Starting phenix.real_space_refine on Sat May 11 10:26:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7box_30135/05_2024/7box_30135.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7box_30135/05_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_30135/05_2024/7box_30135.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7box_30135/05_2024/7box_30135.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7box_30135/05_2024/7box_30135.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7box_30135/05_2024/7box_30135.pdb" } 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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: 9.93, per 1000 atoms: 0.53 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: 6.32 Conformation dependent library (CDL) restraints added in 3.5 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: 1.55 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: 5.29 Time building geometry restraints manager: 6.98 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 2.440 nonbonded pdb=" O ARG P 52 " pdb=" OG SER P 56 " model vdw 2.239 2.440 nonbonded pdb=" O ARG N 52 " pdb=" OG SER N 56 " model vdw 2.244 2.440 nonbonded pdb=" O ARG T 52 " pdb=" OG SER T 56 " model vdw 2.250 2.440 nonbonded pdb=" O ARG O 52 " pdb=" OG SER O 56 " model vdw 2.264 2.440 ... (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 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: 2.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 9.650 Check model and map are aligned: 0.160 Set scattering table: 0.180 Process input model: 48.960 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.340 ------------------------------------------------------------------------------- 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 : 2.227 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: 0.3233 time to fit residues: 511.4439 Evaluate side-chains 505 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 505 time to evaluate : 2.423 ------------------------------------------------------------------------------- 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: 0.9980 chunk 59 optimal weight: 0.0970 chunk 116 optimal weight: 0.9980 chunk 92 optimal weight: 0.5980 chunk 178 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 108 optimal weight: 0.5980 chunk 133 optimal weight: 1.9990 chunk 207 optimal weight: 0.8980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 7 ASN ** M 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 48 ASN M 55 GLN ** 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 42 ASN ** O 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 182 ASN P 18 ASN P 42 ASN ** P 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 182 ASN Q 7 ASN ** Q 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 62 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 42 ASN S 55 GLN ** 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 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 182 ASN U 7 ASN U 42 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 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 182 ASN W 7 ASN ** W 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** X 147 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18942 Z= 0.262 Angle : 0.812 10.265 25656 Z= 0.438 Chirality : 0.047 0.230 2754 Planarity : 0.005 0.035 3444 Dihedral : 7.739 46.108 2664 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 5.17 % Allowed : 20.05 % Favored : 74.78 % 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: -3.07 (0.14), residues: 2310 helix: -1.15 (0.15), residues: 906 sheet: -2.49 (0.41), residues: 144 loop : -2.75 (0.13), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.004 TRP R 137 PHE 0.034 0.002 PHE P 150 TYR 0.026 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 648 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 544 time to evaluate : 2.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 5 ASP cc_start: 0.8482 (OUTLIER) cc_final: 0.8265 (m-30) REVERT: M 112 ARG cc_start: 0.8491 (ptp-170) cc_final: 0.8220 (mpt-90) REVERT: M 145 GLN cc_start: 0.8609 (mt0) cc_final: 0.8387 (mt0) REVERT: M 161 GLN cc_start: 0.8252 (tm-30) cc_final: 0.7926 (tm-30) REVERT: M 176 MET cc_start: 0.8013 (mmm) cc_final: 0.6820 (ptm) REVERT: M 184 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8715 (pp) REVERT: N 55 GLN cc_start: 0.9053 (mp10) cc_final: 0.8335 (mp10) REVERT: N 68 THR cc_start: 0.8938 (t) cc_final: 0.8245 (p) REVERT: O 161 GLN cc_start: 0.8306 (tp40) cc_final: 0.7559 (tp40) REVERT: O 184 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8808 (pp) REVERT: P 49 LYS cc_start: 0.8801 (ttpp) cc_final: 0.8563 (ttpp) REVERT: P 160 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8768 (tm) REVERT: P 172 MET cc_start: 0.7972 (tpp) cc_final: 0.6338 (ptt) REVERT: P 184 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8649 (pp) REVERT: P 194 LEU cc_start: 0.9085 (mp) cc_final: 0.8866 (mp) REVERT: Q 19 ASP cc_start: 0.8010 (m-30) cc_final: 0.7743 (m-30) REVERT: Q 157 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7797 (tm-30) REVERT: Q 172 MET cc_start: 0.8267 (mmm) cc_final: 0.6964 (ptt) REVERT: R 29 VAL cc_start: 0.8277 (OUTLIER) cc_final: 0.7854 (m) REVERT: R 172 MET cc_start: 0.7989 (tpp) cc_final: 0.6609 (ptt) REVERT: S 157 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7682 (tm-30) REVERT: S 172 MET cc_start: 0.8228 (tpp) cc_final: 0.6889 (ptt) REVERT: T 29 VAL cc_start: 0.9046 (p) cc_final: 0.8823 (m) REVERT: T 95 ILE cc_start: 0.9017 (OUTLIER) cc_final: 0.8540 (mm) REVERT: T 172 MET cc_start: 0.8459 (tpp) cc_final: 0.7219 (ptm) REVERT: U 172 MET cc_start: 0.8890 (tpp) cc_final: 0.8448 (tpp) REVERT: U 176 MET cc_start: 0.7621 (mmm) cc_final: 0.6493 (ptm) REVERT: V 26 GLU cc_start: 0.7485 (mp0) cc_final: 0.7110 (mt-10) REVERT: V 49 LYS cc_start: 0.9168 (tttp) cc_final: 0.8901 (tttm) REVERT: V 172 MET cc_start: 0.8244 (tpp) cc_final: 0.6711 (ptt) REVERT: V 184 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8505 (pp) REVERT: V 194 LEU cc_start: 0.8966 (mp) cc_final: 0.8700 (mp) REVERT: W 26 GLU cc_start: 0.7127 (tt0) cc_final: 0.6921 (mt-10) REVERT: W 169 ARG cc_start: 0.7935 (ttp-110) cc_final: 0.7282 (tpp-160) REVERT: W 172 MET cc_start: 0.8827 (tpp) cc_final: 0.8397 (tpp) REVERT: W 184 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8461 (pp) REVERT: X 26 GLU cc_start: 0.7394 (mp0) cc_final: 0.7083 (mt-10) REVERT: X 29 VAL cc_start: 0.9249 (p) cc_final: 0.8987 (m) REVERT: X 172 MET cc_start: 0.8417 (tpp) cc_final: 0.6768 (ptt) outliers start: 104 outliers final: 49 residues processed: 612 average time/residue: 0.2575 time to fit residues: 249.5489 Evaluate side-chains 477 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 419 time to evaluate : 2.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 5 ASP 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 126 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 77 LEU Chi-restraints excluded: chain N residue 126 ASP 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 126 ASP Chi-restraints excluded: chain O residue 184 LEU Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 95 ILE Chi-restraints excluded: chain P residue 126 ASP 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 67 ILE Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 126 ASP Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 35 ASP Chi-restraints excluded: chain R residue 126 ASP 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 50 ILE Chi-restraints excluded: chain S residue 63 ILE Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 126 ASP Chi-restraints excluded: chain S residue 184 LEU Chi-restraints excluded: chain T residue 23 SER 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 U residue 126 ASP Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 184 LEU Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 90 THR Chi-restraints excluded: chain W residue 126 ASP Chi-restraints excluded: chain W residue 184 LEU 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 126 ASP 