Starting phenix.real_space_refine on Sun Jun 15 00:05:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sss_25413/06_2025/7sss_25413.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sss_25413/06_2025/7sss_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/cci-nas-00/data/ceres_data/7sss_25413/06_2025/7sss_25413.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sss_25413/06_2025/7sss_25413.map" model { file = "/net/cci-nas-00/data/ceres_data/7sss_25413/06_2025/7sss_25413.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sss_25413/06_2025/7sss_25413.cif" } 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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 21.75, per 1000 atoms: 1.78 Number of scatterers: 12190 At special positions: 0 Unit cell: (95.795, 104.125, 92.463, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 P 20 15.00 O 2394 8.00 N 2009 7.00 C 7695 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.75 Conformation dependent library (CDL) restraints added in 2.6 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... Secondary structure from input PDB file: 66 helices and 0 sheets defined 82.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 95 through 108 removed outlier: 3.802A pdb=" N LEU A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN A 100 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 127 removed outlier: 3.701A pdb=" N ILE A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER A 127 " --> pdb=" O GLU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 170 Processing helix chain 'A' and resid 177 through 191 Processing helix chain 'A' and resid 192 through 197 Proline residue: A 195 - end of helix No H-bonds generated for 'chain 'A' and resid 192 through 197' Processing helix chain 'A' and resid 199 through 208 Processing helix chain 'A' and resid 212 through 231 Processing helix chain 'A' and resid 238 through 260 removed outlier: 3.681A pdb=" N GLN A 260 " --> pdb=" O LEU A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 265 No H-bonds generated for 'chain 'A' and resid 263 through 265' Processing helix chain 'A' and resid 266 through 282 removed outlier: 3.558A pdb=" N ASN A 282 " --> pdb=" O ASN A 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 108 removed outlier: 3.615A pdb=" N LEU B 108 " --> pdb=" O LEU B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 115 Processing helix chain 'B' and resid 117 through 127 removed outlier: 3.781A pdb=" N ILE B 121 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER B 127 " --> pdb=" O GLU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 171 removed outlier: 3.586A pdb=" N LEU B 170 " --> pdb=" O LYS B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 191 Processing helix chain 'B' and resid 192 through 197 Proline residue: B 195 - end of helix No H-bonds generated for 'chain 'B' and resid 192 through 197' Processing helix chain 'B' and resid 199 through 208 Processing helix chain 'B' and resid 212 through 231 Processing helix chain 'B' and resid 238 through 260 removed outlier: 3.677A pdb=" N GLN B 260 " --> pdb=" O LEU B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 265 No H-bonds generated for 'chain 'B' and resid 263 through 265' Processing helix chain 'B' and resid 266 through 281 Processing helix chain 'C' and resid 96 through 108 removed outlier: 3.580A pdb=" N LEU C 108 " --> pdb=" O LEU C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 127 removed outlier: 3.832A pdb=" N ILE C 121 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 170 removed outlier: 3.569A pdb=" N LEU C 167 " --> pdb=" O GLU C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 191 Processing helix chain 'C' and resid 192 through 197 Proline residue: C 195 - end of helix No H-bonds generated for 'chain 'C' and resid 192 through 197' Processing helix chain 'C' and resid 199 through 208 Processing helix chain 'C' and resid 212 through 231 Processing helix chain 'C' and resid 238 through 260 removed outlier: 3.677A pdb=" N GLN C 260 " --> pdb=" O LEU C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 265 No H-bonds generated for 'chain 'C' and resid 263 through 265' Processing helix chain 'C' and resid 266 through 282 Processing helix chain 'D' and resid 97 through 108 removed outlier: 3.629A pdb=" N LEU D 108 " --> pdb=" O LEU D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 115 Processing helix chain 'D' and resid 117 through 127 removed outlier: 3.722A pdb=" N ILE D 121 " --> pdb=" O THR D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 170 Processing helix chain 'D' and resid 177 through 191 Processing helix chain 'D' and resid 192 through 197 Proline residue: D 195 - end of helix No H-bonds generated for 'chain 'D' and resid 192 through 197' Processing helix chain 'D' and resid 199 through 208 Processing helix chain 'D' and resid 212 through 231 Processing helix chain 'D' and resid 238 through 260 removed outlier: 3.679A pdb=" N GLN D 260 " --> pdb=" O LEU D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 265 No H-bonds generated for 'chain 'D' and resid 263 through 265' Processing helix chain 'D' and resid 266 through 282 Processing helix chain 'E' and resid 46 through 75 removed outlier: 3.568A pdb=" N VAL E 73 " --> pdb=" O GLY E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 105 Processing helix chain 'E' and resid 111 through 126 removed outlier: 3.564A pdb=" N PHE E 120 " --> pdb=" O ASN E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 157 Processing helix chain 'E' and resid 164 through 178 Processing helix chain 'E' and resid 193 through 215 Processing helix chain 'F' and resid 46 through 74 Processing helix chain 'F' and resid 79 through 105 Processing helix chain 'F' and resid 111 through 126 removed outlier: 3.570A pdb=" N VAL F 117 " --> pdb=" O PRO F 113 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE F 120 " --> pdb=" O ASN F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 160 removed outlier: 3.987A pdb=" N GLU F 158 " --> pdb=" O ARG F 154 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU F 159 " --> pdb=" O THR F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 178 removed outlier: 3.512A pdb=" N LEU F 168 " --> pdb=" O TYR F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 217 removed outlier: 3.500A pdb=" N VAL F 198 " --> pdb=" O PRO F 194 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG F 216 " --> pdb=" O TYR F 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 74 Processing helix chain 'G' and resid 79 through 105 Processing helix chain 'G' and resid 111 through 126 removed outlier: 3.546A pdb=" N VAL G 117 " --> pdb=" O PRO G 113 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE G 120 " --> pdb=" O ASN G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 157 Processing helix chain 'G' and resid 164 through 178 Processing helix chain 'G' and resid 193 through 217 removed outlier: 4.012A pdb=" N ARG G 216 " --> pdb=" O TYR G 212 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 74 Processing helix chain 'H' and resid 79 through 105 Processing helix chain 'H' and resid 111 through 126 removed outlier: 3.543A pdb=" N VAL H 117 " --> pdb=" O PRO H 113 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE H 120 " --> pdb=" O ASN H 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 160 removed outlier: 3.661A pdb=" N GLU H 159 " --> pdb=" O THR H 155 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP H 160 " --> pdb=" O LEU H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 178 removed outlier: 3.537A pdb=" N LEU H 168 " --> pdb=" O TYR H 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 193 through 217 removed outlier: 3.506A pdb=" N VAL H 198 " --> pdb=" O PRO H 194 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG H 216 " --> pdb=" O TYR H 212 " (cutoff:3.500A) 878 hydrogen bonds defined for protein. 2644 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.98 Time building geometry restraints manager: 4.