Starting phenix.real_space_refine (version: dev) on Mon Dec 19 02:30:59 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i1x_0326/12_2022/6i1x_0326_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i1x_0326/12_2022/6i1x_0326.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i1x_0326/12_2022/6i1x_0326.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i1x_0326/12_2022/6i1x_0326.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i1x_0326/12_2022/6i1x_0326_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i1x_0326/12_2022/6i1x_0326_neut.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.009 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ASP 168": "OD1" <-> "OD2" Residue "A ARG 232": "NH1" <-> "NH2" Residue "A ARG 236": "NH1" <-> "NH2" Residue "A TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 510": "NH1" <-> "NH2" Residue "A TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 555": "NH1" <-> "NH2" Residue "B ASP 168": "OD1" <-> "OD2" Residue "B ARG 232": "NH1" <-> "NH2" Residue "B ARG 236": "NH1" <-> "NH2" Residue "B GLU 237": "OE1" <-> "OE2" Residue "B TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 510": "NH1" <-> "NH2" Residue "B TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 555": "NH1" <-> "NH2" Residue "C ASP 168": "OD1" <-> "OD2" Residue "C ARG 232": "NH1" <-> "NH2" Residue "C ARG 236": "NH1" <-> "NH2" Residue "C GLU 237": "OE1" <-> "OE2" Residue "C TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 510": "NH1" <-> "NH2" Residue "C TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 555": "NH1" <-> "NH2" Residue "D ASP 168": "OD1" <-> "OD2" Residue "D ARG 232": "NH1" <-> "NH2" Residue "D ARG 236": "NH1" <-> "NH2" Residue "D TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 510": "NH1" <-> "NH2" Residue "D TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 555": "NH1" <-> "NH2" Residue "E ASP 168": "OD1" <-> "OD2" Residue "E ARG 232": "NH1" <-> "NH2" Residue "E ARG 236": "NH1" <-> "NH2" Residue "E TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 510": "NH1" <-> "NH2" Residue "E TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 555": "NH1" <-> "NH2" Residue "F ASP 168": "OD1" <-> "OD2" Residue "F ARG 232": "NH1" <-> "NH2" Residue "F ARG 236": "NH1" <-> "NH2" Residue "F TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 510": "NH1" <-> "NH2" Residue "F TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 555": "NH1" <-> "NH2" Residue "G ASP 168": "OD1" <-> "OD2" Residue "G ARG 232": "NH1" <-> "NH2" Residue "G ARG 236": "NH1" <-> "NH2" Residue "G TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 510": "NH1" <-> "NH2" Residue "G TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 555": "NH1" <-> "NH2" Residue "H ASP 168": "OD1" <-> "OD2" Residue "H ARG 232": "NH1" <-> "NH2" Residue "H ARG 236": "NH1" <-> "NH2" Residue "H TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 510": "NH1" <-> "NH2" Residue "H TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 555": "NH1" <-> "NH2" Residue "I ASP 168": "OD1" <-> "OD2" Residue "I ARG 232": "NH1" <-> "NH2" Residue "I ARG 236": "NH1" <-> "NH2" Residue "I TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 510": "NH1" <-> "NH2" Residue "I TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 555": "NH1" <-> "NH2" Residue "I GLU 616": "OE1" <-> "OE2" Residue "J ASP 168": "OD1" <-> "OD2" Residue "J ARG 232": "NH1" <-> "NH2" Residue "J ARG 236": "NH1" <-> "NH2" Residue "J GLU 237": "OE1" <-> "OE2" Residue "J TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 510": "NH1" <-> "NH2" Residue "J TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 555": "NH1" <-> "NH2" Residue "K ASP 168": "OD1" <-> "OD2" Residue "K ARG 232": "NH1" <-> "NH2" Residue "K ARG 236": "NH1" <-> "NH2" Residue "K GLU 237": "OE1" <-> "OE2" Residue "K TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 510": "NH1" <-> "NH2" Residue "K TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 555": "NH1" <-> "NH2" Residue "L ASP 168": "OD1" <-> "OD2" Residue "L ARG 232": "NH1" <-> "NH2" Residue "L ARG 236": "NH1" <-> "NH2" Residue "L TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 510": "NH1" <-> "NH2" Residue "L TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 555": "NH1" <-> "NH2" Residue "M ASP 168": "OD1" <-> "OD2" Residue "M ARG 232": "NH1" <-> "NH2" Residue "M ARG 236": "NH1" <-> "NH2" Residue "M TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 510": "NH1" <-> "NH2" Residue "M TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 555": "NH1" <-> "NH2" Residue "N ASP 168": "OD1" <-> "OD2" Residue "N ARG 232": "NH1" <-> "NH2" Residue "N ARG 236": "NH1" <-> "NH2" Residue "N TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 510": "NH1" <-> "NH2" Residue "N TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 555": "NH1" <-> "NH2" Residue "O ASP 168": "OD1" <-> "OD2" Residue "O ARG 232": "NH1" <-> "NH2" Residue "O ARG 236": "NH1" <-> "NH2" Residue "O GLU 237": "OE1" <-> "OE2" Residue "O TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 510": "NH1" <-> "NH2" Residue "O TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 555": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 54915 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "B" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "C" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "D" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "E" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "F" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "G" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "H" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "I" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "J" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "K" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "L" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "M" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "N" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "O" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Time building chain proxies: 21.91, per 1000 atoms: 0.40 Number of scatterers: 54915 At special positions: 0 Unit cell: (158.51, 157.3, 182.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 150 16.00 O 10935 8.00 N 9675 7.00 C 34155 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: 16.40 Conformation dependent library (CDL) restraints added in 6.1 seconds 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13290 Finding SS restraints... Secondary structure from input PDB file: 195 helices and 0 sheets defined 32.