Starting phenix.real_space_refine on Tue Nov 14 01:52:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i1x_0326/11_2023/6i1x_0326_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i1x_0326/11_2023/6i1x_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_0326/11_2023/6i1x_0326.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i1x_0326/11_2023/6i1x_0326.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i1x_0326/11_2023/6i1x_0326_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i1x_0326/11_2023/6i1x_0326_neut.pdb" } resolution = 3.7 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 ------------------------------------------------------------------------------- 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 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. 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: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 21.11, per 1000 atoms: 0.38 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: 16.27 Conformation dependent library (CDL) restraints added in 7.9 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: 2.98 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: 11.90 Time building geometry restraints manager: 17.93 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 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: 0.570 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: 5.510 Check model and map are aligned: 0.600 Set scattering table: 0.380 Process input model: 102.910 Find NCS groups from input model: 2.910 Set up NCS constraints: 0.330 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:2.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3237 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 % Allowed : 8.17 % Favored : 87.48 % 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 : 4.879 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: 0.5624 time to fit residues: 1597.3435 Evaluate side-chains 799 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 728 time to evaluate : 4.620 Switching outliers to nearest non-outliers outliers start: 71 outliers final: 0 residues processed: 71 average time/residue: 0.3873 time to fit residues: 59.3097 ------------------------------------------------------------------------------- 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: 0.3242 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 44.659 7785 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 20.46 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.19 % Favored : 96.44 % Rotamer: Outliers : 4.81 % Allowed : 14.92 % Favored : 80.26 % 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 : 4.633 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: 0.5408 time to fit residues: 1046.8813 Evaluate side-chains 776 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 670 time to evaluate : 4.623 Switching outliers to nearest non-outliers outliers start: 106 outliers final: 0 residues processed: 106 average time/residue: 0.4154 time to fit residues: 89.2822 ------------------------------------------------------------------------------- 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: 10.0000 chunk 202 optimal weight: 3.9990 chunk 544 optimal weight: 4.9990 chunk 445 optimal weight: 0.9980 chunk 180 optimal weight: 8.9990 chunk 655 optimal weight: 3.9990 chunk 707 optimal weight: 0.9990 chunk 583 optimal weight: 10.0000 chunk 649 optimal weight: 9.9990 chunk 223 optimal weight: 4.9990 chunk 525 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 B 496 GLN ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 328 GLN C 404 ASN ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 328 GLN ** 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 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 233 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** M 345 ASN ** M 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 328 GLN N 496 GLN ** O 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 186 ASN ** O 233 GLN ** 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 496 GLN O 533 GLN O 559 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3269 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 55485 Z= 0.306 Angle : 0.768 9.934 75255 Z= 0.392 Chirality : 0.049 0.255 9120 Planarity : 0.006 0.102 9855 Dihedral : 6.250 44.260 7785 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 20.35 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.51 % Favored : 95.07 % Rotamer: Outliers : 3.36 % Allowed : 19.32 % Favored : 77.32 % 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: -1.97 (0.09), residues: 7200 helix: -0.31 (0.11), residues: 1950 sheet: -1.07 (0.09), residues: 2445 loop : -2.12 (0.11), residues: 2805 *********************** 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 995 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 792 time to evaluate : 4.711 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 outliers start: 203 outliers final: 115 residues processed: 937 average time/residue: 0.5318 time to fit residues: 847.6407 Evaluate side-chains 729 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 614 time to evaluate : 4.632 Switching outliers to nearest non-outliers outliers start: 115 outliers final: 0 residues processed: 115 average time/residue: 0.4072 time to fit residues: 96.3349 ------------------------------------------------------------------------------- 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: 10.0000 chunk 492 optimal weight: 20.0000 chunk 339 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 312 optimal weight: 0.6980 chunk 439 optimal weight: 3.9990 chunk 657 optimal weight: 2.9990 chunk 695 optimal weight: 0.1980 chunk 343 optimal weight: 9.9990 chunk 623 optimal weight: 30.0000 chunk 187 optimal weight: 7.