Starting phenix.real_space_refine on Fri Jul 3 22:44:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7sss_25413/07_2026/7sss_25413.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sss_25413/07_2026/7sss_25413.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sss_25413/07_2026/7sss_25413.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sss_25413/07_2026/7sss_25413.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7sss_25413/07_2026/7sss_25413.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7sss_25413/07_2026/7sss_25413.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sss_25413/07_2026/7sss_25413.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sss_25413/07_2026/7sss_25413.map" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5095 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 20 5.49 5 S 72 5.16 5 C 7695 2.51 5 N 2009 2.21 5 O 2394 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12190 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1446 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 181, 1437 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Conformer: "B" Number of residues, atoms: 181, 1437 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 bond proxies already assigned to first conformer: 1457 Chain: "B" Number of atoms: 1461 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 181, 1441 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 13 Conformer: "B" Number of residues, atoms: 181, 1441 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 13 bond proxies already assigned to first conformer: 1449 Chain: "C" Number of atoms: 1449 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 181, 1440 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 13 Conformer: "B" Number of residues, atoms: 181, 1440 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 13 bond proxies already assigned to first conformer: 1459 Chain: "D" Number of atoms: 1457 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 181, 1437 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 17 Conformer: "B" Number of residues, atoms: 181, 1437 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 17 bond proxies already assigned to first conformer: 1445 Chain: "E" Number of atoms: 1350 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1341 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 167} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 25 Conformer: "B" Number of residues, atoms: 173, 1341 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 167} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1356 Chain: "F" Number of atoms: 1354 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1345 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 167} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Conformer: "B" Number of residues, atoms: 173, 1345 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 167} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 1360 Chain: "G" Number of atoms: 1354 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1345 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 167} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Conformer: "B" Number of residues, atoms: 173, 1345 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 167} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 1360 Chain: "H" Number of atoms: 1354 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1345 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 167} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Conformer: "B" Number of residues, atoms: 173, 1345 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 167} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 1360 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {'PEV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEV:plan-1': 2, 'PEV:plan-2': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 68 Unusual residues: {'8PP': 1, 'PEV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEV:plan-1': 1, 'PEV:plan-2': 1, '8PP:plan-8': 1, '8PP:plan-9': 1} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 96 Unusual residues: {'PEV': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEV:plan-1': 2, 'PEV:plan-2': 2} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 57 Unusual residues: {'PEV': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEV:plan-1': 3, 'PEV:plan-2': 3} Unresolved non-hydrogen planarities: 24 Chain: "E" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 166 Unusual residues: {'8PP': 1, 'NAD': 1, 'PEV': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'8PP:plan-7': 1, '8PP:plan-8': 1, '8PP:plan-9': 1, 'PEV:plan-1': 1, 'PEV:plan-2': 1} Unresolved non-hydrogen planarities: 20 Chain: "F" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 125 Unusual residues: {'NAD': 1, 'PEV': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEV:plan-1': 3, 'PEV:plan-2': 3} Unresolved non-hydrogen planarities: 23 Chain: "G" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 107 Unusual residues: {'8PP': 1, 'PEV': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 136 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'8PP:plan-7': 1, '8PP:plan-8': 1, '8PP:plan-9': 1, 'PEV:plan-1': 2, 'PEV:plan-2': 2} Unresolved non-hydrogen planarities: 29 Chain: "H" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 133 Unusual residues: {'8PP': 1, 'PEV': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 174 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'8PP:plan-7': 1, '8PP:plan-8': 1, '8PP:plan-9': 1, 'PEV:plan-1': 2, 'PEV:plan-2': 2} Unresolved non-hydrogen planarities: 28 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "B" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "E" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "F" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "H" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Residues with excluded nonbonded symmetry interactions: 10 residue: pdb=" N AGLN A 152 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A 152 " occ=0.50 residue: pdb=" N AGLN B 152 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN B 152 " occ=0.50 residue: pdb=" N AARG B 276 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 276 " occ=0.50 residue: pdb=" N AGLN C 152 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN C 152 " occ=0.50 residue: pdb=" N AGLN D 152 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN D 152 " occ=0.50 residue: pdb=" N AARG D 276 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG D 276 " occ=0.50 residue: pdb=" N ALYS E 96 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS E 96 " occ=0.50 residue: pdb=" N ALYS F 96 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS F 96 " occ=0.50 residue: pdb=" N ALYS G 96 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS G 96 " occ=0.50 residue: pdb=" N ALYS H 96 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS H 96 " occ=0.50 Time building chain proxies: 4.20, per 1000 atoms: 0.34 Number of scatterers: 12190 At special positions: 0 Unit cell: (95.795, 104.125, 92.463, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 P 20 15.00 O 2394 8.00 N 2009 7.00 C 7695 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 0.87 Conformation dependent library (CDL) restraints added in 705.9 milliseconds 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2700 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 0 sheets defined 82.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 95 through 108 removed outlier: 3.802A pdb=" N LEU A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN A 100 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 127 removed outlier: 3.701A pdb=" N ILE A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER A 127 " --> pdb=" O GLU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 170 Processing helix chain 'A' and resid 177 through 191 Processing helix chain 'A' and resid 192 through 197 Proline residue: A 195 - end of helix No H-bonds generated for 'chain 'A' and resid 192 through 197' Processing helix chain 'A' and resid 199 through 208 Processing helix chain 'A' and resid 212 through 231 Processing helix chain 'A' and resid 238 through 260 removed outlier: 3.681A pdb=" N GLN A 260 " --> pdb=" O LEU A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 265 No H-bonds generated for 'chain 'A' and resid 263 through 265' Processing helix chain 'A' and resid 266 through 282 removed outlier: 3.558A pdb=" N ASN A 282 " --> pdb=" O ASN A 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 108 removed outlier: 3.615A pdb=" N LEU B 108 " --> pdb=" O LEU B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 115 Processing helix chain 'B' and resid 117 through 127 removed outlier: 3.781A pdb=" N ILE B 121 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER B 127 " --> pdb=" O GLU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 171 removed outlier: 3.586A pdb=" N LEU B 170 " --> pdb=" O LYS B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 191 Processing helix chain 'B' and resid 192 through 197 Proline residue: B 195 - end of helix No H-bonds generated for 'chain 'B' and resid 192 through 197' Processing helix chain 'B' and resid 199 through 208 Processing helix chain 'B' and resid 212 through 231 Processing helix chain 'B' and resid 238 through 260 removed outlier: 3.677A pdb=" N GLN B 260 " --> pdb=" O LEU B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 265 No H-bonds generated for 'chain 'B' and resid 263 through 265' Processing helix chain 'B' and resid 266 through 281 Processing helix chain 'C' and resid 96 through 108 removed outlier: 3.580A pdb=" N LEU C 108 " --> pdb=" O LEU C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 127 removed outlier: 3.832A pdb=" N ILE C 121 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 170 removed outlier: 3.569A pdb=" N LEU C 167 " --> pdb=" O GLU C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 191 Processing helix chain 'C' and resid 192 through 197 Proline residue: C 195 - end of helix No H-bonds generated for 'chain 'C' and resid 192 through 