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: 0.7980 chunk 64 optimal weight: 0.0030 chunk 172 optimal weight: 1.9990 chunk 140 optimal weight: 0.0870 chunk 57 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 chunk 224 optimal weight: 0.9980 chunk 184 optimal weight: 0.9980 chunk 205 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 166 optimal weight: 0.9980 overall best weight: 0.5568 ------------------------------------------------------------------------------- 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 109 GLN ** M 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 18 ASN ** N 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 62 ASN ** 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** ** P 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 42 ASN 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 55 GLN ** S 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 161 GLN U 53 GLN ** U 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 145 GLN ** 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 ** V 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 53 GLN W 55 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.5737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18942 Z= 0.239 Angle : 0.700 7.852 25656 Z= 0.378 Chirality : 0.045 0.216 2754 Planarity : 0.004 0.035 3444 Dihedral : 6.776 42.231 2664 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 5.67 % Allowed : 21.79 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.80 % Twisted Proline : 0.00 % Twisted General : 0.88 % 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: 0.10 (0.16), residues: 930 sheet: -2.97 (0.43), residues: 108 loop : -2.57 (0.14), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP N 137 PHE 0.026 0.002 PHE P 150 TYR 0.017 0.001 TYR W 136 ARG 0.005 0.001 ARG N 2 *********************** 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 589 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 475 time to evaluate : 2.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 19 ASP cc_start: 0.7785 (m-30) cc_final: 0.7576 (m-30) REVERT: M 161 GLN cc_start: 0.8284 (tm-30) cc_final: 0.7828 (tm-30) REVERT: M 165 ASP cc_start: 0.8139 (OUTLIER) cc_final: 0.7888 (t70) REVERT: M 172 MET cc_start: 0.8482 (mmm) cc_final: 0.6952 (ptt) REVERT: N 68 THR cc_start: 0.8915 (t) cc_final: 0.8562 (p) REVERT: N 113 PHE cc_start: 0.8950 (OUTLIER) cc_final: 0.8653 (p90) REVERT: O 172 MET cc_start: 0.8846 (mmm) cc_final: 0.8511 (tpp) REVERT: P 49 LYS cc_start: 0.9082 (ttpp) cc_final: 0.8788 (ttpp) REVERT: P 164 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8518 (tm-30) REVERT: P 172 MET cc_start: 0.8244 (tpp) cc_final: 0.6587 (ptt) REVERT: P 184 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8345 (pp) REVERT: P 194 LEU cc_start: 0.9042 (mp) cc_final: 0.8737 (mt) REVERT: Q 5 ASP cc_start: 0.8472 (m-30) cc_final: 0.8218 (m-30) REVERT: Q 96 TYR cc_start: 0.9016 (m-10) cc_final: 0.8813 (m-80) REVERT: Q 157 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7936 (tm-30) REVERT: Q 176 MET cc_start: 0.8345 (mmt) cc_final: 0.8053 (mmt) REVERT: Q 184 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8980 (pp) REVERT: R 29 VAL cc_start: 0.8781 (p) cc_final: 0.8515 (m) REVERT: R 172 MET cc_start: 0.8127 (tpp) cc_final: 0.6707 (ptt) REVERT: S 13 GLU cc_start: 0.8243 (pt0) cc_final: 0.8004 (pm20) REVERT: S 172 MET cc_start: 0.8475 (tpp) cc_final: 0.6865 (ptt) REVERT: T 95 ILE cc_start: 0.9066 (mt) cc_final: 0.8558 (mm) REVERT: U 145 GLN cc_start: 0.8041 (mt0) cc_final: 0.6873 (mt0) REVERT: U 172 MET cc_start: 0.8949 (tpp) cc_final: 0.8444 (tpp) REVERT: U 176 MET cc_start: 0.7601 (mmm) cc_final: 0.6733 (ptm) REVERT: U 184 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8851 (pp) REVERT: V 26 GLU cc_start: 0.7338 (mp0) cc_final: 0.7077 (mt-10) REVERT: V 172 MET cc_start: 0.8410 (tpp) cc_final: 0.7012 (ptt) REVERT: W 26 GLU cc_start: 0.7430 (tt0) cc_final: 0.7115 (mt-10) REVERT: W 145 GLN cc_start: 0.7977 (mt0) cc_final: 0.7717 (mt0) REVERT: W 155 GLU cc_start: 0.7291 (pp20) cc_final: 0.6986 (pp20) REVERT: W 169 ARG cc_start: 0.8141 (ttp-110) cc_final: 0.7139 (tpp-160) REVERT: W 173 GLU cc_start: 0.7877 (tt0) cc_final: 0.7367 (tt0) REVERT: W 184 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8659 (pp) REVERT: X 10 THR cc_start: 0.8724 (t) cc_final: 0.8459 (t) REVERT: X 163 GLU cc_start: 0.7882 (tt0) cc_final: 0.7578 (tt0) REVERT: X 170 LEU cc_start: 0.8814 (mm) cc_final: 0.8536 (tp) REVERT: X 172 MET cc_start: 0.8486 (tpp) cc_final: 0.6964 (ptt) outliers start: 114 outliers final: 64 residues processed: 556 average time/residue: 0.2661 time to fit residues: 237.0810 Evaluate side-chains 464 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 393 time to evaluate : 2.276 ------------------------------------------------------------------------------- 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 126 ASP Chi-restraints excluded: chain M residue 165 ASP Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 23 SER Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 63 ILE Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain N residue 113 PHE Chi-restraints excluded: chain N residue 126 ASP 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 90 THR Chi-restraints excluded: chain O residue 126 ASP Chi-restraints excluded: chain P residue 24 ILE Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 65 GLU Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 126 ASP Chi-restraints excluded: chain P residue 164 GLU Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 126 ASP Chi-restraints excluded: chain Q residue 159 VAL Chi-restraints excluded: chain Q residue 184 LEU Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 126 ASP 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 32 LEU Chi-restraints excluded: chain S residue 63 ILE Chi-restraints excluded: chain S residue 87 LEU Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 126 ASP 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 60 THR Chi-restraints excluded: chain T residue 72 ASP Chi-restraints excluded: chain T residue 126 ASP 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 67 ILE Chi-restraints excluded: chain U residue 87 LEU Chi-restraints excluded: chain U residue 90 THR Chi-restraints excluded: chain U residue 126 ASP Chi-restraints excluded: chain U residue 184 LEU Chi-restraints excluded: chain V residue 23 SER 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 126 ASP 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 47 LEU Chi-restraints excluded: chain X residue 59 TRP Chi-restraints excluded: chain X residue 108 SER Chi-restraints excluded: chain X residue 126 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 0.9980 chunk 155 optimal weight: 4.9990 chunk 107 optimal weight: 0.1980 chunk 22 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 208 optimal weight: 0.0470 chunk 220 optimal weight: 0.9980 chunk 108 optimal weight: 0.7980 chunk 197 optimal weight: 0.2980 chunk 59 optimal weight: 1.