Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 10:33:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sss_25413/04_2023/7sss_25413_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sss_25413/04_2023/7sss_25413.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sss_25413/04_2023/7sss_25413.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sss_25413/04_2023/7sss_25413.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sss_25413/04_2023/7sss_25413_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sss_25413/04_2023/7sss_25413_updated.pdb" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5095 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 20 5.49 5 S 72 5.16 5 C 7695 2.51 5 N 2009 2.21 5 O 2394 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 79 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEV:plan-1': 2, 'PEV:plan-2': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 68 Unusual residues: {'8PP': 1, 'PEV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEV:plan-1': 1, '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: 123 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEV:plan-1': 2, 'PEV:plan-2': 2} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 57 Unusual residues: {'PEV': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEV:plan-1': 3, 'PEV:plan-2': 3} Unresolved non-hydrogen planarities: 24 Chain: "E" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 166 Unusual residues: {'8PP': 1, 'NAD': 1, 'PEV': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'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: 127 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEV:plan-1': 3, 'PEV:plan-2': 3} Unresolved non-hydrogen planarities: 23 Chain: "G" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 107 Unusual residues: {'8PP': 1, 'PEV': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 136 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'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: 130 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: 12.31, per 1000 atoms: 1.01 Number of scatterers: 12190 At special positions: 0 Unit cell: (95.795, 104.125, 92.463, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 P 20 15.00 O 2394 8.00 N 2009 7.00 C 7695 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.26 Conformation dependent library (CDL) restraints added in 3.4 seconds 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2700 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 0 sheets defined 76.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 96 through 109 removed outlier: 3.774A pdb=" N GLN A 100 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLU A 109 " --> pdb=" O THR A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 126 Processing helix chain 'A' and resid 143 through 169 Processing helix chain 'A' and resid 178 through 196 removed outlier: 3.816A pdb=" N MET A 192 " --> pdb=" O THR A 188 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU A 193 " --> pdb=" O ARG A 189 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Proline residue: A 195 - end of helix Processing helix chain 'A' and resid 200 through 207 Processing helix chain 'A' and resid 213 through 230 Processing helix chain 'A' and resid 238 through 259 removed outlier: 3.846A pdb=" N ARG A 243 " --> pdb=" O TRP A 240 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG A 244 " --> pdb=" O TYR A 241 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 245 " --> pdb=" O THR A 242 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE A 250 " --> pdb=" O LEU A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 281 removed outlier: 5.803A pdb=" N ASP A 268 " --> pdb=" O ASP A 265 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP A 270 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG A 271 " --> pdb=" O ASP A 268 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP A 279 " --> pdb=" O ARG A 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 109 removed outlier: 3.505A pdb=" N GLN B 100 " --> pdb=" O GLU B 97 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B 104 " --> pdb=" O HIS B 101 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 108 " --> pdb=" O THR B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 114 No H-bonds generated for 'chain 'B' and resid 111 through 114' Processing helix chain 'B' and resid 118 through 126 Processing helix chain 'B' and resid 143 through 170 removed