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1921 1.32 - 1.44: 3132 1.44 - 1.56: 7000 1.56 - 1.68: 40 1.68 - 1.81: 132 Bond restraints: 12225 Sorted by residual: bond pdb=" N ILE A 250 " pdb=" CA ILE A 250 " ideal model delta sigma weight residual 1.461 1.492 -0.031 1.17e-02 7.31e+03 6.94e+00 bond pdb=" N AARG B 276 " pdb=" CA AARG B 276 " ideal model delta sigma weight residual 1.459 1.489 -0.029 1.19e-02 7.06e+03 6.05e+00 bond pdb=" O3 NAD E 306 " pdb=" PA NAD E 306 " ideal model delta sigma weight residual 1.653 1.604 0.049 2.00e-02 2.50e+03 6.04e+00 bond pdb=" O3 NAD F 306 " pdb=" PA NAD F 306 " ideal model delta sigma weight residual 1.653 1.604 0.049 2.00e-02 2.50e+03 5.95e+00 bond pdb=" C1 PEV C 405 " pdb=" O3P PEV C 405 " ideal model delta sigma weight residual 1.407 1.454 -0.047 2.00e-02 2.50e+03 5.57e+00 ... (remaining 12220 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 16157 1.99 - 3.98: 222 3.98 - 5.97: 45 5.97 - 7.96: 2 7.96 - 9.95: 16 Bond angle restraints: 16442 Sorted by residual: angle pdb=" O3P PEV H 301 " pdb=" P PEV H 301 " pdb=" O4P PEV H 301 " ideal model delta sigma weight residual 93.57 103.52 -9.95 3.00e+00 1.11e-01 1.10e+01 angle pdb=" O3P PEV C 401 " pdb=" P PEV C 401 " pdb=" O4P PEV C 401 " ideal model delta sigma weight residual 93.57 103.49 -9.92 3.00e+00 1.11e-01 1.09e+01 angle pdb=" CA AARG B 276 " pdb=" C AARG B 276 " pdb=" O AARG B 276 " ideal model delta sigma weight residual 120.82 117.35 3.47 1.05e+00 9.07e-01 1.09e+01 angle pdb=" O3P PEV H 302 " pdb=" P PEV H 302 " pdb=" O4P PEV H 302 " ideal model delta sigma weight residual 93.57 103.40 -9.83 3.00e+00 1.11e-01 1.07e+01 angle pdb=" O3P PEV C 403 " pdb=" P PEV C 403 " pdb=" O4P PEV C 403 " ideal model delta sigma weight residual 93.57 103.22 -9.65 3.00e+00 1.11e-01 1.03e+01 ... (remaining 16437 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 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: 3838 2.84 - 3.35: 11471 3.35 - 3.87: 20898 3.87 - 4.38: 26733 4.38 - 4.90: 42144 Nonbonded interactions: 105084 Sorted by model distance: nonbonded pdb=" ND1 HIS B 211 " pdb=" OG SER E 201 " model vdw 2.323 3.120 nonbonded pdb=" ND1 HIS A 211 " pdb=" OG SER G 201 " model vdw 2.329 3.120 nonbonded pdb=" ND1 HIS D 211 " pdb=" OG SER H 201 " model vdw 2.330 3.120 nonbonded pdb=" OD2 ASP F 50 " pdb=" O HOH F 401 " model vdw 2.332 3.040 nonbonded pdb=" ND1 HIS C 211 " pdb=" OG SER F 201 " model vdw 2.333 3.120 ... (remaining 105079 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 95 through 151 or resid 153 through 162 or (resid 163 and \ (name N or name CA or name C or name O or name CB )) or resid 164 through 209 or \ (resid 210 and (name N or name CA or name C or name O or name CB or name CD )) \ or resid 211 through 275 or resid 277 through 283)) selection = (chain 'B' and (resid 95 through 97 or (resid 98 and (name N or name CA or name \ C or name O or name CB )) or resid 99 through 151 or resid 153 through 162 or (r \ esid 163 and (name N or name CA or name C or name O or name CB )) or resid 164 t \ hrough 209 or (resid 210 and (name N or name CA or name C or name O or name CB o \ r name CD )) or resid 211 through 275 or resid 277 through 283)) selection = (chain 'C' and (resid 95 through 97 or (resid 98 and (name N or name CA or name \ C or name O or name CB )) or resid 99 through 151 or resid 153 through 162 or (r \ esid 163 and (name N or name CA or name C or name O or name CB )) or resid 164 t \ hrough 275 or resid 277 through 283)) selection = (chain 'D' and (resid 95 through 97 or (resid 98 and (name N or name CA or name \ C or name O or name CB )) or resid 99 through 151 or resid 153 through 209 or (r \ esid 210 and (name N or name CA or name C or name O or name CB or name CD )) or \ resid 211 through 275 or resid 277 through 283)) } ncs_group { reference = (chain 'E' and (resid 45 through 95 or resid 97 through 217 or (resid 301 and (n \ ame C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 o \ r name C2 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 \ or name O11 or name O1P or name O2 or name O2P or name O3 or name O31 or name O \ 3P or name O4P or name P )) or (resid 305 and (name C18 or name C19 or name C20 \ or name C21 or name C22)))) selection = (chain 'F' and (resid 45 through 95 or resid 97 through 182 or (resid 183 and (n \ ame N or name CA or name C or name O or name CB )) or resid 184 through 213 or ( \ resid 214 and (name N or name CA or name C or name O or name CB )) or resid 215 \ through 217 or (resid 301 and (name C1 or name C11 or name C12 or name C13 or na \ me C14 or name C15 or name C16 or name C2 or name C3 or name C31 or name C32 or \ name C33 or name C34 or name C35 or name O11 or name O1P or name O2 or name O2P \ or name O3 or name O31 or name O3P or name O4P or name P )) or (resid 305 and (n \ ame C17 or name C18 or name C19 or name C20 or name C21)))) selection = (chain 'G' and (resid 45 through 95 or resid 97 through 182 or (resid 183 and (n \ ame N or name CA or name C or name O or name CB )) or resid 184 through 213 or ( \ resid 214 and (name N or name CA or name C or name O or name CB )) or resid 215 \ through 217 or (resid 301 and (name C1 or name C11 or name C12 or name C13 or na \ me C14 or name C15 or name C16 or name C2 or name C3 or name C31 or name C32 or \ name C33 or name C34 or name C35 or name O11 or name O1P or name O2 or name O2P \ or name O3 or name O31 or name O3P or name O4P or name P )) or (resid 305 and (n \ ame C18 or name C19 or name C20 or name C21 or name C22)))) selection = (chain 'H' and (resid 45 through 95 or resid 97 through 182 or (resid 183 and (n \ ame N or name CA or name C or name O or name CB )) or resid 184 through 213 or ( \ resid 214 and (name N or name CA or name C or name O or name CB )) or resid 215 \ through 217 or (resid 301 and (name C1 or name C11 or name C12 or name C13 or na \ me C14 or name C15 or name C16 or name C2 or name C3 or name C31 or name C32 or \ name C33 or name C34 or name C35 or name O11 or name O1P or name O2 or name O2P \ or name O3 or name O31 or name O3P or name O4P or name P )) or (resid 305 and (n \ ame C18 or name C19 or name C20 or name C21 or name C22)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 55.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 48.850 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:23.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.230 ------------------------------------------------------------------------------- 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= 0.268 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 Details of bonding type rmsd hydrogen bonds : bond 0.21359 ( 878) hydrogen bonds : angle 6.18914 ( 2644) covalent geometry : bond 0.00559 (12225) covalent geometry : angle 0.66092 (16442) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 325 time to evaluate : 1.311 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: 1.6913 time to fit residues: 582.9934 Evaluate side-chains 270 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 266 time to evaluate : 1.365 ------------------------------------------------------------------------------- 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: 0.9980 chunk 58 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 71 optimal weight: 0.8980 chunk 56 optimal weight: 9.9990 chunk 109 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 ASN C 275 ASN E 98 ASN F 98 ASN F 182 HIS G 98 ASN H 98 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.177087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.138317 restraints weight = 51087.628| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 4.66 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3518 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3518 r_free = 0.3518 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3517 r_free = 0.3517 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3517 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1759 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= 0.131 Angle : 0.544 10.922 16442 Z= 0.279 Chirality : 0.037 0.114 1778 Planarity : 0.005 0.053 2066 Dihedral : 19.068 172.639 2169 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.55 % Allowed : 9.56 % Favored : 88.89 % 