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 48 ASN M 109 GLN ** M 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** P 18 ASN ** P 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 48 ASN ** Q 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 55 GLN ** R 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 148 ASN U 42 ASN U 55 GLN ** U 145 GLN ** 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 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.6329 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= 0.204 Angle : 0.650 8.045 25656 Z= 0.353 Chirality : 0.044 0.197 2754 Planarity : 0.003 0.025 3444 Dihedral : 6.244 39.905 2664 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 6.32 % Allowed : 21.99 % Favored : 71.69 % 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: -1.50 (0.16), residues: 2310 helix: 0.79 (0.17), residues: 930 sheet: -2.12 (0.70), residues: 60 loop : -2.42 (0.14), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP X 137 PHE 0.026 0.002 PHE N 150 TYR 0.021 0.001 TYR M 136 ARG 0.004 0.000 ARG N 2 *********************** 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 600 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 473 time to evaluate : 2.399 Fit side-chains REVERT: M 157 GLU cc_start: 0.8552 (tm-30) cc_final: 0.8304 (tm-30) REVERT: M 161 GLN cc_start: 0.8312 (tm-30) cc_final: 0.8032 (tm-30) REVERT: M 172 MET cc_start: 0.8459 (mmm) cc_final: 0.6630 (ptt) REVERT: M 184 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8826 (pp) REVERT: N 68 THR cc_start: 0.8949 (t) cc_final: 0.8646 (p) REVERT: N 113 PHE cc_start: 0.8934 (OUTLIER) cc_final: 0.8546 (p90) REVERT: N 130 MET cc_start: 0.8623 (mmm) cc_final: 0.8113 (mtp) REVERT: N 148 ASN cc_start: 0.8167 (m-40) cc_final: 0.7799 (m-40) REVERT: O 127 TYR cc_start: 0.8740 (t80) cc_final: 0.8207 (t80) REVERT: O 136 TYR cc_start: 0.9070 (t80) cc_final: 0.8584 (t80) REVERT: O 145 GLN cc_start: 0.7727 (mt0) cc_final: 0.7343 (mt0) REVERT: O 172 MET cc_start: 0.8763 (mmm) cc_final: 0.8457 (tpp) REVERT: P 49 LYS cc_start: 0.9086 (ttpp) cc_final: 0.8716 (ttpp) REVERT: P 163 GLU cc_start: 0.7773 (tt0) cc_final: 0.7540 (tt0) REVERT: P 164 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8463 (tm-30) REVERT: P 172 MET cc_start: 0.8314 (tpp) cc_final: 0.6723 (ptt) REVERT: P 184 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8338 (pp) REVERT: P 194 LEU cc_start: 0.9046 (mp) cc_final: 0.8708 (mp) REVERT: Q 5 ASP cc_start: 0.8455 (m-30) cc_final: 0.8184 (m-30) REVERT: Q 96 TYR cc_start: 0.9070 (m-10) cc_final: 0.8844 (m-80) REVERT: Q 136 TYR cc_start: 0.8675 (t80) cc_final: 0.8343 (t80) REVERT: Q 184 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8679 (pp) REVERT: R 172 MET cc_start: 0.8135 (tpp) cc_final: 0.6868 (ptt) REVERT: S 172 MET cc_start: 0.8483 (tpp) cc_final: 0.7142 (ptt) REVERT: T 95 ILE cc_start: 0.9123 (OUTLIER) cc_final: 0.8832 (mt) REVERT: T 172 MET cc_start: 0.8264 (tpp) cc_final: 0.7252 (ptm) REVERT: T 187 ASP cc_start: 0.5447 (p0) cc_final: 0.5153 (m-30) REVERT: U 112 ARG cc_start: 0.8067 (mpt-90) cc_final: 0.7821 (mtt90) REVERT: U 145 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.7378 (mt0) REVERT: U 157 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7932 (tm-30) REVERT: U 172 MET cc_start: 0.8920 (tpp) cc_final: 0.8448 (tpp) REVERT: U 176 MET cc_start: 0.7431 (mmm) cc_final: 0.6787 (ptm) REVERT: U 184 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8725 (pp) REVERT: V 55 GLN cc_start: 0.8325 (mm-40) cc_final: 0.7992 (mm110) REVERT: V 172 MET cc_start: 0.8417 (tpp) cc_final: 0.6922 (ptt) REVERT: V 184 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8695 (pp) REVERT: V 194 LEU cc_start: 0.8900 (mp) cc_final: 0.8566 (mp) REVERT: W 19 ASP cc_start: 0.8062 (m-30) cc_final: 0.7767 (m-30) REVERT: W 53 GLN cc_start: 0.9031 (tp-100) cc_final: 0.8616 (tp40) REVERT: W 155 GLU cc_start: 0.7232 (pp20) cc_final: 0.6885 (pp20) REVERT: W 164 GLU cc_start: 0.8840 (tm-30) cc_final: 0.8625 (tm-30) REVERT: W 169 ARG cc_start: 0.8207 (ttp-110) cc_final: 0.7227 (tpp-160) REVERT: W 184 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8677 (pp) REVERT: X 163 GLU cc_start: 0.7882 (tt0) cc_final: 0.7552 (tt0) REVERT: X 172 MET cc_start: 0.8478 (tpp) cc_final: 0.6989 (ptt) outliers start: 127 outliers final: 74 residues processed: 567 average time/residue: 0.2631 time to fit residues: 237.4041 Evaluate side-chains 498 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 414 time to evaluate : 2.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 5 ASP Chi-restraints excluded: chain M residue 59 TRP Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain M residue 87 LEU Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 126 ASP Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain N residue 23 SER Chi-restraints excluded: chain N residue 24 ILE 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 113 PHE Chi-restraints excluded: chain N residue 126 ASP Chi-restraints excluded: chain N residue 175 GLU Chi-restraints excluded: chain N residue 191 SER Chi-restraints excluded: chain O residue 59 TRP Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 126 ASP Chi-restraints excluded: chain P residue 4 TYR Chi-restraints excluded: chain P residue 23 SER Chi-restraints excluded: chain P residue 24 ILE Chi-restraints excluded: chain P residue 56 SER 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 126 ASP Chi-restraints excluded: chain P residue 164 GLU Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain Q residue 6 MET 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 126 ASP 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 126 ASP 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 63 ILE Chi-restraints excluded: chain S residue 87 LEU Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 126 ASP 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 59 TRP Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 67 ILE Chi-restraints excluded: chain T residue 72 ASP Chi-restraints excluded: chain T residue 95 ILE Chi-restraints excluded: chain T residue 126 ASP 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 90 THR Chi-restraints excluded: chain U residue 126 ASP Chi-restraints excluded: chain U residue 145 GLN Chi-restraints excluded: chain U residue 170 LEU Chi-restraints excluded: chain U residue 184 LEU Chi-restraints excluded: chain V residue 10 THR Chi-restraints excluded: chain V residue 59 TRP Chi-restraints excluded: chain V residue 78 ILE Chi-restraints excluded: chain V residue 126 ASP Chi-restraints excluded: chain V residue 184 LEU Chi-restraints excluded: chain W residue 6 MET 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 126 ASP Chi-restraints excluded: chain W residue 143 SER Chi-restraints excluded: chain W residue 184 LEU Chi-restraints excluded: chain X residue 5 ASP Chi-restraints excluded: chain X residue 23 SER Chi-restraints excluded: chain X residue 59 TRP Chi-restraints excluded: chain X residue 126 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 0.9990 chunk 125 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 188 optimal weight: 0.9990 chunk 152 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 112 optimal weight: 0.7980 chunk 197 optimal weight: 0.0270 chunk 55 optimal weight: 0.5980 overall best weight: 0.6838 ------------------------------------------------------------------------------- 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 ** M 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 7 ASN O 109 GLN ** O 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 ASN S 145 GLN ** S 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 55 GLN W 161 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.6733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18942 Z= 0.250 Angle : 0.667 8.673 25656 Z= 0.358 Chirality : 0.044 0.190 2754 Planarity : 0.003 0.035 3444 Dihedral : 6.176 39.990 2664 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 6.42 % Allowed : 23.08 % Favored : 70.50 % 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: -1.31 (0.16), residues: 2310 helix: 1.01 (0.16), residues: 936 sheet: -2.12 (0.68), residues: 60 loop : -2.37 (0.14), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 137 PHE 0.026 0.002 PHE P 150 TYR 0.015 0.001 TYR X 80 ARG 0.007 0.000 ARG T 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 572 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 443 time to evaluate : 2.091 Fit side-chains revert: symmetry clash REVERT: M 157 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8341 (tm-30) REVERT: M 161 GLN cc_start: 0.8467 (tm-30) cc_final: 0.8131 (tm-30) REVERT: M 172 MET cc_start: 0.8555 (mmm) cc_final: 0.6885 (ptt) REVERT: M 184 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8753 (pp) REVERT: N 68 THR cc_start: 0.9040 (t) cc_final: 0.8775 (p) REVERT: N 87 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9068 (tm) REVERT: N 113 PHE cc_start: 0.9034 (OUTLIER) cc_final: 0.8683 (p90) REVERT: N 172 MET cc_start: 0.8292 (tpp) cc_final: 0.7965 (mmm) REVERT: O 49 LYS cc_start: 0.8904 (tttp) cc_final: 0.8682 (tttp) REVERT: P 163 GLU cc_start: 0.7779 (tt0) cc_final: 0.7544 (tt0) REVERT: P 172 MET cc_start: 0.8412 (tpp) cc_final: 0.6996 (ptt) REVERT: Q 5 ASP cc_start: 0.8489 (m-30) cc_final: 0.8282 (m-30) REVERT: Q 95 ILE cc_start: 0.9160 (OUTLIER) cc_final: 0.8683 (mt) REVERT: Q 136 TYR cc_start: 0.8724 (t80) cc_final: 0.8333 (t80) REVERT: Q 176 MET cc_start: 0.8181 (mmm) cc_final: 0.7502 (ptm) REVERT: Q 184 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8869 (pp) REVERT: R 39 ASP cc_start: 0.8146 (m-30) cc_final: 0.7747 (m-30) REVERT: R 172 MET cc_start: 0.8202 (tpp) cc_final: 0.6900 (ptt) REVERT: S 14 LEU cc_start: 0.9104 (tt) cc_final: 0.8871 (tp) REVERT: T 75 SER cc_start: 0.7777 (OUTLIER) cc_final: 0.7154 (m) REVERT: T 88 MET cc_start: 0.8411 (mtt) cc_final: 0.8082 (mtt) REVERT: T 95 ILE cc_start: 0.9148 (mt) cc_final: 0.8861 (mt) REVERT: T 187 ASP cc_start: 0.5433 (p0) cc_final: 0.5099 (m-30) REVERT: U 172 MET cc_start: 0.8891 (tpp) cc_final: 0.8532 (tpp) REVERT: U 184 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.8831 (pp) REVERT: V 21 LEU cc_start: 0.9430 (OUTLIER) cc_final: 0.9053 (mm) REVERT: V 172 MET cc_start: 0.8438 (tpp) cc_final: 0.7187 (ptt) REVERT: V 184 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8522 (pp) REVERT: V 194 LEU cc_start: 0.8892 (mp) cc_final: 0.8472 (mp) REVERT: W 19 ASP cc_start: 0.7725 (m-30) cc_final: 0.7515 (m-30) REVERT: W 169 ARG cc_start: 0.8498 (ttp-110) cc_final: 0.7236 (tpp-160) REVERT: W 172 MET cc_start: 0.8734 (mmm) cc_final: 0.8327 (tpp) REVERT: W 184 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8833 (pp) REVERT: X 172 MET cc_start: 0.8546 (tpp) cc_final: 0.7466 (ptt) outliers start: 129 outliers final: 83 residues processed: 541 average time/residue: 0.2569 time to fit residues: 223.9691 Evaluate side-chains 503 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 410 time to evaluate : 2.250 ------------------------------------------------------------------------------- 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 59 TRP Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 126 ASP Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 190 THR Chi-restraints excluded: chain N residue 5 ASP Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 23 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 77 LEU Chi-restraints excluded: chain N residue 87 LEU Chi-restraints excluded: chain N residue 113 PHE Chi-restraints excluded: chain N residue 126 ASP 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 O residue 17 VAL 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 126 ASP 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 56 SER Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 126 ASP Chi-restraints excluded: chain P residue 164 GLU Chi-restraints excluded: chain P residue 191 SER 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 95 ILE Chi-restraints excluded: chain Q residue 126 ASP Chi-restraints excluded: chain Q residue 184 LEU Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 37 ASN Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 126 ASP Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain S residue 6 MET Chi-restraints excluded: chain S residue 32 LEU Chi-restraints excluded: chain S residue 63 ILE Chi-restraints excluded: chain S residue 87 LEU Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 126 ASP 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 59 TRP Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 75 SER Chi-restraints excluded: chain T residue 126 ASP 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 50 ILE 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 126 ASP Chi-restraints excluded: chain U residue 170 LEU Chi-restraints excluded: chain U residue 184 LEU Chi-restraints excluded: chain V residue 10 THR Chi-restraints excluded: chain V residue 21 LEU Chi-restraints excluded: chain V residue 23 SER Chi-restraints excluded: chain V residue 59 TRP 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 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 126 ASP Chi-restraints excluded: chain W residue 143 SER Chi-restraints excluded: chain W residue 184 LEU Chi-restraints excluded: chain X residue 5 ASP 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 126 ASP Chi-restraints excluded: chain X residue 184 LEU 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: 0.0370 chunk 43 optimal weight: 0.9990 chunk 129 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 chunk 220 optimal weight: 0.9980 chunk 183 optimal weight: 0.8980 chunk 102 optimal weight: 0.0020 chunk 18 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 115 optimal weight: 0.7980 overall best weight: 0.4266 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 147 ASN ** N 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 109 GLN R 37 ASN ** S 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 7 ASN W 55 GLN ** W 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.7057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18942 Z= 0.188 Angle : 0.634 7.642 25656 Z= 0.338 Chirality : 0.043 0.189 2754 Planarity : 0.003 0.040 3444 Dihedral : 5.905 40.211 2664 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 6.37 % Allowed : 22.94 % Favored : 70.70 % 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: -1.02 (0.16), residues: 2310 helix: 1.37 (0.17), residues: 912 sheet: -2.23 (0.66), residues: 60 loop : -2.24 (0.15), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP R 59 PHE 0.024 0.002 PHE P 150 TYR 0.017 0.001 TYR M 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 569 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 441 time to evaluate : 2.278 Fit side-chains REVERT: M 157 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8272 (tm-30) REVERT: M 163 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7551 (mt-10) REVERT: M 165 ASP cc_start: 0.8110 (OUTLIER) cc_final: 0.7864 (t0) REVERT: M 172 MET cc_start: 0.8512 (mmm) cc_final: 0.6853 (ptt) REVERT: M 184 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8801 (pp) REVERT: N 21 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9046 (mt) REVERT: N 42 ASN cc_start: 0.8100 (t0) cc_final: 0.7734 (t0) REVERT: N 68 THR cc_start: 0.8877 (t) cc_final: 0.8669 (p) REVERT: N 87 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.9089 (tm) REVERT: N 113 PHE cc_start: 0.9043 (OUTLIER) cc_final: 0.8608 (p90) REVERT: N 130 MET cc_start: 0.8593 (mmm) cc_final: 0.8207 (mtp) REVERT: N 145 GLN cc_start: 0.7816 (mt0) cc_final: 0.7557 (mt0) REVERT: N 172 MET cc_start: 0.8265 (tpp) cc_final: 0.7942 (mmm) REVERT: N 175 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7649 (tt0) REVERT: O 112 ARG cc_start: 0.7243 (mtt180) cc_final: 0.6862 (mtt-85) REVERT: O 145 GLN cc_start: 0.7705 (mt0) cc_final: 0.7388 (mt0) REVERT: O 172 MET cc_start: 0.8779 (mmm) cc_final: 0.8433 (tpp) REVERT: P 172 MET cc_start: 0.8270 (tpp) cc_final: 0.6787 (ptt) REVERT: P 184 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8768 (pp) REVERT: Q 5 ASP cc_start: 0.8469 (m-30) cc_final: 0.8260 (m-30) REVERT: Q 109 GLN cc_start: 0.8072 (mm-40) cc_final: 0.7860 (mp10) REVERT: Q 176 MET cc_start: 0.8192 (mmm) cc_final: 0.7510 (ptm) REVERT: Q 184 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8707 (pp) REVERT: R 39 ASP cc_start: 0.7777 (m-30) cc_final: 0.7494 (m-30) REVERT: R 172 MET cc_start: 0.8001 (tpp) cc_final: 0.6816 (ptt) REVERT: S 14 LEU cc_start: 0.9093 (tt) cc_final: 0.8890 (tp) REVERT: S 172 MET cc_start: 0.8629 (mmm) cc_final: 0.7453 (ptt) REVERT: T 75 SER cc_start: 0.7691 (OUTLIER) cc_final: 0.7178 (m) REVERT: T 88 MET cc_start: 0.8331 (mtt) cc_final: 0.8060 (mtt) REVERT: T 95 ILE cc_start: 0.9136 (OUTLIER) cc_final: 0.8835 (mt) REVERT: T 187 ASP cc_start: 0.5276 (p0) cc_final: 0.4934 (m-30) REVERT: U 53 GLN cc_start: 0.9150 (tp40) cc_final: 0.8574 (tm-30) REVERT: U 184 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8741 (pp) REVERT: V 21 LEU cc_start: 0.9516 (OUTLIER) cc_final: 0.9258 (mm) REVERT: V 172 MET cc_start: 0.8314 (tpp) cc_final: 0.6902 (ptt) REVERT: V 184 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8502 (pp) REVERT: V 194 LEU cc_start: 0.8926 (mp) cc_final: 0.8459 (mp) REVERT: W 75 SER cc_start: 0.8596 (OUTLIER) cc_final: 0.8182 (p) REVERT: W 169 ARG cc_start: 0.8173 (ttp-110) cc_final: 0.7032 (tpp-160) REVERT: X 164 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8164 (tm-30) REVERT: X 172 MET cc_start: 0.8451 (tpp) cc_final: 0.7146 (ptt) outliers start: 128 outliers final: 87 residues processed: 533 average time/residue: 0.2661 time to fit residues: 228.1939 Evaluate side-chains 516 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 414 time to evaluate : 2.