Starting phenix.real_space_refine on Sat Aug 23 11:36:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qqz_18609/08_2025/8qqz_18609.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qqz_18609/08_2025/8qqz_18609.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8qqz_18609/08_2025/8qqz_18609.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qqz_18609/08_2025/8qqz_18609.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qqz_18609/08_2025/8qqz_18609.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qqz_18609/08_2025/8qqz_18609.map" } resolution = 2.63 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 7971 2.51 5 N 1710 2.21 5 O 2140 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11871 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2180 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 272, 2160 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 259} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'FME:plan-2': 1, 'ARG:plan': 3, 'GLU:plan': 3, 'LYR:plan-1': 1} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 272, 2160 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 259} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'FME:plan-2': 1, 'ARG:plan': 3, 'GLU:plan': 3, 'LYR:plan-1': 1} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 2205 Chain: "B" Number of atoms: 2181 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 272, 2161 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 12, 'TRANS': 259} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'FME:plan-2': 1, 'ARG:plan': 3, 'GLU:plan': 3, 'LYR:plan-1': 1} Unresolved non-hydrogen planarities: 23 Conformer: "B" Number of residues, atoms: 272, 2161 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 12, 'TRANS': 259} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'FME:plan-2': 1, 'ARG:plan': 3, 'GLU:plan': 3, 'LYR:plan-1': 1} Unresolved non-hydrogen planarities: 23 bond proxies already assigned to first conformer: 2206 Chain: "C" Number of atoms: 2180 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 272, 2160 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 259} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'FME:plan-2': 1, 'ARG:plan': 3, 'GLU:plan': 3, 'LYR:plan-1': 1} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 272, 2160 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 259} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'FME:plan-2': 1, 'ARG:plan': 3, 'GLU:plan': 3, 'LYR:plan-1': 1} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 2205 Chain: "D" Number of atoms: 2180 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 272, 2160 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 259} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'FME:plan-2': 1, 'ARG:plan': 3, 'GLU:plan': 3, 'LYR:plan-1': 1} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 272, 2160 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 259} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'FME:plan-2': 1, 'ARG:plan': 3, 'GLU:plan': 3, 'LYR:plan-1': 1} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 2205 Chain: "E" Number of atoms: 2180 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 272, 2160 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 259} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'FME:plan-2': 1, 'ARG:plan': 3, 'GLU:plan': 3, 'LYR:plan-1': 1} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 272, 2160 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 259} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'FME:plan-2': 1, 'ARG:plan': 3, 'GLU:plan': 3, 'LYR:plan-1': 1} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 2205 Chain: "A" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 204 Unusual residues: {'LFA': 10, 'LMT': 3} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 101 Chain: "B" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 156 Unusual residues: {'LFA': 9, 'LMT': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 94 Chain: "C" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 136 Unusual residues: {'LFA': 8, 'LMT': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 94 Chain: "D" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 178 Unusual residues: {'LFA': 11, 'LMT': 2} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 112 Chain: "E" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 101 Unusual residues: {'LFA': 8, 'LMT': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 94 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Residues with excluded nonbonded symmetry interactions: 10 residue: pdb=" N AGLN A 67 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A 67 " occ=0.50 residue: pdb=" N APHE A 217 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 217 " occ=0.50 residue: pdb=" N AGLN B 67 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN B 67 " occ=0.50 residue: pdb=" N APHE B 217 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE B 217 " occ=0.50 residue: pdb=" N AGLN C 67 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN C 67 " occ=0.50 residue: pdb=" N APHE C 217 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE C 217 " occ=0.50 residue: pdb=" N AGLN D 67 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN D 67 " occ=0.50 residue: pdb=" N APHE D 217 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE D 217 " occ=0.50 residue: pdb=" N AGLN E 67 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN E 67 " occ=0.50 residue: pdb=" N APHE E 217 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE E 217 " occ=0.50 Time building chain proxies: 6.08, per 1000 atoms: 0.51 Number of scatterers: 11871 At special positions: 0 Unit cell: (92.378, 91.542, 81.092, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 2140 8.00 N 1710 7.00 C 7971 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 1.2 microseconds 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2560 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 5 sheets defined 84.4% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 3 through 8 Processing helix chain 'A' and resid 11 through 38 Processing helix chain 'A' and resid 39 through 43 Processing helix chain 'A' and resid 47 through 75 removed outlier: 3.780A pdb=" N ALA A 51 " --> pdb=" O TYR A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 117 removed outlier: 4.291A pdb=" N TYR A 99 " --> pdb=" O ASN A 95 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASN A 101 " --> pdb=" O TYR A 97 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU A 103 " --> pdb=" O TYR A 99 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ILE A 104 " --> pdb=" O MET A 100 " (cutoff:3.500A) Proline residue: A 107 - end of helix removed outlier: 3.564A pdb=" N LEU A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 146 Processing helix chain 'A' and resid 148 through 153 Processing helix chain 'A' and resid 160 through 188 removed outlier: 3.714A pdb=" N PHE A 164 " --> pdb=" O GLY A 160 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TRP A 165 " --> pdb=" O ALA A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 213 Processing helix chain 'A' and resid 213 through 225 removed outlier: 3.876A pdb=" N APHE A 217 " --> pdb=" O SER A 213 " (cutoff:3.500A) Proline residue: A 222 - end of helix Processing helix chain 'A' and resid 227 through 264 removed outlier: 4.674A pdb=" N PHE A 249 " --> pdb=" O SER A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 271 Processing helix chain 'B' and resid 3 through 8 Processing helix chain 'B' and resid 11 through 38 Processing helix chain 'B' and resid 39 through 43 Processing helix chain 'B' and resid 47 through 75 removed outlier: 3.793A pdb=" N ALA B 51 " --> pdb=" O TYR B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 117 removed outlier: 4.301A pdb=" N TYR B 99 " --> pdb=" O ASN B 95 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N MET B 100 " --> pdb=" O GLY B 96 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN B 101 " --> pdb=" O TYR B 97 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU B 103 " --> pdb=" O TYR B 99 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE B 104 " --> pdb=" O MET B 100 " (cutoff:3.500A) Proline residue: B 107 - end of helix removed outlier: 3.563A pdb=" N LEU B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 146 Processing helix chain 'B' and resid 148 through 153 Processing helix chain 'B' and resid 160 through 188 removed outlier: 3.716A pdb=" N PHE B 164 " --> pdb=" O GLY B 160 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TRP B 165 " --> pdb=" O ALA B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 213 Processing helix chain 'B' and resid 213 through 225 removed outlier: 3.876A pdb=" N APHE B 217 " --> pdb=" O SER B 213 " (cutoff:3.500A) Proline residue: B 222 - end of helix Processing helix chain 'B' and resid 227 through 264 removed outlier: 4.691A pdb=" N PHE B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 271 Processing helix chain 'C' and resid 3 through 8 removed outlier: 3.527A pdb=" N LEU C 8 " --> pdb=" O GLU C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 38 Processing helix chain 'C' and resid 39 through 43 Processing helix chain 'C' and resid 47 through 75 removed outlier: 3.791A pdb=" N ALA C 51 " --> pdb=" O TYR C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 117 removed outlier: 3.714A pdb=" N MET C 100 " --> pdb=" O GLY C 96 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN C 101 " --> pdb=" O TYR C 97 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU C 103 " --> pdb=" O TYR C 99 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ILE C 104 " --> pdb=" O MET C 100 " (cutoff:3.500A) Proline residue: C 107 - end of helix removed outlier: 3.563A pdb=" N LEU C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 146 Processing helix chain 'C' and resid 148 through 153 Processing helix chain 'C' and resid 160 through 188 removed outlier: 3.714A pdb=" N PHE C 164 " --> pdb=" O GLY C 160 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TRP C 165 " --> pdb=" O ALA C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 213 Processing helix chain 'C' and resid 213 through 225 removed outlier: 3.879A pdb=" N APHE C 217 " --> pdb=" O SER C 213 " (cutoff:3.500A) Proline residue: C 222 - end of helix Processing helix chain 'C' and resid 227 through 264 removed outlier: 3.500A pdb=" N VAL C 248 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N PHE C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 271 Processing helix chain 'D' and resid 3 through 8 Processing helix chain 'D' and resid 11 through 38 Processing helix chain 'D' and resid 39 through 43 Processing helix chain 'D' and resid 47 through 75 removed outlier: 3.788A pdb=" N ALA D 51 " --> pdb=" O TYR D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 117 removed outlier: 4.288A pdb=" N TYR D 99 " --> pdb=" O ASN D 95 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N MET D 100 " --> pdb=" O GLY D 96 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASN D 