Starting phenix.real_space_refine on Wed Jul 30 00:01:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qqz_18609/07_2025/8qqz_18609.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qqz_18609/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8qqz_18609/07_2025/8qqz_18609.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qqz_18609/07_2025/8qqz_18609.map" model { file = "/net/cci-nas-00/data/ceres_data/8qqz_18609/07_2025/8qqz_18609.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qqz_18609/07_2025/8qqz_18609.cif" } resolution = 2.63 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.023 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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, 'GLU:plan': 3, 'ARG: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, 'GLU:plan': 3, 'ARG: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, 'GLU:plan': 3, 'ARG: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, 'GLU:plan': 3, 'ARG: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, 'GLU:plan': 3, 'ARG: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, 'GLU:plan': 3, 'ARG: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, 'GLU:plan': 3, 'ARG: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, 'GLU:plan': 3, 'ARG: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, 'GLU:plan': 3, 'ARG: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, 'GLU:plan': 3, 'ARG: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: 16.96, per 1000 atoms: 1.43 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: 3.51 Conformation dependent library (CDL) restraints added in 3.0 seconds 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: 0.88 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: 3.43 Time building geometry restraints manager: 4.12 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: 358.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.610 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 41.240 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.060 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:13.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 414.980 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (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 TRP 0.076 0.012 TRP E 128 HIS 0.009 0.006 HIS A 20 PHE 0.060 0.011 PHE E 12 TYR 0.051 0.012 TYR D 147 ARG 0.035 0.006 ARG B 127 Details of bonding type rmsd hydrogen bonds : bond 0.20926 ( 866) hydrogen bonds : angle 7.58985 ( 2523) covalent geometry : bond 0.01282 (11995) covalent geometry : angle 1.53333 (16214) *********************** 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 : 1.478 Fit side-chains REVERT: A 196 GLU cc_start: 0.8341 (tm-30) cc_final: 0.8052 (tm-30) REVERT: A 199 SER cc_start: 0.8698 (m) cc_final: 0.8282 (p) REVERT: B 196 GLU cc_start: 0.8301 (tm-30) cc_final: 0.8075 (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: 0.8067 (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: 0.8073 (tm-30) REVERT: E 199 SER cc_start: 0.8649 (m) cc_final: 0.8253 (p) outliers start: 25 outliers final: 15 residues processed: 178 average time/residue: 1.7781 time to fit residues: 339.6899 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 : 1.348 ------------------------------------------------------------------------------- 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 113 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 54 optimal weight: 0.0980 chunk 105 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 122 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN B 73 ASN B 235 GLN C 73 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.100785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.082143 restraints weight = 56658.616| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 2.72 r_work: 0.2687 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2596 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2596 r_free = 0.2596 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2596 r_free = 0.2596 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2596 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11995 Z= 0.143 Angle : 0.660 11.945 16214 Z= 0.321 Chirality : 0.040 0.181 1795 Planarity : 0.005 0.039 1925 Dihedral : 13.195 107.009 2497 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.68 % Allowed : 7.66 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.20), residues: 1360 helix: 1.47 (0.14), residues: 1045 sheet: None (None), residues: 0 loop : 0.70 (0.30), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 212 HIS 0.003 0.002 HIS E 20 PHE 0.019 0.002 PHE B 12 TYR 0.013 0.001 TYR D 238 ARG 0.003 0.000 ARG D 200 Details of bonding type rmsd hydrogen bonds : bond 