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain M residue 59 TRP Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 126 ASP 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 8 VAL Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 23 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 126 ASP 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 O residue 17 VAL 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 126 ASP Chi-restraints excluded: chain O residue 170 LEU Chi-restraints excluded: chain O residue 190 THR Chi-restraints excluded: chain P residue 4 TYR 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 56 SER Chi-restraints excluded: chain P residue 59 TRP Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 126 ASP Chi-restraints excluded: chain P residue 161 GLN Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain P residue 191 SER Chi-restraints excluded: chain Q residue 24 ILE Chi-restraints excluded: chain Q residue 77 LEU Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 126 ASP Chi-restraints excluded: chain Q residue 184 LEU 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 126 ASP 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 63 ILE Chi-restraints excluded: chain S residue 87 LEU Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 126 ASP 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 60 THR Chi-restraints excluded: chain T residue 75 SER Chi-restraints excluded: chain T residue 95 ILE Chi-restraints excluded: chain T residue 126 ASP Chi-restraints excluded: chain T residue 184 LEU Chi-restraints excluded: chain U residue 23 SER Chi-restraints excluded: chain U residue 50 ILE Chi-restraints excluded: chain U residue 59 TRP Chi-restraints excluded: chain U residue 87 LEU Chi-restraints excluded: chain U residue 170 LEU Chi-restraints excluded: chain U residue 184 LEU Chi-restraints excluded: chain V residue 10 THR Chi-restraints excluded: chain V residue 21 LEU Chi-restraints excluded: chain V residue 23 SER Chi-restraints excluded: chain V residue 59 TRP Chi-restraints excluded: chain V residue 87 LEU Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain V residue 126 ASP Chi-restraints excluded: chain V residue 184 LEU Chi-restraints excluded: chain V residue 190 THR 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 90 THR Chi-restraints excluded: chain W residue 126 ASP Chi-restraints excluded: chain W residue 143 SER Chi-restraints excluded: chain W residue 191 SER Chi-restraints excluded: chain X residue 5 ASP 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 68 THR Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 108 SER Chi-restraints excluded: chain X residue 126 ASP Chi-restraints excluded: chain X residue 164 GLU Chi-restraints excluded: chain X residue 184 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 125 optimal weight: 0.7980 chunk 161 optimal weight: 0.2980 chunk 124 optimal weight: 0.6980 chunk 185 optimal weight: 0.9990 chunk 123 optimal weight: 0.6980 chunk 219 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 101 optimal weight: 0.1980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 55 GLN ** P 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 145 GLN R 37 ASN ** S 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 109 GLN U 145 GLN ** U 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 55 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.7217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18942 Z= 0.213 Angle : 0.641 7.744 25656 Z= 0.342 Chirality : 0.043 0.189 2754 Planarity : 0.003 0.032 3444 Dihedral : 5.822 39.674 2664 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 6.52 % Allowed : 23.73 % Favored : 69.75 % 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: -0.80 (0.17), residues: 2310 helix: 1.56 (0.16), residues: 936 sheet: -2.39 (0.64), residues: 60 loop : -2.16 (0.15), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP U 137 PHE 0.024 0.002 PHE P 150 TYR 0.019 0.001 TYR M 136 ARG 0.005 0.000 ARG T 168 *********************** 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 554 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 423 time to evaluate : 1.925 Fit side-chains REVERT: M 157 GLU cc_start: 0.8672 (tm-30) cc_final: 0.8358 (tm-30) REVERT: M 163 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7636 (mt-10) REVERT: M 172 MET cc_start: 0.8494 (mmm) cc_final: 0.6866 (ptt) REVERT: M 184 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8813 (pp) REVERT: N 21 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9078 (mt) REVERT: N 42 ASN cc_start: 0.8157 (t0) cc_final: 0.7830 (t0) REVERT: N 87 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9121 (tm) REVERT: N 113 PHE cc_start: 0.9053 (OUTLIER) cc_final: 0.8624 (p90) REVERT: N 130 MET cc_start: 0.8570 (mmm) cc_final: 0.8199 (mtp) REVERT: N 145 GLN cc_start: 0.7822 (mt0) cc_final: 0.7542 (mt0) REVERT: N 175 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7691 (tt0) REVERT: O 136 TYR cc_start: 0.9195 (t80) cc_final: 0.8736 (t80) REVERT: O 145 GLN cc_start: 0.7946 (mt0) cc_final: 0.7733 (mt0) REVERT: O 172 MET cc_start: 0.8791 (mmm) cc_final: 0.8456 (tpp) REVERT: P 172 MET cc_start: 0.8307 (tpp) cc_final: 0.6804 (ptt) REVERT: P 184 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.8807 (pp) REVERT: Q 176 MET cc_start: 0.8230 (mmm) cc_final: 0.7629 (ptm) REVERT: Q 184 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8768 (pp) REVERT: R 39 ASP cc_start: 0.8272 (m-30) cc_final: 0.7645 (m-30) REVERT: R 172 MET cc_start: 0.8009 (tpp) cc_final: 0.6115 (ptt) REVERT: S 14 LEU cc_start: 0.9131 (tt) cc_final: 0.8911 (tp) REVERT: S 172 MET cc_start: 0.8628 (mmm) cc_final: 0.7445 (ptt) REVERT: T 75 SER cc_start: 0.7751 (OUTLIER) cc_final: 0.7286 (m) REVERT: T 88 MET cc_start: 0.8419 (mtt) cc_final: 0.8130 (mtt) REVERT: T 95 ILE cc_start: 0.9157 (mt) cc_final: 0.8876 (mt) REVERT: T 168 ARG cc_start: 0.8303 (ttt90) cc_final: 0.7999 (tpt-90) REVERT: T 187 ASP cc_start: 0.5332 (p0) cc_final: 0.5011 (m-30) REVERT: U 53 GLN cc_start: 0.9199 (tp40) cc_final: 0.8526 (tm-30) REVERT: U 172 MET cc_start: 0.8700 (tpp) cc_final: 0.7274 (ptt) REVERT: U 184 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.8540 (pp) REVERT: V 21 LEU cc_start: 0.9499 (OUTLIER) cc_final: 0.9154 (mm) REVERT: V 172 MET cc_start: 0.8294 (tpp) cc_final: 0.6842 (ptt) REVERT: V 184 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.8618 (pp) REVERT: V 194 LEU cc_start: 0.8953 (mp) cc_final: 0.8520 (mp) REVERT: W 75 SER cc_start: 0.8565 (OUTLIER) cc_final: 0.8137 (p) REVERT: W 169 ARG cc_start: 0.8248 (ttp-110) cc_final: 0.7062 (tpp-160) REVERT: X 164 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8145 (tm-30) REVERT: X 172 MET cc_start: 0.8452 (tpp) cc_final: 0.7129 (ptt) outliers start: 131 outliers final: 101 residues processed: 519 average time/residue: 0.2676 time to fit residues: 223.1200 Evaluate side-chains 518 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 404 time to evaluate : 2.287 ------------------------------------------------------------------------------- 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 59 TRP Chi-restraints excluded: chain M residue 87 LEU Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 126 ASP 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 21 LEU Chi-restraints excluded: chain N residue 23 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 126 ASP 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 