Starting phenix.real_space_refine on Sun Mar 17 09:02:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sss_25413/03_2024/7sss_25413_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sss_25413/03_2024/7sss_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sss_25413/03_2024/7sss_25413.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sss_25413/03_2024/7sss_25413.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sss_25413/03_2024/7sss_25413_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sss_25413/03_2024/7sss_25413_updated.pdb" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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 Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/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: {'GLN:plan1': 2, 'GLU:plan': 1, '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: {'GLN:plan1': 2, 'GLU:plan': 1, '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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 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: {'GLN:plan1': 1, 'GLU:plan': 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: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 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: 104 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: 76 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEV:plan-1': 1, '8PP:plan-8': 1, 'PEV:plan-2': 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: 151 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: 138 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: 121 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEV:plan-1': 1, '8PP:plan-8': 1, '8PP:plan-9': 1, '8PP:plan-7': 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: 163 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: 135 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEV:plan-1': 2, '8PP:plan-8': 1, '8PP:plan-9': 1, '8PP:plan-7': 1, '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: 158 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEV:plan-1': 2, '8PP:plan-8': 1, '8PP:plan-9': 1, '8PP:plan-7': 1, '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: 11.57, per 1000 atoms: 0.95 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.53 Conformation dependent library (CDL) restraints added in 3.7 seconds 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... running ksdssp... Secondary structure from input PDB file: 58 helices and 0 sheets defined 76.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.86 Creating SS restraints... Processing helix chain 'A' and resid 96 through 109 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) removed outlier: 4.506A pdb=" N GLU A 109 " --> pdb=" O THR A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 126 Processing helix chain 'A' and resid 143 through 169 Processing helix chain 'A' and resid 178 through 196 removed outlier: 3.816A pdb=" N MET A 192 " --> pdb=" O THR A 188 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU A 193 " --> pdb=" O ARG A 189 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Proline residue: A 195 - end of helix Processing helix chain 'A' and resid 200 through 207 Processing helix chain 'A' and resid 213 through 230 Processing helix chain 'A' and resid 238 through 259 removed outlier: 3.846A pdb=" N ARG A 243 " --> pdb=" O TRP A 240 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG A 244 " --> pdb=" O TYR A 241 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 245 " --> pdb=" O THR A 242 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE A 250 " --> pdb=" O LEU A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 281 removed outlier: 5.803A pdb=" N ASP A 268 " --> pdb=" O ASP A 265 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP A 270 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG A 271 " --> pdb=" O ASP A 268 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP A 279 " --> pdb=" O ARG A 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 109 removed outlier: 3.505A pdb=" N GLN B 100 " --> pdb=" O GLU B 97 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B 104 " --> pdb=" O HIS B 101 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 108 " --> pdb=" O THR B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 114 No H-bonds generated for 'chain 'B' and resid 111 through 114' Processing helix chain 'B' and resid 118 through 126 Processing helix chain 'B' and resid 143 through 170 removed outlier: 3.586A pdb=" N LEU B 170 " --> pdb=" O LYS B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 196 removed outlier: 3.815A pdb=" N MET B 192 " --> pdb=" O THR B 188 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LEU B 193 " --> pdb=" O ARG B 189 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Proline residue: B 195 - end of helix Processing helix chain 'B' and resid 200 through 207 Processing helix chain 'B' and resid 213 through 230 Processing helix chain 'B' and resid 238 through 259 removed outlier: 3.850A pdb=" N ARG B 243 " --> pdb=" O TRP B 240 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG B 244 " --> pdb=" O TYR B 241 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA B 245 " --> pdb=" O THR B 242 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN B 252 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR B 253 " --> pdb=" O ILE B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 280 removed outlier: 5.827A pdb=" N ASP B 268 " --> pdb=" O ASP B 265 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TRP B 270 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG B 271 " --> pdb=" O ASP B 268 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP B 279 " --> pdb=" O AARG B 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 109 removed outlier: 3.580A pdb=" N LEU C 108 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLU C 109 " --> pdb=" O THR C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 126 Processing helix chain 'C' and resid 143 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 178 through 196 removed outlier: 3.827A pdb=" N MET C 192 " --> pdb=" O THR C 188 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU C 193 " --> pdb=" O ARG C 189 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILE C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Proline residue: C 195 - end of helix Processing helix chain 'C' and resid 200 through 207 Processing helix chain 'C' and resid 213 through 230 Processing helix chain 'C' and resid 238 through 259 removed outlier: 3.851A pdb=" N ARG C 243 " --> pdb=" O TRP C 240 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG C 244 " --> pdb=" O TYR C 241 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA C 245 " --> pdb=" O THR C 242 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN C 252 " --> pdb=" O ALA C 249 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR C 253 " --> pdb=" O ILE C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 281 removed outlier: 5.821A pdb=" N ASP C 268 " --> pdb=" O ASP C 265 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TRP C 270 " --> pdb=" O GLU C 267 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG C 271 " --> pdb=" O ASP C 268 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP C 279 " --> pdb=" O ARG C 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 109 removed outlier: 3.629A pdb=" N LEU D 108 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N GLU D 109 " --> pdb=" O THR D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 114 No H-bonds generated for 'chain 'D' and resid 111 through 114' Processing helix chain 'D' and resid 118 through 126 Processing helix chain 'D' and resid 143 through 169 Processing helix chain 'D' and resid 178 through 196 removed outlier: 3.822A pdb=" N MET D 192 " --> pdb=" O THR D 188 