Starting phenix.real_space_refine (version: dev) on Thu May 12 19:16:49 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i1x_0326/05_2022/6i1x_0326_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i1x_0326/05_2022/6i1x_0326.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i1x_0326/05_2022/6i1x_0326.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i1x_0326/05_2022/6i1x_0326.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i1x_0326/05_2022/6i1x_0326_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i1x_0326/05_2022/6i1x_0326_neut.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ASP 168": "OD1" <-> "OD2" Residue "A ARG 232": "NH1" <-> "NH2" Residue "A ARG 236": "NH1" <-> "NH2" Residue "A TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 510": "NH1" <-> "NH2" Residue "A TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 555": "NH1" <-> "NH2" Residue "B ASP 168": "OD1" <-> "OD2" Residue "B ARG 232": "NH1" <-> "NH2" Residue "B ARG 236": "NH1" <-> "NH2" Residue "B GLU 237": "OE1" <-> "OE2" Residue "B TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 510": "NH1" <-> "NH2" Residue "B TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 555": "NH1" <-> "NH2" Residue "C ASP 168": "OD1" <-> "OD2" Residue "C ARG 232": "NH1" <-> "NH2" Residue "C ARG 236": "NH1" <-> "NH2" Residue "C GLU 237": "OE1" <-> "OE2" Residue "C TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 510": "NH1" <-> "NH2" Residue "C TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 555": "NH1" <-> "NH2" Residue "D ASP 168": "OD1" <-> "OD2" Residue "D ARG 232": "NH1" <-> "NH2" Residue "D ARG 236": "NH1" <-> "NH2" Residue "D TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 510": "NH1" <-> "NH2" Residue "D TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 555": "NH1" <-> "NH2" Residue "E ASP 168": "OD1" <-> "OD2" Residue "E ARG 232": "NH1" <-> "NH2" Residue "E ARG 236": "NH1" <-> "NH2" Residue "E TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 510": "NH1" <-> "NH2" Residue "E TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 555": "NH1" <-> "NH2" Residue "F ASP 168": "OD1" <-> "OD2" Residue "F ARG 232": "NH1" <-> "NH2" Residue "F ARG 236": "NH1" <-> "NH2" Residue "F TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 510": "NH1" <-> "NH2" Residue "F TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 555": "NH1" <-> "NH2" Residue "G ASP 168": "OD1" <-> "OD2" Residue "G ARG 232": "NH1" <-> "NH2" Residue "G ARG 236": "NH1" <-> "NH2" Residue "G TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 510": "NH1" <-> "NH2" Residue "G TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 555": "NH1" <-> "NH2" Residue "H ASP 168": "OD1" <-> "OD2" Residue "H ARG 232": "NH1" <-> "NH2" Residue "H ARG 236": "NH1" <-> "NH2" Residue "H TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 510": "NH1" <-> "NH2" Residue "H TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 555": "NH1" <-> "NH2" Residue "I ASP 168": "OD1" <-> "OD2" Residue "I ARG 232": "NH1" <-> "NH2" Residue "I ARG 236": "NH1" <-> "NH2" Residue "I TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 510": "NH1" <-> "NH2" Residue "I TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 555": "NH1" <-> "NH2" Residue "I GLU 616": "OE1" <-> "OE2" Residue "J ASP 168": "OD1" <-> "OD2" Residue "J ARG 232": "NH1" <-> "NH2" Residue "J ARG 236": "NH1" <-> "NH2" Residue "J GLU 237": "OE1" <-> "OE2" Residue "J TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 510": "NH1" <-> "NH2" Residue "J TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 555": "NH1" <-> "NH2" Residue "K ASP 168": "OD1" <-> "OD2" Residue "K ARG 232": "NH1" <-> "NH2" Residue "K ARG 236": "NH1" <-> "NH2" Residue "K GLU 237": "OE1" <-> "OE2" Residue "K TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 510": "NH1" <-> "NH2" Residue "K TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 555": "NH1" <-> "NH2" Residue "L ASP 168": "OD1" <-> "OD2" Residue "L ARG 232": "NH1" <-> "NH2" Residue "L ARG 236": "NH1" <-> "NH2" Residue "L TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 510": "NH1" <-> "NH2" Residue "L TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 555": "NH1" <-> "NH2" Residue "M ASP 168": "OD1" <-> "OD2" Residue "M ARG 232": "NH1" <-> "NH2" Residue "M ARG 236": "NH1" <-> "NH2" Residue "M TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 510": "NH1" <-> "NH2" Residue "M TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 555": "NH1" <-> "NH2" Residue "N ASP 168": "OD1" <-> "OD2" Residue "N ARG 232": "NH1" <-> "NH2" Residue "N ARG 236": "NH1" <-> "NH2" Residue "N TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 510": "NH1" <-> "NH2" Residue "N TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 555": "NH1" <-> "NH2" Residue "O ASP 168": "OD1" <-> "OD2" Residue "O ARG 232": "NH1" <-> "NH2" Residue "O ARG 236": "NH1" <-> "NH2" Residue "O GLU 237": "OE1" <-> "OE2" Residue "O TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 510": "NH1" <-> "NH2" Residue "O TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 555": "NH1" <-> "NH2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/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: 27.81, per 1000 atoms: 0.51 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: 21.28 Conformation dependent library (CDL) restraints added in 6.3 seconds 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13290 Finding SS restraints... Secondary structure from input PDB file: 195 helices and 0 sheets defined 32.