O residue 17 VAL Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 26 GLU Chi-restraints excluded: chain O residue 50 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 126 ASP Chi-restraints excluded: chain O residue 170 LEU Chi-restraints excluded: chain O residue 190 THR 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 24 ILE Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 78 ILE Chi-restraints excluded: chain P residue 126 ASP Chi-restraints excluded: chain P residue 161 GLN Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain P residue 191 SER Chi-restraints excluded: chain Q residue 24 ILE Chi-restraints excluded: chain Q residue 77 LEU Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 126 ASP 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 37 ASN Chi-restraints excluded: chain R residue 56 SER Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 126 ASP 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 63 ILE Chi-restraints excluded: chain S residue 87 LEU Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 126 ASP Chi-restraints excluded: chain S residue 170 LEU Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 59 TRP Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 67 ILE Chi-restraints excluded: chain T residue 75 SER Chi-restraints excluded: chain T residue 126 ASP Chi-restraints excluded: chain T residue 184 LEU Chi-restraints excluded: chain U residue 23 SER Chi-restraints excluded: chain U residue 50 ILE 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 162 GLU Chi-restraints excluded: chain U residue 170 LEU Chi-restraints excluded: chain U residue 184 LEU Chi-restraints excluded: chain V residue 10 THR Chi-restraints excluded: chain V residue 21 LEU Chi-restraints excluded: chain V residue 23 SER Chi-restraints excluded: chain V residue 59 TRP Chi-restraints excluded: chain V residue 87 LEU Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain V residue 126 ASP Chi-restraints excluded: chain V residue 184 LEU Chi-restraints excluded: chain V residue 190 THR Chi-restraints excluded: chain W residue 5 ASP 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 5 ASP 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 77 LEU Chi-restraints excluded: chain X residue 108 SER Chi-restraints excluded: chain X residue 126 ASP Chi-restraints excluded: chain X residue 164 GLU Chi-restraints excluded: chain X residue 184 LEU Chi-restraints excluded: chain X residue 190 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 139 optimal weight: 0.9990 chunk 149 optimal weight: 0.7980 chunk 108 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 172 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 93 GLN ** N 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 55 GLN ** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 48 ASN ** P 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 93 GLN R 37 ASN ** S 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 145 GLN ** U 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 42 ASN ** W 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.7370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18942 Z= 0.248 Angle : 0.653 7.620 25656 Z= 0.350 Chirality : 0.044 0.191 2754 Planarity : 0.003 0.030 3444 Dihedral : 5.890 40.631 2664 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 6.57 % Allowed : 24.63 % Favored : 68.81 % 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: -0.74 (0.17), residues: 2310 helix: 1.66 (0.16), residues: 936 sheet: -2.60 (0.63), residues: 60 loop : -2.15 (0.15), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP U 137 PHE 0.026 0.002 PHE P 150 TYR 0.021 0.001 TYR M 136 ARG 0.008 0.000 ARG N 168 *********************** 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 534 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 402 time to evaluate : 2.300 Fit side-chains REVERT: M 53 GLN cc_start: 0.8833 (tp-100) cc_final: 0.8103 (tm-30) REVERT: M 157 GLU cc_start: 0.8740 (tm-30) cc_final: 0.8474 (tm-30) REVERT: M 161 GLN cc_start: 0.8504 (tm-30) cc_final: 0.8090 (tm-30) REVERT: M 172 MET cc_start: 0.8485 (mmm) cc_final: 0.6888 (ptt) REVERT: M 184 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8848 (pp) REVERT: N 21 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.9165 (mt) REVERT: N 42 ASN cc_start: 0.8283 (t0) cc_final: 0.7983 (t0) REVERT: N 87 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9066 (tm) REVERT: N 113 PHE cc_start: 0.9062 (OUTLIER) cc_final: 0.8658 (p90) REVERT: O 145 GLN cc_start: 0.7865 (mt0) cc_final: 0.7624 (mt0) REVERT: O 172 MET cc_start: 0.8797 (mmm) cc_final: 0.8425 (tpp) REVERT: P 172 MET cc_start: 0.8401 (tpp) cc_final: 0.7044 (ptt) REVERT: P 184 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.8833 (pp) REVERT: Q 176 MET cc_start: 0.8197 (mmm) cc_final: 0.7727 (ptm) REVERT: Q 184 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8790 (pp) REVERT: R 172 MET cc_start: 0.7732 (tpp) cc_final: 0.6540 (ptt) REVERT: S 172 MET cc_start: 0.8637 (mmm) cc_final: 0.7509 (ptt) REVERT: T 75 SER cc_start: 0.7770 (OUTLIER) cc_final: 0.7467 (m) REVERT: T 88 MET cc_start: 0.8466 (mtt) cc_final: 0.8176 (mtt) REVERT: T 95 ILE cc_start: 0.9191 (mt) cc_final: 0.8908 (mt) REVERT: T 187 ASP cc_start: 0.5727 (p0) cc_final: 0.5394 (m-30) REVERT: U 53 GLN cc_start: 0.9156 (tp40) cc_final: 0.8441 (tm-30) REVERT: U 194 LEU cc_start: 0.9051 (mt) cc_final: 0.8845 (mp) REVERT: V 21 LEU cc_start: 0.9468 (OUTLIER) cc_final: 0.9162 (mm) REVERT: V 172 MET cc_start: 0.8371 (tpp) cc_final: 0.7135 (ptt) REVERT: V 184 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.8653 (pp) REVERT: V 194 LEU cc_start: 0.8916 (mp) cc_final: 0.8517 (mp) REVERT: W 75 SER cc_start: 0.8584 (OUTLIER) cc_final: 0.8129 (p) REVERT: W 169 ARG cc_start: 0.8379 (ttp-110) cc_final: 0.7013 (tpp-160) REVERT: W 172 MET cc_start: 0.8776 (mmm) cc_final: 0.8469 (tpp) REVERT: X 164 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8118 (tm-30) REVERT: X 172 MET cc_start: 0.8383 (tpp) cc_final: 0.7154 (ptt) outliers start: 132 outliers final: 106 residues processed: 500 average time/residue: 0.2500 time to fit residues: 202.1901 Evaluate side-chains 503 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 386 time to evaluate : 2.083 ------------------------------------------------------------------------------- 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 73 VAL Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 126 ASP 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 21 LEU Chi-restraints excluded: chain N residue 23 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 126 ASP Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain N residue 191 SER Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 26 GLU Chi-restraints excluded: chain O residue 50 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 126 ASP Chi-restraints excluded: chain O residue 170 LEU Chi-restraints excluded: chain O residue 190 THR 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 24 ILE Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 126 ASP Chi-restraints excluded: chain P residue 161 GLN Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain P residue 191 SER Chi-restraints excluded: chain Q residue 24 ILE Chi-restraints excluded: chain Q residue 77 LEU Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 126 ASP 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 56 SER Chi-restraints excluded: chain R residue 67 ILE Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 126 ASP 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 63 ILE Chi-restraints excluded: chain S residue 87 LEU Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 126 ASP Chi-restraints excluded: chain S residue 170 LEU Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 59 TRP Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 75 SER Chi-restraints excluded: chain T residue 126 ASP Chi-restraints excluded: chain T residue 184 LEU Chi-restraints excluded: chain U residue 10 THR 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 