Starting phenix.real_space_refine on Fri Feb 16 18:44:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uzy_20964/02_2024/6uzy_20964_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uzy_20964/02_2024/6uzy_20964.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uzy_20964/02_2024/6uzy_20964.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uzy_20964/02_2024/6uzy_20964.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uzy_20964/02_2024/6uzy_20964_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uzy_20964/02_2024/6uzy_20964_updated.pdb" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 7 5.49 5 S 77 5.16 5 C 10948 2.51 5 N 2443 2.21 5 O 2737 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 29": "NH1" <-> "NH2" Residue "A GLU 57": "OE1" <-> "OE2" Residue "A ARG 75": "NH1" <-> "NH2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A ARG 251": "NH1" <-> "NH2" Residue "A ARG 256": "NH1" <-> "NH2" Residue "A ARG 276": "NH1" <-> "NH2" Residue "B ARG 29": "NH1" <-> "NH2" Residue "B GLU 57": "OE1" <-> "OE2" Residue "B ARG 75": "NH1" <-> "NH2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B ARG 251": "NH1" <-> "NH2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B ARG 276": "NH1" <-> "NH2" Residue "C ARG 29": "NH1" <-> "NH2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C ARG 75": "NH1" <-> "NH2" Residue "C ARG 219": "NH1" <-> "NH2" Residue "C ARG 251": "NH1" <-> "NH2" Residue "C ARG 256": "NH1" <-> "NH2" Residue "C ARG 276": "NH1" <-> "NH2" Residue "D ARG 29": "NH1" <-> "NH2" Residue "D GLU 57": "OE1" <-> "OE2" Residue "D ARG 75": "NH1" <-> "NH2" Residue "D ARG 219": "NH1" <-> "NH2" Residue "D ARG 251": "NH1" <-> "NH2" Residue "D ARG 256": "NH1" <-> "NH2" Residue "D ARG 276": "NH1" <-> "NH2" Residue "E ARG 29": "NH1" <-> "NH2" Residue "E GLU 57": "OE1" <-> "OE2" Residue "E ARG 75": "NH1" <-> "NH2" Residue "E ARG 219": "NH1" <-> "NH2" Residue "E ARG 251": "NH1" <-> "NH2" Residue "E ARG 256": "NH1" <-> "NH2" Residue "E ARG 276": "NH1" <-> "NH2" Residue "F ARG 29": "NH1" <-> "NH2" Residue "F GLU 57": "OE1" <-> "OE2" Residue "F ARG 75": "NH1" <-> "NH2" Residue "F ARG 219": "NH1" <-> "NH2" Residue "F ARG 251": "NH1" <-> "NH2" Residue "F ARG 256": "NH1" <-> "NH2" Residue "F ARG 276": "NH1" <-> "NH2" Residue "G ARG 29": "NH1" <-> "NH2" Residue "G GLU 57": "OE1" <-> "OE2" Residue "G ARG 75": "NH1" <-> "NH2" Residue "G ARG 219": "NH1" <-> "NH2" Residue "G ARG 251": "NH1" <-> "NH2" Residue "G ARG 256": "NH1" <-> "NH2" Residue "G ARG 276": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16212 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2260 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 11, 'TRANS': 266} Chain breaks: 3 Chain: "B" Number of atoms: 2260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2260 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 11, 'TRANS': 266} Chain breaks: 3 Chain: "C" Number of atoms: 2260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2260 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 11, 'TRANS': 266} Chain breaks: 3 Chain: "D" Number of atoms: 2260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2260 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 11, 'TRANS': 266} Chain breaks: 3 Chain: "E" Number of atoms: 2260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2260 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 11, 'TRANS': 266} Chain breaks: 3 Chain: "F" Number of atoms: 2260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2260 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 11, 'TRANS': 266} Chain breaks: 3 Chain: "G" Number of atoms: 2260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2260 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 11, 'TRANS': 266} Chain breaks: 3 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {'6OU': 1, 'R16': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'6OU:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {'6OU': 1, 'R16': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'6OU:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {'6OU': 1, 'R16': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'6OU:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {'6OU': 1, 'R16': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'6OU:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {'6OU': 1, 'R16': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'6OU:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {'6OU': 1, 'R16': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'6OU:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {'6OU': 1, 'R16': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'6OU:plan-1': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 8.47, per 1000 atoms: 0.52 Number of scatterers: 16212 At special positions: 0 Unit cell: (107.8, 107.8, 123.