Starting phenix.real_space_refine on Wed Aug 7 02:12:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7box_30135/08_2024/7box_30135.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7box_30135/08_2024/7box_30135.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7box_30135/08_2024/7box_30135.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7box_30135/08_2024/7box_30135.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7box_30135/08_2024/7box_30135.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7box_30135/08_2024/7box_30135.cif" } resolution = 3.8 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= 0.019 sd= 0.574 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: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 11556 2.51 5 N 3168 2.21 5 O 3798 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "M ARG 99": "NH1" <-> "NH2" Residue "N ARG 2": "NH1" <-> "NH2" Residue "N ARG 99": "NH1" <-> "NH2" Residue "O ARG 99": "NH1" <-> "NH2" Residue "P ARG 2": "NH1" <-> "NH2" Residue "P ARG 99": "NH1" <-> "NH2" Residue "Q ARG 99": "NH1" <-> "NH2" Residue "R ARG 2": "NH1" <-> "NH2" Residue "R ARG 99": "NH1" <-> "NH2" Residue "S ARG 99": "NH1" <-> "NH2" Residue "T ARG 2": "NH1" <-> "NH2" Residue "T ARG 99": "NH1" <-> "NH2" Residue "U ARG 99": "NH1" <-> "NH2" Residue "V ARG 2": "NH1" <-> "NH2" Residue "V ARG 99": "NH1" <-> "NH2" Residue "W ARG 99": "NH1" <-> "NH2" Residue "X ARG 2": "NH1" <-> "NH2" Residue "X ARG 99": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 18618 Number of models: 1 Model: "" Number of chains: 12 Chain: "M" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1546 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 187} Chain: "N" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1557 Classifications: {'peptide': 195} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 5, 'TRANS': 187} Chain: "O" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1546 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 187} Chain: "P" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1557 Classifications: {'peptide': 195} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 5, 'TRANS': 187} Chain: "Q" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1546 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 187} Chain: "R" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1557 Classifications: {'peptide': 195} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 5, 'TRANS': 187} Chain: "S" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1546 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 187} Chain: "T" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1557 Classifications: {'peptide': 195} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 5, 'TRANS': 187} Chain: "U" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1546 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 187} Chain: "V" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1557 Classifications: {'peptide': 195} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 5, 'TRANS': 187} Chain: "W" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1546 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 187} Chain: "X" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1557 Classifications: {'peptide': 195} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 5, 'TRANS': 187} Time building chain proxies: 9.69, per 1000 atoms: 0.52 Number of scatterers: 18618 At special positions: 0 Unit cell: (168.91, 168.91, 87.63, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 3798 8.00 N 3168 7.00 C 11556 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 6.70 Conformation dependent library (CDL) restraints added in 3.0 seconds 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4332 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 24 sheets defined 42.9% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'M' and resid 10 through 25 removed outlier: 4.073A pdb=" N ALA M 16 " --> pdb=" O ALA M 12 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE M 24 " --> pdb=" O ILE M 20 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 55 removed outlier: 4.142A pdb=" N GLN M 53 " --> pdb=" O LYS M 49 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 150 removed outlier: 3.580A pdb=" N VAL M 139 " --> pdb=" O ARG M 135 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG M 144 " --> pdb=" O THR M 140 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASN M 147 " --> pdb=" O SER M 143 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE M 150 " --> pdb=" O PHE M 146 " (cutoff:3.500A) Processing helix chain 'M' and resid 153 through 179 removed outlier: 3.552A pdb=" N GLU M 157 " --> pdb=" O ALA M 153 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL M 159 " --> pdb=" O GLU M 155 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU M 160 " --> pdb=" O VAL M 156 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU M 162 " --> pdb=" O GLY M 158 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU M 175 " --> pdb=" O CYS M 171 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N MET M 176 " --> pdb=" O MET M 172 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASP M 177 " --> pdb=" O GLU M 173 " (cutoff:3.500A) Processing helix chain 'N' and resid 11 through 25 Processing helix chain 'N' and resid 37 through 55 removed outlier: 3.649A pdb=" N ALA N 43 " --> pdb=" O ASP N 39 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG N 44 " --> pdb=" O ALA N 40 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLN N 53 " --> pdb=" O LYS N 49 " (cutoff:3.500A) Processing helix chain 'N' and resid 131 through 150 removed outlier: 3.621A pdb=" N VAL N 139 " --> pdb=" O ARG N 135 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG N 144 " --> pdb=" O THR N 140 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN N 147 " --> pdb=" O SER N 143 " (cutoff:3.500A) Processing helix chain 'N' and resid 153 through 179 removed outlier: 3.741A pdb=" N GLU N 157 " --> pdb=" O ALA N 153 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU N 162 " --> pdb=" O GLY N 158 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR N 174 " --> pdb=" O LEU N 170 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU N 175 " --> pdb=" O CYS N 171 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N MET N 176 " --> pdb=" O MET N 172 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP N 177 " --> pdb=" O GLU N 173 " (cutoff:3.500A) Processing helix chain 'O' and resid 10 through 25 removed outlier: 4.004A pdb=" N ALA O 16 " --> pdb=" O ALA O 12 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE O 24 " --> pdb=" O ILE O 20 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 55 removed outlier: 3.502A pdb=" N LEU O 47 " --> pdb=" O ALA O 43 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLN O 53 " --> pdb=" O LYS O 49 " (cutoff:3.500A) Processing helix chain 'O' and resid 131 through 150 removed outlier: 3.508A pdb=" N VAL O 139 " --> pdb=" O ARG O 135 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG O 144 " --> pdb=" O THR O 140 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN O 147 " --> pdb=" O SER O 143 " (cutoff:3.500A) Processing helix chain 'O' and resid 153 through 180 removed outlier: 3.504A pdb=" N GLU O 157 " --> pdb=" O ALA O 153 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL O 159 " --> pdb=" O GLU O 155 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU O 160 " --> pdb=" O VAL O 156 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU O 162 " --> pdb=" O GLY O 158 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR O 174 " --> pdb=" O LEU O 170 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU O 175 " --> pdb=" O CYS O 171 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N MET O 176 " --> pdb=" O MET O 172 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP O 177 " --> pdb=" O GLU O 173 " (cutoff:3.500A) Processing helix chain 'O' and resid 189 through 194 removed outlier: 3.676A pdb=" N LEU O 193 " --> pdb=" O PHE O 189 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU O 194 " --> pdb=" O THR O 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 189 through 194' Processing helix chain 'P' and resid 11 through 25 Processing helix chain 'P' and resid 37 through 57 removed outlier: 3.678A pdb=" N ALA P 43 " --> pdb=" O ASP P 39 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG P 44 " --> pdb=" O ALA P 40 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLN P 53 " --> pdb=" O LYS P 49 " (cutoff:3.500A) Processing helix chain 'P' and resid 131 through 150 removed outlier: 3.589A pdb=" N VAL P 139 " --> pdb=" O ARG P 135 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG P 144 " --> pdb=" O THR P 140 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN P 147 " --> pdb=" O SER P 143 " (cutoff:3.500A) Processing helix chain 'P' and resid 153 through 180 removed outlier: 3.715A pdb=" N GLU P 157 " --> pdb=" O ALA P 153 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU P 162 " --> pdb=" O GLY P 158 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU P 175 " --> pdb=" O CYS P 171 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N MET P 176 " --> pdb=" O MET P 172 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP P 177 " --> pdb=" O GLU P 173 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 25 removed outlier: 3.923A pdb=" N ALA Q 16 " --> pdb=" O ALA Q 12 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE Q 24 " --> pdb=" O ILE Q 20 " (cutoff:3.500A) Processing helix chain 'Q' and resid 37 through 57 removed outlier: 3.527A pdb=" N LEU Q 47 " --> pdb=" O ALA Q 43 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLN Q 53 " --> pdb=" O LYS Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 131 through 150 removed outlier: 3.524A pdb=" N VAL Q 139 " --> pdb=" O ARG Q 135 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG Q 144 " --> pdb=" O THR Q 140 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN Q 147 " --> pdb=" O SER Q 143 " (cutoff:3.500A) Processing helix chain 'Q' and resid 153 through 180 removed outlier: 3.629A pdb=" N VAL Q 159 " --> pdb=" O GLU Q 155 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU Q 160 " --> pdb=" O VAL Q 156 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU Q 162 " --> pdb=" O GLY Q 158 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU Q 175 " --> pdb=" O CYS Q 171 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N MET Q 176 " --> pdb=" O MET Q 172 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP Q 177 " --> pdb=" O GLU Q 173 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY Q 180 " --> pdb=" O MET Q 176 " (cutoff:3.500A) Processing helix chain 'R' and resid 11 through 25 Processing helix chain 'R' and resid 37 through 57 removed outlier: 4.057A pdb=" N GLN R 53 " --> pdb=" O LYS R 49 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 150 removed outlier: 3.543A pdb=" N VAL R 139 " --> pdb=" O ARG R 135 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG R 144 " --> pdb=" O THR R 140 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN R 147 " --> pdb=" O SER R 143 " (cutoff:3.500A) Processing helix chain 'R' and resid 153 through 180 removed outlier: 3.811A pdb=" N GLU R 157 " --> pdb=" O ALA R 153 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU R 162 " --> pdb=" O GLY R 158 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU R 175 " --> pdb=" O CYS R 171 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N MET R 176 " --> pdb=" O MET R 172 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP R 177 " --> pdb=" O GLU R 173 " (cutoff:3.500A) Processing helix chain 'S' and resid 10 through 25 removed outlier: 3.893A pdb=" N ALA S 16 " --> pdb=" O ALA S 12 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE S 24 " --> pdb=" O ILE S 20 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY S 25 " --> pdb=" O LEU S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 55 removed outlier: 4.080A pdb=" N GLN S 53 " --> pdb=" O LYS S 49 " (cutoff:3.500A) Processing helix chain 'S' and resid 131 through 150 removed outlier: 3.510A pdb=" N VAL S 139 " --> pdb=" O ARG S 135 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG S 144 " --> pdb=" O THR S 140 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN S 147 " --> pdb=" O SER S 143 " (cutoff:3.500A) Processing helix chain 'S' and resid 153 through 180 removed outlier: 3.522A pdb=" N VAL S 159 " --> pdb=" O GLU S 155 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU S 160 " --> pdb=" O VAL S 156 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU S 162 " --> pdb=" O GLY S 158 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLU S 175 " --> pdb=" O CYS S 171 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N MET S 176 " --> pdb=" O MET S 172 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP S 177 " --> pdb=" O GLU S 173 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY S 180 " --> pdb=" O MET S 176 " (cutoff:3.500A) Processing helix chain 'T' and resid 11 through 25 Processing helix chain 'T' and resid 37 through 55 removed outlier: 3.581A pdb=" N ALA T 41 " --> pdb=" O ASN T 37 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLN T 53 " --> pdb=" O LYS T 49 " (cutoff:3.500A) Processing helix chain 'T' and resid 131 through 151 removed outlier: 3.631A pdb=" N VAL T 139 " --> pdb=" O ARG T 135 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG T 144 " --> pdb=" O THR T 140 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN T 147 " --> pdb=" O SER T 143 " (cutoff:3.500A) Processing helix chain 'T' and resid 153 through 179 removed outlier: 3.608A pdb=" N GLU T 157 " --> pdb=" O ALA T 153 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU T 162 " --> pdb=" O GLY T 158 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLU T 175 " --> pdb=" O CYS T 171 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N MET T 176 " --> pdb=" O MET T 172 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP T 177 " --> pdb=" O GLU T 173 " (cutoff:3.500A) Processing helix chain 'U' and resid 10 through 25 removed outlier: 3.921A pdb=" N ALA U 16 " --> pdb=" O ALA U 12 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE U 24 " --> pdb=" O ILE U 20 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY U 25 " --> pdb=" O LEU U 21 " (cutoff:3.500A) Processing helix chain 'U' and resid 37 through 55 removed outlier: 4.129A pdb=" N GLN U 53 " --> pdb=" O LYS U 49 " (cutoff:3.500A) Processing helix chain 'U' and resid 131 through 150 removed outlier: 3.563A pdb=" N VAL U 139 " --> pdb=" O ARG U 135 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG U 144 " --> pdb=" O THR U 140 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN U 147 " --> pdb=" O SER U 143 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE U 150 " --> pdb=" O PHE U 146 " (cutoff:3.500A) Processing helix chain 'U' and resid 153 through 179 removed outlier: 3.583A pdb=" N GLU U 157 " --> pdb=" O ALA U 153 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU U 160 " --> pdb=" O VAL U 156 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU U 162 " --> pdb=" O GLY U 158 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR U 174 " --> pdb=" O LEU U 170 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU U 175 " --> pdb=" O CYS U 171 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N MET U 176 " --> pdb=" O MET U 172 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP U 177 " --> pdb=" O GLU U 173 " (cutoff:3.500A) Processing helix chain 'V' and resid 11 through 25 Processing helix chain 'V' and resid 37 through 55 removed outlier: 3.805A pdb=" N ALA V 41 " --> pdb=" O ASN V 37 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLN V 53 " --> pdb=" O LYS V 49 " (cutoff:3.500A) Processing helix chain 'V' and resid 131 through 151 removed outlier: 3.669A pdb=" N VAL V 139 " --> pdb=" O ARG V 135 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG V 144 " --> pdb=" O THR V 140 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN V 147 " --> pdb=" O SER V 143 " (cutoff:3.500A) Processing helix chain 'V' and resid 153 through 179 removed outlier: 3.508A pdb=" N GLU V 157 " --> pdb=" O ALA V 153 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU V 162 " --> pdb=" O GLY V 158 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR V 174 " --> pdb=" O LEU V 170 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU V 175 " --> pdb=" O CYS V 171 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N MET V 176 " --> pdb=" O MET V 172 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP V 177 " --> pdb=" O GLU V 173 " (cutoff:3.500A) Processing helix chain 'W' and resid 10 through 25 removed outlier: 4.004A pdb=" N ALA W 16 " --> pdb=" O ALA W 12 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE W 24 " --> pdb=" O ILE W 20 " (cutoff:3.500A) Processing helix chain 'W' and resid 37 through 55 removed outlier: 4.174A pdb=" N GLN W 53 " --> pdb=" O LYS W 49 " (cutoff:3.500A) Processing helix chain 'W' and resid 131 through 150 removed outlier: 3.590A pdb=" N VAL W 139 " --> pdb=" O ARG W 135 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG W 144 " --> pdb=" O THR W 140 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN W 147 " --> pdb=" O SER W 143 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE W 150 " --> pdb=" O PHE W 146 " (cutoff:3.500A) Processing helix chain 'W' and resid 153 through 179 removed outlier: 3.620A pdb=" N GLU W 157 " --> pdb=" O ALA W 153 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU W 160 " --> pdb=" O VAL W 156 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU W 162 " --> pdb=" O GLY W 158 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR W 174 " --> pdb=" O LEU W 170 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLU W 175 " --> pdb=" O CYS W 171 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N MET W 176 " --> pdb=" O MET W 172 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP W 177 " --> pdb=" O GLU W 173 " (cutoff:3.500A) Processing helix chain 'W' and resid 191 through 195 removed outlier: 3.564A pdb=" N LEU W 194 " --> pdb=" O SER W 191 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR W 195 " --> pdb=" O GLY W 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 191 through 195' Processing helix chain 'X' and resid 11 through 25 Processing helix chain 'X' and resid 37 through 55 removed outlier: 3.501A pdb=" N ALA X 41 " --> pdb=" O ASN X 37 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA X 43 " --> pdb=" O ASP X 39 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLN X 53 " --> pdb=" O LYS X 49 " (cutoff:3.500A) Processing helix chain 'X' and resid 131 through 150 removed outlier: 3.649A pdb=" N VAL X 139 " --> pdb=" O ARG X 135 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG X 144 " --> pdb=" O THR X 140 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN X 147 " --> pdb=" O SER X 143 " (cutoff:3.500A) Processing helix chain 'X' and resid 153 through 179 removed outlier: 3.596A pdb=" N GLU X 157 " --> pdb=" O ALA X 153 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU X 162 " --> pdb=" O GLY X 158 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR X 174 " --> pdb=" O LEU X 170 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU X 175 " --> pdb=" O CYS X 171 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N MET X 176 " --> pdb=" O MET X 172 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASP X 177 " --> pdb=" O GLU X 173 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'M' and resid 63 through 67 removed outlier: 3.550A pdb=" N ILE M 121 " --> pdb=" O GLU M 64 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY M 66 " --> pdb=" O VAL M 119 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N VAL M 119 " --> pdb=" O GLY M 66 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ASN M 120 " --> pdb=" O LEU M 87 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LEU M 87 " --> pdb=" O ASN M 120 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE M 122 " --> pdb=" O LEU M 85 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'M' and resid 96 through 98 Processing sheet with id=AA3, first strand: chain 'N' and resid 63 through 67 removed outlier: 3.508A pdb=" N ILE N 121 " --> pdb=" O GLU N 64 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY N 66 " --> pdb=" O VAL N 119 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N VAL N 119 " --> pdb=" O GLY N 66 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN N 120 " --> pdb=" O LEU N 87 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LEU N 87 " --> pdb=" O ASN N 120 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE N 122 " --> pdb=" O LEU N 85 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'N' and resid 96 through 99 Processing sheet with id=AA5, first strand: chain 'O' and resid 63 through 67 removed outlier: 3.698A pdb=" N GLY O 66 " --> pdb=" O VAL O 119 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N VAL O 119 " --> pdb=" O GLY O 66 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ASN O 120 " --> pdb=" O LEU O 87 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU O 87 " --> pdb=" O ASN O 120 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE O 122 " --> pdb=" O LEU O 85 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'O' and resid 96 through 98 Processing sheet with id=AA7, first strand: chain 'P' and resid 63 through 67 removed outlier: 3.741A pdb=" N GLY P 66 " --> pdb=" O VAL P 119 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N VAL P 119 " --> pdb=" O GLY P 66 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN P 120 " --> pdb=" O LEU P 87 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU P 87 " --> pdb=" O ASN P 120 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ILE P 122 " --> pdb=" O LEU P 85 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'P' and resid 96 through 99 Processing sheet with id=AA9, first strand: chain 'Q' and resid 63 through 67 removed outlier: 3.709A pdb=" N GLY Q 66 " --> pdb=" O VAL Q 119 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N VAL Q 119 " --> pdb=" O GLY Q 66 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ASN Q 120 " --> pdb=" O LEU Q 87 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU Q 87 " --> pdb=" O ASN Q 120 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ILE Q 122 " --> pdb=" O LEU Q 85 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Q' and resid 96 through 98 Processing sheet with id=AB2, first strand: chain 'R' and resid 63 through 67 removed outlier: 3.795A pdb=" N GLY R 66 " --> pdb=" O VAL R 119 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N VAL R 119 " --> pdb=" O GLY R 66 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ASN R 120 " --> pdb=" O LEU R 87 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LEU R 87 " --> pdb=" O ASN R 120 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ILE R 122 " --> pdb=" O LEU R 85 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 96 through 99 Processing sheet with id=AB4, first strand: chain 'S' and resid 63 through 67 removed outlier: 3.505A pdb=" N ILE S 121 " --> pdb=" O GLU S 64 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY S 66 " --> pdb=" O VAL S 119 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N VAL S 119 " --> pdb=" O GLY S 66 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ASN S 120 " --> pdb=" O LEU S 87 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LEU S 87 " --> pdb=" O ASN S 120 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE S 122 " --> pdb=" O LEU S 85 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 96 through 98 Processing sheet with id=AB6, first strand: chain 'T' and resid 63 through 67 removed outlier: 3.604A pdb=" N ILE T 121 " --> pdb=" O GLU T 64 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY T 66 " --> pdb=" O VAL T 119 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N VAL T 119 " --> pdb=" O GLY T 66 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASN T 120 " --> pdb=" O LEU T 87 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LEU T 87 " --> pdb=" O ASN T 120 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ILE T 122 " --> pdb=" O LEU T 85 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'T' and resid 96 through 98 Processing sheet with id=AB8, first strand: chain 'U' and resid 63 through 67 removed outlier: 3.573A pdb=" N ILE U 121 " --> pdb=" O GLU U 64 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY U 66 " --> pdb=" O VAL U 119 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N VAL U 119 " --> pdb=" O GLY U 66 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ASN U 120 " --> pdb=" O LEU U 87 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU U 87 " --> pdb=" O ASN U 120 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE U 122 " --> pdb=" O LEU U 85 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'U' and resid 96 through 98 Processing sheet with id=AC1, first strand: chain 'V' and resid 63 through 67 removed outlier: 3.651A pdb=" N ILE V 121 " --> pdb=" O GLU V 64 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY V 66 " --> pdb=" O VAL V 119 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N VAL V 119 " --> pdb=" O GLY V 66 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASN V 120 " --> pdb=" O LEU V 87 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU V 87 " --> pdb=" O ASN V 120 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE V 122 " --> pdb=" O LEU V 85 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'V' and resid 96 through 99 Processing sheet with id=AC3, first strand: chain 'W' and resid 63 through 67 removed outlier: 3.603A pdb=" N ILE W 121 " --> pdb=" O GLU W 64 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY W 66 " --> pdb=" O VAL W 119 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N VAL W 119 " --> pdb=" O GLY W 66 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ASN W 120 " --> pdb=" O LEU W 87 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU W 87 " --> pdb=" O ASN W 120 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE W 122 " --> pdb=" O LEU W 85 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'W' and resid 96 through 98 Processing sheet with id=AC5, first strand: chain 'X' and resid 63 through 67 removed outlier: 3.626A pdb=" N ILE X 121 " --> pdb=" O GLU X 64 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY X 66 " --> pdb=" O VAL X 119 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N VAL X 119 " --> pdb=" O GLY X 66 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASN X 120 " --> pdb=" O LEU X 87 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LEU X 87 " --> pdb=" O ASN X 120 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE X 122 " --> pdb=" O LEU X 85 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'X' and resid 96 through 99 710 hydrogen bonds defined for protein. 