873 Planarity : 0.004 0.066 3460 Dihedral : 4.605 20.757 2572 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.57 % Allowed : 21.66 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.17), residues: 2285 helix: 1.04 (0.19), residues: 744 sheet: -1.76 (0.39), residues: 158 loop : -0.85 (0.16), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP O 46 HIS 0.005 0.001 HIS G 81 PHE 0.021 0.002 PHE G 315 TYR 0.016 0.001 TYR E 301 ARG 0.007 0.000 ARG E 189 Details of bonding type rmsd hydrogen bonds : bond 0.04076 ( 649) hydrogen bonds : angle 5.82252 ( 1731) metal coordination : bond 0.02128 ( 28) metal coordination : angle 3.40677 ( 21) SS BOND : bond 0.00674 ( 9) SS BOND : angle 2.10228 ( 18) covalent geometry : bond 0.00268 (19269) covalent geometry : angle 0.50888 (26103) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 438 time to evaluate : 2.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8100 (t70) cc_final: 0.7761 (t70) REVERT: A 194 ASP cc_start: 0.7117 (t0) cc_final: 0.6813 (t0) REVERT: A 265 ARG cc_start: 0.7034 (ttm170) cc_final: 0.6564 (tpm170) REVERT: A 269 ARG cc_start: 0.4112 (mtm-85) cc_final: 0.3391 (mtm-85) REVERT: C 60 SER cc_start: 0.8638 (t) cc_final: 0.8366 (m) REVERT: C 112 GLN cc_start: 0.7698 (mt0) cc_final: 0.7489 (mp10) REVERT: C 171 ARG cc_start: 0.7584 (mtm-85) cc_final: 0.5745 (mmt180) REVERT: C 174 ARG cc_start: 0.7553 (mmm-85) cc_final: 0.7297 (mmm-85) REVERT: C 189 ARG cc_start: 0.7746 (ptt180) cc_final: 0.7544 (ptm160) REVERT: C 200 TYR cc_start: 0.7421 (m-80) cc_final: 0.6853 (m-80) REVERT: C 310 PHE cc_start: 0.8401 (t80) cc_final: 0.8107 (t80) REVERT: E 68 ASP cc_start: 0.7185 (p0) cc_final: 0.6851 (p0) REVERT: E 86 LYS cc_start: 0.8122 (mmmm) cc_final: 0.7509 (mtmm) REVERT: G 16 ASN cc_start: 0.7009 (t0) cc_final: 0.6652 (t0) REVERT: G 67 PHE cc_start: 0.7837 (m-10) cc_final: 0.7480 (m-80) REVERT: G 146 GLN cc_start: 0.7768 (tm-30) cc_final: 0.7404 (tp40) REVERT: G 174 ARG cc_start: 0.7418 (mpt90) cc_final: 0.6750 (tpt-90) REVERT: I 54 ILE cc_start: 0.8747 (mt) cc_final: 0.8536 (mt) REVERT: I 102 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.6361 (mm-40) REVERT: I 150 HIS cc_start: 0.7934 (t70) cc_final: 0.6859 (m-70) REVERT: I 171 ARG cc_start: 0.6730 (ptt180) cc_final: 0.5584 (mtt90) REVERT: I 267 GLN cc_start: 0.6251 (mm-40) cc_final: 0.5993 (mm-40) REVERT: K 67 PHE cc_start: 0.7590 (OUTLIER) cc_final: 0.7141 (t80) REVERT: K 103 ASP cc_start: 0.8386 (m-30) cc_final: 0.8156 (m-30) REVERT: K 120 LEU cc_start: 0.8149 (mt) cc_final: 0.7832 (mt) REVERT: K 253 ILE cc_start: 0.6715 (OUTLIER) cc_final: 0.6206 (pp) REVERT: K 269 ARG cc_start: 0.8045 (ptt180) cc_final: 0.7623 (ptt-90) REVERT: K 307 GLU cc_start: 0.7872 (pm20) cc_final: 0.7666 (pm20) REVERT: K 312 ARG cc_start: 0.7877 (ptm160) cc_final: 0.7335 (ttp80) REVERT: M 16 ASN cc_start: 0.7660 (t0) cc_final: 0.7198 (t0) REVERT: M 25 SER cc_start: 0.8066 (t) cc_final: 0.7855 (t) REVERT: M 107 LEU cc_start: 0.7990 (mt) cc_final: 0.7265 (mm) REVERT: M 115 GLN cc_start: 0.8585 (mt0) cc_final: 0.8217 (mt0) REVERT: M 122 TYR cc_start: 0.8193 (m-80) cc_final: 0.7453 (m-80) REVERT: M 141 PHE cc_start: 0.8456 (t80) cc_final: 0.8015 (t80) REVERT: M 188 LEU cc_start: 0.8369 (mp) cc_final: 0.8127 (mm) REVERT: M 204 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8246 (mt) REVERT: O 88 ARG cc_start: 0.7067 (ttm110) cc_final: 0.6785 (ttm110) REVERT: O 112 GLN cc_start: 0.7232 (pm20) cc_final: 0.6745 (pm20) REVERT: O 171 ARG cc_start: 0.7340 (mtm-85) cc_final: 0.6688 (mtt-85) REVERT: O 198 ASN cc_start: 0.7008 (m-40) cc_final: 0.6641 (p0) REVERT: O 269 ARG cc_start: 0.4674 (OUTLIER) cc_final: 0.4149 (pmt-80) REVERT: O 270 ASN cc_start: 0.7440 (t0) cc_final: 0.7038 (m-40) outliers start: 75 outliers final: 32 residues processed: 491 average time/residue: 0.3249 time to fit residues: 234.8208 Evaluate side-chains 435 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 398 time to evaluate : 1.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 36 CYS Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 169 CYS Chi-restraints excluded: chain E residue 195 GLN Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain G residue 294 TYR Chi-restraints excluded: chain I residue 102 GLN Chi-restraints excluded: chain I residue 167 THR Chi-restraints excluded: chain I residue 169 CYS Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 150 HIS Chi-restraints excluded: chain K residue 253 ILE Chi-restraints excluded: chain M residue 90 ILE Chi-restraints excluded: chain M residue 195 GLN Chi-restraints excluded: chain M residue 204 LEU Chi-restraints excluded: chain M residue 240 VAL Chi-restraints excluded: chain M residue 284 THR Chi-restraints excluded: chain M residue 294 TYR Chi-restraints excluded: chain M residue 306 SER Chi-restraints excluded: chain O residue 60 SER Chi-restraints excluded: chain O residue 134 ASN Chi-restraints excluded: chain O residue 149 ILE Chi-restraints excluded: chain O residue 150 HIS Chi-restraints excluded: chain O residue 169 CYS Chi-restraints excluded: chain O residue 224 LEU Chi-restraints excluded: chain O residue 269 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 2 optimal weight: 5.9990 chunk 129 optimal weight: 0.0060 chunk 65 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 112 optimal weight: 0.0030 chunk 9 optimal weight: 0.3980 chunk 230 optimal weight: 5.9990 chunk 178 optimal weight: 0.4980 chunk 157 optimal weight: 3.9990 chunk 213 optimal weight: 0.4980 chunk 136 optimal weight: 0.7980 overall best weight: 0.2806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 199 ASN E 305 ASN I 106 ASN I 164 ASN ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 218 GLN ** O 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 195 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.216530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.192390 restraints weight = 20248.348| |-----------------------------------------------------------------------------| r_work (start): 0.4178 rms_B_bonded: 1.86 r_work: 0.4086 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3954 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 19306 Z= 0.103 Angle : 0.491 8.235 26142 Z= 0.265 Chirality : 0.042 0.148 2873 Planarity : 0.004 0.065 3460 Dihedral : 4.474 18.884 2572 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.38 % Allowed : 22.47 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.17), residues: 2285 helix: 1.13 (0.19), residues: 749 sheet: -1.71 (0.38), residues: 166 loop : -0.81 (0.16), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 46 HIS 0.004 0.001 HIS G 52 PHE 0.028 0.001 PHE G 315 TYR 0.020 0.001 TYR E 301 ARG 0.008 0.000 ARG E 189 Details of bonding type rmsd hydrogen bonds : bond 0.03379 ( 649) hydrogen bonds : angle 5.32605 ( 1731) metal coordination : bond 0.01669 ( 28) metal coordination : angle 2.91494 ( 21) SS BOND : bond 0.00312 ( 9) SS BOND : angle 1.70634 ( 18) covalent geometry : bond 0.00228 (19269) covalent geometry : angle 0.48243 (26103) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 442 time to evaluate : 2.226 Fit side-chains revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8069 (t70) cc_final: 0.7749 (t70) REVERT: A 194 ASP cc_start: 0.7099 (t0) cc_final: 0.6764 (t0) REVERT: A 265 ARG cc_start: 0.7064 (ttm170) cc_final: 0.6570 (tpm170) REVERT: A 269 ARG cc_start: 0.4176 (mtm-85) cc_final: 0.3401 (mtm-85) REVERT: C 43 ASP cc_start: 0.7579 (t0) cc_final: 0.7366 (t0) REVERT: C 60 SER cc_start: 0.8602 (t) cc_final: 0.8307 (m) REVERT: C 171 ARG cc_start: 0.7505 (mtm-85) cc_final: 0.5729 (mmt180) REVERT: C 174 ARG cc_start: 0.7612 (mmm-85) cc_final: 0.7335 (mmm-85) REVERT: C 200 TYR cc_start: 0.7457 (m-80) cc_final: 0.6887 (m-80) REVERT: C 310 PHE cc_start: 0.8323 (t80) cc_final: 0.8032 (t80) REVERT: E 68 ASP cc_start: 0.7192 (p0) cc_final: 0.6783 (p0) REVERT: G 39 ASP cc_start: 0.7614 (OUTLIER) cc_final: 0.7305 (p0) REVERT: G 42 HIS cc_start: 0.7636 (m90) cc_final: 0.6681 (m90) REVERT: G 67 PHE cc_start: 0.7657 (m-10) cc_final: 0.7243 (m-80) REVERT: G 174 ARG cc_start: 0.7543 (mpt90) cc_final: 0.7007 (tpt-90) REVERT: I 150 HIS cc_start: 0.7861 (t70) cc_final: 0.6842 (m-70) REVERT: I 171 ARG cc_start: 0.6745 (ptt180) cc_final: 0.5469 (mpt180) REVERT: K 120 LEU cc_start: 0.8117 (mt) cc_final: 0.7788 (mt) REVERT: K 133 ASP cc_start: 0.7354 (t0) cc_final: 0.6775 (m-30) REVERT: K 149 ILE cc_start: 0.8282 (tt) cc_final: 0.8072 (pt) REVERT: K 150 HIS cc_start: 0.6775 (OUTLIER) cc_final: 0.6079 (m-70) REVERT: K 253 ILE cc_start: 0.6477 (OUTLIER) cc_final: 0.5958 (pp) REVERT: K 269 ARG cc_start: 0.8001 (ptt180) cc_final: 0.7541 (ptt-90) REVERT: K 307 GLU cc_start: 0.7487 (pm20) cc_final: 0.7279 (pm20) REVERT: K 312 ARG cc_start: 0.7867 (ptm160) cc_final: 0.7363 (ttp80) REVERT: M 16 ASN cc_start: 0.7649 (t0) cc_final: 0.7319 (t0) REVERT: M 68 ASP cc_start: 0.5065 (t0) cc_final: 0.4813 (t0) REVERT: M 122 TYR cc_start: 0.8169 (m-80) cc_final: 0.7486 (m-80) REVERT: M 141 PHE cc_start: 0.8457 (t80) cc_final: 0.8002 (t80) REVERT: M 188 LEU cc_start: 0.8356 (mp) cc_final: 0.8130 (mm) REVERT: O 35 PRO cc_start: 0.6773 (Cg_exo) cc_final: 0.6497 (Cg_endo) REVERT: O 51 ASN cc_start: 0.6686 (OUTLIER) cc_final: 0.6310 (t0) REVERT: O 88 ARG cc_start: 0.7043 (ttm110) cc_final: 0.6738 (ttm110) REVERT: O 112 GLN cc_start: 0.7057 (pm20) cc_final: 0.6649 (pm20) REVERT: O 134 ASN cc_start: 0.6726 (OUTLIER) cc_final: 0.6496 (p0) REVERT: O 171 ARG cc_start: 0.7193 (mtm-85) cc_final: 0.6539 (mtt-85) REVERT: O 198 ASN cc_start: 0.6720 (m-40) cc_final: 0.6466 (p0) REVERT: O 269 ARG cc_start: 0.4617 (OUTLIER) cc_final: 0.4146 (pmt-80) REVERT: O 270 ASN cc_start: 0.7407 (t0) cc_final: 0.6982 (m-40) outliers start: 71 outliers final: 42 residues processed: 493 average time/residue: 0.3150 time to fit residues: 230.8085 Evaluate side-chains 452 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 404 time to evaluate : 1.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 36 CYS Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain E residue 51 ASN Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 169 CYS Chi-restraints excluded: chain E residue 195 GLN Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain G residue 294 TYR Chi-restraints excluded: chain I residue 62 MET Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 167 THR Chi-restraints excluded: chain I residue 169 CYS Chi-restraints excluded: chain I residue 229 CYS Chi-restraints excluded: chain I residue 293 THR Chi-restraints excluded: chain K residue 150 HIS Chi-restraints excluded: chain K residue 253 ILE Chi-restraints excluded: chain M residue 57 PHE Chi-restraints excluded: chain M residue 132 CYS Chi-restraints excluded: chain M residue 195 GLN Chi-restraints excluded: chain M residue 221 THR Chi-restraints excluded: chain M residue 242 SER Chi-restraints excluded: chain M residue 294 TYR Chi-restraints excluded: chain M residue 306 SER Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 51 ASN Chi-restraints excluded: chain O residue 120 LEU Chi-restraints excluded: chain O residue 134 ASN Chi-restraints excluded: chain O residue 142 THR Chi-restraints excluded: chain O residue 149 ILE Chi-restraints excluded: chain O residue 150 HIS Chi-restraints excluded: chain O residue 169 CYS Chi-restraints excluded: chain O residue 195 GLN Chi-restraints excluded: chain O residue 224 LEU Chi-restraints excluded: chain O residue 269 ARG Chi-restraints excluded: chain O residue 293 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 187 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 166 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 170 optimal weight: 0.0010 chunk 98 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 199 ASN G 270 ASN ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 124 ASN ** O 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.208772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.183158 restraints weight = 20303.726| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 1.91 r_work: 0.3981 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3842 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 19306 Z= 0.180 Angle : 0.584 13.533 26142 Z= 0.308 Chirality : 0.045 0.156 2873 Planarity : 0.004 0.074 3460 Dihedral : 4.757 21.171 2572 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.47 % Allowed : 22.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.17), residues: 2285 helix: 0.95 (0.19), residues: 717 sheet: -1.37 (0.33), residues: 235 loop : -0.90 (0.16), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 46 HIS 0.008 0.002 HIS C 81 PHE 0.026 0.002 PHE G 315 TYR 0.022 0.002 TYR E 301 ARG 0.009 0.001 ARG E 189 Details of bonding type rmsd hydrogen bonds : bond 0.03902 ( 649) hydrogen bonds : angle 5.49077 ( 1731) metal coordination : bond 0.03122 ( 28) metal coordination : angle 4.68850 ( 21) SS BOND : bond 0.00801 ( 9) SS BOND : angle 2.11727 ( 18) covalent geometry : bond 0.00424 (19269) covalent geometry : angle 0.56596 (26103) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 424 time to evaluate : 2.