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU D 193 " --> pdb=" O ARG D 189 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ILE D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) Proline residue: D 195 - end of helix Processing helix chain 'D' and resid 200 through 207 Processing helix chain 'D' and resid 213 through 230 Processing helix chain 'D' and resid 238 through 259 removed outlier: 3.840A pdb=" N ARG D 243 " --> pdb=" O TRP D 240 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG D 244 " --> pdb=" O TYR D 241 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA D 245 " --> pdb=" O THR D 242 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN D 252 " --> pdb=" O ALA D 249 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR D 253 " --> pdb=" O ILE D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 281 removed outlier: 5.837A pdb=" N ASP D 268 " --> pdb=" O ASP D 265 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP D 270 " --> pdb=" O GLU D 267 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG D 271 " --> pdb=" O ASP D 268 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP D 279 " --> pdb=" O BARG D 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 74 removed outlier: 3.568A pdb=" N VAL E 73 " --> pdb=" O GLY E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 104 Processing helix chain 'E' and resid 112 through 125 removed outlier: 3.564A pdb=" N PHE E 120 " --> pdb=" O ASN E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 160 removed outlier: 4.026A pdb=" N GLU E 158 " --> pdb=" O ARG E 154 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU E 159 " --> pdb=" O THR E 155 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP E 160 " --> pdb=" O LEU E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 177 Processing helix chain 'E' and resid 194 through 216 removed outlier: 3.978A pdb=" N ARG E 216 " --> pdb=" O TYR E 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 73 Processing helix chain 'F' and resid 80 through 104 Processing helix chain 'F' and resid 112 through 125 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 131 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 165 through 179 removed outlier: 3.932A pdb=" N LEU F 179 " --> pdb=" O ARG F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 216 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 73 Processing helix chain 'G' and resid 80 through 104 Processing helix chain 'G' and resid 112 through 125 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 131 through 160 removed outlier: 3.991A pdb=" N GLU G 158 " --> pdb=" O ARG G 154 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU G 159 " --> pdb=" O THR G 155 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP G 160 " --> pdb=" O LEU G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 177 Processing helix chain 'G' and resid 194 through 216 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 73 Processing helix chain 'H' and resid 80 through 104 Processing helix chain 'H' and resid 112 through 125 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 131 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 165 through 177 Processing helix chain 'H' and resid 194 through 216 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) 786 hydrogen bonds defined for protein. 2033 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.27 Time building geometry restraints manager: 4.95 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: 99.52 - 106.47: 352 106.47 - 113.43: 6686 113.43 - 120.39: 4930 120.39 - 127.35: 4291 127.35 - 134.31: 183 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 - 35.86: 7201 35.86 - 71.73: 274 71.73 - 107.59: 16 107.59 - 143.45: 2 143.45 - 179.32: 8 Dihedral angle restraints: 7501 sinusoidal: 3337 harmonic: 4164 Sorted by residual: dihedral pdb=" C3 PEV C 403 " pdb=" C1 PEV C 403 " pdb=" C2 PEV C 403 " pdb=" O3P PEV C 403 " ideal model delta sinusoidal sigma weight residual 292.80 113.48 179.32 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C3 PEV G 303 " pdb=" C1 PEV G 303 " pdb=" C2 PEV G 303 " pdb=" O3P PEV G 303 " ideal model delta sinusoidal sigma weight residual 292.80 116.80 176.00 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C3 PEV H 301 " pdb=" C1 PEV H 301 " pdb=" C2 PEV H 301 " pdb=" O3P PEV H 301 " ideal model delta sinusoidal sigma weight residual -67.20 103.39 -170.59 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 7498 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: 3853 2.84 - 3.35: 11589 3.35 - 3.87: 20860 3.87 - 4.38: 26980 4.38 - 4.90: 42170 Nonbonded interactions: 105452 Sorted by model distance: nonbonded pdb=" ND1 HIS B 211 " pdb=" OG SER E 201 " model vdw 2.323 2.520 nonbonded pdb=" ND1 HIS A 211 " pdb=" OG SER G 201 " model vdw 2.329 2.520 nonbonded pdb=" ND1 HIS D 211 " pdb=" OG SER H 201 " model vdw 2.330 2.520 nonbonded pdb=" OD2 ASP F 50 " pdb=" O HOH F 401 " model vdw 2.332 2.440 nonbonded pdb=" ND1 HIS C 211 " pdb=" OG SER F 201 " model vdw 2.333 2.520 ... (remaining 105447 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 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: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 4.300 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 39.860 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 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= 0.361 Angle : 0.661 9.948 16442 Z= 0.318 Chirality : 0.039 0.197 1778 Planarity : 0.019 0.288 2066 Dihedral : 17.639 179.315 4801 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (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 TRP 0.012 0.002 TRP A 200 HIS 0.003 0.001 HIS C 211 PHE 0.006 0.001 PHE D 149 TYR 0.008 0.001 TYR F 67 ARG 0.004 0.001 ARG A 156 *********************** 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 fitting. rotamer outliers: 0 poor density : 325 time to evaluate : 1.331 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: 1.6302 time to fit residues: 562.3057 Evaluate side-chains 270 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 266 time to evaluate : 1.189 ------------------------------------------------------------------------------- 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 118 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 109 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN A 275 ASN B 260 GLN C 260 GLN C 275 ASN D 169 GLN D 260 GLN E 98 ASN F 98 ASN G 98 ASN H 98 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12225 Z= 0.157 Angle : 0.538 10.177 16442 Z= 0.278 Chirality : 0.037 0.113 1778 Planarity : 0.005 0.040 2066 Dihedral : 18.780 170.103 2169 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.81 % Allowed : 9.47 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.23), residues: 1422 helix: 1.99 (0.15), residues: 1142 sheet: None (None), residues: 0 loop : -0.87 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 200 HIS 0.004 0.001 HIS H 57 PHE 0.011 0.001 PHE D 272 TYR 0.010 0.001 TYR A 230 ARG 0.004 0.001 ARG H 46 *********************** 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 310 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 289 time to evaluate : 1.426 Fit side-chains REVERT: A 109 GLU cc_start: 0.5233 (mt-10) cc_final: 0.4993 (tt0) REVERT: A 123 GLU cc_start: 0.5296 (tt0) cc_final: 0.4750 (tm-30) REVERT: A 163 GLU cc_start: 0.6509 (mt-10) cc_final: 0.6210 (mt-10) REVERT: A 167 LEU cc_start: 0.7033 (mt) cc_final: 0.6645 (tp) REVERT: A 271 ARG cc_start: 0.6902 (ttm110) cc_final: 0.6529 (mtm-85) REVERT: A 274 GLU cc_start: 0.7398 (tt0) cc_final: 0.7061 (tt0) REVERT: A 279 ASP cc_start: 0.6713 (m-30) cc_final: 0.6448 (m-30) REVERT: A 281 MET cc_start: 0.6121 (OUTLIER) cc_final: 0.3707 (mpt) REVERT: B 109 GLU cc_start: 0.5268 (mt-10) cc_final: 0.4875 (tp30) REVERT: B 119 GLU cc_start: 0.5675 (tm-30) cc_final: 