Starting phenix.real_space_refine (version: 1.21rc1) on Wed Oct 18 01:09:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ufm_26477/10_2023/7ufm_26477_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ufm_26477/10_2023/7ufm_26477.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ufm_26477/10_2023/7ufm_26477.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ufm_26477/10_2023/7ufm_26477.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ufm_26477/10_2023/7ufm_26477_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ufm_26477/10_2023/7ufm_26477_updated.pdb" } resolution = 3.9 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= 0.002 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 114 5.49 5 S 154 5.16 5 C 22780 2.51 5 N 6304 2.21 5 O 7040 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 39": "OE1" <-> "OE2" Residue "A GLU 109": "OE1" <-> "OE2" Residue "A ARG 143": "NH1" <-> "NH2" Residue "A ARG 146": "NH1" <-> "NH2" Residue "A TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 220": "OE1" <-> "OE2" Residue "A GLU 266": "OE1" <-> "OE2" Residue "A GLU 293": "OE1" <-> "OE2" Residue "A GLU 296": "OE1" <-> "OE2" Residue "B GLU 39": "OE1" <-> "OE2" Residue "B GLU 109": "OE1" <-> "OE2" Residue "B ARG 143": "NH1" <-> "NH2" Residue "B ARG 146": "NH1" <-> "NH2" Residue "B TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 220": "OE1" <-> "OE2" Residue "B GLU 266": "OE1" <-> "OE2" Residue "B GLU 293": "OE1" <-> "OE2" Residue "B GLU 296": "OE1" <-> "OE2" Residue "C GLU 39": "OE1" <-> "OE2" Residue "C GLU 109": "OE1" <-> "OE2" Residue "C ARG 143": "NH1" <-> "NH2" Residue "C ARG 146": "NH1" <-> "NH2" Residue "C TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 220": "OE1" <-> "OE2" Residue "C GLU 266": "OE1" <-> "OE2" Residue "C GLU 293": "OE1" <-> "OE2" Residue "C GLU 296": "OE1" <-> "OE2" Residue "D GLU 39": "OE1" <-> "OE2" Residue "D GLU 109": "OE1" <-> "OE2" Residue "D ARG 143": "NH1" <-> "NH2" Residue "D ARG 146": "NH1" <-> "NH2" Residue "D TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 220": "OE1" <-> "OE2" Residue "D GLU 266": "OE1" <-> "OE2" Residue "D GLU 293": "OE1" <-> "OE2" Residue "D GLU 296": "OE1" <-> "OE2" Residue "E GLU 39": "OE1" <-> "OE2" Residue "E GLU 109": "OE1" <-> "OE2" Residue "E ARG 143": "NH1" <-> "NH2" Residue "E ARG 146": "NH1" <-> "NH2" Residue "E TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 220": "OE1" <-> "OE2" Residue "E GLU 266": "OE1" <-> "OE2" Residue "E GLU 293": "OE1" <-> "OE2" Residue "E GLU 296": "OE1" <-> "OE2" Residue "F GLU 39": "OE1" <-> "OE2" Residue "F GLU 109": "OE1" <-> "OE2" Residue "F ARG 143": "NH1" <-> "NH2" Residue "F ARG 146": "NH1" <-> "NH2" Residue "F TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 220": "OE1" <-> "OE2" Residue "F GLU 266": "OE1" <-> "OE2" Residue "F GLU 293": "OE1" <-> "OE2" Residue "F GLU 296": "OE1" <-> "OE2" Residue "G GLU 39": "OE1" <-> "OE2" Residue "G GLU 109": "OE1" <-> "OE2" Residue "G ARG 143": "NH1" <-> "NH2" Residue "G ARG 146": "NH1" <-> "NH2" Residue "G TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 220": "OE1" <-> "OE2" Residue "G GLU 266": "OE1" <-> "OE2" Residue "G GLU 293": "OE1" <-> "OE2" Residue "G GLU 296": "OE1" <-> "OE2" Residue "H GLU 39": "OE1" <-> "OE2" Residue "H GLU 109": "OE1" <-> "OE2" Residue "H ARG 143": "NH1" <-> "NH2" Residue "H ARG 146": "NH1" <-> "NH2" Residue "H TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 220": "OE1" <-> "OE2" Residue "H GLU 266": "OE1" <-> "OE2" Residue "H GLU 293": "OE1" <-> "OE2" Residue "H GLU 296": "OE1" <-> "OE2" Residue "I GLU 39": "OE1" <-> "OE2" Residue "I GLU 109": "OE1" <-> "OE2" Residue "I ARG 143": "NH1" <-> "NH2" Residue "I ARG 146": "NH1" <-> "NH2" Residue "I TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 220": "OE1" <-> "OE2" Residue "I GLU 266": "OE1" <-> "OE2" Residue "I GLU 293": "OE1" <-> "OE2" Residue "I GLU 296": "OE1" <-> "OE2" Residue "J GLU 39": "OE1" <-> "OE2" Residue "J GLU 109": "OE1" <-> "OE2" Residue "J ARG 143": "NH1" <-> "NH2" Residue "J ARG 146": "NH1" <-> "NH2" Residue "J TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 220": "OE1" <-> "OE2" Residue "J GLU 266": "OE1" <-> "OE2" Residue "J GLU 293": "OE1" <-> "OE2" Residue "J GLU 296": "OE1" <-> "OE2" Residue "K GLU 39": "OE1" <-> "OE2" Residue "K GLU 109": "OE1" <-> "OE2" Residue "K ARG 143": "NH1" <-> "NH2" Residue "K ARG 146": "NH1" <-> "NH2" Residue "K TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 220": "OE1" <-> "OE2" Residue "K GLU 266": "OE1" <-> "OE2" Residue "K GLU 293": "OE1" <-> "OE2" Residue "K GLU 296": "OE1" <-> "OE2" Residue "L GLU 39": "OE1" <-> "OE2" Residue "L GLU 109": "OE1" <-> "OE2" Residue "L ARG 143": "NH1" <-> "NH2" Residue "L ARG 146": "NH1" <-> "NH2" Residue "L TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 220": "OE1" <-> "OE2" Residue "L GLU 266": "OE1" <-> "OE2" Residue "L GLU 293": "OE1" <-> "OE2" Residue "L GLU 296": "OE1" <-> "OE2" Residue "M GLU 39": "OE1" <-> "OE2" Residue "M GLU 109": "OE1" <-> "OE2" Residue "M ARG 143": "NH1" <-> "NH2" Residue "M ARG 146": "NH1" <-> "NH2" Residue "M PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 220": "OE1" <-> "OE2" Residue "M GLU 266": "OE1" <-> "OE2" Residue "M GLU 293": "OE1" <-> "OE2" Residue "M GLU 296": "OE1" <-> "OE2" Residue "N GLU 39": "OE1" <-> "OE2" Residue "N GLU 109": "OE1" <-> "OE2" Residue "N ARG 143": "NH1" <-> "NH2" Residue "N ARG 146": "NH1" <-> "NH2" Residue "N TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 220": "OE1" <-> "OE2" Residue "N GLU 266": "OE1" <-> "OE2" Residue "N GLU 293": "OE1" <-> "OE2" Residue "N GLU 296": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 36392 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2463 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 16, 'TRANS': 294} Chain: "B" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2463 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 16, 'TRANS': 294} Chain: "C" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2463 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 16, 'TRANS': 294} Chain: "D" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2463 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 16, 'TRANS': 294} Chain: "E" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2463 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 16, 'TRANS': 294} Chain: "F" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2463 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 16, 'TRANS': 294} Chain: "G" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2463 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 16, 'TRANS': 294} Chain: "H" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2463 