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 SER cc_start: 0.8685 (t) cc_final: 0.8331 (p) REVERT: A 43 ASP cc_start: 0.8185 (t70) cc_final: 0.7874 (t70) REVERT: A 150 HIS cc_start: 0.7321 (OUTLIER) cc_final: 0.7108 (m-70) REVERT: A 194 ASP cc_start: 0.7198 (t0) cc_final: 0.6773 (t0) REVERT: A 265 ARG cc_start: 0.7093 (ttm170) cc_final: 0.6595 (tpm170) REVERT: A 269 ARG cc_start: 0.4280 (mtm-85) cc_final: 0.3528 (mtm-85) REVERT: C 60 SER cc_start: 0.8722 (t) cc_final: 0.8387 (m) REVERT: C 102 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.6611 (mm-40) REVERT: C 171 ARG cc_start: 0.7674 (mtm-85) cc_final: 0.5781 (mmt180) REVERT: C 174 ARG cc_start: 0.7661 (mmm-85) cc_final: 0.7385 (mmm-85) REVERT: C 200 TYR cc_start: 0.7858 (m-80) cc_final: 0.7311 (m-80) REVERT: C 267 GLN cc_start: 0.6718 (mt0) cc_final: 0.6100 (mm-40) REVERT: C 310 PHE cc_start: 0.8500 (t80) cc_final: 0.8211 (t80) REVERT: E 68 ASP cc_start: 0.7150 (p0) cc_final: 0.6680 (p0) REVERT: G 39 ASP cc_start: 0.7721 (OUTLIER) cc_final: 0.7472 (p0) REVERT: G 42 HIS cc_start: 0.7755 (m90) cc_final: 0.6741 (m90) REVERT: G 67 PHE cc_start: 0.7771 (m-10) cc_final: 0.7346 (m-80) REVERT: G 174 ARG cc_start: 0.7619 (mpt90) cc_final: 0.7018 (tpt-90) REVERT: G 200 TYR cc_start: 0.8643 (m-80) cc_final: 0.8416 (m-80) REVERT: I 54 ILE cc_start: 0.8676 (mt) cc_final: 0.8452 (mt) REVERT: I 102 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.6387 (mm-40) REVERT: I 150 HIS cc_start: 0.7836 (t70) cc_final: 0.7006 (m-70) REVERT: I 171 ARG cc_start: 0.6896 (ptt180) cc_final: 0.5657 (mtt90) REVERT: K 67 PHE cc_start: 0.7903 (OUTLIER) cc_final: 0.7307 (t80) REVERT: K 120 LEU cc_start: 0.8167 (mt) cc_final: 0.7832 (mt) REVERT: K 133 ASP cc_start: 0.7242 (t0) cc_final: 0.6786 (m-30) REVERT: K 224 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8310 (mt) REVERT: K 253 ILE cc_start: 0.6713 (OUTLIER) cc_final: 0.6209 (pp) REVERT: K 269 ARG cc_start: 0.8028 (ptt180) cc_final: 0.7560 (ptt-90) REVERT: K 312 ARG cc_start: 0.7886 (ptm160) cc_final: 0.7319 (ttp80) REVERT: M 122 TYR cc_start: 0.8335 (m-80) cc_final: 0.7544 (m-80) REVERT: M 141 PHE cc_start: 0.8516 (t80) cc_final: 0.8044 (t80) REVERT: M 188 LEU cc_start: 0.8415 (mp) cc_final: 0.8183 (mm) REVERT: O 51 ASN cc_start: 0.7114 (OUTLIER) cc_final: 0.6765 (t0) REVERT: O 88 ARG cc_start: 0.7067 (ttm110) cc_final: 0.6774 (ttm110) REVERT: O 112 GLN cc_start: 0.7100 (pm20) cc_final: 0.6745 (pm20) REVERT: O 134 ASN cc_start: 0.6768 (OUTLIER) cc_final: 0.6228 (p0) REVERT: O 171 ARG cc_start: 0.7307 (mtm-85) cc_final: 0.6627 (mtt-85) REVERT: O 198 ASN cc_start: 0.6893 (m-40) cc_final: 0.6595 (p0) REVERT: O 270 ASN cc_start: 0.7411 (t0) cc_final: 0.6915 (m-40) outliers start: 94 outliers final: 62 residues processed: 496 average time/residue: 0.3077 time to fit residues: 228.5129 Evaluate side-chains 469 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 398 time to evaluate : 2.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 150 HIS Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 36 CYS Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 102 GLN Chi-restraints excluded: chain C residue 195 GLN Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain E residue 51 ASN Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 169 CYS Chi-restraints excluded: chain E residue 195 GLN Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 59 MET Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain G residue 284 THR Chi-restraints excluded: chain G residue 285 LEU Chi-restraints excluded: chain G residue 294 TYR Chi-restraints excluded: chain I residue 36 CYS Chi-restraints excluded: chain I residue 62 MET Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 102 GLN Chi-restraints excluded: chain I residue 167 THR Chi-restraints excluded: chain I residue 169 CYS Chi-restraints excluded: chain I residue 253 ILE Chi-restraints excluded: chain I residue 293 THR Chi-restraints excluded: chain I residue 311 LEU Chi-restraints excluded: chain K residue 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 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 182 VAL Chi-restraints excluded: chain M residue 195 GLN Chi-restraints excluded: chain M residue 240 VAL Chi-restraints excluded: chain M residue 242 SER Chi-restraints excluded: chain M residue 245 ASP Chi-restraints excluded: chain M residue 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 120 LEU Chi-restraints excluded: chain O residue 134 ASN Chi-restraints excluded: chain O residue 142 THR Chi-restraints excluded: chain O residue 149 ILE Chi-restraints excluded: chain O residue 150 HIS Chi-restraints excluded: chain O residue 169 CYS Chi-restraints excluded: chain O residue 293 THR Chi-restraints excluded: chain O residue 316 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 44 optimal weight: 3.9990 chunk 93 optimal weight: 0.0030 chunk 135 optimal weight: 2.9990 chunk 176 optimal weight: 0.5980 chunk 99 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 142 optimal weight: 0.5980 chunk 94 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 199 ASN I 16 ASN ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 ASN M 115 GLN 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.213417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.188450 restraints weight = 20337.066| |-----------------------------------------------------------------------------| r_work (start): 0.4131 rms_B_bonded: 1.90 r_work: 0.4037 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3901 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 19306 Z= 0.113 Angle : 0.516 8.912 26142 Z= 0.276 Chirality : 0.042 0.150 2873 Planarity : 0.004 0.071 3460 Dihedral : 4.553 19.458 2572 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 4.00 % Allowed : 23.85 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.17), residues: 2285 helix: 1.18 (0.19), residues: 719 sheet: -1.33 (0.33), residues: 235 loop : -0.86 (0.16), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 46 HIS 0.004 0.001 HIS K 81 PHE 0.022 0.001 PHE E 74 TYR 0.017 0.001 TYR E 301 ARG 0.008 0.000 ARG E 189 Details of bonding type rmsd hydrogen bonds : bond 0.03368 ( 649) hydrogen bonds : angle 5.23589 ( 1731) metal coordination : bond 0.01963 ( 28) metal coordination : angle 3.07739 ( 21) SS BOND : bond 0.00336 ( 9) SS BOND : angle 1.80892 ( 18) covalent geometry : bond 0.00260 (19269) covalent geometry : angle 0.50704 (26103) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 403 time to evaluate : 2.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 SER cc_start: 0.8649 (t) cc_final: 0.8305 (p) REVERT: A 43 ASP cc_start: 0.8110 (t70) cc_final: 0.7810 (t70) REVERT: A 194 ASP cc_start: 0.7200 (t0) cc_final: 0.6744 (t0) REVERT: A 265 ARG cc_start: 0.7069 (ttm170) cc_final: 0.6625 (tpm170) REVERT: A 269 ARG cc_start: 0.4392 (mtm-85) cc_final: 0.3275 (mtm180) REVERT: C 60 SER cc_start: 0.8636 (t) cc_final: 0.8333 (m) REVERT: C 102 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.6559 (mm-40) REVERT: C 171 ARG cc_start: 0.7588 (mtm-85) cc_final: 0.5718 (mmt180) REVERT: C 174 ARG cc_start: 0.7640 (mmm-85) cc_final: 0.7352 (mmm-85) REVERT: C 200 TYR cc_start: 0.7511 (m-80) cc_final: 0.6912 (m-80) REVERT: C 222 GLU cc_start: 0.5868 (OUTLIER) cc_final: 0.4887 (mp0) REVERT: C 310 PHE cc_start: 0.8391 (t80) cc_final: 0.8095 (t80) REVERT: E 78 ILE cc_start: 0.7544 (tt) cc_final: 0.7295 (tt) REVERT: E 222 GLU cc_start: 0.7178 (pm20) cc_final: 0.6927 (pm20) REVERT: G 42 HIS cc_start: 0.7760 (m90) cc_final: 0.6720 (m90) REVERT: G 67 PHE cc_start: 0.7669 (m-10) cc_final: 0.7265 (m-80) REVERT: G 174 ARG cc_start: 0.7618 (mpt90) cc_final: 0.7008 (tpt-90) REVERT: I 102 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.6195 (mm-40) REVERT: I 171 ARG cc_start: 0.6859 (ptt180) cc_final: 0.5545 (mpt180) REVERT: I 305 ASN cc_start: 0.8312 (m-40) cc_final: 0.8065 (m-40) REVERT: K 67 PHE cc_start: 0.7862 (OUTLIER) cc_final: 0.7215 (t80) REVERT: K 120 LEU cc_start: 0.8151 (mt) cc_final: 0.7822 (mt) REVERT: K 133 ASP cc_start: 0.7011 (t0) cc_final: 0.6655 (m-30) REVERT: K 149 ILE cc_start: 0.8416 (tt) cc_final: 0.8213 (pt) REVERT: K 253 ILE cc_start: 0.6669 (OUTLIER) cc_final: 0.6148 (pp) REVERT: K 312 ARG cc_start: 0.7863 (ptm160) cc_final: 0.7331 (ttp80) REVERT: M 16 ASN cc_start: 0.7846 (t0) cc_final: 0.7458 (t0) REVERT: M 115 GLN cc_start: 0.8513 (mt0) cc_final: 0.8128 (mt0) REVERT: M 141 PHE cc_start: 0.8541 (t80) cc_final: 0.8087 (t80) REVERT: O 51 ASN cc_start: 0.6825 (OUTLIER) cc_final: 0.6461 (t0) REVERT: O 62 MET cc_start: 0.7110 (mtm) cc_final: 0.6877 (mtp) REVERT: O 88 ARG cc_start: 0.7124 (ttm110) cc_final: 0.6770 (ttm110) REVERT: O 112 GLN cc_start: 0.7187 (pm20) cc_final: 0.5977 (pm20) REVERT: O 134 ASN cc_start: 0.6587 (OUTLIER) cc_final: 0.5611 (p0) REVERT: O 171 ARG cc_start: 0.7165 (mtm-85) cc_final: 0.6457 (mtt-85) REVERT: O 198 ASN cc_start: 0.6746 (m-40) cc_final: 0.6461 (p0) REVERT: O 270 ASN cc_start: 0.7290 (t0) cc_final: 0.6737 (m-40) outliers start: 84 outliers final: 56 residues processed: 465 average time/residue: 0.3115 time to fit residues: 217.6429 Evaluate side-chains 447 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 384 time to evaluate : 2.260 ------------------------------------------------------------------------------- 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 206 ASN 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 102 GLN Chi-restraints excluded: chain C residue 195 GLN Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 51 ASN Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 169 CYS Chi-restraints excluded: chain E residue 195 GLN Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 240 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 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 293 THR Chi-restraints excluded: chain I residue 311 LEU Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 150 HIS Chi-restraints excluded: chain K residue 253 ILE Chi-restraints excluded: chain M residue 57 PHE Chi-restraints excluded: chain M residue 132 CYS Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 168 PHE Chi-restraints excluded: chain M residue 195 GLN Chi-restraints excluded: chain M residue 221 THR Chi-restraints excluded: chain M residue 240 VAL Chi-restraints excluded: chain M residue 242 SER Chi-restraints excluded: chain M residue 245 ASP Chi-restraints excluded: chain M residue 294 TYR Chi-restraints excluded: chain 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 134 ASN Chi-restraints excluded: chain O residue 142 THR Chi-restraints excluded: chain O residue 149 ILE Chi-restraints excluded: chain O residue 150 HIS Chi-restraints excluded: chain O residue 166 ASN Chi-restraints excluded: chain O residue 169 CYS Chi-restraints excluded: chain O residue 195 GLN Chi-restraints excluded: chain O residue 224 LEU Chi-restraints excluded: chain O residue 293 THR Chi-restraints excluded: chain O residue 316 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 211 optimal weight: 0.6980 chunk 28 optimal weight: 10.0000 chunk 30 optimal weight: 0.8980 chunk 229 optimal weight: 3.9990 chunk 169 optimal weight: 0.9990 chunk 110 optimal weight: 0.3980 chunk 87 optimal weight: 0.0050 chunk 104 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 chunk 227 optimal weight: 0.0980 chunk 147 optimal weight: 0.8980 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 199 ASN G 228 ASN ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 251 ASN ** O 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 195 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.215429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.190899 restraints weight = 20278.486| |-----------------------------------------------------------------------------| r_work (start): 0.4153 rms_B_bonded: 1.89 r_work: 0.4058 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3919 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 19306 Z= 0.108 Angle : 0.511 9.249 26142 Z= 0.273 Chirality : 0.042 0.149 2873 Planarity : 0.004 0.071 3460 Dihedral : 4.485 20.423 2572 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.09 % Allowed : 24.18 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.17), residues: 2285 helix: 1.32 (0.20), residues: 719 sheet: -1.23 (0.33), residues: 235 loop : -0.83 (0.16), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 46 HIS 0.004 0.001 HIS K 81 PHE 0.029 0.001 PHE K 315 TYR 0.017 0.001 TYR E 301 ARG 0.011 0.000 ARG E 189 Details of bonding type rmsd hydrogen bonds : bond 0.03261 ( 649) hydrogen bonds : angle 5.11594 ( 1731) metal coordination : bond 0.01824 ( 28) metal coordination : angle 2.98103 ( 21) SS BOND : bond 0.00517 ( 9) SS BOND : angle 1.82929 ( 18) covalent geometry : bond 0.00247 (19269) covalent geometry : angle 0.50167 (26103) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 396 time to evaluate : 2.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 SER cc_start: 0.8642 (t) cc_final: 0.8304 (p) REVERT: A 43 ASP cc_start: 0.8145 (t70) cc_final: 0.7857 (t70) REVERT: A 194 ASP cc_start: 0.7108 (t0) cc_final: 0.6617 (t0) REVERT: A 265 ARG cc_start: 0.7040 (ttm170) cc_final: 0.6616 (tpm170) REVERT: A 269 ARG cc_start: 0.4507 (mtm-85) cc_final: 0.3291 (mtm180) REVERT: C 60 SER cc_start: 0.8610 (t) cc_final: 0.8305 (m) REVERT: C 102 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.6548 (mm-40) REVERT: C 171 ARG cc_start: 0.7576 (mtm-85) cc_final: 0.5716 (mmt180) REVERT: C 174 ARG cc_start: 0.7629 (mmm-85) cc_final: 0.7333 (mmm-85) REVERT: C 200 TYR cc_start: 0.7605 (m-80) cc_final: 0.7000 (m-80) REVERT: C 222 GLU cc_start: 0.5854 (OUTLIER) cc_final: 0.4877 (mp0) REVERT: C 290 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8234 (mt-10) REVERT: C 310 PHE cc_start: 0.8334 (t80) cc_final: 0.8057 (t80) REVERT: E 59 MET cc_start: 0.6599 (mtt) cc_final: 0.6352 (mtm) REVERT: E 78 ILE cc_start: 0.7779 (tt) cc_final: 0.7556 (tt) REVERT: G 39 ASP cc_start: 0.7562 (OUTLIER) cc_final: 0.7204 (p0) REVERT: G 42 HIS cc_start: 0.7735 (m90) cc_final: 0.6696 (m90) REVERT: G 67 PHE cc_start: 0.7665 (m-10) cc_final: 0.7342 (m-80) REVERT: G 174 ARG cc_start: 0.7610 (mpt90) cc_final: 0.7001 (tpt-90) REVERT: I 171 ARG cc_start: 0.6851 (ptt180) cc_final: 0.5547 (mpt180) REVERT: K 67 PHE cc_start: 0.7881 (OUTLIER) cc_final: 0.7185 (t80) REVERT: K 120 LEU cc_start: 0.8120 (mt) cc_final: 0.7761 (mt) REVERT: K 133 ASP cc_start: 0.7078 (t0) cc_final: 0.6764 (m-30) REVERT: K 149 ILE cc_start: 0.8401 (tt) cc_final: 0.8173 (pt) REVERT: K 195 GLN cc_start: 0.7032 (tm-30) cc_final: 0.6664 (pp30) REVERT: K 253 ILE cc_start: 0.6676 (OUTLIER) cc_final: 0.6154 (pp) REVERT: K 312 ARG cc_start: 0.7838 (ptm160) cc_final: 0.7317 (ttp80) REVERT: M 115 GLN cc_start: 0.8495 (mt0) cc_final: 0.8102 (mt0) REVERT: M 141 PHE cc_start: 0.8528 (t80) cc_final: 0.8060 (t80) REVERT: O 112 GLN cc_start: 0.7090 (pm20) cc_final: 0.6837 (pm20) REVERT: O 134 ASN cc_start: 0.6523 (OUTLIER) cc_final: 0.5560 (p0) REVERT: O 171 ARG cc_start: 0.7046 (mtm-85) cc_final: 0.6304 (mtt-85) REVERT: O 198 ASN cc_start: 0.6747 (m-40) cc_final: 0.6440 (p0) REVERT: O 270 ASN cc_start: 0.7291 (t0) cc_final: 0.6740 (m-40) outliers start: 86 outliers final: 56 residues processed: 459 average time/residue: 0.2962 time to fit residues: 205.4503 Evaluate side-chains 447 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 385 time to evaluate : 1.