Starting phenix.real_space_refine on Thu May 9 00:23:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qr0_18610/05_2024/8qr0_18610_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qr0_18610/05_2024/8qr0_18610.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qr0_18610/05_2024/8qr0_18610.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qr0_18610/05_2024/8qr0_18610.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qr0_18610/05_2024/8qr0_18610_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qr0_18610/05_2024/8qr0_18610_updated.pdb" } resolution = 2.5 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= 0.001 sd= 0.066 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 7798 2.51 5 N 1725 2.21 5 O 2025 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 11598 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2167 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 259} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'LYR:plan-1': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2167 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 259} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'LYR:plan-1': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2167 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 259} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'LYR:plan-1': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2167 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 259} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'LYR:plan-1': 1} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2167 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 259} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'LYR:plan-1': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 123 Unusual residues: {'LFA': 7, 'LMT': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 52 Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 89 Unusual residues: {'LFA': 5, 'LMT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 46 Chain: "C" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 120 Unusual residues: {'LFA': 7, 'LMT': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 55 Chain: "D" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 152 Unusual residues: {'LFA': 9, 'LMT': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 63 Chain: "E" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 134 Unusual residues: {'LFA': 8, 'LMT': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 61 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "E" Number of atoms: 29 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" O BHOH A 428 " occ=0.50 residue: pdb=" O BHOH C 428 " occ=0.50 residue: pdb=" O BHOH C 429 " occ=0.50 residue: pdb=" O BHOH D 428 " occ=0.50 residue: pdb=" O BHOH E 428 " occ=0.50 Time building chain proxies: 6.66, per 1000 atoms: 0.57 Number of scatterers: 11598 At special positions: 0 Unit cell: (91.124, 94.468, 82.764, 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 2025 8.00 N 1725 7.00 C 7798 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.97 Conformation dependent library (CDL) restraints added in 2.0 seconds 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2540 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 5 sheets defined 79.4% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.84 Creating SS restraints... Processing helix chain 'A' and resid 4 through 7 Processing helix chain 'A' and resid 12 through 42 removed outlier: 5.631A pdb=" N ARG A 41 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N THR A 42 " --> pdb=" O MET A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 75 removed outlier: 5.502A pdb=" N LEU A 49 " --> pdb=" O ASN A 46 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN A 67 " --> pdb=" O GLU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 117 removed outlier: 3.859A pdb=" N MET A 100 " --> pdb=" O TYR A 97 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N VAL A 106 