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 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: 11.89 Time building geometry restraints manager: 23.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 11082 1.32 - 1.45: 11247 1.45 - 1.58: 32856 1.58 - 1.70: 0 1.70 - 1.83: 300 Bond restraints: 55485 Sorted by residual: bond pdb=" CA TYR F 174 " pdb=" C TYR F 174 " ideal model delta sigma weight residual 1.520 1.545 -0.026 4.80e-03 4.34e+04 2.89e+01 bond pdb=" CA TYR G 174 " pdb=" C TYR G 174 " ideal model delta sigma weight residual 1.520 1.544 -0.025 4.80e-03 4.34e+04 2.65e+01 bond pdb=" CA TYR N 174 " pdb=" C TYR N 174 " ideal model delta sigma weight residual 1.520 1.544 -0.024 4.80e-03 4.34e+04 2.60e+01 bond pdb=" CA TYR K 174 " pdb=" C TYR K 174 " ideal model delta sigma weight residual 1.520 1.544 -0.024 4.80e-03 4.34e+04 2.59e+01 bond pdb=" CA TYR D 174 " pdb=" C TYR D 174 " ideal model delta sigma weight residual 1.520 1.544 -0.024 4.80e-03 4.34e+04 2.59e+01 ... (remaining 55480 not shown) Histogram of bond angle deviations from ideal: 94.24 - 102.35: 371 102.35 - 110.45: 13037 110.45 - 118.55: 35793 118.55 - 126.66: 25710 126.66 - 134.76: 344 Bond angle restraints: 75255 Sorted by residual: angle pdb=" N PRO I 609 " pdb=" CA PRO I 609 " pdb=" CB PRO I 609 " ideal model delta sigma weight residual 103.25 94.24 9.01 1.05e+00 9.07e-01 7.36e+01 angle pdb=" N PRO D 609 " pdb=" CA PRO D 609 " pdb=" CB PRO D 609 " ideal model delta sigma weight residual 103.25 94.43 8.82 1.05e+00 9.07e-01 7.06e+01 angle pdb=" N PRO H 609 " pdb=" CA PRO H 609 " pdb=" CB PRO H 609 " ideal model delta sigma weight residual 103.25 94.45 8.80 1.05e+00 9.07e-01 7.03e+01 angle pdb=" N PRO B 609 " pdb=" CA PRO B 609 " pdb=" CB PRO B 609 " ideal model delta sigma weight residual 103.25 94.49 8.76 1.05e+00 9.07e-01 6.96e+01 angle pdb=" N PRO C 609 " pdb=" CA PRO C 609 " pdb=" CB PRO C 609 " ideal model delta sigma weight residual 103.25 94.50 8.75 1.05e+00 9.07e-01 6.94e+01 ... (remaining 75250 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.10: 30582 18.10 - 36.19: 2588 36.19 - 54.29: 609 54.29 - 72.39: 121 72.39 - 90.49: 30 Dihedral angle restraints: 33930 sinusoidal: 13230 harmonic: 20700 Sorted by residual: dihedral pdb=" CA LYS I 189 " pdb=" C LYS I 189 " pdb=" N ASP I 190 " pdb=" CA ASP I 190 " ideal model delta harmonic sigma weight residual 180.00 150.09 29.91 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA LYS H 189 " pdb=" C LYS H 189 " pdb=" N ASP H 190 " pdb=" CA ASP H 190 " ideal model delta harmonic sigma weight residual 180.00 151.35 28.65 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA LYS G 189 " pdb=" C LYS G 189 " pdb=" N ASP G 190 " pdb=" CA ASP G 190 " ideal model delta harmonic sigma weight residual 180.00 152.60 27.40 0 5.00e+00 4.00e-02 3.00e+01 ... (remaining 33927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3853 0.061 - 0.123: 3239 0.123 - 0.184: 1572 0.184 - 0.245: 391 0.245 - 0.306: 65 Chirality restraints: 9120 Sorted by residual: chirality pdb=" CA LYS E 250 " pdb=" N LYS E 250 " pdb=" C LYS E 250 " pdb=" CB LYS E 250 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CA LYS F 250 " pdb=" N LYS F 250 " pdb=" C LYS F 250 " pdb=" CB LYS F 250 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA LYS L 250 " pdb=" N LYS L 250 " pdb=" C LYS L 250 " pdb=" CB LYS L 250 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.30e+00 ... (remaining 9117 not shown) Planarity restraints: 9855 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL F 613 " 0.018 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" C VAL F 613 " -0.065 2.00e-02 2.50e+03 pdb=" O VAL F 613 " 0.025 2.00e-02 2.50e+03 pdb=" N LEU F 614 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 613 " 0.018 2.00e-02 2.50e+03 3.73e-02 1.39e+01 pdb=" C VAL B 613 " -0.064 2.00e-02 2.50e+03 pdb=" O VAL B 613 " 0.025 2.00e-02 2.50e+03 pdb=" N LEU B 614 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL H 613 " 0.017 2.00e-02 2.50e+03 3.72e-02 1.39e+01 pdb=" C VAL H 613 " -0.064 2.00e-02 2.50e+03 pdb=" O VAL H 613 " 0.025 2.00e-02 2.50e+03 pdb=" N LEU H 614 " 0.022 2.00e-02 2.50e+03 ... (remaining 9852 not shown) Histogram of nonbonded interaction distances: 0.46 - 1.35: 5 1.35 - 2.23: 94 2.23 - 3.12: 45107 3.12 - 4.01: 145267 4.01 - 4.90: 262893 Warning: very small nonbonded interaction distances. Nonbonded interactions: 453366 Sorted by model distance: nonbonded pdb=" CG2 VAL H 139 " pdb=" C ALA I 162 " model vdw 0.458 3.690 nonbonded pdb=" CB VAL H 139 " pdb=" O ALA I 162 " model vdw 0.818 3.470 nonbonded pdb=" CG2 VAL H 139 " pdb=" O ALA I 162 " model vdw 1.091 3.460 nonbonded pdb=" CG2 VAL H 139 " pdb=" N GLY I 163 " model vdw 1.289 3.540 nonbonded pdb=" ND2 ASN I 138 " pdb=" O THR J 198 " model vdw 1.323 2.520 ... (remaining 453361 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 150 5.16 5 C 34155 2.51 5 N 9675 2.21 5 O 10935 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.490 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: 0.030 Extract box with map and model: 7.210 Check model and map are aligned: 0.660 Convert atoms to be neutral: 0.370 Process input model: 115.200 Find NCS groups from input model: 3.200 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3168 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.013 0.061 55485 Z= 0.838 Angle : 1.810 9.397 75255 Z= 1.296 Chirality : 0.098 0.306 9120 Planarity : 0.008 0.072 9855 Dihedral : 14.937 90.487 20640 Min Nonbonded Distance : 0.458 Molprobity Statistics. All-atom Clashscore : 50.06 Ramachandran Plot: Outliers : 1.89 % Allowed : 7.50 % Favored : 90.61 % Rotamer Outliers : 4.35 % Cbeta Deviations : 0.51 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.08), residues: 7200 helix: -2.95 (0.08), residues: 1965 sheet: -1.10 (0.10), residues: 2175 loop : -2.72 (0.08), residues: 3060 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1804 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 263 poor density : 1541 time to evaluate : 4.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 263 outliers final: 71 residues processed: 1752 average time/residue: 0.5360 time to fit residues: 1525.9939 Evaluate side-chains 800 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 729 time to evaluate : 4.895 Switching outliers to nearest non-outliers outliers start: 71 outliers final: 0 residues processed: 71 average time/residue: 0.3685 time to fit residues: 56.4481 ------------------------------------------------------------------------------- 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: 3.9990 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 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 ** 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 ** 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 233 GLN ** 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: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3179 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.079 55485 Z= 0.253 Angle : 0.839 12.667 75255 Z= 0.426 Chirality : 0.051 0.545 9120 Planarity : 0.006 0.086 9855 Dihedral : 6.670 32.960 7785 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 20.22 Ramachandran Plot: Outliers : 0.39 % Allowed : 2.94 % Favored : 96.67 % Rotamer Outliers : 4.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.42 % 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: -1.17 (0.09), residues: 2745 loop : -1.91 (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 1229 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 294 poor density : 935 time to evaluate : 4.810 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: 294 outliers final: 108 residues processed: 1149 average time/residue: 0.5016 time to fit residues: 976.5758 Evaluate side-chains 762 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 654 time to evaluate : 4.871 Switching outliers to nearest non-outliers outliers start: 108 outliers final: 0 residues processed: 108 average time/residue: 0.3866 time to fit residues: 85.2326 ------------------------------------------------------------------------------- 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: 5.9990 chunk 202 optimal weight: 10.0000 chunk 544 optimal weight: 2.9990 chunk 445 optimal weight: 3.9990 chunk 180 optimal weight: 9.9990 chunk 655 optimal weight: 4.9990 chunk 707 optimal weight: 0.9990 chunk 583 optimal weight: 3.9990 chunk 649 optimal weight: 10.0000 chunk 223 optimal weight: 5.9990 chunk 525 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 GLN A 559 ASN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 GLN B 345 ASN B 440 GLN B 475 GLN B 496 GLN ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 392 ASN C 404 ASN ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 496 GLN ** C 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 233 GLN ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 440 GLN ** E 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 496 GLN ** E 533 GLN ** 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 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 138 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 392 ASN ** J 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 496 GLN J 559 ASN ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 392 ASN ** K 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 559 ASN ** L 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 533 GLN L 559 ASN ** M 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 345 ASN ** M 349 GLN ** 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 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 345 ASN 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 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 496 GLN O 533 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3203 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.112 55485 Z= 0.326 Angle : 0.799 15.800 75255 Z= 0.407 Chirality : 0.049 0.253 9120 Planarity : 0.006 0.113 9855 Dihedral : 6.172 35.720 7785 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 20.23 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.40 % Favored : 95.18 % Rotamer Outliers : 3.