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- 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** A 559 ASN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 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 194 GLN ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 GLN G 109 ASN ** G 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 475 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 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 431 ASN ** 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 188 ASN M 233 GLN ** M 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 431 ASN ** 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 188 ASN ** N 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 233 GLN ** 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 ** O 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3267 moved from start: 0.5320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 55485 Z= 0.297 Angle : 0.744 14.269 75255 Z= 0.378 Chirality : 0.048 0.268 9120 Planarity : 0.006 0.093 9855 Dihedral : 6.063 43.035 7785 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 20.48 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.32 % Favored : 94.26 % Rotamer: Outliers : 2.85 % Allowed : 20.98 % Favored : 76.18 % 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: -1.89 (0.09), residues: 7200 helix: -0.06 (0.11), residues: 1995 sheet: -1.24 (0.09), residues: 2580 loop : -2.05 (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 899 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 727 time to evaluate : 4.830 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: 172 outliers final: 81 residues processed: 858 average time/residue: 0.4987 time to fit residues: 740.5079 Evaluate side-chains 684 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 603 time to evaluate : 4.662 Switching outliers to nearest non-outliers outliers start: 81 outliers final: 0 residues processed: 81 average time/residue: 0.3992 time to fit residues: 67.3017 ------------------------------------------------------------------------------- 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: 30.0000 chunk 395 optimal weight: 8.9990 chunk 10 optimal weight: 0.0570 chunk 518 optimal weight: 0.9990 chunk 287 optimal weight: 10.0000 chunk 593 optimal weight: 0.0570 chunk 481 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 355 optimal weight: 2.9990 chunk 624 optimal weight: 30.0000 chunk 175 optimal weight: 0.8980 overall best weight: 1.0020 ------------------------------------------------------------------------------- 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 565 ASN ** 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 ** 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 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 GLN F 233 GLN ** G 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 475 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 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 308 GLN ** J 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 533 GLN ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 188 ASN K 233 GLN ** K 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 431 ASN ** 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 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 233 GLN N 308 GLN ** N 394 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 Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3269 moved from start: 0.5668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 55485 Z= 0.184 Angle : 0.663 11.411 75255 Z= 0.333 Chirality : 0.046 0.267 9120 Planarity : 0.005 0.084 9855 Dihedral : 5.661 41.493 7785 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.94 % Favored : 95.64 % Rotamer: Outliers : 1.75 % Allowed : 21.97 % Favored : 76.28 % 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: -1.51 (0.09), residues: 7200 helix: 0.36 (0.11), residues: 1965 sheet: -1.04 (0.10), residues: 2535 loop : -1.86 (0.11), residues: 2700 *********************** 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 820 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 714 time to evaluate : 4.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 106 outliers final: 51 residues processed: 790 average time/residue: 0.5017 time to fit residues: 690.8283 Evaluate side-chains 647 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 596 time to evaluate : 4.737 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 0 residues processed: 51 average time/residue: 0.4068 time to fit residues: 46.0593 ------------------------------------------------------------------------------- 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: 7.9990 chunk 626 optimal weight: 6.9990 chunk 137 optimal weight: 0.6980 chunk 408 optimal weight: 3.9990 chunk 171 optimal weight: 0.5980 chunk 696 optimal weight: 0.7980 chunk 578 optimal weight: 5.9990 chunk 322 optimal weight: 0.0020 chunk 57 optimal weight: 30.0000 chunk 230 optimal weight: 0.5980 chunk 365 optimal weight: 7.9990 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 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 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 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 GLN F 233 GLN G 138 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 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 496 GLN J 533 GLN ** J 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 109 ASN ** 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 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 431 ASN ** 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 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 587 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3277 moved from start: 0.5905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 55485 Z= 0.170 Angle : 0.646 12.482 75255 Z= 0.324 Chirality : 0.046 0.285 9120 Planarity : 0.005 0.083 9855 Dihedral : 5.441 39.880 7785 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.86 % Favored : 95.72 % Rotamer: Outliers : 1.27 % Allowed : 22.89 % Favored : 75.83 % 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: -1.29 (0.10), residues: 7200 helix: 0.42 (0.11), residues: 2040 sheet: -0.75 (0.10), residues: 2475 loop : -1.87 (0.11), residues: 2685 *********************** 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 739 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 662 time to evaluate : 4.