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Proline residue: A 107 - end of helix removed outlier: 3.578A pdb=" N ALA A 110 " --> pdb=" O PRO A 107 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 115 " --> pdb=" O GLN A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 152 removed outlier: 3.669A pdb=" N TYR A 147 " --> pdb=" O TYR A 143 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N PHE A 148 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLU A 149 " --> pdb=" O GLY A 145 " (cutoff:3.500A) Proline residue: A 150 - end of helix Processing helix chain 'A' and resid 161 through 186 removed outlier: 3.703A pdb=" N TRP A 165 " --> pdb=" O ALA A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 224 removed outlier: 3.735A pdb=" N ILE A 214 " --> pdb=" O ALA A 210 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N TYR A 215 " --> pdb=" O THR A 211 " (cutoff:3.500A) Proline residue: A 216 - end of helix Proline residue: A 222 - end of helix Processing helix chain 'A' and resid 228 through 263 removed outlier: 3.678A pdb=" N VAL A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N PHE A 249 " --> pdb=" O SER A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 271 Processing helix chain 'B' and resid 4 through 7 Processing helix chain 'B' and resid 12 through 42 removed outlier: 5.628A pdb=" N ARG B 41 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N THR B 42 " --> pdb=" O MET B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 75 removed outlier: 5.501A pdb=" N LEU B 49 " --> pdb=" O ASN B 46 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN B 67 " --> pdb=" O GLU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 117 removed outlier: 3.855A pdb=" N MET B 100 " --> pdb=" O TYR B 97 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N VAL B 106 " --> pdb=" O LEU B 103 " (cutoff:3.500A) Proline residue: B 107 - end of helix removed outlier: 3.579A pdb=" N ALA B 110 " --> pdb=" O PRO B 107 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL B 115 " --> pdb=" O GLN B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 152 removed outlier: 3.667A pdb=" N TYR B 147 " --> pdb=" O TYR B 143 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N PHE B 148 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLU B 149 " --> pdb=" O GLY B 145 " (cutoff:3.500A) Proline residue: B 150 - end of helix Processing helix chain 'B' and resid 161 through 186 removed outlier: 3.699A pdb=" N TRP B 165 " --> pdb=" O ALA B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 224 removed outlier: 3.736A pdb=" N ILE B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N TYR B 215 " --> pdb=" O THR B 211 " (cutoff:3.500A) Proline residue: B 216 - end of helix Proline residue: B 222 - end of helix Processing helix chain 'B' and resid 228 through 263 removed outlier: 3.680A pdb=" N VAL B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 271 Processing helix chain 'C' and resid 4 through 7 Processing helix chain 'C' and resid 12 through 42 removed outlier: 5.616A pdb=" N ARG C 41 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N THR C 42 " --> pdb=" O MET C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 75 removed outlier: 5.501A pdb=" N LEU C 49 " --> pdb=" O ASN C 46 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN C 67 " --> pdb=" O GLU C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 117 removed outlier: 3.860A pdb=" N MET C 100 " --> pdb=" O TYR C 97 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N VAL C 106 " --> pdb=" O LEU C 103 " (cutoff:3.500A) Proline residue: C 107 - end of helix removed outlier: 3.580A pdb=" N ALA C 110 " --> pdb=" O PRO C 107 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL C 115 " --> pdb=" O GLN C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 152 removed outlier: 3.668A pdb=" N TYR C 147 " --> pdb=" O TYR C 143 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N PHE C 148 " --> pdb=" O VAL C 144 