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.83 % 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: -0.35 (0.11), residues: 1950 sheet: -1.04 (0.09), residues: 2475 loop : -2.13 (0.11), residues: 2775 *********************** 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 972 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 766 time to evaluate : 4.837 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 outliers start: 206 outliers final: 105 residues processed: 909 average time/residue: 0.5298 time to fit residues: 823.2062 Evaluate side-chains 719 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 614 time to evaluate : 4.843 Switching outliers to nearest non-outliers outliers start: 105 outliers final: 0 residues processed: 105 average time/residue: 0.3836 time to fit residues: 83.7917 ------------------------------------------------------------------------------- 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: 9.9990 chunk 339 optimal weight: 10.0000 chunk 72 optimal weight: 0.5980 chunk 312 optimal weight: 0.6980 chunk 439 optimal weight: 0.0000 chunk 657 optimal weight: 0.9990 chunk 695 optimal weight: 20.0000 chunk 343 optimal weight: 3.9990 chunk 623 optimal weight: 20.0000 chunk 187 optimal weight: 7.9990 overall best weight: 1.2588 ------------------------------------------------------------------------------- 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 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 GLN ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 595 GLN ** D 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 475 GLN E 533 GLN ** E 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 109 ASN ** G 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 392 ASN ** K 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 233 GLN ** L 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 349 GLN L 359 GLN ** L 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 188 ASN M 233 GLN ** M 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 595 GLN ** N 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 328 GLN ** N 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 533 GLN O 559 ASN ** O 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 602 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3199 moved from start: 0.5030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.105 55485 Z= 0.228 Angle : 0.707 15.558 75255 Z= 0.354 Chirality : 0.047 0.277 9120 Planarity : 0.006 0.101 9855 Dihedral : 5.707 34.393 7785 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.38 % Favored : 96.21 % Rotamer Outliers : 2.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.42 % 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: -1.59 (0.09), residues: 7200 helix: 0.09 (0.11), residues: 1950 sheet: -0.94 (0.10), residues: 2535 loop : -1.87 (0.11), residues: 2715 *********************** 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 845 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 707 time to evaluate : 4.844 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 outliers start: 138 outliers final: 63 residues processed: 807 average time/residue: 0.4771 time to fit residues: 668.1148 Evaluate side-chains 661 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 598 time to evaluate : 4.889 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 0 residues processed: 63 average time/residue: 0.3844 time to fit residues: 52.4008 ------------------------------------------------------------------------------- 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: 10.0000 chunk 395 optimal weight: 0.0770 chunk 10 optimal weight: 8.9990 chunk 518 optimal weight: 0.6980 chunk 287 optimal weight: 6.9990 chunk 593 optimal weight: 1.9990 chunk 481 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 355 optimal weight: 0.9990 chunk 624 optimal weight: 30.0000 chunk 175 optimal weight: 6.9990 overall best weight: 2.1544 ------------------------------------------------------------------------------- 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 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 GLN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 GLN B 565 ASN ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 GLN ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN D 233 GLN ** D 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 GLN ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 ASN ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 GLN ** E 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 165 GLN ** 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 186 ASN H 533 GLN ** I 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 186 ASN I 496 GLN ** I 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 533 GLN ** J 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 233 GLN ** K 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 392 ASN ** L 475 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 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 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 188 ASN N 233 GLN ** N 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 533 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3208 moved from start: 0.5432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.198 55485 Z= 0.258 Angle : 0.706 15.020 75255 Z= 0.356 Chirality : 0.047 0.276 9120 Planarity : 0.005 0.102 9855 Dihedral : 5.587 33.368 7785 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 19.26 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.11 % Favored : 94.47 % Rotamer Outliers : 2.