0.5440 (tm-30) REVERT: B 163 GLU cc_start: 0.6771 (mm-30) cc_final: 0.6470 (mt-10) REVERT: B 164 GLU cc_start: 0.7056 (mt-10) cc_final: 0.6733 (mt-10) REVERT: B 218 SER cc_start: 0.8460 (p) cc_final: 0.8123 (t) REVERT: B 271 ARG cc_start: 0.6979 (ttm110) cc_final: 0.6615 (mtm-85) REVERT: B 274 GLU cc_start: 0.7468 (tt0) cc_final: 0.7123 (tt0) REVERT: B 279 ASP cc_start: 0.6802 (m-30) cc_final: 0.6512 (m-30) REVERT: C 109 GLU cc_start: 0.5296 (mt-10) cc_final: 0.4789 (tp30) REVERT: C 162 GLU cc_start: 0.6500 (pt0) cc_final: 0.6080 (pt0) REVERT: C 163 GLU cc_start: 0.6921 (mm-30) cc_final: 0.6629 (mt-10) REVERT: C 164 GLU cc_start: 0.6981 (mt-10) cc_final: 0.6680 (mt-10) REVERT: C 169 GLN cc_start: 0.6333 (mt0) cc_final: 0.5796 (pt0) REVERT: C 177 LYS cc_start: 0.6951 (mtpp) cc_final: 0.6428 (mmtt) REVERT: C 271 ARG cc_start: 0.6901 (ttm110) cc_final: 0.6548 (mtm-85) REVERT: C 274 GLU cc_start: 0.7404 (tt0) cc_final: 0.7058 (tt0) REVERT: C 281 MET cc_start: 0.6229 (OUTLIER) cc_final: 0.3817 (mpt) REVERT: D 108 LEU cc_start: 0.6778 (mp) cc_final: 0.6566 (mm) REVERT: D 109 GLU cc_start: 0.5253 (mt-10) cc_final: 0.4798 (tp30) REVERT: D 123 GLU cc_start: 0.5171 (tt0) cc_final: 0.4610 (tm-30) REVERT: D 167 LEU cc_start: 0.6625 (mt) cc_final: 0.6241 (tp) REVERT: D 177 LYS cc_start: 0.6993 (mtpp) cc_final: 0.6473 (mmtt) REVERT: D 271 ARG cc_start: 0.6994 (ttm110) cc_final: 0.6593 (mtm-85) REVERT: D 274 GLU cc_start: 0.7487 (tt0) cc_final: 0.7171 (tt0) REVERT: D 281 MET cc_start: 0.6098 (mmp) cc_final: 0.5684 (mmm) REVERT: D 283 MET cc_start: 0.3556 (ttp) cc_final: 0.3242 (ptt) REVERT: E 143 GLU cc_start: 0.7084 (mt-10) cc_final: 0.6570 (tt0) REVERT: E 147 HIS cc_start: 0.7397 (t-90) cc_final: 0.7085 (t-170) REVERT: E 180 GLU cc_start: 0.5376 (tp30) cc_final: 0.5068 (tm-30) REVERT: E 199 LEU cc_start: 0.7309 (tp) cc_final: 0.7088 (tp) REVERT: E 215 GLU cc_start: 0.7594 (pt0) cc_final: 0.7070 (pt0) REVERT: F 50 ASP cc_start: 0.7085 (m-30) cc_final: 0.6684 (m-30) REVERT: F 143 GLU cc_start: 0.7001 (mt-10) cc_final: 0.6456 (tt0) REVERT: F 147 HIS cc_start: 0.7261 (t-90) cc_final: 0.6975 (t-170) REVERT: F 199 LEU cc_start: 0.7333 (tp) cc_final: 0.7114 (tp) REVERT: F 215 GLU cc_start: 0.7517 (pt0) cc_final: 0.7227 (pt0) REVERT: G 143 GLU cc_start: 0.7094 (mt-10) cc_final: 0.6576 (tt0) REVERT: G 147 HIS cc_start: 0.7377 (t-90) cc_final: 0.7061 (t-170) REVERT: G 175 ARG cc_start: 0.7958 (tmm-80) cc_final: 0.7724 (tmm160) REVERT: G 199 LEU cc_start: 0.7286 (tp) cc_final: 0.7065 (tp) REVERT: G 208 ARG cc_start: 0.7005 (mtt-85) cc_final: 0.6633 (mmt90) REVERT: G 215 GLU cc_start: 0.7511 (pt0) cc_final: 0.7203 (pt0) REVERT: H 143 GLU cc_start: 0.7082 (mt-10) cc_final: 0.6572 (tt0) REVERT: H 147 HIS cc_start: 0.7357 (t-90) cc_final: 0.7070 (t-170) REVERT: H 199 LEU cc_start: 0.7340 (tp) cc_final: 0.7129 (tp) REVERT: H 215 GLU cc_start: 0.7558 (pt0) cc_final: 0.7242 (pt0) outliers start: 21 outliers final: 4 residues processed: 291 average time/residue: 1.5824 time to fit residues: 488.9009 Evaluate side-chains 269 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 263 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain C residue 281 MET Chi-restraints excluded: chain D residue 226 ASP 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 70 optimal weight: 0.3980 chunk 39 optimal weight: 20.0000 chunk 105 optimal weight: 6.9990 chunk 86 optimal weight: 0.0020 chunk 35 optimal weight: 0.0980 chunk 127 optimal weight: 0.9980 chunk 137 optimal weight: 10.0000 chunk 113 optimal weight: 5.9990 chunk 126 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 102 optimal weight: 9.9990 overall best weight: 1.0990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN A 260 GLN A 275 ASN B 252 ASN B 260 GLN B 275 ASN C 260 GLN C 275 ASN D 260 GLN E 204 GLN F 204 GLN G 204 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.2372 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= 0.143 Angle : 0.485 8.474 16442 Z= 0.249 Chirality : 0.036 0.113 1778 Planarity : 0.004 0.039 2066 Dihedral : 16.975 161.569 2167 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.50 % Allowed : 12.14 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.23), residues: 1422 helix: 2.32 (0.16), residues: 1142 sheet: None (None), residues: 0 loop : -0.91 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 200 HIS 0.004 0.001 HIS E 57 PHE 0.009 0.001 PHE D 272 TYR 0.009 0.001 TYR A 230 ARG 0.004 0.000 ARG G 46 *********************** 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 293 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 264 time to evaluate : 1.386 Fit side-chains REVERT: A 108 LEU cc_start: 0.6656 (OUTLIER) cc_final: 0.6256 (mt) REVERT: A 109 GLU cc_start: 0.5196 (mt-10) cc_final: 0.4993 (tt0) REVERT: A 123 GLU cc_start: 0.5219 (tt0) cc_final: 0.4758 (tm-30) REVERT: A 163 GLU cc_start: 0.6440 (mt-10) cc_final: 0.6168 (mt-10) REVERT: A 167 LEU cc_start: 0.6936 (OUTLIER) cc_final: 0.6588 (tp) REVERT: A 179 ASP cc_start: 0.7298 (p0) cc_final: 0.6957 (p0) REVERT: A 274 GLU cc_start: 0.7489 (tt0) cc_final: 0.7063 (tt0) REVERT: A 279 ASP cc_start: 0.6796 (m-30) cc_final: 0.6182 (t70) REVERT: A 281 MET cc_start: 0.6048 (OUTLIER) cc_final: 0.3570 (mpt) REVERT: B 109 GLU cc_start: 0.5311 (mt-10) cc_final: 0.4880 (tp30) REVERT: B 119 GLU cc_start: 0.5617 (tm-30) cc_final: 0.5235 (tm-30) REVERT: B 271 ARG cc_start: 0.6910 (ttm110) cc_final: 0.6703 (ttp-170) REVERT: B 274 GLU cc_start: 0.7429 (tt0) cc_final: 0.7054 (tt0) REVERT: B 279 ASP cc_start: 0.6853 (m-30) cc_final: 0.6568 (m-30) REVERT: C 108 LEU cc_start: 0.6685 (OUTLIER) cc_final: 0.6348 (mt) REVERT: C 109 GLU cc_start: 0.5364 (mt-10) cc_final: 0.4826 (tp30) REVERT: C 119 GLU cc_start: 0.5505 (tm-30) cc_final: 0.5072 (tm-30) REVERT: C 123 GLU cc_start: 0.5409 (OUTLIER) cc_final: 0.4946 (tm-30) REVERT: C 162 GLU cc_start: 0.6616 (pt0) cc_final: 0.6237 (pt0) REVERT: C 163 GLU cc_start: 0.6808 (mm-30) cc_final: 0.6489 (mt-10) REVERT: C 164 GLU cc_start: 0.6973 (mt-10) cc_final: 0.6673 (mt-10) REVERT: C 177 LYS cc_start: 0.6965 (mtpp) cc_final: 0.6585 (mmtt) REVERT: C 179 ASP cc_start: 0.7229 (p0) cc_final: 0.6930 (p0) REVERT: C 271 ARG cc_start: 0.6879 (ttm110) cc_final: 0.6673 (ttp-170) REVERT: C 274 GLU cc_start: 0.7415 (tt0) cc_final: 0.7043 (tt0) REVERT: C 279 ASP cc_start: 0.6751 (m-30) cc_final: 0.6495 (m-30) REVERT: D 109 GLU cc_start: 0.5239 (mt-10) cc_final: 0.4786 (tp30) REVERT: D 123 GLU cc_start: 0.5269 (tt0) cc_final: 0.4557 (tm-30) REVERT: D 177 LYS cc_start: 0.7016 (mtpp) cc_final: 0.6511 (mmtt) REVERT: D 179 ASP cc_start: 0.7223 (p0) cc_final: 0.6903 (p0) REVERT: D 271 ARG cc_start: 0.6862 (ttm110) cc_final: 0.6422 (mtm-85) REVERT: D 274 GLU cc_start: 0.7522 (tt0) cc_final: 0.7228 (tt0) REVERT: D 281 MET cc_start: 0.5976 (mmp) cc_final: 0.5677 (mmm) REVERT: D 283 MET cc_start: 0.3891 (ttp) cc_final: 0.3353 (ptt) REVERT: E 135 MET cc_start: 0.6698 (mmt) cc_final: 0.6365 (mmm) REVERT: E 143 GLU cc_start: 0.7075 (mt-10) cc_final: 0.6609 (tt0) REVERT: E 147 HIS cc_start: 0.7226 (t-90) cc_final: 0.6986 (t-170) REVERT: E 155 THR cc_start: 0.6833 (m) cc_final: 0.6456 (t) REVERT: E 180 GLU cc_start: 0.5299 (tp30) cc_final: 0.5033 (tm-30) REVERT: E 199 LEU cc_start: 0.7266 (tp) cc_final: 0.7020 (tp) REVERT: F 50 ASP cc_start: 0.7028 (m-30) cc_final: 0.6730 (m-30) REVERT: F 143 GLU cc_start: 0.7054 (mt-10) cc_final: 0.6544 (tt0) REVERT: F 147 HIS cc_start: 0.7110 (t-90) cc_final: 0.6892 (t-170) REVERT: F 199 LEU cc_start: 0.7251 (tp) cc_final: 0.7009 (tp) REVERT: F 215 GLU cc_start: 0.7406 (pt0) cc_final: 0.6970 (pt0) REVERT: G 135 MET cc_start: 0.6705 (mmt) cc_final: 0.6376 (mmm) REVERT: G 143 GLU cc_start: 0.7098 (mt-10) cc_final: 0.6636 (tt0) REVERT: G 147 HIS cc_start: 0.7240 (t-90) cc_final: 0.6993 (t-170) REVERT: G 155 THR cc_start: 0.6764 (m) cc_final: 