197' Processing helix chain 'C' and resid 199 through 208 Processing helix chain 'C' and resid 212 through 231 Processing helix chain 'C' and resid 238 through 260 removed outlier: 3.677A pdb=" N GLN C 260 " --> pdb=" O LEU C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 265 No H-bonds generated for 'chain 'C' and resid 263 through 265' Processing helix chain 'C' and resid 266 through 282 Processing helix chain 'D' and resid 97 through 108 removed outlier: 3.629A pdb=" N LEU D 108 " --> pdb=" O LEU D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 115 Processing helix chain 'D' and resid 117 through 127 removed outlier: 3.722A pdb=" N ILE D 121 " --> pdb=" O THR D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 170 Processing helix chain 'D' and resid 177 through 191 Processing helix chain 'D' and resid 192 through 197 Proline residue: D 195 - end of helix No H-bonds generated for 'chain 'D' and resid 192 through 197' Processing helix chain 'D' and resid 199 through 208 Processing helix chain 'D' and resid 212 through 231 Processing helix chain 'D' and resid 238 through 260 removed outlier: 3.679A pdb=" N GLN D 260 " --> pdb=" O LEU D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 265 No H-bonds generated for 'chain 'D' and resid 263 through 265' Processing helix chain 'D' and resid 266 through 282 Processing helix chain 'E' and resid 46 through 75 removed outlier: 3.568A pdb=" N VAL E 73 " --> pdb=" O GLY E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 105 Processing helix chain 'E' and resid 111 through 126 removed outlier: 3.564A pdb=" N PHE E 120 " --> pdb=" O ASN E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 157 Processing helix chain 'E' and resid 164 through 178 Processing helix chain 'E' and resid 193 through 215 Processing helix chain 'F' and resid 46 through 74 Processing helix chain 'F' and resid 79 through 105 Processing helix chain 'F' and resid 111 through 126 removed outlier: 3.570A pdb=" N VAL F 117 " --> pdb=" O PRO F 113 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE F 120 " --> pdb=" O ASN F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 160 removed outlier: 3.987A pdb=" N GLU F 158 " --> pdb=" O ARG F 154 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU F 159 " --> pdb=" O THR F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 178 removed outlier: 3.512A pdb=" N LEU F 168 " --> pdb=" O TYR F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 217 removed outlier: 3.500A pdb=" N VAL F 198 " --> pdb=" O PRO F 194 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG F 216 " --> pdb=" O TYR F 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 74 Processing helix chain 'G' and resid 79 through 105 Processing helix chain 'G' and resid 111 through 126 removed outlier: 3.546A pdb=" N VAL G 117 " --> pdb=" O PRO G 113 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE G 120 " --> pdb=" O ASN G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 157 Processing helix chain 'G' and resid 164 through 178 Processing helix chain 'G' and resid 193 through 217 removed outlier: 4.012A pdb=" N ARG G 216 " --> pdb=" O TYR G 212 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 74 Processing helix chain 'H' and resid 79 through 105 Processing helix chain 'H' and resid 111 through 126 removed outlier: 3.543A pdb=" N VAL H 117 " --> pdb=" O PRO H 113 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE H 120 " --> pdb=" O ASN H 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 160 removed outlier: 3.661A pdb=" N GLU H 159 " --> pdb=" O THR H 155 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP H 160 " --> pdb=" O LEU H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 178 removed outlier: 3.537A pdb=" N LEU H 168 " --> pdb=" O TYR H 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 193 through 217 removed outlier: 3.506A pdb=" N VAL H 198 " --> pdb=" O PRO H 194 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG H 216 " --> pdb=" O TYR H 212 " (cutoff:3.500A) 878 hydrogen bonds defined for protein. 2644 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: 1.52 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1921 1.32 - 1.44: 3132 1.44 - 1.56: 7000 1.56 - 1.68: 40 1.68 - 1.81: 132 Bond restraints: 12225 Sorted by residual: bond pdb=" N ILE A 250 " pdb=" CA ILE A 250 " ideal model delta sigma weight residual 1.461 1.492 -0.031 1.17e-02 7.31e+03 6.94e+00 bond pdb=" N AARG B 276 " pdb=" CA AARG B 276 " ideal model delta sigma weight residual 1.459 1.489 -0.029 1.19e-02 7.06e+03 6.05e+00 bond pdb=" O3 NAD E 306 " pdb=" PA NAD E 306 " ideal model delta sigma weight residual 1.653 1.604 0.049 2.00e-02 2.50e+03 6.04e+00 bond pdb=" O3 NAD F 306 " pdb=" PA NAD F 306 " ideal model delta sigma weight residual 1.653 1.604 0.049 2.00e-02 2.50e+03 5.95e+00 bond pdb=" C1 PEV C 405 " pdb=" O3P PEV C 405 " ideal model delta sigma weight residual 1.407 1.454 -0.047 2.00e-02 2.50e+03 5.57e+00 ... (remaining 12220 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 16157 1.99 - 3.98: 222 3.98 - 5.97: 45 5.97 - 7.96: 2 7.96 - 9.95: 16 Bond angle restraints: 16442 Sorted by residual: angle pdb=" O3P PEV H 301 " pdb=" P PEV H 301 " pdb=" O4P PEV H 301 " ideal model delta sigma weight residual 93.57 103.52 -9.95 3.00e+00 1.11e-01 1.10e+01 angle pdb=" O3P PEV C 401 " pdb=" P PEV C 401 " pdb=" O4P PEV C 401 " ideal model delta sigma weight residual 93.57 103.49 -9.92 3.00e+00 1.11e-01 1.09e+01 angle pdb=" CA AARG B 276 " pdb=" C AARG B 276 " pdb=" O AARG B 276 " ideal model delta sigma weight residual 120.82 117.35 3.47 1.05e+00 9.07e-01 1.09e+01 angle pdb=" O3P PEV H 302 " pdb=" P PEV H 302 " pdb=" O4P PEV H 302 " ideal model delta sigma weight residual 93.57 103.40 -9.83 3.00e+00 1.11e-01 1.07e+01 angle pdb=" O3P PEV C 403 " pdb=" P PEV C 403 " pdb=" O4P PEV C 403 " ideal model delta sigma weight residual 93.57 103.22 -9.65 3.00e+00 1.11e-01 1.03e+01 ... (remaining 16437 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.99: 6555 15.99 - 31.99: 453 31.99 - 47.98: 161 47.98 - 63.97: 79 63.97 - 79.97: 13 Dihedral angle restraints: 7261 sinusoidal: 3097 harmonic: 4164 Sorted by residual: dihedral pdb=" CA ALA G 127 " pdb=" C ALA G 127 " pdb=" N LEU G 128 " pdb=" CA LEU G 128 " ideal model delta harmonic sigma weight residual 180.00 158.64 21.36 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA ALA E 127 " pdb=" C ALA E 127 " pdb=" N LEU E 128 " pdb=" CA LEU E 128 " ideal model delta harmonic sigma weight residual 180.00 158.78 21.22 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA ALA H 127 " pdb=" C ALA H 127 " pdb=" N LEU H 128 " pdb=" CA LEU H 128 " ideal model delta harmonic sigma weight residual 180.00 158.80 21.20 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 7258 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1285 0.039 - 0.079: 407 0.079 - 0.118: 76 0.118 - 0.158: 8 0.158 - 0.197: 2 Chirality restraints: 1778 Sorted by residual: chirality pdb=" C2 PEV E 304 " pdb=" C1 PEV E 304 " pdb=" C3 PEV E 304 " pdb=" O2 PEV E 304 " both_signs ideal model delta sigma weight residual False 2.36 2.56 -0.20 2.00e-01 2.50e+01 9.71e-01 chirality pdb=" CA ILE A 250 " pdb=" N ILE A 250 " pdb=" C ILE A 250 " pdb=" CB ILE A 250 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.43e-01 chirality pdb=" C1D NAD E 306 " pdb=" C2D NAD E 306 " pdb=" N1N NAD E 306 " pdb=" O4D NAD E 306 " both_signs ideal model delta sigma weight residual False 2.41 2.57 -0.15 2.00e-01 2.50e+01 5.70e-01 ... (remaining 1775 not shown) Planarity restraints: 2066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C32 8PP B 403 " 0.338 2.00e-02 2.50e+03 2.88e-01 1.04e+03 pdb=" C33 8PP B 403 " -0.502 2.00e-02 2.50e+03 pdb=" C34 8PP B 403 " -0.108 2.00e-02 2.50e+03 pdb=" C35 8PP B 403 " 0.109 2.00e-02 2.50e+03 pdb=" C36 8PP B 403 " 0.162 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C22 8PP G 302 " 0.335 2.00e-02 2.50e+03 2.85e-01 1.01e+03 pdb=" C23 8PP G 302 " -0.495 2.00e-02 2.50e+03 pdb=" C24 8PP G 302 " -0.105 2.00e-02 2.50e+03 pdb=" C25 8PP G 302 " 0.167 2.00e-02 2.50e+03 pdb=" C26 8PP G 302 " 0.098 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 8PP B 403 " -0.317 2.00e-02 2.50e+03 2.70e-01 9.12e+02 pdb=" C18 8PP B 403 " 0.467 2.00e-02 2.50e+03 pdb=" C19 8PP B 403 " 0.098 2.00e-02 2.50e+03 pdb=" C20 8PP B 403 " -0.068 2.00e-02 2.50e+03 pdb=" C21 8PP B 403 " -0.179 2.00e-02 2.50e+03 ... (remaining 2063 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 3838 2.84 - 3.35: 11471 3.35 - 3.87: 20898 3.87 - 4.38: 26733 4.38 - 4.90: 42144 Nonbonded interactions: 105084 Sorted by model distance: nonbonded pdb=" ND1 HIS B 211 " pdb=" OG SER E 201 " model vdw 2.323 3.120 nonbonded pdb=" ND1 HIS A 211 " pdb=" OG SER G 201 " model vdw 2.329 3.120 nonbonded pdb=" ND1 HIS D 211 " pdb=" OG SER H 201 " model vdw 2.330 3.120 nonbonded pdb=" OD2 ASP F 50 " pdb=" O HOH F 401 " model vdw 2.332 3.040 nonbonded pdb=" ND1 HIS C 211 " pdb=" OG SER F 201 " model vdw 2.333 3.120 ... (remaining 105079 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 95 through 151 or resid 153 through 162 or (resid 163 and \ (name N or name CA or name C or name O or name CB )) or resid 164 through 209 or \ (resid 210 and (name N or name CA or name C or name O or name CB or name CD )) \ or resid 211 through 275 or resid 277 through 283)) selection = (chain 'B' and (resid 95 through 97 or (resid 98 and (name N or name CA or name \ C or name O or name CB )) or resid 99 through 151 or resid 153 through 162 or (r \ esid 163 and (name N or name CA or name C or name O or name CB )) or resid 164 t \ hrough 209 or (resid 210 and (name N or name CA or name C or name O or name CB o \ r name CD )) or resid 211 through 275 or resid 277 through 283)) selection = (chain 'C' and (resid 95 through 97 or (resid 98 and (name N or name CA or name \ C or name O or name CB )) or resid 99 through 151 or resid 153 through 162 or (r \ esid 163 and (name N or name CA or name C or name O or name CB )) or resid 164 t \ hrough 275 or resid 277 through 283)) selection = (chain 'D' and (resid 95 through 97 or (resid 98 and (name N or