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: 2.68 (0.23), residues: 1422 helix: 2.40 (0.15), residues: 1150 sheet: None (None), residues: 0 loop : -1.05 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 240 HIS 0.004 0.001 HIS H 57 PHE 0.009 0.001 PHE B 272 TYR 0.010 0.001 TYR A 230 ARG 0.003 0.001 ARG H 46 Details of bonding type rmsd hydrogen bonds : bond 0.05823 ( 878) hydrogen bonds : angle 3.53633 ( 2644) covalent geometry : bond 0.00242 (12225) covalent geometry : angle 0.54392 (16442) *********************** 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 299 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 281 time to evaluate : 1.245 Fit side-chains REVERT: A 109 GLU cc_start: 0.5274 (mt-10) cc_final: 0.5046 (tt0) REVERT: A 123 GLU cc_start: 0.5398 (tt0) cc_final: 0.4932 (tm-30) REVERT: A 163 GLU cc_start: 0.6504 (mt-10) cc_final: 0.6200 (mt-10) REVERT: A 167 LEU cc_start: 0.6999 (mt) cc_final: 0.6600 (tp) REVERT: A 260 GLN cc_start: 0.7233 (pt0) cc_final: 0.6459 (pm20) REVERT: A 271 ARG cc_start: 0.7136 (ttm110) cc_final: 0.6810 (mtm-85) REVERT: A 274 GLU cc_start: 0.7739 (tt0) cc_final: 0.7480 (tt0) REVERT: A 276 ARG cc_start: 0.7357 (mmm-85) cc_final: 0.7072 (mmm160) REVERT: A 279 ASP cc_start: 0.6718 (m-30) cc_final: 0.6429 (m-30) REVERT: B 109 GLU cc_start: 0.5315 (mt-10) cc_final: 0.4849 (tp30) REVERT: B 119 GLU cc_start: 0.5938 (tm-30) cc_final: 0.5693 (tm-30) REVERT: B 123 GLU cc_start: 0.5479 (OUTLIER) cc_final: 0.5137 (tm-30) REVERT: B 163 GLU cc_start: 0.6632 (mm-30) cc_final: 0.6360 (mt-10) REVERT: B 164 GLU cc_start: 0.7081 (mt-10) cc_final: 0.6743 (mt-10) REVERT: B 260 GLN cc_start: 0.7311 (pt0) cc_final: 0.6530 (pm20) REVERT: B 271 ARG cc_start: 0.7186 (ttm110) cc_final: 0.6902 (mtm-85) REVERT: B 274 GLU cc_start: 0.7735 (tt0) cc_final: 0.7525 (tt0) REVERT: B 279 ASP cc_start: 0.6703 (m-30) cc_final: 0.6444 (m-30) REVERT: B 281 MET cc_start: 0.6408 (OUTLIER) cc_final: 0.4375 (mpt) REVERT: C 109 GLU cc_start: 0.5309 (mt-10) cc_final: 0.4855 (tp30) REVERT: C 123 GLU cc_start: 0.5708 (tt0) cc_final: 0.5233 (tm-30) REVERT: C 162 GLU cc_start: 0.6373 (pt0) cc_final: 0.5988 (pt0) REVERT: C 163 GLU cc_start: 0.6904 (mm-30) cc_final: 0.6614 (mt-10) REVERT: C 169 GLN cc_start: 0.6315 (mt0) cc_final: 0.5809 (pt0) REVERT: C 177 LYS cc_start: 0.7048 (mtpp) cc_final: 0.6553 (mmtt) REVERT: C 260 GLN cc_start: 0.7196 (pt0) cc_final: 0.6606 (pm20) REVERT: C 271 ARG cc_start: 0.7112 (ttm110) cc_final: 0.6844 (mtm-85) REVERT: C 274 GLU cc_start: 0.7769 (tt0) cc_final: 0.7500 (tt0) REVERT: C 276 ARG cc_start: 0.7410 (mmm-85) cc_final: 0.6616 (mpp-170) REVERT: D 109 GLU cc_start: 0.5251 (mt-10) cc_final: 0.4809 (tp30) REVERT: D 123 GLU cc_start: 0.5041 (tt0) cc_final: 0.4551 (tm-30) REVERT: D 177 LYS cc_start: 0.7025 (mtpp) cc_final: 0.6514 (mmtt) REVERT: D 260 GLN cc_start: 0.7290 (pt0) cc_final: 0.6506 (pm20) REVERT: D 271 ARG cc_start: 0.7174 (ttm110) cc_final: 0.6880 (mtm-85) REVERT: D 274 GLU cc_start: 0.7748 (tt0) cc_final: 0.7537 (tt0) REVERT: D 279 ASP cc_start: 0.6676 (m-30) cc_final: 0.6442 (m-30) REVERT: D 281 MET cc_start: 0.6353 (mmp) cc_final: 0.5972 (mmm) REVERT: E 76 ARG cc_start: 0.7214 (mtt180) cc_final: 0.6217 (mpp-170) REVERT: E 132 GLU cc_start: 0.6930 (mt-10) cc_final: 0.6606 (tt0) REVERT: E 143 GLU cc_start: 0.7355 (mt-10) cc_final: 0.6818 (tt0) REVERT: E 147 HIS cc_start: 0.7537 (t-90) cc_final: 0.7262 (t-90) REVERT: E 180 GLU cc_start: 0.5561 (tp30) cc_final: 0.5174 (tm-30) REVERT: E 215 GLU cc_start: 0.7734 (pt0) cc_final: 0.7324 (pt0) REVERT: F 50 ASP cc_start: 0.7086 (m-30) cc_final: 0.6658 (m-30) REVERT: F 143 GLU cc_start: 0.7294 (mt-10) cc_final: 0.6732 (tt0) REVERT: F 147 HIS cc_start: 0.7373 (t-90) cc_final: 0.7083 (t-170) REVERT: F 215 GLU cc_start: 0.7616 (pt0) cc_final: 0.7353 (pt0) REVERT: G 143 GLU cc_start: 0.7325 (mt-10) cc_final: 0.6860 (tt0) REVERT: G 147 HIS cc_start: 0.7564 (t-90) cc_final: 0.7291 (t-90) REVERT: G 180 GLU cc_start: 0.5709 (tp30) cc_final: 0.5455 (tm-30) REVERT: G 208 ARG cc_start: 0.7298 (mtt-85) cc_final: 0.6920 (mmt90) REVERT: G 215 GLU cc_start: 0.7629 (pt0) cc_final: 0.7347 (pt0) REVERT: H 132 GLU cc_start: 0.6890 (mt-10) cc_final: 0.6598 (tt0) REVERT: H 143 GLU cc_start: 0.7317 (mt-10) cc_final: 0.6788 (tt0) REVERT: H 147 HIS cc_start: 0.7478 (t-90) cc_final: 0.7175 (t-170) REVERT: H 172 LYS cc_start: 0.7611 (mttt) cc_final: 0.7407 (mmmm) REVERT: H 215 GLU cc_start: 0.7656 (pt0) cc_final: 0.7395 (pt0) outliers start: 18 outliers final: 1 residues processed: 283 average time/residue: 1.7070 time to fit residues: 512.2314 Evaluate side-chains 256 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 253 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain F residue 49 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 120 optimal weight: 8.9990 chunk 139 optimal weight: 4.9990 chunk 96 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 15 optimal weight: 9.9990 chunk 110 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 55 optimal weight: 0.0050 chunk 36 optimal weight: 8.9990 overall best weight: 1.9198 ------------------------------------------------------------------------------- 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 C 260 GLN C 275 ASN D 260 GLN E 98 ASN E 204 GLN F 98 ASN G 98 ASN H 98 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.177182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.139007 restraints weight = 56763.365| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 5.09 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3517 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3517 r_free = 0.3517 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3517 r_free = 0.3517 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3517 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12225 Z= 0.139 Angle : 0.564 8.125 16442 Z= 0.287 Chirality : 0.040 0.173 1778 Planarity : 0.005 0.054 2066 Dihedral : 17.692 163.048 2161 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.41 % Allowed : 12.32 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.02 (0.23), residues: 1422 helix: 2.65 (0.15), residues: 1150 sheet: None (None), residues: 0 loop : -1.02 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 200 HIS 0.005 0.002 HIS D 114 PHE 0.010 0.002 PHE G 174 TYR 0.010 0.002 TYR G 67 ARG 0.009 0.001 ARG A 202 Details of bonding type rmsd hydrogen bonds : bond 0.05158 ( 878) hydrogen bonds : angle 3.38996 ( 2644) covalent geometry : bond 0.00292 (12225) covalent geometry : angle 0.56402 (16442) *********************** 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 278 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 250 time to evaluate : 1.292 Fit side-chains REVERT: A 108 LEU cc_start: 0.6671 (OUTLIER) cc_final: 0.6297 (mt) REVERT: A 109 GLU cc_start: 0.5265 (mt-10) cc_final: 0.5003 (tt0) REVERT: A 119 GLU cc_start: 0.5722 (tm-30) cc_final: 0.5462 (tm-30) REVERT: A 123 GLU cc_start: 0.5247 (tt0) cc_final: 0.4729 (tm-30) REVERT: A 163 GLU cc_start: 0.6489 (mt-10) cc_final: 0.6178 (mt-10) REVERT: A 179 ASP cc_start: 0.7328 (p0) cc_final: 0.7070 (p0) REVERT: A 202 ARG cc_start: 0.7491 (tpm170) cc_final: 0.7261 (tpm170) REVERT: A 271 ARG cc_start: 0.7114 (ttm110) cc_final: 0.6787 (mtm-85) REVERT: A 276 ARG cc_start: 0.7304 (mmm-85) cc_final: 0.7015 (mmm160) REVERT: A 279 ASP cc_start: 0.6700 (m-30) cc_final: 0.6229 (t70) REVERT: B 108 LEU cc_start: 0.6720 (mm) cc_final: 0.6363 (mt) REVERT: B 109 GLU cc_start: 0.5380 (mt-10) cc_final: 0.4814 (tp30) REVERT: B 119 GLU cc_start: 0.5737 (tm-30) cc_final: 0.5442 (tm-30) REVERT: B 123 GLU cc_start: 0.5810 (OUTLIER) cc_final: 0.5344 (tm-30) REVERT: B 163 GLU cc_start: 0.6658 (mm-30) cc_final: 0.6337 (mt-10) REVERT: B 167 LEU cc_start: 0.6560 (OUTLIER) cc_final: 0.6343 (tp) REVERT: B 260 GLN cc_start: 0.7209 (pt0) cc_final: 0.6979 (pp30) REVERT: B 271 ARG cc_start: 0.7131 (ttm110) cc_final: 0.6829 (mtm-85) REVERT: B 279 ASP cc_start: 0.6758 (m-30) cc_final: 0.6467 (m-30) REVERT: B 281 MET cc_start: 0.6431 (OUTLIER) cc_final: 0.4553 (mpt) REVERT: C 108 LEU cc_start: 0.6740 (mm) cc_final: 0.6405 (mt) REVERT: C 109 GLU