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 26 residues processed: 718 average time/residue: 0.5100 time to fit residues: 633.3127 Evaluate side-chains 591 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 565 time to evaluate : 4.695 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 26 outliers final: 1 residues processed: 26 average time/residue: 0.4456 time to fit residues: 27.5506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 671 optimal weight: 7.9990 chunk 78 optimal weight: 5.9990 chunk 396 optimal weight: 8.9990 chunk 508 optimal weight: 6.9990 chunk 394 optimal weight: 0.0970 chunk 586 optimal weight: 2.9990 chunk 389 optimal weight: 20.0000 chunk 693 optimal weight: 0.7980 chunk 434 optimal weight: 20.0000 chunk 423 optimal weight: 2.9990 chunk 320 optimal weight: 0.9980 overall best weight: 1.5782 ------------------------------------------------------------------------------- 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** ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 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 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 GLN F 233 GLN ** F 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 496 GLN J 533 GLN ** K 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 431 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 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 431 ASN ** 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 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 301 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 496 GLN ** O 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3282 moved from start: 0.6144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 55485 Z= 0.205 Angle : 0.666 13.831 75255 Z= 0.332 Chirality : 0.046 0.378 9120 Planarity : 0.005 0.082 9855 Dihedral : 5.423 44.776 7785 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.01 % Favored : 94.62 % Rotamer: Outliers : 1.36 % Allowed : 23.64 % Favored : 75.00 % 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: -1.24 (0.10), residues: 7200 helix: 0.49 (0.11), residues: 2040 sheet: -0.77 (0.10), residues: 2475 loop : -1.81 (0.11), residues: 2685 *********************** REFINEMENT MACRO_CYCLE 7 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 685 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 603 time to evaluate : 4.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 82 outliers final: 36 residues processed: 657 average time/residue: 0.5088 time to fit residues: 577.1603 Evaluate side-chains 599 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 563 time to evaluate : 4.623 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.3926 time to fit residues: 33.5265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 429 optimal weight: 9.9990 chunk 277 optimal weight: 3.9990 chunk 414 optimal weight: 0.8980 chunk 209 optimal weight: 0.4980 chunk 136 optimal weight: 1.9990 chunk 134 optimal weight: 7.9990 chunk 441 optimal weight: 30.0000 chunk 472 optimal weight: 3.9990 chunk 343 optimal weight: 20.0000 chunk 64 optimal weight: 4.9990 chunk 545 optimal weight: 9.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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** ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 595 GLN ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 GLN ** F 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 533 GLN ** K 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 431 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 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 431 ASN ** 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 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 431 ASN ** 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** ** N 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 595 GLN ** 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 496 GLN ** O 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3286 moved from start: 0.6409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 55485 Z= 0.244 Angle : 0.679 11.930 75255 Z= 0.341 Chirality : 0.047 0.309 9120 Planarity : 0.005 0.073 9855 Dihedral : 5.528 44.375 7785 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.69 % Favored : 94.04 % Rotamer: Outliers : 1.11 % Allowed : 24.02 % Favored : 74.87 % 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: -1.31 (0.10), residues: 7200 helix: 0.56 (0.11), residues: 2040 sheet: -0.90 (0.10), residues: 2490 loop : -1.87 (0.11), residues: 2670 *********************** REFINEMENT MACRO_CYCLE 8 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 673 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 606 time to evaluate : 4.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 33 residues processed: 657 average time/residue: 0.5047 time to fit residues: 577.8127 Evaluate side-chains 580 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 547 time to evaluate : 4.646 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.4257 time to fit residues: 32.2908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 631 optimal weight: 20.0000 chunk 664 optimal weight: 8.9990 chunk 606 optimal weight: 0.8980 chunk 646 optimal weight: 9.9990 chunk 389 optimal weight: 6.9990 chunk 281 optimal weight: 1.9990 chunk 507 optimal weight: 8.9990 chunk 198 optimal weight: 6.9990 chunk 584 optimal weight: 9.9990 chunk 611 optimal weight: 0.7980 chunk 644 optimal weight: 1.