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 16, 'TRANS': 294} Chain: "I" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2463 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 16, 'TRANS': 294} Chain: "J" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2463 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 16, 'TRANS': 294} Chain: "K" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2463 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 16, 'TRANS': 294} Chain: "L" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2463 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 16, 'TRANS': 294} Chain: "M" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2463 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 16, 'TRANS': 294} Chain: "N" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2463 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 16, 'TRANS': 294} Chain: "O" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 737 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain: "P" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 739 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain breaks: 2 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 19.31, per 1000 atoms: 0.53 Number of scatterers: 36392 At special positions: 0 Unit cell: (147.882, 167.499, 155.427, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 154 16.00 P 114 15.00 O 7040 8.00 N 6304 7.00 C 22780 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: 15.24 Conformation dependent library (CDL) restraints added in 5.0 seconds 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8204 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 196 helices and 14 sheets defined 44.1% alpha, 2.6% beta 33 base pairs and 63 stacking pairs defined. Time for finding SS restraints: 12.48 Creating SS restraints... Processing helix chain 'A' and resid 6 through 13 Processing helix chain 'A' and resid 20 through 33 Processing helix chain 'A' and resid 55 through 73 removed outlier: 7.001A pdb=" N ALA A 69 " --> pdb=" O GLN A 65 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ALA A 70 " --> pdb=" O ALA A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 100 Processing helix chain 'A' and resid 114 through 122 Processing helix chain 'A' and resid 137 through 139 No H-bonds generated for 'chain 'A' and resid 137 through 139' Processing helix chain 'A' and resid 150 through 161 Processing helix chain 'A' and resid 172 through 178 removed outlier: 3.900A pdb=" N LYS A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL A 176 " --> pdb=" O TYR A 173 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A 177 " --> pdb=" O SER A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 187 Processing helix chain 'A' and resid 205 through 216 Processing helix chain 'A' and resid 230 through 237 Processing helix chain 'A' and resid 242 through 258 removed outlier: 3.590A pdb=" N GLU A 255 " --> pdb=" O GLN A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 275 Processing helix chain 'A' and resid 296 through 299 Processing helix chain 'B' and resid 6 through 13 Processing helix chain 'B' and resid 20 through 33 Processing helix chain 'B' and resid 55 through 73 removed outlier: 7.002A pdb=" N ALA B 69 " --> pdb=" O GLN B 65 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ALA B 70 " --> pdb=" O ALA B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 100 Processing helix chain 'B' and resid 114 through 122 Processing helix chain 'B' and resid 137 through 139 No H-bonds generated for 'chain 'B' and resid 137 through 139' Processing helix chain 'B' and resid 150 through 161 Processing helix chain 'B' and resid 172 through 178 removed outlier: 3.898A pdb=" N LYS B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL B 176 " --> pdb=" O TYR B 173 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL B 177 " --> pdb=" O SER B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'B' and resid 205 through 216 Processing helix chain 'B' and resid 230 through 237 Processing helix chain 'B' and resid 242 through 258 removed outlier: 3.590A pdb=" N GLU B 255 " --> pdb=" O GLN B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 275 Processing helix chain 'B' and resid 296 through 299 Processing helix chain 'C' and resid 6 through 13 Processing helix chain 'C' and resid 20 through 33 Processing helix chain 'C' and resid 55 through 73 removed outlier: 7.001A pdb=" N ALA C 69 " --> pdb=" O GLN C 65 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ALA C 70 " --> pdb=" O ALA C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 100 Processing helix chain 'C' and resid 114 through 122 Processing helix chain 'C' and resid 137 through 139 No H-bonds generated for 'chain 'C' and resid 137 through 139' Processing helix chain 'C' and resid 150 through 161 Processing helix chain 'C' and resid 172 through 178 removed outlier: 3.899A pdb=" N LYS C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL C 176 " --> pdb=" O TYR C 173 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL C 177 " --> pdb=" O SER C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 205 through 216 Processing helix chain 'C' and resid 230 through 237 Processing helix chain 'C' and resid 242 through 258 removed outlier: 3.590A pdb=" N GLU C 255 " --> pdb=" O GLN C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 275 Processing helix chain 'C' and resid 296 through 299 Processing helix chain 'D' and resid 6 through 13 Processing helix chain 'D' and resid 20 through 33 Processing helix chain 'D' and resid 55 through 73 removed outlier: 7.001A pdb=" N ALA D 69 " --> pdb=" O GLN D 65 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ALA D 70 " --> pdb=" O ALA D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 100 Processing helix chain 'D' and resid 114 through 122 Processing helix chain 'D' and resid 137 through 139 No H-bonds generated for 'chain 'D' and resid 137 through 139' Processing helix chain 'D' and resid 150 through 161 Processing helix chain 'D' and resid 172 through 178 removed outlier: 3.899A pdb=" N LYS D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL D 176 " --> pdb=" O TYR D 173 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL D 177 " --> pdb=" O SER D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 187 Processing helix chain 'D' and resid 205 through 216 Processing helix chain 'D' and resid 230 through 237 Processing helix chain 'D' and resid 242 through 258 removed outlier: 3.590A pdb=" N GLU D 255 " --> pdb=" O GLN D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 275 Processing helix chain 'D' and resid 296 through 299 Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 