101 " --> pdb=" O TYR D 97 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU D 103 " --> pdb=" O TYR D 99 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ILE D 104 " --> pdb=" O MET D 100 " (cutoff:3.500A) Proline residue: D 107 - end of helix removed outlier: 3.560A pdb=" N LEU D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 146 Processing helix chain 'D' and resid 148 through 153 Processing helix chain 'D' and resid 160 through 188 removed outlier: 3.714A pdb=" N PHE D 164 " --> pdb=" O GLY D 160 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TRP D 165 " --> pdb=" O ALA D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 225 removed outlier: 3.777A pdb=" N ILE D 214 " --> pdb=" O ALA D 210 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N TYR D 215 " --> pdb=" O THR D 211 " (cutoff:3.500A) Proline residue: D 216 - end of helix Proline residue: D 222 - end of helix Processing helix chain 'D' and resid 227 through 264 removed outlier: 4.678A pdb=" N PHE D 249 " --> pdb=" O SER D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 271 Processing helix chain 'E' and resid 3 through 8 removed outlier: 3.532A pdb=" N LEU E 8 " --> pdb=" O GLU E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 38 Processing helix chain 'E' and resid 39 through 43 Processing helix chain 'E' and resid 47 through 75 removed outlier: 3.786A pdb=" N ALA E 51 " --> pdb=" O TYR E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 117 removed outlier: 4.319A pdb=" N TYR E 99 " --> pdb=" O ASN E 95 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N MET E 100 " --> pdb=" O GLY E 96 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASN E 101 " --> pdb=" O TYR E 97 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU E 103 " --> pdb=" O TYR E 99 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ILE E 104 " --> pdb=" O MET E 100 " (cutoff:3.500A) Proline residue: E 107 - end of helix removed outlier: 3.564A pdb=" N LEU E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 146 Processing helix chain 'E' and resid 148 through 153 Processing helix chain 'E' and resid 160 through 188 removed outlier: 3.717A pdb=" N PHE E 164 " --> pdb=" O GLY E 160 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TRP E 165 " --> pdb=" O ALA E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 213 Processing helix chain 'E' and resid 213 through 225 removed outlier: 3.876A pdb=" N APHE E 217 " --> pdb=" O SER E 213 " (cutoff:3.500A) Proline residue: E 222 - end of helix Processing helix chain 'E' and resid 227 through 264 removed outlier: 4.675A pdb=" N PHE E 249 " --> pdb=" O SER E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 271 Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 79 Processing sheet with id=AA2, first strand: chain 'B' and resid 76 through 79 Processing sheet with id=AA3, first strand: chain 'C' and resid 76 through 79 Processing sheet with id=AA4, first strand: chain 'D' and resid 76 through 79 Processing sheet with id=AA5, first strand: chain 'E' and resid 76 through 79 866 hydrogen bonds defined for protein. 2523 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: 2.25 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 3111 1.34 - 1.47: 3691 1.47 - 1.61: 5103 1.61 - 1.74: 0 1.74 - 1.88: 90 Bond restraints: 11995 Sorted by residual: bond pdb=" C6 LYR E 246 " pdb=" C7 LYR E 246 " ideal model delta sigma weight residual 1.444 1.353 0.091 2.00e-02 2.50e+03 2.05e+01 bond pdb=" C6 LYR C 246 " pdb=" C7 LYR C 246 " ideal model delta sigma weight residual 1.444 1.354 0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" C6 LYR A 246 " pdb=" C7 LYR A 246 " ideal model delta sigma weight residual 1.444 1.354 0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" C6 LYR B 246 " pdb=" C7 LYR B 246 " ideal model delta sigma weight residual 1.444 1.355 0.089 2.00e-02 2.50e+03 2.00e+01 bond pdb=" C6 LYR D 246 " pdb=" C7 LYR D 246 " ideal model delta sigma weight residual 1.444 1.355 0.089 2.00e-02 2.50e+03 2.00e+01 ... (remaining 11990 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 14324 2.28 - 4.57: 1693 4.57 - 6.85: 171 6.85 - 9.14: 16 9.14 - 11.42: 10 Bond angle restraints: 16214 Sorted by residual: angle pdb=" CA FME B 1 " pdb=" C FME B 1 " pdb=" N PRO B 2 " ideal model delta sigma weight residual 116.90 128.32 -11.42 1.50e+00 4.44e-01 5.80e+01 angle pdb=" CA FME D 1 " pdb=" C FME D 1 " pdb=" N PRO D 2 " ideal model delta sigma weight residual 116.90 128.23 -11.33 1.50e+00 4.44e-01 5.70e+01 angle pdb=" CA FME A 1 " pdb=" C FME A 1 " pdb=" N PRO A 2 " ideal model delta sigma weight residual 116.90 128.14 -11.24 1.50e+00 4.44e-01 5.61e+01 angle pdb=" CA FME C 1 " pdb=" C FME C 1 " pdb=" N PRO C 2 " ideal model delta sigma weight residual 116.90 128.13 -11.23 1.50e+00 4.44e-01 5.60e+01 angle pdb=" CA FME E 1 " pdb=" C FME E 1 " pdb=" N PRO E 2 " ideal model delta sigma weight residual 116.90 127.90 -11.00 1.50e+00 4.44e-01 5.38e+01 ... (remaining 16209 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.01: 6789 25.01 - 50.03: 378 50.03 - 75.04: 61 75.04 - 100.05: 10 100.05 - 125.07: 5 Dihedral angle restraints: 7243 sinusoidal: 3248 harmonic: 3995 Sorted by residual: dihedral pdb=" C14 LYR C 246 " pdb=" C15 LYR C 246 " pdb=" C16 LYR C 246 " pdb=" C17 LYR C 246 " ideal model delta sinusoidal sigma weight residual 61.52 -63.55 125.07 1 3.00e+01 1.11e-03 1.68e+01 dihedral pdb=" C14 LYR E 246 " pdb=" C15 LYR E 246 " pdb=" C16 LYR E 246 " pdb=" C17 LYR E 246 " ideal model delta sinusoidal sigma weight residual 