0.6427 (t) REVERT: G 199 LEU cc_start: 0.7236 (tp) cc_final: 0.6988 (tp) REVERT: G 208 ARG cc_start: 0.6897 (mtt-85) cc_final: 0.6593 (mmt90) REVERT: G 215 GLU cc_start: 0.7334 (pt0) cc_final: 0.6996 (pt0) REVERT: H 135 MET cc_start: 0.6668 (mmt) cc_final: 0.6332 (mmm) REVERT: H 143 GLU cc_start: 0.7080 (mt-10) cc_final: 0.6554 (tt0) REVERT: H 147 HIS cc_start: 0.7236 (t-90) cc_final: 0.6982 (t-170) REVERT: H 199 LEU cc_start: 0.7278 (tp) cc_final: 0.7047 (tp) REVERT: H 215 GLU cc_start: 0.7427 (pt0) cc_final: 0.7024 (pt0) outliers start: 29 outliers final: 10 residues processed: 271 average time/residue: 1.6933 time to fit residues: 487.0960 Evaluate side-chains 269 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 254 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain B residue 226 ASP 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 144 SER Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain H residue 144 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 60 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 112 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN A 260 GLN A 275 ASN B 260 GLN B 275 ASN C 234 GLN C 260 GLN C 275 ASN D 260 GLN G 182 HIS H 204 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12225 Z= 0.171 Angle : 0.524 9.157 16442 Z= 0.269 Chirality : 0.038 0.119 1778 Planarity : 0.005 0.040 2066 Dihedral : 16.884 152.575 2167 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.76 % Allowed : 12.83 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.23), residues: 1422 helix: 2.23 (0.16), residues: 1138 sheet: None (None), residues: 0 loop : -0.89 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 200 HIS 0.004 0.001 HIS H 57 PHE 0.009 0.001 PHE D 272 TYR 0.011 0.001 TYR B 230 ARG 0.004 0.001 ARG E 46 *********************** 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 287 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 256 time to evaluate : 1.280 Fit side-chains REVERT: A 108 LEU cc_start: 0.6607 (OUTLIER) cc_final: 0.6225 (mt) REVERT: A 109 GLU cc_start: 0.5253 (mt-10) cc_final: 0.4985 (tt0) REVERT: A 119 GLU cc_start: 0.5402 (tm-30) cc_final: 0.5068 (tm-30) REVERT: A 123 GLU cc_start: 0.5126 (tt0) cc_final: 0.4601 (tm-30) REVERT: A 163 GLU cc_start: 0.6435 (mt-10) cc_final: 0.6133 (mt-10) REVERT: A 179 ASP cc_start: 0.7312 (p0) cc_final: 0.6986 (p0) REVERT: A 271 ARG cc_start: 0.6898 (ttm-80) cc_final: 0.6663 (ttp-170) REVERT: A 274 GLU cc_start: 0.7567 (tt0) cc_final: 0.7129 (tt0) REVERT: B 109 GLU cc_start: 0.5305 (mt-10) cc_final: 0.4868 (tp30) REVERT: B 119 GLU cc_start: 0.5521 (tm-30) cc_final: 0.5245 (tm-30) REVERT: B 163 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6517 (mt-10) REVERT: B 167 LEU cc_start: 0.6655 (OUTLIER) cc_final: 0.6427 (tp) REVERT: B 271 ARG cc_start: 0.6934 (ttm110) cc_final: 0.6578 (mtm-85) REVERT: B 274 GLU cc_start: 0.7481 (tt0) cc_final: 0.7066 (tt0) REVERT: C 109 GLU cc_start: 0.5436 (mt-10) cc_final: 0.4874 (tp30) REVERT: C 119 GLU cc_start: 0.5519 (tm-30) cc_final: 0.5171 (tm-30) REVERT: C 123 GLU cc_start: 0.5587 (OUTLIER) cc_final: 0.5313 (tp30) REVERT: C 162 GLU cc_start: 0.6633 (pt0) cc_final: 0.6277 (pt0) REVERT: C 163 GLU cc_start: 0.6782 (OUTLIER) cc_final: 0.6416 (mt-10) REVERT: C 164 GLU cc_start: 0.6932 (mt-10) cc_final: 0.6637 (mt-10) REVERT: C 177 LYS cc_start: 0.7028 (mtpp) cc_final: 0.6644 (mmtt) REVERT: C 179 ASP cc_start: 0.7255 (p0) cc_final: 0.6957 (p0) REVERT: C 271 ARG cc_start: 0.6902 (ttm110) cc_final: 0.6530 (mtm-85) REVERT: C 274 GLU cc_start: 0.7480 (tt0) cc_final: 0.7087 (tt0) REVERT: C 279 ASP cc_start: 0.6893 (m-30) cc_final: 0.6592 (m-30) REVERT: D 108 LEU cc_start: 0.6660 (OUTLIER) cc_final: 0.6315 (mt) REVERT: D 109 GLU cc_start: 0.5263 (mt-10) cc_final: 0.4783 (tp30) REVERT: D 177 LYS cc_start: 0.7065 (mtpp) cc_final: 0.6543 (mmtt) REVERT: D 179 ASP cc_start: 0.7290 (p0) cc_final: 0.6956 (p0) REVERT: D 271 ARG cc_start: 0.6868 (ttm110) cc_final: 0.6506 (mtm-85) REVERT: D 274 GLU cc_start: 0.7534 (tt0) cc_final: 0.7212 (tt0) REVERT: E 143 GLU cc_start: 0.7083 (mt-10) cc_final: 0.6659 (tt0) REVERT: E 147 HIS cc_start: 0.7465 (t-90) cc_final: 0.7205 (t-170) REVERT: E 148 HIS cc_start: 0.7181 (t70) cc_final: 0.6958 (t-170) REVERT: E 155 THR cc_start: 0.6849 (OUTLIER) cc_final: 0.6379 (t) REVERT: E 199 LEU cc_start: 0.7392 (tp) cc_final: 0.7134 (tp) REVERT: F 143 GLU cc_start: 0.7108 (mt-10) cc_final: 0.6665 (mt-10) REVERT: F 147 HIS cc_start: 0.7366 (t-90) cc_final: 0.7100 (t-170) REVERT: F 199 LEU cc_start: 0.7350 (tp) cc_final: 0.7107 (tp) REVERT: F 215 GLU cc_start: 0.7481 (pt0) cc_final: 0.7087 (pt0) REVERT: G 143 GLU cc_start: 0.7097 (mt-10) cc_final: 0.6643 (tt0) REVERT: G 147 HIS cc_start: 0.7476 (t-90) cc_final: 0.7217 (t-170) REVERT: G 148 HIS cc_start: 0.7207 (t70) cc_final: 0.6945 (t-170) REVERT: G 155 THR cc_start: 0.6815 (m) cc_final: 0.6340 (t) REVERT: G 199 LEU cc_start: 0.7288 (tp) cc_final: 0.7043 (tp) REVERT: G 200 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7667 (tttt) REVERT: G 215 GLU cc_start: 0.7514 (pt0) cc_final: 0.7106 (pt0) REVERT: H 143 GLU cc_start: 0.7098 (mt-10) cc_final: 0.6670 (tt0) REVERT: H 147 HIS cc_start: 0.7397 (t-90) cc_final: 0.7132 (t-170) REVERT: H 148 HIS cc_start: 0.7232 (t70) cc_final: 0.6998 (t-90) REVERT: H 199 LEU cc_start: 0.7350 (tp) cc_final: 0.7113 (tp) REVERT: H 215 GLU cc_start: 0.7498 (pt0) cc_final: 0.7151 (pt0) outliers start: 31 outliers final: 12 residues processed: 271 average time/residue: 1.6144 time to fit residues: 464.6243 Evaluate side-chains 272 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 252 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 163 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 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 E residue 144 SER Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 144 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 100 optimal weight: 20.0000 chunk 55 optimal weight: 4.9990 chunk 115 optimal weight: 9.9990 chunk 93 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 34 optimal weight: 0.0050 chunk 45 optimal weight: 6.9990 overall best weight: 1.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN A 260 GLN A 275 ASN B 260 GLN B 275 ASN C 234 GLN C 260 GLN C 275 ASN D 260 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12225 Z= 0.149 Angle : 0.485 8.811 16442 Z= 0.251 Chirality : 0.036 0.113 1778 Planarity : 0.004 0.039 2066 Dihedral : 16.369 142.325 2163 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.67 % Allowed : 13.95 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.23), residues: 1422 helix: 2.34 (0.16), residues: 1138 sheet: None (None), residues: 0 loop : -0.93 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 200 HIS 0.004 0.001 HIS G 57 PHE 0.013 0.001 PHE D 110 TYR 0.009 0.001 TYR A 230 ARG 0.003 0.000 ARG C 159 *********************** 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 279 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 249 time to evaluate : 1.181 Fit side-chains REVERT: A 108 LEU cc_start: 0.6627 (OUTLIER) cc_final: 0.6242 (mt) REVERT: A 109 GLU cc_start: 0.5229 (mt-10) cc_final: 0.4971 (tt0) REVERT: A 119 GLU cc_start: 0.5451 (tm-30) cc_final: 0.5128 (tm-30) REVERT: A 123 GLU cc_start: 0.5155 (tt0) cc_final: 0.4614 (tm-30) REVERT: A 163 GLU cc_start: 0.6332 (mt-10) cc_final: 0.6094 (mt-10) REVERT: A 167 LEU cc_start: 0.6719 (mt) cc_final: 0.6325 (tp) REVERT: A 169 GLN cc_start: 0.6352 (mt0) cc_final: 0.5861 (pt0) REVERT: A 179 ASP cc_start: 0.7306 (p0) cc_final: 0.6976 (p0) REVERT: A 208 MET cc_start: 0.7778 (mtp) cc_final: 0.7450 (mtp) REVERT: A 274 GLU cc_start: 0.7447 (tt0) cc_final: 0.7082 (tt0) REVERT: B 109 GLU cc_start: 0.5293 (mt-10) cc_final: 0.4869 (tp30) REVERT: B 119 GLU cc_start: 0.5501 (tm-30) cc_final: 0.5296 (tm-30) REVERT: B 123 