0.05643 ( 866) hydrogen bonds : angle 4.33473 ( 2523) covalent geometry : bond 0.00288 (11995) covalent geometry : angle 0.66029 (16214) *********************** 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 182 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 164 time to evaluate : 1.218 Fit side-chains REVERT: B 43 THR cc_start: 0.8780 (m) cc_final: 0.8492 (t) REVERT: B 259 ARG cc_start: 0.8390 (ttt180) cc_final: 0.8173 (ttt180) REVERT: C 43 THR cc_start: 0.8780 (m) cc_final: 0.8537 (t) REVERT: D 259 ARG cc_start: 0.8451 (ttt90) cc_final: 0.8167 (ttt180) REVERT: E 43 THR cc_start: 0.8731 (m) cc_final: 0.8449 (t) REVERT: E 259 ARG cc_start: 0.8417 (ttt90) cc_final: 0.8161 (ttt180) outliers start: 18 outliers final: 6 residues processed: 178 average time/residue: 2.1773 time to fit residues: 414.7750 Evaluate side-chains 150 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 144 time to evaluate : 1.180 ------------------------------------------------------------------------------- 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 E residue 208 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 66 optimal weight: 5.9990 chunk 54 optimal weight: 0.0030 chunk 67 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 42 optimal weight: 0.3980 chunk 64 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 123 optimal weight: 0.0970 chunk 23 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 overall best weight: 0.4588 ------------------------------------------------------------------------------- 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 = 0.3070 r_free = 0.3070 target = 0.103896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.085283 restraints weight = 60944.125| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.72 r_work: 0.2725 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2628 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2628 r_free = 0.2628 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 = 0.2629 r_free = 0.2629 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2629 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2045 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= 0.128 Angle : 0.605 10.642 16214 Z= 0.293 Chirality : 0.039 0.157 1795 Planarity : 0.004 0.039 1925 Dihedral : 12.314 107.247 2482 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 0.75 % Allowed : 11.12 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.99 (0.22), residues: 1360 helix: 2.34 (0.15), residues: 1045 sheet: None (None), residues: 0 loop : 0.88 (0.31), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 128 HIS 0.003 0.002 HIS E 20 PHE 0.017 0.002 PHE D 12 TYR 0.009 0.001 TYR A 238 ARG 0.002 0.000 ARG B 98 Details of bonding type rmsd hydrogen bonds : bond 0.04895 ( 866) hydrogen bonds : angle 4.10474 ( 2523) covalent geometry : bond 0.00260 (11995) covalent geometry : angle 0.60530 (16214) *********************** 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 165 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 157 time to evaluate : 1.106 Fit side-chains REVERT: A 196 GLU cc_start: 0.7234 (tm-30) cc_final: 0.6974 (tm-30) REVERT: A 259 ARG cc_start: 0.8427 (ttt180) cc_final: 0.8206 (ttt180) REVERT: B 196 GLU cc_start: 0.7523 (tm-30) cc_final: 0.7257 (tm-30) REVERT: B 259 ARG cc_start: 0.8346 (ttt180) cc_final: 0.8136 (ttt180) REVERT: C 43 THR cc_start: 0.8698 (m) cc_final: 0.8403 (t) REVERT: C 196 GLU cc_start: 0.7450 (tm-30) cc_final: 0.7198 (tm-30) REVERT: C 259 ARG cc_start: 0.8461 (ttt180) cc_final: 0.8236 (ttt180) REVERT: E 43 THR cc_start: 0.8630 (m) cc_final: 0.8319 (t) REVERT: E 196 GLU cc_start: 0.7338 (tm-30) cc_final: 0.7039 (tm-30) REVERT: E 259 ARG cc_start: 0.8393 (ttt90) cc_final: 0.8071 (ttt180) outliers start: 8 outliers final: 3 residues processed: 160 average time/residue: 1.7531 time to fit residues: 297.8532 Evaluate side-chains 146 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 143 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain C residue 81 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 50 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 36 optimal weight: 0.0060 chunk 118 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 111 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.7802 ------------------------------------------------------------------------------- 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 = 0.3045 r_free = 0.3045 target = 0.101862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.083612 restraints weight = 53088.909| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 2.55 r_work: 0.2649 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2609 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2609 