61.52 -63.33 124.85 1 3.00e+01 1.11e-03 1.68e+01 dihedral pdb=" C14 LYR B 246 " pdb=" C15 LYR B 246 " pdb=" C16 LYR B 246 " pdb=" C17 LYR B 246 " ideal model delta sinusoidal sigma weight residual 61.52 -63.18 124.70 1 3.00e+01 1.11e-03 1.67e+01 ... (remaining 7240 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1056 0.060 - 0.121: 507 0.121 - 0.181: 184 0.181 - 0.242: 35 0.242 - 0.302: 13 Chirality restraints: 1795 Sorted by residual: chirality pdb=" CA GLU B 149 " pdb=" N GLU B 149 " pdb=" C GLU B 149 " pdb=" CB GLU B 149 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CA GLU C 149 " pdb=" N GLU C 149 " pdb=" C GLU C 149 " pdb=" CB GLU C 149 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CA GLU E 149 " pdb=" N GLU E 149 " pdb=" C GLU E 149 " pdb=" CB GLU E 149 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.23e+00 ... (remaining 1792 not shown) Planarity restraints: 1925 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 LYR D 246 " -0.090 2.00e-02 2.50e+03 7.54e-02 7.10e+01 pdb=" C2 LYR D 246 " 0.122 2.00e-02 2.50e+03 pdb=" C3 LYR D 246 " 0.020 2.00e-02 2.50e+03 pdb=" C4 LYR D 246 " 0.017 2.00e-02 2.50e+03 pdb=" C5 LYR D 246 " -0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 LYR E 246 " -0.089 2.00e-02 2.50e+03 7.52e-02 7.07e+01 pdb=" C2 LYR E 246 " 0.121 2.00e-02 2.50e+03 pdb=" C3 LYR E 246 " 0.020 2.00e-02 2.50e+03 pdb=" C4 LYR E 246 " 0.017 2.00e-02 2.50e+03 pdb=" C5 LYR E 246 " -0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 LYR B 246 " 0.088 2.00e-02 2.50e+03 7.35e-02 6.76e+01 pdb=" C2 LYR B 246 " -0.119 2.00e-02 2.50e+03 pdb=" C3 LYR B 246 " -0.020 2.00e-02 2.50e+03 pdb=" C4 LYR B 246 " -0.017 2.00e-02 2.50e+03 pdb=" C5 LYR B 246 " 0.068 2.00e-02 2.50e+03 ... (remaining 1922 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1166 2.73 - 3.27: 12321 3.27 - 3.81: 22204 3.81 - 4.36: 29999 4.36 - 4.90: 47094 Nonbonded interactions: 112784 Sorted by model distance: nonbonded pdb=" ND1 HIS C 20 " pdb=" OH TYR D 143 " model vdw 2.182 3.120 nonbonded pdb=" OH TYR A 143 " pdb=" ND1 HIS E 20 " model vdw 2.190 3.120 nonbonded pdb=" O ASN C 73 " pdb=" O HOH C 401 " model vdw 2.197 3.040 nonbonded pdb=" ND1 HIS A 20 " pdb=" OH TYR B 143 " model vdw 2.198 3.120 nonbonded pdb=" ND1 HIS D 20 " pdb=" OH TYR E 143 " model vdw 2.200 3.120 ... (remaining 112779 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 1 through 66 or resid 68 through 216 or resid 218 through \ 272 or (resid 301 and (name C8 or name C9 )) or (resid 305 and (name C16 or name \ C17 or name C18 or name C19 or name C20)) or resid 308)) selection = (chain 'B' and (resid 1 through 66 or resid 68 through 216 or resid 218 through \ 266 or (resid 267 and (name N or name CA or name C or name O or name CB )) or re \ sid 268 through 272 or (resid 301 and (name C8 or name C9 )) or (resid 305 and ( \ name C3 or name C4 or name C5 or name C6 or name C7 )) or resid 308)) selection = (chain 'C' and (resid 1 through 66 or resid 68 through 216 or resid 218 through \ 272 or (resid 301 and (name C8 or name C9 )) or (resid 305 and (name C4 or name \ C5 or name C6 or name C7 or name C8 )) or resid 308)) selection = (chain 'D' and (resid 1 through 66 or resid 68 through 216 or resid 218 through \ 272 or (resid 301 and (name C8 or name C9 )) or resid 305 or (resid 308 and (nam \ e C15 or name C16 or name C17 or name C18 or name C19 or name C20)))) selection = (chain 'E' and (resid 1 through 66 or resid 68 through 216 or resid 218 through \ 272 or (resid 301 and (name C8 or name C9 )) or (resid 305 and (name C16 or name \ C17 or name C18 or name C19 or name C20)) or (resid 308 and (name C15 or name C \ 16 or name C17 or name C18 or name C19 or name C20)))) } 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: 25.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 16.270 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 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 : 0.013 0.091 11995 Z= 0.797 Angle : 1.533 11.420 16214 Z= 0.979 Chirality : 0.080 0.302 1795 Planarity : 0.019 0.290 1925 Dihedral : 15.821 125.066 4683 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 2.34 % Allowed : 4.39 % Favored : 93.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.99 (0.19), residues: 1360 helix: -1.69 (0.12), residues: 1020 sheet: None (None), residues: 0 loop : 0.74 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.035 0.006 ARG B 127 TYR 0.051 0.012 TYR D 147 PHE 0.060 0.011 PHE E 12 TRP 0.076 0.012 TRP E 128 HIS 0.009 0.006 HIS A 20 Details of bonding type rmsd covalent geometry : bond 0.01282 (11995) covalent geometry : angle 1.53333 (16214) hydrogen bonds : bond 0.20926 ( 866) hydrogen bonds : angle 7.58985 ( 2523) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 0.481 Fit side-chains REVERT: A 196 GLU cc_start: 0.8341 (tm-30) cc_final: 0.8037 (tm-30) REVERT: A 199 SER cc_start: 0.8698 (m) cc_final: 0.8283 (p) REVERT: B 196 GLU cc_start: 0.8301 (tm-30) cc_final: 0.8072 (tm-30) REVERT: B 199 SER cc_start: 0.8649 (m) cc_final: 0.8245 (p) REVERT: C 199 SER cc_start: 0.8667 (m) cc_final: 0.8256 (p) REVERT: D 196 GLU cc_start: 0.8339 (tm-30) cc_final: 0.8064 (tm-30) REVERT: D 199 SER cc_start: 0.8648 (m) cc_final: 0.8281 (p) REVERT: E 196 GLU cc_start: 0.8347 (tm-30) cc_final: 0.8071 (tm-30) REVERT: E 199 SER cc_start: 0.8649 (m) cc_final: 0.8252 (p) outliers start: 25 outliers final: 15 residues processed: 178 average time/residue: 0.7182 time to fit residues: 137.1783 Evaluate side-chains 151 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 