outlier: 3.586A pdb=" N LEU B 170 " --> pdb=" O LYS B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 196 removed outlier: 3.815A pdb=" N MET B 192 " --> pdb=" O THR B 188 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LEU B 193 " --> pdb=" O ARG B 189 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Proline residue: B 195 - end of helix Processing helix chain 'B' and resid 200 through 207 Processing helix chain 'B' and resid 213 through 230 Processing helix chain 'B' and resid 238 through 259 removed outlier: 3.850A pdb=" N ARG B 243 " --> pdb=" O TRP B 240 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG B 244 " --> pdb=" O TYR B 241 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA B 245 " --> pdb=" O THR B 242 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN B 252 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR B 253 " --> pdb=" O ILE B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 280 removed outlier: 5.827A pdb=" N ASP B 268 " --> pdb=" O ASP B 265 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TRP B 270 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG B 271 " --> pdb=" O ASP B 268 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP B 279 " --> pdb=" O AARG B 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 109 removed outlier: 3.580A pdb=" N LEU C 108 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLU C 109 " --> pdb=" O THR C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 126 Processing helix chain 'C' and resid 143 through 170 removed outlier: 3.569A pdb=" N LEU C 167 " --> pdb=" O GLU C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 196 removed outlier: 3.827A pdb=" N MET C 192 " --> pdb=" O THR C 188 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU C 193 " --> pdb=" O ARG C 189 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILE C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Proline residue: C 195 - end of helix Processing helix chain 'C' and resid 200 through 207 Processing helix chain 'C' and resid 213 through 230 Processing helix chain 'C' and resid 238 through 259 removed outlier: 3.851A pdb=" N ARG C 243 " --> pdb=" O TRP C 240 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG C 244 " --> pdb=" O TYR C 241 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA C 245 " --> pdb=" O THR C 242 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN C 252 " --> pdb=" O ALA C 249 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR C 253 " --> pdb=" O ILE C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 281 removed outlier: 5.821A pdb=" N ASP C 268 " --> pdb=" O ASP C 265 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TRP C 270 " --> pdb=" O GLU C 267 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG C 271 " --> pdb=" O ASP C 268 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP C 279 " --> pdb=" O ARG C 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 109 removed outlier: 3.629A pdb=" N LEU D 108 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N GLU D 109 " --> pdb=" O THR D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 114 No H-bonds generated for 'chain 'D' and resid 111 through 114' Processing helix chain 'D' and resid 118 through 126 Processing helix chain 'D' and resid 143 through 169 Processing helix chain 'D' and resid 178 through 196 removed outlier: 3.822A pdb=" N MET D 192 " --> pdb=" O THR D 188 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU D 193 " --> pdb=" O ARG D 189 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ILE D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) Proline residue: D 195 - end of helix Processing helix chain 'D' and resid 200 through 207 Processing helix chain 'D' and resid 213 through 230 Processing helix chain 'D' and resid 238 through 259 removed outlier: 3.840A pdb=" N ARG D 243 " --> pdb=" O TRP D 240 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG D 244 " --> pdb=" O TYR D 241 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA D 245 " --> pdb=" O THR D 242 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN D 252 " --> pdb=" O ALA D 249 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR D 253 " --> pdb=" O ILE D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 281 removed outlier: 5.837A pdb=" N ASP D 268 " --> pdb=" O ASP D 265 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP D 270 " --> pdb=" O GLU D 267 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG D 271 " --> pdb=" O ASP D 268 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP D 279 " --> pdb=" O BARG D 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 74 removed outlier: 3.568A pdb=" N VAL E 73 " --> pdb=" O GLY E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 104 Processing helix chain 'E' and resid 112 through 125 removed outlier: 3.564A pdb=" N PHE E 120 " --> pdb=" O ASN E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 160 removed outlier: 4.026A pdb=" N GLU E 158 " --> pdb=" O ARG E 154 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU E 159 " --> pdb=" O THR E 155 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP E 160 " --> pdb=" O LEU E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 177 Processing helix chain 'E' and resid 194 through 216 removed outlier: 3.978A pdb=" N ARG E 216 " --> pdb=" O TYR E 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 73 Processing helix chain 'F' and resid 80 through 104 Processing helix chain 'F' and resid 112 through 125 removed outlier: 3.570A pdb=" N VAL F 117 " --> pdb=" O PRO F 113 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE F 120 " --> pdb=" O ASN F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 160 removed outlier: 3.987A pdb=" N GLU F 158 " --> pdb=" O ARG F 154 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU F 159 " --> pdb=" O THR F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 179 removed outlier: 3.932A pdb=" N LEU F 179 " --> pdb=" O ARG F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 216 removed outlier: 3.500A pdb=" N VAL F 198 " --> pdb=" O PRO F 194 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG F 216 " --> pdb=" O TYR F 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 80 through 104 Processing helix chain 'G' and resid 112 through 125 removed outlier: 3.546A pdb=" N VAL G 117 " --> pdb=" O PRO G 113 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE G 120 " --> pdb=" O ASN G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 160 removed outlier: 3.991A pdb=" N GLU G 158 " --> pdb=" O ARG G 154 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU G 159 " --> pdb=" O THR G 155 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP G 160 " --> pdb=" O LEU G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 177 Processing helix chain 'G' and resid 194 through 216 removed outlier: 4.012A pdb=" N ARG G 216 " --> pdb=" O TYR G 212 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 73 Processing helix chain 'H' and resid 80 through 104 Processing helix chain 'H' and resid 112 through 125 removed outlier: 3.543A pdb=" N VAL H 117 " --> pdb=" O PRO H 113 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE H 120 " --> pdb=" O ASN H 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 160 removed outlier: 3.661A pdb=" N GLU H 159 " --> pdb=" O THR H 155 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP H 160 " --> pdb=" O LEU H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 165 through 177 Processing helix chain 'H' and resid 194 through 216 removed outlier: 3.506A pdb=" N VAL H 198 " --> pdb=" O PRO H 194 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG H 216 " --> pdb=" O TYR H 212 " (cutoff:3.500A) 786 hydrogen bonds defined for protein. 2033 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.33 Time building geometry restraints manager: 5.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1921 1.32 - 1.44: 3132 1.44 - 1.56: 7000 1.56 - 1.68: 40 1.68 - 1.81: 132 Bond restraints: 12225 Sorted by residual: bond pdb=" N ILE A 250 " pdb=" CA ILE A 250 " ideal model delta sigma weight residual 1.461 1.492 -0.031 1.17e-02 7.31e+03 6.94e+00 bond pdb=" N AARG B 276 " pdb=" CA AARG B 276 " ideal model delta sigma weight residual 1.459 1.489 -0.029 1.19e-02 7.06e+03 6.05e+00 bond pdb=" O3 NAD E 306 " pdb=" PA NAD E 306 " ideal model delta sigma weight residual 1.653 1.604 0.049 2.00e-02 2.50e+03 6.04e+00 bond pdb=" O3 NAD F 306 " pdb=" PA NAD F 306 " ideal model delta sigma weight residual 1.653 1.604 0.049 2.00e-02 2.50e+03 5.95e+00 bond pdb=" C1 PEV C 405 " pdb=" O3P PEV C 405 " ideal model delta sigma weight residual 1.407 1.454 -0.047 2.00e-02 2.50e+03 5.57e+00 ... (remaining 12220 not shown) Histogram of bond angle deviations from ideal: 99.52 - 106.47: 352 106.47 - 113.43: 6686 113.43 - 120.39: 4930 120.39 - 127.35: 4291 127.35 - 134.31: 183 Bond angle restraints: 16442 Sorted by residual: angle pdb=" O3P PEV H 301 " pdb=" P PEV H 301 " pdb=" O4P PEV H 301 " ideal model delta sigma weight residual 93.57 103.52 -9.95 3.00e+00 1.11e-01 1.10e+01 angle pdb=" O3P PEV C 401 " pdb=" P PEV C 401 " pdb=" O4P PEV C 401 " ideal model delta sigma weight residual 93.57 103.49 -9.92 3.00e+00 1.11e-01 1.09e+01 angle pdb=" CA AARG B 276 " pdb=" C AARG B 276 " pdb=" O AARG B 276 " ideal model delta sigma weight residual 120.82 117.35 3.47 1.05e+00 9.07e-01 1.09e+01 angle pdb=" O3P PEV H 302 " pdb=" P PEV H 302 " pdb=" O4P PEV H 302 " ideal model delta sigma weight residual 93.57 103.40 -9.83 3.00e+00 1.11e-01 1.07e+01 angle pdb=" O3P PEV C 403 " pdb=" P PEV C 403 " pdb=" O4P PEV C 403 " ideal model delta sigma weight residual 93.57 103.22 -9.65 3.00e+00 1.11e-01 1.03e+01 ... (remaining 16437 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.99: 6555 15.99 - 31.99: 453 31.99 - 47.98: 161 47.98 - 63.97: 79 63.97 - 79.97: 13 Dihedral angle restraints: 7261 sinusoidal: 3097 harmonic: 4164 Sorted by residual: dihedral pdb=" CA ALA G 127 " pdb=" C ALA G 127 " pdb=" N LEU G 128 " pdb=" CA LEU G 128 " ideal model delta harmonic sigma weight residual 180.00 158.64 21.36 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA ALA E 127 " pdb=" C ALA E 127 " pdb=" N LEU E 128 " pdb=" CA LEU E 128 " ideal model delta harmonic sigma weight residual 180.00 158.78 21.22 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA ALA H 127 " pdb=" C ALA H 127 " pdb=" N LEU H 128 " pdb=" CA LEU H 128 " ideal model delta harmonic sigma weight residual 180.00 158.80 21.20 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 7258 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1285 0.039 - 0.079: 407 0.079 - 0.118: 76 0.118 - 0.158: 8 0.158 - 0.197: 2 Chirality restraints: 1778 Sorted by residual: chirality pdb=" C2 PEV E 304 " pdb=" C1 PEV E 304 " pdb=" C3 PEV E 304 " pdb=" O2 PEV E 304 " both_signs ideal model delta sigma weight residual False 2.36 2.56 -0.20 2.00e-01 2.50e+01 9.71e-01 chirality pdb=" CA ILE A 250 " pdb=" N ILE A 250 " pdb=" C ILE A 250 " pdb=" CB ILE A 250 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.43e-01 chirality pdb=" C1D NAD E 306 " pdb=" C2D NAD E 306 " pdb=" N1N NAD E 306 " pdb=" O4D NAD E 306 " both_signs ideal model delta sigma weight residual False 2.41 2.57 -0.15 2.00e-01 2.50e+01 5.70e-01 ... (remaining 1775 not shown) Planarity restraints: 2066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C32 8PP B 403 " 0.338 2.00e-02 2.50e+03 2.88e-01 1.04e+03 pdb=" C33 8PP B 403 " -0.502 2.00e-02 2.50e+03 pdb=" C34 8PP B 403 " -0.108 2.00e-02 2.50e+03 pdb=" C35 8PP B 403 " 0.109 2.00e-02 2.50e+03 pdb=" C36 8PP B 403 " 0.162 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C22 8PP G 302 " 0.335 2.00e-02 2.50e+03 2.85e-01 1.01e+03 pdb=" C23 8PP G 302 " -0.495 2.00e-02 2.50e+03 pdb=" C24 8PP G 302 " -0.105 2.00e-02 2.50e+03 pdb=" C25 8PP G 302 " 0.167 2.00e-02 2.50e+03 pdb=" C26 8PP G 302 " 0.098 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 8PP B 403 " -0.317 2.00e-02 2.50e+03 2.70e-01 9.12e+02 pdb=" C18 8PP B 403 " 0.467 2.00e-02 2.50e+03 pdb=" C19 8PP B 403 " 0.098 2.00e-02 2.50e+03 pdb=" C20 8PP B 403 " -0.068 2.00e-02 2.50e+03 pdb=" C21 8PP B 403 " -0.179 2.00e-02 2.50e+03 ... (remaining 2063 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 3853 2.84 - 3.35: 11589 3.35 - 3.87: 20860 3.87 - 4.38: 26980 4.38 - 4.90: 42170 Nonbonded interactions: 105452 Sorted by model distance: nonbonded pdb=" ND1 HIS B 211 " pdb=" OG SER E 201 " model vdw 2.323 2.520 nonbonded pdb=" ND1 HIS A 211 " pdb=" OG SER G 201 " model vdw 2.329 2.520 nonbonded pdb=" ND1 HIS D 211 " pdb=" OG SER H 201 " model vdw 2.330 2.520 nonbonded pdb=" OD2 ASP F 50 " pdb=" O HOH F 401 " model vdw 2.332 2.440 nonbonded pdb=" ND1 HIS C 211 " pdb=" OG SER F 201 " model vdw 2.333 2.520 ... (remaining 105447 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 95 through 151 or resid 153 through 162 or (resid 163 and \ (name N or name CA or name C or name O or name CB )) or resid 164 through 209 or \ (resid 210 and (name N or name CA or name C or name O or name CB or name CD )) \ or resid 211 through 275 or resid 277 through 283)) selection = (chain 'B' and (resid 95 through 97 or (resid 98 and (name N or name CA or name \ C or name O or name CB )) or resid 99 through 151 or resid 153 through 162 or (r \ esid 163 and (name N or name CA or name C or name O or name CB )) or resid 164 t \ hrough 209 