Starting phenix.real_space_refine on Thu Apr 11 14:19:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uiv_20788/04_2024/6uiv_20788.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uiv_20788/04_2024/6uiv_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_2024/6uiv_20788.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uiv_20788/04_2024/6uiv_20788.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uiv_20788/04_2024/6uiv_20788.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uiv_20788/04_2024/6uiv_20788.pdb" } resolution = 3.3 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= 0.002 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-dev-5288/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: 11.85, per 1000 atoms: 0.52 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: 8.57 Conformation dependent library (CDL) restraints added in 4.4 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: 2.02 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: 7.33 Time building geometry restraints manager: 9.26 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: 2.510 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: 9.210 Check model and map are aligned: 0.340 Set scattering table: 0.220 Process input model: 59.180 Find NCS groups from input model: 1.650 Set up NCS constraints: 0.170 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.040 ------------------------------------------------------------------------------- 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 % Allowed : 11.25 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP E 80 HIS 0.009 0.001 HIS F 88 PHE 0.011 0.002 PHE F 253 TYR 0.013 0.003 TYR F 287 ARG 0.002 0.000 ARG C 298 *********************** 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 : 2.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 ILE cc_start: 0.9198 (tp) cc_final: 0.8808 (tp) REVERT: B 156 ILE cc_start: 0.9187 (tp) cc_final: 0.8749 (tp) REVERT: D 156 ILE cc_start: 0.9187 (tp) cc_final: 0.8822 (tp) REVERT: E 156 ILE cc_start: 0.9189 (tp) cc_final: 0.8835 (tp) REVERT: F 71 ILE cc_start: 0.9483 (mt) cc_final: 0.9281 (mt) REVERT: F 156 ILE cc_start: 0.9178 (tp) cc_final: 0.8789 (tp) REVERT: G 156 ILE cc_start: 0.9225 (tp) cc_final: 0.8838 (tp) REVERT: H 156 ILE cc_start: 0.9232 (tp) cc_final: 0.8832 (tp) REVERT: I 156 ILE cc_start: 0.9182 (tp) cc_final: 0.8741 (tp) REVERT: K 156 ILE cc_start: 0.9187 (tp) cc_final: 0.8787 (tp) outliers start: 22 outliers final: 1 residues processed: 303 average time/residue: 0.2855 time to fit residues: 146.7398 Evaluate side-chains 200 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 199 time to evaluate : 2.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 247 VAL 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 207 HIS K 216 GLN K 226 ASN K 246 ASN K 279 ASN Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1641 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= 0.169 Angle : 0.528 5.836 32285 Z= 0.280 Chirality : 0.037 0.120 3707 Planarity : 0.005 0.057 4169 Dihedral : 4.491 23.214 3455 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.98 % Allowed : 13.35 % Favored : 85.67 % 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: -0.19 (0.13), residues: 3135 helix: 0.69 (0.10), residues: 2233 sheet: None (None), residues: 0 loop : -2.16 (0.18), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 302 HIS 0.024 0.003 HIS J 152 PHE 0.008 0.001 PHE B 69 TYR 0.010 0.001 TYR H 54 ARG 0.005 0.000 ARG J 233 *********************** 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: 19 poor density : 224 time to evaluate : 2.500 Fit side-chains REVERT: F 71 ILE cc_start: 0.9491 (mt) cc_final: 0.9273 (mt) REVERT: H 53 ASN cc_start: 0.7945 (OUTLIER) cc_final: 0.7499 (p0) REVERT: K 53 ASN cc_start: 0.8044 (OUTLIER) cc_final: 0.7736 (p0) outliers start: 19 outliers final: 14 residues processed: 241 average time/residue: 0.2640 time to fit residues: 111.8384 Evaluate side-chains 224 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 208 time to evaluate : 2.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASN Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain C residue 53 ASN Chi-restraints excluded: chain D residue 53 ASN Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain F residue 53 ASN Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain G residue 53 ASN Chi-restraints excluded: chain H residue 53 ASN Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain I residue 53 ASN Chi-restraints excluded: chain J residue 53 ASN Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain K residue 53 ASN 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: 5.9990 chunk 232 optimal weight: 6.9990 chunk 190 optimal weight: 4.9990 chunk 77 optimal weight: 0.5980 chunk 280 optimal weight: 90.0000 chunk 302 optimal weight: 2.9990 chunk 249 optimal weight: 6.9990 chunk 277 optimal weight: 8.9990 chunk 95 optimal weight: 5.9990 chunk 224 optimal weight: 80.0000 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 HIS 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 45 HIS ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 ASN E 45 HIS E 246 ASN 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: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 23529 Z= 0.441 