GLU cc_start: 0.5710 (OUTLIER) cc_final: 0.5100 (tm-30) REVERT: B 163 GLU cc_start: 0.6923 (OUTLIER) cc_final: 0.6515 (mt-10) REVERT: B 179 ASP cc_start: 0.7359 (p0) cc_final: 0.7058 (p0) REVERT: B 271 ARG cc_start: 0.6862 (ttm110) cc_final: 0.6512 (mtm-85) REVERT: B 274 GLU cc_start: 0.7463 (tt0) cc_final: 0.7038 (tt0) REVERT: C 108 LEU cc_start: 0.6671 (OUTLIER) cc_final: 0.6341 (mt) REVERT: C 109 GLU cc_start: 0.5441 (mt-10) cc_final: 0.4859 (tp30) REVERT: C 119 GLU cc_start: 0.5487 (tm-30) cc_final: 0.5207 (tm-30) REVERT: C 123 GLU cc_start: 0.5537 (OUTLIER) cc_final: 0.4927 (tm-30) REVERT: C 162 GLU cc_start: 0.6619 (pt0) cc_final: 0.6285 (pt0) REVERT: C 163 GLU cc_start: 0.6813 (mm-30) cc_final: 0.6487 (mt-10) REVERT: C 164 GLU cc_start: 0.6994 (mt-10) cc_final: 0.6693 (mt-10) REVERT: C 177 LYS cc_start: 0.7042 (mtpp) cc_final: 0.6526 (mmtt) REVERT: C 179 ASP cc_start: 0.7291 (p0) cc_final: 0.6982 (p0) REVERT: C 271 ARG cc_start: 0.6877 (ttm110) cc_final: 0.6525 (mtm-85) REVERT: C 274 GLU cc_start: 0.7429 (tt0) cc_final: 0.7063 (tt0) REVERT: D 109 GLU cc_start: 0.5162 (mt-10) cc_final: 0.4656 (tp30) REVERT: D 119 GLU cc_start: 0.5582 (tm-30) cc_final: 0.5241 (tm-30) REVERT: D 123 GLU cc_start: 0.5389 (tt0) cc_final: 0.4830 (tm-30) REVERT: D 177 LYS cc_start: 0.7060 (mtpp) cc_final: 0.6568 (mmtt) REVERT: D 179 ASP cc_start: 0.7239 (p0) cc_final: 0.6944 (p0) REVERT: D 271 ARG cc_start: 0.6817 (ttm110) cc_final: 0.6484 (ttp-170) REVERT: D 274 GLU cc_start: 0.7500 (tt0) cc_final: 0.7216 (tt0) REVERT: E 143 GLU cc_start: 0.7079 (mt-10) cc_final: 0.6639 (tt0) REVERT: E 147 HIS cc_start: 0.7431 (t-90) cc_final: 0.7172 (t-170) REVERT: E 148 HIS cc_start: 0.7146 (t70) cc_final: 0.6923 (t-170) REVERT: E 155 THR cc_start: 0.6789 (m) cc_final: 0.6418 (t) REVERT: E 199 LEU cc_start: 0.7336 (tp) cc_final: 0.7081 (tp) REVERT: F 147 HIS cc_start: 0.7300 (t-90) cc_final: 0.7040 (t-170) REVERT: F 148 HIS cc_start: 0.7192 (t70) cc_final: 0.6930 (t-170) REVERT: F 199 LEU cc_start: 0.7297 (tp) cc_final: 0.7049 (tp) REVERT: F 215 GLU cc_start: 0.7531 (pt0) cc_final: 0.7144 (pt0) REVERT: G 76 ARG cc_start: 0.7056 (OUTLIER) cc_final: 0.6779 (mtt180) REVERT: G 143 GLU cc_start: 0.7101 (mt-10) cc_final: 0.6675 (tt0) REVERT: G 147 HIS cc_start: 0.7457 (t-90) cc_final: 0.7203 (t-170) REVERT: G 148 HIS cc_start: 0.7173 (t70) cc_final: 0.6915 (t-170) REVERT: G 155 THR cc_start: 0.6794 (m) cc_final: 0.6413 (t) REVERT: G 199 LEU cc_start: 0.7229 (tp) cc_final: 0.6987 (tp) REVERT: G 215 GLU cc_start: 0.7470 (pt0) cc_final: 0.7055 (pt0) REVERT: H 76 ARG cc_start: 0.7038 (OUTLIER) cc_final: 0.6778 (mtt180) REVERT: H 143 GLU cc_start: 0.7058 (mt-10) cc_final: 0.6613 (tt0) REVERT: H 147 HIS cc_start: 0.7350 (t-90) cc_final: 0.7088 (t-170) REVERT: H 148 HIS cc_start: 0.7185 (t70) cc_final: 0.6934 (t-170) REVERT: H 199 LEU cc_start: 0.7321 (tp) cc_final: 0.7071 (tp) REVERT: H 215 GLU cc_start: 0.7539 (pt0) cc_final: 0.7187 (pt0) outliers start: 30 outliers final: 13 residues processed: 262 average time/residue: 1.6427 time to fit residues: 456.5871 Evaluate side-chains 266 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 246 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 163 GLU 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 C residue 108 LEU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 196 TYR Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 76 ARG Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 144 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 79 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 135 optimal weight: 3.9990 chunk 112 optimal weight: 20.0000 chunk 62 optimal weight: 0.3980 chunk 11 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN A 260 GLN A 275 ASN B 260 GLN B 275 ASN C 234 GLN C 260 GLN C 275 ASN D 260 GLN E 182 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.3009 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= 0.122 Angle : 0.453 8.869 16442 Z= 0.235 Chirality : 0.035 0.108 1778 Planarity : 0.004 0.039 2066 Dihedral : 15.501 144.595 2163 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.58 % Allowed : 14.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.77 (0.23), residues: 1422 helix: 2.50 (0.16), residues: 1138 sheet: None (None), residues: 0 loop : -1.05 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 200 HIS 0.003 0.001 HIS F 57 PHE 0.012 0.001 PHE D 110 TYR 0.009 0.001 TYR B 196 ARG 0.003 0.000 ARG C 159 *********************** 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 279 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 250 time to evaluate : 1.168 Fit side-chains REVERT: A 108 LEU cc_start: 0.6581 (OUTLIER) cc_final: 0.6228 (mt) REVERT: A 109 GLU cc_start: 0.5202 (mt-10) cc_final: 0.4953 (tt0) REVERT: A 119 GLU cc_start: 0.5406 (tm-30) cc_final: 0.5130 (tm-30) REVERT: A 123 GLU cc_start: 0.5124 (tt0) cc_final: 0.4587 (tm-30) REVERT: A 163 GLU cc_start: 0.6334 (mt-10) cc_final: 0.6090 (mt-10) REVERT: A 167 LEU cc_start: 0.6578 (mt) cc_final: 0.6311 (tp) REVERT: A 179 ASP cc_start: 0.7311 (p0) cc_final: 0.6956 (p0) REVERT: A 208 MET cc_start: 0.7744 (mtp) cc_final: 0.7392 (mtp) REVERT: A 274 GLU cc_start: 0.7414 (tt0) cc_final: 0.7043 (tt0) REVERT: A 279 ASP cc_start: 0.6852 (m-30) cc_final: 0.6227 (t70) REVERT: B 109 GLU cc_start: 0.5266 (mt-10) cc_final: 0.4853 (tp30) REVERT: B 123 GLU cc_start: 0.5629 (OUTLIER) cc_final: 0.5100 (tm-30) REVERT: B 163 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6521 (mt-10) REVERT: B 179 ASP cc_start: 0.7320 (p0) cc_final: 0.7000 (p0) REVERT: B 271 ARG cc_start: 0.6762 (ttm110) cc_final: 0.6479 (ttp-170) REVERT: B 274 GLU cc_start: 0.7468 (tt0) cc_final: 0.7056 (tt0) REVERT: B 283 MET cc_start: 0.3505 (mmm) cc_final: 0.2144 (ppp) REVERT: C 108 LEU cc_start: 0.6664 (OUTLIER) cc_final: 0.6336 (mt) REVERT: C 109 GLU cc_start: 0.5454 (mt-10) cc_final: 0.4892 (tp30) REVERT: C 119 GLU cc_start: 0.5432 (tm-30) cc_final: 0.5193 (tm-30) REVERT: C 123 GLU cc_start: 0.5509 (tt0) cc_final: 0.4895 (tm-30) REVERT: C 162 GLU cc_start: 0.6688 (pt0) cc_final: 0.6317 (pt0) REVERT: C 163 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.6427 (mt-10) REVERT: C 164 GLU cc_start: 0.6988 (mt-10) cc_final: 0.6688 (mt-10) REVERT: C 177 LYS cc_start: 0.6951 (mtpp) cc_final: 0.6613 (mmtt) REVERT: C 208 MET cc_start: 0.7702 (mtp) cc_final: 0.7331 (mtp) REVERT: C 260 GLN cc_start: 0.7191 (pt0) cc_final: 0.6664 (pm20) REVERT: C 271 ARG cc_start: 0.6789 (ttm110) cc_final: 0.6521 (ttp-170) REVERT: C 274 GLU cc_start: 0.7417 (tt0) cc_final: 0.7060 (tt0) REVERT: D 108 LEU cc_start: 0.6545 (OUTLIER) cc_final: 0.6201 (mt) REVERT: D 109 GLU cc_start: 0.5210 (mt-10) cc_final: 0.4714 (tp30) REVERT: D 119 GLU cc_start: 0.5555 (tm-30) cc_final: 0.5113 (tm-30) REVERT: D 123 GLU cc_start: 0.5527 (tt0) cc_final: 0.4878 (tm-30) REVERT: D 177 LYS cc_start: 0.6957 (mtpp) cc_final: 0.6508 (mmtt) REVERT: D 179 ASP cc_start: 0.7210 (p0) cc_final: 0.6919 (p0) REVERT: D 260 GLN cc_start: 0.7285 (pt0) cc_final: 0.6762 (pm20) REVERT: D 271 ARG cc_start: 0.6768 (ttm110) cc_final: 0.6390 (mtm-85) REVERT: D 274 GLU cc_start: 0.7513 (tt0) cc_final: 0.7220 (tt0) REVERT: E 76 ARG cc_start: 0.7114 (mtt180) cc_final: 0.6483 (mpp-170) REVERT: E 143 GLU cc_start: 0.7012 (mt-10) cc_final: 0.6591 (tt0) REVERT: E 147 HIS cc_start: 0.7258 (t-90) cc_final: 0.7022 (t-170) REVERT: E 148 HIS cc_start: 0.7236 (t70) cc_final: 0.7000 (t-170) REVERT: E 155 THR cc_start: 0.6788 (m) cc_final: 0.6429 (t) REVERT: E 199 LEU cc_start: 0.7237 (tp) cc_final: 0.6993 (tp) REVERT: F 143 GLU cc_start: 0.7030 (mt-10) cc_final: 0.6615 (tt0) REVERT: F 147 HIS cc_start: 0.7189 (t-90) cc_final: 0.6952 (t-170) REVERT: F 148 HIS cc_start: 0.7140 (t70) cc_final: 0.6883 (t-170) REVERT: F 155 THR cc_start: 0.6627 (m) cc_final: 0.6222 (t) REVERT: F 199 LEU cc_start: 