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 77 16.00 P 7 15.00 O 2737 8.00 N 2443 7.00 C 10948 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 267 " distance=2.03 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 248 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 267 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 248 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 267 " distance=2.03 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 248 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 267 " distance=2.03 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 248 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 267 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 248 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 267 " distance=2.03 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 248 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 267 " distance=2.03 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 248 " distance=2.03 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: 6.15 Conformation dependent library (CDL) restraints added in 2.7 seconds 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3794 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 77 helices and 7 sheets defined 66.2% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.55 Creating SS restraints... Processing helix chain 'A' and resid 33 through 60 Proline residue: A 46 - end of helix Processing helix chain 'A' and resid 74 through 85 Processing helix chain 'A' and resid 104 through 107 No H-bonds generated for 'chain 'A' and resid 104 through 107' Processing helix chain 'A' and resid 109 through 130 Proline residue: A 123 - end of helix Processing helix chain 'A' and resid 133 through 157 removed outlier: 3.895A pdb=" N SER A 137 " --> pdb=" O PRO A 133 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ASP A 138 " --> pdb=" O HIS A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 206 removed outlier: 3.656A pdb=" N LYS A 205 " --> pdb=" O TYR A 201 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASN A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 239 removed outlier: 3.765A pdb=" N ILE A 237 " --> pdb=" O LEU A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 297 removed outlier: 3.591A pdb=" N ARG A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU A 277 " --> pdb=" O GLY A 273 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN A 282 " --> pdb=" O LEU A 278 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR A 286 " --> pdb=" O ASN A 282 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) Proline residue: A 291 - end of helix Processing helix chain 'A' and resid 308 through 313 removed outlier: 4.969A pdb=" N VAL A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 339 Processing helix chain 'A' and resid 346 through 356 Processing helix chain 'B' and resid 33 through 60 Proline residue: B 46 - end of helix Processing helix chain 'B' and resid 74 through 85 Processing helix chain 'B' and resid 104 through 107 No H-bonds generated for 'chain 'B' and resid 104 through 107' Processing helix chain 'B' and resid 109 through 130 Proline residue: B 123 - end of helix Processing helix chain 'B' and resid 133 through 157 removed outlier: 3.894A pdb=" N SER B 137 " --> pdb=" O PRO B 133 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASP B 138 " --> pdb=" O HIS B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 206 removed outlier: 3.656A pdb=" N LYS B 205 " --> pdb=" O TYR B 201 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASN B 206 " --> pdb=" O LEU B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 239 removed outlier: 3.765A pdb=" N ILE B 237 " --> pdb=" O LEU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 297 removed outlier: 3.591A pdb=" N ARG B 276 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU B 277 " --> pdb=" O GLY B 273 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN B 282 " --> pdb=" O LEU B 278 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR B 286 " --> pdb=" O ASN B 282 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) Proline residue: B 291 - end of helix Processing helix chain 'B' and resid 308 through 313 removed outlier: 4.970A pdb=" N VAL B 313 " --> pdb=" O LYS B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 339 Processing helix chain 'B' and resid 346 through 356 Processing helix chain 'C' and resid 33 through 60 Proline residue: C 46 - end of helix Processing helix chain 'C' and resid 74 through 85 Processing helix chain 'C' and resid 104 through 107 No H-bonds generated for 'chain 'C' and resid 104 through 107' Processing helix chain 'C' and resid 109 through 130 Proline residue: C 123 - end of helix Processing helix chain 'C' and resid 133 through 157 removed outlier: 3.896A pdb=" N SER C 137 " --> pdb=" O PRO C 133 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASP C 138 " --> pdb=" O HIS C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 206 removed outlier: 3.656A pdb=" N LYS C 205 " --> pdb=" O TYR C 201 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASN C 206 " --> pdb=" O LEU C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 239 removed outlier: 3.765A pdb=" N ILE C 237 " --> pdb=" O LEU C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 297 removed outlier: 3.591A pdb=" N ARG C 276 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU C 277 " --> pdb=" O GLY C 273 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN C 282 " --> pdb=" O LEU C 278 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR C 286 " --> pdb=" O ASN C 282 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET C 290 " --> pdb=" O TYR C 286 " (cutoff:3.500A) Proline residue: C 291 - end of helix Processing helix chain 'C' and resid 308 through 313 removed outlier: 4.969A pdb=" N VAL C 313 " --> pdb=" O LYS C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 339 Processing helix chain 'C' and resid 346 through 356 Processing helix chain 'D' and