2115 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: 4.30 Time building geometry restraints manager: 7.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5289 1.33 - 1.45: 3590 1.45 - 1.57: 9895 1.57 - 1.69: 0 1.69 - 1.81: 168 Bond restraints: 18942 Sorted by residual: bond pdb=" CB ILE Q 24 " pdb=" CG2 ILE Q 24 " ideal model delta sigma weight residual 1.521 1.406 0.115 3.30e-02 9.18e+02 1.21e+01 bond pdb=" CG MET O 176 " pdb=" SD MET O 176 " ideal model delta sigma weight residual 1.803 1.724 0.079 2.50e-02 1.60e+03 9.98e+00 bond pdb=" CB ILE M 24 " pdb=" CG2 ILE M 24 " ideal model delta sigma weight residual 1.521 1.422 0.099 3.30e-02 9.18e+02 9.04e+00 bond pdb=" CB ASN P 42 " pdb=" CG ASN P 42 " ideal model delta sigma weight residual 1.516 1.441 0.075 2.50e-02 1.60e+03 9.01e+00 bond pdb=" CB ILE O 24 " pdb=" CG2 ILE O 24 " ideal model delta sigma weight residual 1.521 1.423 0.098 3.30e-02 9.18e+02 8.80e+00 ... (remaining 18937 not shown) Histogram of bond angle deviations from ideal: 93.96 - 102.01: 76 102.01 - 110.07: 3646 110.07 - 118.12: 10088 118.12 - 126.17: 11625 126.17 - 134.22: 221 Bond angle restraints: 25656 Sorted by residual: angle pdb=" C SER R 75 " pdb=" N ASN R 76 " pdb=" CA ASN R 76 " ideal model delta sigma weight residual 121.70 131.98 -10.28 1.80e+00 3.09e-01 3.26e+01 angle pdb=" C SER P 75 " pdb=" N ASN P 76 " pdb=" CA ASN P 76 " ideal model delta sigma weight residual 121.70 131.97 -10.27 1.80e+00 3.09e-01 3.25e+01 angle pdb=" C GLY P 58 " pdb=" N TRP P 59 " pdb=" CA TRP P 59 " ideal model delta sigma weight residual 120.82 129.01 -8.19 1.47e+00 4.63e-01 3.11e+01 angle pdb=" C SER N 75 " pdb=" N ASN N 76 " pdb=" CA ASN N 76 " ideal model delta sigma weight residual 121.70 131.67 -9.97 1.80e+00 3.09e-01 3.07e+01 angle pdb=" C SER T 75 " pdb=" N ASN T 76 " pdb=" CA ASN T 76 " ideal model delta sigma weight residual 121.70 131.52 -9.82 1.80e+00 3.09e-01 2.98e+01 ... (remaining 25651 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.63: 10356 15.63 - 31.26: 792 31.26 - 46.89: 149 46.89 - 62.52: 31 62.52 - 78.14: 36 Dihedral angle restraints: 11364 sinusoidal: 4566 harmonic: 6798 Sorted by residual: dihedral pdb=" CA ARG T 57 " pdb=" C ARG T 57 " pdb=" N GLY T 58 " pdb=" CA GLY T 58 " ideal model delta harmonic sigma weight residual 180.00 125.79 54.21 0 5.00e+00 4.00e-02 1.18e+02 dihedral pdb=" CA ARG Q 57 " pdb=" C ARG Q 57 " pdb=" N GLY Q 58 " pdb=" CA GLY Q 58 " ideal model delta harmonic sigma weight residual 180.00 125.94 54.06 0 5.00e+00 4.00e-02 1.17e+02 dihedral pdb=" CA ARG S 57 " pdb=" C ARG S 57 " pdb=" N GLY S 58 " pdb=" CA GLY S 58 " ideal model delta harmonic sigma weight residual 180.00 126.64 53.36 0 5.00e+00 4.00e-02 1.14e+02 ... (remaining 11361 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 2322 0.088 - 0.176: 399 0.176 - 0.264: 26 0.264 - 0.352: 2 0.352 - 0.440: 5 Chirality restraints: 2754 Sorted by residual: chirality pdb=" CA ASN P 37 " pdb=" N ASN P 37 " pdb=" C ASN P 37 " pdb=" CB ASN P 37 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.85e+00 chirality pdb=" CA ASN R 37 " pdb=" N ASN R 37 " pdb=" C ASN R 37 " pdb=" CB ASN R 37 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.84e+00 chirality pdb=" CA ASN N 37 " pdb=" N ASN N 37 " pdb=" C ASN N 37 " pdb=" CB ASN N 37 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.72e+00 ... (remaining 2751 not shown) Planarity restraints: 3444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE X 150 " -0.023 2.00e-02 2.50e+03 4.46e-02 1.99e+01 pdb=" C PHE X 150 " 0.077 2.00e-02 2.50e+03 pdb=" O PHE X 150 " -0.028 2.00e-02 2.50e+03 pdb=" N PHE X 151 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA P 38 " -0.021 2.00e-02 2.50e+03 4.24e-02 1.79e+01 pdb=" C ALA P 38 " 0.073 2.00e-02 2.50e+03 pdb=" O ALA P 38 " -0.027 2.00e-02 2.50e+03 pdb=" N ASP P 39 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE P 150 " -0.021 2.00e-02 2.50e+03 4.20e-02 1.77e+01 pdb=" C PHE P 150 " 0.073 2.00e-02 2.50e+03 pdb=" O PHE P 150 " -0.026 2.00e-02 2.50e+03 pdb=" N PHE P 151 " -0.025 2.00e-02 2.50e+03 ... (remaining 3441 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3962 2.77 - 3.30: 17954 3.30 - 3.83: 30222 3.83 - 4.37: 35747 4.37 - 4.90: 56740 Nonbonded interactions: 144625 Sorted by model distance: nonbonded pdb=" O ARG R 52 " pdb=" OG SER R 56 " model vdw 2.236 3.040 nonbonded pdb=" O ARG P 52 " pdb=" OG SER P 56 " model vdw 2.239 3.040 nonbonded pdb=" O ARG N 52 " pdb=" OG SER N 56 " model vdw 2.244 3.040 nonbonded pdb=" O ARG T 52 " pdb=" OG SER T 56 " model vdw 2.250 3.040 nonbonded pdb=" O ARG O 52 " pdb=" OG SER O 56 " model vdw 2.264 3.040 ... (remaining 144620 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 'M' selection = (chain 'N' and resid 3 through 196) selection = chain 'O' selection = (chain 'P' and resid 3 through 196) selection = chain 'Q' selection = (chain 'R' and resid 3 through 196) selection = chain 'S' selection = (chain 'T' and resid 3 through 196) selection = chain 'U' selection = (chain 'V' and resid 3 through 196) selection = chain 'W' selection = (chain 'X' and resid 3 through 196) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.10 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 4.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.700 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 44.830 Find NCS groups from input model: 0.720 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:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 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 : 0.012 0.115 18942 Z= 0.760 Angle : 1.462 14.155 25656 Z= 0.815 Chirality : 0.067 0.440 2754 Planarity : 0.007 0.045 3444 Dihedral : 12.930 78.145 7032 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.05 % Favored : 91.47 % Rotamer: Outliers : 0.05 % Allowed : 7.91 % Favored : 92.04 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.62 % Twisted Proline : 0.00 % Twisted General : 2.12 % 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: -4.94 (0.12), residues: 2310 helix: -3.45 (0.11), residues: 912 sheet: -2.71 (0.57), residues: 72 loop : -3.30 (0.12), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.008 TRP R 59 PHE 0.056 0.007 PHE P 150 TYR 0.026 0.005 TYR P 136 ARG 0.010 0.001 ARG W 196 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1066 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1065 time to evaluate : 2.093 Fit side-chains revert: symmetry clash REVERT: M 166 GLU cc_start: 0.8015 (tt0) cc_final: 0.7750 (tt0) REVERT: M 172 MET cc_start: 0.7536 (tpp) cc_final: 0.6840 (ptt) REVERT: N 47 LEU cc_start: 0.9235 (tt) cc_final: 0.8999 (tt) REVERT: N 64 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7953 (mt-10) REVERT: N 67 ILE cc_start: 0.8697 (pp) cc_final: 0.8235 (pt) REVERT: O 145 GLN cc_start: 0.7841 (mt0) cc_final: 0.6952 (mt0) REVERT: P 172 MET cc_start: 0.7369 (tpp) cc_final: 0.6088 (ptt) REVERT: R 172 MET cc_start: 0.7679 (tpp) cc_final: 0.6248 (ptt) REVERT: S 82 ASP cc_start: 0.7987 (m-30) cc_final: 0.7787 (m-30) REVERT: S 112 ARG cc_start: 0.8043 (mpt-90) cc_final: 0.7793 (mtt90) REVERT: S 172 MET cc_start: 0.7979 (tpp) cc_final: 0.6630 (ptt) REVERT: U 50 ILE cc_start: 0.8678 (mt) cc_final: 0.8175 (mt) REVERT: U 127 TYR cc_start: 0.8948 (t80) cc_final: 0.8569 (t80) REVERT: U 145 GLN cc_start: 0.7673 (mt0) cc_final: 0.6896 (mt0) REVERT: V 9 GLU cc_start: 0.7423 (mt-10) cc_final: 0.6885 (mt-10) REVERT: V 67 ILE cc_start: 0.7573 (pp) cc_final: 0.7316 (pt) REVERT: V 121 ILE cc_start: 0.9531 (mt) cc_final: 0.9097 (mt) REVERT: V 172 MET cc_start: 0.7724 (tpp) cc_final: 0.6753 (ptt) REVERT: W 50 ILE cc_start: 0.8887 (mt) cc_final: 0.8666 (mt) REVERT: W 145 GLN cc_start: 0.7903 (mt0) cc_final: 0.7675 (mt0) REVERT: W 169 ARG cc_start: 0.7551 (ttp-110) cc_final: 0.6764 (tpt170) REVERT: W 183 MET cc_start: 0.7908 (mtm) cc_final: 0.7290 (mtp) REVERT: X 15 SER cc_start: 0.8283 (t) cc_final: 0.8032 (p) REVERT: X 54 ILE cc_start: 0.8825 (mm) cc_final: 0.8547 (mm) REVERT: X 145 GLN cc_start: 0.7747 (mt0) cc_final: 0.7493 (mt0) outliers start: 1 outliers final: 0 residues processed: 1065 average time/residue: 0.3117 time to fit residues: 495.0361 Evaluate side-chains 505 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 505 time to evaluate : 2.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 0.8980 chunk 172 optimal weight: 0.5980 chunk 95 optimal weight: 0.0030 chunk 59 optimal weight: 0.0030 chunk 116 optimal weight: 0.4980 chunk 92 optimal weight: 0.5980 chunk 178 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 108 optimal weight: 0.5980 chunk 133 optimal weight: 2.9990 chunk 207 optimal weight: 0.7980 overall best weight: 0.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 7 ASN ** M 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 55 GLN M 62 ASN ** M 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 182 ASN N 18 ASN N 42 ASN ** N 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 147 ASN N 182 ASN O 7 ASN ** O 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 62 ASN ** O 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 18 ASN P 42 ASN ** P 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 182 ASN Q 7 ASN ** Q 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 109 GLN Q 182 ASN R 42 ASN R 48 ASN ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 182 ASN S 7 ASN S 18 ASN ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 182 ASN T 42 ASN ** T 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 109 GLN ** T 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 182 ASN U 7 ASN ** U 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 182 ASN V 42 ASN V 48 ASN ** V 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 109 GLN ** V 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 182 ASN W 7 ASN ** W 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 182 ASN X 18 ASN X 48 ASN ** X 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 18942 Z= 0.232 Angle : 0.823 10.279 25656 Z= 0.444 Chirality : 0.047 0.230 2754 Planarity : 0.004 0.031 3444 Dihedral : 7.760 45.174 2664 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.83 % Allowed : 20.75 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.80 % Twisted Proline : 0.00 % Twisted General : 0.84 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.14), residues: 2310 helix: -1.07 (0.15), residues: 888 sheet: -2.48 (0.40), residues: 144 loop : -2.67 (0.14), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP R 137 PHE 0.033 0.003 PHE P 150 TYR 0.025 0.002 TYR W 136 ARG 0.007 0.001 ARG N 2 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 558 time to evaluate : 1.763 Fit side-chains revert: symmetry clash REVERT: M 112 ARG cc_start: 0.8446 (ptp-170) cc_final: 0.8177 (mpt-90) REVERT: M 145 GLN cc_start: 0.8634 (mt0) cc_final: 0.8418 (mt0) REVERT: M 161 GLN cc_start: 0.8207 (tm-30) cc_final: 0.7827 (tm-30) REVERT: M 172 MET cc_start: 0.7664 (tpp) cc_final: 0.6871 (ptt) REVERT: M 174 TYR cc_start: 0.9190 (t80) cc_final: 0.8858 (t80) REVERT: M 176 MET cc_start: 0.7932 (mmm) cc_final: 0.6680 (ptm) REVERT: M 184 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8771 (pp) REVERT: M 194 LEU cc_start: 0.8549 (mp) cc_final: 0.8341 (mp) REVERT: N 6 MET cc_start: 0.8430 (tpt) cc_final: 0.8059 (tpt) REVERT: N 55 GLN cc_start: 0.9010 (mp10) cc_final: 0.8530 (mp10) REVERT: N 68 THR cc_start: 0.8853 (t) cc_final: 0.8078 (p) REVERT: O 161 GLN cc_start: 0.8262 (tp40) cc_final: 0.7414 (tp40) REVERT: O 184 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8703 (pp) REVERT: P 49 LYS cc_start: 0.8754 (ttpp) cc_final: 0.8522 (ttpp) REVERT: P 160 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8695 (tm) REVERT: P 164 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8521 (tm-30) REVERT: P 172 MET cc_start: 0.7798 (tpp) cc_final: 0.6333 (ptt) REVERT: P 184 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.8765 (pp) REVERT: P 194 LEU cc_start: 0.9056 (mp) cc_final: 0.8826 (mp) REVERT: Q 19 ASP cc_start: 0.7773 (m-30) cc_final: 0.7471 (m-30) REVERT: Q 172 MET cc_start: 0.8232 (mmm) cc_final: 0.6889 (ptt) REVERT: R 29 VAL cc_start: 0.8233 (OUTLIER) cc_final: 0.7878 (m) REVERT: R 172 MET cc_start: 0.7870 (tpp) cc_final: 0.6540 (ptt) REVERT: S 157 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7521 (tm-30) REVERT: S 172 MET cc_start: 0.8176 (tpp) cc_final: 0.6898 (ptt) REVERT: T 29 VAL cc_start: 0.9102 (p) cc_final: 0.8887 (m) REVERT: T 49 LYS cc_start: 0.9024 (tmtt) cc_final: 0.8786 (tttp) REVERT: T 172 MET cc_start: 0.8460 (tpp) cc_final: 0.7145 (ptm) REVERT: U 19 ASP cc_start: 0.8031 (m-30) cc_final: 0.7631 (m-30) REVERT: U 157 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7681 (tm-30) REVERT: U 172 MET cc_start: 0.8894 (tpp) cc_final: 0.8361 (tpp) REVERT: V 49 LYS cc_start: 0.9151 (tttp) cc_final: 0.8839 (tttm) REVERT: V 62 ASN cc_start: 0.8165 (t0) cc_final: 0.7891 (t0) REVERT: V 163 GLU cc_start: 0.7727 (tt0) cc_final: 0.7350 (tt0) REVERT: V 172 MET cc_start: 0.8087 (tpp) cc_final: 0.6714 (ptt) REVERT: W 169 ARG cc_start: 0.7788 (ttp-110) cc_final: 0.7218 (tpp-160) REVERT: W 172 MET cc_start: 0.8792 (tpp) cc_final: 0.8467 (tpp) REVERT: W 184 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8438 (pp) REVERT: W 190 THR cc_start: 0.9113 (OUTLIER) cc_final: 0.8841 (t) REVERT: X 26 GLU cc_start: 0.7187 (mp0) cc_final: 0.6904 (mt-10) REVERT: X 172 MET cc_start: 0.8424 (tpp) cc_final: 0.6702 (ptt) outliers start: 77 outliers final: 32 residues processed: 611 average time/residue: 0.2129 time to fit residues: 208.5346 Evaluate side-chains 459 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 419 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 59 TRP Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 165 ASP Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain N residue 23 SER Chi-restraints excluded: chain N residue 63 ILE Chi-restraints excluded: chain N residue 161 GLN Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain O residue 77 LEU Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 184 LEU Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 95 ILE Chi-restraints excluded: chain P residue 148 ASN Chi-restraints excluded: chain P residue 160 LEU Chi-restraints excluded: chain P residue 164 GLU Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 49 LYS Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain S residue 6 MET Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 63 ILE Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain T residue 95 ILE Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 90 THR Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 184 LEU Chi-restraints excluded: chain W residue 190 THR Chi-restraints excluded: chain X residue 8 VAL Chi-restraints excluded: chain X residue 23 SER Chi-restraints excluded: chain X residue 59 TRP Chi-restraints excluded: chain X residue 108 SER Chi-restraints excluded: chain X residue 184 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 0.4980 chunk 64 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 224 optimal weight: 0.6980 chunk 184 optimal weight: 0.6980 chunk 205 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 166 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 53 GLN M 55 GLN ** M 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 18 ASN ** N 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 48 ASN ** O 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 182 ASN ** P 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 48 ASN Q 55 GLN ** R 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 18 ASN S 55 GLN S 109 GLN ** S 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 55 GLN ** U 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 48 ASN W 53 GLN W 55 GLN ** W 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 147 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.5753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 18942 Z= 0.262 Angle : 0.722 7.459 25656 Z= 0.393 Chirality : 0.046 0.208 2754 Planarity : 0.004 0.037 3444 Dihedral : 6.865 42.373 2664 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 5.37 % Allowed : 22.04 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.80 % Twisted Proline : 0.00 % Twisted General : 0.93 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.15), residues: 2310 helix: -0.00 (0.16), residues: 930 sheet: -2.42 (0.60), residues: 72 loop : -2.56 (0.14), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.004 TRP T 137 PHE 0.027 0.002 PHE P 150 TYR 0.017 0.002 TYR X 136 ARG 0.006 0.001 ARG T 168 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 487 time to evaluate : 2.232 Fit side-chains revert: symmetry clash REVERT: M 19 ASP cc_start: 0.7752 (m-30) cc_final: 0.7550 (m-30) REVERT: M 161 GLN cc_start: 0.8316 (tm-30) cc_final: 0.7937 (tm-30) REVERT: N 55 GLN cc_start: 0.9068 (mp10) cc_final: 0.8634 (mp10) REVERT: N 68 THR cc_start: 0.8967 (t) cc_final: 0.8606 (p) REVERT: N 113 PHE cc_start: 0.8959 (OUTLIER) cc_final: 0.8665 (p90) REVERT: O 77 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8897 (pp) REVERT: O 161 GLN cc_start: 0.8475 (tp40) cc_final: 0.8162 (tp40) REVERT: O 172 MET cc_start: 0.8886 (tpp) cc_final: 0.6969 (ptt) REVERT: P 49 LYS cc_start: 0.9001 (ttpp) cc_final: 0.8743 (ttpp) REVERT: P 88 MET cc_start: 0.8188 (mtt) cc_final: 0.7987 (mpp) REVERT: P 172 MET cc_start: 0.8292 (tpp) cc_final: 0.6711 (ptt) REVERT: P 184 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8384 (pp) REVERT: P 194 LEU cc_start: 0.9023 (mp) cc_final: 0.8670 (mp) REVERT: Q 96 TYR cc_start: 0.9024 (m-10) cc_final: 0.8820 (m-80) REVERT: Q 163 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7473 (mt-10) REVERT: Q 184 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8881 (pp) REVERT: R 29 VAL cc_start: 0.8762 (p) cc_final: 0.8548 (m) REVERT: R 172 MET cc_start: 0.8134 (tpp) cc_final: 0.6684 (ptt) REVERT: S 70 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8288 (mt) REVERT: S 172 MET cc_start: 0.8555 (tpp) cc_final: 0.6906 (ptt) REVERT: T 95 ILE cc_start: 0.9040 (OUTLIER) cc_final: 0.8790 (mt) REVERT: T 187 ASP cc_start: 0.5520 (p0) cc_final: 0.5249 (m-30) REVERT: U 145 GLN cc_start: 0.8287 (mt0) cc_final: 0.7057 (mt0) REVERT: U 172 MET cc_start: 0.8964 (tpp) cc_final: 0.8304 (tpp) REVERT: U 184 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8632 (pp) REVERT: V 55 GLN cc_start: 0.9000 (mm-40) cc_final: 0.8769 (mm110) REVERT: V 157 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7872 (tm-30) REVERT: V 172 MET cc_start: 0.8411 (tpp) cc_final: 0.6964 (ptt) REVERT: V 184 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8712 (pp) REVERT: W 10 THR cc_start: 0.8086 (t) cc_final: 0.7085 (t) REVERT: W 163 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7935 (mt-10) REVERT: W 169 ARG cc_start: 0.8236 (ttp-110) cc_final: 0.7356 (tpp-160) REVERT: W 172 MET cc_start: 0.8860 (tpp) cc_final: 0.8478 (tpp) REVERT: W 173 GLU cc_start: 0.7793 (tt0) cc_final: 0.7343 (tt0) REVERT: W 184 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8521 (pp) REVERT: W 190 THR cc_start: 0.9222 (OUTLIER) cc_final: 0.8961 (m) REVERT: X 10 THR cc_start: 0.8918 (t) cc_final: 0.8645 (t) REVERT: X 31 THR cc_start: 0.9345 (OUTLIER) cc_final: 0.9031 (p) REVERT: X 163 GLU cc_start: 0.8090 (tt0) cc_final: 0.7848 (tt0) REVERT: X 170 LEU cc_start: 0.8897 (mm) cc_final: 0.8486 (tp) REVERT: X 172 MET cc_start: 0.8603 (tpp) cc_final: 0.7030 (ptt) outliers start: 108 outliers final: 56 residues processed: 566 average time/residue: 0.2183 time to fit residues: 197.5660 Evaluate side-chains 465 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 398 time to evaluate : 1.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 59 TRP Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain N residue 95 ILE Chi-restraints excluded: chain N residue 113 PHE Chi-restraints excluded: chain N residue 133 CYS Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain N residue 191 SER Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain O residue 59 TRP Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain O residue 77 LEU Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain P residue 23 SER Chi-restraints excluded: chain P residue 24 ILE Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 65 GLU Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 97 VAL Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain Q residue 67 ILE Chi-restraints excluded: chain Q residue 77 LEU Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 184 LEU Chi-restraints excluded: chain Q residue 191 SER Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 67 ILE Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain S residue 6 MET Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 63 ILE Chi-restraints excluded: chain S residue 70 LEU Chi-restraints excluded: chain S residue 87 LEU Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 170 LEU Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 95 ILE Chi-restraints excluded: chain T residue 164 GLU Chi-restraints excluded: chain T residue 184 LEU Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 21 LEU Chi-restraints excluded: chain U residue 23 SER Chi-restraints excluded: chain U residue 59 TRP Chi-restraints excluded: chain U residue 63 ILE Chi-restraints excluded: chain U residue 67 ILE Chi-restraints excluded: chain U residue 87 LEU Chi-restraints excluded: chain U residue 90 THR Chi-restraints excluded: chain U residue 170 LEU Chi-restraints excluded: chain U residue 184 LEU Chi-restraints excluded: chain V residue 184 LEU Chi-restraints excluded: chain W residue 21 LEU Chi-restraints excluded: chain W residue 59 TRP Chi-restraints excluded: chain W residue 79 VAL Chi-restraints excluded: chain W residue 90 THR Chi-restraints excluded: chain W residue 184 LEU Chi-restraints excluded: chain W residue 190 THR Chi-restraints excluded: chain X residue 17 VAL Chi-restraints excluded: chain X residue 23 SER Chi-restraints excluded: chain X residue 31 THR Chi-restraints excluded: chain X residue 59 TRP Chi-restraints excluded: chain X residue 78 ILE Chi-restraints excluded: chain X residue 184 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 0.9990 chunk 155 optimal weight: 0.0870 chunk 107 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 139 optimal weight: 0.0980 chunk 208 optimal weight: 0.0570 chunk 220 optimal weight: 0.5980 chunk 108 optimal weight: 0.9980 chunk 197 optimal weight: 0.3980 chunk 59 optimal weight: 2.9990 overall best weight: 0.2476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 109 GLN M 147 ASN ** N 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 7 ASN ** O 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 18 ASN ** P 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 147 ASN Q 48 ASN ** Q 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 48 ASN W 55 GLN ** W 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.6285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18942 Z= 0.171 Angle : 0.658 8.515 25656 Z= 0.358 Chirality : 0.044 0.197 2754 Planarity : 0.003 0.031 3444 Dihedral : 6.257 39.991 2664 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 5.37 % Allowed : 22.54 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.80 % Twisted Proline : 0.00 % Twisted General : 0.75 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.16), residues: 2310 helix: 0.80 (0.17), residues: 906 sheet: -2.13 (0.43), residues: 144 loop : -2.33 (0.15), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP V 137 PHE 0.024 0.002 PHE N 150 TYR 0.018 0.001 TYR Q 136 ARG 0.005 0.000 ARG Q 149 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 459 time to evaluate : 2.104 Fit side-chains REVERT: M 161 GLN cc_start: 0.8290 (tm-30) cc_final: 0.7935 (tm-30) REVERT: M 165 ASP cc_start: 0.8036 (OUTLIER) cc_final: 0.7741 (t0) REVERT: M 172 MET cc_start: 0.8600 (tpp) cc_final: 0.6740 (ptt) REVERT: M 184 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8714 (pp) REVERT: N 68 THR cc_start: 0.8814 (t) cc_final: 0.8465 (p) REVERT: N 113 PHE cc_start: 0.8926 (OUTLIER) cc_final: 0.8607 (p90) REVERT: O 145 GLN cc_start: 0.7941 (mt0) cc_final: 0.7551 (mt0) REVERT: O 161 GLN cc_start: 0.8316 (tp40) cc_final: 0.7793 (tm-30) REVERT: O 172 MET cc_start: 0.8878 (tpp) cc_final: 0.8674 (tpp) REVERT: O 184 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8772 (pp) REVERT: P 49 LYS cc_start: 0.9058 (ttpp) cc_final: 0.8706 (ttpp) REVERT: P 68 THR cc_start: 0.8792 (m) cc_final: 0.8586 (p) REVERT: P 163 GLU cc_start: 0.7765 (tt0) cc_final: 0.7520 (tt0) REVERT: P 172 MET cc_start: 0.8202 (tpp) cc_final: 0.6649 (ptt) REVERT: P 184 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8227 (pp) REVERT: P 194 LEU cc_start: 0.8994 (mp) cc_final: 0.8676 (mt) REVERT: Q 172 MET cc_start: 0.8305 (mmm) cc_final: 0.7039 (ptt) REVERT: Q 176 MET cc_start: 0.8281 (mmm) cc_final: 0.7508 (ptm) REVERT: Q 184 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8750 (pp) REVERT: R 172 MET cc_start: 0.8191 (tpp) cc_final: 0.6749 (ptt) REVERT: S 170 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8946 (mt) REVERT: S 172 MET cc_start: 0.8382 (tpp) cc_final: 0.6877 (ptt) REVERT: T 95 ILE cc_start: 0.8993 (OUTLIER) cc_final: 0.8745 (mt) REVERT: T 172 MET cc_start: 0.8243 (tpp) cc_final: 0.6868 (ptt) REVERT: T 187 ASP cc_start: 0.5314 (p0) cc_final: 0.4932 (m-30) REVERT: U 112 ARG cc_start: 0.7920 (mpt-90) cc_final: 0.7650 (mtt90) REVERT: U 145 GLN cc_start: 0.7683 (mt0) cc_final: 0.7331 (mt0) REVERT: U 157 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7885 (tm-30) REVERT: U 172 MET cc_start: 0.8917 (tpp) cc_final: 0.8293 (tpp) REVERT: U 184 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8595 (pp) REVERT: V 124 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.9011 (tt) REVERT: V 163 GLU cc_start: 0.7362 (tt0) cc_final: 0.7064 (tt0) REVERT: V 172 MET cc_start: 0.8347 (tpp) cc_final: 0.6861 (ptt) REVERT: V 184 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8480 (pp) REVERT: V 194 LEU cc_start: 0.8630 (mp) cc_final: 0.8413 (mp) REVERT: W 10 THR cc_start: 0.8370 (OUTLIER) cc_final: 0.7793 (m) REVERT: W 19 ASP cc_start: 0.8106 (m-30) cc_final: 0.7845 (m-30) REVERT: W 157 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7833 (tm-30) REVERT: W 169 ARG cc_start: 0.8126 (ttp-110) cc_final: 0.7184 (tpp-160) REVERT: W 184 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8846 (pp) REVERT: X 163 GLU cc_start: 0.7889 (tt0) cc_final: 0.7670 (tt0) REVERT: X 172 MET cc_start: 0.8533 (tpp) cc_final: 0.7012 (ptt) outliers start: 108 outliers final: 50 residues processed: 541 average time/residue: 0.2614 time to fit residues: 225.2015 Evaluate side-chains 463 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 400 time to evaluate : 2.