r_free = 0.2609 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2609 r_free = 0.2609 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2609 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11995 Z= 0.141 Angle : 0.622 11.332 16214 Z= 0.301 Chirality : 0.040 0.175 1795 Planarity : 0.004 0.039 1925 Dihedral : 12.315 107.140 2472 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 0.75 % Allowed : 12.80 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.10 (0.22), residues: 1360 helix: 2.42 (0.16), residues: 1045 sheet: None (None), residues: 0 loop : 0.89 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 128 HIS 0.001 0.001 HIS E 20 PHE 0.016 0.002 PHE D 12 TYR 0.010 0.002 TYR B 238 ARG 0.002 0.000 ARG B 98 Details of bonding type rmsd hydrogen bonds : bond 0.05210 ( 866) hydrogen bonds : angle 4.08856 ( 2523) covalent geometry : bond 0.00298 (11995) covalent geometry : angle 0.62247 (16214) *********************** 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 151 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 143 time to evaluate : 1.174 Fit side-chains REVERT: A 196 GLU cc_start: 0.7433 (tm-30) cc_final: 0.7187 (tm-30) REVERT: B 196 GLU cc_start: 0.7651 (tm-30) cc_final: 0.7358 (tm-30) REVERT: B 259 ARG cc_start: 0.8393 (ttt180) cc_final: 0.8084 (ttt180) REVERT: C 43 THR cc_start: 0.8665 (m) cc_final: 0.8352 (t) REVERT: C 196 GLU cc_start: 0.7592 (tm-30) cc_final: 0.7290 (tm-30) REVERT: D 196 GLU cc_start: 0.7213 (tm-30) cc_final: 0.6978 (tm-30) REVERT: E 43 THR cc_start: 0.8595 (m) cc_final: 0.8268 (t) REVERT: E 196 GLU cc_start: 0.7475 (tm-30) cc_final: 0.7187 (tm-30) REVERT: E 259 ARG cc_start: 0.8434 (ttt90) cc_final: 0.8115 (ttt180) outliers start: 8 outliers final: 5 residues processed: 148 average time/residue: 1.7947 time to fit residues: 281.9187 Evaluate side-chains 148 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 143 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 178 MET Chi-restraints excluded: chain E residue 178 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 87 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3097 r_free = 0.3097 target = 0.104520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.090731 restraints weight = 54668.786| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 1.67 r_work: 0.2670 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2545 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2597 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2597 r_free = 0.2597 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2597 r_free = 0.2597 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2597 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11995 Z= 0.159 Angle : 0.650 11.994 16214 Z= 0.314 Chirality : 0.041 0.202 1795 Planarity : 0.005 0.040 1925 Dihedral : 12.652 106.840 2472 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.03 % Allowed : 13.27 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.94 (0.22), residues: 1360 helix: 2.32 (0.15), residues: 1045 sheet: None (None), residues: 0 loop : 0.78 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 128 HIS 0.001 0.001 HIS E 20 PHE 0.017 0.002 PHE A 12 TYR 0.012 0.002 TYR C 10 ARG 0.002 0.000 ARG C 98 Details of bonding type rmsd hydrogen bonds : bond 0.05631 ( 866) hydrogen bonds : angle 4.14958 ( 2523) covalent geometry : bond 0.00352 (11995) covalent geometry : angle 0.64974 (16214) *********************** 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 144 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 1.104 Fit side-chains REVERT: A 196 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7537 (tm-30) REVERT: B 196 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7695 (tm-30) REVERT: B 259 ARG cc_start: 0.8578 (ttt180) cc_final: 0.8371 (ttt180) REVERT: C 43 THR cc_start: 0.8829 (m) cc_final: 0.8547 (t) REVERT: E 196 GLU cc_start: 0.7755 (tm-30) cc_final: 0.7471 (tm-30) REVERT: E 259 ARG cc_start: 0.8602 (ttt90) cc_final: 0.8303 (ttt180) outliers start: 11 outliers final: 5 residues processed: 140 average time/residue: 1.7262 time to fit residues: 256.6218 Evaluate side-chains 137 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 132 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 178 MET Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 247 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 24 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 129 optimal weight: 0.6980 chunk 107 optimal weight: 0.0170 chunk 48 optimal weight: 1.9990 overall best weight: 0.9420 ------------------------------------------------------------------------------- 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 = 0.3022 r_free = 0.3022 target = 0.100702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.082422 restraints weight = 57168.775| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 2.50 r_work: 0.2699 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2655 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2655 r_free = 0.2655 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 = 0.2655 r_free = 0.2655 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2655 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.1994 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= 0.147 Angle : 0.626 11.636 16214 Z= 0.302 Chirality : 0.040 0.185 1795 Planarity : 0.004 0.040 1925 Dihedral : 12.535 107.135 2472 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.12 % Allowed : 13.36 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.00 (0.22), residues: 1360 helix: 2.36 (0.15), residues: 1045 sheet: None (None), residues: 0 loop : 0.78 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 128 HIS 0.002 0.001 HIS E 20 PHE 0.016 0.002 PHE B 12 TYR 0.010 0.002 TYR C 10 ARG 0.002 0.000 ARG C 98 Details of bonding type rmsd hydrogen bonds : bond 0.05353 ( 866) hydrogen bonds : angle 4.10370 ( 2523) covalent geometry : bond 0.00319 (11995) covalent geometry : angle 0.62598 (16214) *********************** 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 151 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 139 time to evaluate : 1.104 Fit side-chains REVERT: B 196 GLU cc_start: 0.7767 (tm-30) cc_final: 0.7551 (tm-30) REVERT: B 259 ARG cc_start: 0.8428 (ttt180) cc_final: 0.8150 (ttt180) REVERT: C 43 THR cc_start: 0.8711 (m) cc_final: 0.8423 (t) REVERT: C 196 GLU cc_start: 0.7563 (tm-30) cc_final: 0.7316 (tm-30) REVERT: E 196 GLU cc_start: 0.7589 (tm-30) cc_final: 0.7283 (tm-30) REVERT: E 259 ARG cc_start: 0.8461 (ttt90) cc_final: 0.8205 (ttt180) outliers start: 12 outliers final: 7 residues processed: 148 average time/residue: 1.7351 time to fit residues: 272.8749 Evaluate side-chains 141 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 134 time to evaluate : 1.096 ------------------------------------------------------------------------------- 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 C residue 81 LEU Chi-restraints excluded: chain C residue 178 MET Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 247 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 82 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 69 optimal weight: 0.3980 chunk 41 optimal weight: 0.6980 chunk 26 optimal weight: 0.0070 chunk 71 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 overall best weight: 0.8202 ------------------------------------------------------------------------------- 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 = 0.3035 r_free = 0.3035 target = 0.101209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.082921 restraints weight = 57941.075| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 2.61 r_work: 0.2644 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2615 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2615 r_free = 0.2615 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2615 r_free = 0.2615 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2615 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11995 Z= 0.140 Angle : 0.614 11.465 16214 Z= 0.296 Chirality : 0.039 0.174 1795 Planarity : 0.004 0.039 1925 Dihedral : 12.400 107.192 2472 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.12 % Allowed : 13.36 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.06 (0.22), residues: 1360 helix: 2.41 (0.15), residues: 1045 sheet: None (None), residues: 0 loop : 0.80 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 167 HIS 0.002 0.001 HIS E 20 PHE 0.015 0.002 PHE E 12 TYR 0.009 0.001 TYR E 219 ARG 0.001 0.000 ARG C 98 Details of bonding type rmsd hydrogen bonds : bond 0.05173 ( 866) hydrogen bonds : angle 4.07071 ( 2523) covalent geometry : bond 0.00300 (11995) covalent geometry : angle 0.61410 (16214) *********************** 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 150 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 1.154 Fit side-chains REVERT: A 196 GLU cc_start: 0.7290 (tm-30) cc_final: 0.6981 (tm-30) REVERT: B 196 GLU cc_start: 0.7691 (tm-30) cc_final: 0.7447 (tm-30) REVERT: B 259 ARG cc_start: 0.8421 (ttt180) cc_final: 0.8133 (ttt180) REVERT: C 43 THR cc_start: 0.8691 (m) cc_final: 0.8357 (t) REVERT: C 196 GLU cc_start: 0.7333 (tm-30) cc_final: 0.7064 (tm-30) REVERT: E 196 GLU cc_start: 0.7491 (tm-30) cc_final: 0.7226 (tm-30) REVERT: E 259 ARG cc_start: 0.8467 (ttt90) cc_final: 0.8225 (ttt180) REVERT: E 264 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7815 (mt-10) outliers start: 