20 through 33 Processing helix chain 'E' and resid 55 through 73 removed outlier: 7.001A pdb=" N ALA E 69 " --> pdb=" O GLN E 65 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ALA E 70 " --> pdb=" O ALA E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 100 Processing helix chain 'E' and resid 114 through 122 Processing helix chain 'E' and resid 137 through 139 No H-bonds generated for 'chain 'E' and resid 137 through 139' Processing helix chain 'E' and resid 150 through 161 Processing helix chain 'E' and resid 172 through 178 removed outlier: 3.899A pdb=" N LYS E 175 " --> pdb=" O PRO E 172 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL E 176 " --> pdb=" O TYR E 173 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL E 177 " --> pdb=" O SER E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 187 Processing helix chain 'E' and resid 205 through 216 Processing helix chain 'E' and resid 230 through 237 Processing helix chain 'E' and resid 242 through 258 removed outlier: 3.590A pdb=" N GLU E 255 " --> pdb=" O GLN E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 275 Processing helix chain 'E' and resid 296 through 299 Processing helix chain 'F' and resid 6 through 13 Processing helix chain 'F' and resid 20 through 33 Processing helix chain 'F' and resid 55 through 73 removed outlier: 7.001A pdb=" N ALA F 69 " --> pdb=" O GLN F 65 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ALA F 70 " --> pdb=" O ALA F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 100 Processing helix chain 'F' and resid 114 through 122 Processing helix chain 'F' and resid 137 through 139 No H-bonds generated for 'chain 'F' and resid 137 through 139' Processing helix chain 'F' and resid 150 through 161 Processing helix chain 'F' and resid 172 through 178 removed outlier: 3.898A pdb=" N LYS F 175 " --> pdb=" O PRO F 172 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL F 176 " --> pdb=" O TYR F 173 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL F 177 " --> pdb=" O SER F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 187 Processing helix chain 'F' and resid 205 through 216 Processing helix chain 'F' and resid 230 through 237 Processing helix chain 'F' and resid 242 through 258 removed outlier: 3.590A pdb=" N GLU F 255 " --> pdb=" O GLN F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 275 Processing helix chain 'F' and resid 296 through 299 Processing helix chain 'G' and resid 6 through 13 Processing helix chain 'G' and resid 20 through 33 Processing helix chain 'G' and resid 55 through 73 removed outlier: 7.001A pdb=" N ALA G 69 " --> pdb=" O GLN G 65 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ALA G 70 " --> pdb=" O ALA G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 100 Processing helix chain 'G' and resid 114 through 122 Processing helix chain 'G' and resid 137 through 139 No H-bonds generated for 'chain 'G' and resid 137 through 139' Processing helix chain 'G' and resid 150 through 161 Processing helix chain 'G' and resid 172 through 178 removed outlier: 3.899A pdb=" N LYS G 175 " --> pdb=" O PRO G 172 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL G 176 " --> pdb=" O TYR G 173 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL G 177 " --> pdb=" O SER G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 182 through 187 Processing helix chain 'G' and resid 205 through 216 Processing helix chain 'G' and resid 230 through 237 Processing helix chain 'G' and resid 242 through 258 removed outlier: 3.590A pdb=" N GLU G 255 " --> pdb=" O GLN G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 275 Processing helix chain 'G' and resid 296 through 299 Processing helix chain 'H' and resid 6 through 13 Processing helix chain 'H' and resid 20 through 33 Processing helix chain 'H' and resid 55 through 73 removed outlier: 7.001A pdb=" N ALA H 69 " --> pdb=" O GLN H 65 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ALA H 70 " --> pdb=" O ALA H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 100 Processing helix chain 'H' and resid 114 through 122 Processing helix chain 'H' and resid 137 through 139 No H-bonds generated for 'chain 'H' and resid 137 through 139' Processing helix chain 'H' and resid 150 through 161 Processing helix chain 'H' and resid 172 through 178 removed outlier: 3.899A pdb=" N LYS H 175 " --> pdb=" O PRO H 172 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL H 176 " --> pdb=" O TYR H 173 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL H 177 " --> pdb=" O SER H 174 " (cutoff:3.500A) Processing helix chain 'H' and resid 182 through 187 Processing helix chain 'H' and resid 205 through 216 Processing helix chain 'H' and resid 230 through 237 Processing helix chain 'H' and resid 242 through 258 removed outlier: 3.590A pdb=" N GLU H 255 " --> pdb=" O GLN H 251 " (cutoff:3.500A) Processing helix chain 'H' and resid 269 through 275 Processing helix chain 'H' and resid 296 through 299 Processing helix chain 'I' and resid 6 through 13 Processing helix chain 'I' and resid 20 through 33 Processing helix chain 'I' and resid 55 through 73 removed outlier: 7.002A pdb=" N ALA I 69 " --> pdb=" O GLN I 65 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ALA I 70 " --> pdb=" O ALA I 66 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 100 Processing helix chain 'I' and resid 114 through 122 Processing helix chain 'I' and resid 137 through 139 No H-bonds generated for 'chain 'I' and resid 137 through 139' Processing helix chain 'I' and resid 150 through 161 Processing helix chain 'I' and resid 172 through 178 removed outlier: 3.898A pdb=" N LYS I 175 " --> pdb=" O PRO I 172 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL I 176 " --> pdb=" O TYR I 173 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL I 177 " --> pdb=" O SER I 174 " (cutoff:3.500A) Processing helix chain 'I' and resid 182 through 187 Processing helix chain 'I' and resid 205 through 216 Processing helix chain 'I' and resid 230 through 237 Processing helix chain 'I' and resid 242 through 258 removed outlier: 3.590A pdb=" N GLU I 255 " --> pdb=" O GLN I 251 " (cutoff:3.500A) Processing helix chain 'I' and resid 269 through 275 Processing helix chain 'I' and resid 296 through 299 Processing helix chain 'J' and resid 6 through 13 Processing helix chain 'J' and resid 20 through 33 Processing helix chain 'J' and resid 55 through 73 removed outlier: 7.001A pdb=" N ALA J 69 " --> pdb=" O GLN J 65 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ALA J 70 " --> pdb=" O ALA J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 90 through 100 Processing helix chain 'J' and resid 114 through 122 Processing helix chain 'J' and