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.42 % 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: -1.53 (0.09), residues: 7200 helix: 0.23 (0.11), residues: 1965 sheet: -1.02 (0.10), residues: 2535 loop : -1.80 (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 784 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 659 time to evaluate : 4.875 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: 125 outliers final: 50 residues processed: 750 average time/residue: 0.5023 time to fit residues: 649.6859 Evaluate side-chains 621 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 571 time to evaluate : 4.955 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 0 residues processed: 50 average time/residue: 0.3899 time to fit residues: 44.2669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 234 optimal weight: 5.9990 chunk 626 optimal weight: 6.9990 chunk 137 optimal weight: 0.0570 chunk 408 optimal weight: 9.9990 chunk 171 optimal weight: 0.0670 chunk 696 optimal weight: 20.0000 chunk 578 optimal weight: 0.7980 chunk 322 optimal weight: 0.7980 chunk 57 optimal weight: 30.0000 chunk 230 optimal weight: 7.9990 chunk 365 optimal weight: 8.9990 overall best weight: 1.5438 ------------------------------------------------------------------------------- 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 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 GLN ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN ** C 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 533 GLN ** E 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 233 GLN ** F 475 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 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 533 GLN ** J 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 188 ASN ** K 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 308 GLN ** L 328 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 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 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 109 ASN ** 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3215 moved from start: 0.5748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.247 55485 Z= 0.243 Angle : 0.697 16.833 75255 Z= 0.352 Chirality : 0.046 0.360 9120 Planarity : 0.005 0.098 9855 Dihedral : 5.457 32.556 7785 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.33 % Favored : 95.25 % Rotamer Outliers : 1.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.42 % 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: -1.39 (0.09), residues: 7200 helix: 0.33 (0.11), residues: 2040 sheet: -0.83 (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 742 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 641 time to evaluate : 5.142 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: 101 outliers final: 39 residues processed: 713 average time/residue: 0.4889 time to fit residues: 603.2790 Evaluate side-chains 596 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 557 time to evaluate : 4.880 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.3922 time to fit residues: 35.6822 ------------------------------------------------------------------------------- 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: 4.9990 chunk 78 optimal weight: 4.9990 chunk 396 optimal weight: 5.9990 chunk 508 optimal weight: 0.0270 chunk 394 optimal weight: 20.0000 chunk 586 optimal weight: 7.9990 chunk 389 optimal weight: 3.9990 chunk 693 optimal weight: 3.9990 chunk 434 optimal weight: 20.0000 chunk 423 optimal weight: 6.9990 chunk 320 optimal weight: 1.9990 overall best weight: 3.0046 ------------------------------------------------------------------------------- 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 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 475 GLN ** 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 194 GLN ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 GLN ** E 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 440 GLN ** G 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 496 GLN ** H 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 533 GLN ** I 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 431 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 ** J 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 440 GLN M 496 GLN ** M 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 109 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3225 moved from start: 0.6136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.238 55485 Z= 0.321 Angle : 0.740 18.516 75255 Z= 0.376 Chirality : 0.048 0.282 9120 Planarity : 0.005 0.103 9855 Dihedral : 5.626 31.987 7785 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 20.31 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.88 % Favored : 93.71 % Rotamer Outliers : 1.