resid 33 through 60 Proline residue: D 46 - end of helix Processing helix chain 'D' and resid 74 through 85 Processing helix chain 'D' and resid 104 through 107 No H-bonds generated for 'chain 'D' and resid 104 through 107' Processing helix chain 'D' and resid 109 through 130 Proline residue: D 123 - end of helix Processing helix chain 'D' and resid 133 through 157 removed outlier: 3.895A pdb=" N SER D 137 " --> pdb=" O PRO D 133 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ASP D 138 " --> pdb=" O HIS D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 206 removed outlier: 3.656A pdb=" N LYS D 205 " --> pdb=" O TYR D 201 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASN D 206 " --> pdb=" O LEU D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 239 removed outlier: 3.765A pdb=" N ILE D 237 " --> pdb=" O LEU D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 297 removed outlier: 3.591A pdb=" N ARG D 276 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU D 277 " --> pdb=" O GLY D 273 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN D 282 " --> pdb=" O LEU D 278 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR D 286 " --> pdb=" O ASN D 282 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) Proline residue: D 291 - end of helix Processing helix chain 'D' and resid 308 through 313 removed outlier: 4.969A pdb=" N VAL D 313 " --> pdb=" O LYS D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 339 Processing helix chain 'D' and resid 346 through 356 Processing helix chain 'E' and resid 33 through 60 Proline residue: E 46 - end of helix Processing helix chain 'E' and resid 74 through 85 Processing helix chain 'E' and resid 104 through 107 No H-bonds generated for 'chain 'E' and resid 104 through 107' Processing helix chain 'E' and resid 109 through 130 Proline residue: E 123 - end of helix Processing helix chain 'E' and resid 133 through 157 removed outlier: 3.895A pdb=" N SER E 137 " --> pdb=" O PRO E 133 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ASP E 138 " --> pdb=" O HIS E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 206 removed outlier: 3.655A pdb=" N LYS E 205 " --> pdb=" O TYR E 201 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASN E 206 " --> pdb=" O LEU E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 239 removed outlier: 3.765A pdb=" N ILE E 237 " --> pdb=" O LEU E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 297 removed outlier: 3.590A pdb=" N ARG E 276 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU E 277 " --> pdb=" O GLY E 273 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN E 282 " --> pdb=" O LEU E 278 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR E 286 " --> pdb=" O ASN E 282 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET E 290 " --> pdb=" O TYR E 286 " (cutoff:3.500A) Proline residue: E 291 - end of helix Processing helix chain 'E' and resid 308 through 313 removed outlier: 4.968A pdb=" N VAL E 313 " --> pdb=" O LYS E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 339 Processing helix chain 'E' and resid 346 through 356 Processing helix chain 'F' and resid 33 through 60 Proline residue: F 46 - end of helix Processing helix chain 'F' and resid 74 through 85 Processing helix chain 'F' and resid 104 through 107 No H-bonds generated for 'chain 'F' and resid 104 through 107' Processing helix chain 'F' and resid 109 through 130 Proline residue: F 123 - end of helix Processing helix chain 'F' and resid 133 through 157 removed outlier: 3.895A pdb=" N SER F 137 " --> pdb=" O PRO F 133 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASP F 138 " --> pdb=" O HIS F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 206 removed outlier: 3.656A pdb=" N LYS F 205 " --> pdb=" O TYR F 201 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASN F 206 " --> pdb=" O LEU F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 239 removed outlier: 3.764A pdb=" N ILE F 237 " --> pdb=" O LEU F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 297 removed outlier: 3.591A pdb=" N ARG F 276 " --> pdb=" O VAL F 272 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU F 277 " --> pdb=" O GLY F 273 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN F 282 " --> pdb=" O LEU F 278 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR F 286 " --> pdb=" O ASN F 282 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET F 290 " --> pdb=" O TYR F 286 " (cutoff:3.500A) Proline residue: F 291 - end of helix Processing helix chain 'F' and resid 308 through 313 removed outlier: 4.969A pdb=" N VAL F 313 " --> pdb=" O LYS F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 339 Processing helix chain 'F' and resid 346 through 356 Processing helix chain 'G' and resid 33 through 60 Proline residue: G 46 - end of helix Processing helix chain 'G' and resid 74 through 85 Processing helix chain 'G' and resid 104 through 107 No H-bonds generated for 'chain 'G' and resid 104 through 107' Processing helix chain 'G' and resid 109 through 130 Proline residue: G 123 - end of helix Processing helix chain 'G' and resid 133 through 157 removed outlier: 3.895A pdb=" N SER G 137 " --> pdb=" O PRO G 133 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASP G 138 " --> pdb=" O HIS G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 206 removed outlier: 3.656A pdb=" N LYS G 205 " --> pdb=" O TYR G 201 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASN G 206 " --> pdb=" O LEU G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 239 removed outlier: 3.765A pdb=" N ILE G 237 " --> pdb=" O LEU G 233 " (cutoff:3.500A) Processing helix chain 'G' and resid 272 through 297 removed outlier: 3.591A pdb=" N ARG G 276 " --> pdb=" O VAL G 272 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU G 277 " --> pdb=" O GLY G 273 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN G 282 " --> pdb=" O LEU G 278 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR G 286 " --> pdb=" O ASN G 282 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET G 290 " --> pdb=" O TYR G 286 " (cutoff:3.500A) Proline residue: G 291 - end of helix Processing helix chain 'G' and resid 308 through 313 removed outlier: 4.969A pdb=" N VAL G 313 " --> pdb=" O LYS G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 329 through 339 Processing helix chain 'G' and resid 346 through 356 Processing sheet with id= A, first strand: chain 'A' and resid 64 through 66 Processing sheet with id= B, first strand: chain 'B' and resid 64 through 66 Processing sheet with id= C, first strand: chain 'C' and resid 64 through 66 Processing sheet with id= D, first strand: chain 'D' and resid 64 through 66 Processing sheet with id= E, first strand: chain 'E' and resid 64 through 66 Processing sheet with id= F, first strand: chain 'F' and resid 64 through 66 Processing sheet with id= G, first strand: chain 'G' and resid 64 through 66 882 hydrogen bonds defined for protein. 2604 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.46 Time building geometry restraints manager: 6.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4238 1.34 - 1.46: 3216 1.46 - 1.58: 8863 1.58 - 1.70: 140 1.70 - 1.82: 112 Bond restraints: 16569 Sorted by residual: bond pdb=" C16 6OU A 501 " pdb=" O18 6OU A 501 " ideal model delta sigma weight residual 1.327 1.463 -0.136 2.00e-02 2.50e+03 4.64e+01 bond pdb=" C16 6OU D 501 " pdb=" O18 6OU D 501 " ideal model delta sigma weight residual 1.327 1.463 -0.136 2.00e-02 2.50e+03 4.64e+01 bond pdb=" C16 6OU B 501 " pdb=" O18 6OU B 501 " ideal model delta sigma weight residual 1.327 1.463 -0.136 2.00e-02 2.50e+03 4.63e+01 bond pdb=" C16 6OU E 501 " pdb=" O18 6OU E 501 " ideal model delta sigma weight residual 1.327 1.463 -0.136 2.00e-02 2.50e+03 4.63e+01 bond pdb=" C16 6OU C 501 " pdb=" O18 6OU C 501 " ideal model delta sigma weight residual 1.327 1.463 -0.136 2.00e-02 2.50e+03 4.61e+01 ... (remaining 16564 not shown) Histogram of bond angle deviations from ideal: 99.27 - 106.27: 369 106.27 - 113.27: 9242 113.27 - 120.27: 6914 120.27 - 127.27: 5714 127.27 - 134.27: 154 Bond angle restraints: 22393 Sorted by residual: angle pdb=" N HIS F 106 " pdb=" CA HIS F 106 " pdb=" C HIS F 106 " ideal model delta sigma weight residual 111.28 118.19 -6.91 1.09e+00 8.42e-01 4.02e+01 angle pdb=" N HIS D 106 " pdb=" CA HIS D 106 " pdb=" C HIS D 106 " ideal model delta sigma weight residual 111.28 118.17 -6.89 1.09e+00 8.42e-01 4.00e+01 angle pdb=" N HIS B 106 " pdb=" CA HIS B 106 " pdb=" C HIS B 106 " ideal model delta sigma weight residual 111.28 118.14 -6.86 1.09e+00 8.42e-01 3.96e+01 angle pdb=" N HIS A 106 " pdb=" CA HIS A 106 " pdb=" C HIS A 106 " ideal model delta sigma weight residual 111.28 118.14 -6.86 1.09e+00 8.42e-01 3.96e+01 angle pdb=" N HIS E 106 " pdb=" CA HIS E 106 " pdb=" C HIS E 106 " ideal model delta sigma weight residual 111.28 118.11 -6.83 1.09e+00 8.42e-01 3.93e+01 ... (remaining 22388 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.10: 9576 32.10 - 64.21: 336 64.21 - 96.31: 21 96.31 - 128.41: 0 128.41 - 160.52: 21 Dihedral angle restraints: 9954 sinusoidal: 4123 harmonic: 5831 Sorted by residual: dihedral pdb=" C ASN B 306 " pdb=" N ASN B 306 " pdb=" CA ASN B 306 " pdb=" CB ASN B 306 " ideal model delta harmonic sigma weight residual -122.60 -136.47 13.87 0 2.50e+00 1.60e-01 3.08e+01 dihedral pdb=" C ASN F 306 " pdb=" N ASN F 306 " pdb=" CA ASN F 306 " pdb=" CB ASN F 306 " ideal model delta harmonic sigma weight residual -122.60 -136.45 13.85 0 2.50e+00 1.60e-01 3.07e+01 dihedral pdb=" C ASN G 306 " pdb=" N ASN G 306 " pdb=" CA ASN G 306 " pdb=" CB ASN G 306 " ideal model delta harmonic sigma weight residual -122.60 -136.42 13.82 0 2.50e+00 1.60e-01 3.06e+01 ... (remaining 9951 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 2457 0.112 - 0.225: 169 0.225 - 0.337: 6 0.337 - 0.450: 0 0.450 - 0.562: 14 Chirality restraints: 2646 Sorted by residual: chirality pdb=" C20 6OU G1002 " pdb=" C19 6OU G1002 " pdb=" C21 6OU G1002 " pdb=" O30 6OU G1002 " both_signs ideal model delta sigma weight residual False 2.35 2.91 -0.56 2.00e-01 2.50e+01 7.91e+00 chirality pdb=" C20 6OU C 501 " pdb=" C19 6OU C 501 " pdb=" C21 6OU C 501 " pdb=" O30 6OU C 501 " both_signs ideal model delta sigma weight residual False 2.35 2.91 -0.56 2.00e-01 2.50e+01 7.90e+00 chirality pdb=" C20 6OU F 501 " pdb=" C19 6OU F 501 " pdb=" C21 6OU F 501 " pdb=" O30 6OU F 501 " both_signs ideal model delta sigma weight residual False 2.35 2.91 -0.56 2.00e-01 2.50e+01 7.88e+00 ... (remaining 2643 not shown) Planarity restraints: 2625 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 290 " -0.032 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO B 291 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 291 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 291 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET E 290 " 0.032 5.00e-02 4.00e+02 4.73e-02 3.57e+00 pdb=" N PRO E 291 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO E 291 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 291 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 132 " -0.032 5.00e-02 4.00e+02 4.72e-02 3.56e+00 pdb=" N PRO E 133 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO E 133 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 133 " -0.027 5.00e-02 4.00e+02 ... (remaining 2622 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 3924 2.79 - 3.32: 14553 3.32 - 3.85: 24862 3.85 - 4.37: 29316 4.37 - 4.90: 52289 Nonbonded interactions: 124944 Sorted by model distance: nonbonded pdb=" NH2 ARG B 75 " pdb=" OD2 ASP C 81 " model vdw 2.265 2.520 nonbonded pdb=" NE2 GLN C 76 " pdb=" O ALA D 68 " model vdw 2.345 2.520 nonbonded pdb=" OH TYR G 311 " pdb=" OG SER G 346 " model vdw 2.361 2.440 nonbonded pdb=" OH TYR F 311 " pdb=" OG SER F 346 " model vdw 2.361 2.440 nonbonded pdb=" OH TYR B 311 " pdb=" OG SER B 346 " model vdw 2.361 2.440 ... (remaining 124939 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' and (resid 25 through 358 or (resid 503 and (name C28 or name C29 or \ name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 \ or name C37)))) selection = (chain 'B' and (resid 25 through 358 or (resid 503 and (name C28 or name C29 or \ name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 \ or name C37)))) selection = (chain 'C' and (resid 25 through 358 or (resid 503 and (name C28 or name C29 or \ name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 \ or name C37)))) selection = (chain 'D' and (resid 25 through 358 or (resid 503 and (name C28 or name C29 or \ name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 \ or name C37)))) selection = (chain 'E' and (resid 25 through 358 or (resid 503 and (name C28 or name C29 or \ name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 \ or name C37)))) selection = (chain 'F' and (resid 25 through 358 or (resid 503 and (name C28 or name C29 or \ name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 \ or name C37)))) selection = (chain 'G' and (resid 25 through 358 or resid 1003)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 0.690 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: 0.010 Extract box with map and model: 4.010 Check model and map are aligned: 0.250 Set scattering table: 0.170 Process input model: 42.430 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.136 16569 Z= 0.753 Angle : 1.097 16.145 22393 Z= 0.617 Chirality : 0.073 0.562 2646 Planarity : 0.006 0.047 2625 Dihedral : 17.598 160.518 6118 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Cbeta Deviations : 0.37 % 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: -3.44 (0.16), residues: 1890 helix: -1.77 (0.12), residues: 1407 sheet: -0.71 (0.54), residues: 77 loop : -3.77 (0.23), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP D 74 HIS 0.003 0.001 HIS G 330 PHE 0.013 0.001 PHE G 246 TYR 0.010 0.001 TYR G 280 ARG 0.003 0.001 ARG B 29 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.648 Fit side-chains REVERT: B 52 LEU cc_start: 0.7829 (mt) cc_final: 0.7546 (mt) REVERT: B 128 ARG cc_start: 0.8262 (ttm170) cc_final: 0.8006 (ttp80) REVERT: D 235 TYR cc_start: 0.7276 (t80) cc_final: 0.7036 (t80) REVERT: D 282 ASN cc_start: 0.8530 (t0) cc_final: 0.8330 (t0) REVERT: E 297 MET cc_start: 0.8656 (mtp) cc_final: 0.8428 (mtm) REVERT: F 52 LEU cc_start: 0.8004 (mt) cc_final: 0.7770 (mt) REVERT: F 235 TYR cc_start: 0.7253 (t80) cc_final: 0.7046 (t80) REVERT: G 290 MET cc_start: 0.7909 (mtp) cc_final: 0.7588 (mtt) REVERT: G 309 LYS cc_start: 0.7944 (mtpp) cc_final: 0.7704 (mtpp) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.3283 time to fit residues: 72.3402 Evaluate side-chains 116 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 2.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 159 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 148 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 110 optimal weight: 0.9980 chunk 171 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16569 Z= 0.169 Angle : 0.515 5.782 22393 Z= 0.257 Chirality : 0.038 0.126 2646 Planarity : 0.004 0.031 2625 Dihedral : 10.962 108.226 2415 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.57 % Allowed : 12.47 % Favored : 86.96 % Cbeta Deviations : 0.00 % 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: -0.94 (0.19), residues: 1890 helix: 0.18 (0.14), residues: 1414 sheet: -0.46 (0.53), residues: 77 loop : -3.40 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 74 HIS 0.003 0.001 HIS G 330 PHE 0.007 0.001 PHE A 349 TYR 0.007 0.001 TYR E 215 ARG 0.003 0.000 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 121 time to evaluate : 1.609 Fit side-chains REVERT: B 128 ARG cc_start: 0.8272 (ttm170) cc_final: 0.7983 (ttp80) REVERT: B 290 MET cc_start: 0.7352 (mtp) cc_final: 0.7103 (mtt) REVERT: E 203 LYS cc_start: 0.8394 (mmmm) cc_final: 0.8186 (mtpt) REVERT: F 52 LEU cc_start: 0.8039 (mt) cc_final: 0.7758 (mt) REVERT: F 282 ASN cc_start: 0.8369 (t0) cc_final: 0.7982 (m-40) outliers start: 10 outliers final: 9 residues processed: 129 average time/residue: 0.2442 time to fit residues: 50.1533 Evaluate side-chains 114 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 105 time to evaluate : 1.