name CA or name \ C or name O or name CB )) or resid 99 through 151 or resid 153 through 209 or (r \ esid 210 and (name N or name CA or name C or name O or name CB or name CD )) or \ resid 211 through 275 or resid 277 through 283)) } ncs_group { reference = (chain 'E' and (resid 45 through 95 or resid 97 through 217 or (resid 301 and (n \ ame C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 o \ r name C2 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 \ or name O11 or name O1P or name O2 or name O2P or name O3 or name O31 or name O \ 3P or name O4P or name P )) or (resid 305 and (name C18 or name C19 or name C20 \ or name C21 or name C22)))) selection = (chain 'F' and (resid 45 through 95 or resid 97 through 182 or (resid 183 and (n \ ame N or name CA or name C or name O or name CB )) or resid 184 through 213 or ( \ resid 214 and (name N or name CA or name C or name O or name CB )) or resid 215 \ through 217 or (resid 301 and (name C1 or name C11 or name C12 or name C13 or na \ me C14 or name C15 or name C16 or name C2 or name C3 or name C31 or name C32 or \ name C33 or name C34 or name C35 or name O11 or name O1P or name O2 or name O2P \ or name O3 or name O31 or name O3P or name O4P or name P )) or (resid 305 and (n \ ame C17 or name C18 or name C19 or name C20 or name C21)))) selection = (chain 'G' and (resid 45 through 95 or resid 97 through 182 or (resid 183 and (n \ ame N or name CA or name C or name O or name CB )) or resid 184 through 213 or ( \ resid 214 and (name N or name CA or name C or name O or name CB )) or resid 215 \ through 217 or (resid 301 and (name C1 or name C11 or name C12 or name C13 or na \ me C14 or name C15 or name C16 or name C2 or name C3 or name C31 or name C32 or \ name C33 or name C34 or name C35 or name O11 or name O1P or name O2 or name O2P \ or name O3 or name O31 or name O3P or name O4P or name P )) or (resid 305 and (n \ ame C18 or name C19 or name C20 or name C21 or name C22)))) selection = (chain 'H' and (resid 45 through 95 or resid 97 through 182 or (resid 183 and (n \ ame N or name CA or name C or name O or name CB )) or resid 184 through 213 or ( \ resid 214 and (name N or name CA or name C or name O or name CB )) or resid 215 \ through 217 or (resid 301 and (name C1 or name C11 or name C12 or name C13 or na \ me C14 or name C15 or name C16 or name C2 or name C3 or name C31 or name C32 or \ name C33 or name C34 or name C35 or name O11 or name O1P or name O2 or name O2P \ or name O3 or name O31 or name O3P or name O4P or name P )) or (resid 305 and (n \ ame C18 or name C19 or name C20 or name C21 or name C22)))) } 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=0.50 max=1.00 mean=0.99 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: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.990 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 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 : 0.006 0.049 12225 Z= 0.268 Angle : 0.661 9.948 16442 Z= 0.318 Chirality : 0.039 0.197 1778 Planarity : 0.019 0.288 2066 Dihedral : 14.287 79.966 4561 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.22), residues: 1422 helix: 0.36 (0.15), residues: 1154 sheet: None (None), residues: 0 loop : -1.12 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 156 TYR 0.008 0.001 TYR F 67 PHE 0.006 0.001 PHE D 149 TRP 0.012 0.002 TRP A 200 HIS 0.003 0.001 HIS C 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.27 (12225) covalent geometry : angle 0.66092 / 0.32 (16442) hydrogen bonds : bond 0.21359 / 14.76 ( 878) hydrogen bonds : angle 6.18914 / 4.44 ( 2644) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 325 time to evaluate : 0.313 Fit side-chains REVERT: A 109 GLU cc_start: 0.5345 (mt-10) cc_final: 0.4907 (tp30) REVERT: A 169 GLN cc_start: 0.6424 (mt0) cc_final: 0.6081 (mt0) REVERT: A 179 ASP cc_start: 0.7380 (p0) cc_final: 0.7021 (p0) REVERT: A 202 ARG cc_start: 0.7391 (tpt90) cc_final: 0.7179 (tpm170) REVERT: A 223 MET cc_start: 0.8782 (ttp) cc_final: 0.8568 (ttp) REVERT: A 271 ARG cc_start: 0.7151 (ttm110) cc_final: 0.6800 (mtm-85) REVERT: A 274 GLU cc_start: 0.7701 (tt0) cc_final: 0.7356 (tt0) REVERT: A 276 ARG cc_start: 0.7448 (mmm-85) cc_final: 0.6569 (mpp-170) REVERT: A 279 ASP cc_start: 0.6740 (m-30) cc_final: 0.6468 (m-30) REVERT: B 109 GLU cc_start: 0.5412 (mt-10) cc_final: 0.4882 (tp30) REVERT: B 164 GLU cc_start: 0.7059 (mt-10) cc_final: 0.6687 (mt-10) REVERT: B 169 GLN cc_start: 0.6480 (mt0) cc_final: 0.5845 (pt0) REVERT: B 179 ASP cc_start: 0.7349 (p0) cc_final: 0.7074 (p0) REVERT: B 202 ARG cc_start: 0.7383 (tpt90) cc_final: 0.7175 (tpm170) REVERT: B 223 MET cc_start: 0.8702 (ttp) cc_final: 0.8449 (ttp) REVERT: B 271 ARG cc_start: 0.7139 (ttm110) cc_final: 0.6771 (mtm-85) REVERT: B 274 GLU cc_start: 0.7715 (tt0) cc_final: 0.7412 (tt0) REVERT: B 279 ASP cc_start: 0.6710 (m-30) cc_final: 0.6428 (m-30) REVERT: C 109 GLU cc_start: 0.5437 (mt-10) cc_final: 0.4900 (tp30) REVERT: C 162 GLU cc_start: 0.6608 (pt0) cc_final: 0.6272 (pt0) REVERT: C 177 LYS cc_start: 0.6948 (mtpp) cc_final: 0.6402 (mmtt) REVERT: C 179 ASP cc_start: 0.7301 (p0) cc_final: 0.6971 (p0) REVERT: C 202 ARG cc_start: 0.7193 (tpt90) cc_final: 0.6970 (tpm170) REVERT: C 223 MET cc_start: 0.8677 (ttp) cc_final: 0.8457 (ttp) REVERT: C 234 GLN cc_start: 0.7822 (mt0) cc_final: 0.7613 (mt0) REVERT: C 271 ARG cc_start: 0.7092 (ttm110) cc_final: 0.6753 (mtm-85) REVERT: C 274 GLU cc_start: 0.7708 (tt0) cc_final: 0.7358 (tt0) REVERT: C 276 ARG cc_start: 0.7496 (mmm-85) cc_final: 0.6615 (mpp-170) REVERT: C 279 ASP cc_start: 0.6722 (m-30) cc_final: 0.6457 (m-30) REVERT: D 109 GLU cc_start: 0.5304 (mt-10) cc_final: 0.4836 (tp30) REVERT: D 167 LEU cc_start: 0.6675 (mt) cc_final: 0.6382 (mt) REVERT: D 177 LYS cc_start: 0.6968 (mtpp) cc_final: 0.6450 (mmtt) REVERT: D 179 ASP cc_start: 0.7312 (p0) cc_final: 0.6977 (p0) REVERT: D 202 ARG cc_start: 0.7430 (tpt90) cc_final: 0.7191 (tpm170) REVERT: D 223 MET cc_start: 0.8763 (ttp) cc_final: 0.8544 (ttp) REVERT: D 271 ARG cc_start: 0.7131 (ttm110) cc_final: 0.6780 (mtm-85) REVERT: D 274 GLU cc_start: 0.7712 (tt0) cc_final: 0.7402 (tt0) REVERT: D 279 ASP cc_start: 0.6735 (m-30) cc_final: 0.6437 (m-30) REVERT: D 281 MET cc_start: 0.6329 (mmp) cc_final: 0.6116 (mmm) REVERT: D 283 MET cc_start: 0.3367 (ttp) cc_final: 0.3059 (ptt) REVERT: E 71 MET cc_start: 0.8547 (tpt) cc_final: 0.8289 (tpt) REVERT: E 99 GLU cc_start: 0.7731 (mt-10) cc_final: 0.6984 (mp0) REVERT: E 132 GLU cc_start: 0.6818 (mt-10) cc_final: 0.6592 (tt0) REVERT: E 143 GLU cc_start: 0.7217 (mt-10) cc_final: 0.6651 (tt0) REVERT: E 147 HIS cc_start: 0.7719 (t-90) cc_final: 0.7355 (t-90) REVERT: E 180 GLU cc_start: 0.5548 (tp30) cc_final: 0.5212 (tm-30) REVERT: E 199 LEU cc_start: 0.7323 (tp) cc_final: 0.7100 (tp) REVERT: E 211 ILE cc_start: 0.8496 (mm) cc_final: 0.8250 (mt) REVERT: F 50 ASP cc_start: 0.7087 (m-30) cc_final: 0.6694 (m-30) REVERT: F 71 MET cc_start: 0.8474 (tpt) cc_final: 0.8224 (tpt) REVERT: F 99 GLU cc_start: 0.7732 (mt-10) cc_final: 0.6998 (mp0) REVERT: F 143 GLU cc_start: 0.7240 (mt-10) cc_final: 0.6672 (tt0) REVERT: F 147 HIS cc_start: 0.7721 (t-90) cc_final: 0.7370 (t-90) REVERT: F 199 LEU cc_start: 0.7387 (tp) cc_final: 0.7170 (tp) REVERT: F 211 ILE cc_start: 0.8479 (mm) cc_final: 0.8227 (mt) REVERT: F 215 GLU cc_start: 0.7692 (pt0) cc_final: 0.7365 (pt0) REVERT: G 99 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7006 (mp0) REVERT: G 143 GLU cc_start: 0.7230 (mt-10) cc_final: 0.6678 (tt0) REVERT: G 147 HIS cc_start: 0.7712 (t-90) cc_final: 0.7360 (t-90) REVERT: G 157 MET cc_start: 0.5043 (mtt) cc_final: 0.4818 (mtm) REVERT: G 175 ARG cc_start: 0.7936 (tmm-80) cc_final: 0.7716 (tmm160) REVERT: G 180 GLU cc_start: 0.5544 (tp30) cc_final: 0.5233 (tm-30) REVERT: G 199 LEU cc_start: 0.7355 (tp) cc_final: 0.7150 (tp) REVERT: G 208 ARG cc_start: 0.7028 (mtt-85) cc_final: 0.6719 (mmt90) REVERT: G 211 ILE cc_start: 0.8539 (mm) cc_final: 0.8291 (mt) REVERT: G 215 GLU cc_start: 0.7700 (pt0) cc_final: 0.7347 (pt0) REVERT: H 71 MET cc_start: 0.8490 (tpt) cc_final: 0.8171 (tpt) REVERT: H 99 GLU cc_start: 0.7719 (mt-10) cc_final: 0.6969 (mp0) REVERT: H 132 GLU cc_start: 0.6790 (mt-10) cc_final: 0.6559 (tt0) REVERT: H 143 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6679 (tt0) REVERT: H 147 HIS cc_start: 0.7741 (t-90) cc_final: 0.7394 (t-90) REVERT: H 199 LEU cc_start: 0.7399 (tp) cc_final: 0.7186 (tp) REVERT: H 211 ILE cc_start: 0.8481 (mm) cc_final: 0.8224 (mt) REVERT: H 215 GLU cc_start: 0.7632 (pt0) cc_final: 0.7282 (pt0) outliers start: 0 outliers final: 4 residues processed: 325 average time/residue: 0.6949 time to fit residues: 239.9124 Evaluate side-chains 270 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 266 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain D residue 226 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 275 ASN C 275 ASN E 98 ASN F 98 ASN G 98 ASN H 98 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.177653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.138640 restraints weight = 53247.849| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 4.85 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3518 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3518 r_free = 0.3518 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3517 r_free = 0.3517 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3517 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12225 Z= 0.123 Angle : 0.540 9.872 16442 Z= 0.278 Chirality : 0.037 0.114 1778 Planarity : 0.005 0.055 2066 Dihedral : 13.128 59.742 1929 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.64 % Allowed : 9.39 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.68 (0.23), residues: 1422 helix: 2.37 (0.15), residues: 1154 sheet: None (None), residues: 0 loop : -1.00 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 46 TYR 0.011 0.001 TYR A 230 PHE 0.010 0.001 PHE B 272 TRP 0.016 0.001 TRP C 240 HIS 0.004 0.001 HIS H 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.12 (12225) covalent geometry : angle 0.53974 / 0.28 (16442) hydrogen bonds : bond 0.05439 / 3.71 ( 878) hydrogen bonds : angle 3.47164 / 2.49 ( 2644) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 283 time to evaluate : 0.422 Fit side-chains REVERT: A 109 GLU cc_start: 0.5285 (mt-10) cc_final: 0.5060 (tt0) REVERT: A 123 GLU cc_start: 0.5344 (tt0) cc_final: 0.4878 (tm-30) REVERT: A 163 GLU cc_start: 0.6486 (mt-10) cc_final: 0.6189 (mt-10) REVERT: A 167 LEU cc_start: 0.6961 (mt) cc_final: 0.6568 (tp) REVERT: A 260 GLN cc_start: 0.7204 (pt0) cc_final: 0.6469 (pm20) REVERT: A 271 ARG cc_start: 0.7119 (ttm110) cc_final: 0.6829 (mtm-85) REVERT: A 274 GLU cc_start: 0.7706 (tt0) cc_final: 0.7470 (tt0) REVERT: A 276 ARG cc_start: 0.7414 (mmm-85) cc_final: 0.7140 (mmm160) REVERT: A 279 ASP cc_start: 0.6685 (m-30) cc_final: 0.6373 (m-30) REVERT: B 109 GLU cc_start: 0.5305 (mt-10) cc_final: 0.4849 (tp30) REVERT: B 123 GLU cc_start: 0.5465 (OUTLIER) cc_final: 0.5077 (tm-30) REVERT: B 163 GLU cc_start: 0.6652 (mm-30) cc_final: 0.6330 (mt-10) REVERT: B 164 GLU cc_start: 0.7084 (mt-10) cc_final: 0.6745 (mt-10) REVERT: B 260 GLN cc_start: 0.7300 (pt0) cc_final: 0.6542 (pm20) REVERT: B 271 ARG cc_start: 0.7179 (ttm110) cc_final: 0.6921 (mtm-85) REVERT: B 274 GLU cc_start: 0.7703 (tt0) cc_final: 0.7497 (tt0) REVERT: B 279 ASP cc_start: 0.6719 (m-30) cc_final: 0.6468 (m-30) REVERT: B 281 MET cc_start: 0.6431 (OUTLIER) cc_final: 0.4399 (mpt) REVERT: C 109 GLU cc_start: 0.5303 (mt-10) cc_final: 0.4857 (tp30) REVERT: C 123 GLU cc_start: 0.5719 (tt0) cc_final: 0.5245 (tm-30) REVERT: C 162 GLU cc_start: 0.6340 (pt0) cc_final: 0.5990 (pt0) REVERT: C 163 GLU cc_start: 0.6936 (mm-30) cc_final: 0.6657 (mt-10) REVERT: C 164 GLU cc_start: 0.7028 (mt-10) cc_final: 0.6701 (mt-10) REVERT: C 169 GLN cc_start: 0.6335 (mt0) cc_final: 0.5668 (pt0) REVERT: C 177 LYS cc_start: 0.7050 (mtpp) cc_final: 0.6568 (mmtt) REVERT: C 260 GLN cc_start: 0.7161 (pt0) cc_final: 0.6571 (pm20) REVERT: C 271 ARG cc_start: 0.7110 (ttm110) cc_final: 0.6821 (mtm-85) REVERT: C 274 GLU cc_start: 0.7733 (tt0) cc_final: 0.7473 (tt0) REVERT: C 276 ARG cc_start: 0.7417 (mmm-85) cc_final: 0.7216 (mmm160) REVERT: C 281 MET cc_start: 0.6653 (OUTLIER) cc_final: 0.5117 (mpt) REVERT: D 109 GLU cc_start: 0.5243 (mt-10) cc_final: 0.4819 (tp30) REVERT: D 119 GLU cc_start: 0.5725 (tm-30) cc_final: 0.5497 (tm-30) REVERT: D 123 GLU cc_start: 0.5103 (tt0) cc_final: 0.4592 (tm-30) REVERT: D 167 LEU cc_start: 0.6566 (mt) cc_final: 0.6108 (tp) REVERT: D 177 LYS cc_start: 0.7020 (mtpp) cc_final: 0.6525 (mmtt) REVERT: D 260 GLN cc_start: 0.7286 (pt0) cc_final: 0.6539 (pm20) REVERT: D 271 ARG cc_start: 0.7171 (ttm110) cc_final: 0.6811 (mtm-85) REVERT: D 279 ASP cc_start: 0.6644 (m-30) cc_final: 0.6420 (m-30) REVERT: D 281 MET cc_start: 0.6355 (mmp) cc_final: 0.5965 (mmm) REVERT: E 76 ARG cc_start: 0.7198 (mtt180) cc_final: 0.6247 (mpp-170) REVERT: E 132 GLU cc_start: 0.6797 (mt-10) cc_final: 0.6537 (tt0) REVERT: E 143 GLU cc_start: 0.7341 (mt-10) cc_final: 0.6802 (tt0) REVERT: E 147 HIS cc_start: 0.7502 (t-90) cc_final: 0.7209 (t-90) REVERT: E 180 GLU cc_start: 0.5567 (tp30) cc_final: 0.5201 (tm-30) REVERT: E 215 GLU cc_start: 0.7710 (pt0) cc_final: 0.7295 (pt0) REVERT: F 50 ASP cc_start: 0.7108 (m-30) cc_final: 0.6705 (m-30) REVERT: F 143 GLU cc_start: 0.7159 (mt-10) cc_final: 0.6572 (tt0) REVERT: F 147 HIS cc_start: 0.7361 (t-90) cc_final: 0.7057 (t-170) REVERT: F 215 GLU cc_start: 0.7621 (pt0) cc_final: 0.7371 (pt0) REVERT: G 143 GLU cc_start: 0.7308 (mt-10) cc_final: 0.6806 (tt0) REVERT: G 147 HIS cc_start: 0.7485 (t-90) cc_final: 0.7176 (t-170) REVERT: G 180 GLU cc_start: 0.5718 (tp30) cc_final: 0.5486 (tm-30) REVERT: G 208 ARG cc_start: 0.7334 (mtt-85) cc_final: 0.6998 (mmt90) REVERT: G 215 GLU cc_start: 0.7613 (pt0) cc_final: 0.7364 (pt0) REVERT: H 132 GLU cc_start: 0.6816 (mt-10) cc_final: 0.6556 (tt0) REVERT: H 143 GLU cc_start: 0.7289 (mt-10) cc_final: 0.6750 (tt0) REVERT: H 147 HIS cc_start: 0.7422 (t-90) cc_final: 0.7115 (t-170) REVERT: H 215 GLU cc_start: 0.7666 (pt0) cc_final: 0.7407 (pt0) outliers start: 19 outliers final: 1 residues processed: 285 average time/residue: 0.6716 time to fit residues: 203.2872 Evaluate side-chains 260 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 256 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain C residue 281 MET Chi-restraints excluded: chain F residue 49 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 16 optimal weight: 0.5980 chunk 118 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 39 optimal weight: 50.0000 chunk 112 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 234 GLN A 260 GLN A 275 ASN B 252 ASN B 260 GLN C 252 ASN C 260 GLN C 275 ASN D 260 GLN E 204 GLN F 98 ASN F 204 GLN G 204 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.177655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.139371 restraints weight = 50847.717| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 4.61 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3528 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3528 r_free = 0.3528 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3528 r_free = 0.3528 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3528 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12225 Z= 0.127 Angle : 0.536 8.527 16442 Z= 0.272 Chirality : 0.038 0.149 1778 Planarity : 0.005 0.063 2066 Dihedral : 12.002 59.944 1921 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.41 % Allowed : 12.58 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.21 (0.23), residues: 1422 helix: 2.79 (0.15), residues: 1150 sheet: None (None), residues: 0 loop : -0.99 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 202 TYR 0.010 0.001 TYR G 67 PHE 0.009 0.002 PHE G 174 TRP 0.013 0.002 TRP B 240 HIS 0.004 0.001 HIS G 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.13 (12225) covalent geometry : angle 0.53556 / 0.27 (16442) hydrogen bonds : bond 0.04860 / 3.32 ( 878) hydrogen bonds : angle 3.28109 / 2.35 ( 2644) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 251 time to evaluate : 0.273 Fit side-chains REVERT: A 108 LEU cc_start: 0.6726 (OUTLIER) cc_final: 0.6330 (mt) REVERT: A 109 GLU cc_start: 0.5247 (mt-10) cc_final: 0.5044 (tt0) REVERT: A 119 GLU cc_start: 0.5647 (tm-30) cc_final: 0.5298 (tm-30) REVERT: A 123 GLU cc_start: 0.5271 (tt0) cc_final: 0.4860 (tm-30) REVERT: A 163 GLU cc_start: 0.6515 (mt-10) cc_final: 0.6205 (mt-10) REVERT: A 179 ASP cc_start: 0.7306 (p0) cc_final: 0.7046 (p0) REVERT: A 271 ARG cc_start: 0.7131 (ttm110) cc_final: 0.6798 (mtm-85) REVERT: A 276 ARG cc_start: 0.7331 (mmm-85) cc_final: 0.7037 (mmm160) REVERT: A 279 ASP cc_start: 0.6703 (m-30) cc_final: 0.6287 (t70) REVERT: B 108 LEU cc_start: 0.6741 (OUTLIER) cc_final: 0.6383 (mt) REVERT: B 109 GLU cc_start: 0.5353 (mt-10) cc_final: 0.4872 (tp30) REVERT: B 123 GLU cc_start: 0.5728 (OUTLIER) cc_final: 0.5327 (tm-30) REVERT: B 163 GLU cc_start: 0.6741 (mm-30) cc_final: 0.6436 (mt-10) REVERT: B 271 ARG cc_start: 0.7146 (ttm110) cc_final: 0.6850 (mtm-85) REVERT: B 279 ASP cc_start: 0.6770 (m-30) cc_final: 0.6464 (m-30) REVERT: B 281 MET cc_start: 0.6441 (OUTLIER) cc_final: 0.4608 (mpt) REVERT: C 108 LEU cc_start: 0.6752 (mm) cc_final: 0.6422 (mt) REVERT: C 109 GLU cc_start: 0.5381 (mt-10) cc_final: 0.4891 (tp30) REVERT: C 119 GLU cc_start: 0.5644 (tm-30) cc_final: 0.5277 (tm-30) REVERT: C 123 GLU cc_start: 0.5574 (OUTLIER) cc_final: 0.5220 (tm-30) REVERT: C 162 GLU cc_start: 0.6545 (pt0) cc_final: 0.6242 (pt0) REVERT: C 163 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.6565 (mt-10) REVERT: C 164 GLU cc_start: 0.6983 (mt-10) cc_final: 0.6687 (mt-10) REVERT: C 177 LYS cc_start: 0.7077 (mtpp) cc_final: 0.6579 (mmtt) REVERT: C 179 ASP cc_start: 0.7364 (p0) cc_final: 0.7076 (p0) REVERT: C 271 ARG cc_start: 0.7119 (ttm110) cc_final: 0.6801 (mtm-85) REVERT: C 274 GLU cc_start: 0.7682 (tt0) cc_final: 0.7457 (tt0) REVERT: C 276 ARG cc_start: 0.7387 (mmm-85) cc_final: 0.7186 (mmm160) REVERT: C 279 ASP cc_start: 0.6592 (m-30) cc_final: 0.6323 (m-30) REVERT: D 108 LEU cc_start: 0.6808 (mm) cc_final: 0.6415 (mt) REVERT: D 109 GLU cc_start: 0.5263 (mt-10) cc_final: 0.4838 (tp30) REVERT: D 119 GLU cc_start: 0.5667 (tm-30) cc_final: 0.5344 (tm-30) REVERT: D 123 GLU cc_start: 0.5182 (tt0) cc_final: 0.4653 (tm-30) REVERT: D 177 LYS cc_start: 0.7058 (mtpp) cc_final: 0.6572 (mmtt) REVERT: D 179 ASP cc_start: 0.7323 (p0) cc_final: 0.7071 (p0) REVERT: D 271 ARG cc_start: 0.7167 (ttm110) cc_final: 0.6818 (mtm-85) REVERT: D 279 ASP cc_start: 0.6845 (m-30) cc_final: 0.6540 (m-30) REVERT: D 281 MET cc_start: 0.6474 (mmp) cc_final: 0.6266 (mmm) REVERT: E 143 GLU cc_start: 0.7363 (mt-10) cc_final: 0.6964 (mt-10) REVERT: E 147 HIS cc_start: 0.7396 (t-90) cc_final: 0.7167 (t-170) REVERT: E 155 THR cc_start: 0.6684 (m) cc_final: 0.6338 (t) REVERT: E 180 GLU cc_start: 0.5468 (tp30) cc_final: 0.5165 (tm-30) REVERT: E 215 GLU cc_start: 0.7702 (pt0) cc_final: 0.7202 (pt0) REVERT: F 50 ASP cc_start: 0.7095 (m-30) cc_final: 0.6843 (m-30) REVERT: F 147 HIS cc_start: 0.7278 (t-90) cc_final: 0.7033 (t-170) REVERT: F 215 GLU cc_start: 0.7549 (pt0) cc_final: 0.7191 (pt0) REVERT: G 143 GLU cc_start: 0.7385 (mt-10) cc_final: 0.6915 (tt0) REVERT: G 147 HIS cc_start: 0.7474 (t-90) cc_final: 0.7212 (t-170) REVERT: G 155 THR cc_start: 0.6750 (m) cc_final: 0.6392 (t) REVERT: G 180 GLU cc_start: 0.5540 (tp30) cc_final: 0.5239 (tm-30) REVERT: G 208 ARG cc_start: 0.7273 (mtt-85) cc_final: 0.6964 (mmt90) REVERT: G 215 GLU cc_start: 0.7471 (pt0) cc_final: 0.7149 (pt0) REVERT: H 143 GLU cc_start: 0.7299 (mt-10) cc_final: 0.6882 (tt0) REVERT: H 147 HIS cc_start: 0.7453 (t-90) cc_final: 0.7225 (t-170) REVERT: H 215 GLU cc_start: 0.7551 (pt0) cc_final: 0.7244 (pt0) outliers start: 28 outliers final: 9 residues processed: 255 average time/residue: 0.6798 time to fit residues: 183.7671 Evaluate side-chains 252 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 237 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 246 MET Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain G residue 49 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 65 optimal weight: 10.0000 chunk 26 optimal weight: 0.8980 chunk 92 optimal weight: 9.9990 chunk 23 optimal weight: 0.9980 chunk 84 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 24 optimal weight: 0.0980 chunk 53 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 126 optimal weight: 9.