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 111 through 114 removed outlier: 3.723A pdb=" N GLU A 114 " --> pdb=" O SER A 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 111 through 114' Processing helix chain 'A' and resid 115 through 124 Processing helix chain 'A' and resid 145 through 163 removed outlier: 3.888A pdb=" N GLY A 163 " --> pdb=" O VAL A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 186 Processing helix chain 'A' and resid 199 through 203 Processing helix chain 'A' and resid 220 through 234 removed outlier: 3.596A pdb=" N GLN A 229 " --> pdb=" O ALA A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 266 removed outlier: 3.852A pdb=" N GLU A 259 " --> pdb=" O LYS A 255 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 260 " --> pdb=" O ASP A 256 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY A 263 " --> pdb=" O GLU A 259 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL A 264 " --> pdb=" O VAL A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 323 Processing helix chain 'A' and resid 366 through 377 Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 543 through 547 Processing helix chain 'A' and resid 549 through 554 Processing helix chain 'A' and resid 578 through 607 removed outlier: 3.655A pdb=" N GLY A 583 " --> pdb=" O ASN A 579 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS A 588 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N TYR A 605 " --> pdb=" O ALA A 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 114 removed outlier: 3.729A pdb=" N GLU B 114 " --> pdb=" O SER B 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 111 through 114' Processing helix chain 'B' and resid 115 through 124 Processing helix chain 'B' and resid 145 through 163 removed outlier: 3.910A pdb=" N GLY B 163 " --> pdb=" O VAL B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 186 Processing helix chain 'B' and resid 199 through 203 Processing helix chain 'B' and resid 220 through 235 removed outlier: 3.589A pdb=" N GLN B 229 " --> pdb=" O ALA B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 266 removed outlier: 3.851A pdb=" N GLU B 259 " --> pdb=" O LYS B 255 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL B 260 " --> pdb=" O ASP B 256 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY B 263 " --> pdb=" O GLU B 259 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL B 264 " --> pdb=" O VAL B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 323 Processing helix chain 'B' and resid 366 through 377 Processing helix chain 'B' and resid 383 through 390 Processing helix chain 'B' and resid 543 through 547 Processing helix chain 'B' and resid 549 through 554 Processing helix chain 'B' and resid 578 through 607 removed outlier: 3.658A pdb=" N GLY B 583 " --> pdb=" O ASN B 579 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS B 588 " --> pdb=" O ILE B 584 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N TYR B 605 " --> pdb=" O ALA B 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 114 removed outlier: 3.736A pdb=" N GLU C 114 " --> pdb=" O SER C 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 111 through 114' Processing helix chain 'C' and resid 115 through 124 Processing helix chain 'C' and resid 145 through 163 removed outlier: 3.896A pdb=" N GLY C 163 " --> pdb=" O VAL C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 186 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 220 through 234 removed outlier: 3.590A pdb=" N GLN C 229 " --> pdb=" O ALA C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 266 removed outlier: 3.847A pdb=" N GLU C 259 " --> pdb=" O LYS C 255 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL C 260 " --> pdb=" O ASP C 256 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY C 263 " --> pdb=" O GLU C 259 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL C 264 " --> pdb=" O VAL C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 323 Processing helix chain 'C' and resid 366 through 377 Processing helix chain 'C' and resid 383 through 390 Processing helix chain 'C' and resid 543 through 547 Processing helix chain 'C' and resid 549 through 554 Processing helix chain 'C' and resid 578 through 607 removed outlier: 3.659A pdb=" N GLY C 583 " --> pdb=" O ASN C 579 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS C 588 " --> pdb=" O ILE C 584 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TYR C 605 " --> pdb=" O ALA C 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 114 removed outlier: 3.720A pdb=" N GLU D 114 " --> pdb=" O SER D 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 111 through 114' Processing helix chain 'D' and resid 115 through 124 Processing helix chain 'D' and resid 145 through 163 removed outlier: 3.892A pdb=" N GLY D 163 " --> pdb=" O VAL D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 186 Processing helix chain 'D' and resid 199 through 203 Processing helix chain 'D' and resid 220 through 234 removed outlier: 3.601A pdb=" N GLN D 229 " --> pdb=" O ALA D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 266 removed outlier: 3.837A pdb=" N GLU D 259 " --> pdb=" O LYS D 255 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL D 260 " --> pdb=" O ASP D 256 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY D 263 " --> pdb=" O GLU D 259 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL D 264 " --> pdb=" O VAL D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 323 Processing helix chain 'D' and resid 366 through 377 Processing helix chain 'D' and resid 383 through 390 Processing helix chain 'D' and resid 543 through 547 Processing helix chain 'D' and resid 549 through 554 Processing helix chain 'D' and resid 578 through 607 removed outlier: 3.659A pdb=" N GLY D 583 " --> pdb=" O ASN D 579 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS D 588 " --> pdb=" O ILE D 584 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N TYR D 605 " --> pdb=" O ALA D 601 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 114 removed outlier: 3.725A pdb=" N GLU E 114 " --> pdb=" O SER E 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 111 through 114' Processing helix chain 'E' and resid 115 through 124 Processing helix chain 'E' and resid 145 through 