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 6 MET Chi-restraints excluded: chain M residue 59 TRP Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 87 LEU Chi-restraints excluded: chain M residue 165 ASP Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain N residue 5 ASP Chi-restraints excluded: chain N residue 59 TRP Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain N residue 113 PHE Chi-restraints excluded: chain N residue 175 GLU Chi-restraints excluded: chain N residue 191 SER Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain O residue 59 TRP Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain O residue 184 LEU Chi-restraints excluded: chain P residue 24 ILE Chi-restraints excluded: chain P residue 59 TRP Chi-restraints excluded: chain P residue 65 GLU Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain P residue 191 SER Chi-restraints excluded: chain Q residue 67 ILE Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 77 LEU Chi-restraints excluded: chain Q residue 78 ILE Chi-restraints excluded: chain Q residue 184 LEU Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain S residue 6 MET Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 32 LEU Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 170 LEU Chi-restraints excluded: chain S residue 191 SER Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 59 TRP Chi-restraints excluded: chain T residue 67 ILE Chi-restraints excluded: chain T residue 88 MET Chi-restraints excluded: chain T residue 95 ILE Chi-restraints excluded: chain T residue 164 GLU Chi-restraints excluded: chain T residue 184 LEU Chi-restraints excluded: chain U residue 23 SER Chi-restraints excluded: chain U residue 59 TRP Chi-restraints excluded: chain U residue 95 ILE Chi-restraints excluded: chain U residue 184 LEU Chi-restraints excluded: chain V residue 59 TRP Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 78 ILE Chi-restraints excluded: chain V residue 87 LEU Chi-restraints excluded: chain V residue 124 LEU Chi-restraints excluded: chain V residue 175 GLU Chi-restraints excluded: chain V residue 184 LEU Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain W residue 59 TRP Chi-restraints excluded: chain W residue 79 VAL Chi-restraints excluded: chain W residue 87 LEU Chi-restraints excluded: chain W residue 90 THR Chi-restraints excluded: chain W residue 184 LEU Chi-restraints excluded: chain X residue 5 ASP Chi-restraints excluded: chain X residue 59 TRP Chi-restraints excluded: chain X residue 78 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 0.2980 chunk 125 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 164 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 112 optimal weight: 0.7980 chunk 197 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 7 ASN M 109 GLN ** N 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 48 ASN ** O 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN ** Q 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 55 GLN ** U 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 55 GLN W 161 GLN ** X 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 55 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.6643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18942 Z= 0.288 Angle : 0.695 7.579 25656 Z= 0.376 Chirality : 0.046 0.197 2754 Planarity : 0.004 0.036 3444 Dihedral : 6.308 41.268 2664 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 6.32 % Allowed : 21.44 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.80 % Twisted Proline : 0.00 % Twisted General : 0.97 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.16), residues: 2310 helix: 0.87 (0.16), residues: 930 sheet: -2.00 (0.68), residues: 60 loop : -2.32 (0.14), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP R 137 PHE 0.028 0.002 PHE P 150 TYR 0.018 0.002 TYR M 127 ARG 0.004 0.001 ARG R 168 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 412 time to evaluate : 2.316 Fit side-chains REVERT: M 161 GLN cc_start: 0.8467 (tm-30) cc_final: 0.8209 (tm-30) REVERT: M 172 MET cc_start: 0.8565 (tpp) cc_final: 0.7004 (ptt) REVERT: M 184 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8918 (pp) REVERT: N 68 THR cc_start: 0.9067 (t) cc_final: 0.8814 (p) REVERT: N 87 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9039 (tm) REVERT: N 113 PHE cc_start: 0.9010 (OUTLIER) cc_final: 0.8692 (p90) REVERT: N 130 MET cc_start: 0.8652 (mmm) cc_final: 0.8215 (mtp) REVERT: N 172 MET cc_start: 0.8289 (tpp) cc_final: 0.8029 (mmm) REVERT: O 161 GLN cc_start: 0.8409 (tp40) cc_final: 0.8161 (tp40) REVERT: O 184 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8699 (pp) REVERT: P 172 MET cc_start: 0.8453 (tpp) cc_final: 0.7098 (ptt) REVERT: Q 172 MET cc_start: 0.8325 (mmm) cc_final: 0.7130 (ptt) REVERT: Q 176 MET cc_start: 0.8247 (mmm) cc_final: 0.7651 (ptm) REVERT: Q 184 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8918 (pp) REVERT: R 39 ASP cc_start: 0.8302 (m-30) cc_final: 0.7801 (m-30) REVERT: R 172 MET cc_start: 0.8207 (tpp) cc_final: 0.6960 (ptt) REVERT: S 5 ASP cc_start: 0.8563 (t0) cc_final: 0.8343 (m-30) REVERT: S 70 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8113 (mt) REVERT: S 88 MET cc_start: 0.8812 (mmm) cc_final: 0.8508 (mmm) REVERT: S 145 GLN cc_start: 0.8423 (mm-40) cc_final: 0.8180 (mm110) REVERT: S 172 MET cc_start: 0.8608 (tpp) cc_final: 0.8378 (tpp) REVERT: T 95 ILE cc_start: 0.9175 (OUTLIER) cc_final: 0.8909 (mt) REVERT: T 172 MET cc_start: 0.7998 (tpp) cc_final: 0.6890 (ptt) REVERT: T 187 ASP cc_start: 0.5346 (p0) cc_final: 0.4996 (m-30) REVERT: U 145 GLN cc_start: 0.7675 (mt0) cc_final: 0.7404 (mm-40) REVERT: U 172 MET cc_start: 0.8999 (tpp) cc_final: 0.8432 (tpp) REVERT: U 176 MET cc_start: 0.8093 (mmt) cc_final: 0.6556 (ptm) REVERT: U 184 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.8805 (pp) REVERT: V 21 LEU cc_start: 0.9472 (OUTLIER) cc_final: 0.9057 (mm) REVERT: V 75 SER cc_start: 0.7743 (OUTLIER) cc_final: 0.7489 (t) REVERT: V 124 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.9090 (tt) REVERT: V 163 GLU cc_start: 0.7436 (tt0) cc_final: 0.6434 (tt0) REVERT: V 172 MET cc_start: 0.8434 (tpp) cc_final: 0.7019 (ptt) REVERT: V 184 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8760 (pp) REVERT: W 19 ASP cc_start: 0.7750 (m-30) cc_final: 0.7541 (m-30) REVERT: W 62 ASN cc_start: 0.8754 (t0) cc_final: 0.8478 (t0) REVERT: W 75 SER cc_start: 0.8714 (OUTLIER) cc_final: 0.8461 (p) REVERT: W 169 ARG cc_start: 0.8473 (ttp-110) cc_final: 0.7349 (tpp-160) REVERT: W 172 MET cc_start: 0.8776 (mmm) cc_final: 0.8319 (tpp) REVERT: W 184 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8817 (pp) REVERT: X 172 MET cc_start: 0.8492 (tpp) cc_final: 0.7093 (ptt) outliers start: 127 outliers final: 70 residues processed: 509 average time/residue: 0.2728 time to fit residues: 225.4583 Evaluate side-chains 460 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 376 time to evaluate : 2.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 59 TRP Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain M residue 183 MET Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 59 TRP Chi-restraints excluded: chain N residue 63 ILE Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain N residue 87 LEU Chi-restraints excluded: chain N residue 113 PHE Chi-restraints excluded: chain N residue 161 GLN Chi-restraints excluded: chain N residue 175 GLU Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain N residue 191 SER Chi-restraints excluded: chain N residue 194 LEU Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 184 LEU Chi-restraints excluded: chain O residue 191 SER Chi-restraints excluded: chain P residue 4 TYR Chi-restraints excluded: chain P residue 23 SER Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 191 SER Chi-restraints excluded: chain Q residue 67 ILE Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 77 LEU Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 184 LEU Chi-restraints excluded: chain Q residue 191 SER Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 148 ASN Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain S residue 6 MET Chi-restraints excluded: chain S residue 32 LEU Chi-restraints excluded: chain S residue 70 LEU Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain S residue 87 LEU Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 170 LEU Chi-restraints excluded: chain S residue 191 SER Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 59 TRP Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain T residue 95 ILE Chi-restraints excluded: chain T residue 112 ARG Chi-restraints excluded: chain T residue 164 GLU Chi-restraints excluded: chain T residue 184 LEU Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 23 SER Chi-restraints excluded: chain U residue 87 LEU Chi-restraints excluded: chain U residue 90 THR Chi-restraints excluded: chain U residue 95 ILE Chi-restraints excluded: chain U residue 170 LEU Chi-restraints excluded: chain U residue 184 LEU Chi-restraints excluded: chain U residue 191 SER Chi-restraints excluded: chain V residue 21 LEU Chi-restraints excluded: chain V residue 59 TRP Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 75 SER Chi-restraints excluded: chain V residue 124 LEU Chi-restraints excluded: chain V residue 175 GLU Chi-restraints excluded: chain V residue 184 LEU Chi-restraints excluded: chain W residue 59 TRP Chi-restraints excluded: chain W residue 63 ILE Chi-restraints excluded: chain W residue 75 SER Chi-restraints excluded: chain W residue 79 VAL Chi-restraints excluded: chain W residue 87 LEU Chi-restraints excluded: chain W residue 90 THR Chi-restraints excluded: chain W residue 143 SER Chi-restraints excluded: chain W residue 184 LEU Chi-restraints excluded: chain W residue 191 SER Chi-restraints excluded: chain X residue 23 SER Chi-restraints excluded: chain X residue 59 TRP Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 78 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 1.9990 chunk 198 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 129 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 220 optimal weight: 0.8980 chunk 183 optimal weight: 0.4980 chunk 102 optimal weight: 1.9990 chunk 18 optimal weight: 0.0050 chunk 72 optimal weight: 0.4980 chunk 115 optimal weight: 0.8980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 145 GLN ** O 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 7 ASN ** W 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.6933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18942 Z= 0.217 Angle : 0.665 8.277 25656 Z= 0.359 Chirality : 0.044 0.193 2754 Planarity : 0.003 0.036 3444 Dihedral : 6.116 39.975 2664 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 5.52 % Allowed : 22.64 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.80 % Twisted Proline : 0.00 % Twisted General : 0.84 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.16), residues: 2310 helix: 1.20 (0.16), residues: 912 sheet: -2.18 (0.67), residues: 60 loop : -2.21 (0.14), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 59 PHE 0.024 0.002 PHE P 150 TYR 0.016 0.001 TYR O 136 ARG 0.005 0.000 ARG R 149 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 416 time to evaluate : 2.126 Fit side-chains REVERT: M 157 GLU cc_start: 0.8658 (tm-30) cc_final: 0.8296 (tm-30) REVERT: M 161 GLN cc_start: 0.8417 (tm-30) cc_final: 0.7867 (tm-30) REVERT: M 163 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7512 (mt-10) REVERT: M 165 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7848 (t70) REVERT: M 172 MET cc_start: 0.8610 (tpp) cc_final: 0.6870 (ptt) REVERT: M 184 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8746 (pp) REVERT: N 68 THR cc_start: 0.8971 (t) cc_final: 0.8764 (p) REVERT: N 87 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9024 (tm) REVERT: N 113 PHE cc_start: 0.8934 (OUTLIER) cc_final: 0.8560 (p90) REVERT: N 130 MET cc_start: 0.8585 (mmm) cc_final: 0.8337 (mtp) REVERT: N 145 GLN cc_start: 0.7929 (mt0) cc_final: 0.7652 (mt0) REVERT: N 172 MET cc_start: 0.8254 (tpp) cc_final: 0.7965 (mmm) REVERT: N 175 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7663 (tt0) REVERT: O 172 MET cc_start: 0.8764 (tpp) cc_final: 0.7189 (ptt) REVERT: O 184 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8638 (pp) REVERT: P 172 MET cc_start: 0.8337 (tpp) cc_final: 0.6976 (ptt) REVERT: P 184 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.8725 (pp) REVERT: P 194 LEU cc_start: 0.8810 (mp) cc_final: 0.8576 (mp) REVERT: Q 80 TYR cc_start: 