Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 11:31:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uiv_20788/04_2023/6uiv_20788.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uiv_20788/04_2023/6uiv_20788.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uiv_20788/04_2023/6uiv_20788.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uiv_20788/04_2023/6uiv_20788.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uiv_20788/04_2023/6uiv_20788.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uiv_20788/04_2023/6uiv_20788.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 77 5.16 5 C 14861 2.51 5 N 4191 2.21 5 O 3773 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 109": "NH1" <-> "NH2" Residue "A ARG 159": "NH1" <-> "NH2" Residue "A ARG 178": "NH1" <-> "NH2" Residue "A ARG 224": "NH1" <-> "NH2" Residue "A ARG 275": "NH1" <-> "NH2" Residue "B ARG 109": "NH1" <-> "NH2" Residue "B ARG 159": "NH1" <-> "NH2" Residue "B ARG 178": "NH1" <-> "NH2" Residue "B ARG 224": "NH1" <-> "NH2" Residue "B ARG 275": "NH1" <-> "NH2" Residue "C ARG 109": "NH1" <-> "NH2" Residue "C ARG 159": "NH1" <-> "NH2" Residue "C ARG 178": "NH1" <-> "NH2" Residue "C ARG 224": "NH1" <-> "NH2" Residue "C ARG 275": "NH1" <-> "NH2" Residue "D ARG 109": "NH1" <-> "NH2" Residue "D ARG 159": "NH1" <-> "NH2" Residue "D ARG 178": "NH1" <-> "NH2" Residue "D ARG 224": "NH1" <-> "NH2" Residue "D ARG 275": "NH1" <-> "NH2" Residue "E ARG 109": "NH1" <-> "NH2" Residue "E ARG 159": "NH1" <-> "NH2" Residue "E ARG 178": "NH1" <-> "NH2" Residue "E ARG 224": "NH1" <-> "NH2" Residue "E ARG 275": "NH1" <-> "NH2" Residue "F ARG 109": "NH1" <-> "NH2" Residue "F ARG 159": "NH1" <-> "NH2" Residue "F PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 178": "NH1" <-> "NH2" Residue "F ARG 224": "NH1" <-> "NH2" Residue "F ARG 275": "NH1" <-> "NH2" Residue "G ARG 109": "NH1" <-> "NH2" Residue "G ARG 159": "NH1" <-> "NH2" Residue "G ARG 178": "NH1" <-> "NH2" Residue "G ARG 224": "NH1" <-> "NH2" Residue "G ARG 275": "NH1" <-> "NH2" Residue "H ARG 109": "NH1" <-> "NH2" Residue "H ARG 159": "NH1" <-> "NH2" Residue "H PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 178": "NH1" <-> "NH2" Residue "H ARG 224": "NH1" <-> "NH2" Residue "H ARG 275": "NH1" <-> "NH2" Residue "I ARG 109": "NH1" <-> "NH2" Residue "I ARG 159": "NH1" <-> "NH2" Residue "I PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 178": "NH1" <-> "NH2" Residue "I ARG 224": "NH1" <-> "NH2" Residue "I ARG 275": "NH1" <-> "NH2" Residue "J ARG 109": "NH1" <-> "NH2" Residue "J ARG 159": "NH1" <-> "NH2" Residue "J ARG 178": "NH1" <-> "NH2" Residue "J ARG 224": "NH1" <-> "NH2" Residue "J ARG 275": "NH1" <-> "NH2" Residue "K ARG 109": "NH1" <-> "NH2" Residue "K ARG 159": "NH1" <-> "NH2" Residue "K ARG 178": "NH1" <-> "NH2" Residue "K ARG 224": "NH1" <-> "NH2" Residue "K ARG 275": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 22902 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2082 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 14, 'TRANS': 272} Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 6, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 131 Chain: "B" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2082 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 14, 'TRANS': 272} Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 6, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 131 Chain: "C" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2082 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 14, 'TRANS': 272} Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 6, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 131 Chain: "D" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2082 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 14, 'TRANS': 272} Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 6, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 131 Chain: "E" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2082 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 14, 'TRANS': 272} Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 6, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 131 Chain: "F" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2082 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 14, 'TRANS': 272} Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 6, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 131 Chain: "G" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2082 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 14, 'TRANS': 272} Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 6, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 131 Chain: "H" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2082 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 14, 'TRANS': 272} Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 6, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 131 Chain: "I" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2082 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 14, 'TRANS': 272} Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 6, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 131 Chain: "J" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2082 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 14, 'TRANS': 272} Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 6, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 131 Chain: "K" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2082 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 14, 'TRANS': 272} Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 6, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 131 Time building chain proxies: 12.22, per 1000 atoms: 0.53 Number of scatterers: 22902 At special positions: 0 Unit cell: (145.692, 146.718, 103.626, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 77 16.00 O 3773 8.00 N 4191 7.00 C 14861 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 130 " distance=2.03 Simple disulfide: pdb=" SG CYS A 48 " - pdb=" SG CYS A 162 " distance=2.03 Simple disulfide: pdb=" SG CYS B 46 " - pdb=" SG CYS B 130 " distance=2.03 Simple disulfide: pdb=" SG CYS B 48 " - pdb=" SG CYS B 162 " distance=2.03 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 130 " distance=2.03 Simple disulfide: pdb=" SG CYS C 48 " - pdb=" SG CYS C 162 " distance=2.03 Simple disulfide: pdb=" SG CYS D 46 " - pdb=" SG CYS D 130 " distance=2.03 Simple disulfide: pdb=" SG CYS D 48 " - pdb=" SG CYS D 162 " distance=2.02 Simple disulfide: pdb=" SG CYS E 46 " - pdb=" SG CYS E 130 " distance=2.03 Simple disulfide: pdb=" SG CYS E 48 " - pdb=" SG CYS E 162 " distance=2.02 Simple disulfide: pdb=" SG CYS F 46 " - pdb=" SG CYS F 130 " distance=2.03 Simple disulfide: pdb=" SG CYS F 48 " - pdb=" SG CYS F 162 " distance=2.02 Simple disulfide: pdb=" SG CYS G 46 " - pdb=" SG CYS G 130 " distance=2.03 Simple disulfide: pdb=" SG CYS G 48 " - pdb=" SG CYS G 162 " distance=2.03 Simple disulfide: pdb=" SG CYS H 46 " - pdb=" SG CYS H 130 " distance=2.03 Simple disulfide: pdb=" SG CYS H 48 " - pdb=" SG CYS H 162 " distance=2.02 Simple disulfide: pdb=" SG CYS I 46 " - pdb=" SG CYS I 130 " distance=2.03 Simple disulfide: pdb=" SG CYS I 48 " - pdb=" SG CYS I 162 " distance=2.03 Simple disulfide: pdb=" SG CYS J 46 " - pdb=" SG CYS J 130 " distance=2.03 Simple disulfide: pdb=" SG CYS J 48 " - pdb=" SG CYS J 162 " distance=2.03 Simple disulfide: pdb=" SG CYS K 46 " - pdb=" SG CYS K 130 " distance=2.03 Simple disulfide: pdb=" SG CYS K 48 " - pdb=" SG CYS K 162 " 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: 9.00 Conformation dependent library (CDL) restraints added in 3.5 seconds 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5984 Finding SS restraints... Secondary structure from input PDB file: 165 helices and 11 sheets defined 77.4% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 20 through 38 removed outlier: 3.520A pdb=" N LEU A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 75 removed outlier: 3.533A pdb=" N TYR A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Proline residue: A 64 - end of helix Processing helix chain 'A' and resid 77 through 89 removed outlier: 3.564A pdb=" N ARG A 89 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 124 removed outlier: 3.519A pdb=" N LEU A 101 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ALA A 113 " --> pdb=" O ARG A 109 " (cutoff:3.500A) Proline residue: A 114 - end of helix Processing helix chain 'A' and resid 125 through 133 removed outlier: 3.532A pdb=" N SER A 133 " --> pdb=" O VAL A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 136 No H-bonds generated for 'chain 'A' and resid 134 through 136' Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 152 through 159 removed outlier: 3.548A pdb=" N ILE A 156 " --> pdb=" O HIS A 152 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 163 Processing helix chain 'A' and resid 166 through 168 No H-bonds generated for 'chain 'A' and resid 166 through 168' Processing helix chain 'A' and resid 169 through 209 Processing helix chain 'A' and resid 214 through 251 Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 274 through 282 Processing helix chain 'A' and resid 297 through 306 Processing helix chain 'B' and resid 21 through 38 removed outlier: 3.520A pdb=" N LEU B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 75 removed outlier: 3.533A pdb=" N TYR B 56 " --> pdb=" O ARG B 52 " (cutoff:3.500A) Proline residue: B 64 - end of helix Processing helix chain 'B' and resid 77 through 89 removed outlier: 3.563A pdb=" N ARG B 89 " --> pdb=" O GLU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 124 removed outlier: 3.519A pdb=" N LEU B 101 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ALA B 113 " --> pdb=" O ARG B 109 " (cutoff:3.500A) Proline residue: B 114 - end of helix Processing helix chain 'B' and resid 125 through 133 removed outlier: 3.533A pdb=" N SER B 133 " --> pdb=" O VAL B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 136 No H-bonds generated for 'chain 'B' and resid 134 through 136' Processing helix chain 'B' and resid 149 through 151 No H-bonds generated for 'chain 'B' and resid 149 through 151' Processing helix chain 'B' and resid 152 through 159 removed outlier: 3.548A pdb=" N ILE B 156 " --> pdb=" O HIS B 152 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 163 Processing helix chain 'B' and resid 166 through 168 No H-bonds generated for 'chain 'B' and resid 166 through 168' Processing helix chain 'B' and resid 169 through 209 Processing helix chain 'B' and resid 214 through 251 Processing helix chain 'B' and resid 257 through 267 Processing helix chain 'B' and resid 274 through 282 Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'C' and resid 21 through 38 removed outlier: 3.521A pdb=" N LEU C 38 " --> pdb=" O GLY C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 75 removed outlier: 3.534A pdb=" N TYR C 56 " --> pdb=" O ARG C 52 " (cutoff:3.500A) Proline residue: C 64 - end of helix Processing helix chain 'C' and resid 77 through 89 removed outlier: 3.564A pdb=" N ARG C 89 " --> pdb=" O GLU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 124 removed outlier: 3.519A pdb=" N LEU C 101 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ALA C 113 " --> pdb=" O ARG C 109 " (cutoff:3.500A) Proline residue: C 114 - end of helix Processing helix chain 'C' and resid 125 through 133 removed outlier: 3.532A pdb=" N SER C 133 " --> pdb=" O VAL C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 136 No H-bonds generated for 'chain 'C' and resid 134 through 136' Processing helix chain 'C' and resid 149 through 151 No H-bonds generated for 'chain 'C' and resid 149 through 151' Processing helix chain 'C' and resid 152 through 159 removed outlier: 3.547A pdb=" N ILE C 156 " --> pdb=" O HIS C 152 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 163 Processing helix chain 'C' and resid 166 through 168 No H-bonds generated for 'chain 'C' and resid 166 through 168' Processing helix chain 'C' and resid 169 through 209 Processing helix chain 'C' and resid 214 through 251 Processing helix chain 'C' and resid 257 through 267 Processing helix chain 'C' and resid 274 through 