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 234 GLN A 275 ASN C 260 GLN C 275 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.176873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.136883 restraints weight = 51819.837| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 4.56 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3490 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3490 r_free = 0.3490 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3490 r_free = 0.3490 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3490 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12225 Z= 0.116 Angle : 0.506 8.888 16442 Z= 0.259 Chirality : 0.037 0.119 1778 Planarity : 0.004 0.050 2066 Dihedral : 11.758 59.967 1921 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.24 % Allowed : 13.09 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.40 (0.23), residues: 1422 helix: 2.89 (0.15), residues: 1158 sheet: None (None), residues: 0 loop : -0.89 (0.40), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 159 TYR 0.009 0.002 TYR E 67 PHE 0.008 0.001 PHE C 272 TRP 0.013 0.001 TRP B 200 HIS 0.004 0.001 HIS G 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.12 (12225) covalent geometry : angle 0.50574 / 0.26 (16442) hydrogen bonds : bond 0.04446 / 3.02 ( 878) hydrogen bonds : angle 3.21920 / 2.31 ( 2644) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 244 time to evaluate : 0.292 Fit side-chains REVERT: A 108 LEU cc_start: 0.6684 (OUTLIER) cc_final: 0.6273 (mt) REVERT: A 109 GLU cc_start: 0.5247 (mt-10) cc_final: 0.4997 (tt0) REVERT: A 119 GLU cc_start: 0.5453 (tm-30) cc_final: 0.5099 (tm-30) REVERT: A 123 GLU cc_start: 0.5160 (tt0) cc_final: 0.4703 (tm-30) REVERT: A 163 GLU cc_start: 0.6528 (mt-10) cc_final: 0.6247 (mt-10) REVERT: A 167 LEU cc_start: 0.6874 (mt) cc_final: 0.6540 (tp) REVERT: A 179 ASP cc_start: 0.7400 (p0) cc_final: 0.7087 (p0) REVERT: A 271 ARG cc_start: 0.7122 (ttm110) cc_final: 0.6754 (mtm-85) REVERT: A 276 ARG cc_start: 0.7305 (mmm-85) cc_final: 0.7003 (mmm160) REVERT: A 279 ASP cc_start: 0.6703 (m-30) cc_final: 0.6237 (t70) REVERT: B 108 LEU cc_start: 0.6772 (mm) cc_final: 0.6410 (mt) REVERT: B 109 GLU cc_start: 0.5386 (mt-10) cc_final: 0.4911 (tp30) REVERT: B 119 GLU cc_start: 0.5816 (tm-30) cc_final: 0.4855 (tp30) REVERT: B 123 GLU cc_start: 0.5689 (OUTLIER) cc_final: 0.5201 (tm-30) REVERT: B 163 GLU cc_start: 0.6713 (mm-30) cc_final: 0.6418 (mt-10) REVERT: B 167 LEU cc_start: 0.6583 (OUTLIER) cc_final: 0.6378 (tp) REVERT: B 271 ARG cc_start: 0.7069 (ttm110) cc_final: 0.6727 (mtm-85) REVERT: B 279 ASP cc_start: 0.6783 (m-30) cc_final: 0.6475 (m-30) REVERT: B 281 MET cc_start: 0.6503 (OUTLIER) cc_final: 0.4633 (mpt) REVERT: C 108 LEU cc_start: 0.6739 (OUTLIER) cc_final: 0.6402 (mt) REVERT: C 109 GLU cc_start: 0.5354 (mt-10) cc_final: 0.4895 (tp30) REVERT: C 119 GLU cc_start: 0.5550 (tm-30) cc_final: 0.5287 (tm-30) REVERT: C 123 GLU cc_start: 0.5527 (OUTLIER) cc_final: 0.5143 (tm-30) REVERT: C 159 ARG cc_start: 0.7144 (mtm-85) cc_final: 0.6821 (mtt180) REVERT: C 162 GLU cc_start: 0.6582 (pt0) cc_final: 0.6245 (pt0) REVERT: C 163 GLU cc_start: 0.6800 (OUTLIER) cc_final: 0.6482 (mt-10) REVERT: C 164 GLU cc_start: 0.7038 (mt-10) cc_final: 0.6753 (mt-10) REVERT: C 177 LYS cc_start: 0.7121 (mtpp) cc_final: 0.6596 (mmtt) REVERT: C 179 ASP cc_start: 0.7414 (p0) cc_final: 0.7135 (p0) REVERT: C 260 GLN cc_start: 0.7097 (pt0) cc_final: 0.6876 (pp30) REVERT: C 271 ARG cc_start: 0.7112 (ttm110) cc_final: 0.6771 (mtm-85) REVERT: C 274 GLU cc_start: 0.7709 (tt0) cc_final: 0.7458 (tt0) REVERT: C 276 ARG cc_start: 0.7387 (mmm-85) cc_final: 0.7175 (mmm160) REVERT: C 279 ASP cc_start: 0.6626 (m-30) cc_final: 0.6356 (m-30) REVERT: D 109 GLU cc_start: 0.5208 (mt-10) cc_final: 0.4782 (tp30) REVERT: D 119 GLU cc_start: 0.5450 (tm-30) cc_final: 0.5165 (tm-30) REVERT: D 123 GLU cc_start: 0.5123 (tt0) cc_final: 0.4641 (tm-30) REVERT: D 177 LYS cc_start: 0.7124 (mtpp) cc_final: 0.6624 (mmtt) REVERT: D 179 ASP cc_start: 0.7412 (p0) cc_final: 0.7101 (p0) REVERT: D 271 ARG cc_start: 0.7141 (ttm110) cc_final: 0.6896 (mtm-85) REVERT: D 279 ASP cc_start: 0.6803 (m-30) cc_final: 0.6484 (m-30) REVERT: D 281 MET cc_start: 0.6670 (mmp) cc_final: 0.6428 (mmm) REVERT: E 143 GLU cc_start: 0.7375 (mt-10) cc_final: 0.6922 (tt0) REVERT: E 147 HIS cc_start: 0.7445 (t-90) cc_final: 0.7202 (t-170) REVERT: E 148 HIS cc_start: 0.7269 (t70) cc_final: 0.7060 (t-90) REVERT: E 155 THR cc_start: 0.6817 (m) cc_final: 0.6369 (t) REVERT: E 200 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7758 (tttt) REVERT: E 215 GLU cc_start: 0.7700 (pt0) cc_final: 0.7204 (pt0) REVERT: F 50 ASP cc_start: 0.7039 (m-30) cc_final: 0.6812 (m-30) REVERT: F 143 GLU cc_start: 0.7351 (mt-10) cc_final: 0.6952 (mt-10) REVERT: F 147 HIS cc_start: 0.7360 (t-90) cc_final: 0.7133 (t-170) REVERT: F 215 GLU cc_start: 0.7561 (pt0) cc_final: 0.7215 (pt0) REVERT: G 143 GLU cc_start: 0.7375 (mt-10) cc_final: 0.6965 (tt0) REVERT: G 147 HIS cc_start: 0.7570 (t-90) cc_final: 0.7312 (t-170) REVERT: G 148 HIS cc_start: 0.7290 (t70) cc_final: 0.7064 (t-170) REVERT: G 155 THR cc_start: 0.6845 (m) cc_final: 0.6441 (t) REVERT: G 215 GLU cc_start: 0.7438 (pt0) cc_final: 0.7115 (pt0) REVERT: H 143 GLU cc_start: 0.7352 (mt-10) cc_final: 0.6883 (tt0) REVERT: H 147 HIS cc_start: 0.7483 (t-90) cc_final: 0.7248 (t-170) REVERT: H 215 GLU cc_start: 0.7574 (pt0) cc_final: 0.7263 (pt0) outliers start: 25 outliers final: 11 residues processed: 250 average time/residue: 0.6755 time to fit residues: 179.5391 Evaluate side-chains 256 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 237 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain E residue 76 ARG Chi-restraints excluded: chain E residue 200 LYS Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 139 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 128 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 57 optimal weight: 20.0000 chunk 120 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 GLN A 234 GLN A 275 ASN B 252 ASN C 275 ASN H 204 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.175276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.134307 restraints weight = 52686.811| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 4.56 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3453 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3453 r_free = 0.3453 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3452 r_free = 0.3452 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3452 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12225 Z= 0.164 Angle : 0.610 8.688 16442 Z= 0.309 Chirality : 0.041 0.215 1778 Planarity : 0.005 0.043 2066 Dihedral : 12.706 59.938 1921 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.67 % Allowed : 13.52 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.91 (0.23), residues: 1422 helix: 2.52 (0.15), residues: 1170 sheet: None (None), residues: 0 loop : -1.08 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 276 TYR 0.012 0.002 TYR G 67 PHE 0.010 0.002 PHE D 272 TRP 0.017 0.002 TRP C 200 HIS 0.005 0.002 HIS D 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (12225) covalent geometry : angle 0.60951 / 0.31 (16442) hydrogen bonds : bond 0.05515 / 3.78 ( 878) hydrogen bonds : angle 3.48563 / 2.49 ( 2644) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 245 time to evaluate : 0.357 Fit side-chains REVERT: A 108 LEU cc_start: 0.6701 (OUTLIER) cc_final: 0.6292 (mt) REVERT: A 109 GLU cc_start: 0.5359 (mt-10) cc_final: 0.5067 (tt0) REVERT: A 119 GLU cc_start: 0.5552 (tm-30) cc_final: 0.5249 (tm-30) REVERT: A 163 GLU cc_start: 0.6467 (mt-10) cc_final: 0.6229 (mt-10) REVERT: A 179 ASP cc_start: 0.7402 (p0) cc_final: 0.7085 (p0) REVERT: A 208 MET cc_start: 0.8038 (mtp) cc_final: 0.7661 (mtp) REVERT: A 271 ARG cc_start: 0.7157 (ttm110) cc_final: 0.6865 (mtm-85) REVERT: A 276 ARG cc_start: 0.7452 (mmm-85) cc_final: 0.7139 (mmm160) REVERT: A 279 ASP cc_start: 0.6551 (m-30) cc_final: 0.6138 (t70) REVERT: B 109 GLU cc_start: 0.5520 (mt-10) cc_final: 0.5044 (tp30) REVERT: B 119 GLU cc_start: 0.5811 (tm-30) cc_final: 0.4890 (tp30) REVERT: B 123 GLU cc_start: 0.5788 (OUTLIER) cc_final: 0.5113 (tm-30) REVERT: B 163 GLU cc_start: 0.6676 (mm-30) cc_final: 0.6352 (mt-10) REVERT: B 167 LEU cc_start: 0.6612 (OUTLIER) cc_final: 0.6362 (tp) REVERT: B 169 GLN cc_start: 0.6451 (mt0) cc_final: 0.6145 (pt0) REVERT: B 271 ARG cc_start: 0.7128 (ttm110) cc_final: 0.6922 (mtm-85) REVERT: B 279 ASP cc_start: 0.6793 (m-30) cc_final: 0.6482 (m-30) REVERT: B 281 MET cc_start: 0.6476 (OUTLIER) cc_final: 0.4417 (mpt) REVERT: B 283 MET cc_start: 0.3365 (mmm) cc_final: 0.2134 (ppp) REVERT: C 108 LEU cc_start: 0.6731 (OUTLIER) cc_final: 0.6427 (mt) REVERT: C 109 GLU cc_start: 0.5488 (mt-10) cc_final: 0.5023 (tp30) REVERT: C 119 GLU cc_start: 0.5557 (tm-30) cc_final: 0.5352 (tm-30) REVERT: C 123 GLU cc_start: 0.5878 (OUTLIER) cc_final: 0.5215 (tm-30) REVERT: C 162 GLU cc_start: 0.6529 (pt0) cc_final: 0.6244 (pt0) REVERT: C 163 GLU cc_start: 0.6861 (OUTLIER) cc_final: 0.6453 (mt-10) REVERT: C 164 GLU cc_start: 0.6993 (mt-10) cc_final: 0.6707 (mt-10) REVERT: C 177 LYS cc_start: 0.7212 (mtpp) cc_final: 0.6661 (mmtt) REVERT: C 179 ASP cc_start: 0.7398 (p0) cc_final: 0.7100 (p0) REVERT: C 208 MET cc_start: 0.8030 (mtp) cc_final: 0.7743 (mtp) REVERT: C 260 GLN cc_start: 0.7023 (pt0) cc_final: 0.6797 (pp30) REVERT: C 271 ARG cc_start: 0.7103 (ttm110) cc_final: 0.6809 (mtm-85) REVERT: C 274 GLU cc_start: 0.7743 (tt0) cc_final: 0.7462 (tt0) REVERT: C 276 ARG cc_start: 0.7459 (mmm-85) cc_final: 0.7213 (mmm160) REVERT: C 279 ASP cc_start: 0.6731 (m-30) cc_final: 0.6480 (m-30) REVERT: D 109 GLU cc_start: 0.5320 (mt-10) cc_final: 0.4846 (tp30) REVERT: D 119 GLU cc_start: 0.5465 (tm-30) cc_final: 0.5245 (tm-30) REVERT: D 177 LYS cc_start: 0.7143 (mtpp) cc_final: 0.6624 (mmtt) REVERT: D 179 ASP