cc_start: 0.5401 (mt-10) cc_final: 0.4866 (tp30) REVERT: C 119 GLU cc_start: 0.5492 (tm-30) cc_final: 0.5160 (tm-30) REVERT: C 123 GLU cc_start: 0.5685 (OUTLIER) cc_final: 0.5200 (tm-30) REVERT: C 162 GLU cc_start: 0.6425 (pt0) cc_final: 0.6127 (pt0) REVERT: C 163 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.6550 (mt-10) REVERT: C 164 GLU cc_start: 0.6958 (mt-10) cc_final: 0.6647 (mt-10) REVERT: C 177 LYS cc_start: 0.7140 (mtpp) cc_final: 0.6658 (mmtt) REVERT: C 179 ASP cc_start: 0.7364 (p0) cc_final: 0.7115 (p0) REVERT: C 271 ARG cc_start: 0.7074 (ttm110) cc_final: 0.6764 (mtm-85) REVERT: C 274 GLU cc_start: 0.7677 (tt0) cc_final: 0.7435 (tt0) REVERT: C 276 ARG cc_start: 0.7483 (mmm-85) cc_final: 0.7259 (mmm160) REVERT: C 279 ASP cc_start: 0.6606 (m-30) cc_final: 0.6333 (m-30) REVERT: D 108 LEU cc_start: 0.6810 (mm) cc_final: 0.6432 (mt) REVERT: D 109 GLU cc_start: 0.5248 (mt-10) cc_final: 0.4744 (tp30) REVERT: D 119 GLU cc_start: 0.5621 (tm-30) cc_final: 0.5241 (tm-30) REVERT: D 167 LEU cc_start: 0.6648 (OUTLIER) cc_final: 0.6258 (tp) REVERT: D 177 LYS cc_start: 0.7066 (mtpp) cc_final: 0.6577 (mmtt) REVERT: D 179 ASP cc_start: 0.7337 (p0) cc_final: 0.7080 (p0) REVERT: D 271 ARG cc_start: 0.7152 (ttm110) cc_final: 0.6823 (mtm-85) REVERT: D 274 GLU cc_start: 0.7760 (tt0) cc_final: 0.7551 (tt0) REVERT: D 279 ASP cc_start: 0.6865 (m-30) cc_final: 0.6557 (m-30) REVERT: D 281 MET cc_start: 0.6549 (mmp) cc_final: 0.6324 (mmm) REVERT: E 143 GLU cc_start: 0.7265 (mt-10) cc_final: 0.6765 (tt0) REVERT: E 147 HIS cc_start: 0.7531 (t-90) cc_final: 0.7283 (t-170) REVERT: E 155 THR cc_start: 0.6701 (m) cc_final: 0.6306 (t) REVERT: E 180 GLU cc_start: 0.5486 (tp30) cc_final: 0.5154 (tm-30) REVERT: E 215 GLU cc_start: 0.7744 (pt0) cc_final: 0.7289 (pt0) REVERT: F 50 ASP cc_start: 0.7068 (m-30) cc_final: 0.6855 (m-30) REVERT: F 147 HIS cc_start: 0.7372 (t-90) cc_final: 0.7109 (t-170) REVERT: F 215 GLU cc_start: 0.7607 (pt0) cc_final: 0.7266 (pt0) REVERT: G 143 GLU cc_start: 0.7278 (mt-10) cc_final: 0.6740 (tt0) REVERT: G 147 HIS cc_start: 0.7585 (t-90) cc_final: 0.7311 (t-170) REVERT: G 155 THR cc_start: 0.6761 (m) cc_final: 0.6356 (t) REVERT: G 180 GLU cc_start: 0.5577 (tp30) cc_final: 0.5340 (tm-30) REVERT: G 208 ARG cc_start: 0.7299 (mtt-85) cc_final: 0.7015 (mmt90) REVERT: G 215 GLU cc_start: 0.7601 (pt0) cc_final: 0.7224 (pt0) REVERT: H 143 GLU cc_start: 0.7226 (mt-10) cc_final: 0.6766 (tt0) REVERT: H 147 HIS cc_start: 0.7511 (t-90) cc_final: 0.7271 (t-170) REVERT: H 215 GLU cc_start: 0.7623 (pt0) cc_final: 0.7276 (pt0) outliers start: 28 outliers final: 8 residues processed: 257 average time/residue: 2.2155 time to fit residues: 603.1709 Evaluate side-chains 256 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 241 time to evaluate : 1.654 ------------------------------------------------------------------------------- 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 143 SER Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 246 MET Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain G residue 49 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 44 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 138 optimal weight: 1.9990 chunk 133 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN A 275 ASN C 260 GLN C 275 ASN G 204 GLN H 93 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.174396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.133110 restraints weight = 54758.410| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 5.05 r_work: 0.3013 rms_B_bonded: 5.02 restraints_weight: 2.0000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2988 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12225 Z= 0.202 Angle : 0.680 9.056 16442 Z= 0.343 Chirality : 0.044 0.256 1778 Planarity : 0.005 0.044 2066 Dihedral : 18.737 169.998 2161 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.93 % Allowed : 12.49 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.22), residues: 1422 helix: 2.21 (0.15), residues: 1162 sheet: None (None), residues: 0 loop : -1.00 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 200 HIS 0.006 0.002 HIS H 182 PHE 0.016 0.003 PHE D 110 TYR 0.012 0.002 TYR E 67 ARG 0.005 0.001 ARG H 46 Details of bonding type rmsd hydrogen bonds : bond 0.06182 ( 878) hydrogen bonds : angle 3.68216 ( 2644) covalent geometry : bond 0.00454 (12225) covalent geometry : angle 0.68037 (16442) *********************** 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 274 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 241 time to evaluate : 1.372 Fit side-chains REVERT: A 108 LEU cc_start: 0.6456 (OUTLIER) cc_final: 0.6042 (mt) REVERT: A 109 GLU cc_start: 0.5461 (mt-10) cc_final: 0.5010 (tt0) REVERT: A 119 GLU cc_start: 0.5399 (tm-30) cc_final: 0.5071 (tm-30) REVERT: A 163 GLU cc_start: 0.6797 (mt-10) cc_final: 0.6523 (mt-10) REVERT: A 179 ASP cc_start: 0.7852 (p0) cc_final: 0.7530 (p0) REVERT: A 208 MET cc_start: 0.8534 (mtp) cc_final: 0.8266 (mtp) REVERT: A 271 ARG cc_start: 0.7767 (ttm110) cc_final: 0.7366 (mtm-85) REVERT: A 276 ARG cc_start: 0.7407 (mmm-85) cc_final: 0.7018 (mmm160) REVERT: A 279 ASP cc_start: 0.7002 (m-30) cc_final: 0.6380 (t70) REVERT: B 109 GLU cc_start: 0.5646 (mt-10) cc_final: 0.4853 (tp30) REVERT: B 119 GLU cc_start: 0.5342 (tm-30) cc_final: 0.5126 (tm-30) REVERT: B 163 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6546 (mt-10) REVERT: B 169 GLN cc_start: 0.6450 (mt0) cc_final: 0.6040 (pt0) REVERT: B 260 GLN cc_start: 0.7204 (pt0) cc_final: 0.6999 (pp30) REVERT: B 271 ARG cc_start: 0.7732 (ttm110) cc_final: 0.7415 (mtm-85) REVERT: B 279 ASP cc_start: 0.7170 (m-30) cc_final: 0.6871 (m-30) REVERT: C 109 GLU cc_start: 0.5623 (mt-10) cc_final: 0.4777 (tp30) REVERT: C 119 GLU cc_start: 0.5313 (tm-30) cc_final: 0.5062 (tm-30) REVERT: C 123 GLU cc_start: 0.5406 (OUTLIER) cc_final: 0.4588 (tm-30) REVERT: C 162 GLU cc_start: 0.7164 (pt0) cc_final: 0.6796 (pt0) REVERT: C 163 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.6779 (mt-10) REVERT: C 177 LYS cc_start: 0.7327 (mtpp) cc_final: 0.6820 (mmtt) REVERT: C 179 ASP cc_start: 0.7789 (p0) cc_final: 0.7470 (p0) REVERT: C 260 GLN cc_start: 0.7439 (pt0) cc_final: 0.7231 (pp30) REVERT: C 271 ARG cc_start: 0.7732 (ttm110) cc_final: 0.7385 (mtm-85) REVERT: C 274 GLU cc_start: 0.8238 (tt0) cc_final: 0.7974 (tt0) REVERT: C 276 ARG cc_start: 0.7607 (mmm-85) cc_final: 0.7280 (mmm160) REVERT: C 279 ASP cc_start: 0.7115 (m-30) cc_final: 0.6859 (m-30) REVERT: D 109 GLU cc_start: 0.5553 (mt-10) cc_final: 0.4703 (tp30) REVERT: D 119 GLU cc_start: 0.5320 (tm-30) cc_final: 0.5005 (tm-30) REVERT: D 123 GLU cc_start: 0.4951 (tt0) cc_final: 0.4206 (tm-30) REVERT: D 167 LEU cc_start: 0.6656 (OUTLIER) cc_final: 0.6113 (tp) REVERT: D 177 LYS cc_start: 0.7333 (mtpp) cc_final: 0.7080 (mttm) REVERT: D 179 ASP cc_start: 0.7753 (p0) cc_final: 0.7408 (p0) REVERT: D 271 ARG cc_start: 0.7727 (ttm110) cc_final: 0.7360 (mtm-85) REVERT: D 274 GLU cc_start: 0.8324 (tt0) cc_final: 0.8090 (tt0) REVERT: D 281 MET cc_start: 0.6924 (mmp) cc_final: 0.6688 (mmm) REVERT: E 76 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.6325 (mpp-170) REVERT: E 132 GLU cc_start: 0.7273 (mt-10) cc_final: 0.7003 (tt0) REVERT: E 143 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7369 (tt0) REVERT: E 155 THR cc_start: 0.6758 (OUTLIER) cc_final: 0.6328 (t) REVERT: F 147 HIS cc_start: 0.7965 (t-90) cc_final: 0.7667 (t-170) REVERT: G 143 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7407 (tt0) REVERT: G 155 THR cc_start: 0.6694 (m) cc_final: 0.6246 (t) REVERT: H 143 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7401 (tt0) REVERT: H 147 HIS cc_start: 0.7988 (t-90) cc_final: 0.7699 (t-170) outliers start: 33 outliers final: 15 residues processed: 250 average time/residue: 1.6943 time to fit residues: 449.5926 Evaluate side-chains 257 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 236 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain 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 167 LEU Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 246 MET Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 