0.8417 (t80) cc_final: 0.8099 (t80) REVERT: Q 172 MET cc_start: 0.8354 (mmm) cc_final: 0.7130 (ptt) REVERT: Q 176 MET cc_start: 0.8117 (mmm) cc_final: 0.7516 (ptm) REVERT: Q 184 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8738 (pp) REVERT: R 88 MET cc_start: 0.8684 (mmm) cc_final: 0.8322 (mtp) REVERT: R 172 MET cc_start: 0.8034 (tpp) cc_final: 0.6159 (ptt) REVERT: R 176 MET cc_start: 0.8145 (mmt) cc_final: 0.7942 (mpp) REVERT: S 70 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8081 (mt) REVERT: S 157 GLU cc_start: 0.8281 (tm-30) cc_final: 0.7897 (tm-30) REVERT: T 95 ILE cc_start: 0.9179 (OUTLIER) cc_final: 0.8913 (mt) REVERT: T 112 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7746 (ptp-110) REVERT: T 172 MET cc_start: 0.7835 (OUTLIER) cc_final: 0.6825 (ptt) REVERT: T 187 ASP cc_start: 0.5394 (p0) cc_final: 0.5090 (m-30) REVERT: U 145 GLN cc_start: 0.7583 (mt0) cc_final: 0.7369 (mm-40) REVERT: U 172 MET cc_start: 0.8890 (tpp) cc_final: 0.8509 (tpp) REVERT: U 176 MET cc_start: 0.7943 (mmt) cc_final: 0.7118 (ptm) REVERT: U 184 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.8773 (pp) REVERT: V 21 LEU cc_start: 0.9507 (OUTLIER) cc_final: 0.9181 (mm) REVERT: V 75 SER cc_start: 0.7863 (OUTLIER) cc_final: 0.7542 (t) REVERT: V 109 GLN cc_start: 0.8249 (mm-40) cc_final: 0.7943 (mm-40) REVERT: V 157 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7699 (tm-30) REVERT: V 163 GLU cc_start: 0.7415 (tt0) cc_final: 0.6439 (tt0) REVERT: V 172 MET cc_start: 0.8447 (tpp) cc_final: 0.6995 (ptt) REVERT: V 184 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8642 (pp) REVERT: W 62 ASN cc_start: 0.8712 (t0) cc_final: 0.8499 (t0) REVERT: W 169 ARG cc_start: 0.8146 (ttp-110) cc_final: 0.7047 (tpp-160) REVERT: W 172 MET cc_start: 0.8684 (mmm) cc_final: 0.8328 (tpp) REVERT: W 175 GLU cc_start: 0.8266 (tm-30) cc_final: 0.7779 (tm-30) REVERT: X 163 GLU cc_start: 0.7932 (tt0) cc_final: 0.7650 (tt0) REVERT: X 172 MET cc_start: 0.8457 (tpp) cc_final: 0.7159 (ptt) outliers start: 111 outliers final: 76 residues processed: 510 average time/residue: 0.2468 time to fit residues: 202.9814 Evaluate side-chains 476 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 384 time to evaluate : 2.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 59 TRP Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 165 ASP Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 191 SER Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 59 TRP Chi-restraints excluded: chain N residue 63 ILE Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain N residue 87 LEU Chi-restraints excluded: chain N residue 113 PHE Chi-restraints excluded: chain N residue 133 CYS Chi-restraints excluded: chain N residue 175 GLU Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain O residue 26 GLU Chi-restraints excluded: chain O residue 59 TRP Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain O residue 77 LEU Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 184 LEU Chi-restraints excluded: chain O residue 191 SER Chi-restraints excluded: chain P residue 4 TYR Chi-restraints excluded: chain P residue 23 SER Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 78 ILE Chi-restraints excluded: chain P residue 91 SER Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain P residue 191 SER Chi-restraints excluded: chain Q residue 5 ASP Chi-restraints excluded: chain Q residue 24 ILE Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 77 LEU Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 184 LEU Chi-restraints excluded: chain Q residue 191 SER Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 59 TRP Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 148 ASN Chi-restraints excluded: chain R residue 161 GLN Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain S residue 6 MET Chi-restraints excluded: chain S residue 32 LEU Chi-restraints excluded: chain S residue 70 LEU Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain S residue 87 LEU Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 170 LEU Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 59 TRP Chi-restraints excluded: chain T residue 63 ILE Chi-restraints excluded: chain T residue 77 LEU Chi-restraints excluded: chain T residue 95 ILE Chi-restraints excluded: chain T residue 112 ARG Chi-restraints excluded: chain T residue 172 MET Chi-restraints excluded: chain T residue 184 LEU Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 23 SER Chi-restraints excluded: chain U residue 59 TRP Chi-restraints excluded: chain U residue 87 LEU Chi-restraints excluded: chain U residue 90 THR Chi-restraints excluded: chain U residue 95 ILE Chi-restraints excluded: chain U residue 170 LEU Chi-restraints excluded: chain U residue 184 LEU Chi-restraints excluded: chain U residue 191 SER Chi-restraints excluded: chain V residue 21 LEU Chi-restraints excluded: chain V residue 59 TRP Chi-restraints excluded: chain V residue 75 SER Chi-restraints excluded: chain V residue 78 ILE Chi-restraints excluded: chain V residue 87 LEU Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain V residue 112 ARG Chi-restraints excluded: chain V residue 175 GLU Chi-restraints excluded: chain V residue 184 LEU Chi-restraints excluded: chain W residue 59 TRP Chi-restraints excluded: chain W residue 63 ILE Chi-restraints excluded: chain W residue 79 VAL Chi-restraints excluded: chain W residue 87 LEU Chi-restraints excluded: chain W residue 90 THR Chi-restraints excluded: chain W residue 143 SER Chi-restraints excluded: chain W residue 191 SER Chi-restraints excluded: chain X residue 23 SER Chi-restraints excluded: chain X residue 59 TRP Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 78 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 0.7980 chunk 24 optimal weight: 0.1980 chunk 125 optimal weight: 0.6980 chunk 161 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 185 optimal weight: 0.9980 chunk 123 optimal weight: 0.3980 chunk 219 optimal weight: 1.9990 chunk 137 optimal weight: 0.6980 chunk 133 optimal weight: 3.9990 chunk 101 optimal weight: 0.2980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 53 GLN O 55 GLN ** O 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.7164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18942 Z= 0.199 Angle : 0.654 7.689 25656 Z= 0.354 Chirality : 0.044 0.190 2754 Planarity : 0.003 0.031 3444 Dihedral : 5.925 39.099 2664 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 5.47 % Allowed : 23.58 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.80 % Twisted Proline : 0.00 % Twisted General : 0.71 % 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: -0.89 (0.16), residues: 2310 helix: 1.46 (0.16), residues: 912 sheet: -2.28 (0.67), residues: 60 loop : -2.14 (0.15), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 59 PHE 0.022 0.002 PHE P 150 TYR 0.017 0.001 TYR U 80 ARG 0.005 0.000 ARG R 149 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 422 time to evaluate : 2.531 Fit side-chains REVERT: M 10 THR cc_start: 0.8525 (OUTLIER) cc_final: 0.8256 (p) REVERT: M 157 GLU cc_start: 0.8651 (tm-30) cc_final: 0.8364 (tm-30) REVERT: M 161 GLN cc_start: 0.8401 (tm-30) cc_final: 0.8018 (tm-30) REVERT: M 172 MET cc_start: 0.8630 (tpp) cc_final: 0.6776 (ptt) REVERT: M 184 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8817 (pp) REVERT: N 87 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9124 (tm) REVERT: N 113 PHE cc_start: 0.8962 (OUTLIER) cc_final: 0.8623 (p90) REVERT: N 132 GLU cc_start: 0.8858 (tp30) cc_final: 0.8518 (tm-30) REVERT: N 172 MET cc_start: 0.8249 (tpp) cc_final: 0.7938 (mmm) REVERT: N 175 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7738 (tt0) REVERT: O 112 ARG cc_start: 0.7228 (mtt180) cc_final: 0.6779 (mtt-85) REVERT: O 163 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7407 (tt0) REVERT: O 172 MET cc_start: 0.8797 (tpp) cc_final: 0.7193 (ptt) REVERT: O 184 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8631 (pp) REVERT: P 49 LYS cc_start: 0.9230 (ttpp) cc_final: 0.8822 (tttm) REVERT: P 172 MET cc_start: 0.8319 (tpp) cc_final: 0.6781 (ptt) REVERT: P 184 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.8847 (pp) REVERT: P 194 LEU cc_start: 0.8834 (mp) cc_final: 0.8485 (mp) REVERT: Q 80 TYR cc_start: 0.8355 (t80) cc_final: 0.8112 (t80) REVERT: Q 172 MET cc_start: 0.8281 (mmm) cc_final: 0.6945 (ptt) REVERT: Q 176 MET cc_start: 0.8025 (mmm) cc_final: 0.7511 (ptm) REVERT: Q 184 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8747 (pp) REVERT: R 88 MET cc_start: 0.8620 (mmm) cc_final: 0.8151 (mtp) REVERT: R 172 MET cc_start: 0.7983 (tpp) cc_final: 0.6146 (ptt) REVERT: S 157 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7956 (tm-30) REVERT: S 172 MET cc_start: 0.8482 (tpp) cc_final: 0.7096 (ptt) REVERT: T 95 ILE cc_start: 0.9187 (OUTLIER) cc_final: 0.8915 (mt) REVERT: T 112 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7699 (ptp-110) REVERT: T 172 MET cc_start: 0.7781 (OUTLIER) cc_final: 0.6800 (ptt) REVERT: T 184 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.8831 (pp) REVERT: T 187 ASP cc_start: 0.5334 (p0) cc_final: 0.5014 (m-30) REVERT: U 145 GLN cc_start: 0.7656 (mt0) cc_final: 0.7456 (mm-40) REVERT: U 184 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.8745 (pp) REVERT: V 21 LEU cc_start: 0.9525 (OUTLIER) cc_final: 0.9181 (mm) REVERT: V 157 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7708 (tm-30) REVERT: V 163 GLU cc_start: 0.7389 (tt0) cc_final: 0.6471 (tt0) REVERT: V 172 MET cc_start: 0.8329 (tpp) cc_final: 0.6808 (ptt) REVERT: V 184 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8590 (pp) REVERT: W 75 SER cc_start: 0.8692 (OUTLIER) cc_final: 0.8413 (p) REVERT: W 109 GLN cc_start: 0.7995 (mm-40) cc_final: 0.7783 (mp10) REVERT: W 169 ARG cc_start: 0.8181 (ttp-110) cc_final: 0.7076 (tpp-160) REVERT: W 183 MET cc_start: 0.8078 (ttm) cc_final: 0.7148 (pmm) REVERT: X 164 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8281 (tm-30) REVERT: X 172 MET cc_start: 0.8380 (tpp) cc_final: 0.7010 (ptt) outliers start: 110 outliers final: 77 residues processed: 513 average time/residue: 0.2640 time to fit residues: 217.3669 Evaluate side-chains 476 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 381 time to evaluate : 2.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 59 TRP Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 191 SER Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 59 TRP Chi-restraints excluded: chain N residue 63 ILE Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain N residue 87 LEU Chi-restraints excluded: chain N residue 113 PHE Chi-restraints excluded: chain N residue 133 CYS Chi-restraints excluded: chain N residue 175 GLU Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain N residue 191 SER Chi-restraints excluded: chain N residue 194 LEU Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 59 TRP Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain O residue 77 LEU Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 163 GLU Chi-restraints excluded: chain O residue 184 LEU Chi-restraints excluded: chain O residue 191 SER Chi-restraints excluded: chain P residue 4 TYR Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 59 TRP Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 78 ILE Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain P residue 191 SER Chi-restraints excluded: chain Q residue 5 ASP Chi-restraints excluded: chain Q residue 24 ILE Chi-restraints excluded: chain Q residue 67 ILE Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 77 LEU Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 184 LEU Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain R residue 59 TRP Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 148 ASN Chi-restraints excluded: chain R residue 161 GLN Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain S residue 6 MET Chi-restraints excluded: chain S residue 59 TRP Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain S residue 87 LEU Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 59 TRP Chi-restraints excluded: chain T residue 77 LEU Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain T residue 95 ILE Chi-restraints excluded: chain T residue 112 ARG Chi-restraints excluded: chain T residue 172 MET Chi-restraints excluded: chain T residue 184 LEU Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 23 SER Chi-restraints excluded: chain U residue 59 TRP Chi-restraints excluded: chain U residue 87 LEU Chi-restraints excluded: chain U residue 90 THR Chi-restraints excluded: chain U residue 95 ILE Chi-restraints excluded: chain U residue 170 LEU Chi-restraints excluded: chain U residue 184 LEU Chi-restraints excluded: chain U residue 191 SER Chi-restraints excluded: chain V residue 21 LEU Chi-restraints excluded: chain V residue 59 TRP Chi-restraints excluded: chain V residue 78 ILE Chi-restraints excluded: chain V residue 87 LEU Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain V residue 112 ARG Chi-restraints excluded: chain V residue 175 GLU Chi-restraints excluded: chain V residue 184 LEU Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 59 TRP Chi-restraints excluded: chain W residue 63 ILE Chi-restraints excluded: chain W residue 75 SER Chi-restraints excluded: chain W residue 79 VAL Chi-restraints excluded: chain W residue 87 LEU Chi-restraints excluded: chain W residue 90 THR Chi-restraints excluded: chain W residue 143 SER Chi-restraints excluded: chain W residue 191 SER Chi-restraints excluded: chain X residue 23 SER Chi-restraints excluded: chain X residue 59 TRP Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 78 ILE Chi-restraints excluded: chain X residue 164 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 0.0870 chunk 87 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 43 optimal weight: 0.0980 chunk 42 optimal weight: 0.6980 chunk 139 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 172 optimal weight: 0.9980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 48 ASN Q 93 GLN ** Q 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 ASN ** R 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 55 GLN ** X 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.7317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18942 Z= 0.217 Angle : 0.657 7.470 25656 Z= 0.356 Chirality : 0.044 0.188 2754 Planarity : 0.003 0.027 3444 Dihedral : 5.899 39.218 2664 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 5.57 % Allowed : 23.63 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.80 % Twisted Proline : 0.00 % Twisted General : 0.71 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.16), residues: 2310 helix: 1.60 (0.16), residues: 906 sheet: -2.41 (0.67), residues: 60 loop : -2.07 (0.15), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 59 PHE 0.020 0.002 PHE P 150 TYR 0.014 0.001 TYR O 80 ARG 0.007 0.000 ARG P 44 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 397 time to evaluate : 2.033 Fit side-chains REVERT: M 10 THR cc_start: 0.8687 (OUTLIER) cc_final: 0.8296 (p) REVERT: M 157 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8404 (tm-30) REVERT: M 161 GLN cc_start: 0.8397 (tm-30) cc_final: 0.7993 (tm-30) REVERT: M 172 MET cc_start: 0.8673 (tpp) cc_final: 0.6824 (ptt) REVERT: M 184 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8832 (pp) REVERT: N 42 ASN cc_start: 0.8266 (t0) cc_final: 0.7920 (t0) REVERT: N 113 PHE cc_start: 0.8949 (OUTLIER) cc_final: 0.8618 (p90) REVERT: N 175 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7793 (tt0) REVERT: O 49 LYS cc_start: 0.8732 (tttm) cc_final: 0.8353 (tttm) REVERT: O 184 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8784 (pp) REVERT: P 49 LYS cc_start: 0.9264 (ttpp) cc_final: 0.8871 (tttm) REVERT: P 172 MET cc_start: 0.8325 (tpp) cc_final: 0.6893 (ptt) REVERT: P 184 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.8812 (pp) REVERT: P 194 LEU cc_start: 0.8840 (mp) cc_final: 0.8501 (mp) REVERT: Q 80 TYR cc_start: 0.8427 (t80) cc_final: 0.8126 (t80) REVERT: Q 172 MET cc_start: 0.8346 (mmm) cc_final: 0.7007 (ptt) REVERT: Q 176 MET cc_start: 0.8023 (mmm) cc_final: 0.7509 (ptm) REVERT: Q 184 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8751 (pp) REVERT: R 39 ASP cc_start: 0.8168 (m-30) cc_final: 0.7470 (m-30) REVERT: R 145 GLN cc_start: 0.7727 (mt0) cc_final: 0.7522 (mt0) REVERT: R 172 MET cc_start: 0.7686 (tpp) cc_final: 0.6425 (ptt) REVERT: S 172 MET cc_start: 0.8517 (tpp) cc_final: 0.7276 (ptt) REVERT: T 95 ILE cc_start: 0.9223 (OUTLIER) cc_final: 0.8917 (mt) REVERT: T 112 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7839 (ptp-110) REVERT: T 172 MET cc_start: 0.7806 (OUTLIER) cc_final: 0.6790 (ptt) REVERT: T 184 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.8884 (pp) REVERT: T 187 ASP cc_start: 0.5368 (p0) cc_final: 0.5036 (m-30) REVERT: U 145 GLN cc_start: 0.7672 (mt0) cc_final: 0.7459 (mm-40) REVERT: U 184 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.8537 (pp) REVERT: V 21 LEU cc_start: 0.9517 (OUTLIER) cc_final: 0.9197 (mm) REVERT: V 157 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7726 (tm-30) REVERT: V 163 GLU cc_start: 0.7414 (tt0) cc_final: 0.6514 (tt0) REVERT: V 172 MET cc_start: 0.8365 (tpp) cc_final: 0.6928 (ptt) REVERT: V 184 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8581 (pp) REVERT: W 75 SER cc_start: 0.8543 (OUTLIER) cc_final: 0.8296 (p) REVERT: W 169 ARG cc_start: 0.8249 (ttp-110) cc_final: 0.7118 (tpp-160) REVERT: W 183 MET cc_start: 0.8113 (ttm) cc_final: 0.7104 (pmm) REVERT: X 130 MET cc_start: 0.8283 (mtp) cc_final: 0.7773 (mmm) REVERT: X 164 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8151 (tm-30) REVERT: X 172 MET cc_start: 0.8245 (tpp) cc_final: 0.6788 (ptt) REVERT: X 173 GLU cc_start: 0.6674 (tm-30) cc_final: 0.6229 (tm-30) outliers start: 112 outliers final: 82 residues processed: 488 average time/residue: 0.2583 time to fit residues: 202.3831 Evaluate side-chains 477 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 379 time to evaluate : 2.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 59 TRP Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 191 SER Chi-restraints excluded: chain N residue 5 ASP Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 59 TRP Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain N residue 113 PHE Chi-restraints excluded: chain N residue 133 CYS Chi-restraints excluded: chain N residue 175 GLU Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain N residue 191 SER Chi-restraints excluded: chain N residue 194 LEU Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 26 GLU Chi-restraints excluded: chain O residue 59 TRP Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 184 LEU Chi-restraints excluded: chain O residue 191 SER Chi-restraints excluded: chain P residue 4 TYR Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 59 TRP Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain P residue 191 SER Chi-restraints excluded: chain Q residue 5 ASP Chi-restraints excluded: chain Q residue 24 ILE Chi-restraints excluded: chain Q residue 67 ILE Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 77 LEU Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 184 LEU Chi-restraints excluded: chain Q residue 191 SER Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 37 ASN Chi-restraints excluded: chain R residue 59 TRP Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 148 ASN Chi-restraints excluded: chain R residue 161 GLN Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain S residue 6 MET Chi-restraints excluded: chain S residue 32 LEU Chi-restraints excluded: chain S residue 59 TRP Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain S residue 78 ILE Chi-restraints excluded: chain S residue 87 LEU Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 191 SER Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 59 TRP Chi-restraints excluded: chain T residue 63 ILE Chi-restraints excluded: chain T residue 67 ILE Chi-restraints excluded: chain T residue 77 LEU Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain T residue 95 ILE Chi-restraints excluded: chain T residue 112 ARG Chi-restraints excluded: chain T residue 172 MET Chi-restraints excluded: chain T residue 184 LEU Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 23 SER Chi-restraints excluded: chain U residue 59 TRP Chi-restraints excluded: chain U residue 87 LEU Chi-restraints excluded: chain U residue 90 THR Chi-restraints excluded: chain U residue 95 ILE Chi-restraints excluded: chain U residue 170 LEU Chi-restraints excluded: chain U residue 184 LEU Chi-restraints excluded: chain U residue 191 SER Chi-restraints excluded: chain V residue 21 LEU Chi-restraints excluded: chain V residue 59 TRP Chi-restraints excluded: chain V residue 78 ILE Chi-restraints excluded: chain V residue 87 LEU Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain V residue 112 ARG Chi-restraints excluded: chain V residue 175 GLU Chi-restraints excluded: chain V residue 184 LEU Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 59 TRP Chi-restraints excluded: chain W residue 63 ILE Chi-restraints excluded: chain W residue 75 SER Chi-restraints excluded: chain W residue 79 VAL Chi-restraints excluded: chain W residue 87 LEU Chi-restraints excluded: chain W residue 90 THR Chi-restraints excluded: chain W residue 143 SER Chi-restraints excluded: chain W residue 191 SER Chi-restraints excluded: chain X residue 13 GLU Chi-restraints excluded: chain X residue 23 SER Chi-restraints excluded: chain X residue 59 TRP Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 78 ILE Chi-restraints excluded: chain X residue 161 GLN Chi-restraints excluded: chain X residue 164 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 0.7980 chunk 210 optimal weight: 0.7980 chunk 192 optimal weight: 0.7980 chunk 204 optimal weight: 0.5980 chunk 123 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 160 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 185 optimal weight: 0.7980 chunk 193 optimal weight: 1.9990 chunk 134 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 55 GLN ** N 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 ASN ** R 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.7444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 18942 Z= 0.270 Angle : 0.686 7.381 25656 Z= 0.371 Chirality : 0.045 0.199 2754 Planarity : 0.003 0.033 3444 Dihedral : 5.978 39.542 2664 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 5.37 % Allowed : 24.18 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.80 % Twisted Proline : 0.00 % Twisted General : 0.80 % 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: -0.83 (0.16), residues: 2310 helix: 1.55 (0.16), residues: 906 sheet: -2.72 (0.48), residues: 102 loop : -2.04 (0.15), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP X 137 PHE 0.019 0.002 PHE P 150 TYR 0.015 0.001 TYR M 127 ARG 0.009 0.000 ARG X 168 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 389 time to evaluate : 2.100 Fit side-chains REVERT: M 10 THR cc_start: 0.8680 (OUTLIER) cc_final: 0.8382 (p) REVERT: M 161 GLN cc_start: 0.8446 (tm-30) cc_final: 0.8083 (tm-30) REVERT: M 172 MET cc_start: 0.8645 (tpp) cc_final: 0.6847 (ptt) REVERT: M 184 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8883 (pp) REVERT: N 42 ASN cc_start: 0.8427 (t0) cc_final: 0.8065 (t0) REVERT: N 113 PHE cc_start: 0.8972 (OUTLIER) cc_final: 0.8647 (p90) REVERT: N 132 GLU cc_start: 0.8929 (tp30) cc_final: 0.8577 (tm-30) REVERT: O 172 MET cc_start: 0.8646 (tpp) cc_final: 0.7167 (ptt) REVERT: O 184 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8738 (pp) REVERT: P 49 LYS cc_start: 0.9276 (ttpp) cc_final: 0.8961 (tttm) REVERT: P 172 MET cc_start: 0.8429 (tpp) cc_final: 0.7106 (ptt) REVERT: P 184 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.8866 (pp) REVERT: P 194 LEU cc_start: 0.8845 (mp) cc_final: 0.8536 (mp) REVERT: Q 80 TYR cc_start: 0.8539 (t80) cc_final: 0.8176 (t80) REVERT: Q 176 MET cc_start: 0.7909 (mmm) cc_final: 0.7559 (ptm) REVERT: Q 184 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8706 (pp) REVERT: R 39 ASP cc_start: 0.8176 (m-30) cc_final: 0.7488 (m-30) REVERT: R 172 MET cc_start: 0.7755 (tpp) cc_final: 0.6559 (ptt) REVERT: S 172 MET cc_start: 0.8550 (tpp) cc_final: 0.7303 (ptt) REVERT: T 95 ILE cc_start: 0.9243 (OUTLIER) cc_final: 0.8954 (mt) REVERT: T 112 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7876 (ptp-110) REVERT: T 172 MET cc_start: 0.7926 (OUTLIER) cc_final: 0.6984 (ptt) REVERT: T 184 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.8824 (pp) REVERT: T 187 ASP cc_start: 0.5414 (p0) cc_final: 0.5103 (m-30) REVERT: U 112 ARG cc_start: 0.7893 (mtt90) cc_final: 0.7627 (mtp85) REVERT: U 145 GLN cc_start: 0.7648 (mt0) cc_final: 0.7434 (mm-40) REVERT: U 184 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8919 (pp) REVERT: V 21 LEU cc_start: 0.9525 (OUTLIER) cc_final: 0.9228 (mm) REVERT: V 109 GLN cc_start: 0.8615 (mm-40) cc_final: 0.8398 (mm-40) REVERT: V 163 GLU cc_start: 0.7422 (tt0) cc_final: 0.6415 (tt0) REVERT: V 172 MET cc_start: 0.8387 (tpp) cc_final: 0.6909 (ptt) REVERT: V 184 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8660 (pp) REVERT: W 75 SER cc_start: 0.8548 (OUTLIER) cc_final: 0.8323 (p) REVERT: W 169 ARG cc_start: 0.8376 (ttp-110) cc_final: 0.7069 (tpp-160) REVERT: W 172 MET cc_start: 0.8666 (tpp) cc_final: 0.8370 (tpp) REVERT: W 183 MET cc_start: 0.8069 (ttm) cc_final: 0.7130 (pmm) REVERT: X 130 MET cc_start: 0.8304 (mtp) cc_final: 0.7832 (mmm) REVERT: X 172 MET cc_start: 0.8395 (tpp) cc_final: 0.7346 (ptt) REVERT: X 173 GLU cc_start: 0.6651 (tm-30) cc_final: 0.6245 (tm-30) outliers start: 108 outliers final: 81 residues processed: 476 average time/residue: 0.2548 time to fit residues: 196.6828 Evaluate side-chains 460 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 365 time to evaluate : 2.