0.7247 (tp) cc_final: 0.6995 (tp) REVERT: F 215 GLU cc_start: 0.7326 (pt0) cc_final: 0.6994 (pt0) REVERT: G 71 MET cc_start: 0.8400 (tpt) cc_final: 0.8111 (mmm) REVERT: G 76 ARG cc_start: 0.7084 (OUTLIER) cc_final: 0.6409 (mpp-170) REVERT: G 143 GLU cc_start: 0.7033 (mt-10) cc_final: 0.6627 (tt0) REVERT: G 147 HIS cc_start: 0.7327 (t-90) cc_final: 0.7063 (t-170) REVERT: G 148 HIS cc_start: 0.7217 (t70) cc_final: 0.6952 (t-170) REVERT: G 155 THR cc_start: 0.6815 (m) cc_final: 0.6450 (t) REVERT: G 199 LEU cc_start: 0.7203 (tp) cc_final: 0.6958 (tp) REVERT: G 215 GLU cc_start: 0.7373 (pt0) cc_final: 0.6976 (pt0) REVERT: H 76 ARG cc_start: 0.7064 (OUTLIER) cc_final: 0.6788 (mtt180) REVERT: H 143 GLU cc_start: 0.6961 (mt-10) cc_final: 0.6523 (tt0) REVERT: H 147 HIS cc_start: 0.7221 (t-90) cc_final: 0.6978 (t-170) REVERT: H 148 HIS cc_start: 0.7169 (t70) cc_final: 0.6945 (t-170) REVERT: H 199 LEU cc_start: 0.7199 (tp) cc_final: 0.6953 (tp) outliers start: 29 outliers final: 15 residues processed: 263 average time/residue: 1.6513 time to fit residues: 460.3672 Evaluate side-chains 268 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 245 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR 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 143 SER Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 196 TYR Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 196 TYR Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 76 ARG Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 144 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 76 optimal weight: 6.9990 chunk 114 optimal weight: 10.0000 chunk 75 optimal weight: 0.0570 chunk 134 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 83 optimal weight: 0.0970 overall best weight: 0.9900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN A 260 GLN A 275 ASN B 260 GLN B 275 ASN C 234 GLN C 275 ASN G 150 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.3033 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= 0.132 Angle : 0.464 8.766 16442 Z= 0.239 Chirality : 0.035 0.111 1778 Planarity : 0.004 0.039 2066 Dihedral : 15.323 145.229 2163 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.50 % Allowed : 14.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.79 (0.23), residues: 1422 helix: 2.51 (0.16), residues: 1134 sheet: None (None), residues: 0 loop : -0.97 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 200 HIS 0.004 0.001 HIS G 57 PHE 0.009 0.001 PHE D 110 TYR 0.010 0.001 TYR B 230 ARG 0.003 0.000 ARG C 159 *********************** 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 269 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 241 time to evaluate : 1.426 Fit side-chains REVERT: A 108 LEU cc_start: 0.6603 (OUTLIER) cc_final: 0.6246 (mt) REVERT: A 109 GLU cc_start: 0.5201 (mt-10) cc_final: 0.4951 (tt0) REVERT: A 119 GLU cc_start: 0.5405 (tm-30) cc_final: 0.5135 (tm-30) REVERT: A 123 GLU cc_start: 0.5108 (tt0) cc_final: 0.4581 (tm-30) REVERT: A 163 GLU cc_start: 0.6328 (mt-10) cc_final: 0.6074 (mt-10) REVERT: A 167 LEU cc_start: 0.6577 (OUTLIER) cc_final: 0.6303 (tp) REVERT: A 179 ASP cc_start: 0.7313 (p0) cc_final: 0.6985 (p0) REVERT: A 274 GLU cc_start: 0.7411 (tt0) cc_final: 0.7036 (tt0) REVERT: B 109 GLU cc_start: 0.5258 (mt-10) cc_final: 0.4846 (tp30) REVERT: B 119 GLU cc_start: 0.5726 (tm-30) cc_final: 0.4758 (tp30) REVERT: B 123 GLU cc_start: 0.5606 (OUTLIER) cc_final: 0.5002 (tm-30) REVERT: B 163 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.6421 (mt-10) REVERT: B 167 LEU cc_start: 0.6610 (OUTLIER) cc_final: 0.6395 (tp) REVERT: B 179 ASP cc_start: 0.7318 (p0) cc_final: 0.7005 (p0) REVERT: B 271 ARG cc_start: 0.6754 (ttm110) cc_final: 0.6452 (ttp-170) REVERT: B 274 GLU cc_start: 0.7427 (tt0) cc_final: 0.7002 (tt0) REVERT: C 109 GLU cc_start: 0.5503 (mt-10) cc_final: 0.4908 (tp30) REVERT: C 119 GLU cc_start: 0.5522 (tm-30) cc_final: 0.5294 (tm-30) REVERT: C 123 GLU cc_start: 0.5524 (OUTLIER) cc_final: 0.4925 (tm-30) REVERT: C 162 GLU cc_start: 0.6684 (pt0) cc_final: 0.6315 (pt0) REVERT: C 163 GLU cc_start: 0.6761 (OUTLIER) cc_final: 0.6425 (mt-10) REVERT: C 164 GLU cc_start: 0.6998 (mt-10) cc_final: 0.6688 (mt-10) REVERT: C 177 LYS cc_start: 0.6962 (mtpp) cc_final: 0.6438 (mmtp) REVERT: C 260 GLN cc_start: 0.7220 (pt0) cc_final: 0.6694 (pm20) REVERT: C 271 ARG cc_start: 0.6782 (ttm110) cc_final: 0.6456 (ttp-170) REVERT: C 274 GLU cc_start: 0.7429 (tt0) cc_final: 0.7214 (tt0) REVERT: D 109 GLU cc_start: 0.5303 (mt-10) cc_final: 0.4757 (tp30) REVERT: D 119 GLU cc_start: 0.5545 (tm-30) cc_final: 0.5116 (tm-30) REVERT: D 123 GLU cc_start: 0.5476 (tt0) cc_final: 0.4856 (tm-30) REVERT: D 177 LYS cc_start: 0.6944 (mtpp) cc_final: 0.6502 (mmtt) REVERT: D 179 ASP cc_start: 0.7228 (p0) cc_final: 0.6926 (p0) REVERT: D 271 ARG cc_start: 0.6748 (ttm110) cc_final: 0.6349 (mtm-85) REVERT: D 274 GLU cc_start: 0.7532 (tt0) cc_final: 0.7244 (tt0) REVERT: E 76 ARG cc_start: 0.7075 (mtt180) cc_final: 0.6489 (mpp-170) REVERT: E 143 GLU cc_start: 0.7010 (mt-10) cc_final: 0.6596 (tt0) REVERT: E 147 HIS cc_start: 0.7309 (t-90) cc_final: 0.7078 (t-170) REVERT: E 148 HIS cc_start: 0.7223 (t70) cc_final: 0.6971 (t-170) REVERT: E 155 THR cc_start: 0.6805 (m) cc_final: 0.6431 (t) REVERT: E 199 LEU cc_start: 0.7323 (tp) cc_final: 0.7078 (tp) REVERT: F 143 GLU cc_start: 0.7050 (mt-10) cc_final: 0.6640 (mt-10) REVERT: F 147 HIS cc_start: 0.7283 (t-90) cc_final: 0.7061 (t-170) REVERT: F 148 HIS cc_start: 0.7178 (t70) cc_final: 0.6916 (t-170) REVERT: F 155 THR cc_start: 0.6616 (m) cc_final: 0.6231 (t) REVERT: F 199 LEU cc_start: 0.7280 (tp) cc_final: 0.7028 (tp) REVERT: G 71 MET cc_start: 0.8388 (tpt) cc_final: 0.8090 (mmm) REVERT: G 76 ARG cc_start: 0.7085 (OUTLIER) cc_final: 0.6729 (mtt180) REVERT: G 143 GLU cc_start: 0.7034 (mt-10) cc_final: 0.6630 (tt0) REVERT: G 147 HIS cc_start: 0.7350 (t-90) cc_final: 0.7097 (t-170) REVERT: G 148 HIS cc_start: 0.7236 (t70) cc_final: 0.6964 (t-170) REVERT: G 155 THR cc_start: 0.6789 (m) cc_final: 0.6382 (t) REVERT: G 215 GLU cc_start: 0.7413 (pt0) cc_final: 0.7039 (pt0) REVERT: H 76 ARG cc_start: 0.7070 (OUTLIER) cc_final: 0.6717 (mtt180) REVERT: H 143 GLU cc_start: 0.7001 (mt-10) cc_final: 0.6592 (tt0) REVERT: H 147 HIS cc_start: 0.7264 (t-90) cc_final: 0.7038 (t-170) REVERT: H 148 HIS cc_start: 0.7172 (t70) cc_final: 0.6938 (t-170) REVERT: H 199 LEU cc_start: 0.7331 (tp) cc_final: 0.7089 (tp) outliers start: 28 outliers final: 16 residues processed: 254 average time/residue: 1.6286 time to fit residues: 439.6633 Evaluate side-chains 267 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 242 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 163 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 C residue 105 THR Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 196 TYR Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 196 TYR Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 76 ARG Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 144 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 66 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 129 optimal weight: 8.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN A 260 GLN A 275 ASN B 260 GLN B 275 ASN C 234 GLN C 275 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.3105 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= 0.139 Angle : 0.472 8.731 16442 Z= 0.243 Chirality : 0.036 0.113 1778 Planarity : 0.004 0.040 2066 Dihedral : 15.314 145.978 2163 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.50 % Allowed : 14.