253 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN B 235 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.101520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.083333 restraints weight = 59899.242| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 2.57 r_work: 0.2681 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2644 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2644 r_free = 0.2644 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2644 r_free = 0.2644 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2644 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11995 Z= 0.152 Angle : 0.675 12.506 16214 Z= 0.329 Chirality : 0.041 0.193 1795 Planarity : 0.005 0.039 1925 Dihedral : 13.345 106.819 2497 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.87 % Allowed : 7.94 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.20), residues: 1360 helix: 1.40 (0.14), residues: 1045 sheet: None (None), residues: 0 loop : 0.68 (0.30), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 200 TYR 0.013 0.002 TYR D 238 PHE 0.020 0.002 PHE B 12 TRP 0.012 0.002 TRP D 212 HIS 0.003 0.002 HIS E 20 Details of bonding type rmsd covalent geometry : bond 0.00316 (11995) covalent geometry : angle 0.67470 (16214) hydrogen bonds : bond 0.05862 ( 866) hydrogen bonds : angle 4.36720 ( 2523) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 0.500 Fit side-chains REVERT: A 43 THR cc_start: 0.8832 (m) cc_final: 0.8601 (t) REVERT: B 43 THR cc_start: 0.8827 (m) cc_final: 0.8548 (t) REVERT: C 43 THR cc_start: 0.8834 (m) cc_final: 0.8587 (t) REVERT: D 259 ARG cc_start: 0.8448 (ttt90) cc_final: 0.8133 (ttt180) REVERT: E 43 THR cc_start: 0.8773 (m) cc_final: 0.8512 (t) REVERT: E 259 ARG cc_start: 0.8479 (ttt90) cc_final: 0.8228 (ttt180) outliers start: 20 outliers final: 7 residues processed: 179 average time/residue: 0.7776 time to fit residues: 148.6244 Evaluate side-chains 152 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 145 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain E residue 208 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 9 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.103799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.089999 restraints weight = 52364.351| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 1.59 r_work: 0.2661 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2540 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2596 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2596 r_free = 0.2596 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2596 r_free = 0.2596 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2596 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11995 Z= 0.162 Angle : 0.667 12.981 16214 Z= 0.322 Chirality : 0.041 0.210 1795 Planarity : 0.005 0.040 1925 Dihedral : 13.031 106.910 2484 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.50 % Allowed : 10.93 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.64 (0.21), residues: 1360 helix: 2.08 (0.15), residues: 1045 sheet: None (None), residues: 0 loop : 0.79 (0.31), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 98 TYR 0.011 0.002 TYR A 238 PHE 0.020 0.002 PHE D 12 TRP 0.010 0.002 TRP C 212 HIS 0.002 0.001 HIS E 20 Details of bonding type rmsd covalent geometry : bond 0.00354 (11995) covalent geometry : angle 0.66693 (16214) hydrogen bonds : bond 0.05768 ( 866) hydrogen bonds : angle 4.24270 ( 2523) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.468 Fit side-chains REVERT: A 43 THR cc_start: 0.8843 (m) cc_final: 0.8617 (t) REVERT: A 196 GLU cc_start: 0.7665 (tm-30) cc_final: 0.7404 (tm-30) REVERT: B 196 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7534 (tm-30) REVERT: B 259 ARG cc_start: 0.8513 (ttt180) cc_final: 0.8243 (ttt180) REVERT: C 43 THR cc_start: 0.8847 (m) cc_final: 0.8607 (t) REVERT: C 196 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7486 (tm-30) REVERT: C 259 ARG cc_start: 0.8499 (ttt180) cc_final: 0.8243 (ttt180) REVERT: D 259 ARG cc_start: 0.8526 (ttt90) cc_final: 0.8267 (ttt180) REVERT: E 43 THR cc_start: 0.8780 (m) cc_final: 0.8523 (t) REVERT: E 196 GLU cc_start: 0.7629 (tm-30) cc_final: 0.7337 (tm-30) REVERT: E 259 ARG cc_start: 0.8535 (ttt90) cc_final: 0.8234 (ttt180) outliers start: 16 outliers final: 10 residues processed: 149 average time/residue: 0.8928 time to fit residues: 140.9432 Evaluate side-chains 145 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 208 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 54 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.103930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.089721 restraints weight = 59742.594| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 1.74 r_work: 0.2654 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2528 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2574 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2574 r_free = 0.2574 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2574 r_free = 0.2574 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2574 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11995 Z= 0.159 Angle : 0.656 12.868 16214 Z= 0.316 Chirality : 0.041 0.206 1795 Planarity : 0.005 0.040 1925 Dihedral : 12.933 107.073 2482 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.21 % Allowed : 11.96 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.81 (0.22), residues: 1360 helix: 2.22 (0.15), residues: 1045 sheet: None (None), residues: 0 loop : 0.76 (0.31), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 