cc_start: 0.7435 (p0) cc_final: 0.7130 (p0) REVERT: D 271 ARG cc_start: 0.7135 (ttm110) cc_final: 0.6880 (mtm-85) REVERT: E 143 GLU cc_start: 0.7400 (mt-10) cc_final: 0.6950 (mt-10) REVERT: E 147 HIS cc_start: 0.7642 (t-90) cc_final: 0.7366 (t-170) REVERT: E 155 THR cc_start: 0.6778 (m) cc_final: 0.6357 (t) REVERT: E 200 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7862 (tttt) REVERT: E 215 GLU cc_start: 0.7801 (pt0) cc_final: 0.7355 (pt0) REVERT: F 147 HIS cc_start: 0.7559 (t-90) cc_final: 0.7262 (t-170) REVERT: F 215 GLU cc_start: 0.7633 (pt0) cc_final: 0.7356 (pt0) REVERT: G 143 GLU cc_start: 0.7375 (mt-10) cc_final: 0.6970 (mt-10) REVERT: G 147 HIS cc_start: 0.7699 (t-90) cc_final: 0.7402 (t-170) REVERT: G 155 THR cc_start: 0.6830 (m) cc_final: 0.6382 (t) REVERT: G 215 GLU cc_start: 0.7684 (pt0) cc_final: 0.7426 (pt0) REVERT: H 143 GLU cc_start: 0.7345 (mt-10) cc_final: 0.6919 (mt-10) REVERT: H 147 HIS cc_start: 0.7634 (t-90) cc_final: 0.7365 (t-170) outliers start: 30 outliers final: 14 residues processed: 255 average time/residue: 0.7211 time to fit residues: 195.4812 Evaluate side-chains 260 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 238 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 246 MET Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 200 LYS Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 49 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 8.9990 chunk 46 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 59 optimal weight: 7.9990 chunk 136 optimal weight: 9.9990 chunk 30 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 106 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 119 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 234 GLN A 275 ASN B 275 ASN C 275 ASN E 93 HIS E 148 HIS H 93 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.177898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.137523 restraints weight = 55538.685| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 4.64 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3487 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3487 r_free = 0.3487 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3487 r_free = 0.3487 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3487 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 12225 Z= 0.106 Angle : 0.493 8.855 16442 Z= 0.253 Chirality : 0.036 0.117 1778 Planarity : 0.004 0.051 2066 Dihedral : 11.692 59.988 1921 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.81 % Allowed : 14.64 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.51 (0.23), residues: 1422 helix: 3.00 (0.15), residues: 1154 sheet: None (None), residues: 0 loop : -0.99 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 159 TYR 0.009 0.001 TYR E 67 PHE 0.012 0.001 PHE D 110 TRP 0.014 0.001 TRP B 240 HIS 0.003 0.001 HIS G 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.11 (12225) covalent geometry : angle 0.49311 / 0.25 (16442) hydrogen bonds : bond 0.04163 / 2.82 ( 878) hydrogen bonds : angle 3.19450 / 2.29 ( 2644) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 248 time to evaluate : 0.311 Fit side-chains REVERT: A 108 LEU cc_start: 0.6619 (OUTLIER) cc_final: 0.6190 (mt) REVERT: A 109 GLU cc_start: 0.5236 (mt-10) cc_final: 0.4909 (tt0) REVERT: A 119 GLU cc_start: 0.5513 (tm-30) cc_final: 0.5232 (tm-30) REVERT: A 163 GLU cc_start: 0.6442 (mt-10) cc_final: 0.6188 (mt-10) REVERT: A 172 GLN cc_start: 0.4931 (mt0) cc_final: 0.4448 (mt0) REVERT: A 179 ASP cc_start: 0.7404 (p0) cc_final: 0.7091 (p0) REVERT: A 208 MET cc_start: 0.7904 (mtp) cc_final: 0.7508 (mtp) REVERT: A 271 ARG cc_start: 0.7083 (ttm110) cc_final: 0.6786 (mtm-85) REVERT: A 276 ARG cc_start: 0.7281 (mmm-85) cc_final: 0.6983 (mmm160) REVERT: A 279 ASP cc_start: 0.6489 (m-30) cc_final: 0.6077 (t70) REVERT: B 108 LEU cc_start: 0.6815 (mm) cc_final: 0.6440 (mt) REVERT: B 109 GLU cc_start: 0.5453 (mt-10) cc_final: 0.4972 (tp30) REVERT: B 119 GLU cc_start: 0.5745 (tm-30) cc_final: 0.4753 (tp30) REVERT: B 163 GLU cc_start: 0.6692 (mm-30) cc_final: 0.6413 (mt-10) REVERT: B 169 GLN cc_start: 0.6451 (mt0) cc_final: 0.6144 (pt0) REVERT: B 271 ARG cc_start: 0.7114 (ttm110) cc_final: 0.6841 (mtm-85) REVERT: B 279 ASP cc_start: 0.6713 (m-30) cc_final: 0.6283 (t70) REVERT: B 281 MET cc_start: 0.6563 (OUTLIER) cc_final: 0.4736 (mpt) REVERT: B 283 MET cc_start: 0.3303 (mmm) cc_final: 0.2083 (ppp) REVERT: C 108 LEU cc_start: 0.6756 (OUTLIER) cc_final: 0.6451 (mt) REVERT: C 109 GLU cc_start: 0.5466 (mt-10) cc_final: 0.4958 (tp30) REVERT: C 119 GLU cc_start: 0.5533 (tm-30) cc_final: 0.4637 (tp30) REVERT: C 123 GLU cc_start: 0.5636 (OUTLIER) cc_final: 0.5096 (tm-30) REVERT: C 162 GLU cc_start: 0.6560 (pt0) cc_final: 0.6228 (pt0) REVERT: C 163 GLU cc_start: 0.6806 (mm-30) cc_final: 0.6485 (mt-10) REVERT: C 164 GLU cc_start: 0.7057 (mt-10) cc_final: 0.6776 (mt-10) REVERT: C 177 LYS cc_start: 0.7143 (mtpp) cc_final: 0.6636 (mmtt) REVERT: C 179 ASP cc_start: 0.7444 (p0) cc_final: 0.7140 (p0) REVERT: C 260 GLN cc_start: 0.7022 (pt0) cc_final: 0.6731 (pp30) REVERT: C 271 ARG cc_start: 0.7119 (ttm110) cc_final: 0.6807 (mtm-85) REVERT: C 274 GLU cc_start: 0.7695 (tt0) cc_final: 0.7457 (tt0) REVERT: C 276 ARG cc_start: 0.7474 (mmm-85) cc_final: 0.7257 (mmm160) REVERT: C 279 ASP cc_start: 0.6679 (m-30) cc_final: 0.6456 (m-30) REVERT: D 108 LEU cc_start: 0.6576 (mm) cc_final: 0.6213 (mt) REVERT: D 109 GLU cc_start: 0.5242 (mt-10) cc_final: 0.4754 (tp30) REVERT: D 119 GLU cc_start: 0.5468 (tm-30) cc_final: 0.5262 (tm-30) REVERT: D 123 GLU cc_start: 0.5373 (tt0) cc_final: 0.4900 (tm-30) REVERT: D 177 LYS cc_start: 0.7123 (mtpp) cc_final: 0.6626 (mmtt) REVERT: D 179 ASP cc_start: 0.7460 (p0) cc_final: 0.7166 (p0) REVERT: D 271 ARG cc_start: 0.7124 (ttm110) cc_final: 0.6755 (mtm-85) REVERT: E 76 ARG cc_start: 0.7041 (OUTLIER) cc_final: 0.6730 (mtt180) REVERT: E 143 GLU cc_start: 0.7327 (mt-10) cc_final: 0.6916 (tt0) REVERT: E 147 HIS cc_start: 0.7481 (t-90) cc_final: 0.7241 (t-170) REVERT: E 155 THR cc_start: 0.6545 (m) cc_final: 0.6255 (t) REVERT: E 215 GLU cc_start: 0.7709 (pt0) cc_final: 0.7214 (pt0) REVERT: F 143 GLU cc_start: 0.7271 (mt-10) cc_final: 0.6861 (mt-10) REVERT: F 147 HIS cc_start: 0.7424 (t-90) cc_final: 0.7161 (t-170) REVERT: F 148 HIS cc_start: 0.7233 (t70) cc_final: 0.6978 (t-170) REVERT: F 155 THR cc_start: 0.6489 (m) cc_final: 0.6085 (t) REVERT: F 215 GLU cc_start: 0.7556 (pt0) cc_final: 0.7225 (pt0) REVERT: G 135 MET cc_start: 0.6891 (mmt) cc_final: 0.6575 (mmm) REVERT: G 143 GLU cc_start: 0.7314 (mt-10) cc_final: 0.6897 (tt0) REVERT: G 147 HIS cc_start: 0.7566 (t-90) cc_final: 0.7289 (t-170) REVERT: G 148 HIS cc_start: 0.7208 (t70) cc_final: 0.6971 (t-170) REVERT: G 155 THR cc_start: 0.6710 (m) cc_final: 0.6372 (t) REVERT: G 215 GLU cc_start: 0.7541 (pt0) cc_final: 0.7243 (pt0) REVERT: H 143 GLU cc_start: 0.7268 (mt-10) cc_final: 0.6864 (mt-10) REVERT: H 147 HIS cc_start: 0.7442 (t-90) cc_final: 0.7194 (t-170) REVERT: H 148 HIS cc_start: 0.7245 (t70) cc_final: 0.7011 (t-170) REVERT: H 215 GLU cc_start: 0.7499 (pt0) cc_final: 0.7204 (pt0) outliers start: 20 outliers final: 10 residues processed: 254 average time/residue: 0.7362 time to fit residues: 198.6760 Evaluate side-chains 256 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 241 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain E residue 76 ARG Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 49 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 9 optimal weight: 0.0030 chunk 96 optimal weight: 0.6980 chunk 120 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 chunk 88 optimal weight: 8.9990 chunk 56 optimal weight: 9.9990 chunk 86 optimal weight: 0.9980 chunk 131 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 overall best weight: 1.1192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 234 GLN A 275 ASN B 275 ASN C 234 GLN C 275 ASN E 148 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.177873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.136507 restraints weight = 49077.092| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 4.39 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3489 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3489 r_free = 0.3489 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3489 r_free = 0.3489 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3489 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12225 Z= 0.109 Angle : 0.503 8.851 16442 Z= 0.256 Chirality : 0.037 0.130 1778 Planarity : 0.004 0.049 2066 Dihedral : 11.219 59.809 1921 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.55 % Allowed : 15.25 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.60 (0.23), residues: 1422 helix: 3.07 (0.15), residues: 1154 sheet: None (None), residues: 0 loop : -0.98 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 159 TYR 0.013 0.001 TYR H 212 PHE 0.015 0.001 PHE D 110 TRP 0.013 0.001 TRP B 240 HIS 0.004 0.001 HIS H 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.11 (12225) covalent geometry : angle 0.50325 / 0.26 (16442) hydrogen bonds : bond 0.04187 / 2.84 ( 878) hydrogen bonds : angle 3.19015 / 2.29 ( 2644) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 243 time to evaluate : 0.349 Fit side-chains REVERT: A 108 LEU cc_start: 0.6670 (OUTLIER) cc_final: 0.6264 (mt) REVERT: A 109 GLU cc_start: 0.5360 (mt-10) cc_final: 0.5056 (tt0) REVERT: A 119 GLU cc_start: 0.5505 (tm-30) cc_final: 0.5234 (tm-30) REVERT: A 163 GLU cc_start: 0.6461 (mt-10) cc_final: 0.6189 (mt-10) REVERT: A 172 GLN cc_start: 0.4851 (mt0) cc_final: 0.4433 (mt0) REVERT: A 179 ASP cc_start: 0.7427 (p0) cc_final: 0.7099 (p0) REVERT: A 208 MET cc_start: 0.7871 (mtp) cc_final: 0.7473 (mtp) REVERT: A 271 ARG cc_start: 0.7126 (ttm110) cc_final: 0.6872 (mtm-85) REVERT: A 276 ARG cc_start: 0.7261 (mmm-85) cc_final: 0.6895 (mtp85) REVERT: A 279 ASP cc_start: 0.6399 (m-30) cc_final: 0.6056 (t70) REVERT: B 108 LEU cc_start: 0.6718 (mm) cc_final: 0.6344 (mt) REVERT: B 109 GLU cc_start: 0.5447 (mt-10) cc_final: 0.4943 (tp30) REVERT: B 119 GLU cc_start: 0.5821 (tm-30) cc_final: 0.4843 (tp30) REVERT: B 163 GLU