163 removed outlier: 3.887A pdb=" N GLY E 163 " --> pdb=" O VAL E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 186 Processing helix chain 'E' and resid 199 through 203 Processing helix chain 'E' and resid 220 through 234 removed outlier: 3.625A pdb=" N GLN E 229 " --> pdb=" O ALA E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 266 removed outlier: 3.805A pdb=" N GLU E 259 " --> pdb=" O LYS E 255 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL E 260 " --> pdb=" O ASP E 256 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY E 263 " --> pdb=" O GLU E 259 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL E 264 " --> pdb=" O VAL E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 323 Processing helix chain 'E' and resid 366 through 377 Processing helix chain 'E' and resid 383 through 390 Processing helix chain 'E' and resid 543 through 547 Processing helix chain 'E' and resid 549 through 554 Processing helix chain 'E' and resid 578 through 607 removed outlier: 3.644A pdb=" N GLY E 583 " --> pdb=" O ASN E 579 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS E 588 " --> pdb=" O ILE E 584 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N TYR E 605 " --> pdb=" O ALA E 601 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 114 removed outlier: 3.713A pdb=" N GLU F 114 " --> pdb=" O SER F 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 111 through 114' Processing helix chain 'F' and resid 115 through 124 Processing helix chain 'F' and resid 145 through 163 removed outlier: 3.887A pdb=" N GLY F 163 " --> pdb=" O VAL F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 186 Processing helix chain 'F' and resid 199 through 203 Processing helix chain 'F' and resid 220 through 234 removed outlier: 3.632A pdb=" N GLN F 229 " --> pdb=" O ALA F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 266 removed outlier: 3.822A pdb=" N GLU F 259 " --> pdb=" O LYS F 255 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL F 260 " --> pdb=" O ASP F 256 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY F 263 " --> pdb=" O GLU F 259 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL F 264 " --> pdb=" O VAL F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 323 Processing helix chain 'F' and resid 366 through 377 Processing helix chain 'F' and resid 383 through 390 Processing helix chain 'F' and resid 543 through 547 Processing helix chain 'F' and resid 549 through 554 Processing helix chain 'F' and resid 578 through 607 removed outlier: 3.665A pdb=" N GLY F 583 " --> pdb=" O ASN F 579 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS F 588 " --> pdb=" O ILE F 584 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N TYR F 605 " --> pdb=" O ALA F 601 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 114 removed outlier: 3.704A pdb=" N GLU G 114 " --> pdb=" O SER G 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 111 through 114' Processing helix chain 'G' and resid 115 through 124 Processing helix chain 'G' and resid 145 through 163 removed outlier: 3.878A pdb=" N GLY G 163 " --> pdb=" O VAL G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 186 Processing helix chain 'G' and resid 199 through 203 Processing helix chain 'G' and resid 220 through 234 removed outlier: 3.644A pdb=" N GLN G 229 " --> pdb=" O ALA G 225 " (cutoff:3.500A) Processing helix chain 'G' and resid 253 through 266 removed outlier: 3.804A pdb=" N GLU G 259 " --> pdb=" O LYS G 255 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL G 260 " --> pdb=" O ASP G 256 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY G 263 " --> pdb=" O GLU G 259 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL G 264 " --> pdb=" O VAL G 260 " (cutoff:3.500A) Processing helix chain 'G' and resid 308 through 323 Processing helix chain 'G' and resid 366 through 377 Processing helix chain 'G' and resid 383 through 390 Processing helix chain 'G' and resid 543 through 547 Processing helix chain 'G' and resid 549 through 554 Processing helix chain 'G' and resid 578 through 607 removed outlier: 3.660A pdb=" N GLY G 583 " --> pdb=" O ASN G 579 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS G 588 " --> pdb=" O ILE G 584 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N TYR G 605 " --> pdb=" O ALA G 601 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 114 removed outlier: 3.713A pdb=" N GLU H 114 " --> pdb=" O SER H 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 111 through 114' Processing helix chain 'H' and resid 115 through 124 Processing helix chain 'H' and resid 145 through 163 removed outlier: 3.907A pdb=" N GLY H 163 " --> pdb=" O VAL H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 186 Processing helix chain 'H' and resid 199 through 203 Processing helix chain 'H' and resid 220 through 234 removed outlier: 3.623A pdb=" N GLN H 229 " --> pdb=" O ALA H 225 " (cutoff:3.500A) Processing helix chain 'H' and resid 253 through 266 removed outlier: 3.840A pdb=" N GLU H 259 " --> pdb=" O LYS H 255 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL H 260 " --> pdb=" O ASP H 256 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY H 263 " --> pdb=" O GLU H 259 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL H 264 " --> pdb=" O VAL H 260 " (cutoff:3.500A) Processing helix chain 'H' and resid 308 through 323 Processing helix chain 'H' and resid 366 through 377 Processing helix chain 'H' and resid 383 through 390 Processing helix chain 'H' and resid 543 through 547 Processing helix chain 'H' and resid 549 through 554 Processing helix chain 'H' and resid 578 through 607 removed outlier: 3.662A pdb=" N GLY H 583 " --> pdb=" O ASN H 579 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS H 588 " --> pdb=" O ILE H 584 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N TYR H 605 " --> pdb=" O ALA H 601 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 114 removed outlier: 3.758A pdb=" N GLU I 114 " --> pdb=" O SER I 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 111 through 114' Processing helix chain 'I' and resid 115 through 124 Processing helix chain 'I' and resid 145 through 163 removed outlier: 3.863A pdb=" N GLY I 163 " --> pdb=" O VAL I 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 176 through 186 Processing helix chain 'I' and resid 199 through 203 Processing helix chain 'I' and resid 220 through 235 removed outlier: 3.637A pdb=" N GLN I 