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 316 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 95 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 142 optimal weight: 0.7980 chunk 116 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 171 optimal weight: 3.9990 chunk 185 optimal weight: 0.3980 chunk 153 optimal weight: 10.0000 chunk 170 optimal weight: 0.8980 chunk 58 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 355 ASN E 355 ASN F 355 ASN G 355 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16569 Z= 0.141 Angle : 0.476 5.544 22393 Z= 0.235 Chirality : 0.036 0.126 2646 Planarity : 0.003 0.027 2625 Dihedral : 9.409 103.801 2415 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.96 % Allowed : 15.42 % Favored : 83.62 % Cbeta Deviations : 0.00 % 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: 0.16 (0.20), residues: 1890 helix: 0.99 (0.14), residues: 1414 sheet: 0.82 (0.75), residues: 42 loop : -2.93 (0.26), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 74 HIS 0.002 0.000 HIS G 330 PHE 0.006 0.001 PHE C 109 TYR 0.007 0.001 TYR A 215 ARG 0.002 0.000 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 115 time to evaluate : 1.810 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 128 ARG cc_start: 0.8271 (ttm170) cc_final: 0.8022 (ttp80) REVERT: F 52 LEU cc_start: 0.8086 (mt) cc_final: 0.7743 (mt) outliers start: 17 outliers final: 8 residues processed: 128 average time/residue: 0.2569 time to fit residues: 52.1201 Evaluate side-chains 110 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 102 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain D residue 203 LYS Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain G residue 316 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 169 optimal weight: 0.9980 chunk 129 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 172 optimal weight: 2.9990 chunk 182 optimal weight: 0.4980 chunk 90 optimal weight: 0.7980 chunk 163 optimal weight: 2.9990 chunk 49 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 ASN C 63 GLN ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16569 Z= 0.141 Angle : 0.466 5.472 22393 Z= 0.229 Chirality : 0.036 0.123 2646 Planarity : 0.003 0.027 2625 Dihedral : 8.949 105.219 2415 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.42 % Allowed : 16.67 % Favored : 81.92 % Cbeta Deviations : 0.00 % 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: 0.57 (0.20), residues: 1890 helix: 1.39 (0.15), residues: 1407 sheet: -2.88 (0.54), residues: 84 loop : -2.56 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 74 HIS 0.001 0.000 HIS C 330 PHE 0.006 0.001 PHE C 109 TYR 0.006 0.001 TYR A 215 ARG 0.003 0.000 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 102 time to evaluate : 1.724 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.7347 (OUTLIER) cc_final: 0.6004 (mtt180) REVERT: B 29 ARG cc_start: 0.7420 (OUTLIER) cc_final: 0.5961 (mtt180) REVERT: B 128 ARG cc_start: 0.8274 (ttm170) cc_final: 0.8008 (ttp80) REVERT: C 29 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.6320 (mtt180) REVERT: D 203 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8116 (ttmt) REVERT: F 235 TYR cc_start: 0.7268 (t80) cc_final: 0.7060 (t80) REVERT: G 29 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.6306 (mtt180) outliers start: 25 outliers final: 17 residues processed: 120 average time/residue: 0.2821 time to fit residues: 51.5292 Evaluate side-chains 119 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 97 time to evaluate : 1.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain D residue 203 LYS Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 290 MET Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain G residue 29 ARG Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 316 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 152 optimal weight: 6.9990 chunk 103 optimal weight: 0.3980 chunk 2 optimal weight: 0.6980 chunk 136 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 155 optimal weight: 0.7980 chunk 126 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 355 ASN ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16569 Z= 0.194 Angle : 0.496 5.525 22393 Z= 0.245 Chirality : 0.038 0.124 2646 Planarity : 0.003 0.027 2625 Dihedral : 9.187 110.823 2415 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.81 % Allowed : 17.40 % Favored : 80.78 % Cbeta Deviations : 0.00 % 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: 0.69 (0.20), residues: 1890 helix: 1.48 (0.14), residues: 1407 sheet: -2.37 (0.44), residues: 119 loop : -2.60 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 127 HIS 0.002 0.001 HIS E 330 PHE 0.008 0.001 PHE B 333 TYR 0.007 0.001 TYR B 215 ARG 0.003 0.000 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 99 time to evaluate : 1.702 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.6340 (mtt180) REVERT: B 128 ARG cc_start: 0.8305 (ttm170) cc_final: 0.8067 (ttp80) REVERT: D 203 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8136 (ttmt) REVERT: D 235 TYR cc_start: 0.7500 (t80) cc_final: 0.7207 (t80) outliers start: 32 outliers final: 24 residues processed: 124 average time/residue: 0.3040 time to fit residues: 56.1209 Evaluate side-chains 123 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 97 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain D residue 203 LYS Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 290 MET Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain G residue 29 