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.77 (0.23), residues: 1422 helix: 2.50 (0.16), residues: 1134 sheet: None (None), residues: 0 loop : -0.98 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 200 HIS 0.003 0.001 HIS G 57 PHE 0.009 0.001 PHE D 110 TYR 0.010 0.001 TYR H 212 ARG 0.003 0.000 ARG C 159 *********************** 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 271 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 243 time to evaluate : 1.381 Fit side-chains REVERT: A 109 GLU cc_start: 0.5208 (mt-10) cc_final: 0.4953 (tt0) REVERT: A 119 GLU cc_start: 0.5397 (tm-30) cc_final: 0.5117 (tm-30) REVERT: A 123 GLU cc_start: 0.5139 (tt0) cc_final: 0.4516 (tm-30) REVERT: A 163 GLU cc_start: 0.6342 (mt-10) cc_final: 0.6072 (mt-10) REVERT: A 167 LEU cc_start: 0.6645 (mt) cc_final: 0.6364 (tp) REVERT: A 208 MET cc_start: 0.7712 (mtp) cc_final: 0.7358 (mtp) REVERT: B 109 GLU cc_start: 0.5320 (mt-10) cc_final: 0.4914 (tp30) REVERT: B 119 GLU cc_start: 0.5776 (tm-30) cc_final: 0.4826 (tp30) REVERT: B 123 GLU cc_start: 0.5627 (OUTLIER) cc_final: 0.4983 (tm-30) REVERT: B 163 GLU cc_start: 0.6857 (OUTLIER) cc_final: 0.6439 (mt-10) REVERT: B 167 LEU cc_start: 0.6605 (OUTLIER) cc_final: 0.6381 (tp) REVERT: B 179 ASP cc_start: 0.7321 (p0) cc_final: 0.7010 (p0) REVERT: B 271 ARG cc_start: 0.6772 (ttm110) cc_final: 0.6457 (ttp-170) REVERT: B 274 GLU cc_start: 0.7426 (tt0) cc_final: 0.6997 (tt0) REVERT: B 283 MET cc_start: 0.3437 (mmm) cc_final: 0.2137 (ppp) REVERT: C 108 LEU cc_start: 0.6630 (mm) cc_final: 0.6332 (mt) REVERT: C 109 GLU cc_start: 0.5475 (mt-10) cc_final: 0.4854 (tp30) REVERT: C 119 GLU cc_start: 0.5498 (tm-30) cc_final: 0.5272 (tm-30) REVERT: C 123 GLU cc_start: 0.5459 (OUTLIER) cc_final: 0.4857 (tm-30) REVERT: C 162 GLU cc_start: 0.6710 (pt0) cc_final: 0.6340 (pt0) REVERT: C 163 GLU cc_start: 0.6771 (OUTLIER) cc_final: 0.6440 (mt-10) REVERT: C 164 GLU cc_start: 0.6931 (mt-10) cc_final: 0.6649 (mt-10) REVERT: C 177 LYS cc_start: 0.6997 (mtpp) cc_final: 0.6622 (mmmt) REVERT: C 271 ARG cc_start: 0.6782 (ttm110) cc_final: 0.6446 (ttp-170) REVERT: C 274 GLU cc_start: 0.7382 (tt0) cc_final: 0.7166 (tt0) REVERT: D 108 LEU cc_start: 0.6564 (OUTLIER) cc_final: 0.6228 (mt) REVERT: D 109 GLU cc_start: 0.5251 (mt-10) cc_final: 0.4716 (tp30) REVERT: D 119 GLU cc_start: 0.5489 (tm-30) cc_final: 0.5107 (tm-30) REVERT: D 123 GLU cc_start: 0.5363 (tt0) cc_final: 0.4748 (tm-30) REVERT: D 177 LYS cc_start: 0.6942 (mtpp) cc_final: 0.6501 (mmtt) REVERT: D 179 ASP cc_start: 0.7260 (p0) cc_final: 0.6953 (p0) REVERT: D 274 GLU cc_start: 0.7533 (tt0) cc_final: 0.7215 (tt0) REVERT: E 143 GLU cc_start: 0.7018 (mt-10) cc_final: 0.6607 (tt0) REVERT: E 147 HIS cc_start: 0.7343 (t-90) cc_final: 0.7103 (t-170) REVERT: E 155 THR cc_start: 0.6837 (m) cc_final: 0.6426 (t) REVERT: F 147 HIS cc_start: 0.7302 (t-90) cc_final: 0.7074 (t-170) REVERT: F 148 HIS cc_start: 0.7219 (t70) cc_final: 0.6965 (t-170) REVERT: F 155 THR cc_start: 0.6587 (m) cc_final: 0.6220 (t) REVERT: F 199 LEU cc_start: 0.7281 (tp) cc_final: 0.7018 (tp) REVERT: G 143 GLU cc_start: 0.7034 (mt-10) cc_final: 0.6627 (tt0) REVERT: G 147 HIS cc_start: 0.7411 (t-90) cc_final: 0.7164 (t-170) REVERT: G 148 HIS cc_start: 0.7199 (t70) cc_final: 0.6920 (t-170) REVERT: G 155 THR cc_start: 0.6859 (m) cc_final: 0.6465 (t) REVERT: G 215 GLU cc_start: 0.7411 (pt0) cc_final: 0.7042 (pt0) REVERT: H 143 GLU cc_start: 0.7002 (mt-10) cc_final: 0.6600 (tt0) REVERT: H 147 HIS cc_start: 0.7274 (t-90) cc_final: 0.7030 (t-170) REVERT: H 148 HIS cc_start: 0.7180 (t70) cc_final: 0.6936 (t-170) REVERT: H 199 LEU cc_start: 0.7311 (tp) cc_final: 0.7074 (tp) outliers start: 28 outliers final: 17 residues processed: 257 average time/residue: 1.6428 time to fit residues: 448.8549 Evaluate side-chains 263 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 240 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR 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 163 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 C residue 105 THR Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 196 TYR Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 196 TYR Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain H residue 144 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 0.0170 chunk 125 optimal weight: 7.9990 chunk 129 optimal weight: 5.9990 chunk 75 optimal weight: 0.0970 chunk 54 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 113 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 overall best weight: 2.8222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN A 260 GLN A 275 ASN B 252 ASN B 260 GLN B 275 ASN C 234 GLN E 93 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12225 Z= 0.226 Angle : 0.585 8.687 16442 Z= 0.298 Chirality : 0.040 0.124 1778 Planarity : 0.005 0.042 2066 Dihedral : 16.541 143.690 2163 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.24 % Allowed : 14.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.23), residues: 1422 helix: 2.09 (0.15), residues: 1146 sheet: None (None), residues: 0 loop : -0.92 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 200 HIS 0.005 0.002 HIS E 181 PHE 0.010 0.002 PHE D 272 TYR 0.013 0.002 TYR G 212 ARG 0.004 0.001 ARG G 46 *********************** 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 253 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 228 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 LEU cc_start: 0.6646 (OUTLIER) cc_final: 0.6284 (mt) REVERT: A 109 GLU cc_start: 0.5251 (mt-10) cc_final: 0.4985 (tt0) REVERT: A 119 GLU cc_start: 0.5400 (tm-30) cc_final: 0.5148 (tm-30) REVERT: A 163 GLU cc_start: 0.6422 (mt-10) cc_final: 0.6163 (mt-10) REVERT: A 179 ASP cc_start: 0.7342 (p0) cc_final: 0.7112 (p0) REVERT: A 279 ASP cc_start: 0.6776 (m-30) cc_final: 0.6541 (m-30) REVERT: B 108 LEU cc_start: 0.6746 (OUTLIER) cc_final: 0.6448 (mt) REVERT: B 109 GLU cc_start: 0.5356 (mt-10) cc_final: 0.4953 (tp30) REVERT: B 119 GLU cc_start: 0.5768 (tm-30) cc_final: 0.4755 (tp30) REVERT: B 163 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6430 (mt-10) REVERT: B 167 LEU cc_start: 0.6675 (OUTLIER) cc_final: 0.6398 (tp) REVERT: B 179 ASP cc_start: 0.7316 (p0) cc_final: 0.7034 (p0) REVERT: B 260 GLN cc_start: 0.7280 (pt0) cc_final: 0.7058 (pp30) REVERT: B 271 ARG cc_start: 0.6939 (ttm110) cc_final: 0.6559 (mtm-85) REVERT: B 274 GLU cc_start: 0.7489 (tt0) cc_final: 0.7117 (tt0) REVERT: B 283 MET cc_start: 0.3358 (mmm) cc_final: 0.2182 (ppp) REVERT: C 108 LEU cc_start: 0.6648 (mm) cc_final: 0.6326 (mt) REVERT: C 109 GLU cc_start: 0.5536 (mt-10) cc_final: 0.4889 (tp30) REVERT: C 119 GLU cc_start: 0.5534 (tm-30) cc_final: 0.5298 (tm-30) REVERT: C 123 GLU cc_start: 0.5594 (OUTLIER) cc_final: 0.5285 (tp30) REVERT: C 162 GLU cc_start: 0.6597 (pt0) cc_final: 0.6277 (pt0) REVERT: C 163 GLU cc_start: 0.6792 (OUTLIER) cc_final: 0.6426 (mt-10) REVERT: C 177 LYS cc_start: 0.7009 (mtpp) cc_final: 0.6505 (mmtt) REVERT: C 179 ASP cc_start: 0.7317 (p0) cc_final: 0.7041 (p0) REVERT: C 208 MET cc_start: 0.7787 (mtp) cc_final: 0.7454 (mtp) REVERT: C 271 ARG cc_start: 0.6912 (ttm110) cc_final: 0.6500 (mtm-85) REVERT: C 274 GLU cc_start: 0.7466 (tt0) cc_final: 0.7087 (tt0) REVERT: D 108 LEU cc_start: 0.6612 (OUTLIER) cc_final: 0.6235 (mt) REVERT: D 109 GLU cc_start: 0.5424 (mt-10) cc_final: 0.4780 (tp30) REVERT: D 119 GLU cc_start: 0.5469 (tm-30) cc_final: 0.5126 (tm-30) REVERT: D 177 LYS cc_start: 0.7045 (mtpp) cc_final: 0.6544 (mmtt) REVERT: D 179 ASP cc_start: 0.7288 (p0) cc_final: 0.6994 (p0) REVERT: D 208 MET cc_start: 0.7800 (mtp) cc_final: 0.7443 (mtp) REVERT: D 274 GLU cc_start: 0.7575 (tt0) cc_final: 0.7214 (tt0) REVERT: E 143 GLU cc_start: 0.7088 (mt-10) cc_final: 0.6691 (mt-10) REVERT: E 147 HIS cc_start: 0.7530 (t-90) cc_final: 0.7262 (t-170) REVERT: E 155 THR cc_start: 0.6818 (m) cc_final: 0.6416 (t) REVERT: F 147 HIS cc_start: 0.7500 (t-90) cc_final: 0.7209 (t-170) REVERT: F 148 HIS cc_start: 0.7181 (t70) cc_final: 0.6897 (t-170) REVERT: F 155 THR cc_start: 0.6594 (m) cc_final: 0.6211 (t) REVERT: F 215 GLU cc_start: 0.7577 (pt0) cc_final: 0.7251 (pt0) REVERT: G 