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.42 % 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: -1.57 (0.10), residues: 7200 helix: 0.30 (0.11), residues: 2040 sheet: -1.03 (0.10), residues: 2580 loop : -2.01 (0.11), residues: 2580 *********************** 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 719 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 617 time to evaluate : 5.841 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: 102 outliers final: 48 residues processed: 683 average time/residue: 0.4940 time to fit residues: 587.4185 Evaluate side-chains 589 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 541 time to evaluate : 4.872 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 0.4063 time to fit residues: 42.5746 ------------------------------------------------------------------------------- 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: 10.0000 chunk 277 optimal weight: 1.9990 chunk 414 optimal weight: 0.8980 chunk 209 optimal weight: 0.7980 chunk 136 optimal weight: 20.0000 chunk 134 optimal weight: 3.9990 chunk 441 optimal weight: 30.0000 chunk 472 optimal weight: 1.9990 chunk 343 optimal weight: 20.0000 chunk 64 optimal weight: 8.9990 chunk 545 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 475 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 GLN ** E 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** ** I 533 GLN ** 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 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 533 GLN ** J 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 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 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 602 GLN ** O 109 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3226 moved from start: 0.6187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.472 55485 Z= 0.375 Angle : 0.817 73.894 75255 Z= 0.403 Chirality : 0.049 0.737 9120 Planarity : 0.006 0.112 9855 Dihedral : 5.650 32.231 7785 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 21.64 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.76 % Favored : 93.82 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.42 % 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: -1.58 (0.10), residues: 7200 helix: 0.31 (0.11), residues: 2040 sheet: -0.97 (0.10), residues: 2520 loop : -2.10 (0.11), residues: 2640 *********************** 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 617 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 554 time to evaluate : 4.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 32 residues processed: 597 average time/residue: 0.4803 time to fit residues: 500.7563 Evaluate side-chains 561 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 529 time to evaluate : 4.832 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.4222 time to fit residues: 31.5568 ------------------------------------------------------------------------------- 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: 9.9990 chunk 664 optimal weight: 10.0000 chunk 606 optimal weight: 0.7980 chunk 646 optimal weight: 20.0000 chunk 389 optimal weight: 7.9990 chunk 281 optimal weight: 0.9980 chunk 507 optimal weight: 20.0000 chunk 198 optimal weight: 20.0000 chunk 584 optimal weight: 1.9990 chunk 611 optimal weight: 3.9990 chunk 644 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 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** ** 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 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 431 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** ** I 533 GLN ** 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 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 533 GLN ** J 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 595 GLN ** 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 602 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** ** N 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 109 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 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3227 moved from start: 0.6288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.599 55485 Z= 0.324 Angle : 0.791 62.666 75255 Z= 0.386 Chirality : 0.048 0.320 9120 Planarity : 0.005 0.111 9855 Dihedral : 5.625 32.122 7785 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 19.91 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.76 % Favored : 93.82 % Rotamer Outliers : 0.