Angle : 0.627 6.100 32285 Z= 0.334 Chirality : 0.042 0.149 3707 Planarity : 0.004 0.053 4169 Dihedral : 4.326 17.179 3454 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.98 % Allowed : 15.87 % Favored : 81.15 % 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: 0.95 (0.15), residues: 3135 helix: 1.63 (0.11), residues: 2233 sheet: None (None), residues: 0 loop : -2.00 (0.18), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 302 HIS 0.005 0.001 HIS J 152 PHE 0.013 0.001 PHE K 69 TYR 0.016 0.002 TYR K 287 ARG 0.004 0.000 ARG J 233 *********************** 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 232 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 174 time to evaluate : 2.881 Fit side-chains revert: symmetry clash REVERT: A 126 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8556 (pm20) REVERT: E 229 GLN cc_start: 0.8284 (tm-30) cc_final: 0.7975 (tm-30) REVERT: F 71 ILE cc_start: 0.9520 (mt) cc_final: 0.9306 (mt) REVERT: H 53 ASN cc_start: 0.8205 (OUTLIER) cc_final: 0.7746 (p0) REVERT: K 53 ASN cc_start: 0.8184 (OUTLIER) cc_final: 0.7831 (p0) outliers start: 58 outliers final: 46 residues processed: 214 average time/residue: 0.2718 time to fit residues: 100.6023 Evaluate side-chains 216 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 167 time to evaluate : 2.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASN Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain C residue 53 ASN Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain D residue 53 ASN Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 214 TYR Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 53 ASN Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 260 ASP Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 53 ASN Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 260 ASP Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain I residue 53 ASN Chi-restraints excluded: chain I residue 260 ASP Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain J residue 53 ASN Chi-restraints excluded: chain J residue 120 ILE Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 260 ASP Chi-restraints excluded: chain J residue 281 ILE Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain K residue 53 ASN Chi-restraints excluded: chain K residue 120 ILE Chi-restraints excluded: chain K residue 285 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 276 optimal weight: 0.0980 chunk 210 optimal weight: 0.1980 chunk 145 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 133 optimal weight: 0.6980 chunk 188 optimal weight: 0.6980 chunk 281 optimal weight: 0.4980 chunk 297 optimal weight: 0.8980 chunk 146 optimal weight: 1.9990 chunk 266 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 207 HIS 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 246 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 23529 Z= 0.150 Angle : 0.491 5.706 32285 Z= 0.255 Chirality : 0.037 0.161 3707 Planarity : 0.004 0.050 4169 Dihedral : 3.997 16.996 3454 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.08 % Allowed : 19.88 % Favored : 79.04 % 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: 1.89 (0.15), residues: 3135 helix: 2.21 (0.11), residues: 2277 sheet: None (None), residues: 0 loop : -1.50 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 80 HIS 0.003 0.001 HIS H 88 PHE 0.007 0.001 PHE B 69 TYR 0.008 0.001 TYR E 54 ARG 0.003 0.000 ARG J 233 *********************** 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 209 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 188 time to evaluate : 2.527 Fit side-chains REVERT: A 198 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9158 (tp) REVERT: A 229 GLN cc_start: 0.7991 (tm-30) cc_final: 0.7782 (tm-30) REVERT: C 260 ASP cc_start: 0.7943 (m-30) cc_final: 0.7733 (m-30) REVERT: E 229 GLN cc_start: 0.8241 (tm-30) cc_final: 0.7935 (tm-30) REVERT: F 71 ILE cc_start: 0.9483 (mt) cc_final: 0.9254 (mt) REVERT: I 198 LEU cc_start: 0.9456 (OUTLIER) cc_final: 0.9186 (tp) REVERT: J 198 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9137 (tt) REVERT: K 198 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9144 (tt) outliers start: 21 outliers final: 11 residues processed: 206 average time/residue: 0.2636 time to fit residues: 95.0602 Evaluate side-chains 197 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 182 time to evaluate : 2.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain C residue 214 TYR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain D residue 214 TYR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain I residue 198 LEU Chi-restraints excluded: chain J residue 198 LEU Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain K residue 198 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 247 optimal weight: 0.4980 chunk 168 optimal weight: 80.0000 chunk 4 optimal weight: 0.9980 chunk 221 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 254 optimal weight: 7.9990 chunk 205 optimal weight: 5.9990 chunk 0 optimal weight: 80.0000 chunk 152 optimal weight: 4.9990 chunk 267 optimal weight: 1.9990 chunk 75 optimal weight: 0.4980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS ** 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** C 246 ASN ** D 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 