76 ARG Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 155 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 101 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 chunk 12 optimal weight: 0.6980 chunk 114 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN A 275 ASN B 275 ASN C 165 GLN C 275 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.176852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.136649 restraints weight = 54514.150| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 5.00 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3480 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3480 r_free = 0.3480 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3480 r_free = 0.3480 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3480 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12225 Z= 0.115 Angle : 0.514 8.676 16442 Z= 0.265 Chirality : 0.037 0.116 1778 Planarity : 0.004 0.048 2066 Dihedral : 17.488 171.319 2161 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.89 % Allowed : 14.47 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.19 (0.23), residues: 1422 helix: 2.76 (0.15), residues: 1162 sheet: None (None), residues: 0 loop : -1.13 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 200 HIS 0.004 0.001 HIS G 57 PHE 0.016 0.002 PHE D 110 TYR 0.009 0.001 TYR A 230 ARG 0.003 0.000 ARG H 175 Details of bonding type rmsd hydrogen bonds : bond 0.04540 ( 878) hydrogen bonds : angle 3.32735 ( 2644) covalent geometry : bond 0.00233 (12225) covalent geometry : angle 0.51449 (16442) *********************** 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 269 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 248 time to evaluate : 1.208 Fit side-chains REVERT: A 108 LEU cc_start: 0.6707 (OUTLIER) cc_final: 0.6283 (mt) REVERT: A 109 GLU cc_start: 0.5308 (mt-10) cc_final: 0.4922 (tt0) REVERT: A 119 GLU cc_start: 0.5484 (tm-30) cc_final: 0.5275 (tm-30) REVERT: A 163 GLU cc_start: 0.6392 (mt-10) cc_final: 0.6132 (mt-10) REVERT: A 167 LEU cc_start: 0.6716 (mt) cc_final: 0.6343 (tp) REVERT: A 179 ASP cc_start: 0.7412 (p0) cc_final: 0.7088 (p0) REVERT: A 271 ARG cc_start: 0.7065 (ttm110) cc_final: 0.6768 (mtm-85) REVERT: A 276 ARG cc_start: 0.7283 (mmm-85) cc_final: 0.6986 (mmm160) REVERT: A 279 ASP cc_start: 0.6656 (m-30) cc_final: 0.6183 (t70) REVERT: B 109 GLU cc_start: 0.5396 (mt-10) cc_final: 0.4910 (tp30) REVERT: B 119 GLU cc_start: 0.5565 (tm-30) cc_final: 0.5364 (tm-30) REVERT: B 123 GLU cc_start: 0.5743 (OUTLIER) cc_final: 0.5076 (tm-30) REVERT: B 163 GLU cc_start: 0.6621 (mm-30) cc_final: 0.6278 (mt-10) REVERT: B 169 GLN cc_start: 0.6440 (mt0) cc_final: 0.6043 (pt0) REVERT: B 271 ARG cc_start: 0.7066 (ttm110) cc_final: 0.6781 (mtm-85) REVERT: B 279 ASP cc_start: 0.6749 (m-30) cc_final: 0.6475 (m-30) REVERT: B 281 MET cc_start: 0.6652 (OUTLIER) cc_final: 0.4693 (mpt) REVERT: B 283 MET cc_start: 0.3336 (mmm) cc_final: 0.2169 (ppp) REVERT: C 108 LEU cc_start: 0.6554 (mp) cc_final: 0.6212 (mt) REVERT: C 109 GLU cc_start: 0.5494 (mt-10) cc_final: 0.4927 (tp30) REVERT: C 119 GLU cc_start: 0.5452 (tm-30) cc_final: 0.4545 (tp30) REVERT: C 123 GLU cc_start: 0.5718 (OUTLIER) cc_final: 0.5090 (tm-30) REVERT: C 162 GLU cc_start: 0.6470 (pt0) cc_final: 0.6210 (pt0) REVERT: C 163 GLU cc_start: 0.6786 (OUTLIER) cc_final: 0.6367 (mt-10) REVERT: C 164 GLU cc_start: 0.7033 (mt-10) cc_final: 0.6761 (mt-10) REVERT: C 177 LYS cc_start: 0.7161 (mtpp) cc_final: 0.6610 (mmtt) REVERT: C 179 ASP cc_start: 0.7428 (p0) cc_final: 0.7126 (p0) REVERT: C 208 MET cc_start: 0.7954 (mtp) cc_final: 0.7627 (mtp) REVERT: C 271 ARG cc_start: 0.7045 (ttm110) cc_final: 0.6699 (mtm-85) REVERT: C 274 GLU cc_start: 0.7664 (tt0) cc_final: 0.7412 (tt0) REVERT: C 276 ARG cc_start: 0.7464 (mmm-85) cc_final: 0.7219 (mmm160) REVERT: C 279 ASP cc_start: 0.6672 (m-30) cc_final: 0.6392 (m-30) REVERT: C 281 MET cc_start: 0.6717 (OUTLIER) cc_final: 0.5298 (mpt) REVERT: D 108 LEU cc_start: 0.6682 (mm) cc_final: 0.6293 (mt) REVERT: D 109 GLU cc_start: 0.5378 (mt-10) cc_final: 0.4758 (tp30) REVERT: D 119 GLU cc_start: 0.5370 (tm-30) cc_final: 0.5143 (tm-30) REVERT: D 123 GLU cc_start: 0.5327 (tt0) cc_final: 0.4837 (tm-30) REVERT: D 167 LEU cc_start: 0.6682 (mt) cc_final: 0.6243 (tp) REVERT: D 177 LYS cc_start: 0.7156 (mtpp) cc_final: 0.6632 (mmtt) REVERT: D 179 ASP cc_start: 0.7382 (p0) cc_final: 0.7079 (p0) REVERT: D 208 MET cc_start: 0.7970 (mtp) cc_final: 0.7646 (mtp) REVERT: D 260 GLN cc_start: 0.6877 (OUTLIER) cc_final: 0.6633 (pp30) REVERT: D 271 ARG cc_start: 0.7094 (ttm110) cc_final: 0.6855 (mtm-85) REVERT: D 274 GLU cc_start: 0.7729 (tt0) cc_final: 0.7506 (tt0) REVERT: D 279 ASP cc_start: 0.6754 (m-30) cc_final: 0.6461 (m-30) REVERT: E 143 GLU cc_start: 0.7176 (mt-10) cc_final: 0.6705 (tt0) REVERT: E 148 HIS cc_start: 0.7210 (t70) cc_final: 0.7003 (t-170) REVERT: E 155 THR cc_start: 0.6502 (m) cc_final: 0.6217 (t) REVERT: E 215 GLU cc_start: 0.7773 (pt0) cc_final: 0.7291 (pt0) REVERT: F 143 GLU cc_start: 0.7366 (mt-10) cc_final: 0.6948 (mt-10) REVERT: F 147 HIS cc_start: 0.7456 (t-90) cc_final: 0.7181 (t-170) REVERT: F 155 THR cc_start: 0.6441 (m) cc_final: 0.6045 (t) REVERT: G 143 GLU cc_start: 0.7205 (mt-10) cc_final: 0.6731 (tt0) REVERT: G 155 THR cc_start: 0.6677 (m) cc_final: 0.6349 (t) REVERT: H 143 GLU cc_start: 0.7175 (mt-10) cc_final: 0.6635 (tt0) REVERT: H 147 HIS cc_start: 0.7532 (t-90) cc_final: 0.7241 (t-170) REVERT: H 166 GLU cc_start: 0.5848 (mm-30) cc_final: 0.5573 (mt-10) REVERT: H 215 GLU cc_start: 0.7696 (pt0) cc_final: 0.7408 (pt0) outliers start: 21 outliers final: 8 residues processed: 256 average time/residue: 1.6976 time to fit residues: 460.8970 Evaluate side-chains 249 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 234 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 281 MET Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 49 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 20 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 chunk 95 optimal weight: 8.9990 chunk 130 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN A 275 ASN B 275 ASN C 234 GLN C 275 ASN E 93 HIS E 182 HIS H 204 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.174502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.134121 restraints weight = 53551.081| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 5.00 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3456 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3456 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12225 Z= 0.229 Angle : 0.734 9.113 16442 Z= 0.370 Chirality : 0.046 0.289 1778 Planarity : 0.006 0.041 2066 Dihedral : 18.637 173.953 2161 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.19 % Allowed : 13.44 % 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: 2.26 (0.22), residues: 1422 helix: 2.07 (0.15), residues: 1162 sheet: None (None), residues: 0 loop : -1.17 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 200 HIS 0.008 0.002 HIS A 199 PHE 0.017 0.003 PHE D 110 TYR 0.015 0.003 TYR G 212 ARG 0.008 0.001 ARG G 46 Details of bonding type rmsd hydrogen bonds : bond 0.06346 ( 878) hydrogen bonds : angle 3.76234 ( 2644) covalent geometry : bond 0.00535 (12225) covalent geometry : angle 0.73406 (16442) *********************** 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 270 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 234 time to evaluate : 1.422 Fit side-chains REVERT: A 108 LEU cc_start: 0.6629 (OUTLIER) cc_final: 0.6241 (mt) REVERT: A 109 GLU cc_start: 0.5498 (mt-10) cc_final: 0.5083 (tt0) REVERT: A 119 GLU cc_start: 0.5486 (tm-30) cc_final: 0.5235 (tm-30) REVERT: A 163 GLU cc_start: 0.6365 (mt-10) cc_final: 0.6151 (mt-10) REVERT: A 179 ASP cc_start: 0.7428 (p0) cc_final: 0.7188 (p0) REVERT: A 208 MET cc_start: 0.8010 (mtp) cc_final: 0.7610 (mtp) REVERT: A 271 ARG cc_start: 0.7128 (ttm110) cc_final: 0.6732 (mtm-85) REVERT: A 276 ARG cc_start: 0.7383 (mmm-85) cc_final: 0.7110 (mmm160) REVERT: A 279 ASP cc_start: 0.6627 (m-30) cc_final: 0.6143 (t70) REVERT: A 281 MET cc_start: 0.6601 (OUTLIER) cc_final: 0.4578 (mpt) REVERT: B 109 GLU cc_start: 0.5560 (mt-10) cc_final: 0.5144 (tt0) REVERT: B 119 GLU cc_start: 0.5687 (tm-30) cc_final: 0.4756 (tp30) REVERT: B 123 GLU cc_start: 0.5775 (OUTLIER) cc_final: 0.5485 (tt0) REVERT: B 163 GLU cc_start: 0.6638 (mm-30) cc_final: 0.6205 (mt-10) REVERT: B 169 GLN cc_start: 0.6439 (mt0) cc_final: 0.6046 (pt0) REVERT: B 271 ARG cc_start: 0.7166 (ttm110) cc_final: 0.6802 (mtm-85) REVERT: B 279 ASP cc_start: 0.6798 (m-30) cc_final: 0.6503 (m-30) REVERT: C 109 GLU cc_start: 0.5676 (mt-10) cc_final: 0.4977 (tp30) REVERT: C 119 GLU cc_start: 0.5387 (tm-30) cc_final: 0.4448 (tp30) REVERT: C 123 GLU cc_start: 0.5762 (OUTLIER) cc_final: 0.5055 (tm-30) REVERT: C 162 GLU cc_start: 0.6501 (pt0) cc_final: 0.6241 (pt0) REVERT: C 177 LYS cc_start: 0.7123 (mtpp) cc_final: 0.6549 (mmtt) REVERT: C 179 ASP cc_start: 0.7469 (p0) cc_final: 0.7171 (p0) REVERT: C 208 MET cc_start: 0.7976 (mtp) cc_final: 0.7693 (mtp) REVERT: C 271 ARG cc_start: 0.7133 (ttm110) cc_final: 0.6809 (mtm-85) REVERT: C 274 GLU cc_start: 0.7753 (tt0) cc_final: 0.7458 (tt0) REVERT: C 276 ARG cc_start: 0.7562 (mmm-85) cc_final: 0.7298 (mmm160) REVERT: C 279 ASP cc_start: 0.6758 (m-30) cc_final: 0.6465 (m-30) REVERT: D 109 GLU cc_start: 0.5449 (mt-10) cc_final: 0.4782 (tp30) REVERT: D 119 GLU cc_start: 0.5480 (tm-30) cc_final: 0.5173 (tm-30) REVERT: D 123 GLU cc_start: 0.5348 (tt0) cc_final: 0.4738 (tm-30) REVERT: D 167 LEU cc_start: 0.6786 (mt) cc_final: 0.6261 (tp) REVERT: D 177 LYS cc_start: 0.7150 (mtpp) cc_final: 0.6576 (mmtt) REVERT: D 179 ASP cc_start: 0.7439 (p0) cc_final: 0.7143 (p0) REVERT: D 271 ARG cc_start: 0.7154 (ttm110) cc_final: 0.6792 (mtm-85) REVERT: D 274 GLU cc_start: 0.7826 (tt0) cc_final: 0.7574 (tt0) REVERT: E 143 GLU cc_start: 0.7290 (mt-10) cc_final: 0.6831 (tt0) REVERT: F 155 THR cc_start: 0.6444 (m) cc_final: 0.6013 (t) REVERT: G 143 GLU cc_start: 0.7298 (mt-10) cc_final: 0.6795 (tt0) REVERT: G 155 THR cc_start: 0.6574 (OUTLIER) cc_final: 0.6287 (t) REVERT: H 143 GLU cc_start: 0.7350 (mt-10) cc_final: 0.6941 (mt-10) REVERT: H 147 HIS cc_start: 0.7737 (t-90) cc_final: 0.7431 (t-170) REVERT: H 166 GLU cc_start: 0.5838 (OUTLIER) cc_final: 0.5544 (mt-10) outliers start: 36 outliers final: 20 residues processed: 247 average time/residue: 2.1643 time to fit residues: 568.7665 Evaluate side-chains 258 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 232 time to evaluate : 2.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 246 MET Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 155 THR Chi-restraints excluded: chain H residue 166 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 109 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 70 optimal weight: 0.4980 chunk 17 optimal weight: 6.9990 chunk 134 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 27 optimal weight: 0.3980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN A 275 ASN B 275 ASN C 234 GLN C 275 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.176939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.136341 restraints weight = 53932.702| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 4.96 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3482 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3482 r_free = 0.3482 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3482 r_free = 0.3482 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3482 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3189 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= 0.120 Angle : 0.535 8.666 16442 Z= 0.275 Chirality : 0.038 0.129 1778 Planarity : 0.004 0.047 2066 Dihedral : 17.685 174.757 2161 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.07 % Allowed : 14.81 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.01 (0.23), residues: 1422 helix: 2.65 (0.15), residues: 1162 sheet: None (None), residues: 0 loop : -1.24 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 240 HIS 0.004 0.001 HIS F 57 PHE 0.013 0.002 PHE D 110 TYR 0.012 0.001 TYR G 212 ARG 0.007 0.000 ARG G 76 Details of bonding type rmsd hydrogen bonds : bond 0.04620 ( 878) hydrogen bonds : angle 3.38279 ( 2644) covalent geometry : bond 0.00246 (12225) covalent geometry : angle 0.53549 (16442) *********************** 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 256 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 234 time to evaluate : 1.464 Fit side-chains REVERT: A 108 LEU cc_start: 0.6695 (OUTLIER) cc_final: 0.6272 (mt) REVERT: A 109 GLU cc_start: 0.5414 (mt-10) cc_final: 0.5024 (tt0) REVERT: A 119 GLU cc_start: 0.5487 (tm-30) cc_final: 0.5241 (tm-30) REVERT: A 163 GLU cc_start: 0.6407 (mt-10) cc_final: 0.6152 (mt-10) REVERT: A 167 LEU cc_start: 0.6690 (mt) cc_final: 0.6285 (tp) REVERT: A 179 ASP cc_start: 0.7396 (p0) cc_final: 0.7074 (p0) REVERT: A 208 MET cc_start: 0.7904 (mtp) cc_final: 0.7575 (mtp) REVERT: A 271 ARG cc_start: 0.7073 (ttm110) cc_final: 0.6717 (mtm-85) REVERT: A 276 ARG cc_start: 0.7298 (mmm-85) cc_final: 0.7047 (mmm160) REVERT: A 279 ASP cc_start: 0.6356 (m-30) cc_final: 0.5968 (t70) REVERT: B 109 GLU cc_start: 0.5551 (mt-10) cc_final: 0.4935 (tp30) REVERT: B 119 GLU cc_start: 0.5698 (tm-30) cc_final: 0.4793 (tp30) REVERT: B 123 GLU cc_start: 0.5830 (OUTLIER) cc_final: 0.5630 (tt0) REVERT: B 163 GLU cc_start: 0.6601 (mm-30) cc_final: 0.6256 (mt-10) REVERT: B 169 GLN cc_start: 0.6396 (mt0) cc_final: 0.6027 (pt0) REVERT: B 271 ARG cc_start: 0.7076 (ttm110) cc_final: 0.6754 (mtm-85) REVERT: B 279 ASP cc_start: 0.6749 (m-30) cc_final: 0.6432 (m-30) REVERT: B 283 MET cc_start: 0.3412 (mmm) cc_final: 0.2248 (ppp) REVERT: C 109 GLU cc_start: 0.5614 (mt-10) cc_final: 0.4911 (tp30) REVERT: C 119 GLU cc_start: 0.5477 (tm-30) cc_final: 0.4615 (tp30) REVERT: C 123 GLU cc_start: 0.5681 (OUTLIER) cc_final: 0.4993 (tm-30) REVERT: C 162 GLU cc_start: 0.6467 (pt0) cc_final: 0.6251 (pt0) REVERT: C 163 GLU cc_start: 0.6723 (OUTLIER) cc_final: 0.6340 (mt-10) REVERT: C 164 GLU cc_start: 0.7122 (mt-10) cc_final: 0.6834 (mt-10) REVERT: C 177 LYS cc_start: 0.7109 (mtpp) cc_final: 0.6590 (mmtt) REVERT: C 179 ASP cc_start: 0.7464 (p0) cc_final: 0.7149 (p0) REVERT: C 208 MET cc_start: 0.7935 (mtp) cc_final: 0.7594 (mtp) REVERT: C 271 ARG cc_start: 0.7064 (ttm110) cc_final: 0.6739 (mtm-85) REVERT: C 274 GLU cc_start: 0.7665 (tt0) cc_final: 0.7409 (tt0) REVERT: C 276 ARG cc_start: 0.7446 (mmm-85) cc_final: 0.7221 (mmm160) REVERT: C 279 ASP cc_start: 0.6712 (m-30) cc_final: 0.6471 (m-30) REVERT: D 108 LEU cc_start: 0.6582 (mm) cc_final: 0.6326 (mt) REVERT: D 109 GLU cc_start: 0.5364 (mt-10) cc_final: 0.5018 (tt0) REVERT: D 119 GLU cc_start: 0.5430 (tm-30) cc_final: 0.5184 (tm-30) REVERT: D 167 LEU cc_start: 0.6703 (mt) cc_final: 0.6229 (tp) REVERT: D 177 LYS cc_start: 0.7143 (mtpp) cc_final: 0.6622 (mmtt) REVERT: D 179 ASP cc_start: 0.7384 (p0) cc_final: 0.7088 (p0) REVERT: D 208 MET cc_start: 0.7923 (mtp) cc_final: 0.7596 (mtp) REVERT: D 271 ARG cc_start: 0.7117 (ttm110) cc_final: 0.6743 (mtm-85) REVERT: D 274 GLU cc_start: 0.7730 (tt0) cc_final: 0.7517 (tt0) REVERT: E 76 ARG cc_start: 0.6958 (mtt180) cc_final: 0.6179 (mpp-170) REVERT: E 143 GLU cc_start: 0.7161 (mt-10) cc_final: 0.6710 (tt0) REVERT: E 148 HIS cc_start: 0.7182 (t70) cc_final: 0.6970 (t-170) REVERT: F 143 GLU cc_start: 0.7336 (mt-10) cc_final: 0.6961 (mt-10) REVERT: F 155 THR cc_start: 0.6467 (m) cc_final: 0.6102 (t) REVERT: G 143 GLU cc_start: 0.7174 (mt-10) cc_final: 0.6713 (tt0) REVERT: H 143 GLU cc_start: 0.7351 (mt-10) cc_final: 0.6904 (mt-10) REVERT: H 147 HIS cc_start: 0.7545 (t-90) cc_final: 0.7297 (t-170) REVERT: H 166 GLU cc_start: 0.5950 (mm-30) cc_final: 0.5646 (mt-10) outliers start: 22 outliers final: 11 residues processed: 242 average time/residue: 1.7620 time to fit residues: 453.2209 Evaluate side-chains 241 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 226 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 139 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 132 optimal weight: 0.6980 chunk 1 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN A 275 ASN B 275 ASN C 234 GLN C 275 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.176172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.133435 