282 Processing helix chain 'C' and resid 297 through 306 Processing helix chain 'D' and resid 21 through 38 removed outlier: 3.520A pdb=" N LEU D 38 " --> pdb=" O GLY D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 75 removed outlier: 3.533A pdb=" N TYR D 56 " --> pdb=" O ARG D 52 " (cutoff:3.500A) Proline residue: D 64 - end of helix Processing helix chain 'D' and resid 77 through 89 removed outlier: 3.563A pdb=" N ARG D 89 " --> pdb=" O GLU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 124 removed outlier: 3.519A pdb=" N LEU D 101 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ALA D 113 " --> pdb=" O ARG D 109 " (cutoff:3.500A) Proline residue: D 114 - end of helix Processing helix chain 'D' and resid 125 through 133 removed outlier: 3.532A pdb=" N SER D 133 " --> pdb=" O VAL D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 136 No H-bonds generated for 'chain 'D' and resid 134 through 136' Processing helix chain 'D' and resid 149 through 151 No H-bonds generated for 'chain 'D' and resid 149 through 151' Processing helix chain 'D' and resid 152 through 159 removed outlier: 3.548A pdb=" N ILE D 156 " --> pdb=" O HIS D 152 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 163 Processing helix chain 'D' and resid 166 through 168 No H-bonds generated for 'chain 'D' and resid 166 through 168' Processing helix chain 'D' and resid 169 through 209 Processing helix chain 'D' and resid 214 through 251 Processing helix chain 'D' and resid 257 through 267 Processing helix chain 'D' and resid 274 through 282 Processing helix chain 'D' and resid 297 through 306 Processing helix chain 'E' and resid 21 through 38 removed outlier: 3.520A pdb=" N LEU E 38 " --> pdb=" O GLY E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 75 removed outlier: 3.533A pdb=" N TYR E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Proline residue: E 64 - end of helix Processing helix chain 'E' and resid 77 through 89 removed outlier: 3.565A pdb=" N ARG E 89 " --> pdb=" O GLU E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 124 removed outlier: 3.519A pdb=" N LEU E 101 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ALA E 113 " --> pdb=" O ARG E 109 " (cutoff:3.500A) Proline residue: E 114 - end of helix Processing helix chain 'E' and resid 125 through 133 removed outlier: 3.532A pdb=" N SER E 133 " --> pdb=" O VAL E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 136 No H-bonds generated for 'chain 'E' and resid 134 through 136' Processing helix chain 'E' and resid 149 through 151 No H-bonds generated for 'chain 'E' and resid 149 through 151' Processing helix chain 'E' and resid 152 through 159 removed outlier: 3.548A pdb=" N ILE E 156 " --> pdb=" O HIS E 152 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 163 Processing helix chain 'E' and resid 166 through 168 No H-bonds generated for 'chain 'E' and resid 166 through 168' Processing helix chain 'E' and resid 169 through 209 Processing helix chain 'E' and resid 214 through 251 Processing helix chain 'E' and resid 257 through 267 Processing helix chain 'E' and resid 274 through 282 Processing helix chain 'E' and resid 297 through 306 Processing helix chain 'F' and resid 21 through 38 removed outlier: 3.520A pdb=" N LEU F 38 " --> pdb=" O GLY F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 75 removed outlier: 3.534A pdb=" N TYR F 56 " --> pdb=" O ARG F 52 " (cutoff:3.500A) Proline residue: F 64 - end of helix Processing helix chain 'F' and resid 77 through 89 removed outlier: 3.564A pdb=" N ARG F 89 " --> pdb=" O GLU F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 124 removed outlier: 3.520A pdb=" N LEU F 101 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ALA F 113 " --> pdb=" O ARG F 109 " (cutoff:3.500A) Proline residue: F 114 - end of helix Processing helix chain 'F' and resid 125 through 133 removed outlier: 3.532A pdb=" N SER F 133 " --> pdb=" O VAL F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 136 No H-bonds generated for 'chain 'F' and resid 134 through 136' Processing helix chain 'F' and resid 149 through 151 No H-bonds generated for 'chain 'F' and resid 149 through 151' Processing helix chain 'F' and resid 152 through 159 removed outlier: 3.548A pdb=" N ILE F 156 " --> pdb=" O HIS F 152 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG F 159 " --> pdb=" O GLU F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 163 Processing helix chain 'F' and resid 166 through 168 No H-bonds generated for 'chain 'F' and resid 166 through 168' Processing helix chain 'F' and resid 169 through 209 Processing helix chain 'F' and resid 214 through 251 Processing helix chain 'F' and resid 257 through 267 Processing helix chain 'F' and resid 274 through 282 Processing helix chain 'F' and resid 297 through 306 Processing helix chain 'G' and resid 21 through 38 removed outlier: 3.520A pdb=" N LEU G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 52 through 75 removed outlier: 3.533A pdb=" N TYR G 56 " --> pdb=" O ARG G 52 " (cutoff:3.500A) Proline residue: G 64 - end of helix Processing helix chain 'G' and resid 77 through 89 removed outlier: 3.564A pdb=" N ARG G 89 " --> pdb=" O GLU G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 124 removed outlier: 3.520A pdb=" N LEU G 101 " --> pdb=" O ALA G 97 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ALA G 113 " --> pdb=" O ARG G 109 " (cutoff:3.500A) Proline residue: G 114 - end of helix Processing helix chain 'G' and resid 125 through 133 removed outlier: 3.532A pdb=" N SER G 133 " --> pdb=" O VAL G 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 136 No H-bonds generated for 'chain 'G' and resid 134 through 136' Processing helix chain 'G' and resid 149 through 151 No H-bonds generated for 'chain 'G' and resid 149 through 151' Processing helix chain 'G' and resid 152 through 159 removed outlier: 3.548A pdb=" N ILE G 156 " --> pdb=" O HIS G 152 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG G 159 " --> pdb=" O GLU G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 163 Processing helix chain 'G' and resid 166 through 168 No H-bonds generated