Starting phenix.real_space_refine on Thu Nov 16 04:04:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcf_6551/11_2023/3jcf_6551.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcf_6551/11_2023/3jcf_6551.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcf_6551/11_2023/3jcf_6551.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcf_6551/11_2023/3jcf_6551.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcf_6551/11_2023/3jcf_6551.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcf_6551/11_2023/3jcf_6551.pdb" } resolution = 3.8 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= 0.005 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 Mg 13 5.21 5 S 40 5.16 5 C 9250 2.51 5 N 2305 2.21 5 O 2620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 165": "NH1" <-> "NH2" Residue "A TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 210": "NH1" <-> "NH2" Residue "A ARG 216": "NH1" <-> "NH2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 269": "NH1" <-> "NH2" Residue "A TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 165": "NH1" <-> "NH2" Residue "B TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 210": "NH1" <-> "NH2" Residue "B ARG 216": "NH1" <-> "NH2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 269": "NH1" <-> "NH2" Residue "B TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 165": "NH1" <-> "NH2" Residue "C TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 210": "NH1" <-> "NH2" Residue "C ARG 216": "NH1" <-> "NH2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 269": "NH1" <-> "NH2" Residue "C TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 165": "NH1" <-> "NH2" Residue "D TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 210": "NH1" <-> "NH2" Residue "D ARG 216": "NH1" <-> "NH2" Residue "D ARG 237": "NH1" <-> "NH2" Residue "D TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 269": "NH1" <-> "NH2" Residue "D TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 165": "NH1" <-> "NH2" Residue "E TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 210": "NH1" <-> "NH2" Residue "E ARG 216": "NH1" <-> "NH2" Residue "E ARG 237": "NH1" <-> "NH2" Residue "E TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 269": "NH1" <-> "NH2" Residue "E TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 14228 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2843 Classifications: {'peptide': 349} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 15, 'TRANS': 333} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 2843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2843 Classifications: {'peptide': 349} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 15, 'TRANS': 333} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 2843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2843 Classifications: {'peptide': 349} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 15, 'TRANS': 333} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "D" Number of atoms: 2843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2843 Classifications: {'peptide': 349} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 15, 'TRANS': 333} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "E" Number of atoms: 2843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2843 Classifications: {'peptide': 349} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 15, 'TRANS': 333} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 7.83, per 1000 atoms: 0.55 Number of scatterers: 14228 At special positions: 0 Unit cell: (116.025, 113.475, 124.95, 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 40 16.00 Mg 13 11.99 O 2620 8.00 N 2305 7.00 C 9250 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.61 Conformation dependent library (CDL) restraints added in 2.5 seconds 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3360 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 5 sheets defined 57.6% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 50 through 56 removed outlier: 3.576A pdb=" N PHE A 53 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP A 55 " --> pdb=" O PRO A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 80 removed outlier: 3.527A pdb=" N VAL A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 92 Processing helix chain 'A' and resid 147 through 156 Processing helix chain 'A' and resid 159 through 163 removed outlier: 4.106A pdb=" N ARG A 162 " --> pdb=" O GLY A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 201 removed outlier: 3.596A pdb=" N TYR A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE A 182 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 237 Proline residue: A 227 - end of helix removed outlier: 4.170A pdb=" N GLU A 230 " --> pdb=" O TRP A 226 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A 235 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG A 237 " --> pdb=" O SER A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 299 removed outlier: 3.929A pdb=" N TYR A 250 " --> pdb=" O GLU A 246 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP A 253 " --> pdb=" O PRO A 249 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE A 259 " --> pdb=" O TYR A 255 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY A 274 " --> pdb=" O ASP A 270 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ASP