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 36 CYS Chi-restraints excluded: chain C residue 102 GLN Chi-restraints excluded: chain C residue 195 GLN Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 51 ASN Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 169 CYS Chi-restraints excluded: chain E residue 195 GLN Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 294 TYR Chi-restraints excluded: chain I residue 36 CYS Chi-restraints excluded: chain I residue 62 MET Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 167 THR Chi-restraints excluded: chain I residue 169 CYS Chi-restraints excluded: chain I residue 229 CYS Chi-restraints excluded: chain I residue 253 ILE Chi-restraints excluded: chain I residue 293 THR Chi-restraints excluded: chain I residue 311 LEU Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 150 HIS Chi-restraints excluded: chain K residue 253 ILE Chi-restraints excluded: chain M residue 57 PHE Chi-restraints excluded: chain M residue 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 221 THR Chi-restraints excluded: chain M residue 240 VAL Chi-restraints excluded: chain M residue 242 SER Chi-restraints excluded: chain M residue 294 TYR Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 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 160 LEU Chi-restraints excluded: chain O residue 166 ASN Chi-restraints excluded: chain O residue 169 CYS Chi-restraints excluded: chain O residue 195 GLN Chi-restraints excluded: chain O residue 224 LEU Chi-restraints excluded: chain O residue 293 THR Chi-restraints excluded: chain O residue 316 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 49 optimal weight: 0.0870 chunk 152 optimal weight: 6.9990 chunk 101 optimal weight: 7.9990 chunk 150 optimal weight: 0.7980 chunk 86 optimal weight: 5.9990 chunk 228 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 chunk 142 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 45 optimal weight: 9.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 199 ASN I 16 ASN ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 195 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.216898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.194278 restraints weight = 20164.915| |-----------------------------------------------------------------------------| r_work (start): 0.4145 rms_B_bonded: 1.64 r_work: 0.4053 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3922 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 19306 Z= 0.136 Angle : 0.542 10.241 26142 Z= 0.287 Chirality : 0.043 0.151 2873 Planarity : 0.004 0.071 3460 Dihedral : 4.551 21.815 2572 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.24 % Allowed : 24.37 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.17), residues: 2285 helix: 1.32 (0.20), residues: 714 sheet: -1.22 (0.35), residues: 215 loop : -0.88 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 46 HIS 0.005 0.001 HIS C 81 PHE 0.023 0.002 PHE E 74 TYR 0.017 0.001 TYR E 301 ARG 0.012 0.000 ARG E 189 Details of bonding type rmsd hydrogen bonds : bond 0.03400 ( 649) hydrogen bonds : angle 5.15634 ( 1731) metal coordination : bond 0.02274 ( 28) metal coordination : angle 3.61084 ( 21) SS BOND : bond 0.00476 ( 9) SS BOND : angle 2.06356 ( 18) covalent geometry : bond 0.00318 (19269) covalent geometry : angle 0.52971 (26103) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 401 time to evaluate : 2.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 SER cc_start: 0.8576 (t) cc_final: 0.8261 (p) REVERT: A 43 ASP cc_start: 0.8087 (t70) cc_final: 0.7807 (t70) REVERT: A 134 ASN cc_start: 0.7138 (m-40) cc_final: 0.6907 (m-40) REVERT: A 194 ASP cc_start: 0.6924 (t0) cc_final: 0.6495 (t0) REVERT: A 265 ARG cc_start: 0.7050 (ttm170) cc_final: 0.6809 (tpm170) REVERT: A 269 ARG cc_start: 0.4439 (mtm-85) cc_final: 0.3136 (mtm180) REVERT: C 60 SER cc_start: 0.8596 (t) cc_final: 0.8289 (m) REVERT: C 102 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.6607 (mm-40) REVERT: C 171 ARG cc_start: 0.7662 (mtm-85) cc_final: 0.5888 (mmt180) REVERT: C 174 ARG cc_start: 0.7716 (mmm-85) cc_final: 0.7456 (mmm-85) REVERT: C 200 TYR cc_start: 0.7464 (m-80) cc_final: 0.6953 (m-80) REVERT: C 224 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8133 (mt) REVERT: C 267 GLN cc_start: 0.6819 (mt0) cc_final: 0.6135 (mm-40) REVERT: C 310 PHE cc_start: 0.8335 (t80) cc_final: 0.8086 (t80) REVERT: E 59 MET cc_start: 0.6700 (mtt) cc_final: 0.6447 (mtm) REVERT: G 39 ASP cc_start: 0.7481 (OUTLIER) cc_final: 0.7221 (p0) REVERT: G 42 HIS cc_start: 0.7649 (m90) cc_final: 0.6741 (m90) REVERT: G 67 PHE cc_start: 0.7685 (m-10) cc_final: 0.7343 (m-80) REVERT: G 174 ARG cc_start: 0.7566 (mpt90) cc_final: 0.7097 (tpt-90) REVERT: G 273 LYS cc_start: 0.8186 (ptmt) cc_final: 0.7621 (pttm) REVERT: I 19 ILE cc_start: 0.7655 (OUTLIER) cc_final: 0.7277 (tp) REVERT: I 102 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.6359 (mm-40) REVERT: I 171 ARG cc_start: 0.6897 (ptt180) cc_final: 0.5657 (mpt180) REVERT: K 67 PHE cc_start: 0.7950 (OUTLIER) cc_final: 0.7281 (t80) REVERT: K 120 LEU cc_start: 0.8192 (mt) cc_final: 0.7850 (mt) REVERT: K 133 ASP cc_start: 0.7134 (t0) cc_final: 0.6917 (m-30) REVERT: K 149 ILE cc_start: 0.8381 (tt) cc_final: 0.8139 (pt) REVERT: K 253 ILE cc_start: 0.6675 (OUTLIER) cc_final: 0.6165 (pp) REVERT: K 312 ARG cc_start: 0.7769 (ptm160) cc_final: 0.7319 (ttp80) REVERT: M 115 GLN cc_start: 0.8514 (mt0) cc_final: 0.8188 (mt0) REVERT: M 141 PHE cc_start: 0.8498 (t80) cc_final: 0.8128 (t80) REVERT: O 134 ASN cc_start: 0.6556 (OUTLIER) cc_final: 0.5885 (p0) REVERT: O 171 ARG cc_start: 0.7052 (mtm-85) cc_final: 0.6450 (mtt-85) REVERT: O 198 ASN cc_start: 0.6693 (m-40) cc_final: 0.6331 (p0) REVERT: O 270 ASN cc_start: 0.7268 (t0) cc_final: 0.6833 (m-40) outliers start: 89 outliers final: 69 residues processed: 470 average time/residue: 0.3080 time to fit residues: 218.3556 Evaluate side-chains 461 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 384 time to evaluate : 2.