Starting phenix.real_space_refine (version: 1.21rc1) on Mon Oct 9 08:57:44 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7box_30135/10_2023/7box_30135.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7box_30135/10_2023/7box_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_30135/10_2023/7box_30135.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7box_30135/10_2023/7box_30135.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7box_30135/10_2023/7box_30135.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7box_30135/10_2023/7box_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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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: 9.45, per 1000 atoms: 0.51 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: 7.39 Conformation dependent library (CDL) restraints added in 3.0 seconds 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4332 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 24 sheets defined 42.9% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 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: 4.51 Time building geometry restraints manager: 8.02 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: 2.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 9.760 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 46.910 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.670 ------------------------------------------------------------------------------- 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 *********************** 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 : 2.321 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 1065 average time/residue: 0.3089 time to fit residues: 486.9880 Evaluate side-chains 496 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 496 time to evaluate : 2.273 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8907 ------------------------------------------------------------------------------- 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: 0.6980 chunk 207 optimal weight: 0.3980 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 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 62 ASN ** 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 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 147 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.4824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18942 Z= 0.236 Angle : 0.794 11.284 25656 Z= 0.429 Chirality : 0.047 0.232 2754 Planarity : 0.004 0.043 3444 Dihedral : 7.637 45.459 2664 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 4.83 % Allowed : 20.80 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.80 % Twisted Proline : 0.00 % Twisted General : 0.84 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.14), residues: 2310 helix: -1.16 (0.15), residues: 894 sheet: -2.48 (0.41), residues: 144 loop : -2.72 (0.13), residues: 1272 *********************** 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 653 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 556 time to evaluate : 2.131 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 97 outliers final: 40 residues processed: 619 average time/residue: 0.2576 time to fit residues: 252.6815 Evaluate side-chains 435 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 395 time to evaluate : 2.158 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.1662 time to fit residues: 15.2499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 0.6980 chunk 64 optimal weight: 0.0970 chunk 172 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 57 optimal weight: 0.0570 chunk 207 optimal weight: 1.9990 chunk 224 optimal weight: 0.7980 chunk 184 optimal weight: 0.6980 chunk 205 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 166 optimal weight: 0.9990 overall best weight: 0.4696 ------------------------------------------------------------------------------- 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 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 48 ASN ** O 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 42 ASN Q 48 ASN Q 55 GLN ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 48 ASN S 55 GLN ** S 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 161 GLN U 53 GLN ** 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 42 ASN W 48 ASN W 53 GLN W 55 GLN ** W 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.5753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18942 Z= 0.220 Angle : 0.701 8.626 25656 Z= 0.378 Chirality : 0.045 0.211 2754 Planarity : 0.004 0.040 3444 Dihedral : 6.753 42.114 2664 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 3.83 % Allowed : 22.44 % Favored : 73.73 % 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: -2.17 (0.15), residues: 2310 helix: -0.01 (0.16), residues: 924 sheet: -2.23 (0.44), residues: 144 loop : -2.58 (0.14), residues: 1242 *********************** 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 554 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 477 time to evaluate : 2.391 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 34 residues processed: 530 average time/residue: 0.2702 time to fit residues: 228.5017 Evaluate side-chains 425 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 391 time to evaluate : 2.559 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.2005 time to fit residues: 16.0141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 0.3980 chunk 155 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 98 optimal weight: 0.0170 chunk 139 optimal weight: 0.4980 chunk 208 optimal weight: 0.0270 chunk 220 optimal weight: 0.0470 chunk 108 optimal weight: 0.0000 chunk 197 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 overall best weight: 0.0978 ------------------------------------------------------------------------------- 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 ** N 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 48 ASN ** O 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 48 ASN ** Q 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 55 GLN ** U 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 48 ASN ** W 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8125 moved from start: 0.6282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 18942 Z= 0.156 Angle : 0.652 9.370 25656 Z= 0.349 Chirality : 0.043 0.195 2754 Planarity : 0.003 0.029 3444 Dihedral : 6.101 38.695 2664 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 3.33 % Allowed : 22.59 