restraints weight = 47151.711| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 4.88 r_work: 0.3064 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12225 Z= 0.151 Angle : 0.598 8.771 16442 Z= 0.304 Chirality : 0.040 0.201 1778 Planarity : 0.004 0.041 2066 Dihedral : 17.754 172.788 2161 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.41 % Allowed : 14.90 % Favored : 82.69 % 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: 2.82 (0.23), residues: 1422 helix: 2.50 (0.15), residues: 1170 sheet: None (None), residues: 0 loop : -1.35 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 200 HIS 0.005 0.002 HIS G 57 PHE 0.014 0.002 PHE D 110 TYR 0.011 0.002 TYR H 67 ARG 0.006 0.001 ARG G 76 Details of bonding type rmsd hydrogen bonds : bond 0.05242 ( 878) hydrogen bonds : angle 3.49516 ( 2644) covalent geometry : bond 0.00337 (12225) covalent geometry : angle 0.59810 (16442) *********************** 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 251 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 225 time to evaluate : 1.441 Fit side-chains REVERT: A 108 LEU cc_start: 0.6430 (OUTLIER) cc_final: 0.5965 (mt) REVERT: A 109 GLU cc_start: 0.5457 (mt-10) cc_final: 0.4956 (tt0) REVERT: A 163 GLU cc_start: 0.6855 (mt-10) cc_final: 0.6615 (mt-10) REVERT: A 179 ASP cc_start: 0.7821 (p0) cc_final: 0.7498 (p0) REVERT: A 208 MET cc_start: 0.8501 (mtp) cc_final: 0.8163 (mtp) REVERT: A 271 ARG cc_start: 0.7765 (ttm110) cc_final: 0.7387 (mtm-85) REVERT: A 276 ARG cc_start: 0.7323 (mmm-85) cc_final: 0.7017 (mmm160) REVERT: A 281 MET cc_start: 0.6523 (OUTLIER) cc_final: 0.4328 (mpt) REVERT: B 109 GLU cc_start: 0.5598 (mt-10) cc_final: 0.5072 (tt0) REVERT: B 119 GLU cc_start: 0.5325 (tm-30) cc_final: 0.4423 (tp30) REVERT: B 123 GLU cc_start: 0.5507 (OUTLIER) cc_final: 0.5213 (tt0) REVERT: B 163 GLU cc_start: 0.7052 (mm-30) cc_final: 0.6507 (mt-10) REVERT: B 169 GLN cc_start: 0.6416 (mt0) cc_final: 0.5974 (pt0) REVERT: B 271 ARG cc_start: 0.7769 (ttm110) cc_final: 0.7418 (mtm-85) REVERT: B 279 ASP cc_start: 0.7051 (m-30) cc_final: 0.6731 (m-30) REVERT: B 281 MET cc_start: 0.6538 (OUTLIER) cc_final: 0.4355 (mpt) REVERT: B 283 MET cc_start: 0.3637 (mmm) cc_final: 0.2401 (ppp) REVERT: C 109 GLU cc_start: 0.5642 (mt-10) cc_final: 0.5127 (tt0) REVERT: C 119 GLU cc_start: 0.5213 (tm-30) cc_final: 0.4216 (tp30) REVERT: C 123 GLU cc_start: 0.5313 (OUTLIER) cc_final: 0.5066 (tt0) REVERT: C 162 GLU cc_start: 0.7172 (pt0) cc_final: 0.6852 (pt0) REVERT: C 163 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.6722 (mt-10) REVERT: C 177 LYS cc_start: 0.7344 (mtpp) cc_final: 0.6869 (mmtt) REVERT: C 179 ASP cc_start: 0.7804 (p0) cc_final: 0.7489 (p0) REVERT: C 271 ARG cc_start: 0.7677 (ttm110) cc_final: 0.7340 (mtm-85) REVERT: C 274 GLU cc_start: 0.8206 (tt0) cc_final: 0.7953 (tt0) REVERT: C 276 ARG cc_start: 0.7441 (mmm-85) cc_final: 0.7160 (mmm160) REVERT: C 279 ASP cc_start: 0.7130 (m-30) cc_final: 0.6878 (m-30) REVERT: D 109 GLU cc_start: 0.5498 (mt-10) cc_final: 0.4972 (tt0) REVERT: D 119 GLU cc_start: 0.5238 (tm-30) cc_final: 0.4999 (tm-30) REVERT: D 177 LYS cc_start: 0.7335 (mtpp) cc_final: 0.6855 (mmtt) REVERT: D 179 ASP cc_start: 0.7802 (p0) cc_final: 0.7489 (p0) REVERT: D 208 MET cc_start: 0.8405 (mtp) cc_final: 0.8106 (mtp) REVERT: D 271 ARG cc_start: 0.7707 (ttm110) cc_final: 0.7338 (mtm-85) REVERT: D 274 GLU cc_start: 0.8320 (tt0) cc_final: 0.8114 (tt0) REVERT: D 281 MET cc_start: 0.6960 (mpm) cc_final: 0.6729 (mmm) REVERT: E 143 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7272 (tt0) REVERT: E 148 HIS cc_start: 0.7361 (t70) cc_final: 0.7146 (t-170) REVERT: F 155 THR cc_start: 0.6459 (m) cc_final: 0.6042 (t) REVERT: G 143 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7288 (tt0) REVERT: G 148 HIS cc_start: 0.7380 (t70) cc_final: 0.7155 (t-170) REVERT: H 143 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7425 (mt-10) REVERT: H 147 HIS cc_start: 0.7893 (t-90) cc_final: 0.7642 (t-170) REVERT: H 166 GLU cc_start: 0.6026 (OUTLIER) cc_final: 0.5640 (mt-10) outliers start: 26 outliers final: 10 residues processed: 235 average time/residue: 1.7026 time to fit residues: 425.3586 Evaluate side-chains 234 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 217 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 166 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 14 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 27 optimal weight: 0.4980 chunk 101 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN A 275 ASN B 275 ASN C 234 GLN C 275 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.177692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.135285 restraints weight = 49456.289| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 5.27 r_work: 0.3093 rms_B_bonded: 5.05 restraints_weight: 2.0000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3041 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3041 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12225 Z= 0.116 Angle : 0.530 8.674 16442 Z= 0.271 Chirality : 0.037 0.146 1778 Planarity : 0.004 0.049 2066 Dihedral : 17.271 173.987 2161 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.89 % Allowed : 15.50 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.20 (0.23), residues: 1422 helix: 2.80 (0.15), residues: 1162 sheet: None (None), residues: 0 loop : -1.27 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 240 HIS 0.004 0.001 HIS G 57 PHE 0.013 0.002 PHE D 110 TYR 0.009 0.001 TYR G 212 ARG 0.004 0.000 ARG G 76 Details of bonding type rmsd hydrogen bonds : bond 0.04464 ( 878) hydrogen bonds : angle 3.32099 ( 2644) covalent geometry : bond 0.00239 (12225) covalent geometry : angle 0.53047 (16442) *********************** 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 248 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 228 time to evaluate : 1.444 Fit side-chains revert: symmetry clash REVERT: A 108 LEU cc_start: 0.6465 (OUTLIER) cc_final: 0.5974 (mt) REVERT: A 109 GLU cc_start: 0.5411 (mt-10) cc_final: 0.4924 (tt0) REVERT: A 119 GLU cc_start: 0.5410 (tm-30) cc_final: 0.4418 (tp30) REVERT: A 163 GLU cc_start: 0.6821 (mt-10) cc_final: 0.6539 (mt-10) REVERT: A 179 ASP cc_start: 0.7818 (p0) cc_final: 0.7532 (p0) REVERT: A 208 MET cc_start: 0.8463 (mtp) cc_final: 0.8128 (mtp) REVERT: A 271 ARG cc_start: 0.7739 (ttm110) cc_final: 0.7402 (mtm-85) REVERT: A 276 ARG cc_start: 0.7331 (mmm-85) cc_final: 0.7027 (mmm160) REVERT: B 109 GLU cc_start: 0.5592 (mt-10) cc_final: 0.5089 (tt0) REVERT: B 119 GLU cc_start: 0.5305 (tm-30) cc_final: 0.4426 (tp30) REVERT: B 123 GLU cc_start: 0.5444 (OUTLIER) cc_final: 0.5199 (tt0) REVERT: B 163 GLU cc_start: 0.6975 (mm-30) cc_final: 0.6437 (mt-10) REVERT: B 169 GLN cc_start: 0.6432 (mt0) cc_final: 0.5946 (pt0) REVERT: B 271 ARG cc_start: 0.7751 (ttm110) cc_final: 0.7380 (mtm-85) REVERT: B 279 ASP cc_start: 0.7044 (m-30) cc_final: 0.6717 (m-30) REVERT: B 281 MET cc_start: 0.6464 (OUTLIER) cc_final: 0.4423 (mpt) REVERT: B 283 MET cc_start: 0.3589 (mmm) cc_final: 0.2359 (ppp) REVERT: C 109 GLU cc_start: 0.5537 (mt-10) cc_final: 0.5007 (tt0) REVERT: C 119 GLU cc_start: 0.5307 (tm-30) cc_final: 0.4385 (tp30) REVERT: C 162 GLU cc_start: 0.7144 (pt0) cc_final: 0.6792 (pt0) REVERT: C 163 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6669 (mt-10) REVERT: C 164 GLU cc_start: 0.7094 (mt-10) cc_final: 0.6811 (mt-10) REVERT: C 177 LYS cc_start: 0.7324 (mtpp) cc_final: 0.6861 (mmtt) REVERT: C 179 ASP cc_start: 0.7793 (p0) cc_final: 0.7483 (p0) REVERT: C 271 ARG cc_start: 0.7681 (ttm110) cc_final: 0.7352 (mtm-85) REVERT: C 274 GLU cc_start: 0.8187 (tt0) cc_final: 0.7937 (tt0) REVERT: C 276 ARG cc_start: 0.7463 (mmm-85) cc_final: 0.7186 (mmm160) REVERT: C 279 ASP cc_start: 0.7088 (m-30) cc_final: 0.6854 (m-30) REVERT: C 281 MET cc_start: 0.6854 (OUTLIER) cc_final: 0.5497 (mpt) REVERT: D 109 GLU cc_start: 0.5410 (mt-10) cc_final: 0.4894 (tt0) REVERT: D 119 GLU cc_start: 0.5233 (tm-30) cc_final: 0.5000 (tm-30) REVERT: D 177 LYS cc_start: 0.7345 (mtpp) cc_final: 0.6900 (mmtt) REVERT: D 179 ASP cc_start: 0.7823 (p0) cc_final: 