for 'chain 'G' and resid 166 through 168' Processing helix chain 'G' and resid 169 through 209 Processing helix chain 'G' and resid 214 through 251 Processing helix chain 'G' and resid 257 through 267 Processing helix chain 'G' and resid 274 through 282 Processing helix chain 'G' and resid 297 through 306 Processing helix chain 'H' and resid 21 through 38 removed outlier: 3.520A pdb=" N LEU H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 75 removed outlier: 3.533A pdb=" N TYR H 56 " --> pdb=" O ARG H 52 " (cutoff:3.500A) Proline residue: H 64 - end of helix Processing helix chain 'H' and resid 77 through 89 removed outlier: 3.564A pdb=" N ARG H 89 " --> pdb=" O GLU H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 124 removed outlier: 3.519A pdb=" N LEU H 101 " --> pdb=" O ALA H 97 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ALA H 113 " --> pdb=" O ARG H 109 " (cutoff:3.500A) Proline residue: H 114 - end of helix Processing helix chain 'H' and resid 125 through 133 removed outlier: 3.532A pdb=" N SER H 133 " --> pdb=" O VAL H 129 " (cutoff:3.500A) Processing helix chain 'H' and resid 134 through 136 No H-bonds generated for 'chain 'H' and resid 134 through 136' Processing helix chain 'H' and resid 149 through 151 No H-bonds generated for 'chain 'H' and resid 149 through 151' Processing helix chain 'H' and resid 152 through 159 removed outlier: 3.548A pdb=" N ILE H 156 " --> pdb=" O HIS H 152 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG H 159 " --> pdb=" O GLU H 155 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 163 Processing helix chain 'H' and resid 166 through 168 No H-bonds generated for 'chain 'H' and resid 166 through 168' Processing helix chain 'H' and resid 169 through 209 Processing helix chain 'H' and resid 214 through 251 Processing helix chain 'H' and resid 257 through 267 Processing helix chain 'H' and resid 274 through 282 Processing helix chain 'H' and resid 297 through 306 Processing helix chain 'I' and resid 21 through 38 removed outlier: 3.520A pdb=" N LEU I 38 " --> pdb=" O GLY I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 75 removed outlier: 3.533A pdb=" N TYR I 56 " --> pdb=" O ARG I 52 " (cutoff:3.500A) Proline residue: I 64 - end of helix Processing helix chain 'I' and resid 77 through 89 removed outlier: 3.564A pdb=" N ARG I 89 " --> pdb=" O GLU I 85 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 124 removed outlier: 3.520A pdb=" N LEU I 101 " --> pdb=" O ALA I 97 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ALA I 113 " --> pdb=" O ARG I 109 " (cutoff:3.500A) Proline residue: I 114 - end of helix Processing helix chain 'I' and resid 125 through 133 removed outlier: 3.533A pdb=" N SER I 133 " --> pdb=" O VAL I 129 " (cutoff:3.500A) Processing helix chain 'I' and resid 134 through 136 No H-bonds generated for 'chain 'I' and resid 134 through 136' Processing helix chain 'I' and resid 149 through 151 No H-bonds generated for 'chain 'I' and resid 149 through 151' Processing helix chain 'I' and resid 152 through 159 removed outlier: 3.548A pdb=" N ILE I 156 " --> pdb=" O HIS I 152 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG I 159 " --> pdb=" O GLU I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 163 Processing helix chain 'I' and resid 166 through 168 No H-bonds generated for 'chain 'I' and resid 166 through 168' Processing helix chain 'I' and resid 169 through 209 Processing helix chain 'I' and resid 214 through 251 Processing helix chain 'I' and resid 257 through 267 Processing helix chain 'I' and resid 274 through 282 Processing helix chain 'I' and resid 297 through 306 Processing helix chain 'J' and resid 21 through 38 removed outlier: 3.521A pdb=" N LEU J 38 " --> pdb=" O GLY J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 75 removed outlier: 3.534A pdb=" N TYR J 56 " --> pdb=" O ARG J 52 " (cutoff:3.500A) Proline residue: J 64 - end of helix Processing helix chain 'J' and resid 77 through 89 removed outlier: 3.564A pdb=" N ARG J 89 " --> pdb=" O GLU J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 124 removed outlier: 3.519A pdb=" N LEU J 101 " --> pdb=" O ALA J 97 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ALA J 113 " --> pdb=" O ARG J 109 " (cutoff:3.500A) Proline residue: J 114 - end of helix Processing helix chain 'J' and resid 125 through 133 removed outlier: 3.533A pdb=" N SER J 133 " --> pdb=" O VAL J 129 " (cutoff:3.500A) Processing helix chain 'J' and resid 134 through 136 No H-bonds generated for 'chain 'J' and resid 134 through 136' Processing helix chain 'J' and resid 149 through 151 No H-bonds generated for 'chain 'J' and resid 149 through 151' Processing helix chain 'J' and resid 152 through 159 removed outlier: 3.548A pdb=" N ILE J 156 " --> pdb=" O HIS J 152 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG J 159 " --> pdb=" O GLU J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 160 through 163 Processing helix chain 'J' and resid 166 through 168 No H-bonds generated for 'chain 'J' and resid 166 through 168' Processing helix chain 'J' and resid 169 through 209 Processing helix chain 'J' and resid 214 through 251 Processing helix chain 'J' and resid 257 through 267 Processing helix chain 'J' and resid 274 through 282 Processing helix chain 'J' and resid 297 through 306 Processing helix chain 'K' and resid 21 through 38 removed outlier: 3.520A pdb=" N LEU K 38 " --> pdb=" O GLY K 34 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 75 removed outlier: 3.533A pdb=" N TYR K 56 " --> pdb=" O ARG K 52 " (cutoff:3.500A) Proline residue: K 64 - end of helix Processing helix chain 'K' and resid 77 through 89 removed outlier: 3.564A pdb=" N ARG K 89 " --> pdb=" O GLU K 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 97 through 124 removed outlier: 3.519A pdb=" N LEU K 101 " --> pdb=" O ALA K 97 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ALA K 113 " --> pdb=" O ARG K 109 " (cutoff:3.500A) Proline residue: K 114 - end of helix Processing helix chain 'K' and resid 125 through 133 removed outlier: 3.532A pdb=" N SER K 133 " --> pdb=" O VAL K 129 " (cutoff:3.500A) Processing helix chain 'K' and resid 134 through 136 No H-bonds generated for 'chain 'K' and resid 134 through 136' Processing helix chain 'K' and resid 149 through 151 No H-bonds generated for 'chain 'K' and resid 149 through 151' Processing helix chain 'K' and resid 152 through 159 removed outlier: 3.548A pdb=" N ILE K 156 " --> pdb=" O HIS K 152 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG K 159 " --> pdb=" O GLU K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 160 through 163 Processing helix chain 'K' and resid 166 through 168 No H-bonds generated for 'chain 'K' and resid 166 through 168' Processing helix chain 'K' and resid 169 through 209 Processing helix chain 'K' and resid 214 through 251 Processing helix chain 'K' and resid 257 through 267 Processing helix chain 'K' and resid 274 through 282 Processing helix chain 'K' and resid 297 through 306 Processing sheet with id=AA1, first strand: chain 'A' and resid 289 through 290 Processing sheet with id=AA2, first strand: chain 'B' and resid 289 through 290 Processing sheet with id=AA3, first strand: chain 'C' and resid 289 through 290 Processing sheet with id=AA4, first strand: chain 'D' and resid 289 through 290 Processing sheet with id=AA5, first strand: chain 'E' and resid 289 through 290 Processing sheet with id=AA6, first strand: chain 'F' and resid 289 through 290 Processing sheet with id=AA7, first strand: chain 'G' and resid 289 through 290 Processing sheet with id=AA8, first strand: chain 'H' and resid 289 through 290 Processing sheet with id=AA9, first strand: chain 'I' and resid 289 through 290 Processing sheet with id=AB1, first strand: chain 'J' and resid 289 through 290 Processing sheet with id=AB2, first strand: chain 'K' and resid 289 through 290 1695 hydrogen bonds defined for protein. 5019 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: 6.75 Time building geometry restraints manager: 9.77 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: 7472 1.34 - 1.46: 5166 1.46 - 1.58: 10814 1.58 - 1.69: 0 1.69 - 1.81: 77 Bond restraints: 23529 Sorted by residual: bond pdb=" N THR G 272 " pdb=" CA THR G 272 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.23e-02 6.61e+03 9.65e+00 bond pdb=" N THR F 272 " pdb=" CA THR F 272 " ideal model delta sigma weight residual 1.454 1.491 -0.038 1.23e-02 6.61e+03 9.50e+00 bond pdb=" N THR K 272 " pdb=" CA THR K 272 " ideal model delta sigma weight residual 1.454 1.491 -0.038 1.23e-02 6.61e+03 9.45e+00 bond pdb=" N THR J 272 " pdb=" CA THR J 272 " ideal model delta sigma weight residual 1.454 1.491 -0.038 1.23e-02 6.61e+03 9.45e+00 bond pdb=" N THR H 272 " pdb=" CA THR H 272 " ideal model delta sigma weight residual 1.454 1.491 -0.038 1.23e-02 6.61e+03 9.45e+00 ... (remaining 23524 not shown) Histogram of bond angle deviations from ideal: 102.19 - 108.62: 1366 108.62 - 115.05: 13102 115.05 - 121.48: 12721 121.48 - 127.91: 4789 127.91 - 134.35: 307 Bond angle restraints: 32285 Sorted by residual: angle pdb=" C GLN E 36 " pdb=" N GLU E 37 " pdb=" CA GLU E 37 " ideal model delta sigma weight residual 120.28 126.20 -5.92 1.34e+00 5.57e-01 1.95e+01 angle pdb=" C GLN A 36 " pdb=" N GLU A 37 " pdb=" CA GLU A 37 " ideal model delta sigma weight residual 120.28 126.18 -5.90 1.34e+00 5.57e-01 1.94e+01 angle pdb=" C GLN F 36 " pdb=" N GLU F 37 " pdb=" CA GLU F 37 " ideal model delta sigma weight residual 120.28 126.15 -5.87 1.34e+00 5.57e-01 1.92e+01 angle pdb=" C GLN C 36 " pdb=" N GLU C 37 " pdb=" CA GLU C 37 " ideal model delta sigma weight residual 120.28 126.13 -5.85 1.34e+00 5.57e-01 1.91e+01 angle pdb=" C ALA I 43 " pdb=" N PHE I 44 " pdb=" CA PHE I 44 " ideal model delta sigma weight residual 121.54 113.23 8.31 1.91e+00 2.74e-01 1.89e+01 ... (remaining 32280 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.44: 12384 16.44 - 32.88: 1080 32.88 - 49.32: 176 49.32 - 65.76: 11 65.76 - 82.20: 33 Dihedral angle restraints: 13684 sinusoidal: 4433 harmonic: 9251 Sorted by residual: dihedral pdb=" CA ALA J 96 " pdb=" C ALA J 96 " pdb=" N ALA J 97 " pdb=" CA ALA J 97 " ideal model delta harmonic sigma weight residual -180.00 -156.94 -23.06 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA ALA H 96 " pdb=" C ALA H 96 " pdb=" N ALA H 97 " pdb=" CA ALA H 97 " ideal model delta harmonic sigma weight residual -180.00 -156.94 -23.06 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA ALA F 96 " pdb=" C ALA F 96 " pdb=" N ALA F 97 " pdb=" CA ALA F 97 " ideal model delta harmonic sigma weight residual 180.00 -156.96 -23.04 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 13681 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2952 0.066 - 0.132: 656 0.132 - 0.199: 88 0.199 - 0.265: 0 0.265 - 0.331: 11 Chirality restraints: 3707 Sorted by residual: chirality pdb=" CB VAL J 83 " pdb=" CA VAL J 83 " pdb=" CG1 VAL J 83 " pdb=" CG2 VAL J 83 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" CB VAL G 83 " pdb=" CA VAL G 83 " pdb=" CG1 VAL G 83 " pdb=" CG2 VAL G 83 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CB VAL I 83 " pdb=" CA VAL I 83 " pdb=" CG1 VAL I 83 " pdb=" CG2 VAL I 83 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.72e+00 ... (remaining 3704 not shown) Planarity restraints: 4169 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA E 97 " 0.054 5.00e-02 4.00e+02 8.19e-02 1.07e+01 pdb=" N PRO E 98 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO E 98 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO E 98 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA I 97 " -0.054 5.00e-02 4.00e+02 8.18e-02 1.07e+01 pdb=" N PRO I 98 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO I 98 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO I 98 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA H 97 " -0.054 5.00e-02 4.00e+02 8.18e-02 1.07e+01 pdb=" N PRO H 98 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO H 98 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO H 98 " -0.045 5.00e-02 4.00e+02 ... (remaining 4166 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 3715 2.75 - 3.29: 22524 3.29 - 3.83: 39959 3.83 - 4.36: 43001 