resid 137 through 139 No H-bonds generated for 'chain 'J' and resid 137 through 139' Processing helix chain 'J' and resid 150 through 161 Processing helix chain 'J' and resid 172 through 178 removed outlier: 3.899A pdb=" N LYS J 175 " --> pdb=" O PRO J 172 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL J 176 " --> pdb=" O TYR J 173 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL J 177 " --> pdb=" O SER J 174 " (cutoff:3.500A) Processing helix chain 'J' and resid 182 through 187 Processing helix chain 'J' and resid 205 through 216 Processing helix chain 'J' and resid 230 through 237 Processing helix chain 'J' and resid 242 through 258 removed outlier: 3.589A pdb=" N GLU J 255 " --> pdb=" O GLN J 251 " (cutoff:3.500A) Processing helix chain 'J' and resid 269 through 275 Processing helix chain 'J' and resid 296 through 299 Processing helix chain 'K' and resid 6 through 13 Processing helix chain 'K' and resid 20 through 33 Processing helix chain 'K' and resid 55 through 73 removed outlier: 7.001A pdb=" N ALA K 69 " --> pdb=" O GLN K 65 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ALA K 70 " --> pdb=" O ALA K 66 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 100 Processing helix chain 'K' and resid 114 through 122 Processing helix chain 'K' and resid 137 through 139 No H-bonds generated for 'chain 'K' and resid 137 through 139' Processing helix chain 'K' and resid 150 through 161 Processing helix chain 'K' and resid 172 through 178 removed outlier: 3.899A pdb=" N LYS K 175 " --> pdb=" O PRO K 172 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL K 176 " --> pdb=" O TYR K 173 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL K 177 " --> pdb=" O SER K 174 " (cutoff:3.500A) Processing helix chain 'K' and resid 182 through 187 Processing helix chain 'K' and resid 205 through 216 Processing helix chain 'K' and resid 230 through 237 Processing helix chain 'K' and resid 242 through 258 removed outlier: 3.590A pdb=" N GLU K 255 " --> pdb=" O GLN K 251 " (cutoff:3.500A) Processing helix chain 'K' and resid 269 through 275 Processing helix chain 'K' and resid 296 through 299 Processing helix chain 'L' and resid 6 through 13 Processing helix chain 'L' and resid 20 through 33 Processing helix chain 'L' and resid 55 through 73 removed outlier: 7.001A pdb=" N ALA L 69 " --> pdb=" O GLN L 65 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ALA L 70 " --> pdb=" O ALA L 66 " (cutoff:3.500A) Processing helix chain 'L' and resid 90 through 100 Processing helix chain 'L' and resid 114 through 122 Processing helix chain 'L' and resid 137 through 139 No H-bonds generated for 'chain 'L' and resid 137 through 139' Processing helix chain 'L' and resid 150 through 161 Processing helix chain 'L' and resid 172 through 178 removed outlier: 3.899A pdb=" N LYS L 175 " --> pdb=" O PRO L 172 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL L 176 " --> pdb=" O TYR L 173 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL L 177 " --> pdb=" O SER L 174 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 187 Processing helix chain 'L' and resid 205 through 216 Processing helix chain 'L' and resid 230 through 237 Processing helix chain 'L' and resid 242 through 258 removed outlier: 3.590A pdb=" N GLU L 255 " --> pdb=" O GLN L 251 " (cutoff:3.500A) Processing helix chain 'L' and resid 269 through 275 Processing helix chain 'L' and resid 296 through 299 Processing helix chain 'M' and resid 6 through 13 Processing helix chain 'M' and resid 20 through 33 Processing helix chain 'M' and resid 55 through 73 removed outlier: 7.001A pdb=" N ALA M 69 " --> pdb=" O GLN M 65 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ALA M 70 " --> pdb=" O ALA M 66 " (cutoff:3.500A) Processing helix chain 'M' and resid 90 through 100 Processing helix chain 'M' and resid 114 through 122 Processing helix chain 'M' and resid 137 through 139 No H-bonds generated for 'chain 'M' and resid 137 through 139' Processing helix chain 'M' and resid 150 through 161 Processing helix chain 'M' and resid 172 through 178 removed outlier: 3.899A pdb=" N LYS M 175 " --> pdb=" O PRO M 172 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL M 176 " --> pdb=" O TYR M 173 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL M 177 " --> pdb=" O SER M 174 " (cutoff:3.500A) Processing helix chain 'M' and resid 182 through 187 Processing helix chain 'M' and resid 205 through 216 Processing helix chain 'M' and resid 230 through 237 Processing helix chain 'M' and resid 242 through 258 removed outlier: 3.589A pdb=" N GLU M 255 " --> pdb=" O GLN M 251 " (cutoff:3.500A) Processing helix chain 'M' and resid 269 through 275 Processing helix chain 'M' and resid 296 through 299 Processing helix chain 'N' and resid 6 through 13 Processing helix chain 'N' and resid 20 through 33 Processing helix chain 'N' and resid 55 through 73 removed outlier: 7.002A pdb=" N ALA N 69 " --> pdb=" O GLN N 65 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ALA N 70 " --> pdb=" O ALA N 66 " (cutoff:3.500A) Processing helix chain 'N' and resid 90 through 100 Processing helix chain 'N' and resid 114 through 122 Processing helix chain 'N' and resid 137 through 139 No H-bonds generated for 'chain 'N' and resid 137 through 139' Processing helix chain 'N' and resid 150 through 161 Processing helix chain 'N' and resid 172 through 178 removed outlier: 3.899A pdb=" N LYS N 175 " --> pdb=" O PRO N 172 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL N 176 " --> pdb=" O TYR N 173 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL N 177 " --> pdb=" O SER N 174 " (cutoff:3.500A) Processing helix chain 'N' and resid 182 through 187 Processing helix chain 'N' and resid 205 through 216 Processing helix chain 'N' and resid 230 through 237 Processing helix chain 'N' and resid 242 through 258 removed outlier: 3.590A pdb=" N GLU N 255 " --> pdb=" O GLN N 251 " (cutoff:3.500A) Processing helix chain 'N' and resid 269 through 275 Processing helix chain 'N' and resid 296 through 299 Processing sheet with id= A, first strand: chain 'A' and resid 79 through 82 removed outlier: 7.006A pdb=" N LEU A 130 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ILE A 82 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE A 132 " --> pdb=" O ILE A 82 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 79 through 82 removed outlier: 7.007A pdb=" N LEU B 130 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N ILE B 82 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE B 132 " --> pdb=" O ILE B 82 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 79 through 82 removed outlier: 7.005A pdb=" N LEU C 130 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N