229 " --> pdb=" O ALA I 225 " (cutoff:3.500A) Processing helix chain 'I' and resid 253 through 266 removed outlier: 3.833A pdb=" N GLU I 259 " --> pdb=" O LYS I 255 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL I 260 " --> pdb=" O ASP I 256 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY I 263 " --> pdb=" O GLU I 259 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL I 264 " --> pdb=" O VAL I 260 " (cutoff:3.500A) Processing helix chain 'I' and resid 308 through 323 Processing helix chain 'I' and resid 366 through 377 removed outlier: 3.512A pdb=" N VAL I 370 " --> pdb=" O GLY I 366 " (cutoff:3.500A) Processing helix chain 'I' and resid 383 through 390 Processing helix chain 'I' and resid 543 through 547 Processing helix chain 'I' and resid 549 through 554 Processing helix chain 'I' and resid 578 through 607 removed outlier: 3.673A pdb=" N GLY I 583 " --> pdb=" O ASN I 579 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS I 588 " --> pdb=" O ILE I 584 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N TYR I 605 " --> pdb=" O ALA I 601 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 114 removed outlier: 3.744A pdb=" N GLU J 114 " --> pdb=" O SER J 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 111 through 114' Processing helix chain 'J' and resid 115 through 124 Processing helix chain 'J' and resid 145 through 163 removed outlier: 3.897A pdb=" N GLY J 163 " --> pdb=" O VAL J 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 176 through 186 Processing helix chain 'J' and resid 199 through 203 Processing helix chain 'J' and resid 220 through 235 removed outlier: 3.587A pdb=" N GLN J 229 " --> pdb=" O ALA J 225 " (cutoff:3.500A) Processing helix chain 'J' and resid 253 through 266 removed outlier: 3.845A pdb=" N GLU J 259 " --> pdb=" O LYS J 255 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL J 260 " --> pdb=" O ASP J 256 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY J 263 " --> pdb=" O GLU J 259 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL J 264 " --> pdb=" O VAL J 260 " (cutoff:3.500A) Processing helix chain 'J' and resid 308 through 323 Processing helix chain 'J' and resid 366 through 377 Processing helix chain 'J' and resid 383 through 390 Processing helix chain 'J' and resid 543 through 547 Processing helix chain 'J' and resid 549 through 554 Processing helix chain 'J' and resid 578 through 607 removed outlier: 3.655A pdb=" N GLY J 583 " --> pdb=" O ASN J 579 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS J 588 " --> pdb=" O ILE J 584 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N TYR J 605 " --> pdb=" O ALA J 601 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 114 removed outlier: 3.720A pdb=" N GLU K 114 " --> pdb=" O SER K 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 111 through 114' Processing helix chain 'K' and resid 115 through 124 Processing helix chain 'K' and resid 145 through 163 removed outlier: 3.899A pdb=" N GLY K 163 " --> pdb=" O VAL K 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 176 through 186 Processing helix chain 'K' and resid 199 through 203 Processing helix chain 'K' and resid 220 through 234 removed outlier: 3.601A pdb=" N GLN K 229 " --> pdb=" O ALA K 225 " (cutoff:3.500A) Processing helix chain 'K' and resid 253 through 266 removed outlier: 3.840A pdb=" N GLU K 259 " --> pdb=" O LYS K 255 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL K 260 " --> pdb=" O ASP K 256 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY K 263 " --> pdb=" O GLU K 259 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL K 264 " --> pdb=" O VAL K 260 " (cutoff:3.500A) Processing helix chain 'K' and resid 308 through 323 Processing helix chain 'K' and resid 366 through 377 Processing helix chain 'K' and resid 383 through 390 Processing helix chain 'K' and resid 543 through 547 Processing helix chain 'K' and resid 549 through 554 Processing helix chain 'K' and resid 578 through 607 removed outlier: 3.656A pdb=" N GLY K 583 " --> pdb=" O ASN K 579 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS K 588 " --> pdb=" O ILE K 584 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N TYR K 605 " --> pdb=" O ALA K 601 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 114 removed outlier: 3.729A pdb=" N GLU L 114 " --> pdb=" O SER L 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 111 through 114' Processing helix chain 'L' and resid 115 through 124 Processing helix chain 'L' and resid 145 through 163 removed outlier: 3.901A pdb=" N GLY L 163 " --> pdb=" O VAL L 159 " (cutoff:3.500A) Processing helix chain 'L' and resid 176 through 186 Processing helix chain 'L' and resid 199 through 203 Processing helix chain 'L' and resid 220 through 235 removed outlier: 3.594A pdb=" N GLN L 229 " --> pdb=" O ALA L 225 " (cutoff:3.500A) Processing helix chain 'L' and resid 253 through 266 removed outlier: 3.845A pdb=" N GLU L 259 " --> pdb=" O LYS L 255 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL L 260 " --> pdb=" O ASP L 256 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY L 263 " --> pdb=" O GLU L 259 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL L 264 " --> pdb=" O VAL L 260 " (cutoff:3.500A) Processing helix chain 'L' and resid 308 through 323 Processing helix chain 'L' and resid 366 through 377 Processing helix chain 'L' and resid 383 through 390 Processing helix chain 'L' and resid 543 through 547 Processing helix chain 'L' and resid 549 through 554 Processing helix chain 'L' and resid 578 through 607 removed outlier: 3.654A pdb=" N GLY L 583 " --> pdb=" O ASN L 579 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS L 588 " --> pdb=" O ILE L 584 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N TYR L 605 " --> pdb=" O ALA L 601 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 114 removed outlier: 3.735A pdb=" N GLU M 114 " --> pdb=" O SER M 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 111 through 114' Processing helix chain 'M' and resid 115 through 124 Processing helix chain 'M' and resid 145 through 163 removed outlier: 3.903A pdb=" N GLY M 163 " --> pdb=" O VAL M 159 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 186 Processing helix chain 'M' and resid 199 through 203 Processing helix chain 'M' and resid 220 through 235 removed outlier: 3.594A pdb=" N GLN M 229 " --> pdb=" O ALA M 225 " (cutoff:3.500A) Processing helix chain 'M' and