Starting phenix.real_space_refine on Thu Nov 16 17:56:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uzy_20964/11_2023/6uzy_20964_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uzy_20964/11_2023/6uzy_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_20964/11_2023/6uzy_20964.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uzy_20964/11_2023/6uzy_20964.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uzy_20964/11_2023/6uzy_20964_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uzy_20964/11_2023/6uzy_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: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 24 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: 24 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: 24 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: 24 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: 24 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: 24 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: 24 Planarities with less than four sites: {'6OU:plan-1': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 8.19, per 1000 atoms: 0.51 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: 6.03 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: 2.68 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: 4.30 Time building geometry restraints manager: 6.55 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 - 16.91: 8604 16.91 - 33.82: 977 33.82 - 50.73: 261 50.73 - 67.63: 42 67.63 - 84.54: 14 Dihedral angle restraints: 9898 sinusoidal: 4067 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 9895 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: 0.980 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: 3.960 Check model and map are aligned: 0.240 Set scattering table: 0.130 Process input model: 41.240 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.100 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.600 ------------------------------------------------------------------------------- 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 : 15.174 84.542 6062 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 *********************** 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 : 1.792 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.3081 time to fit residues: 67.8511 Evaluate side-chains 116 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.824 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6880 ------------------------------------------------------------------------------- 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: 0.7980 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: 0.8980 ------------------------------------------------------------------------------- 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 D 282 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16569 Z= 0.166 Angle : 0.514 5.755 22393 Z= 0.258 Chirality : 0.037 0.126 2646 Planarity : 0.004 0.030 2625 Dihedral : 7.629 57.233 2359 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.68 % Allowed : 12.30 % Favored : 87.02 % 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: -0.99 (0.19), residues: 1890 helix: 0.17 (0.14), residues: 1407 sheet: -0.37 (0.53), residues: 77 loop : -3.50 (0.24), residues: 406 *********************** 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 127 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 115 time to evaluate : 1.805 Fit side-chains outliers start: 12 outliers final: 10 residues processed: 123 average time/residue: 0.2337 time to fit residues: 46.9039 Evaluate side-chains 114 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 104 time to evaluate : 1.849 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1395 time to fit residues: 5.0494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 95 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 171 optimal weight: 3.9990 chunk 185 optimal weight: 1.9990 chunk 153 optimal weight: 0.4980 chunk 170 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 137 optimal weight: 0.0060 overall best weight: 0.6196 ------------------------------------------------------------------------------- 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 282 ASN D 355 ASN E 355 ASN F 355 ASN G 355 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1626 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= 0.138 Angle : 0.472 5.545 22393 Z= 0.233 Chirality : 0.036 0.124 2646 Planarity : 0.003 0.027 2625 Dihedral : 5.820 37.302 2359 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.74 % Allowed : 14.46 % Favored : 84.81 % 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: 0.04 (0.20), residues: 1890 helix: 0.95 (0.14), residues: 1414 sheet: -2.82 (0.55), residues: 84 loop : -2.65 (0.28), residues: 392 *********************** 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 130 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 117 time to evaluate : 1.671 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 4 residues processed: 127 average time/residue: 0.2436 time to fit residues: 49.9046 Evaluate side-chains 104 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 100 time to evaluate : 1.661 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1433 time to fit residues: 3.5725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 169 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 19 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 172 optimal weight: 1.9990 chunk 182 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 163 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 ASN B 200 GLN B 355 ASN C 63 GLN ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1761 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= 0.165 Angle : 0.479 5.470 22393 Z= 0.237 Chirality : 0.037 0.123 2646 Planarity : 0.003 0.027 2625 Dihedral : 5.674 36.292 2359 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.91 % Allowed : 16.55 % Favored : 82.54 % 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: 0.43 (0.20), residues: 1890 helix: 1.29 (0.14), residues: 1407 sheet: -2.93 (0.53), residues: 84 loop : -2.60 (0.29), residues: 399 *********************** 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 118 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 102 time to evaluate : 1.854 Fit side-chains outliers start: 16 outliers final: 8 residues processed: 112 average time/residue: 0.2818 time to fit residues: 48.5478 Evaluate side-chains 104 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 96 time to evaluate : 1.782 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1460 time to fit residues: 4.7049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 152 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 136 optimal weight: 0.5980 chunk 75 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 126 optimal weight: 0.1980 chunk 0 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.7789 moved from start: 0.1977 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= 0.140 Angle : 0.458 5.442 22393 Z= 0.226 Chirality : 0.036 0.123 2646 Planarity : 0.003 0.028 2625 Dihedral : 5.305 32.629 2359 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.45 % Allowed : 17.06 % Favored : 82.48 % 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: 0.82 (0.21), residues: 1890 helix: 1.56 (0.14), residues: 1407 sheet: -2.83 (0.53), residues: 84 loop : -2.41 (0.30), residues: 399 *********************** 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 110 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 102 time to evaluate : 1.743 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 109 average time/residue: 0.2521 time to fit residues: 43.9570 Evaluate side-chains 102 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 99 time to evaluate : 1.746 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1388 time to fit residues: 