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 GLN F 440 GLN F 496 GLN ** F 595 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 I 109 ASN ** I 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 533 GLN ** K 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 431 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 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 431 ASN ** 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 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 488 GLN ** M 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 213 ASN ** O 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3290 moved from start: 0.6662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 55485 Z= 0.261 Angle : 0.706 12.170 75255 Z= 0.352 Chirality : 0.048 0.348 9120 Planarity : 0.005 0.071 9855 Dihedral : 5.604 41.699 7785 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 19.12 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.03 % Favored : 93.71 % Rotamer: Outliers : 0.61 % Allowed : 24.53 % Favored : 74.86 % 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: -1.42 (0.10), residues: 7200 helix: 0.54 (0.11), residues: 2040 sheet: -0.95 (0.10), residues: 2550 loop : -2.02 (0.11), residues: 2610 *********************** REFINEMENT MACRO_CYCLE 9 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 638 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 601 time to evaluate : 5.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 17 residues processed: 619 average time/residue: 0.5103 time to fit residues: 547.6334 Evaluate side-chains 554 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 537 time to evaluate : 6.102 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.4451 time to fit residues: 21.5535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 424 optimal weight: 6.9990 chunk 683 optimal weight: 1.9990 chunk 417 optimal weight: 0.0870 chunk 324 optimal weight: 0.0670 chunk 475 optimal weight: 4.9990 chunk 717 optimal weight: 0.7980 chunk 660 optimal weight: 0.0470 chunk 571 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 441 optimal weight: 0.0020 chunk 350 optimal weight: 2.9990 overall best weight: 0.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 440 GLN ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 GLN ** E 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 109 ASN ** G 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 533 GLN ** K 431 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 328 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 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 488 GLN ** M 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 301 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3295 moved from start: 0.6805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 55485 Z= 0.166 Angle : 0.659 13.545 75255 Z= 0.326 Chirality : 0.046 0.362 9120 Planarity : 0.004 0.094 9855 Dihedral : 5.318 41.667 7785 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.32 % Favored : 96.43 % Rotamer: Outliers : 0.26 % Allowed : 25.28 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -0.99 (0.10), residues: 7200 helix: 0.75 (0.11), residues: 2055 sheet: -0.66 (0.11), residues: 2490 loop : -1.67 (0.11), residues: 2655 ********************** REFINEMENT MACRO_CYCLE 10 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 630 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 614 time to evaluate : 4.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 6 residues processed: 625 average time/residue: 0.5255 time to fit residues: 564.4343 Evaluate side-chains 555 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 549 time to evaluate : 4.661 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.4805 time to fit residues: 11.9750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 453 optimal weight: 4.9990 chunk 608 optimal weight: 0.8980 chunk 174 optimal weight: 0.9980 chunk 526 optimal weight: 1.9990 chunk 84 optimal weight: 0.0030 chunk 158 optimal weight: 10.0000 chunk 572 optimal weight: 0.9990 chunk 239 optimal weight: 9.9990 chunk 587 optimal weight: 20.0000 chunk 72 optimal weight: 9.9990 chunk 105 optimal weight: 30.0000 overall best weight: 0.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 488 GLN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 496 GLN ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** I 109 ASN ** I 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 533 GLN ** K 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 431 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 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 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 301 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4885 r_free = 0.4885 target = 0.228834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.213700 restraints weight = 70975.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.211925 restraints weight = 117699.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.209213 restraints weight = 69397.921| |-----------------------------------------------------------------------------| r_work (final): 0.4710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5916 moved from start: 0.6907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 55485 Z= 0.182 Angle : 0.657 12.020 75255 Z= 0.324 Chirality : 0.046 0.336 9120 Planarity : 0.004 0.086 9855 Dihedral : 5.208 39.384 7785 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.81 % Favored : 94.96 % Rotamer: Outliers : 0.30 % Allowed : 25.84 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -0.88 (0.10), residues: 7200 helix: 0.81 (0.11), residues: 2055 sheet: -0.56 (0.11), residues: 2505 loop : -1.63 (0.12), residues: 2640 =============================================================================== Job complete usr+sys time: 12004.16 seconds wall clock time: 212 minutes 19.61 seconds (12739.61 seconds total)