resid 253 through 266 removed outlier: 3.842A pdb=" N GLU M 259 " --> pdb=" O LYS M 255 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL M 260 " --> pdb=" O ASP M 256 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY M 263 " --> pdb=" O GLU M 259 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL M 264 " --> pdb=" O VAL M 260 " (cutoff:3.500A) Processing helix chain 'M' and resid 308 through 323 Processing helix chain 'M' and resid 366 through 377 Processing helix chain 'M' and resid 383 through 390 Processing helix chain 'M' and resid 543 through 547 Processing helix chain 'M' and resid 549 through 554 Processing helix chain 'M' and resid 578 through 607 removed outlier: 3.654A pdb=" N GLY M 583 " --> pdb=" O ASN M 579 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS M 588 " --> pdb=" O ILE M 584 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N TYR M 605 " --> pdb=" O ALA M 601 " (cutoff:3.500A) Processing helix chain 'N' and resid 111 through 114 removed outlier: 3.722A pdb=" N GLU N 114 " --> pdb=" O SER N 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 111 through 114' Processing helix chain 'N' and resid 115 through 124 Processing helix chain 'N' and resid 145 through 163 removed outlier: 3.895A pdb=" N GLY N 163 " --> pdb=" O VAL N 159 " (cutoff:3.500A) Processing helix chain 'N' and resid 176 through 186 Processing helix chain 'N' and resid 199 through 203 Processing helix chain 'N' and resid 220 through 234 removed outlier: 3.600A pdb=" N GLN N 229 " --> pdb=" O ALA N 225 " (cutoff:3.500A) Processing helix chain 'N' and resid 253 through 266 removed outlier: 3.839A pdb=" N GLU N 259 " --> pdb=" O LYS N 255 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL N 260 " --> pdb=" O ASP N 256 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY N 263 " --> pdb=" O GLU N 259 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL N 264 " --> pdb=" O VAL N 260 " (cutoff:3.500A) Processing helix chain 'N' and resid 308 through 323 Processing helix chain 'N' and resid 366 through 377 Processing helix chain 'N' and resid 383 through 390 Processing helix chain 'N' and resid 543 through 547 Processing helix chain 'N' and resid 549 through 554 Processing helix chain 'N' and resid 578 through 607 removed outlier: 3.657A pdb=" N GLY N 583 " --> pdb=" O ASN N 579 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS N 588 " --> pdb=" O ILE N 584 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N TYR N 605 " --> pdb=" O ALA N 601 " (cutoff:3.500A) Processing helix chain 'O' and resid 111 through 114 removed outlier: 3.724A pdb=" N GLU O 114 " --> pdb=" O SER O 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 111 through 114' Processing helix chain 'O' and resid 115 through 124 Processing helix chain 'O' and resid 145 through 163 removed outlier: 3.899A pdb=" N GLY O 163 " --> pdb=" O VAL O 159 " (cutoff:3.500A) Processing helix chain 'O' and resid 176 through 186 Processing helix chain 'O' and resid 199 through 203 Processing helix chain 'O' and resid 220 through 234 removed outlier: 3.598A pdb=" N GLN O 229 " --> pdb=" O ALA O 225 " (cutoff:3.500A) Processing helix chain 'O' and resid 253 through 266 removed outlier: 3.839A pdb=" N GLU O 259 " --> pdb=" O LYS O 255 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL O 260 " --> pdb=" O ASP O 256 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY O 263 " --> pdb=" O GLU O 259 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL O 264 " --> pdb=" O VAL O 260 " (cutoff:3.500A) Processing helix chain 'O' and resid 308 through 323 Processing helix chain 'O' and resid 366 through 377 Processing helix chain 'O' and resid 383 through 390 Processing helix chain 'O' and resid 543 through 547 Processing helix chain 'O' and resid 549 through 554 Processing helix chain 'O' and resid 578 through 607 removed outlier: 3.655A pdb=" N GLY O 583 " --> pdb=" O ASN O 579 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS O 588 " --> pdb=" O ILE O 584 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N TYR O 605 " --> pdb=" O ALA O 601 " (cutoff:3.500A) 1459 hydrogen bonds defined for protein. 4062 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.52 Time building geometry restraints manager: 18.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 11082 1.32 - 1.45: 11247 1.45 - 1.58: 32856 1.58 - 1.70: 0 1.70 - 1.83: 300 Bond restraints: 55485 Sorted by residual: bond pdb=" CA TYR F 174 " pdb=" C TYR F 174 " ideal model delta sigma weight residual 1.520 1.545 -0.026 4.80e-03 4.34e+04 2.89e+01 bond pdb=" CA TYR G 174 " pdb=" C TYR G 174 " ideal model delta sigma weight residual 1.520 1.544 -0.025 4.80e-03 4.34e+04 2.65e+01 bond pdb=" CA TYR N 174 " pdb=" C TYR N 174 " ideal model delta sigma weight residual 1.520 1.544 -0.024 4.80e-03 4.34e+04 2.60e+01 bond pdb=" CA TYR K 174 " pdb=" C TYR K 174 " ideal model delta sigma weight residual 1.520 1.544 -0.024 4.80e-03 4.34e+04 2.59e+01 bond pdb=" CA TYR D 174 " pdb=" C TYR D 174 " ideal model delta sigma weight residual 1.520 1.544 -0.024 4.80e-03 4.34e+04 2.59e+01 ... (remaining 55480 not shown) Histogram of bond angle deviations from ideal: 94.24 - 102.35: 371 102.35 - 110.45: 13037 110.45 - 118.55: 35793 118.55 - 126.66: 25710 126.66 - 134.76: 344 Bond angle restraints: 75255 Sorted by residual: angle pdb=" N PRO I 609 " pdb=" CA PRO I 609 " pdb=" CB PRO I 609 " ideal model delta sigma weight residual 103.25 94.24 9.01 1.05e+00 9.07e-01 7.36e+01 angle pdb=" N PRO D 609 " pdb=" CA PRO D 609 " pdb=" CB PRO D 609 " ideal model delta sigma weight residual 103.25 94.43 8.82 1.05e+00 9.07e-01 7.06e+01 angle pdb=" N PRO H 609 " pdb=" CA PRO H 609 " pdb=" CB PRO H 609 " ideal model delta sigma weight residual 103.25 94.45 8.80 1.05e+00 9.07e-01 7.03e+01 angle pdb=" N PRO B 609 " pdb=" CA PRO B 609 " pdb=" CB PRO B 609 " ideal model delta sigma weight residual 103.25 94.49 8.76 1.05e+00 9.07e-01 6.96e+01 angle pdb=" N PRO C 609 " pdb=" CA PRO C 609 " pdb=" CB PRO C 609 " ideal model delta sigma weight residual 103.25 94.50 8.75 1.05e+00 9.07e-01 6.94e+01 ... (remaining 75250 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.10: 30582 18.10 - 36.19: 2588 36.19 - 54.29: 609 54.29 - 72.39: 121 72.39 - 90.49: 30 Dihedral angle restraints: 33930 sinusoidal: 13230 harmonic: 20700 Sorted by residual: dihedral pdb=" CA LYS I 189 " pdb=" C LYS I 189 " pdb=" N ASP I 190 " pdb=" CA ASP I 