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 60 SER 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 173 SER Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 36 CYS Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 102 GLN Chi-restraints excluded: chain C residue 195 GLN Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 51 ASN Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 169 CYS Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 195 GLN Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 59 MET Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 36 CYS Chi-restraints excluded: chain I residue 62 MET Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 102 GLN Chi-restraints excluded: chain I residue 167 THR Chi-restraints excluded: chain I residue 169 CYS Chi-restraints excluded: chain I residue 229 CYS Chi-restraints excluded: chain I residue 253 ILE Chi-restraints excluded: chain I residue 293 THR Chi-restraints excluded: chain I residue 311 LEU Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 131 ILE Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 150 HIS Chi-restraints excluded: chain K residue 253 ILE Chi-restraints excluded: chain M residue 57 PHE Chi-restraints excluded: chain M residue 90 ILE Chi-restraints excluded: chain M residue 132 CYS Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 168 PHE Chi-restraints excluded: chain M residue 182 VAL Chi-restraints excluded: chain M residue 195 GLN Chi-restraints excluded: chain M residue 221 THR Chi-restraints excluded: chain M residue 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 O residue 15 VAL Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 134 ASN Chi-restraints excluded: chain O residue 142 THR Chi-restraints excluded: chain O residue 149 ILE Chi-restraints excluded: chain O residue 150 HIS Chi-restraints excluded: chain O residue 166 ASN Chi-restraints excluded: chain O residue 169 CYS Chi-restraints excluded: chain O residue 195 GLN Chi-restraints excluded: chain O residue 224 LEU Chi-restraints excluded: chain O residue 293 THR Chi-restraints excluded: chain O residue 297 LEU Chi-restraints excluded: chain O residue 316 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 221 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 160 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 161 optimal weight: 4.9990 chunk 102 optimal weight: 8.9990 chunk 3 optimal weight: 0.5980 chunk 230 optimal weight: 0.0970 overall best weight: 1.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN C 51 ASN I 123 ASN ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 134 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.209959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.186734 restraints weight = 20259.311| |-----------------------------------------------------------------------------| r_work (start): 0.4082 rms_B_bonded: 1.65 r_work: 0.3987 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3856 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.118 19306 Z= 0.212 Angle : 0.634 13.131 26142 Z= 0.332 Chirality : 0.046 0.191 2873 Planarity : 0.005 0.073 3460 Dihedral : 4.924 23.065 2572 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 4.38 % Allowed : 24.46 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.17), residues: 2285 helix: 0.89 (0.19), residues: 712 sheet: -1.23 (0.35), residues: 213 loop : -1.02 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 46 HIS 0.009 0.002 HIS M 81 PHE 0.027 0.002 PHE G 315 TYR 0.021 0.002 TYR M 216 ARG 0.014 0.001 ARG E 189 Details of bonding type rmsd hydrogen bonds : bond 0.03905 ( 649) hydrogen bonds : angle 5.48855 ( 1731) metal coordination : bond 0.03552 ( 28) metal coordination : angle 5.05589 ( 21) SS BOND : bond 0.00920 ( 9) SS BOND : angle 2.99957 ( 18) covalent geometry : bond 0.00503 (19269) covalent geometry : angle 0.61280 (26103) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 390 time to evaluate : 2.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 SER cc_start: 0.8571 (t) cc_final: 0.8278 (p) REVERT: A 43 ASP cc_start: 0.8126 (t70) cc_final: 0.7853 (t70) REVERT: A 265 ARG cc_start: 0.7122 (ttm170) cc_final: 0.6810 (tpm170) REVERT: C 43 ASP cc_start: 0.7518 (t0) cc_final: 0.7248 (t0) REVERT: C 102 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.6832 (mm-40) REVERT: C 171 ARG cc_start: 0.7767 (mtm-85) cc_final: 0.5947 (mmt180) REVERT: C 174 ARG cc_start: 0.7737 (mmm-85) cc_final: 0.7241 (mmm-85) REVERT: C 200 TYR cc_start: 0.7940 (m-80) cc_final: 0.7416 (m-80) REVERT: C 224 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8064 (mt) REVERT: C 310 PHE cc_start: 0.8441 (t80) cc_final: 0.8188 (t80) REVERT: G 39 ASP cc_start: 0.7662 (OUTLIER) cc_final: 0.7458 (p0) REVERT: G 42 HIS cc_start: 0.7713 (m90) cc_final: 0.6802 (m90) REVERT: G 67 PHE cc_start: 0.7844 (m-10) cc_final: 0.7604 (m-80) REVERT: G 111 MET cc_start: 0.8041 (mtp) cc_final: 0.7838 (mtp) REVERT: G 174 ARG cc_start: 0.7629 (mpt90) cc_final: 0.7123 (tpt-90) REVERT: I 19 ILE cc_start: 0.7833 (OUTLIER) cc_final: 0.7496 (tp) REVERT: I 102 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.6395 (mm-40) REVERT: I 171 ARG cc_start: 0.6935 (ptt180) cc_final: 0.5672 (mpt180) REVERT: K 67 PHE cc_start: 0.8175 (OUTLIER) cc_final: 0.7450 (t80) REVERT: K 120 LEU cc_start: 0.8272 (mt) cc_final: 0.7952 (mt) REVERT: K 149 ILE cc_start: 0.8387 (tt) cc_final: 0.8153 (pt) REVERT: K 253 ILE cc_start: 0.6698 (OUTLIER) cc_final: 0.6194 (pp) REVERT: K 312 ARG cc_start: 0.7837 (ptm160) cc_final: 0.7378 (ttp80) REVERT: M 141 PHE cc_start: 0.8506 (t80) cc_final: 0.8142 (t80) REVERT: M 218 GLN cc_start: 0.8144 (OUTLIER) cc_final: 0.7435 (tt0) REVERT: O 134 ASN cc_start: 0.6594 (OUTLIER) cc_final: 0.5932 (p0) REVERT: O 171 ARG cc_start: 0.7236 (mtm-85) cc_final: 0.6491 (mtt-85) REVERT: O 198 ASN cc_start: 0.6811 (m-40) cc_final: 0.6367 (p0) REVERT: O 301 TYR cc_start: 0.8078 (t80) cc_final: 0.7650 (t80) outliers start: 92 outliers final: 69 residues processed: 460 average time/residue: 0.3037 time to fit residues: 211.1191 Evaluate side-chains 461 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 383 time to evaluate : 2.261 ------------------------------------------------------------------------------- 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 173 SER Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain 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 195 GLN Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 51 ASN Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 169 CYS Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 195 GLN Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 59 MET Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 284 THR Chi-restraints excluded: chain G residue 285 LEU Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 36 CYS Chi-restraints excluded: chain I residue 62 MET Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 102 GLN Chi-restraints excluded: chain I residue 167 THR Chi-restraints excluded: chain I residue 169 CYS Chi-restraints excluded: chain I residue 253 ILE Chi-restraints excluded: chain I residue 293 THR Chi-restraints excluded: chain I residue 311 LEU Chi-restraints excluded: chain K residue 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 253 ILE Chi-restraints excluded: chain M residue 57 PHE Chi-restraints excluded: chain M residue 90 ILE Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 168 PHE Chi-restraints excluded: chain M residue 182 VAL 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 O residue 15 VAL Chi-restraints excluded: chain O residue 24 VAL 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 