98 TYR 0.011 0.002 TYR C 10 PHE 0.018 0.002 PHE D 12 TRP 0.009 0.002 TRP B 128 HIS 0.002 0.001 HIS E 20 Details of bonding type rmsd covalent geometry : bond 0.00349 (11995) covalent geometry : angle 0.65560 (16214) hydrogen bonds : bond 0.05633 ( 866) hydrogen bonds : angle 4.17548 ( 2523) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 137 time to evaluate : 0.465 Fit side-chains REVERT: A 196 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7463 (tm-30) REVERT: B 196 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7733 (tm-30) REVERT: C 43 THR cc_start: 0.8861 (m) cc_final: 0.8569 (t) REVERT: C 196 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7698 (tm-30) REVERT: D 259 ARG cc_start: 0.8499 (ttt90) cc_final: 0.8297 (ttt180) REVERT: E 43 THR cc_start: 0.8802 (m) cc_final: 0.8506 (t) REVERT: E 196 GLU cc_start: 0.7763 (tm-30) cc_final: 0.7533 (tm-30) REVERT: E 259 ARG cc_start: 0.8612 (ttt90) cc_final: 0.8397 (ttt180) outliers start: 13 outliers final: 12 residues processed: 146 average time/residue: 0.8303 time to fit residues: 129.1824 Evaluate side-chains 146 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 178 MET Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 258 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 39 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.096181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.078864 restraints weight = 56752.598| |-----------------------------------------------------------------------------| r_work (start): 0.2711 rms_B_bonded: 2.27 r_work: 0.2546 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2527 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2527 r_free = 0.2527 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2527 r_free = 0.2527 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2527 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 11995 Z= 0.235 Angle : 0.759 15.397 16214 Z= 0.363 Chirality : 0.047 0.273 1795 Planarity : 0.005 0.041 1925 Dihedral : 13.758 105.783 2482 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.50 % Allowed : 12.15 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.57 (0.21), residues: 1360 helix: 1.96 (0.15), residues: 1030 sheet: None (None), residues: 0 loop : 1.08 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 260 TYR 0.016 0.003 TYR C 10 PHE 0.020 0.003 PHE B 12 TRP 0.013 0.002 TRP E 128 HIS 0.002 0.001 HIS A 20 Details of bonding type rmsd covalent geometry : bond 0.00549 (11995) covalent geometry : angle 0.75885 (16214) hydrogen bonds : bond 0.06767 ( 866) hydrogen bonds : angle 4.36320 ( 2523) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.408 Fit side-chains REVERT: B 196 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7578 (tm-30) REVERT: D 259 ARG cc_start: 0.8405 (ttt90) cc_final: 0.8116 (ttt180) REVERT: E 196 GLU cc_start: 0.7682 (tm-30) cc_final: 0.7400 (tm-30) REVERT: E 259 ARG cc_start: 0.8521 (ttt90) cc_final: 0.8240 (ttt180) outliers start: 16 outliers final: 12 residues processed: 143 average time/residue: 0.7304 time to fit residues: 111.3214 Evaluate side-chains 143 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 178 MET Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 258 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 60 optimal weight: 0.7980 chunk 115 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 130 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.101167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.083164 restraints weight = 68514.015| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 2.58 r_work: 0.2607 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2575 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2575 r_free = 0.2575 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2575 r_free = 0.2575 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2575 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11995 Z= 0.140 Angle : 0.617 11.734 16214 Z= 0.298 Chirality : 0.040 0.181 1795 Planarity : 0.005 0.040 1925 Dihedral : 12.903 107.177 2482 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.68 % Allowed : 12.06 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.86 (0.22), residues: 1360 helix: 2.28 (0.15), residues: 1045 sheet: None (None), residues: 0 loop : 0.71 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 98 TYR 0.009 0.001 TYR B 238 PHE 0.016 0.002 PHE D 12 TRP 0.008 0.001 TRP B 167 HIS 0.002 0.002 HIS E 20 Details of bonding type rmsd covalent geometry : bond 0.00299 (11995) covalent geometry : angle 0.61666 (16214) hydrogen bonds : bond 0.05188 ( 866) hydrogen bonds : angle 4.10990 ( 2523) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 0.467 Fit side-chains REVERT: A 43 THR cc_start: 0.8772 (m) cc_final: 0.8507 (t) REVERT: A 196 GLU cc_start: 0.7233 (tm-30) cc_final: 0.7017 (tm-30) REVERT: B 196 GLU cc_start: 0.7610 (tm-30) cc_final: 0.7410 (tm-30) REVERT: C 43 THR cc_start: 0.8746 (m) cc_final: 0.8445 (t) REVERT: C 196 GLU cc_start: 0.7526 (tm-30) cc_final: 0.7245 (tm-30) REVERT: D 259 ARG cc_start: 0.8328 (ttt90) cc_final: 0.8103 (ttt180) REVERT: E 43 THR cc_start: 0.8698 (m) cc_final: 0.8394 (t) REVERT: E 196 GLU cc_start: 0.7573 (tm-30) cc_final: 0.7273 (tm-30) REVERT: E 259 ARG cc_start: 0.8482 (ttt90) cc_final: 0.8189 (ttt180) REVERT: E 264 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7868 (mt-10) outliers start: 18 outliers final: 12 residues processed: 151 average time/residue: 0.7260 time to fit residues: 116.8556 Evaluate