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 5 ASP Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 59 TRP Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain N residue 5 ASP Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 59 TRP Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain N residue 113 PHE Chi-restraints excluded: chain N residue 133 CYS Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain N residue 191 SER Chi-restraints excluded: chain N residue 194 LEU Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 26 GLU Chi-restraints excluded: chain O residue 59 TRP Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain O residue 77 LEU Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 184 LEU Chi-restraints excluded: chain O residue 191 SER Chi-restraints excluded: chain P residue 4 TYR Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain P residue 191 SER Chi-restraints excluded: chain Q residue 5 ASP Chi-restraints excluded: chain Q residue 24 ILE Chi-restraints excluded: chain Q residue 67 ILE Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 77 LEU Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 184 LEU Chi-restraints excluded: chain Q residue 191 SER Chi-restraints excluded: chain R residue 13 GLU Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 37 ASN Chi-restraints excluded: chain R residue 67 ILE Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 148 ASN Chi-restraints excluded: chain R residue 161 GLN Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain S residue 6 MET Chi-restraints excluded: chain S residue 32 LEU Chi-restraints excluded: chain S residue 59 TRP Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain S residue 78 ILE Chi-restraints excluded: chain S residue 87 LEU Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 191 SER Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 59 TRP Chi-restraints excluded: chain T residue 63 ILE Chi-restraints excluded: chain T residue 77 LEU Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain T residue 95 ILE Chi-restraints excluded: chain T residue 112 ARG Chi-restraints excluded: chain T residue 172 MET Chi-restraints excluded: chain T residue 184 LEU Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 23 SER Chi-restraints excluded: chain U residue 59 TRP Chi-restraints excluded: chain U residue 63 ILE Chi-restraints excluded: chain U residue 87 LEU Chi-restraints excluded: chain U residue 90 THR Chi-restraints excluded: chain U residue 95 ILE Chi-restraints excluded: chain U residue 170 LEU Chi-restraints excluded: chain U residue 184 LEU Chi-restraints excluded: chain U residue 191 SER Chi-restraints excluded: chain V residue 21 LEU Chi-restraints excluded: chain V residue 59 TRP Chi-restraints excluded: chain V residue 78 ILE Chi-restraints excluded: chain V residue 87 LEU Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain V residue 112 ARG Chi-restraints excluded: chain V residue 184 LEU Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 59 TRP Chi-restraints excluded: chain W residue 63 ILE Chi-restraints excluded: chain W residue 75 SER Chi-restraints excluded: chain W residue 79 VAL Chi-restraints excluded: chain W residue 87 LEU Chi-restraints excluded: chain W residue 90 THR Chi-restraints excluded: chain W residue 143 SER Chi-restraints excluded: chain W residue 191 SER Chi-restraints excluded: chain X residue 13 GLU Chi-restraints excluded: chain X residue 23 SER Chi-restraints excluded: chain X residue 59 TRP Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 78 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 2.9990 chunk 132 optimal weight: 0.4980 chunk 102 optimal weight: 0.7980 chunk 150 optimal weight: 0.6980 chunk 227 optimal weight: 0.6980 chunk 209 optimal weight: 0.8980 chunk 180 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 143 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 48 ASN N 147 ASN ** O 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 ASN R 145 GLN ** R 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.7561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18942 Z= 0.249 Angle : 0.678 7.388 25656 Z= 0.366 Chirality : 0.044 0.182 2754 Planarity : 0.003 0.053 3444 Dihedral : 5.978 39.767 2664 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 5.02 % Allowed : 24.73 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.80 % Twisted Proline : 0.00 % Twisted General : 0.80 % 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: -0.71 (0.17), residues: 2310 helix: 1.60 (0.16), residues: 924 sheet: -2.79 (0.48), residues: 102 loop : -1.96 (0.15), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP X 137 PHE 0.017 0.002 PHE P 150 TYR 0.025 0.001 TYR X 96 ARG 0.009 0.000 ARG X 168 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 377 time to evaluate : 2.189 Fit side-chains REVERT: M 10 THR cc_start: 0.8627 (OUTLIER) cc_final: 0.8342 (p) REVERT: M 157 GLU cc_start: 0.8705 (tm-30) cc_final: 0.8419 (tm-30) REVERT: M 161 GLN cc_start: 0.8447 (tm-30) cc_final: 0.8026 (tm-30) REVERT: M 172 MET cc_start: 0.8635 (tpp) cc_final: 0.6857 (ptt) REVERT: M 184 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8879 (pp) REVERT: N 42 ASN cc_start: 0.8382 (t0) cc_final: 0.8015 (t0) REVERT: N 113 PHE cc_start: 0.8945 (OUTLIER) cc_final: 0.8602 (p90) REVERT: N 132 GLU cc_start: 0.8918 (tp30) cc_final: 0.8698 (tm-30) REVERT: O 172 MET cc_start: 0.8634 (tpp) cc_final: 0.7126 (ptt) REVERT: O 184 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8737 (pp) REVERT: P 49 LYS cc_start: 0.9331 (ttpp) cc_final: 0.9024 (tttm) REVERT: P 172 MET cc_start: 0.8428 (tpp) cc_final: 0.7038 (ptt) REVERT: P 184 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.8797 (pp) REVERT: P 194 LEU cc_start: 0.8829 (mp) cc_final: 0.8488 (mp) REVERT: Q 33 GLU cc_start: 0.8065 (pt0) cc_final: 0.7864 (mm-30) REVERT: Q 80 TYR cc_start: 0.8540 (t80) cc_final: 0.8228 (t80) REVERT: Q 172 MET cc_start: 0.8427 (mmm) cc_final: 0.7060 (ptt) REVERT: Q 176 MET cc_start: 0.7890 (mmm) cc_final: 0.7611 (ptm) REVERT: Q 184 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8768 (pp) REVERT: R 39 ASP cc_start: 0.8145 (m-30) cc_final: 0.7427 (m-30) REVERT: R 145 GLN cc_start: 0.7860 (mt0) cc_final: 0.7653 (mt0) REVERT: R 172 MET cc_start: 0.7671 (tpp) cc_final: 0.6524 (ptt) REVERT: S 172 MET cc_start: 0.8547 (tpp) cc_final: 0.7328 (ptt) REVERT: T 95 ILE cc_start: 0.9256 (OUTLIER) cc_final: 0.8962 (mt) REVERT: T 112 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7830 (ptp-110) REVERT: T 172 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.6807 (ptt) REVERT: T 184 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.8917 (pp) REVERT: T 187 ASP cc_start: 0.5352 (p0) cc_final: 0.5056 (m-30) REVERT: U 112 ARG cc_start: 0.8091 (mtt90) cc_final: 0.7748 (mtp85) REVERT: U 145 GLN cc_start: 0.7668 (mt0) cc_final: 0.7459 (mm-40) REVERT: U 172 MET cc_start: 0.8766 (mmm) cc_final: 0.8524 (tpp) REVERT: U 184 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.9035 (pp) REVERT: V 21 LEU cc_start: 0.9524 (OUTLIER) cc_final: 0.9238 (mm) REVERT: V 163 GLU cc_start: 0.7409 (tt0) cc_final: 0.6433 (tt0) REVERT: V 172 MET cc_start: 0.8318 (tpp) cc_final: 0.6940 (ptt) REVERT: V 184 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8651 (pp) REVERT: W 75 SER cc_start: 0.8565 (OUTLIER) cc_final: 0.8276 (p) REVERT: W 169 ARG cc_start: 0.8327 (ttp-110) cc_final: 0.6920 (tpp-160) REVERT: W 183 MET cc_start: 0.8063 (ttm) cc_final: 0.7050 (pmm) REVERT: X 130 MET cc_start: 0.8244 (mtp) cc_final: 0.7765 (mmm) REVERT: X 172 MET cc_start: 0.8326 (tpp) cc_final: 0.7279 (ptt) REVERT: X 173 GLU cc_start: 0.6650 (tm-30) cc_final: 0.6231 (tm-30) outliers start: 101 outliers final: 82 residues processed: 459 average time/residue: 0.2556 time to fit residues: 190.2542 Evaluate side-chains 461 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 365 time to evaluate : 2.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 5 ASP Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 59 TRP Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain N residue 5 ASP Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 59 TRP Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain N residue 113 PHE Chi-restraints excluded: chain N residue 133 CYS Chi-restraints excluded: chain N residue 183 MET Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain N residue 191 SER Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 26 GLU Chi-restraints excluded: chain O residue 59 TRP Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain O residue 77 LEU Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 184 LEU Chi-restraints excluded: chain O residue 191 SER Chi-restraints excluded: chain P residue 4 TYR Chi-restraints excluded: chain P residue 23 SER Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain P residue 191 SER Chi-restraints excluded: chain Q residue 5 ASP Chi-restraints excluded: chain Q residue 24 ILE Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 77 LEU Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 184 LEU Chi-restraints excluded: chain Q residue 191 SER Chi-restraints excluded: chain R residue 13 GLU Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 37 ASN Chi-restraints excluded: chain R residue 59 TRP Chi-restraints excluded: chain R residue 67 ILE Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 161 GLN Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain S residue 6 MET Chi-restraints excluded: chain S residue 32 LEU Chi-restraints excluded: chain S residue 59 TRP Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain S residue 78 ILE Chi-restraints excluded: chain S residue 87 LEU Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 191 SER Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 59 TRP Chi-restraints excluded: chain T residue 63 ILE Chi-restraints excluded: chain T residue 77 LEU Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain T residue 95 ILE Chi-restraints excluded: chain T residue 112 ARG Chi-restraints excluded: chain T residue 172 MET Chi-restraints excluded: chain T residue 184 LEU Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 23 SER Chi-restraints excluded: chain U residue 59 TRP Chi-restraints excluded: chain U residue 63 ILE Chi-restraints excluded: chain U residue 87 LEU Chi-restraints excluded: chain U residue 90 THR Chi-restraints excluded: chain U residue 95 ILE Chi-restraints excluded: chain U residue 170 LEU Chi-restraints excluded: chain U residue 184 LEU Chi-restraints excluded: chain U residue 191 SER Chi-restraints excluded: chain V residue 21 LEU Chi-restraints excluded: chain V residue 59 TRP Chi-restraints excluded: chain V residue 78 ILE Chi-restraints excluded: chain V residue 87 LEU Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain V residue 184 LEU Chi-restraints excluded: chain W residue 5 ASP Chi-restraints excluded: chain W residue 10 THR Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 59 TRP Chi-restraints excluded: chain W residue 63 ILE Chi-restraints excluded: chain W residue 75 SER Chi-restraints excluded: chain W residue 79 VAL Chi-restraints excluded: chain W residue 87 LEU Chi-restraints excluded: chain W residue 90 THR Chi-restraints excluded: chain W residue 143 SER Chi-restraints excluded: chain W residue 191 SER Chi-restraints excluded: chain X residue 13 GLU Chi-restraints excluded: chain X residue 23 SER Chi-restraints excluded: chain X residue 59 TRP Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 78 ILE Chi-restraints excluded: chain X residue 161 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.3637 > 50: distance: 112 - 138: 32.821 distance: 129 - 135: 21.253 distance: 135 - 136: 26.522 distance: 136 - 137: 17.904 distance: 136 - 139: 16.009 distance: 139 - 140: 40.842 distance: 139 - 141: 55.464 distance: 140 - 142: 32.518 distance: 144 - 145: 38.920 distance: 144 - 147: 47.408 distance: 145 - 146: 3.193 distance: 145 - 154: 39.212 distance: 147 - 148: 31.785 distance: 148 - 149: 6.253 distance: 150 - 151: 24.278 distance: 151 - 152: 41.423 distance: 151 - 153: 54.919 distance: 154 - 155: 44.291 distance: 155 - 156: 30.691 distance: 155 - 158: 20.107 distance: 156 - 162: 16.376 distance: 158 - 159: 11.911 distance: 159 - 160: 20.084 distance: 159 - 161: 46.414 distance: 162 - 163: 28.440 distance: 163 - 164: 18.502 distance: 163 - 166: 7.378 distance: 164 - 165: 10.911 distance: 164 - 173: 29.052 distance: 166 - 167: 13.813 distance: 167 - 168: 8.861 distance: 168 - 169: 34.863 distance: 169 - 170: 28.778 distance: 170 - 171: 3.156 distance: 170 - 172: 11.526 distance: 173 - 174: 22.643 distance: 174 - 175: 19.563 distance: 174 - 177: 43.326 distance: 175 - 176: 34.940 distance: 175 - 181: 17.486 distance: 177 - 178: 34.411 distance: 178 - 179: 39.648 distance: 178 - 180: 5.154 distance: 181 - 182: 19.286 distance: 182 - 183: 32.782 distance: 183 - 184: 18.813 distance: 183 - 193: 28.193 distance: 185 - 186: 23.499 distance: 186 - 187: 22.882 distance: 186 - 188: 41.456 distance: 187 - 189: 11.858 distance: 188 - 190: 3.206 distance: 189 - 191: 19.039 distance: 190 - 191: 26.662 distance: 191 - 192: 24.714 distance: 193 - 194: 19.281 distance: 194 - 195: 17.501 distance: 194 - 197: 16.864 distance: 195 - 196: 11.670 distance: 195 - 201: 33.107 distance: 197 - 198: 46.911 distance: 198 - 199: 21.588 distance: 201 - 202: 38.161 distance: 202 - 203: 32.966 distance: 202 - 205: 38.800 distance: 203 - 204: 56.524 distance: 203 - 210: 36.359 distance: 205 - 206: 20.784 distance: 206 - 207: 7.745 distance: 210 - 211: 51.252 distance: 211 - 212: 53.293 distance: 211 - 214: 35.542 distance: 212 - 218: 55.025 distance: 214 - 215: 26.068 distance: 215 - 216: 37.198 distance: 216 - 217: 14.673 distance: 218 - 219: 38.706 distance: 219 - 220: 40.923 distance: 220 - 221: 27.622 distance: 220 - 225: 29.804 distance: 221 - 243: 35.970 distance: 223 - 224: 39.500