or (resid 210 and (name N or name CA or name C or name O or name CB o \ r name CD )) or resid 211 through 275 or resid 277 through 283)) selection = (chain 'C' and (resid 95 through 97 or (resid 98 and (name N or name CA or name \ C or name O or name CB )) or resid 99 through 151 or resid 153 through 162 or (r \ esid 163 and (name N or name CA or name C or name O or name CB )) or resid 164 t \ hrough 275 or resid 277 through 283)) selection = (chain 'D' and (resid 95 through 97 or (resid 98 and (name N or name CA or name \ C or name O or name CB )) or resid 99 through 151 or resid 153 through 209 or (r \ esid 210 and (name N or name CA or name C or name O or name CB or name CD )) or \ resid 211 through 275 or resid 277 through 283)) } ncs_group { reference = (chain 'E' and (resid 45 through 95 or resid 97 through 217 or (resid 301 and (n \ ame C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 o \ r name C2 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 \ or name O11 or name O1P or name O2 or name O2P or name O3 or name O31 or name O \ 3P or name O4P or name P )) or (resid 305 and (name C18 or name C19 or name C20 \ or name C21 or name C22)))) selection = (chain 'F' and (resid 45 through 95 or resid 97 through 182 or (resid 183 and (n \ ame N or name CA or name C or name O or name CB )) or resid 184 through 213 or ( \ resid 214 and (name N or name CA or name C or name O or name CB )) or resid 215 \ through 217 or (resid 301 and (name C1 or name C11 or name C12 or name C13 or na \ me C14 or name C15 or name C16 or name C2 or name C3 or name C31 or name C32 or \ name C33 or name C34 or name C35 or name O11 or name O1P or name O2 or name O2P \ or name O3 or name O31 or name O3P or name O4P or name P )) or (resid 305 and (n \ ame C17 or name C18 or name C19 or name C20 or name C21)))) selection = (chain 'G' and (resid 45 through 95 or resid 97 through 182 or (resid 183 and (n \ ame N or name CA or name C or name O or name CB )) or resid 184 through 213 or ( \ resid 214 and (name N or name CA or name C or name O or name CB )) or resid 215 \ through 217 or (resid 301 and (name C1 or name C11 or name C12 or name C13 or na \ me C14 or name C15 or name C16 or name C2 or name C3 or name C31 or name C32 or \ name C33 or name C34 or name C35 or name O11 or name O1P or name O2 or name O2P \ or name O3 or name O31 or name O3P or name O4P or name P )) or (resid 305 and (n \ ame C18 or name C19 or name C20 or name C21 or name C22)))) selection = (chain 'H' and (resid 45 through 95 or resid 97 through 182 or (resid 183 and (n \ ame N or name CA or name C or name O or name CB )) or resid 184 through 213 or ( \ resid 214 and (name N or name CA or name C or name O or name CB )) or resid 215 \ through 217 or (resid 301 and (name C1 or name C11 or name C12 or name C13 or na \ me C14 or name C15 or name C16 or name C2 or name C3 or name C31 or name C32 or \ name C33 or name C34 or name C35 or name O11 or name O1P or name O2 or name O2P \ or name O3 or name O31 or name O3P or name O4P or name P )) or (resid 305 and (n \ ame C18 or name C19 or name C20 or name C21 or name C22)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 4.860 Check model and map are aligned: 0.190 Set scattering table: 0.130 Process input model: 41.680 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.049 12225 Z= 0.361 Angle : 0.661 9.948 16442 Z= 0.318 Chirality : 0.039 0.197 1778 Planarity : 0.019 0.288 2066 Dihedral : 14.287 79.966 4561 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer Outliers : 0.00 % 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 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 325 time to evaluate : 1.365 Fit side-chains outliers start: 0 outliers final: 4 residues processed: 325 average time/residue: 1.6996 time to fit residues: 585.9201 Evaluate side-chains 238 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 234 time to evaluate : 1.399 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 4 average time/residue: 0.2481 time to fit residues: 3.2367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 8.9990 chunk 106 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 36 optimal weight: 10.0000 chunk 71 optimal weight: 0.7980 chunk 56 optimal weight: 7.9990 chunk 109 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 127 optimal weight: 0.8980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN A 275 ASN B 169 GLN B 260 GLN C 260 GLN C 275 ASN D 169 GLN D 260 GLN E 