A 277 " --> pdb=" O SER A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 313 Processing helix chain 'A' and resid 325 through 345 removed outlier: 3.566A pdb=" N VAL A 329 " --> pdb=" O TRP A 325 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 56 removed outlier: 3.575A pdb=" N PHE B 53 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP B 55 " --> pdb=" O PRO B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 80 removed outlier: 3.527A pdb=" N VAL B 73 " --> pdb=" O ARG B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'B' and resid 147 through 156 Processing helix chain 'B' and resid 159 through 163 removed outlier: 4.105A pdb=" N ARG B 162 " --> pdb=" O GLY B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 201 removed outlier: 3.598A pdb=" N TYR B 181 " --> pdb=" O LEU B 177 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE B 182 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL B 183 " --> pdb=" O ASP B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 237 Proline residue: B 227 - end of helix removed outlier: 4.169A pdb=" N GLU B 230 " --> pdb=" O TRP B 226 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU B 235 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG B 237 " --> pdb=" O SER B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 299 removed outlier: 3.928A pdb=" N TYR B 250 " --> pdb=" O GLU B 246 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP B 253 " --> pdb=" O PRO B 249 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE B 259 " --> pdb=" O TYR B 255 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY B 274 " --> pdb=" O ASP B 270 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU B 276 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ASP B 277 " --> pdb=" O SER B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 313 Processing helix chain 'B' and resid 325 through 345 removed outlier: 3.568A pdb=" N VAL B 329 " --> pdb=" O TRP B 325 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 56 removed outlier: 3.576A pdb=" N PHE C 53 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP C 55 " --> pdb=" O PRO C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 80 removed outlier: 3.527A pdb=" N VAL C 73 " --> pdb=" O ARG C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 92 Processing helix chain 'C' and resid 147 through 156 Processing helix chain 'C' and resid 159 through 163 removed outlier: 4.104A pdb=" N ARG C 162 " --> pdb=" O GLY C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 201 removed outlier: 3.596A pdb=" N TYR C 181 " --> pdb=" O LEU C 177 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE C 182 " --> pdb=" O VAL C 178 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL C 183 " --> pdb=" O ASP C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 237 Proline residue: C 227 - end of helix removed outlier: 4.170A pdb=" N GLU C 230 " --> pdb=" O TRP C 226 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU C 235 " --> pdb=" O VAL C 231 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG C 237 " --> pdb=" O SER C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 299 removed outlier: 3.928A pdb=" N TYR C 250 " --> pdb=" O GLU C 246 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASP C 253 " --> pdb=" O PRO C 249 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE C 259 " --> pdb=" O TYR C 255 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY C 274 " --> pdb=" O ASP C 270 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU C 276 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ASP C 277 " --> pdb=" O SER C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 313 Processing helix chain 'C' and resid 325 through 345 removed outlier: 3.563A pdb=" N VAL C 329 " --> pdb=" O TRP C 325 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY C 335 " --> pdb=" O LEU C 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 56 removed outlier: 3.575A pdb=" N PHE D 53 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP D 55 " --> pdb=" O PRO D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 80 removed outlier: 3.526A pdb=" N VAL D 73 " --> pdb=" O ARG D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 92 Processing helix chain 'D' and resid 147 through 156 Processing helix chain 'D' and resid 159 through 163 removed outlier: 4.106A pdb=" N ARG D 162 " --> pdb=" O GLY D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 201 removed outlier: 3.597A pdb=" N TYR D 181 " --> pdb=" O LEU D 177 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE D 182 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL D 183 " --> pdb=" O ASP D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 237 Proline residue: D 227 - end of helix removed outlier: 4.169A pdb=" N GLU D 230 " --> pdb=" O TRP D 226 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU D 235 " --> pdb=" O VAL D 231 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG D 237 " --> pdb=" O SER D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 299 removed outlier: 3.928A pdb=" N TYR D 250 " --> pdb=" O GLU D 246 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP D 253 " --> pdb=" O PRO D 249 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE D 259 " --> pdb=" O TYR D 255 