side-chains 148 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain C residue 178 MET Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 264 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 27 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.096807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.079491 restraints weight = 57879.516| |-----------------------------------------------------------------------------| r_work (start): 0.2726 rms_B_bonded: 2.28 r_work: 0.2564 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2535 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2535 r_free = 0.2535 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2535 r_free = 0.2535 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2535 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 11995 Z= 0.215 Angle : 0.729 14.889 16214 Z= 0.348 Chirality : 0.045 0.260 1795 Planarity : 0.005 0.041 1925 Dihedral : 13.573 105.847 2482 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.87 % Allowed : 12.06 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.44 (0.21), residues: 1360 helix: 1.92 (0.15), residues: 1060 sheet: None (None), residues: 0 loop : 0.69 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 260 TYR 0.014 0.002 TYR C 10 PHE 0.019 0.003 PHE B 12 TRP 0.011 0.002 TRP E 128 HIS 0.001 0.001 HIS A 20 Details of bonding type rmsd covalent geometry : bond 0.00500 (11995) covalent geometry : angle 0.72938 (16214) hydrogen bonds : bond 0.06482 ( 866) hydrogen bonds : angle 4.30459 ( 2523) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.301 Fit side-chains REVERT: A 196 GLU cc_start: 0.7511 (tm-30) cc_final: 0.7302 (tm-30) REVERT: C 196 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7417 (tm-30) REVERT: D 259 ARG cc_start: 0.8375 (ttt90) cc_final: 0.8097 (ttt180) REVERT: E 259 ARG cc_start: 0.8509 (ttt90) cc_final: 0.8306 (ttt180) REVERT: E 264 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7872 (mt-10) outliers start: 20 outliers final: 16 residues processed: 148 average time/residue: 0.7122 time to fit residues: 112.4893 Evaluate side-chains 150 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 178 MET Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 264 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 2.9990 chunk 49 optimal weight: 0.0370 chunk 59 optimal weight: 2.9990 chunk 126 optimal weight: 0.2980 chunk 62 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.102907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.084549 restraints weight = 59204.329| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 2.68 r_work: 0.2665 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2685 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2685 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11995 Z= 0.127 Angle : 0.591 10.538 16214 Z= 0.285 Chirality : 0.038 0.155 1795 Planarity : 0.004 0.040 1925 Dihedral : 12.569 107.423 2482 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.65 % Allowed : 13.36 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.05 (0.22), residues: 1360 helix: 2.39 (0.16), residues: 1045 sheet: None (None), residues: 0 loop : 0.86 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 259 TYR 0.008 0.001 TYR B 238 PHE 0.015 0.001 PHE D 12 TRP 0.008 0.001 TRP A 13 HIS 0.002 0.002 HIS E 20 Details of bonding type rmsd covalent geometry : bond 0.00262 (11995) covalent geometry : angle 0.59124 (16214) hydrogen bonds : bond 0.04768 ( 866) hydrogen bonds : angle 4.04294 ( 2523) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 144 time to evaluate : 0.305 Fit side-chains REVERT: A 43 THR cc_start: 0.8602 (m) cc_final: 0.8338 (t) REVERT: A 196 GLU cc_start: 0.7066 (tm-30) cc_final: 0.6800 (tm-30) REVERT: B 196 GLU cc_start: 0.7358 (tm-30) cc_final: 0.7107 (tm-30) REVERT: C 43 THR cc_start: 0.8625 (m) cc_final: 0.8294 (t) REVERT: C 196 GLU cc_start: 0.7277 (tm-30) cc_final: 0.6965 (tm-30) REVERT: D 259 ARG cc_start: 0.8193 (ttt90) cc_final: 0.7962 (ttt180) REVERT: E 43 THR cc_start: 0.8545 (m) cc_final: 0.8202 (t) REVERT: E 196 GLU cc_start: 0.7220 (tm-30) cc_final: 0.6935 (tm-30) REVERT: E 259 ARG cc_start: 0.8327 (ttt90) cc_final: 0.8054 (ttt180) REVERT: E 264 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7775 (mt-10) outliers start: 7 outliers final: 5 residues processed: 146 average time/residue: 0.6904 time to fit residues: 107.4671 Evaluate side-chains 144 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 138 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain C residue 178 MET Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 264 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 23 optimal weight: 1.9990 chunk 131 optimal weight: 0.6980 chunk 120 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 128 optimal weight: 0.6980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.099431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.081682 restraints weight = 61678.904| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 2.46 r_work: 0.2597 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2625 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2625 r_free = 0.2625 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2625 r_free = 0.2625 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2625 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11995 Z= 0.167 Angle : 0.661 12.054 16214 Z= 0.317 Chirality : 0.042 0.216 1795 Planarity : 0.005 0.040 1925 Dihedral : 12.944 106.362 2472 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 