12 outliers final: 8 residues processed: 146 average time/residue: 1.7064 time to fit residues: 265.0200 Evaluate side-chains 148 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 139 time to evaluate : 1.105 ------------------------------------------------------------------------------- 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 81 LEU Chi-restraints excluded: chain C residue 178 MET Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 247 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 14 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 123 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3093 r_free = 0.3093 target = 0.104407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.090678 restraints weight = 51340.699| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 1.60 r_work: 0.2686 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2566 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2605 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2605 r_free = 0.2605 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2606 r_free = 0.2606 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2606 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11995 Z= 0.155 Angle : 0.637 11.935 16214 Z= 0.307 Chirality : 0.041 0.195 1795 Planarity : 0.005 0.039 1925 Dihedral : 12.625 106.997 2472 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 0.93 % Allowed : 13.36 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.95 (0.22), residues: 1360 helix: 2.33 (0.15), residues: 1045 sheet: None (None), residues: 0 loop : 0.78 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 128 HIS 0.001 0.001 HIS E 20 PHE 0.015 0.002 PHE A 12 TYR 0.011 0.002 TYR C 10 ARG 0.002 0.000 ARG C 98 Details of bonding type rmsd hydrogen bonds : bond 0.05493 ( 866) hydrogen bonds : angle 4.11936 ( 2523) covalent geometry : bond 0.00339 (11995) covalent geometry : angle 0.63720 (16214) *********************** 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 145 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 0.993 Fit side-chains REVERT: A 196 GLU cc_start: 0.7534 (tm-30) cc_final: 0.7294 (tm-30) REVERT: E 196 GLU cc_start: 0.7755 (tm-30) cc_final: 0.7498 (tm-30) REVERT: E 259 ARG cc_start: 0.8592 (ttt90) cc_final: 0.8338 (ttt180) REVERT: E 264 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7968 (mt-10) outliers start: 10 outliers final: 7 residues processed: 141 average time/residue: 2.3748 time to fit residues: 356.4606 Evaluate side-chains 141 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 133 time to evaluate : 1.401 ------------------------------------------------------------------------------- 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 C residue 81 LEU Chi-restraints excluded: chain C residue 178 MET Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 247 LEU 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 112 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 126 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.3095 r_free = 0.3095 target = 0.104578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.090225 restraints weight = 63888.095| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 1.88 r_work: 0.2653 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2617 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2617 r_free = 0.2617 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 = 0.2617 r_free = 0.2617 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2617 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.1997 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 : 0.634 11.857 16214 Z= 0.305 Chirality : 0.040 0.191 1795 Planarity : 0.005 0.039 1925 Dihedral : 12.666 107.047 2472 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.03 % Allowed : 13.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.96 (0.22), residues: 1360 helix: 2.34 (0.15), residues: 1045 sheet: None (None), residues: 0 loop : 0.76 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 128 HIS 0.002 0.001 HIS D 20 PHE 0.015 0.002 PHE B 12 TYR 0.010 0.002 TYR C 10 ARG 0.001 0.000 ARG C 98 Details of bonding type rmsd hydrogen bonds : bond 0.05433 ( 866) hydrogen bonds : angle 4.11479 ( 2523) covalent geometry : bond 0.00333 (11995) covalent geometry : angle 0.63432 (16214) *********************** 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 147 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 1.091 Fit side-chains REVERT: E 196 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7522 (tm-30) REVERT: E 259 ARG cc_start: 0.8617 (ttt90) cc_final: 0.8369 (ttt180) REVERT: E 264 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8014 (mt-10) outliers start: 11 outliers final: 7 