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY D 274 " --> pdb=" O ASP D 270 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU D 276 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ASP D 277 " --> pdb=" O SER D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 313 Processing helix chain 'D' and resid 325 through 345 removed outlier: 3.567A pdb=" N VAL D 329 " --> pdb=" O TRP D 325 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY D 335 " --> pdb=" O LEU D 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 56 removed outlier: 3.574A pdb=" N PHE E 53 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP E 55 " --> pdb=" O PRO E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 80 removed outlier: 3.526A pdb=" N VAL E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 92 Processing helix chain 'E' and resid 147 through 156 Processing helix chain 'E' and resid 159 through 163 removed outlier: 4.105A pdb=" N ARG E 162 " --> pdb=" O GLY E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 201 removed outlier: 3.597A pdb=" N TYR E 181 " --> pdb=" O LEU E 177 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE E 182 " --> pdb=" O VAL E 178 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL E 183 " --> pdb=" O ASP E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 237 Proline residue: E 227 - end of helix removed outlier: 4.170A pdb=" N GLU E 230 " --> pdb=" O TRP E 226 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU E 235 " --> pdb=" O VAL E 231 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG E 237 " --> pdb=" O SER E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 299 removed outlier: 3.927A pdb=" N TYR E 250 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASP E 253 " --> pdb=" O PRO E 249 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE E 259 " --> pdb=" O TYR E 255 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY E 274 " --> pdb=" O ASP E 270 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU E 276 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ASP E 277 " --> pdb=" O SER E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 313 Processing helix chain 'E' and resid 325 through 345 removed outlier: 3.566A pdb=" N VAL E 329 " --> pdb=" O TRP E 325 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY E 335 " --> pdb=" O LEU E 331 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 39 through 44 Processing sheet with id= B, first strand: chain 'B' and resid 39 through 44 Processing sheet with id= C, first strand: chain 'C' and resid 39 through 44 Processing sheet with id= D, first strand: chain 'D' and resid 39 through 44 Processing sheet with id= E, first strand: chain 'E' and resid 39 through 44 880 hydrogen bonds defined for protein. 2565 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: 3.96 Time building geometry restraints manager: 6.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4471 1.34 - 1.46: 1966 1.46 - 1.57: 8013 1.57 - 1.69: 0 1.69 - 1.80: 75 Bond restraints: 14525 Sorted by residual: bond pdb=" CA PRO C 240 " pdb=" C PRO C 240 " ideal model delta sigma weight residual 1.517 1.546 -0.028 9.30e-03 1.16e+04 9.35e+00 bond pdb=" CA PRO E 240 " pdb=" C PRO E 240 " ideal model delta sigma weight residual 1.517 1.545 -0.028 9.30e-03 1.16e+04 9.11e+00 bond pdb=" CA PRO A 240 " pdb=" C PRO A 240 " ideal model delta sigma weight residual 1.517 1.545 -0.028 9.30e-03 1.16e+04 8.95e+00 bond pdb=" CA PRO B 240 " pdb=" C PRO B 240 " ideal model delta sigma weight residual 1.517 1.545 -0.028 9.30e-03 1.16e+04 8.92e+00 bond pdb=" CA PRO D 240 " pdb=" C PRO D 240 " ideal model delta sigma weight residual 1.517 1.545 -0.028 9.30e-03 1.16e+04 8.78e+00 ... (remaining 14520 not shown) Histogram of bond angle deviations from ideal: 100.71 - 107.60: 440 107.60 - 114.48: 8668 114.48 - 121.37: 6666 121.37 - 128.26: 3856 128.26 - 135.14: 100 Bond angle restraints: 19730 Sorted by residual: angle pdb=" C PRO C 240 " pdb=" N PRO C 241 " pdb=" CA PRO C 241 " ideal model delta sigma weight residual 119.84 113.54 6.30 1.25e+00 6.40e-01 2.54e+01 angle pdb=" C PRO B 240 " pdb=" N PRO B 241 " pdb=" CA PRO B 241 " ideal model delta sigma weight residual 119.84 113.59 6.25 1.25e+00 6.40e-01 2.50e+01 angle pdb=" C PRO D 240 " pdb=" N PRO D 241 " pdb=" CA PRO D 241 " ideal model delta sigma weight residual 119.84 113.59 6.25 1.25e+00 6.40e-01 2.50e+01 angle pdb=" C PRO E 240 " pdb=" N PRO E 241 " pdb=" CA PRO E 241 " ideal model delta sigma weight residual 119.84 113.60 6.24 1.25e+00 6.40e-01 2.49e+01 angle pdb=" C PRO A 240 " pdb=" N PRO A 241 " pdb=" CA PRO A 241 " ideal model delta sigma weight residual 119.84 113.62 6.22 1.25e+00 6.40e-01 2.48e+01 ... (remaining 19725 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 7.97: 7974 7.97 - 15.93: 576 15.93 - 23.90: 118 23.90 - 31.86: 59 31.86 - 39.83: 28 Dihedral angle restraints: 8755 sinusoidal: 3570 harmonic: 5185 Sorted by residual: dihedral pdb=" CA LEU C 131 " pdb=" CB LEU C 131 " pdb=" CG LEU C 131 " pdb=" CD1 LEU C 131 " ideal model delta sinusoidal sigma weight residual 180.00 140.17 39.83 3 1.50e+01 4.44e-03 7.07e+00 dihedral pdb=" CA LEU A 131 " pdb=" CB LEU A 131 " pdb=" CG LEU A 131 " pdb=" CD1 LEU A 131 " ideal model delta sinusoidal sigma weight residual 180.00 140.19 39.81 3 1.50e+01 4.44e-03 7.07e+00 dihedral