4.36 - 4.90: 75811 Nonbonded interactions: 185010 Sorted by model distance: nonbonded pdb=" N GLN B 273 " pdb=" OE1 GLN B 273 " model vdw 2.218 2.520 nonbonded pdb=" N GLN I 273 " pdb=" OE1 GLN I 273 " model vdw 2.219 2.520 nonbonded pdb=" N GLN D 273 " pdb=" OE1 GLN D 273 " model vdw 2.219 2.520 nonbonded pdb=" N GLN G 273 " pdb=" OE1 GLN G 273 " model vdw 2.219 2.520 nonbonded pdb=" N GLN H 273 " pdb=" OE1 GLN H 273 " model vdw 2.219 2.520 ... (remaining 185005 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } 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: 2.440 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: 0.020 Extract box with map and model: 10.480 Check model and map are aligned: 0.340 Set scattering table: 0.210 Process input model: 55.510 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.140 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:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 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 : 0.007 0.068 23529 Z= 0.476 Angle : 0.890 8.305 32285 Z= 0.540 Chirality : 0.056 0.331 3707 Planarity : 0.008 0.082 4169 Dihedral : 13.351 82.197 7634 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer Outliers : 1.13 % 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: -3.51 (0.10), residues: 3135 helix: -2.00 (0.07), residues: 2211 sheet: None (None), residues: 0 loop : -2.74 (0.17), residues: 924 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 281 time to evaluate : 2.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 1 residues processed: 303 average time/residue: 0.2915 time to fit residues: 149.2047 Evaluate side-chains 189 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 188 time to evaluate : 2.960 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2087 time to fit residues: 4.1832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 260 optimal weight: 8.9990 chunk 233 optimal weight: 0.8980 chunk 129 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 chunk 157 optimal weight: 0.9990 chunk 124 optimal weight: 50.0000 chunk 241 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 146 optimal weight: 2.9990 chunk 179 optimal weight: 0.9990 chunk 279 optimal weight: 0.3980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN A 216 GLN A 226 ASN A 246 ASN A 279 ASN B 185 GLN ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN B 246 ASN B 279 ASN C 185 GLN ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN C 246 ASN C 279 ASN D 185 GLN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 ASN D 246 ASN D 279 ASN E 185 GLN E 216 GLN E 226 ASN E 246 ASN E 279 ASN F 185 GLN F 216 GLN F 226 ASN F 246 ASN F 279 ASN G 185 GLN G 216 GLN G 226 ASN G 246 ASN G 279 ASN H 185 GLN H 216 GLN H 226 ASN H 246 ASN H 279 ASN I 185 GLN ** I 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 226 ASN I 246 ASN I 279 ASN J 185 GLN J 216 GLN J 226 ASN J 246 ASN J 279 ASN K 185 GLN K 216 GLN K 226 ASN K 246 ASN K 279 ASN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 23529 Z= 0.167 Angle : 0.531 5.811 32285 Z= 0.282 Chirality : 0.037 0.118 3707 Planarity : 0.005 0.057 4169 Dihedral : 4.466 17.190 3454 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.13), residues: 3135 helix: 0.70 (0.10), residues: 2233 sheet: None (None), residues: 0 loop : -2.13 (0.18), residues: 902 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 225 time to evaluate : 2.793 Fit side-chains outliers start: 18 outliers final: 14 residues processed: 241 average time/residue: 0.2708 time to fit residues: 113.7469 Evaluate side-chains 223 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 209 time to evaluate : 2.923 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1962 time to fit residues: 8.9824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 155 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 chunk 232 optimal weight: 5.9990 chunk 190 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 280 optimal weight: 90.0000 chunk 302 optimal weight: 2.9990 chunk 249 optimal weight: 0.0970 chunk 277 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 224 optimal weight: 80.0000 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 ASN B 45 HIS ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 ASN C 45 HIS ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 ASN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 ASN E 45 HIS E 246 ASN F 207 HIS F 246 ASN G 45 HIS G 246 ASN H 45 HIS H 246 ASN I 45 HIS ** I 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 246 ASN J 45 HIS J 246 ASN K 222 GLN K 246 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 23529 Z= 0.297 Angle : 0.545 5.856 32285 Z= 0.288 Chirality : 0.040 0.160 3707 Planarity : 0.004 0.053 4169 Dihedral : 4.202 16.501 3454 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer Outliers : 1.13 % 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: 1.10 (0.15), residues: 3135 helix: 1.69 (0.11), residues: 2244 sheet: None (None), residues: 0 loop : -1.83 (0.19), residues: 891 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 176 time to evaluate : 2.846 Fit side-chains outliers start: 22 outliers final: 9 residues processed: 189 average time/residue: 0.2747 time to fit residues: 91.4704 Evaluate side-chains 182 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 173 time to evaluate : 2.703 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2421 time to fit residues: 7.5120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 276 optimal weight: 6.9990 chunk 210 optimal weight: 6.9990 chunk 145 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 133 optimal weight: 0.7980 chunk 188 optimal weight: 1.9990 chunk 281 optimal weight: 20.0000 chunk 297 optimal weight: 3.9990 chunk 146 optimal weight: 6.9990 chunk 266 optimal weight: 0.0570 chunk 80 optimal weight: 1.9990 overall best weight: 1.