cc_start: 0.6679 (mm-30) cc_final: 0.6401 (mt-10) REVERT: B 169 GLN cc_start: 0.6458 (mt0) cc_final: 0.6170 (pt0) REVERT: B 271 ARG cc_start: 0.7101 (ttm110) cc_final: 0.6837 (mtm-85) REVERT: B 281 MET cc_start: 0.6555 (OUTLIER) cc_final: 0.4651 (mpt) REVERT: B 283 MET cc_start: 0.3261 (mmm) cc_final: 0.2096 (ppp) REVERT: C 108 LEU cc_start: 0.6766 (OUTLIER) cc_final: 0.6451 (mt) REVERT: C 109 GLU cc_start: 0.5467 (mt-10) cc_final: 0.4978 (tp30) REVERT: C 119 GLU cc_start: 0.5545 (tm-30) cc_final: 0.4654 (tp30) REVERT: C 123 GLU cc_start: 0.5618 (OUTLIER) cc_final: 0.5093 (tm-30) REVERT: C 162 GLU cc_start: 0.6594 (pt0) cc_final: 0.6292 (pt0) REVERT: C 163 GLU cc_start: 0.6781 (mm-30) cc_final: 0.6460 (mt-10) REVERT: C 164 GLU cc_start: 0.7040 (mt-10) cc_final: 0.6757 (mt-10) REVERT: C 177 LYS cc_start: 0.7093 (mtpp) cc_final: 0.6614 (mmtt) REVERT: C 179 ASP cc_start: 0.7463 (p0) cc_final: 0.7162 (p0) REVERT: C 271 ARG cc_start: 0.7135 (ttm110) cc_final: 0.6843 (mtm-85) REVERT: C 274 GLU cc_start: 0.7719 (tt0) cc_final: 0.7459 (tt0) REVERT: C 279 ASP cc_start: 0.6634 (m-30) cc_final: 0.6412 (m-30) REVERT: D 108 LEU cc_start: 0.6603 (mm) cc_final: 0.6245 (mt) REVERT: D 109 GLU cc_start: 0.5310 (mt-10) cc_final: 0.4827 (tp30) REVERT: D 119 GLU cc_start: 0.5497 (tm-30) cc_final: 0.5284 (tm-30) REVERT: D 123 GLU cc_start: 0.5282 (tt0) cc_final: 0.4919 (tm-30) REVERT: D 177 LYS cc_start: 0.7058 (mtpp) cc_final: 0.6600 (mmtt) REVERT: D 179 ASP cc_start: 0.7479 (p0) cc_final: 0.7176 (p0) REVERT: D 271 ARG cc_start: 0.7143 (ttm110) cc_final: 0.6829 (mtm-85) REVERT: E 143 GLU cc_start: 0.7251 (mt-10) cc_final: 0.6901 (mt-10) REVERT: E 147 HIS cc_start: 0.7494 (t-90) cc_final: 0.7242 (t-170) REVERT: E 155 THR cc_start: 0.6512 (m) cc_final: 0.6255 (t) REVERT: F 143 GLU cc_start: 0.7270 (mt-10) cc_final: 0.6889 (mt-10) REVERT: F 147 HIS cc_start: 0.7395 (t-90) cc_final: 0.7135 (t-170) REVERT: F 148 HIS cc_start: 0.7183 (t70) cc_final: 0.6913 (t-170) REVERT: F 155 THR cc_start: 0.6575 (m) cc_final: 0.6187 (t) REVERT: F 215 GLU cc_start: 0.7453 (pt0) cc_final: 0.7108 (pt0) REVERT: G 135 MET cc_start: 0.6892 (mmt) cc_final: 0.6571 (mmm) REVERT: G 143 GLU cc_start: 0.7212 (mt-10) cc_final: 0.6854 (mt-10) REVERT: G 147 HIS cc_start: 0.7569 (t-90) cc_final: 0.7288 (t-170) REVERT: G 148 HIS cc_start: 0.7184 (t70) cc_final: 0.6917 (t-170) REVERT: G 155 THR cc_start: 0.6599 (m) cc_final: 0.6294 (t) REVERT: G 215 GLU cc_start: 0.7487 (pt0) cc_final: 0.7168 (pt0) REVERT: H 135 MET cc_start: 0.6798 (mmt) cc_final: 0.6469 (mmm) REVERT: H 143 GLU cc_start: 0.7245 (mt-10) cc_final: 0.6863 (mt-10) REVERT: H 147 HIS cc_start: 0.7429 (t-90) cc_final: 0.7191 (t-170) REVERT: H 148 HIS cc_start: 0.7214 (t70) cc_final: 0.6972 (t-170) REVERT: H 215 GLU cc_start: 0.7478 (pt0) cc_final: 0.7185 (pt0) outliers start: 17 outliers final: 9 residues processed: 247 average time/residue: 0.7205 time to fit residues: 188.9433 Evaluate side-chains 250 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 237 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 246 MET Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 49 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 79 optimal weight: 0.7980 chunk 127 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 62 optimal weight: 0.8980 chunk 134 optimal weight: 0.0270 chunk 126 optimal weight: 5.9990 chunk 123 optimal weight: 0.8980 chunk 139 optimal weight: 7.9990 chunk 25 optimal weight: 8.9990 chunk 13 optimal weight: 0.4980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 234 GLN A 275 ASN B 275 ASN C 234 GLN C 275 ASN E 148 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.179791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.136685 restraints weight = 51103.525| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 5.41 r_work: 0.3108 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3108 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3108 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 12225 Z= 0.097 Angle : 0.474 8.738 16442 Z= 0.242 Chirality : 0.035 0.114 1778 Planarity : 0.004 0.055 2066 Dihedral : 10.514 57.790 1921 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.46 % Allowed : 15.68 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.72 (0.23), residues: 1422 helix: 3.17 (0.15), residues: 1158 sheet: None (None), residues: 0 loop : -1.10 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 76 TYR 0.011 0.001 TYR B 196 PHE 0.013 0.001 PHE D 110 TRP 0.015 0.001 TRP B 240 HIS 0.003 0.001 HIS C 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00188 / 0.10 (12225) covalent geometry : angle 0.47401 / 0.24 (16442) hydrogen bonds : bond 0.03659 / 2.47 ( 878) hydrogen bonds : angle 3.06449 / 2.20 ( 2644) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 240 time to evaluate : 0.393 Fit side-chains REVERT: A 108 LEU cc_start: 0.6349 (OUTLIER) cc_final: 0.5910 (mt) REVERT: A 109 GLU cc_start: 0.5372 (mt-10) cc_final: 0.4900 (tt0) REVERT: A 119 GLU cc_start: 0.5240 (tm-30) cc_final: 0.5001 (tm-30) REVERT: A 163 GLU cc_start: 0.6702 (mt-10) cc_final: 0.6419 (mt-10) REVERT: A 172 GLN cc_start: 0.4973 (mt0) cc_final: 0.4449 (mt0) REVERT: A 179 ASP cc_start: 0.7823 (p0) cc_final: 0.7482 (p0) REVERT: A 271 ARG cc_start: 0.7696 (ttm110) cc_final: 0.7350 (mtm-85) REVERT: A 276 ARG cc_start: 0.7245 (mmm-85) cc_final: 0.6803 (mtp85) REVERT: B 108 LEU cc_start: 0.6419 (mm) cc_final: 0.5979 (mt) REVERT: B 109 GLU cc_start: 0.5438 (mt-10) cc_final: 0.4694 (tp30) REVERT: B 119 GLU cc_start: 0.5287 (tm-30) cc_final: 0.4322 (tp30) REVERT: B 163 GLU cc_start: 0.7064 (mm-30) cc_final: 0.6496 (mt-10) REVERT: B 169 GLN cc_start: 0.6318 (mt0) cc_final: 0.5962 (pt0) REVERT: B 271 ARG cc_start: 0.7694 (ttm110) cc_final: 0.7345 (mtm-85) REVERT: B 281 MET cc_start: 0.6482 (OUTLIER) cc_final: 0.4708 (mpt) REVERT: B 283 MET cc_start: 0.3282 (mmm) cc_final: 0.2143 (ppp) REVERT: C 108 LEU cc_start: 0.6430 (OUTLIER) cc_final: 0.6066 (mt) REVERT: C 109 GLU cc_start: 0.5514 (mt-10) cc_final: 0.4768 (tp30) REVERT: C 119 GLU cc_start: 0.5206 (tm-30) cc_final: 0.4252 (tp30) REVERT: C 123 GLU cc_start: 0.5333 (OUTLIER) cc_final: 0.4551 (tm-30) REVERT: C 162 GLU cc_start: 0.7159 (pt0) cc_final: 0.6699 (pt0) REVERT: C 163 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6634 (mt-10) REVERT: C 164 GLU cc_start: 0.7082 (mt-10) cc_final: 0.6796 (mt-10) REVERT: C 177 LYS cc_start: 0.7271 (mtpp) cc_final: 0.6828 (mmtt) REVERT: C 179 ASP cc_start: 0.7806 (p0) cc_final: 0.7453 (p0) REVERT: C 208 MET cc_start: 0.8330 (mtp) cc_final: 0.8046 (mtp) REVERT: C 271 ARG cc_start: 0.7644 (ttm110) cc_final: 0.7285 (mtm-85) REVERT: C 274 GLU cc_start: 0.8179 (tt0) cc_final: 0.7916 (tt0) REVERT: D 108 LEU cc_start: 0.6353 (OUTLIER) cc_final: 0.5937 (mt) REVERT: D 109 GLU cc_start: 0.5340 (mt-10) cc_final: 0.4613 (tp30) REVERT: D 123 GLU cc_start: 0.4933 (tt0) cc_final: 0.4323 (tm-30) REVERT: D 177 LYS cc_start: 0.7255 (mtpp) cc_final: 0.6849 (mmtt) REVERT: D 179 ASP cc_start: 0.7822 (p0) cc_final: 0.7493 (p0) REVERT: D 271 ARG cc_start: 0.7668 (ttm110) cc_final: 0.7281 (mtm-85) REVERT: E 76 ARG cc_start: 0.7484 (mtt180) cc_final: 0.7219 (mmm-85) REVERT: E 135 MET cc_start: 0.7249 (mmt) cc_final: 0.7004 (mmm) REVERT: E 143 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7382 (mt-10) REVERT: E 155 THR cc_start: 0.6447 (m) cc_final: 0.6184 (t) REVERT: F 143 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7384 (mt-10) REVERT: F 147 HIS cc_start: 0.7602 (t-90) cc_final: 0.7369 (t-170) REVERT: F 148 HIS cc_start: 0.7306 (t70) cc_final: 0.7036 (t-170) REVERT: F 155 THR cc_start: 0.6350 (m) cc_final: 0.5955 (t) REVERT: F 215 GLU cc_start: 0.7644 (pt0) cc_final: 0.7390 (pt0) REVERT: G 143 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7364 (mt-10) REVERT: G 147 HIS cc_start: 0.7747 (t-90) cc_final: 0.7503 (t-170) REVERT: G 148 HIS cc_start: 0.7329 (t70) cc_final: 0.7060 (t-170) REVERT: G 155 THR cc_start: 0.6450 (m) cc_final: 0.6192 (t) REVERT: G 215 GLU cc_start: 0.7618 (pt0) cc_final: 0.7326 (pt0) REVERT: H 143 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7336 (mt-10) REVERT: H 147 HIS cc_start: 0.7587 (t-90) cc_final: 0.7356 (t-170) REVERT: H 148 HIS cc_start: 0.7301 (t70) cc_final: 0.7072 (t-170) outliers start: 16 outliers final: 7 residues processed: 244 average time/residue: 0.6905 time to fit residues: 179.1508 Evaluate side-chains 253 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 241 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 226 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 26 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 73 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 106 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 GLN A 275 ASN B 275 ASN C 165 GLN C 234 GLN C 275 ASN E 148 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.178114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.137482 restraints weight = 54020.114| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 4.67 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3513 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3513 r_free = 0.3513 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3513 r_free = 0.3513 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.3513 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12225 Z= 0.113 Angle : 0.511 8.689 16442 Z= 0.260 Chirality : 0.037 0.139 1778 Planarity : 0.004 0.048 2066 Dihedral : 10.659 58.904 1921 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.29 % Allowed : 16.11 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.63 (0.23), residues: 1422 helix: 3.09 (0.15), residues: 1154 sheet: None (None), residues: 0 loop : -0.98 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 159 TYR 0.010 0.001 TYR E 67 PHE 0.012 0.001 PHE D 110 TRP 0.014 0.002 TRP B 200 HIS 0.004 0.001 HIS H 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (12225) covalent geometry : angle 0.51089 / 0.26 (16442) hydrogen bonds : bond 0.04278 / 2.91 ( 878) hydrogen bonds : angle 3.19209 / 2.29 ( 2644) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 244 