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLU C 149 " --> pdb=" O GLY C 145 " (cutoff:3.500A) Proline residue: C 150 - end of helix Processing helix chain 'C' and resid 161 through 186 removed outlier: 3.703A pdb=" N TRP C 165 " --> pdb=" O ALA C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 224 removed outlier: 3.735A pdb=" N ILE C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N TYR C 215 " --> pdb=" O THR C 211 " (cutoff:3.500A) Proline residue: C 216 - end of helix Proline residue: C 222 - end of helix Processing helix chain 'C' and resid 228 through 263 removed outlier: 3.678A pdb=" N VAL C 248 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N PHE C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 271 Processing helix chain 'D' and resid 4 through 7 Processing helix chain 'D' and resid 12 through 42 removed outlier: 5.634A pdb=" N ARG D 41 " --> pdb=" O ALA D 37 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N THR D 42 " --> pdb=" O MET D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 75 removed outlier: 5.505A pdb=" N LEU D 49 " --> pdb=" O ASN D 46 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN D 67 " --> pdb=" O GLU D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 117 removed outlier: 3.859A pdb=" N MET D 100 " --> pdb=" O TYR D 97 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N VAL D 106 " --> pdb=" O LEU D 103 " (cutoff:3.500A) Proline residue: D 107 - end of helix removed outlier: 3.578A pdb=" N ALA D 110 " --> pdb=" O PRO D 107 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL D 115 " --> pdb=" O GLN D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 152 removed outlier: 3.667A pdb=" N TYR D 147 " --> pdb=" O TYR D 143 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N PHE D 148 " --> pdb=" O VAL D 144 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLU D 149 " --> pdb=" O GLY D 145 " (cutoff:3.500A) Proline residue: D 150 - end of helix Processing helix chain 'D' and resid 161 through 186 removed outlier: 3.698A pdb=" N TRP D 165 " --> pdb=" O ALA D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 224 removed outlier: 3.737A pdb=" N ILE D 214 " --> pdb=" O ALA D 210 " (cutoff:3.500A) removed outlier: 4.315A 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 228 through 263 removed outlier: 3.674A pdb=" N VAL D 248 " --> pdb=" O SER D 244 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N PHE D 249 " --> pdb=" O SER D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 271 Processing helix chain 'E' and resid 4 through 7 Processing helix chain 'E' and resid 12 through 42 removed outlier: 5.631A pdb=" N ARG E 41 " --> pdb=" O ALA E 37 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N THR E 42 " --> pdb=" O MET E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 75 removed outlier: 5.504A pdb=" N LEU E 49 " --> pdb=" O ASN E 46 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN E 67 " --> pdb=" O GLU E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 117 removed outlier: 3.859A pdb=" N MET E 100 " --> pdb=" O TYR E 97 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N VAL E 106 " --> pdb=" O LEU E 103 " (cutoff:3.500A) Proline residue: E 107 - end of helix removed outlier: 3.579A pdb=" N ALA E 110 " --> pdb=" O PRO E 107 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL E 115 " --> pdb=" O GLN E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 152 removed outlier: 3.665A pdb=" N TYR E 147 " --> pdb=" O TYR E 143 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE E 148 " --> pdb=" O VAL E 144 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLU E 149 " --> pdb=" O GLY E 145 " (cutoff:3.500A) Proline residue: E 150 - end of helix Processing helix chain 'E' and resid 161 through 186 removed outlier: 3.701A pdb=" N TRP E 165 " --> pdb=" O ALA E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 224 removed outlier: 3.734A pdb=" N ILE E 214 " --> pdb=" O ALA E 210 