0.65 % Allowed : 13.93 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.87 (0.22), residues: 1360 helix: 2.26 (0.15), residues: 1045 sheet: None (None), residues: 0 loop : 0.80 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 98 TYR 0.011 0.002 TYR C 10 PHE 0.017 0.002 PHE D 12 TRP 0.010 0.002 TRP B 167 HIS 0.001 0.001 HIS C 20 Details of bonding type rmsd covalent geometry : bond 0.00373 (11995) covalent geometry : angle 0.66140 (16214) hydrogen bonds : bond 0.05706 ( 866) hydrogen bonds : angle 4.15997 ( 2523) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 132 time to evaluate : 0.282 Fit side-chains REVERT: A 196 GLU cc_start: 0.7377 (tm-30) cc_final: 0.7166 (tm-30) REVERT: B 196 GLU cc_start: 0.7482 (tm-30) cc_final: 0.7281 (tm-30) REVERT: C 196 GLU cc_start: 0.7532 (tm-30) cc_final: 0.7295 (tm-30) REVERT: D 259 ARG cc_start: 0.8274 (ttt90) cc_final: 0.8062 (ttt180) REVERT: E 196 GLU cc_start: 0.7470 (tm-30) cc_final: 0.7224 (tm-30) REVERT: E 259 ARG cc_start: 0.8439 (ttt90) cc_final: 0.8161 (ttt180) REVERT: E 264 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7814 (mt-10) outliers start: 7 outliers final: 5 residues processed: 135 average time/residue: 0.7400 time to fit residues: 106.1703 Evaluate side-chains 138 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 132 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain C residue 178 MET Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 264 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 95 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 0.0970 chunk 22 optimal weight: 0.0570 chunk 47 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.101904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.083297 restraints weight = 58607.837| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.74 r_work: 0.2723 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2653 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2653 r_free = 0.2653 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2653 r_free = 0.2653 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2653 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11995 Z= 0.127 Angle : 0.602 10.597 16214 Z= 0.288 Chirality : 0.038 0.153 1795 Planarity : 0.004 0.040 1925 Dihedral : 12.429 107.319 2472 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.75 % Allowed : 14.11 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.20 (0.22), residues: 1360 helix: 2.51 (0.16), residues: 1045 sheet: None (None), residues: 0 loop : 0.86 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 98 TYR 0.008 0.001 TYR B 238 PHE 0.014 0.001 PHE C 12 TRP 0.008 0.001 TRP B 167 HIS 0.003 0.002 HIS E 20 Details of bonding type rmsd covalent geometry : bond 0.00261 (11995) covalent geometry : angle 0.60220 (16214) hydrogen bonds : bond 0.04800 ( 866) hydrogen bonds : angle 4.02217 ( 2523) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 139 time to evaluate : 0.295 Fit side-chains REVERT: A 196 GLU cc_start: 0.7005 (tm-30) cc_final: 0.6768 (tm-30) REVERT: B 196 GLU cc_start: 0.7118 (tm-30) cc_final: 0.6843 (tm-30) REVERT: C 196 GLU cc_start: 0.7185 (tm-30) cc_final: 0.6919 (tm-30) REVERT: D 259 ARG cc_start: 0.8130 (ttt90) cc_final: 0.7867 (ttt180) REVERT: E 196 GLU cc_start: 0.7185 (tm-30) cc_final: 0.6966 (tm-30) REVERT: E 259 ARG cc_start: 0.8296 (ttt90) cc_final: 0.8041 (ttt180) REVERT: E 264 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7665 (mt-10) outliers start: 8 outliers final: 6 residues processed: 143 average time/residue: 0.7182 time to fit residues: 109.0254 Evaluate side-chains 145 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 138 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain C residue 178 MET Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 264 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 77 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 16 optimal weight: 0.4980 chunk 1 optimal weight: 0.8980 chunk 27 optimal weight: 0.0270 chunk 109 optimal weight: 0.7980 chunk 122 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 80 optimal weight: 0.3980 chunk 76 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.103665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.085081 restraints weight = 60817.186| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 2.73 r_work: 0.2724 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2653 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2653 r_free = 0.2653 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2653 r_free = 0.2653 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2653 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11995 Z= 0.124 Angle : 0.594 10.532 16214 Z= 0.283 Chirality : 0.038 0.149 1795 Planarity : 0.004 0.039 1925 Dihedral : 11.997 107.374 2472 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 0.65 % Allowed : 14.30 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.39 (0.22), residues: 1360 helix: 2.64 (0.16), residues: 1045 sheet: None (None), residues: 0 loop : 0.96 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 98 TYR 0.008 0.001 TYR B 238 PHE 0.014 0.001 PHE B 12 TRP 0.008 0.001 TRP A 13 HIS 0.002 0.001 HIS E 20 Details of bonding type rmsd covalent geometry : bond 0.00256 (11995) covalent geometry : angle 0.59387 (16214) hydrogen bonds : bond 0.04634 ( 866) hydrogen bonds : angle 3.95767 ( 2523) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4240.88 seconds wall clock time: 73 minutes 23.70 seconds (4403.70 seconds total)