3.3091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 61 optimal weight: 0.8980 chunk 164 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 45 optimal weight: 9.9990 chunk 182 optimal weight: 2.9990 chunk 151 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7804 moved from start: 0.2070 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= 0.154 Angle : 0.465 5.433 22393 Z= 0.229 Chirality : 0.036 0.123 2646 Planarity : 0.003 0.046 2625 Dihedral : 5.285 31.975 2359 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.57 % Allowed : 17.91 % Favored : 81.52 % 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: 1.08 (0.20), residues: 1890 helix: 1.70 (0.14), residues: 1407 sheet: -0.52 (0.52), residues: 84 loop : -2.68 (0.29), residues: 399 *********************** 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 113 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 103 time to evaluate : 1.720 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 106 average time/residue: 0.2489 time to fit residues: 42.8124 Evaluate side-chains 105 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 99 time to evaluate : 1.697 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1525 time to fit residues: 4.0747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 176 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 104 optimal weight: 0.6980 chunk 133 optimal weight: 2.9990 chunk 103 optimal weight: 0.0020 chunk 153 optimal weight: 8.9990 chunk 102 optimal weight: 0.8980 chunk 182 optimal weight: 0.7980 chunk 114 optimal weight: 4.9990 chunk 111 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7780 moved from start: 0.2202 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= 0.131 Angle : 0.448 5.419 22393 Z= 0.221 Chirality : 0.036 0.121 2646 Planarity : 0.003 0.033 2625 Dihedral : 5.052 30.505 2359 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.11 % Allowed : 18.76 % Favored : 81.12 % 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: 1.38 (0.20), residues: 1890 helix: 1.91 (0.14), residues: 1407 sheet: -0.40 (0.52), residues: 84 loop : -2.54 (0.30), residues: 399 *********************** 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 109 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 107 time to evaluate : 2.258 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 109 average time/residue: 0.2487 time to fit residues: 43.9677 Evaluate side-chains 102 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 101 time to evaluate : 1.735 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1459 time to fit residues: 2.6911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 112 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 90 optimal weight: 0.0870 chunk 16 optimal weight: 0.9980 chunk 143 optimal weight: 0.5980 chunk 165 optimal weight: 10.0000 overall best weight: 0.6760 ------------------------------------------------------------------------------- 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: 0.7787 moved from start: 0.2248 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= 0.140 Angle : 0.453 5.418 22393 Z= 0.223 Chirality : 0.036 0.122 2646 Planarity : 0.003 0.033 2625 Dihedral : 5.020 30.777 2359 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.11 % Allowed : 19.33 % Favored : 80.56 % 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: 1.55 (0.21), residues: 1890 helix: 2.03 (0.14), residues: 1407 sheet: -0.30 (0.52), residues: 84 loop : -2.49 (0.30), residues: 399 *********************** 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 104 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 102 time to evaluate : 1.746 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 103 average time/residue: 0.2402 time to fit residues: 41.0456 Evaluate side-chains 99 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 98 time to evaluate : 1.903 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1770 time to fit residues: 2.6604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 174 optimal weight: 2.9990 chunk 159 optimal weight: 0.6980 chunk 169 optimal weight: 0.9990 chunk 102 optimal weight: 0.0470 chunk 73 optimal weight: 0.8980 chunk 133 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 153 optimal weight: 5.9990 chunk 160 optimal weight: 0.8980 chunk 111 optimal weight: 10.0000 chunk 179 optimal weight: 0.4980 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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: 0.7778 moved from start: 0.2335 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= 0.133 Angle : 0.447 5.416 22393 Z= 0.220 Chirality : 0.036 0.122 2646 Planarity : 0.003 0.030 2625 Dihedral : 4.928 30.013 2359 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.11 % Allowed : 19.61 % Favored : 80.27 % 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: 1.72 (0.21), residues: 1890 helix: 2.15 (0.14), residues: 1407 sheet: -0.17 (0.52), residues: 84 loop : -2.45 (0.31), residues: 399 *********************** 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 100 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 98 time to evaluate : 1.876 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 99 average time/residue: 0.2514 time to fit residues: 40.5792 Evaluate side-chains 97 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 1.790 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 109 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 188 optimal weight: 2.9990 chunk 173 optimal weight: 0.9980 chunk 149 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 115 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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: 0.7807 moved from start: 0.2285 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= 0.161 Angle : 0.466 5.433 22393 Z= 0.230 Chirality : 0.037 0.123 2646 Planarity : 0.003 0.033 2625 Dihedral : 5.104 32.391 2359 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.23 % Allowed : 19.78 % Favored : 79.99 % 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: 1.61 (0.21), residues: 1890 helix: 2.13 (0.14), residues: 1407 sheet: -1.91 (0.46), residues: 119 loop : -2.21 (0.33), residues: 364 ********************** 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 101 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 97 time to evaluate : 1.964 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 99 average time/residue: 0.2416 time to fit residues: 39.8993 Evaluate side-chains 99 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 95 time to evaluate : 2.167 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1461 time to fit residues: 3.7344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 45 optimal weight: 0.8980 chunk 138 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 41 optimal weight: 0.1980 chunk 150 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 154 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 27 optimal weight: 0.0030 chunk 131 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- 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 = 0.3549 r_free = 0.3549 target = 0.145178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.112241 restraints weight = 16478.367| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.71 r_work: 0.3041 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2398 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= 0.128 Angle : 0.443 5.401 22393 Z= 0.218 Chirality : 0.036 0.122 2646 Planarity : 0.003 0.027 2625 Dihedral : 4.863 30.317 2359 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.17 % Allowed : 19.78 % Favored : 80.05 % 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: 1.87 (0.21), residues: 1890 helix: 2.30 (0.14), residues: 1400 sheet: -0.06 (0.53), residues: 84 loop : -2.46 (0.31), residues: 406 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2513.16 seconds wall clock time: 47 minutes 22.80 seconds (2842.80 seconds total)