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N TYR E 215 " --> pdb=" O THR E 211 " (cutoff:3.500A) Proline residue: E 216 - end of helix Proline residue: E 222 - end of helix Processing helix chain 'E' and resid 228 through 263 removed outlier: 3.676A pdb=" N VAL E 248 " --> pdb=" O SER E 244 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N PHE E 249 " --> pdb=" O SER E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 271 Processing sheet with id= A, first strand: chain 'A' and resid 76 through 79 Processing sheet with id= B, first strand: chain 'B' and resid 76 through 79 Processing sheet with id= C, first strand: chain 'C' and resid 76 through 79 Processing sheet with id= D, first strand: chain 'D' and resid 76 through 79 Processing sheet with id= E, first strand: chain 'E' and resid 76 through 79 800 hydrogen bonds defined for protein. 1785 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: 3.56 Time building geometry restraints manager: 5.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2419 1.33 - 1.45: 3506 1.45 - 1.57: 5747 1.57 - 1.69: 0 1.69 - 1.82: 90 Bond restraints: 11762 Sorted by residual: bond pdb=" C6 LMT C 303 " pdb=" C7 LMT C 303 " ideal model delta sigma weight residual 1.527 1.415 0.112 2.00e-02 2.50e+03 3.14e+01 bond pdb=" C6 LYR C 246 " pdb=" C7 LYR C 246 " ideal model delta sigma weight residual 1.444 1.339 0.105 2.00e-02 2.50e+03 2.75e+01 bond pdb=" C6 LYR E 246 " pdb=" C7 LYR E 246 " ideal model delta sigma weight residual 1.444 1.339 0.105 2.00e-02 2.50e+03 2.75e+01 bond pdb=" C6 LYR D 246 " pdb=" C7 LYR D 246 " ideal model delta sigma weight residual 1.444 1.339 0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" C6 LYR A 246 " pdb=" C7 LYR A 246 " ideal model delta sigma weight residual 1.444 1.339 0.105 2.00e-02 2.50e+03 2.74e+01 ... (remaining 11757 not shown) Histogram of bond angle deviations from ideal: 95.03 - 102.91: 165 102.91 - 110.79: 3569 110.79 - 118.67: 5669 118.67 - 126.55: 6267 126.55 - 134.43: 226 Bond angle restraints: 15896 Sorted by residual: angle pdb=" N PRO B 226 " pdb=" CA PRO B 226 " pdb=" CB PRO B 226 " ideal model delta sigma weight residual 102.36 97.44 4.92 7.80e-01 1.64e+00 3.98e+01 angle pdb=" N PRO E 226 " pdb=" CA PRO E 226 " pdb=" CB PRO E 226 " ideal model delta sigma weight residual 102.36 97.47 4.89 7.80e-01 1.64e+00 3.94e+01 angle pdb=" N PRO A 226 " pdb=" CA PRO A 226 " pdb=" CB PRO A 226 " ideal model delta sigma weight residual 102.36 97.66 4.70 7.80e-01 1.64e+00 3.63e+01 angle pdb=" N PRO D 226 " pdb=" CA PRO D 226 " pdb=" CB PRO D 226 " ideal model delta sigma weight residual 102.36 97.66 4.70 7.80e-01 1.64e+00 3.62e+01 angle pdb=" N PRO C 226 " pdb=" CA PRO C 226 " pdb=" CB PRO C 226 " ideal model delta sigma weight residual 102.36 97.67 4.69 7.80e-01 1.64e+00 3.62e+01 ... (remaining 15891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.67: 6474 23.67 - 47.34: 389 47.34 - 71.00: 77 71.00 - 94.67: 15 94.67 - 118.34: 5 Dihedral angle restraints: 6960 sinusoidal: 3005 harmonic: 3955 Sorted by residual: dihedral pdb=" C GLU E 149 " pdb=" N GLU E 149 " pdb=" CA GLU E 149 " pdb=" CB GLU E 149 " ideal model delta harmonic sigma weight residual -122.60 -133.13 10.53 0 2.50e+00 1.60e-01 1.78e+01 dihedral pdb=" C GLU A 149 " pdb=" N GLU A 149 " pdb=" CA GLU A 149 " pdb=" CB GLU A 149 " ideal model delta harmonic sigma weight residual -122.60 -133.10 10.50 0 2.50e+00 1.60e-01 1.76e+01 dihedral pdb=" C GLU C 149 " pdb=" N GLU C 149 " pdb=" CA GLU C 149 " pdb=" CB GLU C 149 " ideal model delta harmonic sigma weight residual -122.60 -132.99 10.39 0 2.50e+00 1.60e-01 1.73e+01 ... (remaining 6957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1033 0.066 - 0.132: 437 0.132 - 0.198: 209 0.198 - 0.264: 41 0.264 - 0.330: 15 Chirality restraints: 1735 Sorted by residual: chirality pdb=" CA GLU A 149 " pdb=" N GLU A 149 " pdb=" C GLU A 149 " pdb=" CB GLU A 149 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.72e+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 