ARG Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 316 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 61 optimal weight: 0.6980 chunk 164 optimal weight: 0.4980 chunk 36 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 45 optimal weight: 10.0000 chunk 182 optimal weight: 3.9990 chunk 151 optimal weight: 6.9990 chunk 84 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16569 Z= 0.141 Angle : 0.459 5.426 22393 Z= 0.226 Chirality : 0.036 0.122 2646 Planarity : 0.003 0.050 2625 Dihedral : 8.889 109.685 2415 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.36 % Allowed : 18.54 % Favored : 80.10 % Cbeta Deviations : 0.00 % 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: 1.03 (0.21), residues: 1890 helix: 1.71 (0.14), residues: 1407 sheet: -2.28 (0.44), residues: 119 loop : -2.41 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 74 HIS 0.001 0.000 HIS D 330 PHE 0.005 0.001 PHE B 333 TYR 0.006 0.000 TYR C 215 ARG 0.004 0.000 ARG F 29 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 98 time to evaluate : 1.717 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.6004 (mtt180) REVERT: B 29 ARG cc_start: 0.7493 (OUTLIER) cc_final: 0.6027 (mtt180) REVERT: B 128 ARG cc_start: 0.8282 (ttm170) cc_final: 0.8015 (ttp80) REVERT: C 29 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.6352 (mtt180) REVERT: D 203 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8158 (ttmt) REVERT: D 235 TYR cc_start: 0.7417 (t80) cc_final: 0.7102 (t80) outliers start: 24 outliers final: 15 residues processed: 114 average time/residue: 0.2874 time to fit residues: 49.7527 Evaluate side-chains 113 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 94 time to evaluate : 1.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 203 LYS Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 290 MET Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain G residue 29 ARG Chi-restraints excluded: chain G residue 316 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 176 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 104 optimal weight: 0.4980 chunk 133 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 153 optimal weight: 8.9990 chunk 102 optimal weight: 0.9980 chunk 182 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 111 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16569 Z= 0.185 Angle : 0.485 5.539 22393 Z= 0.238 Chirality : 0.037 0.123 2646 Planarity : 0.003 0.043 2625 Dihedral : 9.041 112.051 2415 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.47 % Allowed : 18.93 % Favored : 79.59 % Cbeta Deviations : 0.00 % 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: 1.11 (0.21), residues: 1890 helix: 1.75 (0.14), residues: 1407 sheet: -2.13 (0.44), residues: 119 loop : -2.33 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 127 HIS 0.002 0.000 HIS E 330 PHE 0.008 0.001 PHE B 333 TYR 0.006 0.001 TYR C 215 ARG 0.004 0.000 ARG F 29 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 96 time to evaluate : 1.782 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.7490 (OUTLIER) cc_final: 0.6185 (mtt180) REVERT: B 128 ARG cc_start: 0.8315 (ttm170) cc_final: 0.8076 (ttp80) REVERT: C 29 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.6653 (mtt180) REVERT: D 203 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8187 (ttmt) outliers start: 26 outliers final: 23 residues processed: 114 average time/residue: 0.2951 time to fit residues: 50.6540 Evaluate side-chains 121 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 95 time to evaluate : 1.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 203 LYS Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 290 MET Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain G residue 29 ARG Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 316 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 112 optimal weight: 0.2980 chunk 72 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 143 optimal weight: 0.5980 chunk 165 optimal weight: 8.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16569 Z= 0.188 Angle : 0.484 5.521 22393 Z= 0.238 Chirality : 0.037 0.123 2646 Planarity : 0.003 0.041 2625 Dihedral : 9.087 113.586 2415 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.70 % Allowed : 19.39 % Favored : 78.91 % Cbeta Deviations : 0.00 % 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: 1.24 (0.21), residues: 1890 helix: 1.82 (0.14), residues: 1407 sheet: -2.04 (0.45), residues: 119 loop : -2.19 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 74 HIS 0.002 0.000 HIS E 330 PHE 0.007 0.001 PHE B 333 TYR 0.007 0.001 TYR A 215 ARG 0.004 0.000 ARG F 29 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 101 time to evaluate : 1.882 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.6114 (mtt180) REVERT: B 128 ARG cc_start: 0.8302 (ttm170) cc_final: 0.8066 (ttp80) REVERT: C 29 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.6499 (mtt180) REVERT: D 203 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8181 (ttmt) outliers start: 30 outliers final: 24 residues processed: 122 average time/residue: 0.3064 time to fit residues: 56.1831 Evaluate side-chains 124 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 97 time to evaluate : 2.