114 ASP Chi-restraints excluded: chain U residue 162 GLU Chi-restraints excluded: chain U residue 170 LEU Chi-restraints excluded: chain U residue 191 SER Chi-restraints excluded: chain V residue 10 THR Chi-restraints excluded: chain V residue 21 LEU Chi-restraints excluded: chain V residue 23 SER 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 126 ASP Chi-restraints excluded: chain V residue 184 LEU Chi-restraints excluded: chain V residue 190 THR 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 126 ASP Chi-restraints excluded: chain W residue 143 SER Chi-restraints excluded: chain W residue 191 SER Chi-restraints excluded: chain X residue 8 VAL 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 68 THR Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 108 SER Chi-restraints excluded: chain X residue 117 ILE Chi-restraints excluded: chain X residue 126 ASP Chi-restraints excluded: chain X residue 161 GLN Chi-restraints excluded: chain X residue 164 GLU Chi-restraints excluded: chain X residue 184 LEU Chi-restraints excluded: chain X residue 190 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 2.9990 chunk 210 optimal weight: 0.4980 chunk 192 optimal weight: 0.0670 chunk 204 optimal weight: 0.4980 chunk 123 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 160 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 185 optimal weight: 0.5980 chunk 193 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 48 ASN ** N 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 109 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.7542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18942 Z= 0.200 Angle : 0.638 7.872 25656 Z= 0.340 Chirality : 0.043 0.240 2754 Planarity : 0.003 0.034 3444 Dihedral : 5.742 39.598 2664 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 5.67 % Allowed : 25.57 % Favored : 68.76 % 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: -0.58 (0.17), residues: 2310 helix: 1.85 (0.16), residues: 924 sheet: -2.79 (0.63), residues: 60 loop : -2.07 (0.15), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP U 59 PHE 0.023 0.002 PHE P 150 TYR 0.017 0.001 TYR M 136 ARG 0.007 0.000 ARG N 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 528 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 414 time to evaluate : 2.251 Fit side-chains REVERT: M 53 GLN cc_start: 0.8766 (tp-100) cc_final: 0.8195 (tm-30) REVERT: M 157 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8378 (tm-30) REVERT: M 163 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7627 (mt-10) REVERT: M 172 MET cc_start: 0.8481 (mmm) cc_final: 0.6820 (ptt) REVERT: M 184 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8810 (pp) REVERT: N 21 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9054 (mt) REVERT: N 42 ASN cc_start: 0.8228 (t0) cc_final: 0.7886 (t0) REVERT: N 87 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9026 (tm) REVERT: N 113 PHE cc_start: 0.8999 (OUTLIER) cc_final: 0.8539 (p90) REVERT: N 130 MET cc_start: 0.8695 (mmm) cc_final: 0.8371 (mtp) REVERT: N 147 ASN cc_start: 0.8803 (t160) cc_final: 0.8585 (t0) REVERT: O 145 GLN cc_start: 0.7914 (mt0) cc_final: 0.7683 (mt0) REVERT: O 172 MET cc_start: 0.8787 (mmm) cc_final: 0.8436 (tpp) REVERT: P 172 MET cc_start: 0.8303 (tpp) cc_final: 0.6675 (ptt) REVERT: P 184 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.8798 (pp) REVERT: Q 176 MET cc_start: 0.8071 (mmm) cc_final: 0.7580 (ptm) REVERT: Q 184 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8866 (pp) REVERT: R 39 ASP cc_start: 0.8463 (m-30) cc_final: 0.7739 (m-30) REVERT: R 172 MET cc_start: 0.7724 (tpp) cc_final: 0.6477 (ptt) REVERT: S 172 MET cc_start: 0.8623 (mmm) cc_final: 0.7471 (ptt) REVERT: T 75 SER cc_start: 0.7721 (OUTLIER) cc_final: 0.7477 (m) REVERT: T 88 MET cc_start: 0.8414 (mtt) cc_final: 0.8129 (mtt) REVERT: T 95 ILE cc_start: 0.9192 (mt) cc_final: 0.8923 (mt) REVERT: T 172 MET cc_start: 0.8291 (mmm) cc_final: 0.6551 (ptm) REVERT: T 187 ASP cc_start: 0.5392 (p0) cc_final: 0.5089 (m-30) REVERT: U 53 GLN cc_start: 0.9079 (tp40) cc_final: 0.8482 (tm-30) REVERT: U 112 ARG cc_start: 0.7801 (mtt90) cc_final: 0.7538 (mtp85) REVERT: U 172 MET cc_start: 0.8622 (tpp) cc_final: 0.7090 (ptt) REVERT: U 183 MET cc_start: 0.8044 (ttm) cc_final: 0.7084 (pmm) REVERT: V 21 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9153 (mm) REVERT: V 157 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7714 (tm-30) REVERT: V 172 MET cc_start: 0.8342 (tpp) cc_final: 0.7158 (ptt) REVERT: V 184 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.8592 (pp) REVERT: V 194 LEU cc_start: 0.8925 (mp) cc_final: 0.8487 (mp) REVERT: W 75 SER cc_start: 0.8567 (OUTLIER) cc_final: 0.8163 (p) REVERT: W 169 ARG cc_start: 0.8339 (ttp-110) cc_final: 0.6946 (tpp-160) REVERT: W 183 MET cc_start: 0.8054 (ttm) cc_final: 0.7128 (pmm) REVERT: X 172 MET cc_start: 0.8368 (tpp) cc_final: 0.6935 (ptt) outliers start: 114 outliers final: 93 residues processed: 500 average time/residue: 0.2512 time to fit residues: 203.3431 Evaluate side-chains 492 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 389 time to evaluate : 2.295 ------------------------------------------------------------------------------- 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 73 VAL Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 126 ASP Chi-restraints excluded: chain M residue 160 LEU 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 21 LEU Chi-restraints excluded: chain N residue 23 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 126 ASP Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain N residue 191 SER Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 26 GLU Chi-restraints excluded: chain O residue 50 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 126 ASP Chi-restraints excluded: chain O residue 170 LEU Chi-restraints excluded: chain O residue 190 THR 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 31 THR Chi-restraints excluded: chain P residue 59 TRP Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 126 ASP Chi-restraints excluded: chain P residue 161 GLN Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain P residue 191 SER Chi-restraints excluded: chain Q residue 24 ILE Chi-restraints excluded: chain Q residue 77 LEU Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 126 ASP Chi-restraints excluded: chain Q residue 184 LEU Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 31 THR Chi-restraints excluded: chain R residue 56 SER 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 126 ASP 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 63 ILE Chi-restraints excluded: chain S residue 87 LEU Chi-restraints excluded: chain S residue 126 ASP Chi-restraints excluded: chain S residue 170 LEU Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 59 TRP Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 75 SER Chi-restraints excluded: chain T residue 126 ASP 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 170 LEU Chi-restraints excluded: chain V residue 10 THR Chi-restraints excluded: chain V residue 21 LEU Chi-restraints excluded: chain V residue 23 SER 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 126 ASP 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 126 ASP Chi-restraints excluded: chain W residue 143 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 108 SER Chi-restraints excluded: chain X residue 126 ASP Chi-restraints excluded: chain X residue 184 LEU Chi-restraints excluded: chain X residue 190 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 0.2980 chunk 132 optimal weight: 0.3980 chunk 102 optimal weight: 0.5980 chunk 150 optimal weight: 0.9980 chunk 227 optimal weight: 0.0770 chunk 209 optimal weight: 0.8980 chunk 180 optimal weight: 1.9990 chunk 18 optimal weight: 0.0050 chunk 139 optimal weight: 0.0270 chunk 110 optimal weight: 0.6980 chunk 143 optimal weight: 2.9990 overall best weight: 0.1610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 53 GLN M 62 ASN N 48 ASN ** N 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 147 ASN ** P 