2.18 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CA GLU D 149 " pdb=" N GLU D 149 " pdb=" C GLU D 149 " pdb=" CB GLU D 149 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.65e+00 ... (remaining 1732 not shown) Planarity restraints: 1905 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 128 " 0.055 2.00e-02 2.50e+03 3.47e-02 3.01e+01 pdb=" CG TRP C 128 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP C 128 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP C 128 " -0.037 2.00e-02 2.50e+03 pdb=" NE1 TRP C 128 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP C 128 " -0.016 2.00e-02 2.50e+03 pdb=" CE3 TRP C 128 " -0.048 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 128 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 128 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP C 128 " 0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 128 " 0.050 2.00e-02 2.50e+03 3.28e-02 2.68e+01 pdb=" CG TRP B 128 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP B 128 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP B 128 " -0.036 2.00e-02 2.50e+03 pdb=" NE1 TRP B 128 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP B 128 " -0.014 2.00e-02 2.50e+03 pdb=" CE3 TRP B 128 " -0.047 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 128 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 128 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP B 128 " 0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 72 " -0.008 2.00e-02 2.50e+03 3.09e-02 2.39e+01 pdb=" CG TRP B 72 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TRP B 72 " 0.065 2.00e-02 2.50e+03 pdb=" CD2 TRP B 72 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP B 72 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TRP B 72 " -0.021 2.00e-02 2.50e+03 pdb=" CE3 TRP B 72 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 72 " -0.041 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 72 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP B 72 " 0.047 2.00e-02 2.50e+03 ... (remaining 1902 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 4541 2.87 - 3.38: 12064 3.38 - 3.88: 21915 3.88 - 4.39: 27036 4.39 - 4.90: 42575 Nonbonded interactions: 108131 Sorted by model distance: nonbonded pdb=" ND1 HIS B 20 " pdb=" OH TYR C 143 " model vdw 2.361 2.520 nonbonded pdb=" OH TYR A 143 " pdb=" ND1 HIS E 20 " model vdw 2.363 2.520 nonbonded pdb=" ND1 HIS C 20 " pdb=" OH TYR D 143 " model vdw 2.364 2.520 nonbonded pdb=" OG SER D 194 " pdb=" OE1 GLU D 263 " model vdw 2.367 2.440 nonbonded pdb=" ND1 HIS D 20 " pdb=" OH TYR E 143 " model vdw 2.367 2.520 ... (remaining 108126 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 272 or resid 304)) selection = (chain 'B' and (resid 1 through 272 or (resid 304 and (name C10 or name C11 or n \ ame C12 or name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or nam \ e C8 or name C9 )))) selection = (chain 'C' and (resid 1 through 272 or (resid 304 and (name C10 or name C11 or n \ ame C12 or name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or nam \ e C8 or name C9 )))) selection = (chain 'D' and (resid 1 through 272 or (resid 304 and (name C10 or name C11 or n \ ame C12 or name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or nam \ e C8 or name C9 )))) selection = (chain 'E' and (resid 1 through 272 or (resid 304 and (name C10 or name C11 or n \ ame C12 or name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or nam \ e C8 or name C9 )))) } 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=1.00 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: 1.380 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: 0.020 Extract box with map and model: 7.490 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 34.240 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 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 : 0.014 0.112 11762 Z= 0.919 Angle : 1.669 9.435 15896 Z= 1.063 Chirality : 0.091 0.330 