190 " ideal model delta harmonic sigma weight residual 180.00 150.09 29.91 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA LYS H 189 " pdb=" C LYS H 189 " pdb=" N ASP H 190 " pdb=" CA ASP H 190 " ideal model delta harmonic sigma weight residual 180.00 151.35 28.65 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA LYS G 189 " pdb=" C LYS G 189 " pdb=" N ASP G 190 " pdb=" CA ASP G 190 " ideal model delta harmonic sigma weight residual 180.00 152.60 27.40 0 5.00e+00 4.00e-02 3.00e+01 ... (remaining 33927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3853 0.061 - 0.123: 3239 0.123 - 0.184: 1572 0.184 - 0.245: 391 0.245 - 0.306: 65 Chirality restraints: 9120 Sorted by residual: chirality pdb=" CA LYS E 250 " pdb=" N LYS E 250 " pdb=" C LYS E 250 " pdb=" CB LYS E 250 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CA LYS F 250 " pdb=" N LYS F 250 " pdb=" C LYS F 250 " pdb=" CB LYS F 250 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA LYS L 250 " pdb=" N LYS L 250 " pdb=" C LYS L 250 " pdb=" CB LYS L 250 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.30e+00 ... (remaining 9117 not shown) Planarity restraints: 9855 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL F 613 " 0.018 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" C VAL F 613 " -0.065 2.00e-02 2.50e+03 pdb=" O VAL F 613 " 0.025 2.00e-02 2.50e+03 pdb=" N LEU F 614 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 613 " 0.018 2.00e-02 2.50e+03 3.73e-02 1.39e+01 pdb=" C VAL B 613 " -0.064 2.00e-02 2.50e+03 pdb=" O VAL B 613 " 0.025 2.00e-02 2.50e+03 pdb=" N LEU B 614 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL H 613 " 0.017 2.00e-02 2.50e+03 3.72e-02 1.39e+01 pdb=" C VAL H 613 " -0.064 2.00e-02 2.50e+03 pdb=" O VAL H 613 " 0.025 2.00e-02 2.50e+03 pdb=" N LEU H 614 " 0.022 2.00e-02 2.50e+03 ... (remaining 9852 not shown) Histogram of nonbonded interaction distances: 0.46 - 1.35: 5 1.35 - 2.23: 94 2.23 - 3.12: 45107 3.12 - 4.01: 145267 4.01 - 4.90: 262893 Warning: very small nonbonded interaction distances. Nonbonded interactions: 453366 Sorted by model distance: nonbonded pdb=" CG2 VAL H 139 " pdb=" C ALA I 162 " model vdw 0.458 3.690 nonbonded pdb=" CB VAL H 139 " pdb=" O ALA I 162 " model vdw 0.818 3.470 nonbonded pdb=" CG2 VAL H 139 " pdb=" O ALA I 162 " model vdw 1.091 3.460 nonbonded pdb=" CG2 VAL H 139 " pdb=" N GLY I 163 " model vdw 1.289 3.540 nonbonded pdb=" ND2 ASN I 138 " pdb=" O THR J 198 " model vdw 1.323 2.520 ... (remaining 453361 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' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 150 5.16 5 C 34155 2.51 5 N 9675 2.21 5 O 10935 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.630 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: 0.050 Extract box with map and model: 7.120 Check model and map are aligned: 0.630 Convert atoms to be neutral: 0.360 Process input model: 94.630 Find NCS groups from input model: 3.030 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3168 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 : 0.013 0.061 55485 Z= 0.838 Angle : 1.810 9.397 75255 Z= 1.296 Chirality : 0.098 0.306 9120 Planarity : 0.008 0.072 9855 Dihedral : 14.937 90.487 20640 Min Nonbonded Distance : 0.458 Molprobity Statistics. All-atom Clashscore : 50.06 Ramachandran Plot: Outliers : 1.89 % Allowed : 7.50 % Favored : 90.61 % Rotamer Outliers : 4.35 % Cbeta Deviations : 0.51 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.08), residues: 7200 helix: -2.95 (0.08), residues: 1965 sheet: -1.10 (0.10), residues: 2175 loop : -2.72 (0.08), residues: 3060 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1804 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 263 poor density : 1541 time to evaluate : 4.667 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 outliers start: 263 outliers final: 71 residues processed: 1752 average time/residue: 0.5428 time to fit residues: 1547.8160 Evaluate side-chains 799 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 728 time to evaluate : 4.658 Switching outliers to nearest non-outliers outliers start: 71 outliers final: 0 residues processed: 71 average time/residue: 0.3727 time to fit residues: 56.8548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 607 optimal weight: 0.9990 chunk 545 optimal weight: 2.9990 chunk 302 optimal weight: 3.9990 chunk 186 optimal weight: 5.9990 chunk 368 optimal weight: 0.7980 chunk 291 optimal weight: 7.9990 chunk 564 optimal weight: 5.9990 chunk 218 optimal weight: 0.3980 chunk 343 optimal weight: 1.9990 chunk 420 optimal weight: 0.9980 chunk 653 optimal weight: 10.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN A 188 ASN ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 GLN A 496 GLN A 595 GLN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 ASN B 328 GLN ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 565 ASN ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 ASN C 440 GLN C 533 GLN ** C 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 ASN ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 ASN F 188 ASN ** F 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 475 GLN G 186 ASN G 233 GLN ** G 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN H 188 ASN ** H 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 186 ASN I 188 ASN I 328 GLN I 345 ASN I 359 GLN I 440 GLN I 533 GLN ** J 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 440 GLN ** J 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 ASN L 188 ASN ** L 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 345 ASN ** M 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 440 GLN ** N 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 186 ASN O 188 ASN ** O 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 349 GLN O 440 GLN ** O 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3177 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 55485 Z= 0.251 Angle : 0.829 12.531 75255 Z= 0.419 Chirality : 0.051 0.622 9120 Planarity : 0.007 0.121 9855 Dihedral : 6.755 44.658 7785 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 20.47 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.19 % Favored : 96.44 % Rotamer Outliers : 4.