HIS ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 ASN ** 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 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** J 207 HIS ** K 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2560 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= 0.175 Angle : 0.484 5.676 32285 Z= 0.251 Chirality : 0.037 0.165 3707 Planarity : 0.004 0.050 4169 Dihedral : 3.840 15.713 3454 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.88 % Allowed : 19.47 % Favored : 77.66 % 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: 2.42 (0.16), residues: 3135 helix: 2.63 (0.11), residues: 2266 sheet: None (None), residues: 0 loop : -1.33 (0.21), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 302 HIS 0.003 0.001 HIS H 88 PHE 0.008 0.001 PHE J 69 TYR 0.009 0.001 TYR H 214 ARG 0.003 0.000 ARG J 233 *********************** 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 253 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 197 time to evaluate : 2.646 Fit side-chains REVERT: A 198 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.9197 (tt) REVERT: C 260 ASP cc_start: 0.7970 (m-30) cc_final: 0.7723 (m-30) REVERT: E 229 GLN cc_start: 0.8236 (tm-30) cc_final: 0.7931 (tm-30) REVERT: F 71 ILE cc_start: 0.9467 (mt) cc_final: 0.9226 (mt) REVERT: G 198 LEU cc_start: 0.9420 (OUTLIER) cc_final: 0.9220 (tt) REVERT: I 198 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9170 (tp) REVERT: J 198 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9150 (tt) REVERT: K 198 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9134 (tt) outliers start: 56 outliers final: 42 residues processed: 246 average time/residue: 0.2657 time to fit residues: 114.2873 Evaluate side-chains 228 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 181 time to evaluate : 2.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 214 TYR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 214 TYR Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 213 SER Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 213 SER Chi-restraints excluded: chain H residue 214 TYR Chi-restraints excluded: chain H residue 281 ILE Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 198 LEU Chi-restraints excluded: chain I residue 213 SER Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 198 LEU Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 213 SER Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 198 LEU Chi-restraints excluded: chain K residue 213 SER Chi-restraints excluded: chain K residue 272 THR 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: 10.0000 chunk 58 optimal weight: 5.9990 chunk 174 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 298 optimal weight: 0.8980 chunk 247 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 156 optimal weight: 9.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 ASN ** B 76 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 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 ** 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 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** ** I 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 246 ASN ** K 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23529 Z= 0.226 Angle : 0.511 5.991 32285 Z= 0.266 Chirality : 0.038 0.172 3707 Planarity : 0.004 0.050 4169 Dihedral : 3.818 15.771 3454 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.01 % Allowed : 19.41 % Favored : 76.58 % 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: 2.58 (0.16), residues: 3135 helix: 2.70 (0.11), residues: 2277 sheet: None (None), residues: 0 loop : -1.17 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 302 HIS 0.002 0.001 HIS H 88 PHE 0.009 0.001 PHE B 69 TYR 0.009 0.001 TYR H 223 ARG 0.003 0.000 ARG G 233 *********************** 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 273 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 195 time to evaluate : 2.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.9211 (tt) REVERT: B 198 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9279 (tt) REVERT: E 229 GLN cc_start: 0.8202 (tm-30) cc_final: 0.7901 (tm-30) REVERT: F 71 ILE cc_start: 0.9483 (mt) cc_final: 0.9262 (mt) REVERT: G 198 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9205 (tt) REVERT: H 53 ASN cc_start: 0.8202 (OUTLIER) cc_final: 0.7935 (p0) REVERT: H 229 GLN cc_start: 0.8355 (tm-30) cc_final: 0.8042 (tm-30) REVERT: I 198 LEU cc_start: 0.9433 (OUTLIER) cc_final: 0.9174 (tp) REVERT: J 198 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9172 (tt) REVERT: K 198 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9145 (tt) outliers start: 78 outliers final: 64 residues processed: 263 average time/residue: 0.2783 time to fit residues: 125.4234 Evaluate side-chains 246 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 175 time to evaluate : 2.