98 ASN E 182 HIS F 98 ASN G 98 ASN G 182 HIS H 98 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2129 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= 0.162 Angle : 0.547 9.520 16442 Z= 0.284 Chirality : 0.038 0.115 1778 Planarity : 0.005 0.039 2066 Dihedral : 13.182 59.999 1921 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer Outliers : 2.50 % 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: 2.15 (0.23), residues: 1422 helix: 1.97 (0.15), residues: 1142 sheet: None (None), residues: 0 loop : -0.84 (0.38), residues: 280 *********************** 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 279 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 250 time to evaluate : 1.361 Fit side-chains outliers start: 29 outliers final: 4 residues processed: 255 average time/residue: 1.5825 time to fit residues: 430.3663 Evaluate side-chains 236 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 232 time to evaluate : 1.474 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 4 average time/residue: 0.2515 time to fit residues: 3.3428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 105 optimal weight: 9.9990 chunk 86 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 chunk 127 optimal weight: 1.9990 chunk 137 optimal weight: 10.0000 chunk 113 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN A 260 GLN A 275 ASN B 260 GLN B 275 ASN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 GLN C 260 GLN C 275 ASN D 260 GLN E 98 ASN E 204 GLN G 98 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 12225 Z= 0.248 Angle : 0.633 8.731 16442 Z= 0.321 Chirality : 0.042 0.233 1778 Planarity : 0.006 0.038 2066 Dihedral : 13.486 59.890 1921 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer Outliers : 3.70 % 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: 2.00 (0.23), residues: 1422 helix: 1.85 (0.15), residues: 1138 sheet: None (None), residues: 0 loop : -0.79 (0.38), residues: 284 *********************** 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 283 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 241 time to evaluate : 1.468 Fit side-chains outliers start: 42 outliers final: 23 residues processed: 252 average time/residue: 1.7414 time to fit residues: 466.4894 Evaluate side-chains 251 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 228 time to evaluate : 1.391 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 14 residues processed: 13 average time/residue: 0.6276 time to fit residues: 11.2647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 0.7980 chunk 95 optimal weight: 8.9990 chunk 66 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 chunk 135 optimal weight: 9.9990 chunk 121 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 chunk 112 optimal weight: 8.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN A 260 GLN A 275 ASN B 260 GLN B 275 ASN C 234 GLN C 260 GLN C 275 ASN D 260 GLN E 93 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 12225 Z= 0.266 Angle : 0.649 8.565 16442 Z= 0.329 Chirality : 0.043 0.224 1778 Planarity : 0.006 0.042 2066 Dihedral : 13.189 59.669 1921 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer Outliers : 4.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.22), residues: 1422 helix: 1.67 (0.15), residues: 1146 sheet: None (None), residues: 0 loop : -0.95 (0.37), residues: 276 *********************** 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 281 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 235 time to evaluate : 1.471 Fit side-chains outliers start: 46 outliers final: 27 residues processed: 254 average time/residue: 1.5832 time to fit residues: 428.7785 Evaluate side-chains 249 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 222 time to evaluate : 1.399 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 20 residues processed: 11 average time/residue: 0.4480 time to fit residues: 7.8398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 chunk 100 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 115 optimal weight: 9.9990 chunk 93 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 34 optimal weight: 0.0670 chunk 45 optimal weight: 2.9990 overall best weight: 0.7718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN A 260 GLN A 275 ASN B 275 ASN C 234 GLN C 260 GLN C 275 ASN F 150 ASN G 150 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 12225 Z= 0.137 Angle : 0.498 8.598 16442 Z= 0.256 Chirality : 0.036 0.116 1778 