143 GLU cc_start: 0.7103 (mt-10) cc_final: 0.6673 (tt0) REVERT: G 147 HIS cc_start: 0.7570 (t-90) cc_final: 0.7283 (t-170) REVERT: G 155 THR cc_start: 0.6808 (m) cc_final: 0.6405 (t) REVERT: G 199 LEU cc_start: 0.7360 (tp) cc_final: 0.7146 (tp) REVERT: G 215 GLU cc_start: 0.7590 (pt0) cc_final: 0.7256 (pt0) REVERT: H 143 GLU cc_start: 0.7057 (mt-10) cc_final: 0.6695 (mt-10) REVERT: H 147 HIS cc_start: 0.7455 (t-90) cc_final: 0.7181 (t-170) REVERT: H 148 HIS cc_start: 0.7136 (t70) cc_final: 0.6898 (t-170) REVERT: H 199 LEU cc_start: 0.7367 (tp) cc_final: 0.7132 (tp) outliers start: 25 outliers final: 17 residues processed: 245 average time/residue: 1.5907 time to fit residues: 414.8669 Evaluate side-chains 248 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 224 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR 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 143 SER Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain C residue 105 THR 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 108 LEU Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 144 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 92 optimal weight: 0.0030 chunk 139 optimal weight: 6.9990 chunk 128 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 118 optimal weight: 9.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN A 260 GLN A 275 ASN B 275 ASN C 234 GLN C 260 GLN D 260 GLN F 150 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.3264 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 : 0.466 8.822 16442 Z= 0.240 Chirality : 0.035 0.109 1778 Planarity : 0.004 0.038 2066 Dihedral : 15.513 146.257 2161 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.72 % Allowed : 15.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.72 (0.23), residues: 1422 helix: 2.55 (0.16), residues: 1118 sheet: None (None), residues: 0 loop : -1.22 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 200 HIS 0.003 0.001 HIS C 148 PHE 0.013 0.001 PHE A 110 TYR 0.011 0.001 TYR B 196 ARG 0.003 0.000 ARG C 159 ********************** 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 253 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 234 time to evaluate : 1.339 Fit side-chains revert: symmetry clash REVERT: A 108 LEU cc_start: 0.6614 (OUTLIER) cc_final: 0.6233 (mt) REVERT: A 109 GLU cc_start: 0.5222 (mt-10) cc_final: 0.4888 (tt0) REVERT: A 119 GLU cc_start: 0.5363 (tm-30) cc_final: 0.5150 (tm-30) REVERT: A 163 GLU cc_start: 0.6388 (mt-10) cc_final: 0.6139 (mt-10) REVERT: A 179 ASP cc_start: 0.7323 (p0) cc_final: 0.7048 (p0) REVERT: A 208 MET cc_start: 0.7751 (mtp) cc_final: 0.7407 (mtp) REVERT: A 271 ARG cc_start: 0.7017 (ttp80) cc_final: 0.6497 (mtm-85) REVERT: B 108 LEU cc_start: 0.6753 (mm) cc_final: 0.6466 (mt) REVERT: B 109 GLU cc_start: 0.5294 (mt-10) cc_final: 0.4925 (tp30) REVERT: B 119 GLU cc_start: 0.5759 (tm-30) cc_final: 0.4704 (tp30) REVERT: B 163 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.6382 (mt-10) REVERT: B 179 ASP cc_start: 0.7315 (p0) cc_final: 0.7001 (p0) REVERT: B 260 GLN cc_start: 0.7301 (pt0) cc_final: 0.7044 (pp30) REVERT: B 271 ARG cc_start: 0.6798 (ttm110) cc_final: 0.6499 (ttp-170) REVERT: B 274 GLU cc_start: 0.7436 (tt0) cc_final: 0.7021 (tt0) REVERT: B 283 MET cc_start: 0.3365 (mmm) cc_final: 0.2283 (ppp) REVERT: C 108 LEU cc_start: 0.6670 (mm) cc_final: 0.6354 (mt) REVERT: C 109 GLU cc_start: 0.5501 (mt-10) cc_final: 0.4874 (tp30) REVERT: C 123 GLU cc_start: 0.5549 (tt0) cc_final: 0.4900 (tm-30) REVERT: C 162 GLU cc_start: 0.6727 (pt0) cc_final: 0.6319 (pt0) REVERT: C 163 GLU cc_start: 0.6766 (OUTLIER) cc_final: 0.6440 (mt-10) REVERT: C 164 GLU cc_start: 0.6930 (mt-10) cc_final: 0.6649 (mt-10) REVERT: C 177 LYS cc_start: 0.6985 (mtpp) cc_final: 0.6591 (mmmt) REVERT: C 179 ASP cc_start: 0.7268 (p0) cc_final: 0.6982 (p0) REVERT: C 208 MET cc_start: 0.7722 (mtp) cc_final: 0.7357 (mtp) REVERT: C 260 GLN cc_start: 0.7252 (pt0) cc_final: 0.6728 (pm20) REVERT: C 271 ARG cc_start: 0.6830 (ttm110) cc_final: 0.6511 (ttp-170) REVERT: C 274 GLU cc_start: 0.7356 (tt0) cc_final: 0.7141 (tt0) REVERT: D 108 LEU cc_start: 0.6619 (OUTLIER) cc_final: 0.6221 (mt) REVERT: D 109 GLU cc_start: 0.5233 (mt-10) cc_final: 0.4732 (tp30) REVERT: D 119 GLU cc_start: 0.5468 (tm-30) cc_final: 0.5108 (tm-30) REVERT: D 177 LYS cc_start: 0.6974 (mtpp) cc_final: 0.6496 (mmtt) REVERT: D 179 ASP cc_start: 0.7306 (p0) cc_final: 0.6998 (p0) REVERT: D 260 GLN cc_start: 0.7247 (pt0) cc_final: 0.6717 (pm20) REVERT: D 271 ARG cc_start: 0.7018 (ttp80) cc_final: 0.6640 (ttp-170) REVERT: D 274 GLU cc_start: 0.7503 (tt0) cc_final: 0.7209 (tt0) REVERT: E 76 ARG cc_start: 0.7097 (mtt180) cc_final: 0.6487 (mpp-170) REVERT: E 135 MET cc_start: 0.6570 (mmp) cc_final: 0.6356 (mmm) REVERT: E 143 GLU cc_start: 0.7013 (mt-10) cc_final: 0.6623 (tt0) REVERT: E 147 HIS cc_start: 0.7393 (t-90) cc_final: 0.7154 (t-170) REVERT: E 155 THR cc_start: 0.6741 (m) cc_final: 0.6357 (t) REVERT: F 71 MET cc_start: 0.8348 (tpt) cc_final: 0.8044 (mmm) REVERT: F 147 HIS cc_start: 0.7360 (t-90) cc_final: 0.7094 (t-170) REVERT: F 148 HIS cc_start: 0.7178 (t70) cc_final: 0.6931 (t-170) REVERT: F 155 THR cc_start: 0.6507 (m) cc_final: 0.6182 (t) REVERT: F 199 LEU cc_start: 0.7254 (tp) cc_final: 0.7001 (tp) REVERT: G 76 ARG cc_start: 0.7397 (mmm-85) cc_final: 0.6357 (mpp-170) REVERT: G 143 GLU cc_start: 0.7050 (mt-10) cc_final: 0.6646 (tt0) REVERT: G 147 HIS cc_start: 0.7437 (t-90) cc_final: 0.7175 (t-170) REVERT: G 155 THR cc_start: 0.6744 (m) cc_final: 0.6358 (t) REVERT: G 215 GLU cc_start: 0.7478 (pt0) cc_final: 0.7101 (pt0) REVERT: H 71 MET cc_start: 0.8339 (tpt) cc_final: 0.8049 (mmm) REVERT: H 143 GLU cc_start: 0.7026 (mt-10) cc_final: 0.6641 (tt0) REVERT: H 147 HIS cc_start: 0.7284 (t-90) cc_final: 0.7059 (t-170) REVERT: H 148 HIS cc_start: 0.7141 (t70) cc_final: 0.6910 (t-170) REVERT: H 199 LEU cc_start: 0.7285 (tp) cc_final: 0.7039 (tp) outliers start: 19 outliers final: 14 residues processed: 246 average time/residue: 1.6354 time to fit residues: 427.5780 Evaluate side-chains 251 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 233 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR 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 143 SER Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain C residue 105 THR 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 E residue 144 SER Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain H residue 144 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 0.7980 chunk 102 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 20 optimal weight: 0.0020 chunk 97 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN B 275 ASN C 234 GLN F 150 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.178998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.138544 restraints weight = 56685.862| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 5.25 r_work: 0.3089 rms_B_bonded: 5.19 restraints_weight: 2.0000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3074 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3073 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3341 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= 0.124 Angle : 0.464 8.786 16442 Z= 0.237 Chirality : 0.035 0.109 1778 Planarity : 0.004 0.038 2066 Dihedral : 14.820 146.809 2161 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.72 % Allowed : 15.85 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.83 (0.23), residues: 1422 helix: 2.66 (0.16), residues: 1114 sheet: None (None), residues: 0 loop : -1.24 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 200 HIS 0.003 0.001 HIS F 57 PHE 0.012 0.001 PHE A 110 TYR 0.016 0.001 TYR F 212 ARG 0.003 0.000 ARG C 159 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6494.55 seconds wall clock time: 114 minutes 17.29 seconds (6857.29 seconds total)