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASN Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain C residue 53 ASN Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 214 TYR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain D residue 53 ASN Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 214 TYR Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain G residue 53 ASN Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 213 SER Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 53 ASN Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 182 TYR Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 213 SER Chi-restraints excluded: chain H residue 214 TYR Chi-restraints excluded: chain H residue 272 THR Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain I residue 53 ASN Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 198 LEU Chi-restraints excluded: chain I residue 213 SER Chi-restraints excluded: chain I residue 281 ILE Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain J residue 53 ASN Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 198 LEU Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 213 SER Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 198 LEU Chi-restraints excluded: chain K residue 213 SER Chi-restraints excluded: chain K residue 260 ASP Chi-restraints excluded: chain K residue 272 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 287 optimal weight: 0.0270 chunk 33 optimal weight: 3.9990 chunk 169 optimal weight: 0.9980 chunk 217 optimal weight: 0.5980 chunk 168 optimal weight: 40.0000 chunk 250 optimal weight: 4.9990 chunk 166 optimal weight: 0.9980 chunk 296 optimal weight: 7.9990 chunk 185 optimal weight: 0.8980 chunk 180 optimal weight: 4.9990 chunk 137 optimal weight: 6.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 ASN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 ASN ** E 81 ASN ** 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** F 246 ASN ** G 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 152 HIS ** 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 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2862 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= 0.156 Angle : 0.481 6.292 32285 Z= 0.249 Chirality : 0.037 0.176 3707 Planarity : 0.004 0.050 4169 Dihedral : 3.694 14.654 3454 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.49 % Allowed : 20.44 % Favored : 76.07 % 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: 2.74 (0.16), residues: 3135 helix: 2.84 (0.11), residues: 2266 sheet: None (None), residues: 0 loop : -1.13 (0.21), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 220 HIS 0.002 0.001 HIS E 88 PHE 0.007 0.001 PHE J 69 TYR 0.007 0.001 TYR B 287 ARG 0.003 0.000 ARG G 233 *********************** 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 256 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 188 time to evaluate : 2.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 229 GLN cc_start: 0.8197 (tm-30) cc_final: 0.7889 (tm-30) REVERT: F 71 ILE cc_start: 0.9454 (mt) cc_final: 0.9233 (mt) REVERT: H 229 GLN cc_start: 0.8335 (tm-30) cc_final: 0.7312 (tm-30) REVERT: K 198 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9167 (tt) REVERT: K 229 GLN cc_start: 0.8349 (tm-30) cc_final: 0.8021 (tm-30) outliers start: 68 outliers final: 56 residues processed: 251 average time/residue: 0.2775 time to fit residues: 118.9241 Evaluate side-chains 233 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 176 time to evaluate : 2.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain D residue 182 TYR Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 182 TYR Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 182 TYR Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 182 TYR Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 213 SER Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 182 TYR Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 213 SER Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 182 TYR Chi-restraints excluded: chain I residue 195 VAL Chi-restraints excluded: chain I residue 213 SER Chi-restraints excluded: chain I residue 281 ILE Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 182 TYR Chi-restraints excluded: chain J residue 195 VAL Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 213 SER Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 182 TYR Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain K residue 198 LEU Chi-restraints excluded: chain K residue 213 SER Chi-restraints excluded: chain K residue 272 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 183 optimal weight: 9.9990 chunk 118 optimal weight: 5.9990 chunk 177 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 57 optimal weight: 40.0000 chunk 188 optimal weight: 1.9990 chunk 202 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 233 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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** D 216 GLN ** E 81 ASN ** 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 81 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** ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 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** ** J 76 ASN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2974 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 : 0.505 9.377 32285 Z= 0.257 Chirality : 0.037 0.170 3707 Planarity : 0.004 0.050 4169 Dihedral : 3.660 14.771 3454 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 4.01 % Allowed : 20.70 % Favored : 75.30 % 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: 2.79 (0.16), residues: 3135 helix: 2.88 (0.11), residues: 2266 sheet: None (None), residues: 0 loop : -1.12 (0.21), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 302 HIS 0.002 0.001 HIS J 88 PHE 0.007 0.001 PHE J 69 TYR 0.016 0.001 TYR H 214 ARG 0.014 0.000 ARG H 233 *********************** 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 263 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 185 time to evaluate : 2.