ILE C 82 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE C 132 " --> pdb=" O ILE C 82 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 79 through 82 removed outlier: 7.007A pdb=" N LEU D 130 " --> pdb=" O LEU D 80 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N ILE D 82 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE D 132 " --> pdb=" O ILE D 82 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 79 through 82 removed outlier: 7.007A pdb=" N LEU E 130 " --> pdb=" O LEU E 80 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N ILE E 82 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE E 132 " --> pdb=" O ILE E 82 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 79 through 82 removed outlier: 7.006A pdb=" N LEU F 130 " --> pdb=" O LEU F 80 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N ILE F 82 " --> pdb=" O LEU F 130 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE F 132 " --> pdb=" O ILE F 82 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'G' and resid 79 through 82 removed outlier: 7.006A pdb=" N LEU G 130 " --> pdb=" O LEU G 80 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N ILE G 82 " --> pdb=" O LEU G 130 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE G 132 " --> pdb=" O ILE G 82 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'H' and resid 79 through 82 removed outlier: 7.007A pdb=" N LEU H 130 " --> pdb=" O LEU H 80 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N ILE H 82 " --> pdb=" O LEU H 130 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE H 132 " --> pdb=" O ILE H 82 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'I' and resid 79 through 82 removed outlier: 7.006A pdb=" N LEU I 130 " --> pdb=" O LEU I 80 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N ILE I 82 " --> pdb=" O LEU I 130 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE I 132 " --> pdb=" O ILE I 82 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'J' and resid 79 through 82 removed outlier: 7.006A pdb=" N LEU J 130 " --> pdb=" O LEU J 80 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N ILE J 82 " --> pdb=" O LEU J 130 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE J 132 " --> pdb=" O ILE J 82 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'K' and resid 79 through 82 removed outlier: 7.006A pdb=" N LEU K 130 " --> pdb=" O LEU K 80 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N ILE K 82 " --> pdb=" O LEU K 130 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE K 132 " --> pdb=" O ILE K 82 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'L' and resid 79 through 82 removed outlier: 7.007A pdb=" N LEU L 130 " --> pdb=" O LEU L 80 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N ILE L 82 " --> pdb=" O LEU L 130 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE L 132 " --> pdb=" O ILE L 82 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'M' and resid 79 through 82 removed outlier: 7.006A pdb=" N LEU M 130 " --> pdb=" O LEU M 80 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N ILE M 82 " --> pdb=" O LEU M 130 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE M 132 " --> pdb=" O ILE M 82 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'N' and resid 79 through 82 removed outlier: 7.006A pdb=" N LEU N 130 " --> pdb=" O LEU N 80 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N ILE N 82 " --> pdb=" O LEU N 130 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE N 132 " --> pdb=" O ILE N 82 " (cutoff:3.500A) 1120 hydrogen bonds defined for protein. 3276 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 81 hydrogen bonds 162 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 63 stacking parallelities Total time for adding SS restraints: 10.34 Time building geometry restraints manager: 16.24 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: 9609 1.33 - 1.45: 6905 1.45 - 1.57: 20110 1.57 - 1.69: 378 1.69 - 1.81: 266 Bond restraints: 37268 Sorted by residual: bond pdb=" C4 ATP A 401 " pdb=" C5 ATP A 401 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.21e+01 bond pdb=" C4 ATP H 401 " pdb=" C5 ATP H 401 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.19e+01 bond pdb=" C4 ATP I 401 " pdb=" C5 ATP I 401 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.17e+01 bond pdb=" C4 ATP G 401 " pdb=" C5 ATP G 401 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.14e+01 bond pdb=" C4 ATP J 401 " pdb=" C5 ATP J 401 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.14e+01 ... (remaining 37263 not shown) Histogram of bond angle deviations from ideal: 98.45 - 105.90: 1568 105.90 - 113.35: 19435 113.35 - 120.80: 17960 120.80 - 128.25: 11431 128.25 - 135.70: 404 Bond angle restraints: 50798 Sorted by residual: angle pdb=" PB ATP A 401 " pdb=" O3B ATP A 401 " pdb=" PG ATP A 401 " ideal model delta sigma weight residual 139.87 118.01 21.86 1.00e+00 1.00e+00 4.78e+02 angle pdb=" PB ATP M 401 " pdb=" O3B ATP M 401 " pdb=" PG ATP M 401 " ideal model delta sigma weight residual 139.87 118.01 21.86 1.00e+00 1.00e+00 4.78e+02 angle pdb=" PB ATP L 401 " pdb=" O3B ATP L 401 " pdb=" PG ATP L 401 " ideal model delta sigma weight residual 139.87 118.03 21.84 1.00e+00 1.00e+00 4.77e+02 angle pdb=" PB ATP K 401 " pdb=" O3B ATP K 401 " pdb=" PG ATP K 401 " ideal model delta sigma weight residual 139.87 118.03 21.84 1.00e+00 1.00e+00 4.77e+02 angle pdb=" PB ATP H 401 " pdb=" O3B ATP H 401 " pdb=" PG ATP H 401 " ideal model delta sigma weight residual 139.87 118.04 21.83 1.00e+00 1.00e+00 4.76e+02 ... (remaining 50793 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.12: 18050 18.12 - 36.24: 2384 36.24 - 54.36: 1552 54.36 - 72.48: 252 72.48 - 90.60: 114 Dihedral angle restraints: 22352 sinusoidal: 9668 harmonic: 12684 Sorted by residual: dihedral pdb=" CA LEU D 105 " pdb=" C LEU D 105 " pdb=" N ALA D 106 " pdb=" CA ALA D 106 " ideal model delta harmonic sigma weight residual 180.00 141.71 38.29 0 5.00e+00 4.00e-02 5.86e+01 dihedral pdb=" CA LEU G 105 " pdb=" C LEU G 105 " pdb=" N ALA G 106 " pdb=" CA ALA G 106 " ideal model delta harmonic sigma weight residual 180.00 141.74 38.26 0 5.00e+00 4.00e-02 5.86e+01 dihedral pdb=" CA LEU F 105 " pdb=" C LEU F 105 " pdb=" N ALA F 106 " pdb=" CA ALA F 106 " ideal model delta harmonic sigma weight residual 180.00 141.76 38.24 0 5.00e+00 4.00e-02 5.85e+01 ... (remaining 22349 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 5190 0.122 - 0.245: 444 0.245 - 0.367: 2 0.367 - 0.489: 28 0.489 - 0.612: 14 Chirality restraints: 5678 Sorted by residual: chirality pdb=" CB ILE L 77 " pdb=" CA ILE L 77 " pdb=" CG1 ILE L 77 " pdb=" CG2 ILE L 77 " both_signs ideal model delta sigma weight residual False 2.64 2.03 