pdb=" CA LEU B 131 " pdb=" CB LEU B 131 " pdb=" CG LEU B 131 " pdb=" CD1 LEU B 131 " ideal model delta sinusoidal sigma weight residual 180.00 140.22 39.78 3 1.50e+01 4.44e-03 7.06e+00 ... (remaining 8752 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 1630 0.024 - 0.047: 245 0.047 - 0.071: 109 0.071 - 0.095: 178 0.095 - 0.119: 128 Chirality restraints: 2290 Sorted by residual: chirality pdb=" CA ILE C 160 " pdb=" N ILE C 160 " pdb=" C ILE C 160 " pdb=" CB ILE C 160 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.51e-01 chirality pdb=" CA ILE B 160 " pdb=" N ILE B 160 " pdb=" C ILE B 160 " pdb=" CB ILE B 160 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.38e-01 chirality pdb=" CA ILE B 143 " pdb=" N ILE B 143 " pdb=" C ILE B 143 " pdb=" CB ILE B 143 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.37e-01 ... (remaining 2287 not shown) Planarity restraints: 2490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL E 239 " -0.024 5.00e-02 4.00e+02 3.65e-02 2.13e+00 pdb=" N PRO E 240 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO E 240 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 240 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 239 " 0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO C 240 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO C 240 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 240 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 239 " 0.024 5.00e-02 4.00e+02 3.62e-02 2.10e+00 pdb=" N PRO B 240 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 240 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 240 " 0.021 5.00e-02 4.00e+02 ... (remaining 2487 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 181 2.63 - 3.19: 13699 3.19 - 3.76: 22099 3.76 - 4.33: 30360 4.33 - 4.90: 49384 Nonbonded interactions: 115723 Sorted by model distance: nonbonded pdb=" OD1 ASP C 253 " pdb="MG MG D 402 " model vdw 2.057 2.170 nonbonded pdb=" OD1 ASP B 253 " pdb="MG MG C 402 " model vdw 2.058 2.170 nonbonded pdb=" OD1 ASP D 253 " pdb="MG MG E 402 " model vdw 2.059 2.170 nonbonded pdb=" OD1 ASP A 253 " pdb="MG MG B 402 " model vdw 2.059 2.170 nonbonded pdb=" OD1 ASP E 253 " pdb="MG MG A 402 " model vdw 2.062 2.170 ... (remaining 115718 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = (chain 'E' and (resid 3 through 351 or resid 402 through 501)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.290 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: 4.490 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 37.930 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 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 : 0.004 0.028 14525 Z= 0.247 Angle : 1.028 10.141 19730 Z= 0.718 Chirality : 0.039 0.119 2290 Planarity : 0.003 0.036 2490 Dihedral : 6.812 39.830 5395 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % 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: -1.63 (0.18), residues: 1735 helix: -0.43 (0.14), residues: 910 sheet: -1.06 (0.32), residues: 240 loop : -1.96 (0.24), residues: 585 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 335 time to evaluate : 1.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 335 average time/residue: 0.2871 time to fit residues: 138.2966 Evaluate side-chains 149 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 1.830 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 0.9980 chunk 128 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 68 optimal weight: 20.0000 chunk 133 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 154 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 HIS A 314 ASN B 94 HIS B 95 GLN B 260 GLN B 314 ASN C 95 GLN C 140 GLN C 314 ASN D 94 HIS D 126 GLN D 213 GLN D 314 ASN ** E 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 HIS E 95 GLN E 140 GLN E 314 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14525 Z= 0.222 Angle : 0.666 8.860 19730 Z= 0.350 Chirality : 0.043 0.195 2290 Planarity : 0.004 0.046 2490 Dihedral : 4.078 14.014 1925 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.36 % Allowed : 6.62 % Favored : 91.02 % 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: 0.27 (0.20), residues: 1735 helix: 1.55 (0.17), residues: 940 sheet: -0.69 (0.29), residues: 285 loop : -1.91 (0.26), residues: 510 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 180 time to evaluate : 1.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 21 residues processed: 202 average time/residue: 0.1864 time to fit residues: 62.8929 Evaluate side-chains 155 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 134 time to evaluate : 1.807 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1253 time to fit residues: 7.3666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 chunk 42 optimal weight: 0.9990 chunk 154 optimal weight: 0.9980 chunk 167 optimal weight: 0.0170 chunk 137 optimal weight: 4.9990 chunk 153 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 overall best weight: 0.9822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS ** B 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 GLN C 126 GLN ** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14525 Z= 0.204 Angle : 0.618 7.970 19730 Z= 0.316 Chirality : 0.042 0.143 2290 Planarity : 0.004 0.048 2490 Dihedral : 3.952 15.113 1925 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.34 % Allowed : 8.15 % Favored : 90.51 % 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: 0.93 (0.21), residues: 1735 helix: 2.12 (0.17), residues: 935 sheet: -0.34 (0.29), residues: 285 loop : -1.70 (0.27), residues: 515 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 146 time to evaluate : 2.128 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 11 residues processed: 159 average time/residue: 0.2116 time to fit residues: 57.1028 Evaluate side-chains 129 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 118 time to evaluate : 1.934 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1393 time to fit residues: 5.6252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 2.9990 chunk 116 optimal weight: 0.3980 chunk 80 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 103 optimal weight: 0.9980 chunk 155 optimal weight: 0.9990 chunk 164 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 147 optimal weight: 8.9990 chunk 44 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 GLN ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 GLN C 213 GLN ** D 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14525 Z= 0.215 Angle : 0.601 8.464 19730 Z= 0.308 Chirality : 0.042 0.176 2290 Planarity : 0.004 0.048 2490 Dihedral : 3.900 14.607 1925 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.21 % Allowed : 9.94 % Favored : 88.85 % 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: 1.26 (0.21), residues: 1735 helix: 2.26 (0.17), residues: 940 sheet: 0.00 (0.30), residues: 280 loop : -1.44 (0.27), residues: 515 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 134 time to evaluate : 1.943 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 10 residues processed: 147 average time/residue: 0.1987 time to fit residues: 49.1894 Evaluate side-chains 129 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 119 time to evaluate : 2.186 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1483 time to fit residues: 5.3198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 20.0000 chunk 93 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 122 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 83 optimal weight: 4.9990 chunk 147 optimal weight: 7.9990 chunk 41 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS ** B 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 GLN ** D 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 126 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 14525 Z= 0.476 Angle : 0.750 10.236 19730 Z= 0.378 Chirality : 0.045 0.165 2290 Planarity : 0.005 0.051 2490 Dihedral : 4.237 17.760 1925 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.29 % Allowed : 10.19 % Favored : 87.52 % 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: 1.19 (0.21), residues: 1735 helix: 2.23 (0.16), residues: 950 sheet: -0.37 (0.31), residues: 270 loop : -1.36 (0.28), residues: 515 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 120 time to evaluate : 1.890 Fit side-chains outliers start: 36 outliers final: 20 residues processed: 142 average time/residue: 0.1910 time to fit residues: 46.0132 Evaluate side-chains 125 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 105 time to evaluate : 1.764 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1271 time to fit residues: 7.1448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 0.6980 chunk 147 optimal weight: 2.9990 chunk 32 optimal weight: 0.4980 chunk 96 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 164 optimal weight: 1.9990 chunk 136 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 HIS D 83 HIS ** E 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14525 Z= 0.195 Angle : 0.617 10.771 19730 Z= 0.311 Chirality : 0.041 0.156 2290 Planarity : 0.004 0.047 2490 Dihedral : 3.974 16.482 1925 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.76 % Allowed : 11.34 % Favored : 87.90 % 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: 1.58 (0.21), residues: 1735 helix: 2.51 (0.17), residues: 940 sheet: 0.03 (0.32), residues: 265 loop : -1.18 (0.28), residues: 530 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 137 time to evaluate : 1.760 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 146 average time/residue: 0.1855 time to fit residues: 46.3326 Evaluate side-chains 117 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 111 time to evaluate : 1.949 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1379 time to fit residues: 4.0947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 0.3980 chunk 18 optimal weight: 0.8980 chunk 93 optimal weight: 6.9990 chunk 120 optimal weight: 3.9990 chunk 138 optimal weight: 8.9990 chunk 91 optimal weight: 0.7980 chunk 163 optimal weight: 0.8980 chunk 102 optimal weight: 7.9990 chunk 99 optimal weight: 0.8980 chunk 75 optimal weight: 8.9990 chunk 101 optimal weight: 9.