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.42 % 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: -1.59 (0.10), residues: 7200 helix: 0.34 (0.11), residues: 2040 sheet: -1.00 (0.10), residues: 2520 loop : -2.11 (0.11), residues: 2640 *********************** 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 610 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 564 time to evaluate : 4.841 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: 46 outliers final: 19 residues processed: 593 average time/residue: 0.4839 time to fit residues: 498.0627 Evaluate side-chains 542 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 523 time to evaluate : 4.843 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.3803 time to fit residues: 20.5438 ------------------------------------------------------------------------------- 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: 0.0980 chunk 683 optimal weight: 10.0000 chunk 417 optimal weight: 0.0170 chunk 324 optimal weight: 9.9990 chunk 475 optimal weight: 5.9990 chunk 717 optimal weight: 1.9990 chunk 660 optimal weight: 9.9990 chunk 571 optimal weight: 0.9980 chunk 59 optimal weight: 9.9990 chunk 441 optimal weight: 30.0000 chunk 350 optimal weight: 10.0000 overall best weight: 1.8222 ------------------------------------------------------------------------------- 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 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 488 GLN E 533 GLN ** E 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 431 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** ** I 533 GLN ** 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 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 533 GLN ** J 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 595 GLN ** 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** ** 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** ** O 109 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3228 moved from start: 0.6367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.609 55485 Z= 0.306 Angle : 0.784 63.253 75255 Z= 0.383 Chirality : 0.048 0.368 9120 Planarity : 0.005 0.160 9855 Dihedral : 5.594 37.470 7785 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 20.02 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.60 % Favored : 94.00 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.42 % 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: -1.52 (0.10), residues: 7200 helix: 0.40 (0.11), residues: 2040 sheet: -0.92 (0.10), residues: 2505 loop : -2.10 (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 567 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 548 time to evaluate : 4.877 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: 19 outliers final: 8 residues processed: 559 average time/residue: 0.4921 time to fit residues: 476.5881 Evaluate side-chains 534 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 526 time to evaluate : 4.868 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3780 time to fit residues: 12.5169 ------------------------------------------------------------------------------- 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: 0.9980 chunk 608 optimal weight: 0.8980 chunk 174 optimal weight: 7.9990 chunk 526 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 158 optimal weight: 9.9990 chunk 572 optimal weight: 0.9990 chunk 239 optimal weight: 9.9990 chunk 587 optimal weight: 4.9990 chunk 72 optimal weight: 20.0000 chunk 105 optimal weight: 30.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 GLN ** E 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 440 GLN F 496 GLN ** G 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 431 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** ** I 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 533 GLN ** 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 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 533 GLN ** J 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 595 GLN ** 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** ** 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** ** O 109 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 = 0.4803 r_free = 0.4803 target = 0.219582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.205895 restraints weight = 71362.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.202341 restraints weight = 122246.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.201285 restraints weight = 71882.660| |-----------------------------------------------------------------------------| r_work (final): 0.4619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6055 moved from start: 0.6442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.586 55485 Z= 0.295 Angle : 0.773 57.643 75255 Z= 0.379 Chirality : 0.047 0.370 9120 Planarity : 0.006 0.146 9855 Dihedral : 5.538 39.644 7785 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.78 % Favored : 93.82 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.42 % 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: -1.44 (0.10), residues: 7200 helix: 0.43 (0.11), residues: 2040 sheet: -0.85 (0.10), residues: 2475 loop : -2.06 (0.11), residues: 2685 =============================================================================== Job complete usr+sys time: 11135.15 seconds wall clock time: 197 minutes 15.35 seconds (11835.35 seconds total)