1735 Planarity : 0.018 0.190 1905 Dihedral : 16.281 118.337 4420 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 4.26 % Allowed : 6.02 % Favored : 89.72 % Cbeta Deviations : 0.79 % 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: -1.18 (0.21), residues: 1335 helix: -0.84 (0.14), residues: 1005 sheet: None (None), residues: 0 loop : 0.07 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.017 TRP C 72 HIS 0.012 0.007 HIS B 20 PHE 0.042 0.013 PHE C 203 TYR 0.037 0.015 TYR C 147 ARG 0.022 0.004 ARG D 200 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 170 time to evaluate : 1.317 Fit side-chains REVERT: A 67 GLN cc_start: 0.8742 (pt0) cc_final: 0.8186 (mt0) REVERT: A 162 GLU cc_start: 0.7722 (pm20) cc_final: 0.7510 (pm20) REVERT: A 194 SER cc_start: 0.8147 (OUTLIER) cc_final: 0.7850 (p) REVERT: A 259 ARG cc_start: 0.8658 (tpt-90) cc_final: 0.8311 (tpt-90) REVERT: B 38 MET cc_start: 0.9252 (mtp) cc_final: 0.8910 (mtp) REVERT: B 67 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8143 (mt0) REVERT: B 163 GLN cc_start: 0.8863 (mm-40) cc_final: 0.8610 (mm-40) REVERT: B 184 ASN cc_start: 0.8274 (t0) cc_final: 0.7849 (m-40) REVERT: B 226 PRO cc_start: 0.8544 (OUTLIER) cc_final: 0.8293 (Cg_endo) REVERT: B 259 ARG cc_start: 0.8664 (tpt-90) cc_final: 0.8254 (tpt-90) REVERT: C 184 ASN cc_start: 0.8105 (t0) cc_final: 0.7727 (m-40) REVERT: C 229 ASP cc_start: 0.8516 (m-30) cc_final: 0.8166 (m-30) REVERT: C 259 ARG cc_start: 0.8635 (tpt-90) cc_final: 0.8160 (tpt-90) REVERT: D 67 GLN cc_start: 0.8620 (pt0) cc_final: 0.8197 (mt0) REVERT: D 184 ASN cc_start: 0.8088 (t0) cc_final: 0.7689 (m110) REVERT: D 194 SER cc_start: 0.7969 (OUTLIER) cc_final: 0.7697 (p) REVERT: D 221 MET cc_start: 0.8577 (tpp) cc_final: 0.8309 (tpt) REVERT: D 226 PRO cc_start: 0.8723 (OUTLIER) cc_final: 0.8483 (Cg_endo) REVERT: D 259 ARG cc_start: 0.8594 (tpt-90) cc_final: 0.8183 (tpt-90) REVERT: E 38 MET cc_start: 0.9223 (mtp) cc_final: 0.8894 (mtp) REVERT: E 67 GLN cc_start: 0.8766 (pt0) cc_final: 0.8233 (mt0) REVERT: E 184 ASN cc_start: 0.8056 (t0) cc_final: 0.7698 (m-40) REVERT: E 194 SER cc_start: 0.8083 (OUTLIER) cc_final: 0.7817 (p) REVERT: E 259 ARG cc_start: 0.8619 (tpt-90) cc_final: 0.8217 (tpt-90) outliers start: 46 outliers final: 18 residues processed: 210 average time/residue: 1.5157 time to fit residues: 339.8236 Evaluate side-chains 167 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 143 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 226 PRO Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 226 PRO Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 226 PRO Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 226 PRO Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 226 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 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 163 GLN A 184 ASN B 67 GLN C 163 GLN D 163 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 11762 Z= 0.191 Angle : 0.665 10.472 15896 Z= 0.334 Chirality : 0.040 0.158 1735 Planarity : 0.006 0.025 1905 Dihedral : 13.898 104.006 2246 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Rotamer: Outliers : 1.94 % Allowed : 7.78 % Favored : 90.28 % 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: 1.69 (0.23), residues: 1335 helix: 1.32 (0.16), residues: 985 sheet: 0.33 (0.81), residues: 50 loop : 0.94 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 128 HIS 0.002 0.001 HIS B 20 PHE 0.014 0.002 PHE A 12 TYR 0.023 0.002 TYR C 97 ARG 0.003 0.000 ARG E 198 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 147 time to evaluate : 1.303 Fit side-chains REVERT: A 97 TYR cc_start: 0.8913 (OUTLIER) cc_final: 0.7147 (t80) REVERT: A 162 GLU cc_start: 0.7669 (pm20) cc_final: 0.7371 (pm20) REVERT: A 184 ASN cc_start: 0.8342 (t0) cc_final: 0.7693 (m-40) REVERT: A 259 ARG cc_start: 0.8657 (tpt-90) cc_final: 0.8313 (tpt-90) REVERT: B 149 GLU cc_start: 0.9111 (pt0) cc_final: 0.8729 (pt0) REVERT: B 184 ASN cc_start: 0.8301 (t0) cc_final: 0.7782 (m-40) REVERT: C 184 ASN cc_start: 0.8269 (t0) cc_final: 0.7784 (m-40) REVERT: C 259 ARG cc_start: 0.8628 (tpt-90) cc_final: 0.8133 (tpt-90) REVERT: D 97 TYR cc_start: 0.8855 (OUTLIER) cc_final: 0.7049 (t80) REVERT: D 149 GLU cc_start: 0.9141 (pt0) cc_final: 0.8908 (pt0) REVERT: D 259 ARG cc_start: 0.8540 (tpt-90) cc_final: 0.8121 (tpt-90) REVERT: E 97 TYR cc_start: 0.8869 (OUTLIER) cc_final: 0.7106 (t80) REVERT: E 184 ASN cc_start: 0.8310 (t0) cc_final: 0.7805 (m-40) outliers start: 21 outliers final: 13 residues processed: 166 average time/residue: 1.6231 time to fit residues: 287.1599 Evaluate side-chains 158 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 142 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 97 TYR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 97 TYR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 97 TYR Chi-restraints excluded: chain E residue 122 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 11762 Z= 0.245 Angle : 0.659 10.500 15896 Z= 0.323 Chirality : 0.041 0.158 1735 Planarity : 0.006 0.030 1905 Dihedral : 13.108 74.782 2217 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 2.13 % Allowed : 10.00 % Favored : 87.87 % 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: 1.75 (0.22), residues: 1335 helix: 1.33 (0.16), residues: 985 sheet: 0.50 (0.76), residues: 50 loop : 1.07 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 128 HIS 0.002 0.001 HIS B 20 PHE 0.014 0.002 PHE B 7 TYR 0.018 0.002 TYR C 238 ARG 0.003 0.000 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 143 time to evaluate : 1.221 Fit side-chains REVERT: A 97 TYR cc_start: 0.8834 (OUTLIER) cc_final: 0.6949 (t80) REVERT: A 184 ASN cc_start: 0.8343 (t0) cc_final: 0.7677 (m-40) REVERT: A 259 ARG cc_start: 0.8654 (tpt-90) cc_final: 0.8332 (tpt-90) REVERT: B 149 GLU cc_start: 0.9088 (pt0) cc_final: 0.8809 (pt0) REVERT: C 184 ASN cc_start: 0.8338 (t0) cc_final: 0.7789 (m-40) REVERT: C 259 ARG cc_start: 0.8613 (tpt-90) cc_final: 0.8114 (tpt-90) REVERT: D 97 TYR cc_start: 0.8830 (OUTLIER) cc_final: 0.6922 (t80) REVERT: D 149 GLU cc_start: 0.9159 (pt0) cc_final: 0.8901 (pt0) REVERT: D 162 GLU cc_start: 0.7875 (pm20) cc_final: 0.7500 (pm20) REVERT: D 259 ARG cc_start: 0.8558 (tpt-90) cc_final: 0.8152 (tpt-90) REVERT: E 97 TYR cc_start: 0.8816 (OUTLIER) cc_final: 0.6947 (t80) REVERT: E 184 ASN cc_start: 0.8293 (t0) cc_final: 0.7722 (m-40) outliers start: 23 outliers final: 14 residues processed: 164 average time/residue: 1.6451 time to fit residues: 287.4208 Evaluate side-chains 147 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 130 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 97 TYR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 97 TYR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 97 TYR Chi-restraints excluded: chain E residue 122 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 116 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 ASN ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 ASN E 112 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 11762 Z= 0.311 Angle : 0.662 11.234 15896 Z= 0.331 Chirality : 0.043 0.186 1735 Planarity : 0.006 0.033 1905 Dihedral : 12.678 78.608 2217 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 2.78 % Allowed : 10.28 % Favored : 86.94 % 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: 1.64 (0.22), residues: 1335 helix: 1.25 (0.16), residues: 985 sheet: 0.71 (0.77), residues: 50 loop : 1.00 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 128 HIS 0.002 0.001 HIS B 20 PHE 0.015 0.002 PHE B 7 TYR 0.020 0.002 TYR D 97 ARG 0.003 0.000 ARG C 98 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 133 time to evaluate : 1.402 Fit side-chains REVERT: A 97 TYR cc_start: 0.8905 (OUTLIER) cc_final: 0.7004 (t80) REVERT: A 184 ASN cc_start: 0.8345 (t0) cc_final: 0.7685 (m-40) REVERT: B 184 ASN cc_start: 0.8332 (t0) cc_final: 0.7751 (m110) REVERT: C 184 ASN cc_start: 0.8366 (t0) cc_final: 