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.09), residues: 7200 helix: -0.73 (0.11), residues: 1935 sheet: -1.16 (0.09), residues: 2745 loop : -1.94 (0.11), residues: 2520 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1217 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 291 poor density : 926 time to evaluate : 4.723 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 outliers start: 291 outliers final: 106 residues processed: 1138 average time/residue: 0.5153 time to fit residues: 999.2221 Evaluate side-chains 776 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 670 time to evaluate : 4.672 Switching outliers to nearest non-outliers outliers start: 106 outliers final: 0 residues processed: 106 average time/residue: 0.4106 time to fit residues: 87.8230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 363 optimal weight: 8.9990 chunk 202 optimal weight: 0.0980 chunk 544 optimal weight: 3.9990 chunk 445 optimal weight: 0.9990 chunk 180 optimal weight: 10.0000 chunk 655 optimal weight: 7.9990 chunk 707 optimal weight: 0.9990 chunk 583 optimal weight: 20.0000 chunk 649 optimal weight: 9.9990 chunk 223 optimal weight: 4.9990 chunk 525 optimal weight: 6.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 GLN B 440 GLN B 475 GLN ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 328 GLN C 404 ASN C 496 GLN C 533 GLN ** C 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 ASN E 188 ASN E 233 GLN ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 440 GLN E 496 GLN ** E 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 437 ASN ** F 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 194 GLN H 328 GLN ** H 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 345 ASN I 496 GLN ** I 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 345 ASN ** J 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 496 GLN ** J 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 559 ASN ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 392 ASN ** K 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 559 ASN ** L 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 533 GLN L 559 ASN ** M 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 328 GLN M 345 ASN ** M 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 496 GLN ** O 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 186 ASN O 233 GLN ** O 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 496 GLN O 533 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3204 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 55485 Z= 0.258 Angle : 0.734 10.120 75255 Z= 0.374 Chirality : 0.048 0.256 9120 Planarity : 0.006 0.102 9855 Dihedral : 6.116 44.184 7785 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 19.00 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.01 % Favored : 95.57 % Rotamer Outliers : 2.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.09), residues: 7200 helix: -0.23 (0.11), residues: 1950 sheet: -0.97 (0.09), residues: 2505 loop : -1.99 (0.11), residues: 2745 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 966 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 790 time to evaluate : 4.648 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 outliers start: 176 outliers final: 97 residues processed: 912 average time/residue: 0.5352 time to fit residues: 837.8239 Evaluate side-chains 724 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 627 time to evaluate : 4.691 Switching outliers to nearest non-outliers outliers start: 97 outliers final: 0 residues processed: 97 average time/residue: 0.3958 time to fit residues: 80.0215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 647 optimal weight: 3.9990 chunk 492 optimal weight: 40.0000 chunk 339 optimal weight: 8.9990 chunk 72 optimal weight: 0.0980 chunk 312 optimal weight: 0.9990 chunk 439 optimal weight: 6.9990 chunk 657 optimal weight: 3.9990 chunk 695 optimal weight: 8.9990 chunk 343 optimal weight: 6.9990 chunk 623 optimal weight: 20.0000 chunk 187 optimal weight: 8.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 559 ASN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 496 GLN ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 595 GLN D 188 ASN ** D 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 GLN F 328 GLN F 437 ASN ** F 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 109 ASN ** G 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 HIS H 533 GLN ** I 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 533 GLN ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 392 ASN ** K 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 233 GLN ** L 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 349 GLN L 359 GLN ** L 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 188 ASN M 233 GLN ** M 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 595 GLN ** N 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 328 GLN ** N 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 533 GLN O 559 ASN ** O 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3204 moved from start: 0.5212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.080 55485 Z= 0.306 Angle : 0.745 13.102 75255 Z= 0.378 Chirality : 0.048 0.267 9120 Planarity : 0.006 0.092 9855 Dihedral : 6.019 43.134 7785 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 19.87 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.24 % Favored : 94.35 % Rotamer Outliers : 3.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.09), residues: 7200 helix: -0.01 (0.11), residues: 1980 sheet: -1.20 (0.09), residues: 2595 loop : -2.03 (0.11), residues: 2625 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 922 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 730 time to evaluate : 4.757 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 outliers start: 192 outliers final: 94 residues processed: 877 average time/residue: 0.4760 time to fit residues: 723.4498 Evaluate side-chains 696 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 602 time to evaluate : 4.706 Switching outliers to nearest non-outliers outliers start: 94 outliers final: 0 residues processed: 94 average time/residue: 0.3859 time to fit residues: 74.5686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 579 optimal weight: 0.9980 chunk 395 optimal weight: 10.0000 chunk 10 optimal weight: 0.0980 chunk 518 optimal weight: 0.3980 chunk 287 optimal weight: 4.9990 chunk 593 optimal weight: 9.9990 chunk 481 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 355 optimal weight: 0.8980 chunk 624 optimal weight: 30.0000 chunk 175 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 