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 229 GLN cc_start: 0.8194 (tm-30) cc_final: 0.7890 (tm-30) REVERT: F 71 ILE cc_start: 0.9461 (mt) cc_final: 0.9236 (mt) REVERT: H 53 ASN cc_start: 0.8155 (OUTLIER) cc_final: 0.7914 (p0) REVERT: K 198 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9177 (tt) REVERT: K 229 GLN cc_start: 0.8303 (tm-30) cc_final: 0.7962 (tm-30) outliers start: 78 outliers final: 64 residues processed: 260 average time/residue: 0.2722 time to fit residues: 122.6727 Evaluate side-chains 244 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 178 time to evaluate : 2.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASN Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain C residue 53 ASN Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain D residue 53 ASN Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 182 TYR Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 182 TYR Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 182 TYR Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain G residue 53 ASN Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 182 TYR Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 213 SER Chi-restraints excluded: chain H residue 53 ASN Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 182 TYR Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 213 SER Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain I residue 53 ASN Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 182 TYR Chi-restraints excluded: chain I residue 195 VAL Chi-restraints excluded: chain I residue 213 SER Chi-restraints excluded: chain I residue 281 ILE Chi-restraints excluded: chain J residue 53 ASN Chi-restraints excluded: chain J residue 182 TYR Chi-restraints excluded: chain J residue 195 VAL Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 213 SER Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 182 TYR Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain K residue 198 LEU Chi-restraints excluded: chain K residue 213 SER Chi-restraints excluded: chain K residue 272 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 270 optimal weight: 5.9990 chunk 284 optimal weight: 6.9990 chunk 259 optimal weight: 3.9990 chunk 276 optimal weight: 0.8980 chunk 166 optimal weight: 0.6980 chunk 120 optimal weight: 5.9990 chunk 217 optimal weight: 0.7980 chunk 84 optimal weight: 80.0000 chunk 249 optimal weight: 3.9990 chunk 261 optimal weight: 0.0970 chunk 275 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ** 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 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 81 ASN ** 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 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 81 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3141 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= 0.158 Angle : 0.497 7.135 32285 Z= 0.253 Chirality : 0.037 0.207 3707 Planarity : 0.004 0.051 4169 Dihedral : 3.587 13.924 3454 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.70 % Allowed : 20.85 % Favored : 75.45 % 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: 2.83 (0.16), residues: 3135 helix: 2.92 (0.11), residues: 2277 sheet: None (None), residues: 0 loop : -1.20 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 80 HIS 0.003 0.000 HIS I 88 PHE 0.007 0.001 PHE A 69 TYR 0.013 0.001 TYR H 214 ARG 0.010 0.000 ARG H 233 *********************** 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 258 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 186 time to evaluate : 2.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 229 GLN cc_start: 0.8178 (tm-30) cc_final: 0.7879 (tm-30) REVERT: F 71 ILE cc_start: 0.9431 (mt) cc_final: 0.9205 (mt) REVERT: K 229 GLN cc_start: 0.8261 (tm-30) cc_final: 0.7913 (tm-30) outliers start: 72 outliers final: 64 residues processed: 255 average time/residue: 0.2716 time to fit residues: 118.4661 Evaluate side-chains 243 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 179 time to evaluate : 2.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain C residue 53 ASN Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain D residue 53 ASN Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 182 TYR Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 182 TYR Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 182 TYR Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 182 TYR Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 213 SER Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 182 TYR Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 213 SER Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain I residue 53 ASN Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 182 TYR Chi-restraints excluded: chain I residue 195 VAL Chi-restraints excluded: chain I residue 213 SER Chi-restraints excluded: chain I residue 281 ILE Chi-restraints excluded: chain J residue 53 