224 LEU Chi-restraints excluded: chain O residue 229 CYS Chi-restraints excluded: chain O residue 293 THR Chi-restraints excluded: chain O residue 297 LEU Chi-restraints excluded: chain O residue 316 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 125 optimal weight: 0.9980 chunk 226 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 60 optimal weight: 0.0870 chunk 204 optimal weight: 0.9990 chunk 202 optimal weight: 0.9980 chunk 205 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 overall best weight: 0.7758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 199 ASN I 123 ASN ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 115 GLN M 270 ASN ** O 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.211757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.186505 restraints weight = 20339.259| |-----------------------------------------------------------------------------| r_work (start): 0.4109 rms_B_bonded: 1.91 r_work: 0.4015 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3879 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 19306 Z= 0.133 Angle : 0.567 11.165 26142 Z= 0.299 Chirality : 0.043 0.154 2873 Planarity : 0.004 0.072 3460 Dihedral : 4.755 24.276 2572 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.95 % Allowed : 25.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.17), residues: 2285 helix: 1.12 (0.20), residues: 712 sheet: -1.26 (0.35), residues: 213 loop : -0.97 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 46 HIS 0.005 0.001 HIS O 81 PHE 0.023 0.002 PHE A 315 TYR 0.018 0.001 TYR E 301 ARG 0.014 0.000 ARG E 189 Details of bonding type rmsd hydrogen bonds : bond 0.03413 ( 649) hydrogen bonds : angle 5.30992 ( 1731) metal coordination : bond 0.02315 ( 28) metal coordination : angle 3.68597 ( 21) SS BOND : bond 0.00499 ( 9) SS BOND : angle 2.88411 ( 18) covalent geometry : bond 0.00309 (19269) covalent geometry : angle 0.55240 (26103) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 396 time to evaluate : 2.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 SER cc_start: 0.8619 (t) cc_final: 0.8297 (p) REVERT: A 43 ASP cc_start: 0.8186 (t70) cc_final: 0.7909 (t70) REVERT: A 265 ARG cc_start: 0.7138 (ttm170) cc_final: 0.6700 (tpm170) REVERT: C 102 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.6762 (mm-40) REVERT: C 171 ARG cc_start: 0.7676 (mtm-85) cc_final: 0.5786 (mmt180) REVERT: C 174 ARG cc_start: 0.7667 (mmm-85) cc_final: 0.7399 (mmm-85) REVERT: C 200 TYR cc_start: 0.7623 (m-80) cc_final: 0.7038 (m-80) REVERT: C 224 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8122 (mt) REVERT: C 310 PHE cc_start: 0.8409 (t80) cc_final: 0.8132 (t80) REVERT: E 318 ARG cc_start: 0.7314 (ttm110) cc_final: 0.6945 (ttp-170) REVERT: G 39 ASP cc_start: 0.7606 (OUTLIER) cc_final: 0.7242 (p0) REVERT: G 42 HIS cc_start: 0.7774 (m90) cc_final: 0.6735 (m90) REVERT: G 67 PHE cc_start: 0.7832 (m-10) cc_final: 0.7575 (m-80) REVERT: G 91 LYS cc_start: 0.8505 (mtmt) cc_final: 0.8247 (mtmm) REVERT: G 174 ARG cc_start: 0.7667 (mpt90) cc_final: 0.7050 (tpt-90) REVERT: G 288 TYR cc_start: 0.5888 (m-80) cc_final: 0.4522 (m-80) REVERT: I 19 ILE cc_start: 0.7683 (OUTLIER) cc_final: 0.7340 (tp) REVERT: I 102 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.6424 (mm-40) REVERT: I 171 ARG cc_start: 0.6857 (ptt180) cc_final: 0.5581 (mpt180) REVERT: K 67 PHE cc_start: 0.8086 (OUTLIER) cc_final: 0.7310 (t80) REVERT: K 120 LEU cc_start: 0.8169 (mt) cc_final: 0.7832 (mt) REVERT: K 133 ASP cc_start: 0.7313 (t0) cc_final: 0.6520 (m-30) REVERT: K 149 ILE cc_start: 0.8306 (tt) cc_final: 0.8086 (pt) REVERT: K 195 GLN cc_start: 0.7023 (tm-30) cc_final: 0.6702 (pp30) REVERT: K 253 ILE cc_start: 0.6759 (OUTLIER) cc_final: 0.6245 (pp) REVERT: K 312 ARG cc_start: 0.7858 (ptm160) cc_final: 0.7371 (ttp80) REVERT: M 115 GLN cc_start: 0.8527 (mt0) cc_final: 0.8042 (mt0) REVERT: M 141 PHE cc_start: 0.8518 (t80) cc_final: 0.8078 (t80) REVERT: M 307 GLU cc_start: 0.6802 (mp0) cc_final: 0.6503 (mt-10) REVERT: O 171 ARG cc_start: 0.7091 (mtm-85) cc_final: 0.6214 (mtt-85) REVERT: O 198 ASN cc_start: 0.6971 (m-40) cc_final: 0.6398 (p0) REVERT: O 270 ASN cc_start: 0.7509 (t0) cc_final: 0.7007 (m-40) outliers start: 83 outliers final: 61 residues processed: 457 average time/residue: 0.3251 time to fit residues: 223.2974 Evaluate side-chains 450 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 382 time to evaluate : 2.279 ------------------------------------------------------------------------------- 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 173 SER 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 224 LEU Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 51 ASN Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 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 39 ASP Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 36 CYS Chi-restraints excluded: chain I residue 62 MET Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 102 GLN Chi-restraints excluded: chain I residue 167 THR Chi-restraints excluded: chain I residue 169 CYS Chi-restraints excluded: chain I residue 229 CYS Chi-restraints excluded: chain I residue 253 ILE Chi-restraints excluded: chain I residue 293 THR Chi-restraints excluded: chain I residue 311 LEU Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 150 HIS Chi-restraints excluded: chain K residue 253 ILE Chi-restraints excluded: chain M residue 57 PHE Chi-restraints excluded: chain M residue 90 ILE Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 168 PHE Chi-restraints excluded: chain M residue 182 VAL Chi-restraints excluded: chain M residue 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 245 ASP Chi-restraints excluded: chain M residue 294 TYR Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 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 188 LEU Chi-restraints excluded: chain O residue 195 GLN Chi-restraints excluded: chain O residue 224 LEU Chi-restraints excluded: chain O residue 293 THR Chi-restraints excluded: chain O residue 297 LEU Chi-restraints excluded: chain O residue 316 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 207 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 151 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 170 optimal weight: 0.6980 chunk 137 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 64 optimal weight: 0.4980 chunk 79 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 123 ASN ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 134 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.212102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.187226 restraints weight = 20260.866| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 1.89 r_work: 0.4030 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3893 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.2536 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= 0.131 Angle : 0.564 11.403 26142 Z= 0.298 Chirality : 0.043 0.157 2873 Planarity : 0.004 0.072 3460 Dihedral : 4.680 24.589 2572 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.71 % Allowed : 25.18 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.17), residues: 2285 helix: 1.22 (0.20), residues: 712 sheet: -1.31 (0.35), residues: 213 loop : -0.95 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 46 HIS 0.005 0.001 HIS K 81 PHE 0.022 0.002 PHE O 203 TYR 0.026 0.001 TYR E 301 ARG 0.015 0.001 ARG E 189 Details of bonding type rmsd hydrogen bonds : bond 0.03344 ( 649) hydrogen bonds : angle 5.22323 ( 1731) metal coordination : bond 0.02305 ( 28) metal coordination : angle 3.69905 ( 21) SS BOND : bond 0.00402 ( 9) SS BOND : angle 2.66152 ( 18) covalent geometry : bond 0.00306 (19269) covalent geometry : angle 0.55034 (26103) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 388 time to evaluate : 2.