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 203 LYS Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 290 MET Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain G residue 29 ARG Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 316 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 174 optimal weight: 0.7980 chunk 159 optimal weight: 2.9990 chunk 169 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 chunk 133 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 chunk 111 optimal weight: 10.0000 chunk 179 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16569 Z= 0.164 Angle : 0.470 5.451 22393 Z= 0.231 Chirality : 0.037 0.123 2646 Planarity : 0.003 0.036 2625 Dihedral : 9.000 113.566 2415 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.76 % Allowed : 19.67 % Favored : 78.57 % Cbeta Deviations : 0.00 % 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: 1.39 (0.21), residues: 1890 helix: 1.93 (0.15), residues: 1407 sheet: -1.96 (0.46), residues: 119 loop : -2.13 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 74 HIS 0.001 0.000 HIS E 330 PHE 0.007 0.001 PHE B 333 TYR 0.006 0.001 TYR F 215 ARG 0.003 0.000 ARG F 29 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 95 time to evaluate : 1.634 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 29 ARG cc_start: 0.7574 (OUTLIER) cc_final: 0.6131 (mtt180) REVERT: B 128 ARG cc_start: 0.8299 (ttm170) cc_final: 0.8046 (ttp80) REVERT: C 29 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.6374 (mtt180) REVERT: D 28 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8150 (mp) REVERT: D 203 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8212 (ttmt) REVERT: D 235 TYR cc_start: 0.7437 (t80) cc_final: 0.7144 (t80) outliers start: 31 outliers final: 25 residues processed: 118 average time/residue: 0.2829 time to fit residues: 50.6293 Evaluate side-chains 123 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 94 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 203 LYS Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain E residue 290 MET Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain G residue 29 ARG Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 316 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 109 optimal weight: 0.9990 chunk 85 optimal weight: 0.0030 chunk 124 optimal weight: 5.9990 chunk 188 optimal weight: 0.0870 chunk 173 optimal weight: 3.9990 chunk 149 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 115 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 119 optimal weight: 0.9990 chunk 159 optimal weight: 0.9990 overall best weight: 0.4568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16569 Z= 0.122 Angle : 0.441 5.403 22393 Z= 0.217 Chirality : 0.036 0.122 2646 Planarity : 0.003 0.043 2625 Dihedral : 8.740 112.049 2415 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.08 % Allowed : 20.29 % Favored : 78.63 % Cbeta Deviations : 0.00 % 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: 1.66 (0.21), residues: 1890 helix: 2.09 (0.15), residues: 1414 sheet: -1.90 (0.46), residues: 119 loop : -1.94 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 74 HIS 0.001 0.000 HIS C 330 PHE 0.005 0.001 PHE F 333 TYR 0.010 0.000 TYR B 209 ARG 0.004 0.000 ARG A 29 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 103 time to evaluate : 1.743 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 29 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.5983 (mtt180) REVERT: B 128 ARG cc_start: 0.8267 (ttm170) cc_final: 0.7998 (ttp80) REVERT: C 29 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.6298 (mtt180) REVERT: D 203 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8206 (ttmt) REVERT: D 235 TYR cc_start: 0.7449 (t80) cc_final: 0.7132 (t80) REVERT: G 29 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.6301 (mtt180) REVERT: G 143 MET cc_start: 0.7951 (mtt) cc_final: 0.7570 (mtt) outliers start: 19 outliers final: 13 residues processed: 114 average time/residue: 0.2922 time to fit residues: 50.2287 Evaluate side-chains 115 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 98 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 203 LYS Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain E residue 290 MET Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain G residue 29 ARG Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 316 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 45 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 150 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 154 optimal weight: 0.0670 chunk 19 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 131 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.143608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.110884 restraints weight = 16521.475| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.68 r_work: 0.3014 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16569 Z= 0.147 Angle : 0.458 5.424 22393 Z= 0.225 Chirality : 0.036 0.123 2646 Planarity : 0.003 0.040 2625 Dihedral : 8.795 113.138 2415 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.08 % Allowed : 20.18 % Favored : 78.74 % Cbeta Deviations : 0.00 % 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: 1.71 (0.21), residues: 1890 helix: 2.16 (0.14), residues: 1407 sheet: -1.82 (0.47), residues: 119 loop : -2.04 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 74 HIS 0.001 0.000 HIS B 330 PHE 0.007 0.001 PHE B 333 TYR 0.009 0.001 TYR B 209 ARG 0.004 0.000 ARG A 29 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2641.48 seconds wall clock time: 49 minutes 39.06 seconds (2979.06 seconds total)