ASN Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 182 TYR Chi-restraints excluded: chain J residue 195 VAL Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 213 SER Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 182 TYR Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain K residue 213 SER Chi-restraints excluded: chain K residue 272 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 181 optimal weight: 3.9990 chunk 292 optimal weight: 30.0000 chunk 178 optimal weight: 0.9990 chunk 138 optimal weight: 0.9980 chunk 203 optimal weight: 9.9990 chunk 306 optimal weight: 5.9990 chunk 282 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 188 optimal weight: 2.9990 chunk 149 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 ** 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 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 ASN ** 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 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 ASN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 246 ASN ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23529 Z= 0.195 Angle : 0.527 10.471 32285 Z= 0.266 Chirality : 0.038 0.206 3707 Planarity : 0.004 0.050 4169 Dihedral : 3.603 14.246 3454 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.49 % Allowed : 21.31 % Favored : 75.19 % 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: 2.84 (0.16), residues: 3135 helix: 2.94 (0.11), residues: 2277 sheet: None (None), residues: 0 loop : -1.24 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 80 HIS 0.002 0.001 HIS I 88 PHE 0.009 0.001 PHE G 69 TYR 0.011 0.001 TYR H 214 ARG 0.011 0.000 ARG H 233 ********************** 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 248 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 180 time to evaluate : 2.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 229 GLN cc_start: 0.8195 (tm-30) cc_final: 0.7913 (tm-30) REVERT: F 71 ILE cc_start: 0.9439 (mt) cc_final: 0.9214 (mt) REVERT: H 53 ASN cc_start: 0.8080 (OUTLIER) cc_final: 0.7852 (p0) outliers start: 68 outliers final: 65 residues processed: 245 average time/residue: 0.2813 time to fit residues: 118.1092 Evaluate side-chains 244 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 178 time to evaluate : 2.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASN Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain C residue 53 ASN Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain D residue 53 ASN Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 182 TYR Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 182 TYR Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 182 TYR Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 182 TYR Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 213 SER Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain H residue 53 ASN Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 182 TYR Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 213 SER Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain I residue 53 ASN Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 182 TYR Chi-restraints excluded: chain I residue 195 VAL Chi-restraints excluded: chain I residue 213 SER Chi-restraints excluded: chain I residue 281 ILE Chi-restraints excluded: chain J residue 53 ASN Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 182 TYR Chi-restraints excluded: chain J residue 195 VAL Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 213 SER Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 182 TYR Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain K residue 213 SER Chi-restraints excluded: chain K residue 272 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 194 optimal weight: 0.8980 chunk 260 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 225 optimal weight: 0.7980 chunk 36 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 244 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 251 optimal weight: 0.9980 chunk 30 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 ** 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 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 ASN ** 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 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 ASN H 76 ASN H 246 ASN ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.089524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.067098 restraints weight = 76496.021| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 3.05 r_work: 0.3241 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3240 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= 0.181 Angle : 0.517 8.618 32285 Z= 0.262 Chirality : 0.038 0.192 3707 Planarity : 0.004 0.051 4169 Dihedral : 3.582 18.037 3454 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.70 % Allowed : 21.11 % Favored : 75.19 % 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: 2.89 (0.16), residues: 3135 helix: 2.97 (0.11), residues: 2277 sheet: None (None), residues: 0 loop : -1.19 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 80 HIS 0.002 0.000 HIS I 88 PHE 0.008 0.001 PHE A 69 TYR 0.011 0.001 TYR H 214 ARG 0.011 0.000 ARG H 233 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4033.74 seconds wall clock time: 74 minutes 45.98 seconds (4485.98 seconds total)