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 53 GLN ** R 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 62 ASN ** U 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 147 ASN ** X 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.7787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18942 Z= 0.161 Angle : 0.628 7.675 25656 Z= 0.334 Chirality : 0.042 0.256 2754 Planarity : 0.003 0.034 3444 Dihedral : 5.464 37.760 2664 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 4.28 % Allowed : 27.36 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.80 % Twisted Proline : 0.00 % Twisted General : 0.53 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.17), residues: 2310 helix: 2.07 (0.17), residues: 924 sheet: -2.85 (0.63), residues: 60 loop : -2.00 (0.15), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 59 PHE 0.019 0.002 PHE W 189 TYR 0.017 0.001 TYR Q 80 ARG 0.008 0.000 ARG U 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 540 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 454 time to evaluate : 2.547 Fit side-chains REVERT: M 157 GLU cc_start: 0.8656 (tm-30) cc_final: 0.8370 (tm-30) REVERT: M 172 MET cc_start: 0.8495 (mmm) cc_final: 0.6808 (ptt) REVERT: M 184 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8884 (pp) REVERT: N 39 ASP cc_start: 0.6813 (m-30) cc_final: 0.6571 (m-30) REVERT: N 113 PHE cc_start: 0.8973 (OUTLIER) cc_final: 0.8560 (p90) REVERT: N 130 MET cc_start: 0.8621 (mmm) cc_final: 0.8261 (mtp) REVERT: O 145 GLN cc_start: 0.7904 (mt0) cc_final: 0.7644 (mt0) REVERT: O 172 MET cc_start: 0.8667 (mmm) cc_final: 0.8377 (tpp) REVERT: P 6 MET cc_start: 0.9003 (tpp) cc_final: 0.8787 (tpt) REVERT: P 62 ASN cc_start: 0.8691 (t0) cc_final: 0.8451 (t0) REVERT: P 77 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8873 (pp) REVERT: P 172 MET cc_start: 0.8251 (tpp) cc_final: 0.6749 (ptt) REVERT: P 184 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8702 (pp) REVERT: Q 172 MET cc_start: 0.8276 (mmm) cc_final: 0.6778 (ptm) REVERT: Q 176 MET cc_start: 0.7903 (mmm) cc_final: 0.7592 (ptm) REVERT: Q 184 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8767 (pp) REVERT: R 79 VAL cc_start: 0.9262 (p) cc_final: 0.8891 (m) REVERT: R 172 MET cc_start: 0.7517 (tpp) cc_final: 0.6416 (ptt) REVERT: S 62 ASN cc_start: 0.8802 (t0) cc_final: 0.8541 (t0) REVERT: S 172 MET cc_start: 0.8482 (mmm) cc_final: 0.7128 (ptt) REVERT: T 75 SER cc_start: 0.7690 (OUTLIER) cc_final: 0.7440 (m) REVERT: T 88 MET cc_start: 0.8383 (mtt) cc_final: 0.8099 (mtt) REVERT: T 95 ILE cc_start: 0.9129 (mt) cc_final: 0.8817 (mt) REVERT: T 172 MET cc_start: 0.8260 (mmm) cc_final: 0.6517 (ptm) REVERT: T 187 ASP cc_start: 0.5295 (p0) cc_final: 0.5024 (m-30) REVERT: U 53 GLN cc_start: 0.8950 (tp40) cc_final: 0.8488 (tm-30) REVERT: U 109 GLN cc_start: 0.8171 (mp10) cc_final: 0.7735 (mp10) REVERT: U 112 ARG cc_start: 0.7779 (mtt90) cc_final: 0.7453 (mtt180) REVERT: U 172 MET cc_start: 0.8600 (tpp) cc_final: 0.6809 (ptt) REVERT: U 183 MET cc_start: 0.7906 (ttm) cc_final: 0.7094 (pmm) REVERT: V 21 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9188 (mm) REVERT: V 157 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7716 (tm-30) REVERT: V 172 MET cc_start: 0.8188 (tpp) cc_final: 0.6702 (ptt) REVERT: V 184 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8569 (pp) REVERT: V 194 LEU cc_start: 0.8882 (mp) cc_final: 0.8461 (mp) REVERT: W 62 ASN cc_start: 0.8861 (t0) cc_final: 0.8582 (t0) REVERT: W 75 SER cc_start: 0.8488 (OUTLIER) cc_final: 0.8139 (p) REVERT: W 161 GLN cc_start: 0.8122 (tm-30) cc_final: 0.7517 (tm-30) REVERT: W 169 ARG cc_start: 0.8178 (ttp-110) cc_final: 0.6871 (tpp-160) REVERT: W 176 MET cc_start: 0.8305 (mpp) cc_final: 0.8023 (mmt) REVERT: W 183 MET cc_start: 0.8073 (ttm) cc_final: 0.7013 (pmm) REVERT: X 172 MET cc_start: 0.8447 (tpp) cc_final: 0.7079 (ptt) outliers start: 86 outliers final: 58 residues processed: 516 average time/residue: 0.2645 time to fit residues: 218.4642 Evaluate side-chains 481 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 414 time to evaluate : 2.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain M residue 59 TRP Chi-restraints excluded: chain M residue 126 ASP Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain N residue 5 ASP Chi-restraints excluded: chain N residue 23 SER 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 126 ASP Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain N residue 191 SER 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 170 LEU Chi-restraints excluded: chain P residue 4 TYR Chi-restraints excluded: chain P residue 19 ASP 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 126 ASP Chi-restraints excluded: chain P residue 161 GLN Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain Q residue 24 ILE Chi-restraints excluded: chain Q residue 77 LEU Chi-restraints excluded: chain Q residue 184 LEU Chi-restraints excluded: chain R residue 56 SER Chi-restraints excluded: chain R residue 59 TRP Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain R residue 126 ASP 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 78 ILE Chi-restraints excluded: chain S residue 87 LEU Chi-restraints excluded: chain S residue 112 ARG Chi-restraints excluded: chain T residue 59 TRP Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 75 SER Chi-restraints excluded: chain T residue 126 ASP 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 87 LEU Chi-restraints excluded: chain U residue 90 THR Chi-restraints excluded: chain U residue 170 LEU Chi-restraints excluded: chain V residue 10 THR Chi-restraints excluded: chain V residue 21 LEU Chi-restraints excluded: chain V residue 59 TRP Chi-restraints excluded: chain V residue 87 LEU Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain V residue 126 ASP 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 87 LEU Chi-restraints excluded: chain X residue 59 TRP Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 108 SER Chi-restraints excluded: chain X residue 126 ASP Chi-restraints excluded: chain X residue 190 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 166 optimal weight: 0.7980 chunk 26 optimal weight: 0.0070 chunk 50 optimal weight: 0.0270 chunk 181 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 chunk 186 optimal weight: 0.0000 chunk 22 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 159 optimal weight: 0.3980 overall best weight: 0.2060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 53 GLN ** P 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN ** R 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 42 ASN ** S 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 55 GLN ** T 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 109 GLN W 55 GLN ** W 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.108566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.099130 restraints weight = 34715.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.101553 restraints weight = 16931.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.103131 restraints weight = 9991.550| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3217 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| r_final: 0.3196 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.7899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18942 Z= 0.167 Angle : 0.635 7.496 25656 Z= 0.337 Chirality : 0.042 0.256 2754 Planarity : 0.003 0.035 3444 Dihedral : 5.357 37.182 2664 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 3.53 % Allowed : 28.31 % Favored : 68.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.80 % Twisted Proline : 0.00 % Twisted General : 0.53 % 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: -0.30 (0.17), residues: 2310 helix: 2.16 (0.16), residues: 924 sheet: None (None), residues: 0 loop : -2.02 (0.15), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP U 59 PHE 0.024 0.002 PHE O 146 TYR 0.018 0.001 TYR X 96 ARG 0.007 0.000 ARG V 168 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4718.67 seconds wall clock time: 86 minutes 16.47 seconds (5176.47 seconds total)