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 GLN ** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14525 Z= 0.186 Angle : 0.616 13.417 19730 Z= 0.307 Chirality : 0.041 0.185 2290 Planarity : 0.004 0.047 2490 Dihedral : 3.877 16.677 1925 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.38 % Allowed : 12.87 % Favored : 86.75 % 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: 1.67 (0.21), residues: 1735 helix: 2.56 (0.17), residues: 940 sheet: 0.24 (0.32), residues: 265 loop : -1.18 (0.28), residues: 530 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 134 time to evaluate : 1.336 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 139 average time/residue: 0.1537 time to fit residues: 36.0193 Evaluate side-chains 118 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 117 time to evaluate : 1.703 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1220 time to fit residues: 2.5430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 0.3980 chunk 97 optimal weight: 0.0970 chunk 49 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 111 optimal weight: 0.0470 chunk 81 optimal weight: 7.9990 chunk 15 optimal weight: 0.4980 chunk 128 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 GLN C 83 HIS C 95 GLN ** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 HIS ** E 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 14525 Z= 0.176 Angle : 0.634 13.682 19730 Z= 0.317 Chirality : 0.041 0.176 2290 Planarity : 0.003 0.046 2490 Dihedral : 3.836 16.246 1925 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.32 % Allowed : 14.08 % Favored : 85.61 % 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: 1735 helix: 2.58 (0.17), residues: 940 sheet: 0.52 (0.32), residues: 270 loop : -1.28 (0.28), residues: 525 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 131 time to evaluate : 1.998 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 135 average time/residue: 0.1965 time to fit residues: 44.5527 Evaluate side-chains 121 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 120 time to evaluate : 1.789 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1278 time to fit residues: 2.6018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 0.9990 chunk 143 optimal weight: 0.9980 chunk 152 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 46 optimal weight: 9.9990 chunk 137 optimal weight: 0.3980 chunk 144 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 chunk 161 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS ** B 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 14525 Z= 0.203 Angle : 0.631 12.770 19730 Z= 0.315 Chirality : 0.042 0.187 2290 Planarity : 0.004 0.047 2490 Dihedral : 3.831 16.464 1925 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.13 % Allowed : 14.52 % Favored : 85.35 % 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: 1.75 (0.21), residues: 1735 helix: 2.59 (0.17), residues: 940 sheet: 0.42 (0.31), residues: 265 loop : -1.14 (0.28), residues: 530 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 126 time to evaluate : 1.754 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 128 average time/residue: 0.1936 time to fit residues: 41.9395 Evaluate side-chains 117 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 116 time to evaluate : 1.624 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1160 time to fit residues: 2.4718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.8980 chunk 76 optimal weight: 0.0020 chunk 112 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 155 optimal weight: 0.7980 chunk 134 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 104 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 143 optimal weight: 6.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14525 Z= 0.186 Angle : 0.634 13.679 19730 Z= 0.317 Chirality : 0.042 0.193 2290 Planarity : 0.003 0.046 2490 Dihedral : 3.795 16.222 1925 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.19 % Allowed : 14.71 % Favored : 85.10 % 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: 1.78 (0.21), residues: 1735 helix: 2.65 (0.17), residues: 935 sheet: 0.65 (0.32), residues: 255 loop : -1.27 (0.27), residues: 545 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 123 time to evaluate : 1.820 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 125 average time/residue: 0.1957 time to fit residues: 41.4268 Evaluate side-chains 121 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 118 time to evaluate : 1.682 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1291 time to fit residues: 2.8648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 0.9990 chunk 124 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 135 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 138 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 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 = 0.3352 r_free = 0.3352 target = 0.071393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.058932 restraints weight = 46655.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.061079 restraints weight = 26773.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.062614 restraints weight = 18290.832| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14525 Z= 0.187 Angle : 0.626 13.443 19730 Z= 0.313 Chirality : 0.042 0.189 2290 Planarity : 0.003 0.046 2490 Dihedral : 3.773 16.271 1925 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.06 % Allowed : 14.84 % Favored : 85.10 % 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: 1.84 (0.21), residues: 1735 helix: 2.69 (0.17), residues: 935 sheet: 0.72 (0.32), residues: 255 loop : -1.26 (0.27), residues: 545 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2324.78 seconds wall clock time: 45 minutes 37.69 seconds (2737.69 seconds total)