0.61 2.00e-01 2.50e+01 9.35e+00 chirality pdb=" CB ILE M 77 " pdb=" CA ILE M 77 " pdb=" CG1 ILE M 77 " pdb=" CG2 ILE M 77 " both_signs ideal model delta sigma weight residual False 2.64 2.04 0.61 2.00e-01 2.50e+01 9.29e+00 chirality pdb=" CB ILE I 77 " pdb=" CA ILE I 77 " pdb=" CG1 ILE I 77 " pdb=" CG2 ILE I 77 " both_signs ideal model delta sigma weight residual False 2.64 2.04 0.61 2.00e-01 2.50e+01 9.26e+00 ... (remaining 5675 not shown) Planarity restraints: 6232 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE K 206 " 0.029 2.00e-02 2.50e+03 2.56e-02 1.15e+01 pdb=" CG PHE K 206 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 PHE K 206 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE K 206 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE K 206 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE K 206 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE K 206 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 206 " 0.029 2.00e-02 2.50e+03 2.55e-02 1.14e+01 pdb=" CG PHE D 206 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 PHE D 206 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE D 206 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE D 206 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 206 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE D 206 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE L 206 " 0.029 2.00e-02 2.50e+03 2.55e-02 1.14e+01 pdb=" CG PHE L 206 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 PHE L 206 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE L 206 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE L 206 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE L 206 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE L 206 " 0.006 2.00e-02 2.50e+03 ... (remaining 6229 not shown) Histogram of nonbonded interaction distances: 1.08 - 1.84: 7 1.84 - 2.61: 604 2.61 - 3.37: 46781 3.37 - 4.14: 90419 4.14 - 4.90: 154094 Nonbonded interactions: 291905 Sorted by model distance: nonbonded pdb=" OE1 GLN E 200 " pdb=" CD1 LEU E 299 " model vdw 1.075 3.460 nonbonded pdb=" NE2 GLN C 200 " pdb=" CB LEU C 299 " model vdw 1.349 3.520 nonbonded pdb=" NE2 GLN H 200 " pdb=" CD2 TYR H 235 " model vdw 1.398 3.420 nonbonded pdb=" NE2 GLN C 200 " pdb=" CD1 LEU C 299 " model vdw 1.604 3.540 nonbonded pdb=" NE2 GLN C 200 " pdb=" CG LEU C 299 " model vdw 1.652 3.550 ... (remaining 291900 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.450 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: 0.040 Extract box with map and model: 4.310 Check model and map are aligned: 0.540 Set scattering table: 0.320 Process input model: 95.220 Find NCS groups from input model: 2.610 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6545 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 : 0.009 0.082 37268 Z= 0.552 Angle : 1.769 21.862 50798 Z= 1.038 Chirality : 0.079 0.612 5678 Planarity : 0.009 0.058 6232 Dihedral : 22.533 90.602 14148 Min Nonbonded Distance : 1.075 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.05 % Favored : 88.95 % Rotamer: Outliers : 24.41 % Allowed : 17.56 % Favored : 58.02 % Cbeta Deviations : 0.34 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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: -4.66 (0.10), residues: 4326 helix: -3.36 (0.07), residues: 2324 sheet: -1.47 (0.30), residues: 406 loop : -2.80 (0.13), residues: 1596 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2468 residues out of total 3752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 916 poor density : 1552 time to evaluate : 4.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 916 outliers final: 369 residues processed: 2142 average time/residue: 0.5554 time to fit residues: 1824.2995 Evaluate side-chains 1701 residues out of total 3752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 369 poor density : 1332 time to evaluate : 3.827 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 369 outliers final: 4 residues processed: 369 average time/residue: 0.4372 time to fit residues: 276.4875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 371 optimal weight: 0.2980 chunk 333 optimal weight: 1.9990 chunk 185 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 chunk 224 optimal weight: 0.4980 chunk 178 optimal weight: 1.9990 chunk 344 optimal weight: 0.9990 chunk 133 optimal weight: 0.9990 chunk 209 optimal weight: 5.9990 chunk 256 optimal weight: 1.9990 chunk 399 optimal weight: 0.0010 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 GLN B 241 ASN C 222 GLN C 231 GLN ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 GLN E 87 ASN E 179 GLN E 185 HIS F 81 HIS ** F 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 251 GLN G 64 ASN G 185 HIS ** H 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 179 GLN ** H 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 185 HIS J 64 ASN J 160 ASN J 183 GLN J 227 ASN ** K 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 185 HIS L 65 GLN L 87 ASN ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 185 HIS N 231 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6600 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 37268 Z= 0.256 Angle : 0.881 11.511 50798 Z= 0.449 Chirality : 0.049 0.272 5678 Planarity : 0.006 0.079 6232 Dihedral : 14.771 89.503 5496 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 4.90 % Allowed : 27.96 % Favored : 67.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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: -3.29 (0.12), residues: 4326 helix: -1.91 (0.09), residues: 2268 sheet: -1.80 (0.27), residues: 476 loop : -2.48 (0.14), residues: 1582 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1563 residues out of total 3752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 1379 time to evaluate : 3.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 184 outliers final: 78 residues processed: 1468 average time/residue: 0.5542 time to fit residues: 1240.3736 Evaluate side-chains 1334 residues out of total 3752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 1256 time to evaluate : 3.792 Switching outliers to nearest non-outliers outliers start: 78 outliers final: 0 residues processed: 78 average time/residue: 0.3671 time to fit residues: 56.6628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 222 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 332 optimal weight: 0.0970 chunk 272 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 400 optimal weight: 0.8980 chunk 432 optimal weight: 0.0970 chunk 356 optimal weight: 0.8980 chunk 396 optimal weight: 5.9990 chunk 136 optimal weight: 0.9990 chunk 321 optimal weight: 3.