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 246 ASN ** B 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 ASN ** C 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 ASN ** D 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 HIS ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 ASN ** E 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 HIS E 246 ASN ** F 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 246 ASN ** G 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 ASN ** H 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 207 HIS H 246 ASN ** I 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 207 HIS ** I 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 246 ASN ** J 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 246 ASN ** K 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 207 HIS K 246 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 23529 Z= 0.193 Angle : 0.501 5.787 32285 Z= 0.262 Chirality : 0.038 0.163 3707 Planarity : 0.004 0.050 4169 Dihedral : 3.989 16.694 3454 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer Outliers : 0.51 % 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: 1.87 (0.15), residues: 3135 helix: 2.19 (0.11), residues: 2277 sheet: None (None), residues: 0 loop : -1.49 (0.20), residues: 858 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 185 time to evaluate : 2.705 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 188 average time/residue: 0.2840 time to fit residues: 92.9581 Evaluate side-chains 187 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 182 time to evaluate : 2.958 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1929 time to fit residues: 5.4374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 247 optimal weight: 5.9990 chunk 168 optimal weight: 80.0000 chunk 4 optimal weight: 0.8980 chunk 221 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 254 optimal weight: 0.0970 chunk 205 optimal weight: 3.9990 chunk 0 optimal weight: 80.0000 chunk 152 optimal weight: 0.0970 chunk 267 optimal weight: 1.9990 chunk 75 optimal weight: 0.0970 overall best weight: 0.6376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 207 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 23529 Z= 0.151 Angle : 0.475 6.721 32285 Z= 0.245 Chirality : 0.036 0.169 3707 Planarity : 0.004 0.050 4169 Dihedral : 3.777 15.447 3454 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer Outliers : 2.05 % 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: 2.43 (0.15), residues: 3135 helix: 2.63 (0.11), residues: 2266 sheet: None (None), residues: 0 loop : -1.29 (0.21), residues: 869 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 199 time to evaluate : 2.913 Fit side-chains revert: symmetry clash outliers start: 40 outliers final: 28 residues processed: 234 average time/residue: 0.2793 time to fit residues: 113.8614 Evaluate side-chains 215 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 187 time to evaluate : 2.649 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.2184 time to fit residues: 15.0995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 100 optimal weight: 10.0000 chunk 268 optimal weight: 9.9990 chunk 58 optimal weight: 8.9990 chunk 174 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 298 optimal weight: 0.9990 chunk 247 optimal weight: 5.9990 chunk 137 optimal weight: 0.7980 chunk 24 optimal weight: 0.0170 chunk 98 optimal weight: 10.0000 chunk 156 optimal weight: 9.9990 overall best weight: 2.1624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 ASN B 76 ASN ** B 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 ASN ** D 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 GLN D 246 ASN ** E 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 ASN ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 246 ASN ** G 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 ASN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 246 ASN ** I 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 246 ASN ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 ASN ** K 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 23529 Z= 0.258 Angle : 0.534 9.972 32285 Z= 0.275 Chirality : 0.039 0.166 3707 Planarity : 0.004 0.049 4169 Dihedral : 3.813 15.637 3454 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer Outliers : 1.80 % 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: 2.54 (0.16), residues: 3135 helix: 2.67 (0.11), residues: 2277 sheet: None (None), residues: 0 loop : -1.17 (0.21), residues: 858 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 205 time to evaluate : 2.879 Fit side-chains revert: symmetry clash outliers start: 35 outliers final: 25 residues processed: 234 average time/residue: 0.2948 time to fit residues: 117.6283 Evaluate side-chains 206 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 181 time to evaluate : 2.882 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.2190 time to fit residues: 13.7283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 287 optimal weight: 0.0470 chunk 33 optimal weight: 3.9990 chunk 169 optimal weight: 0.8980 chunk 217 optimal weight: 0.5980 chunk 168 optimal weight: 50.0000 chunk 250 optimal weight: 4.9990 chunk 166 optimal weight: 4.9990 chunk 296 optimal weight: 10.0000 chunk 185 optimal weight: 2.9990 chunk 180 optimal weight: 0.7980 chunk 137 optimal weight: 5.9990 overall best weight: 1.0680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 ASN ** D 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 ASN ** E 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 ASN ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 246 ASN G 246 ASN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 246 ASN ** I 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 246 ASN ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 23529 Z= 0.179 Angle : 0.504 7.111 32285 Z= 0.259 Chirality : 0.037 0.180 3707 Planarity : 0.004 0.050 4169 Dihedral : 3.742 14.986 3454 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer Outliers : 1.34 % 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: 2.67 (0.16), residues: 3135 helix: 2.75 (0.11), residues: 2277 sheet: None (None), residues: 0 loop : -1.06 (0.21), residues: 858 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 198 time to evaluate : 2.887 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 