Planarity : 0.004 0.034 2066 Dihedral : 12.188 58.960 1921 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer Outliers : 2.93 % 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: 2.49 (0.23), residues: 1422 helix: 2.28 (0.16), residues: 1134 sheet: None (None), residues: 0 loop : -1.00 (0.36), residues: 288 *********************** 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 268 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 235 time to evaluate : 1.469 Fit side-chains outliers start: 33 outliers final: 18 residues processed: 257 average time/residue: 1.5872 time to fit residues: 434.7960 Evaluate side-chains 237 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 219 time to evaluate : 1.433 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 15 residues processed: 3 average time/residue: 0.7696 time to fit residues: 4.5154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 79 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 135 optimal weight: 0.1980 chunk 112 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 chunk 130 optimal weight: 7.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN A 260 GLN A 275 ASN B 275 ASN C 234 GLN C 260 GLN C 275 ASN F 204 GLN G 204 GLN H 204 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 12225 Z= 0.127 Angle : 0.476 8.742 16442 Z= 0.243 Chirality : 0.035 0.112 1778 Planarity : 0.004 0.036 2066 Dihedral : 11.338 59.705 1921 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer Outliers : 1.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.71 (0.23), residues: 1422 helix: 2.46 (0.16), residues: 1134 sheet: None (None), residues: 0 loop : -1.01 (0.36), residues: 288 *********************** 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 255 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 233 time to evaluate : 1.297 Fit side-chains outliers start: 22 outliers final: 17 residues processed: 249 average time/residue: 1.5715 time to fit residues: 417.5054 Evaluate side-chains 247 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 230 time to evaluate : 1.403 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 15 residues processed: 2 average time/residue: 2.0860 time to fit residues: 6.1836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 84 optimal weight: 9.9990 chunk 82 optimal weight: 6.9990 chunk 62 optimal weight: 0.6980 chunk 83 optimal weight: 6.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 ASN C 234 GLN C 275 ASN ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 HIS F 148 HIS G 148 HIS H 148 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 12225 Z= 0.193 Angle : 0.552 8.461 16442 Z= 0.280 Chirality : 0.038 0.175 1778 Planarity : 0.005 0.038 2066 Dihedral : 11.607 58.874 1921 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer Outliers : 2.50 % 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: 2.45 (0.23), residues: 1422 helix: 2.26 (0.16), residues: 1134 sheet: None (None), residues: 0 loop : -1.02 (0.36), residues: 288 *********************** 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 258 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 230 time to evaluate : 1.415 Fit side-chains outliers start: 28 outliers final: 18 residues processed: 246 average time/residue: 1.6014 time to fit residues: 420.6460 Evaluate side-chains 239 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 221 time to evaluate : 1.337 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 14 residues processed: 4 average time/residue: 0.1793 time to fit residues: 2.9455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 1.9990 chunk 80 optimal weight: 0.2980 chunk 40 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 106 optimal weight: 0.9990 chunk 122 optimal weight: 8.9990 chunk 129 optimal weight: 6.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN A 260 GLN A 275 ASN B 260 GLN B 275 ASN C 234 GLN C 260 GLN C 275 ASN D 260 GLN E 148 HIS F 148 HIS G 148 HIS H 148 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 12225 Z= 0.126 Angle : 0.480 8.554 16442 Z= 0.244 Chirality : 0.035 0.129 1778 Planarity : 0.004 0.036 2066 Dihedral : 10.822 58.227 1921 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer Outliers : 1.