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 GLN C 64 ASN C 81 HIS D 81 HIS ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 HIS E 179 GLN ** E 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 HIS E 286 ASN F 65 GLN F 153 ASN F 181 ASN ** F 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 ASN G 185 HIS ** H 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 231 GLN J 87 ASN J 160 ASN ** J 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 81 HIS ** K 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 191 GLN ** L 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 87 ASN ** L 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 179 GLN M 181 ASN ** M 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 251 GLN N 185 HIS ** N 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6621 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 37268 Z= 0.235 Angle : 0.833 13.724 50798 Z= 0.417 Chirality : 0.047 0.281 5678 Planarity : 0.006 0.099 6232 Dihedral : 14.326 89.925 5496 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 4.02 % Allowed : 30.22 % Favored : 65.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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: -2.68 (0.12), residues: 4326 helix: -1.32 (0.10), residues: 2282 sheet: -1.70 (0.27), residues: 476 loop : -2.28 (0.15), residues: 1568 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1450 residues out of total 3752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 1299 time to evaluate : 3.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 151 outliers final: 57 residues processed: 1375 average time/residue: 0.5657 time to fit residues: 1184.0018 Evaluate side-chains 1310 residues out of total 3752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 1253 time to evaluate : 3.970 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 0 residues processed: 57 average time/residue: 0.3568 time to fit residues: 42.2321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 395 optimal weight: 6.9990 chunk 300 optimal weight: 7.9990 chunk 207 optimal weight: 8.9990 chunk 44 optimal weight: 0.3980 chunk 191 optimal weight: 5.9990 chunk 268 optimal weight: 2.9990 chunk 401 optimal weight: 0.9980 chunk 425 optimal weight: 7.9990 chunk 209 optimal weight: 10.0000 chunk 380 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 GLN ** B 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 HIS ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 HIS F 81 HIS ** F 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 185 HIS ** F 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 179 GLN G 185 HIS ** H 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 87 ASN J 160 ASN ** J 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 ASN ** K 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 191 GLN ** L 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 183 GLN ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 81 HIS ** M 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 81 HIS N 185 HIS ** N 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 314 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 moved from start: 0.4864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 37268 Z= 0.312 Angle : 0.840 14.172 50798 Z= 0.427 Chirality : 0.049 0.299 5678 Planarity : 0.005 0.059 6232 Dihedral : 14.092 85.200 5496 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 21.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 3.76 % Allowed : 31.82 % Favored : 64.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -2.45 (0.12), residues: 4326 helix: -1.08 (0.10), residues: 2282 sheet: -1.89 (0.26), residues: 476 loop : -2.17 (0.15), residues: 1568 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1443 residues out of total 3752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 1302 time to evaluate : 3.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 141 outliers final: 64 residues processed: 1376 average time/residue: 0.5637 time to fit residues: 1173.2363 Evaluate side-chains 1329 residues out of total 3752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 1265 time to evaluate : 3.981 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 0 residues processed: 64 average time/residue: 0.3806 time to fit residues: 49.5568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 354 optimal weight: 0.5980 chunk 241 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 316 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 chunk 362 optimal weight: 2.9990 chunk 293 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 217 optimal weight: 20.0000 chunk 381 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 GLN ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 ASN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN E 185 HIS ** F 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 185 HIS ** H 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 64 ASN ** I 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 87 ASN J 160 ASN ** J 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 286 ASN ** L 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 179 GLN ** M 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 185 HIS ** N 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 231 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.5384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 37268 Z= 0.308 Angle : 0.857 15.106 50798 Z= 0.430 Chirality : 0.049 0.222 5678 Planarity : 0.005 0.067 6232 Dihedral : 14.128 88.575 5496 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 22.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 3.60 % Allowed : 33.93 % Favored : 62.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -2.46 (0.12), residues: 4326 helix: -1.09 (0.10), residues: 2282 sheet: -1.99 (0.26), residues: 476 loop : -2.13 (0.15), residues: 1568 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1432 residues out of total 3752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 1297 time to evaluate : 4.