19 residues processed: 221 average time/residue: 0.2867 time to fit residues: 108.9047 Evaluate side-chains 203 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 184 time to evaluate : 2.766 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2448 time to fit residues: 11.7270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 183 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 177 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 188 optimal weight: 1.9990 chunk 202 optimal weight: 0.9980 chunk 146 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 233 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 ASN ** B 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 GLN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 ASN ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 ASN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 246 ASN ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 23529 Z= 0.187 Angle : 0.512 9.699 32285 Z= 0.261 Chirality : 0.038 0.187 3707 Planarity : 0.004 0.050 4169 Dihedral : 3.713 14.916 3454 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer Outliers : 0.77 % 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: 2.70 (0.16), residues: 3135 helix: 2.81 (0.11), residues: 2266 sheet: None (None), residues: 0 loop : -1.14 (0.21), residues: 869 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 193 time to evaluate : 2.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 205 average time/residue: 0.2856 time to fit residues: 100.5691 Evaluate side-chains 190 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 184 time to evaluate : 2.724 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2129 time to fit residues: 5.9334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 270 optimal weight: 1.9990 chunk 284 optimal weight: 6.9990 chunk 259 optimal weight: 20.0000 chunk 276 optimal weight: 10.0000 chunk 166 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 217 optimal weight: 0.6980 chunk 84 optimal weight: 80.0000 chunk 249 optimal weight: 1.9990 chunk 261 optimal weight: 0.9980 chunk 275 optimal weight: 0.6980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 ASN ** B 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 ASN ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 ASN H 76 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 246 ASN ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 23529 Z= 0.169 Angle : 0.506 8.191 32285 Z= 0.258 Chirality : 0.037 0.186 3707 Planarity : 0.004 0.051 4169 Dihedral : 3.651 14.352 3454 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer Outliers : 0.31 % 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: 2.73 (0.15), residues: 3135 helix: 2.85 (0.11), residues: 2277 sheet: None (None), residues: 0 loop : -1.25 (0.21), residues: 858 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 184 time to evaluate : 2.917 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 0 residues processed: 189 average time/residue: 0.2898 time to fit residues: 94.5137 Evaluate side-chains 179 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 2.654 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 181 optimal weight: 10.0000 chunk 292 optimal weight: 30.0000 chunk 178 optimal weight: 9.9990 chunk 138 optimal weight: 0.9990 chunk 203 optimal weight: 5.9990 chunk 306 optimal weight: 4.9990 chunk 282 optimal weight: 4.9990 chunk 244 optimal weight: 0.6980 chunk 25 optimal weight: 0.0970 chunk 188 optimal weight: 2.9990 chunk 149 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 ASN ** B 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 ASN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 ASN ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 246 ASN ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 23529 Z= 0.183 Angle : 0.516 10.121 32285 Z= 0.264 Chirality : 0.037 0.190 3707 Planarity : 0.004 0.050 4169 Dihedral : 3.628 14.283 3454 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer Outliers : 0.41 % 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: 2.76 (0.15), residues: 3135 helix: 2.87 (0.11), residues: 2277 sheet: None (None), residues: 0 loop : -1.23 (0.21), residues: 858 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 178 time to evaluate : 2.962 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 184 average time/residue: 0.2711 time to fit residues: 87.2459 Evaluate side-chains 180 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 176 time to evaluate : 2.782 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2168 time to fit residues: 5.2476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 194 optimal weight: 0.5980 chunk 260 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 225 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 67 optimal weight: 8.9990 chunk 244 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 251 optimal weight: 0.4980 chunk 30 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 ASN B 76 ASN ** B 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 ASN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 ASN ** E 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 246 ASN G 246 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 246 ASN ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.088671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.066532 restraints weight = 75724.810| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 3.04 r_work: 0.3212 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 23529 Z= 0.233 Angle : 0.536 7.918 32285 Z= 0.276 Chirality : 0.039 0.198 3707 Planarity : 0.004 0.051 4169 Dihedral : 3.681 14.177 3454 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer Outliers : 0.21 % 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: 2.71 (0.15), residues: 3135 helix: 2.80 (0.11), residues: 2288 sheet: None (None), residues: 0 loop : -1.18 (0.21), residues: 847 =============================================================================== Job complete usr+sys time: 3861.83 seconds wall clock time: 71 minutes 51.98 seconds (4311.98 seconds total)