residues processed: 143 average time/residue: 1.7767 time to fit residues: 269.7527 Evaluate side-chains 139 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 131 time to evaluate : 1.062 ------------------------------------------------------------------------------- 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 C residue 81 LEU Chi-restraints excluded: chain C residue 178 MET Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 247 LEU 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 115 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 41 optimal weight: 0.0770 chunk 27 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 64 optimal weight: 8.9990 chunk 52 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 overall best weight: 0.7342 ------------------------------------------------------------------------------- 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 = 0.3034 r_free = 0.3034 target = 0.101406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.083111 restraints weight = 57057.520| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 2.59 r_work: 0.2709 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2602 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2602 r_free = 0.2602 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2602 r_free = 0.2602 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2602 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11995 Z= 0.137 Angle : 0.610 11.331 16214 Z= 0.293 Chirality : 0.039 0.168 1795 Planarity : 0.004 0.039 1925 Dihedral : 12.454 107.199 2472 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 0.84 % Allowed : 13.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.08 (0.22), residues: 1360 helix: 2.43 (0.15), residues: 1045 sheet: None (None), residues: 0 loop : 0.79 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 167 HIS 0.002 0.001 HIS A 20 PHE 0.015 0.002 PHE C 12 TYR 0.008 0.001 TYR E 219 ARG 0.001 0.000 ARG C 98 Details of bonding type rmsd hydrogen bonds : bond 0.05076 ( 866) hydrogen bonds : angle 4.06548 ( 2523) covalent geometry : bond 0.00289 (11995) covalent geometry : angle 0.61014 (16214) ********************** 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: 9 poor density : 138 time to evaluate : 1.130 Fit side-chains REVERT: B 196 GLU cc_start: 0.7390 (tm-30) cc_final: 0.7104 (tm-30) REVERT: B 259 ARG cc_start: 0.8326 (ttt180) cc_final: 0.8123 (ttt180) REVERT: C 43 THR cc_start: 0.8711 (m) cc_final: 0.8370 (t) REVERT: E 196 GLU cc_start: 0.7528 (tm-30) cc_final: 0.7260 (tm-30) REVERT: E 259 ARG cc_start: 0.8462 (ttt90) cc_final: 0.8171 (ttt180) REVERT: E 264 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7844 (mt-10) outliers start: 9 outliers final: 7 residues processed: 143 average time/residue: 1.7416 time to fit residues: 264.4406 Evaluate side-chains 143 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 135 time to evaluate : 0.960 ------------------------------------------------------------------------------- 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 C residue 81 LEU Chi-restraints excluded: chain C residue 178 MET Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 247 LEU 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 112 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- 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 = 0.2960 r_free = 0.2960 target = 0.095829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.078092 restraints weight = 53303.747| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 2.45 r_work: 0.2625 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2602 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2602 r_free = 0.2602 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2602 r_free = 0.2602 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2602 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 11995 Z= 0.249 Angle : 0.765 13.937 16214 Z= 0.368 Chirality : 0.048 0.289 1795 Planarity : 0.005 0.040 1925 Dihedral : 13.596 104.734 2472 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.93 % Allowed : 13.74 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.22), residues: 1360 helix: 1.87 (0.15), residues: 1060 sheet: None (None), residues: 0 loop : 0.62 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 128 HIS 0.001 0.001 HIS A 20 PHE 0.018 0.003 PHE B 12 TYR 0.018 0.003 TYR C 10 ARG 0.003 0.001 ARG C 259 Details of bonding type rmsd hydrogen bonds : bond 0.06866 ( 866) hydrogen bonds : angle 4.36616 ( 2523) covalent geometry : bond 0.00585 (11995) covalent geometry : angle 0.76541 (16214) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10423.61 seconds wall clock time: 186 minutes 44.95 seconds (11204.95 seconds total)