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.80 % Twisted Proline : 0.00 % Twisted General : 0.62 % 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: -1.55 (0.16), residues: 2310 helix: 0.79 (0.17), residues: 906 sheet: -2.16 (0.43), residues: 144 loop : -2.40 (0.15), residues: 1260 *********************** 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 524 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 457 time to evaluate : 2.352 Fit side-chains revert: symmetry clash outliers start: 67 outliers final: 32 residues processed: 500 average time/residue: 0.2711 time to fit residues: 215.5865 Evaluate side-chains 417 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 385 time to evaluate : 2.276 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.1985 time to fit residues: 14.9825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 0.6980 chunk 125 optimal weight: 0.2980 chunk 3 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 188 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 112 optimal weight: 0.4980 chunk 197 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 109 GLN ** N 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 7 ASN ** O 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 18 ASN ** P 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 55 GLN ** Q 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 48 ASN ** U 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 55 GLN ** X 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 55 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.6632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18942 Z= 0.226 Angle : 0.651 7.393 25656 Z= 0.351 Chirality : 0.044 0.188 2754 Planarity : 0.003 0.030 3444 Dihedral : 5.965 38.209 2664 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 3.33 % Allowed : 23.53 % Favored : 73.13 % 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: -1.32 (0.16), residues: 2310 helix: 1.02 (0.16), residues: 918 sheet: -2.14 (0.66), residues: 60 loop : -2.35 (0.14), residues: 1332 *********************** 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 472 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 405 time to evaluate : 2.213 Fit side-chains outliers start: 67 outliers final: 23 residues processed: 446 average time/residue: 0.2527 time to fit residues: 181.9545 Evaluate side-chains 374 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 351 time to evaluate : 2.389 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1980 time to fit residues: 10.8494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 43 optimal weight: 0.5980 chunk 129 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 220 optimal weight: 0.9980 chunk 183 optimal weight: 0.6980 chunk 102 optimal weight: 0.0040 chunk 18 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 115 optimal weight: 0.7980 overall best weight: 0.5592 ------------------------------------------------------------------------------- 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 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 ASN S 145 GLN ** S 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 148 ASN ** W 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 161 GLN ** X 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.6957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18942 Z= 0.221 Angle : 0.649 8.318 25656 Z= 0.346 Chirality : 0.044 0.189 2754 Planarity : 0.003 0.036 3444 Dihedral : 5.867 38.687 2664 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 2.54 % Allowed : 24.93 % Favored : 72.54 % 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: -1.16 (0.16), residues: 2310 helix: 1.20 (0.16), residues: 918 sheet: -2.36 (0.63), residues: 60 loop : -2.28 (0.14), residues: 1332 *********************** 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 459 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 408 time to evaluate : 2.190 Fit side-chains outliers start: 51 outliers final: 28 residues processed: 439 average time/residue: 0.2567 time to fit residues: 182.2707 Evaluate side-chains 415 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 387 time to evaluate : 2.189 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.1723 time to fit residues: 11.7926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 chunk 125 optimal weight: 0.9980 chunk 161 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 185 optimal weight: 0.6980 chunk 123 optimal weight: 0.8980 chunk 219 optimal weight: 2.9990 chunk 137 optimal weight: 0.6980 chunk 133 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 55 GLN ** S 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.7236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 18942 Z= 0.271 Angle : 0.671 7.870 25656 Z= 0.358 Chirality : 0.044 0.190 2754 Planarity : 0.003 0.034 3444 Dihedral : 5.987 43.109 2664 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.92 % Favored : 92.03 % Rotamer: Outliers : 2.04 % Allowed : 26.27 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.80 % Twisted Proline : 0.00 % Twisted General : 0.84 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.16), residues: 2310 helix: 1.24 (0.16), residues: 918 sheet: -2.56 (0.62), residues: 60 loop : -2.26 (0.14), residues: 1332 *********************** 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 443 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 402 time to evaluate : 2.083 Fit side-chains outliers start: 41 outliers final: 24 residues processed: 423 average time/residue: 0.2597 time to fit residues: 175.2819 Evaluate side-chains 392 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 368 time to evaluate : 2.137 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1709 time to fit residues: 10.5556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 139 optimal weight: 0.5980 chunk 149 optimal weight: 0.8980 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 109 GLN ** M 148 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 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 148 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 145 GLN ** U 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 109 GLN ** V 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 148 ASN ** X 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.7437 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= 0.253 Angle : 0.660 7.730 25656 Z= 0.353 Chirality : 0.044 0.191 2754 Planarity : 0.003 0.027 3444 Dihedral : 5.961 41.465 2664 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 1.79 % Allowed : 26.52 % Favored : 71.69 % 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: -1.04 (0.16), residues: 2310 helix: 1.32 (0.16), residues: 918 sheet: -2.76 (0.60), residues: 60 loop : -2.19 (0.15), residues: 1332 *********************** 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 426 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 390 time to evaluate : 2.144 Fit side-chains outliers start: 36 outliers final: 22 residues processed: 413 average time/residue: 0.2567 time to fit residues: 170.3326 Evaluate side-chains 385 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 363 time to evaluate : 2.180 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1693 time to fit residues: 9.9984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 0.1980 chunk 210 optimal weight: 0.7980 chunk 192 optimal weight: 0.1980 chunk 204 optimal weight: 0.5980 chunk 123 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 160 optimal weight: 0.2980 chunk 62 optimal weight: 0.2980 chunk 185 optimal weight: 0.1980 chunk 193 optimal weight: 0.8980 chunk 134 optimal weight: 0.6980 overall best weight: 0.2380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 42 ASN ** N 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 109 GLN ** R 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 148 ASN T 145 GLN ** 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 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 147 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.7675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18942 Z= 0.168 Angle : 0.627 7.618 25656 Z= 0.335 Chirality : 0.043 0.266 2754 Planarity : 0.003 0.026 3444 Dihedral : 5.646 40.269 2664 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 0.85 % Allowed : 27.46 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.80 % Twisted Proline : 0.00 % Twisted General : 0.66 % 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: -0.75 (0.17), residues: 2310 helix: 1.67 (0.17), residues: 912 sheet: -2.95 (0.60), residues: 60 loop : -2.09 (0.15), residues: 1338 *********************** 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 441 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 424 time to evaluate : 2.114 Fit side-chains outliers start: 17 outliers final: 11 residues processed: 436 average time/residue: 0.2609 time to fit residues: 181.5433 Evaluate side-chains 395 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 384 time to evaluate : 2.279 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1869 time to fit residues: 6.7011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 chunk 150 optimal weight: 0.4980 chunk 227 optimal weight: 0.0470 chunk 209 optimal weight: 1.9990 chunk 180 optimal weight: 0.0970 chunk 18 optimal weight: 0.0000 chunk 139 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 143 optimal weight: 0.4980 overall best weight: 0.2280 ------------------------------------------------------------------------------- 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 48 ASN N 53 GLN ** N 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 145 GLN ** O 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 182 ASN P 55 GLN ** Q 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 53 GLN R 145 GLN ** R 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 42 ASN T 145 GLN ** T 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 93 GLN ** 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 148 ASN ** X 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.7793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18942 Z= 0.174 Angle : 0.637 7.568 25656 Z= 0.340 Chirality : 0.042 0.184 2754 Planarity : 0.003 0.030 3444 Dihedral : 5.529 39.335 2664 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 0.50 % Allowed : 28.26 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.80 % Twisted Proline : 0.00 % Twisted General : 0.66 % 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: -0.69 (0.17), residues: 2310 helix: 1.76 (0.17), residues: 900 sheet: -3.02 (0.61), residues: 60 loop : -2.04 (0.15), residues: 1350 ********************** 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 422 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 412 time to evaluate : 2.171 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 418 average time/residue: 0.2574 time to fit residues: 172.8746 Evaluate side-chains 384 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 380 time to evaluate : 2.303 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1646 time to fit residues: 4.2307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 166 optimal weight: 0.6980 chunk 26 optimal weight: 0.0060 chunk 50 optimal weight: 0.5980 chunk 181 optimal weight: 0.0570 chunk 75 optimal weight: 0.9990 chunk 186 optimal weight: 0.1980 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 159 optimal weight: 1.9990 overall best weight: 0.2914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 145 GLN ** T 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 93 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 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 109 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.108873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.099549 restraints weight = 34768.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.101960 restraints weight = 16859.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.103549 restraints weight = 9921.303| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3224 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 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 = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 35 | |-----------------------------------------------------------------------------| r_final: 0.3204 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.7881 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= 0.177 Angle : 0.638 8.117 25656 Z= 0.340 Chirality : 0.042 0.181 2754 Planarity : 0.003 0.027 3444 Dihedral : 5.478 39.416 2664 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 0.45 % Allowed : 28.31 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.80 % Twisted Proline : 0.00 % Twisted General : 0.66 % 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: -0.63 (0.17), residues: 2310 helix: 1.83 (0.17), residues: 900 sheet: -3.10 (0.60), residues: 60 loop : -2.01 (0.15), residues: 1350 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4407.38 seconds wall clock time: 80 minutes 1.58 seconds (4801.58 seconds total)