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 135 outliers final: 68 residues processed: 1363 average time/residue: 0.5652 time to fit residues: 1171.0801 Evaluate side-chains 1333 residues out of total 3752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 1265 time to evaluate : 4.093 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 0 residues processed: 68 average time/residue: 0.3634 time to fit residues: 50.2240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 143 optimal weight: 3.9990 chunk 383 optimal weight: 1.9990 chunk 84 optimal weight: 0.0870 chunk 249 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 425 optimal weight: 5.9990 chunk 353 optimal weight: 4.9990 chunk 197 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 140 optimal weight: 0.8980 chunk 223 optimal weight: 3.9990 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN ** B 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 GLN ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 HIS F 81 HIS F 179 GLN G 185 HIS ** H 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 GLN J 87 ASN ** J 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 87 ASN ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 moved from start: 0.5723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 37268 Z= 0.260 Angle : 0.861 17.457 50798 Z= 0.425 Chirality : 0.048 0.516 5678 Planarity : 0.006 0.099 6232 Dihedral : 14.082 87.885 5496 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 21.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 2.77 % Allowed : 34.97 % Favored : 62.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.31 (0.12), residues: 4326 helix: -0.95 (0.10), residues: 2282 sheet: -1.94 (0.26), residues: 476 loop : -2.09 (0.15), residues: 1568 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1399 residues out of total 3752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 1295 time to evaluate : 3.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 104 outliers final: 45 residues processed: 1338 average time/residue: 0.5719 time to fit residues: 1160.9690 Evaluate side-chains 1304 residues out of total 3752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 1259 time to evaluate : 4.175 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.3859 time to fit residues: 36.1538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 410 optimal weight: 9.9990 chunk 47 optimal weight: 0.0970 chunk 242 optimal weight: 1.9990 chunk 310 optimal weight: 0.9990 chunk 240 optimal weight: 10.0000 chunk 358 optimal weight: 0.7980 chunk 237 optimal weight: 0.9980 chunk 424 optimal weight: 0.3980 chunk 265 optimal weight: 0.3980 chunk 258 optimal weight: 0.0980 chunk 195 optimal weight: 3.9990 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 GLN ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 150 GLN G 153 ASN G 185 HIS ** H 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 185 HIS L 191 GLN ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 179 GLN ** M 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 145 ASN N 200 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.5930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 37268 Z= 0.236 Angle : 0.879 18.761 50798 Z= 0.429 Chirality : 0.048 0.435 5678 Planarity : 0.005 0.126 6232 Dihedral : 14.007 88.017 5496 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 20.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 1.84 % Allowed : 37.29 % Favored : 60.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.13 (0.13), residues: 4326 helix: -0.82 (0.10), residues: 2282 sheet: -1.63 (0.27), residues: 448 loop : -2.06 (0.15), residues: 1596 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1328 residues out of total 3752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 1259 time to evaluate : 4.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 37 residues processed: 1283 average time/residue: 0.5684 time to fit residues: 1101.0594 Evaluate side-chains 1264 residues out of total 3752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 1227 time to evaluate : 3.883 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.4037 time to fit residues: 31.2135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 262 optimal weight: 4.9990 chunk 169 optimal weight: 3.9990 chunk 253 optimal weight: 7.9990 chunk 127 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 269 optimal weight: 0.9980 chunk 288 optimal weight: 0.9980 chunk 209 optimal weight: 10.0000 chunk 39 optimal weight: 0.0970 chunk 333 optimal weight: 8.9990 overall best weight: 0.8178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 GLN ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 HIS ** F 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 185 HIS ** H 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 GLN J 160 ASN ** J 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 185 HIS L 191 GLN ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 moved from start: 0.6168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 37268 Z= 0.245 Angle : 0.892 17.718 50798 Z= 0.438 Chirality : 0.048 0.452 5678 Planarity : 0.005 0.085 6232 Dihedral : 13.933 89.660 5496 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 20.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 1.49 % Allowed : 37.90 % Favored : 60.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.45 % Twisted General : 0.12 % 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: -2.14 (0.13), residues: 4326 helix: -0.79 (0.11), residues: 2296 sheet: -1.95 (0.25), residues: 476 loop : -2.01 (0.16), residues: 1554 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1332 residues out of total 3752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 1276 time to evaluate : 4.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 34 residues processed: 1294 average time/residue: 0.5789 time to fit residues: 1139.1262 Evaluate side-chains 1277 residues out of total 3752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 1243 time to evaluate : 3.919 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.4098 time to fit residues: 29.6031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.4171 > 50: distance: 109 - 200: 36.830 distance: 122 - 203: 33.814 distance: 165 - 170: 34.667 distance: 171 - 172: 56.936 distance: 172 - 173: 55.894 distance: 174 - 175: 56.554 distance: 177 - 178: 39.226 distance: 180 - 181: 39.448 distance: 183 - 184: 41.742 distance: 185 - 191: 56.337 distance: 186 - 187: 39.537 distance: 186 - 189: 39.558 distance: 189 - 190: 69.119 distance: 192 - 193: 38.952 distance: 193 - 196: 56.926 distance: 196 - 198: 55.204 distance: 197 - 199: 40.590 distance: 200 - 201: 56.475 distance: 202 - 203: 56.076 distance: 202 - 207: 35.318 distance: 204 - 205: 39.182 distance: 207 - 208: 50.597 distance: 208 - 209: 37.994 distance: 209 - 215: 3.898 distance: 215 - 216: 55.554 distance: 216 - 219: 56.934 distance: 217 - 226: 40.246 distance: 219 - 220: 56.583 distance: 220 - 221: 39.401 distance: 223 - 225: 40.756 distance: 228 - 229: 40.375 distance: 228 - 230: 55.918 distance: 232 - 233: 39.441 distance: 232 - 238: 56.268 distance: 234 - 235: 40.920 distance: 235 - 236: 41.202 distance: 236 - 237: 49.002 distance: 239 - 240: 56.817 distance: 239 - 242: 38.621 distance: 240 - 241: 38.812 distance: 240 - 245: 34.801 distance: 242 - 243: 40.668