0.7510 (p0) REVERT: D 271 ARG cc_start: 0.7710 (ttm110) cc_final: 0.7344 (mtm-85) REVERT: E 143 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7270 (tt0) REVERT: E 148 HIS cc_start: 0.7354 (t70) cc_final: 0.7136 (t-170) REVERT: F 143 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7378 (mt-10) REVERT: F 155 THR cc_start: 0.6551 (m) cc_final: 0.6136 (t) REVERT: G 143 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7280 (tt0) REVERT: G 148 HIS cc_start: 0.7333 (t70) cc_final: 0.7109 (t-170) REVERT: H 143 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7360 (mt-10) REVERT: H 147 HIS cc_start: 0.7826 (t-90) cc_final: 0.7596 (t-170) REVERT: H 166 GLU cc_start: 0.6217 (OUTLIER) cc_final: 0.5803 (mt-10) outliers start: 20 outliers final: 10 residues processed: 236 average time/residue: 1.6277 time to fit residues: 408.9989 Evaluate side-chains 241 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 225 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 281 MET Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 166 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 39 optimal weight: 0.0060 chunk 22 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 87 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 124 optimal weight: 8.9990 chunk 100 optimal weight: 0.0570 chunk 123 optimal weight: 0.9990 chunk 119 optimal weight: 0.5980 overall best weight: 0.5316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN A 275 ASN B 275 ASN C 234 GLN C 275 ASN D 165 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.180466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.141142 restraints weight = 54952.128| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 4.84 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3539 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3539 r_free = 0.3539 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3539 r_free = 0.3539 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3539 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.3451 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= 0.098 Angle : 0.486 8.661 16442 Z= 0.249 Chirality : 0.036 0.131 1778 Planarity : 0.004 0.055 2066 Dihedral : 16.313 175.808 2161 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.69 % Allowed : 16.62 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.57 (0.23), residues: 1422 helix: 3.08 (0.15), residues: 1162 sheet: None (None), residues: 0 loop : -1.26 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 240 HIS 0.005 0.001 HIS F 147 PHE 0.014 0.001 PHE D 110 TYR 0.008 0.001 TYR A 230 ARG 0.003 0.000 ARG D 159 Details of bonding type rmsd hydrogen bonds : bond 0.03596 ( 878) hydrogen bonds : angle 3.11870 ( 2644) covalent geometry : bond 0.00191 (12225) covalent geometry : angle 0.48648 (16442) ********************** 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 241 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 235 time to evaluate : 1.291 Fit side-chains REVERT: A 108 LEU cc_start: 0.6681 (OUTLIER) cc_final: 0.6254 (mt) REVERT: A 109 GLU cc_start: 0.5360 (mt-10) cc_final: 0.5065 (tt0) REVERT: A 119 GLU cc_start: 0.5655 (tm-30) cc_final: 0.4764 (tp30) REVERT: A 163 GLU cc_start: 0.6357 (mt-10) cc_final: 0.6100 (mt-10) REVERT: A 172 GLN cc_start: 0.4991 (mt0) cc_final: 0.4536 (mt0) REVERT: A 179 ASP cc_start: 0.7397 (p0) cc_final: 0.7084 (p0) REVERT: A 208 MET cc_start: 0.7834 (mtp) cc_final: 0.7496 (mtp) REVERT: A 271 ARG cc_start: 0.7091 (ttm110) cc_final: 0.6776 (mtm-85) REVERT: A 276 ARG cc_start: 0.7250 (mmm-85) cc_final: 0.6908 (mtp85) REVERT: B 109 GLU cc_start: 0.5412 (mt-10) cc_final: 0.4846 (tp30) REVERT: B 119 GLU cc_start: 0.5575 (tm-30) cc_final: 0.4764 (tp30) REVERT: B 163 GLU cc_start: 0.6605 (mm-30) cc_final: 0.6384 (mt-10) REVERT: B 169 GLN cc_start: 0.6443 (mt0) cc_final: 0.6052 (pt0) REVERT: B 198 GLU cc_start: 0.6567 (tt0) cc_final: 0.6270 (tt0) REVERT: B 271 ARG cc_start: 0.7057 (ttm110) cc_final: 0.6754 (mtm-85) REVERT: B 283 MET cc_start: 0.3562 (mmm) cc_final: 0.2467 (ppp) REVERT: C 109 GLU cc_start: 0.5433 (mt-10) cc_final: 0.5130 (tt0) REVERT: C 119 GLU cc_start: 0.5495 (tm-30) cc_final: 0.4644 (tp30) REVERT: C 163 GLU cc_start: 0.6745 (mm-30) cc_final: 0.6402 (mt-10) REVERT: C 164 GLU cc_start: 0.7032 (mt-10) cc_final: 0.6766 (mt-10) REVERT: C 169 GLN cc_start: 0.5922 (mt0) cc_final: 0.5621 (pt0) REVERT: C 177 LYS cc_start: 0.7057 (mtpp) cc_final: 0.6589 (mmtt) REVERT: C 179 ASP cc_start: 0.7450 (p0) cc_final: 0.7146 (p0) REVERT: C 208 MET cc_start: 0.7926 (mtp) cc_final: 0.7622 (mtp) REVERT: C 271 ARG cc_start: 0.7097 (ttm110) cc_final: 0.6782 (mtm-85) REVERT: C 276 ARG cc_start: 0.7489 (mmm-85) cc_final: 0.7094 (mmm160) REVERT: C 279 ASP cc_start: 0.6528 (m-30) cc_final: 0.6125 (t70) REVERT: D 109 GLU cc_start: 0.5254 (mt-10) cc_final: 0.4969 (tt0) REVERT: D 119 GLU cc_start: 0.5406 (tm-30) cc_final: 0.5110 (tm-30) REVERT: D 177 LYS cc_start: 0.7053 (mtpp) cc_final: 0.6622 (mmtt) REVERT: D 179 ASP cc_start: 0.7408 (p0) cc_final: 0.7119 (p0) REVERT: D 271 ARG cc_start: 0.7122 (ttm110) cc_final: 0.6785 (mtm-85) REVERT: E 143 GLU cc_start: 0.7079 (mt-10) cc_final: 0.6652 (tt0) REVERT: E 148 HIS cc_start: 0.7256 (t70) cc_final: 0.7022 (t-170) REVERT: E 155 THR cc_start: 0.6516 (m) cc_final: 0.6242 (t) REVERT: F 71 MET cc_start: 0.8287 (tpt) cc_final: 0.7974 (mmm) REVERT: F 135 MET cc_start: 0.6869 (mmt) cc_final: 0.6623 (mmm) REVERT: F 143 GLU cc_start: 0.7233 (mt-10) cc_final: 0.6868 (mt-10) REVERT: F 148 HIS cc_start: 0.7210 (t70) cc_final: 0.6977 (t-170) REVERT: F 155 THR cc_start: 0.6604 (m) cc_final: 0.6257 (t) REVERT: F 173 LYS cc_start: 0.7776 (ttmt) cc_final: 0.7498 (ttmt) REVERT: G 143 GLU cc_start: 0.7137 (mt-10) cc_final: 0.6666 (tt0) REVERT: G 148 HIS cc_start: 0.7225 (t70) cc_final: 0.6976 (t-170) REVERT: G 155 THR cc_start: 0.6555 (m) cc_final: 0.6266 (t) REVERT: H 71 MET cc_start: 0.8324 (tpt) cc_final: 0.7982 (mmm) REVERT: H 135 MET cc_start: 0.6776 (mmt) cc_final: 0.6520 (mmm) REVERT: H 143 GLU cc_start: 0.7197 (mt-10) cc_final: 0.6827 (mt-10) REVERT: H 147 HIS cc_start: 0.7358 (t-90) cc_final: 0.7143 (t-170) REVERT: H 148 HIS cc_start: 0.7188 (t70) cc_final: 0.6970 (t-170) REVERT: H 155 THR cc_start: 0.6473 (m) cc_final: 0.5976 (t) REVERT: H 173 LYS cc_start: 0.7769 (ttmt) cc_final: 0.7439 (ttmt) outliers start: 6 outliers final: 4 residues processed: 236 average time/residue: 1.7585 time to fit residues: 439.3864 Evaluate side-chains 228 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 223 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain D residue 226 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 23 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 38 optimal weight: 9.9990 chunk 129 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 64 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN A 275 ASN B 275 ASN C 275 ASN F 204 GLN H 204 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.178005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.137415 restraints weight = 48150.434| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 4.42 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3499 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3499 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12225 Z= 0.118 Angle : 0.533 9.371 16442 Z= 0.272 Chirality : 0.038 0.163 1778 Planarity : 0.004 0.047 2066 Dihedral : 16.472 174.020 2161 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.86 % Allowed : 16.80 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.40 (0.23), residues: 1422 helix: 2.94 (0.15), residues: 1162 sheet: None (None), residues: 0 loop : -1.25 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 200 HIS 0.006 0.001 HIS F 147 PHE 0.011 0.002 PHE D 110 TYR 0.011 0.001 TYR B 196 ARG 0.007 0.000 ARG E 76 Details of bonding type rmsd hydrogen bonds : bond 0.04353 ( 878) hydrogen bonds : angle 3.25878 ( 2644) covalent geometry : bond 0.00249 (12225) covalent geometry : angle 0.53252 (16442) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11070.44 seconds wall clock time: 193 minutes 28.94 seconds (11608.94 seconds total)