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.71 (0.23), residues: 1422 helix: 2.44 (0.16), residues: 1138 sheet: None (None), residues: 0 loop : -0.97 (0.36), residues: 284 *********************** 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 250 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 228 time to evaluate : 1.520 Fit side-chains outliers start: 22 outliers final: 18 residues processed: 243 average time/residue: 1.6296 time to fit residues: 421.7097 Evaluate side-chains 244 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 226 time to evaluate : 1.287 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 14 residues processed: 4 average time/residue: 0.7053 time to fit residues: 5.0579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 0.0070 chunk 125 optimal weight: 7.9990 chunk 129 optimal weight: 2.9990 chunk 75 optimal weight: 0.0000 chunk 54 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 113 optimal weight: 0.9990 chunk 118 optimal weight: 9.9990 chunk 82 optimal weight: 4.9990 chunk 132 optimal weight: 9.9990 overall best weight: 1.6008 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 ASN C 234 GLN C 275 ASN E 148 HIS F 148 HIS G 148 HIS H 148 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 12225 Z= 0.165 Angle : 0.523 8.574 16442 Z= 0.266 Chirality : 0.037 0.154 1778 Planarity : 0.004 0.037 2066 Dihedral : 10.955 59.540 1921 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer Outliers : 1.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.23), residues: 1422 helix: 2.43 (0.16), residues: 1118 sheet: None (None), residues: 0 loop : -1.16 (0.35), residues: 304 *********************** 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 243 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 223 time to evaluate : 1.533 Fit side-chains outliers start: 20 outliers final: 18 residues processed: 238 average time/residue: 1.6159 time to fit residues: 410.0203 Evaluate side-chains 241 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 223 time to evaluate : 1.404 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 15 residues processed: 3 average time/residue: 0.7953 time to fit residues: 4.6079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 139 optimal weight: 0.7980 chunk 128 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 88 optimal weight: 0.7980 chunk 118 optimal weight: 5.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 ASN C 234 GLN C 275 ASN ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 HIS F 148 HIS G 148 HIS H 148 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 12225 Z= 0.136 Angle : 0.500 8.549 16442 Z= 0.252 Chirality : 0.036 0.131 1778 Planarity : 0.004 0.036 2066 Dihedral : 10.638 59.345 1921 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.68 (0.23), residues: 1422 helix: 2.52 (0.16), residues: 1118 sheet: None (None), residues: 0 loop : -1.20 (0.34), residues: 304 ********************** 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 247 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 228 time to evaluate : 1.457 Fit side-chains outliers start: 19 outliers final: 18 residues processed: 244 average time/residue: 1.5822 time to fit residues: 412.0054 Evaluate side-chains 243 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 225 time to evaluate : 1.427 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 15 residues processed: 3 average time/residue: 1.2498 time to fit residues: 5.9252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 6 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN A 260 GLN A 275 ASN B 275 ASN C 234 GLN C 275 ASN E 148 HIS F 148 HIS G 148 HIS H 148 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.176950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.136883 restraints weight = 56999.471| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 4.85 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3477 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3477 r_free = 0.3477 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3477 r_free = 0.3477 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3477 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 12225 Z= 0.214 Angle : 0.587 8.528 16442 Z= 0.297 Chirality : 0.039 0.199 1778 Planarity : 0.005 0.038 2066 Dihedral : 11.523 58.314 1921 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.23), residues: 1422 helix: 2.17 (0.16), residues: 1126 sheet: None (None), residues: 0 loop : -1.05 (0.35), residues: 296 =============================================================================== Job complete usr+sys time: 6070.84 seconds wall clock time: 107 minutes 32.49 seconds (6452.49 seconds total)