233 GLN ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 GLN ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 GLN ** D 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 431 ASN E 533 GLN F 233 GLN G 165 GLN ** G 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 533 GLN ** I 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 186 ASN I 496 GLN ** I 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 533 GLN ** J 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 188 ASN K 233 GLN ** K 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 188 ASN N 233 GLN ** N 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 533 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3207 moved from start: 0.5569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.078 55485 Z= 0.178 Angle : 0.662 10.595 75255 Z= 0.331 Chirality : 0.047 0.272 9120 Planarity : 0.005 0.084 9855 Dihedral : 5.611 41.486 7785 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.62 % Favored : 95.96 % Rotamer Outliers : 1.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.09), residues: 7200 helix: 0.43 (0.11), residues: 1950 sheet: -0.93 (0.10), residues: 2535 loop : -1.81 (0.11), residues: 2715 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 812 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 720 time to evaluate : 4.724 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 outliers start: 92 outliers final: 42 residues processed: 786 average time/residue: 0.4898 time to fit residues: 673.8261 Evaluate side-chains 637 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 595 time to evaluate : 4.675 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.3858 time to fit residues: 37.5616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 234 optimal weight: 5.9990 chunk 626 optimal weight: 10.0000 chunk 137 optimal weight: 6.9990 chunk 408 optimal weight: 7.9990 chunk 171 optimal weight: 0.0570 chunk 696 optimal weight: 20.0000 chunk 578 optimal weight: 9.9990 chunk 322 optimal weight: 1.9990 chunk 57 optimal weight: 30.0000 chunk 230 optimal weight: 5.9990 chunk 365 optimal weight: 10.0000 overall best weight: 4.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 GLN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 565 ASN ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 GLN ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 GLN ** F 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 440 GLN ** G 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 496 GLN ** H 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 533 GLN ** I 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 496 GLN ** I 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 308 GLN ** J 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 533 GLN ** J 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 602 GLN ** L 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 392 ASN ** L 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 440 GLN M 496 GLN ** M 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 440 GLN O 496 GLN O 533 GLN ** O 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 602 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3220 moved from start: 0.6075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.058 55485 Z= 0.373 Angle : 0.777 13.310 75255 Z= 0.397 Chirality : 0.050 0.280 9120 Planarity : 0.006 0.092 9855 Dihedral : 6.021 40.223 7785 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 22.04 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.58 % Favored : 93.00 % Rotamer Outliers : 2.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.09), residues: 7200 helix: 0.18 (0.11), residues: 2040 sheet: -1.10 (0.10), residues: 2505 loop : -2.25 (0.11), residues: 2655 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 788 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 645 time to evaluate : 4.737 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 outliers start: 143 outliers final: 78 residues processed: 752 average time/residue: 0.4796 time to fit residues: 626.7228 Evaluate side-chains 633 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 555 time to evaluate : 4.694 Switching outliers to nearest non-outliers outliers start: 78 outliers final: 0 residues processed: 78 average time/residue: 0.4185 time to fit residues: 66.0417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/iotbx/cli_parser.py", line 864, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 63.6683 > 50: distance: 112 - 117: 8.748 distance: 117 - 118: 14.796 distance: 118 - 119: 6.614 distance: 119 - 120: 8.448 distance: 119 - 124: 6.070 distance: 121 - 122: 6.666 distance: 121 - 123: 7.586 distance: 124 - 125: 13.172 distance: 125 - 126: 16.865 distance: 125 - 128: 18.322 distance: 126 - 127: 11.518 distance: 128 - 129: 23.105 distance: 128 - 130: 9.259 distance: 131 - 132: 16.310 distance: 132 - 133: 4.538 distance: 132 - 135: 15.708 distance: 133 - 134: 31.727 distance: 133 - 139: 14.816 distance: 135 - 136: 10.727 distance: 136 - 137: 14.467 distance: 136 - 138: 23.106 distance: 139 - 140: 31.256 distance: 140 - 141: 25.391 distance: 141 - 142: 34.668 distance: 141 - 143: 31.188 distance: 144 - 145: 25.966 distance: 145 - 146: 33.203 distance: 145 - 147: 9.212 distance: 147 - 148: 7.940 distance: 148 - 149: 7.082 distance: 148 - 151: 7.089 distance: 149 - 150: 15.041 distance: 149 - 155: 8.715 distance: 151 - 152: 23.249 distance: 152 - 153: 6.123 distance: 152 - 154: 12.261 distance: 155 - 156: 9.314 distance: 156 - 157: 13.300 distance: 156 - 159: 5.772 distance: 157 - 158: 14.559 distance: 157 - 163: 3.217 distance: 159 - 160: 11.211 distance: 160 - 161: 12.842 distance: 161 - 162: 15.104 distance: 164 - 165: 6.272 distance: 164 - 167: 7.345 distance: 165 - 166: 6.313 distance: 165 - 171: 7.902 distance: 167 - 168: 8.224 distance: 168 - 169: 11.325 distance: 168 - 170: 11.486 distance: 171 - 172: 7.853 distance: 172 - 173: 4.671 distance: 172 - 175: 9.682 distance: 173 - 174: 5.116 distance: 173 - 180: 5.577 distance: 175 - 176: 13.963 distance: 176 - 177: 20.012 distance: 177 - 178: 12.623 distance: 177 - 179: 4.365 distance: 180 - 181: 3.550 distance: 181 - 182: 8.454 distance: 181 - 184: 12.005 distance: 182 - 183: 8.545 distance: 182 - 189: 10.336 distance: 184 - 185: 16.903 distance: 185 - 186: 7.861 distance: 186 - 187: 12.357 distance: 186 - 188: 13.370