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 SER cc_start: 0.8616 (t) cc_final: 0.8286 (p) REVERT: A 43 ASP cc_start: 0.8189 (t70) cc_final: 0.7925 (t70) REVERT: A 265 ARG cc_start: 0.7108 (ttm170) cc_final: 0.6691 (tpm170) REVERT: C 102 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.6593 (mm-40) REVERT: C 171 ARG cc_start: 0.7670 (mtm-85) cc_final: 0.5818 (mmt180) REVERT: C 174 ARG cc_start: 0.7677 (mmm-85) cc_final: 0.7408 (mmm-85) REVERT: C 200 TYR cc_start: 0.7473 (m-80) cc_final: 0.6898 (m-80) REVERT: C 224 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8150 (mt) REVERT: C 310 PHE cc_start: 0.8409 (t80) cc_final: 0.8133 (t80) REVERT: G 39 ASP cc_start: 0.7584 (OUTLIER) cc_final: 0.7253 (p0) REVERT: G 42 HIS cc_start: 0.7754 (m90) cc_final: 0.6728 (m90) REVERT: G 67 PHE cc_start: 0.7791 (m-10) cc_final: 0.7539 (m-80) REVERT: G 91 LYS cc_start: 0.8496 (mtmt) cc_final: 0.8235 (mtmm) REVERT: G 174 ARG cc_start: 0.7660 (mpt90) cc_final: 0.7056 (tpt-90) REVERT: G 288 TYR cc_start: 0.5766 (m-80) cc_final: 0.4461 (m-80) REVERT: I 19 ILE cc_start: 0.7638 (OUTLIER) cc_final: 0.7292 (tp) REVERT: I 102 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.6235 (mm-40) REVERT: I 171 ARG cc_start: 0.6889 (ptt180) cc_final: 0.5590 (mpt180) REVERT: K 67 PHE cc_start: 0.8052 (OUTLIER) cc_final: 0.7302 (t80) REVERT: K 120 LEU cc_start: 0.8155 (mt) cc_final: 0.7810 (mt) REVERT: K 133 ASP cc_start: 0.7289 (t0) cc_final: 0.6510 (m-30) REVERT: K 149 ILE cc_start: 0.8436 (tt) cc_final: 0.8209 (pt) REVERT: K 195 GLN cc_start: 0.7039 (tm-30) cc_final: 0.6719 (pp30) REVERT: K 253 ILE cc_start: 0.6577 (OUTLIER) cc_final: 0.6059 (pp) REVERT: K 312 ARG cc_start: 0.7851 (ptm160) cc_final: 0.7372 (ttp80) REVERT: M 115 GLN cc_start: 0.8522 (mt0) cc_final: 0.8138 (mt0) REVERT: M 141 PHE cc_start: 0.8556 (t80) cc_final: 0.8090 (t80) REVERT: M 270 ASN cc_start: 0.7894 (m-40) cc_final: 0.7692 (m-40) REVERT: M 307 GLU cc_start: 0.6764 (mp0) cc_final: 0.6472 (mt-10) REVERT: O 110 MET cc_start: 0.4620 (mtt) cc_final: 0.2434 (tpp) REVERT: O 134 ASN cc_start: 0.6593 (OUTLIER) cc_final: 0.5999 (p0) REVERT: O 171 ARG cc_start: 0.7135 (mtm-85) cc_final: 0.6190 (mtt-85) REVERT: O 198 ASN cc_start: 0.6943 (m-40) cc_final: 0.6404 (p0) REVERT: O 270 ASN cc_start: 0.7560 (t0) cc_final: 0.6962 (m-40) outliers start: 78 outliers final: 64 residues processed: 448 average time/residue: 0.3138 time to fit residues: 209.7823 Evaluate side-chains 449 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 377 time to evaluate : 2.026 ------------------------------------------------------------------------------- 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 229 CYS 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 224 LEU Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 51 ASN Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 169 CYS Chi-restraints excluded: chain E residue 195 GLN Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 36 CYS Chi-restraints excluded: chain I residue 62 MET Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 102 GLN Chi-restraints excluded: chain I residue 167 THR Chi-restraints excluded: chain I residue 169 CYS Chi-restraints excluded: chain I residue 229 CYS Chi-restraints excluded: chain I residue 253 ILE Chi-restraints excluded: chain I residue 293 THR Chi-restraints excluded: chain I residue 311 LEU Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 150 HIS Chi-restraints excluded: chain K residue 253 ILE Chi-restraints excluded: chain M residue 57 PHE Chi-restraints excluded: chain M residue 90 ILE Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 168 PHE Chi-restraints excluded: chain M residue 182 VAL Chi-restraints excluded: chain M residue 195 GLN Chi-restraints excluded: chain M residue 221 THR Chi-restraints excluded: chain M residue 222 GLU Chi-restraints excluded: chain M residue 240 VAL Chi-restraints excluded: chain M residue 242 SER Chi-restraints excluded: chain M residue 245 ASP Chi-restraints excluded: chain M residue 294 TYR Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain O residue 24 VAL 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 188 LEU Chi-restraints excluded: chain O residue 195 GLN Chi-restraints excluded: chain O residue 224 LEU Chi-restraints excluded: chain O residue 229 CYS Chi-restraints excluded: chain O residue 293 THR Chi-restraints excluded: chain O residue 297 LEU Chi-restraints excluded: chain O residue 316 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 74 optimal weight: 0.0370 chunk 28 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 160 optimal weight: 10.0000 chunk 196 optimal weight: 0.2980 chunk 32 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.2664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 123 ASN ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 251 ASN ** O 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.211990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.187108 restraints weight = 20411.870| |-----------------------------------------------------------------------------| r_work (start): 0.4121 rms_B_bonded: 1.89 r_work: 0.4025 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3891 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 19306 Z= 0.162 Angle : 0.739 59.198 26142 Z= 0.425 Chirality : 0.046 0.866 2873 Planarity : 0.004 0.072 3460 Dihedral : 4.687 24.545 2572 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.57 % Allowed : 25.32 % Favored : 71.11 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.17), residues: 2285 helix: 1.20 (0.20), residues: 712 sheet: -1.32 (0.35), residues: 213 loop : -0.95 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 46 HIS 0.005 0.001 HIS C 81 PHE 0.023 0.002 PHE C 315 TYR 0.023 0.001 TYR E 301 ARG 0.013 0.000 ARG E 318 Details of bonding type rmsd hydrogen bonds : bond 0.03345 ( 649) hydrogen bonds : angle 5.22431 ( 1731) metal coordination : bond 0.02359 ( 28) metal coordination : angle 3.86786 ( 21) SS BOND : bond 0.00435 ( 9) SS BOND : angle 2.66301 ( 18) covalent geometry : bond 0.00367 (19269) covalent geometry : angle 0.72825 (26103) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11293.10 seconds wall clock time: 195 minutes 12.65 seconds (11712.65 seconds total)