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: A 108 LEU cc_start: 0.6621 (OUTLIER) cc_final: 0.6242 (mt) REVERT: A 109 GLU cc_start: 0.5353 (mt-10) cc_final: 0.5025 (tt0) REVERT: A 119 GLU cc_start: 0.5521 (tm-30) cc_final: 0.5243 (tm-30) REVERT: A 163 GLU cc_start: 0.6488 (mt-10) cc_final: 0.6188 (mt-10) REVERT: A 172 GLN cc_start: 0.4833 (mt0) cc_final: 0.4413 (mt0) REVERT: A 179 ASP cc_start: 0.7358 (p0) cc_final: 0.7045 (p0) REVERT: A 208 MET cc_start: 0.7891 (mtp) cc_final: 0.7527 (mtp) REVERT: A 271 ARG cc_start: 0.7098 (ttm110) cc_final: 0.6768 (mtm-85) REVERT: A 276 ARG cc_start: 0.7241 (mmm-85) cc_final: 0.6875 (mtp85) REVERT: B 108 LEU cc_start: 0.6658 (mm) cc_final: 0.6255 (mt) REVERT: B 109 GLU cc_start: 0.5330 (mt-10) cc_final: 0.4856 (tp30) REVERT: B 119 GLU cc_start: 0.5701 (tm-30) cc_final: 0.4806 (tp30) REVERT: B 163 GLU cc_start: 0.6631 (mm-30) cc_final: 0.6347 (mt-10) REVERT: B 169 GLN cc_start: 0.6446 (mt0) cc_final: 0.6162 (pt0) REVERT: B 271 ARG cc_start: 0.7080 (ttm110) cc_final: 0.6714 (mtm-85) REVERT: B 281 MET cc_start: 0.6505 (OUTLIER) cc_final: 0.4620 (mpt) REVERT: B 283 MET cc_start: 0.3324 (mmm) cc_final: 0.2183 (ppp) REVERT: C 109 GLU cc_start: 0.5492 (mt-10) cc_final: 0.4952 (tp30) REVERT: C 119 GLU cc_start: 0.5536 (tm-30) cc_final: 0.4649 (tp30) REVERT: C 123 GLU cc_start: 0.5629 (OUTLIER) cc_final: 0.5085 (tm-30) REVERT: C 162 GLU cc_start: 0.6593 (pt0) cc_final: 0.6256 (pt0) REVERT: C 163 GLU cc_start: 0.6755 (mm-30) cc_final: 0.6408 (mt-10) REVERT: C 164 GLU cc_start: 0.7013 (mt-10) cc_final: 0.6731 (mt-10) REVERT: C 177 LYS cc_start: 0.7059 (mtpp) cc_final: 0.6586 (mmtt) REVERT: C 179 ASP cc_start: 0.7481 (p0) cc_final: 0.7149 (p0) REVERT: C 271 ARG cc_start: 0.7113 (ttm110) cc_final: 0.6825 (mtm-85) REVERT: C 274 GLU cc_start: 0.7715 (tt0) cc_final: 0.7448 (tt0) REVERT: D 108 LEU cc_start: 0.6612 (OUTLIER) cc_final: 0.6249 (mt) REVERT: D 109 GLU cc_start: 0.5300 (mt-10) cc_final: 0.4799 (tp30) REVERT: D 123 GLU cc_start: 0.5253 (tt0) cc_final: 0.4885 (tm-30) REVERT: D 177 LYS cc_start: 0.7044 (mtpp) cc_final: 0.6618 (mmtt) REVERT: D 179 ASP cc_start: 0.7456 (p0) cc_final: 0.7143 (p0) REVERT: D 271 ARG cc_start: 0.7151 (ttm110) cc_final: 0.6836 (mtm-85) REVERT: E 143 GLU cc_start: 0.7303 (mt-10) cc_final: 0.6945 (mt-10) REVERT: E 155 THR cc_start: 0.6447 (m) cc_final: 0.6207 (t) REVERT: F 143 GLU cc_start: 0.7289 (mt-10) cc_final: 0.6954 (mt-10) REVERT: F 147 HIS cc_start: 0.7410 (t-90) cc_final: 0.7142 (t-170) REVERT: F 148 HIS cc_start: 0.7230 (t70) cc_final: 0.6966 (t-170) REVERT: F 155 THR cc_start: 0.6522 (m) cc_final: 0.6170 (t) REVERT: F 215 GLU cc_start: 0.7460 (pt0) cc_final: 0.7194 (pt0) REVERT: G 135 MET cc_start: 0.6932 (mmt) cc_final: 0.6586 (mmm) REVERT: G 143 GLU cc_start: 0.7332 (mt-10) cc_final: 0.6984 (mt-10) REVERT: G 147 HIS cc_start: 0.7567 (t-90) cc_final: 0.7287 (t-170) REVERT: G 148 HIS cc_start: 0.7279 (t70) cc_final: 0.6997 (t-170) REVERT: G 155 THR cc_start: 0.6620 (m) cc_final: 0.6359 (t) REVERT: G 215 GLU cc_start: 0.7488 (pt0) cc_final: 0.7146 (pt0) REVERT: H 143 GLU cc_start: 0.7257 (mt-10) cc_final: 0.6934 (mt-10) REVERT: H 147 HIS cc_start: 0.7378 (t-90) cc_final: 0.7135 (t-170) REVERT: H 148 HIS cc_start: 0.7205 (t70) cc_final: 0.6971 (t-170) outliers start: 14 outliers final: 8 residues processed: 247 average time/residue: 0.6859 time to fit residues: 180.1795 Evaluate side-chains 248 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 236 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 246 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 66 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 83 optimal weight: 7.9990 chunk 137 optimal weight: 0.0030 chunk 28 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 3 optimal weight: 40.0000 chunk 94 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 overall best weight: 1.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 GLN A 275 ASN B 275 ASN C 234 GLN C 275 ASN E 148 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.177623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.136398 restraints weight = 46759.155| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 4.29 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3499 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3499 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12225 Z= 0.119 Angle : 0.526 8.660 16442 Z= 0.268 Chirality : 0.037 0.153 1778 Planarity : 0.004 0.046 2066 Dihedral : 10.886 57.087 1921 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.29 % Allowed : 16.11 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.53 (0.23), residues: 1422 helix: 3.02 (0.15), residues: 1154 sheet: None (None), residues: 0 loop : -0.99 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 159 TYR 0.010 0.001 TYR E 67 PHE 0.013 0.002 PHE D 110 TRP 0.014 0.002 TRP C 200 HIS 0.004 0.001 HIS G 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (12225) covalent geometry : angle 0.52552 / 0.27 (16442) hydrogen bonds : bond 0.04475 / 3.04 ( 878) hydrogen bonds : angle 3.25744 / 2.33 ( 2644) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 236 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 108 LEU cc_start: 0.6635 (OUTLIER) cc_final: 0.6247 (mt) REVERT: A 109 GLU cc_start: 0.5319 (mt-10) cc_final: 0.5003 (tt0) REVERT: A 119 GLU cc_start: 0.5526 (tm-30) cc_final: 0.5254 (tm-30) REVERT: A 163 GLU cc_start: 0.6433 (mt-10) cc_final: 0.6150 (mt-10) REVERT: A 179 ASP cc_start: 0.7409 (p0) cc_final: 0.7084 (p0) REVERT: A 208 MET cc_start: 0.7896 (mtp) cc_final: 0.7541 (mtp) REVERT: A 271 ARG cc_start: 0.7144 (ttm110) cc_final: 0.6887 (mtm-85) REVERT: A 276 ARG cc_start: 0.7244 (mmm-85) cc_final: 0.6861 (mtp85) REVERT: B 108 LEU cc_start: 0.6675 (mm) cc_final: 0.6310 (mt) REVERT: B 109 GLU cc_start: 0.5429 (mt-10) cc_final: 0.4947 (tp30) REVERT: B 119 GLU cc_start: 0.5592 (tm-30) cc_final: 0.4751 (tp30) REVERT: B 163 GLU cc_start: 0.6673 (mm-30) cc_final: 0.6392 (mt-10) REVERT: B 169 GLN cc_start: 0.6474 (mt0) cc_final: 0.6188 (pt0) REVERT: B 271 ARG cc_start: 0.7112 (ttm110) cc_final: 0.6842 (mtm-85) REVERT: B 281 MET cc_start: 0.6340 (OUTLIER) cc_final: 0.4368 (mpt) REVERT: B 283 MET cc_start: 0.3336 (mmm) cc_final: 0.2203 (ppp) REVERT: C 108 LEU cc_start: 0.6708 (mm) cc_final: 0.6401 (mt) REVERT: C 109 GLU cc_start: 0.5555 (mt-10) cc_final: 0.5019 (tp30) REVERT: C 119 GLU cc_start: 0.5707 (tm-30) cc_final: 0.4849 (tp30) REVERT: C 123 GLU cc_start: 0.5647 (OUTLIER) cc_final: 0.5088 (tm-30) REVERT: C 162 GLU cc_start: 0.6630 (pt0) cc_final: 0.6312 (pt0) REVERT: C 163 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.6450 (mt-10) REVERT: C 164 GLU cc_start: 0.7031 (mt-10) cc_final: 0.6751 (mt-10) REVERT: C 177 LYS cc_start: 0.7076 (mtpp) cc_final: 0.6603 (mmtt) REVERT: C 179 ASP cc_start: 0.7500 (p0) cc_final: 0.7189 (p0) REVERT: C 271 ARG cc_start: 0.7116 (ttm110) cc_final: 0.6833 (mtm-85) REVERT: C 274 GLU cc_start: 0.7742 (tt0) cc_final: 0.7448 (tt0) REVERT: D 108 LEU cc_start: 0.6632 (OUTLIER) cc_final: 0.6273 (mt) REVERT: D 109 GLU cc_start: 0.5307 (mt-10) cc_final: 0.4837 (tp30) REVERT: D 123 GLU cc_start: 0.5282 (tt0) cc_final: 0.4951 (tm-30) REVERT: D 177 LYS cc_start: 0.7022 (mtpp) cc_final: 0.6608 (mmtt) REVERT: D 179 ASP cc_start: 0.7456 (p0) cc_final: 0.7143 (p0) REVERT: D 271 ARG cc_start: 0.7160 (ttm110) cc_final: 0.6792 (mtm-85) REVERT: E 143 GLU cc_start: 0.7285 (mt-10) cc_final: 0.6912 (mt-10) REVERT: E 155 THR cc_start: 0.6630 (m) cc_final: 0.6365 (t) REVERT: F 143 GLU cc_start: 0.7248 (mt-10) cc_final: 0.6917 (mt-10) REVERT: F 147 HIS cc_start: 0.7484 (t-90) cc_final: 0.7190 (t-170) REVERT: F 148 HIS cc_start: 0.7179 (t70) cc_final: 0.6897 (t-170) REVERT: F 155 THR cc_start: 0.6557 (m) cc_final: 0.6217 (t) REVERT: F 215 GLU cc_start: 0.7580 (pt0) cc_final: 0.7290 (pt0) REVERT: G 143 GLU cc_start: 0.7274 (mt-10) cc_final: 0.6909 (mt-10) REVERT: G 147 HIS cc_start: 0.7596 (t-90) cc_final: 0.7305 (t-170) REVERT: G 148 HIS cc_start: 0.7234 (t70) cc_final: 0.6990 (t-170) REVERT: G 155 THR cc_start: 0.6557 (m) cc_final: 0.6300 (t) REVERT: H 143 GLU cc_start: 0.7220 (mt-10) cc_final: 0.6877 (mt-10) REVERT: H 147 HIS cc_start: 0.7464 (t-90) cc_final: 0.7192 (t-170) REVERT: H 148 HIS cc_start: 0.7221 (t70) cc_final: 0.6994 (t-170) outliers start: 14 outliers final: 8 residues processed: 239 average time/residue: 0.6646 time to fit residues: 168.7337 Evaluate side-chains 248 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 235 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 246 MET Chi-restraints excluded: chain E residue 112 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 120 optimal weight: 0.0050 chunk 8 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 overall best weight: 2.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 275 ASN B 275 ASN C 234 GLN C 275 ASN E 148 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.176554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.134290 restraints weight = 47951.896| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 4.92 r_work: 0.3066 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3037 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3037 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12225 Z= 0.150 Angle : 0.595 9.364 16442 Z= 0.301 Chirality : 0.040 0.202 1778 Planarity : 0.005 0.043 2066 Dihedral : 11.687 59.847 1921 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.29 % Allowed : 16.19 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.22 (0.23), residues: 1422 helix: 2.75 (0.15), residues: 1162 sheet: None (None), residues: 0 loop : -0.95 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 46 TYR 0.013 0.002 TYR G 212 PHE 0.014 0.002 PHE D 110 TRP 0.017 0.002 TRP C 200 HIS 0.005 0.002 HIS D 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (12225) covalent geometry : angle 0.59488 / 0.30 (16442) hydrogen bonds : bond 0.05156 / 3.53 ( 878) hydrogen bonds : angle 3.44808 / 2.46 ( 2644) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4250.72 seconds wall clock time: 72 minutes 50.58 seconds (4370.58 seconds total)