0.7855 (m-40) REVERT: C 259 ARG cc_start: 0.8576 (tpt-90) cc_final: 0.8078 (tpt-90) REVERT: D 97 TYR cc_start: 0.8885 (OUTLIER) cc_final: 0.7159 (t80) REVERT: D 184 ASN cc_start: 0.8249 (t0) cc_final: 0.7734 (m-40) REVERT: D 259 ARG cc_start: 0.8566 (tpt-90) cc_final: 0.8184 (tpt-90) REVERT: E 184 ASN cc_start: 0.8259 (t0) cc_final: 0.7685 (m-40) outliers start: 30 outliers final: 19 residues processed: 162 average time/residue: 1.5880 time to fit residues: 275.0912 Evaluate side-chains 160 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 139 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 97 TYR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 97 TYR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 97 TYR Chi-restraints excluded: chain E residue 122 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 66 optimal weight: 0.2980 chunk 117 optimal weight: 5.9990 chunk 32 optimal weight: 0.5980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 11762 Z= 0.277 Angle : 0.637 10.974 15896 Z= 0.319 Chirality : 0.042 0.171 1735 Planarity : 0.006 0.033 1905 Dihedral : 12.531 72.219 2217 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 3.06 % Allowed : 9.91 % Favored : 87.04 % 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: 1.71 (0.22), residues: 1335 helix: 1.28 (0.16), residues: 985 sheet: 0.82 (0.78), residues: 50 loop : 1.06 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 13 HIS 0.002 0.001 HIS B 20 PHE 0.015 0.002 PHE B 164 TYR 0.018 0.002 TYR E 97 ARG 0.004 0.000 ARG A 259 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 139 time to evaluate : 1.381 Fit side-chains REVERT: A 97 TYR cc_start: 0.8912 (OUTLIER) cc_final: 0.7110 (t80) REVERT: A 184 ASN cc_start: 0.8359 (t0) cc_final: 0.7693 (m-40) REVERT: A 200 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.8149 (mtt180) REVERT: B 184 ASN cc_start: 0.8337 (t0) cc_final: 0.7737 (m110) REVERT: C 149 GLU cc_start: 0.9121 (pt0) cc_final: 0.8919 (pt0) REVERT: C 184 ASN cc_start: 0.8338 (t0) cc_final: 0.7783 (m110) REVERT: C 259 ARG cc_start: 0.8584 (tpt-90) cc_final: 0.8087 (tpt-90) REVERT: D 97 TYR cc_start: 0.8862 (OUTLIER) cc_final: 0.7103 (t80) REVERT: D 149 GLU cc_start: 0.9174 (pt0) cc_final: 0.8956 (pt0) REVERT: D 184 ASN cc_start: 0.8240 (t0) cc_final: 0.7711 (m-40) REVERT: D 259 ARG cc_start: 0.8558 (tpt-90) cc_final: 0.8190 (tpt-90) REVERT: E 184 ASN cc_start: 0.8270 (t0) cc_final: 0.7682 (m-40) outliers start: 33 outliers final: 19 residues processed: 170 average time/residue: 1.3378 time to fit residues: 242.4442 Evaluate side-chains 155 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 133 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 200 ARG Chi-restraints excluded: chain B residue 97 TYR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 97 TYR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 97 TYR Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 152 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11762 Z= 0.177 Angle : 0.567 10.036 15896 Z= 0.284 Chirality : 0.038 0.147 1735 Planarity : 0.005 0.032 1905 Dihedral : 11.590 68.670 2213 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.69 % Allowed : 10.74 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.91 (0.23), residues: 1335 helix: 1.43 (0.16), residues: 985 sheet: 0.77 (0.79), residues: 50 loop : 1.17 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 13 HIS 0.001 0.001 HIS C 20 PHE 0.012 0.001 PHE C 12 TYR 0.011 0.001 TYR C 97 ARG 0.004 0.000 ARG A 259 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 140 time to evaluate : 1.321 Fit side-chains REVERT: A 97 TYR cc_start: 0.8764 (OUTLIER) cc_final: 0.7043 (t80) REVERT: A 184 ASN cc_start: 0.8314 (t0) cc_final: 0.7635 (m-40) REVERT: A 200 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.8145 (mtt180) REVERT: B 149 GLU cc_start: 0.9026 (pt0) cc_final: 0.8764 (pt0) REVERT: C 184 ASN cc_start: 0.8323 (t0) cc_final: 0.7735 (m110) REVERT: C 259 ARG cc_start: 0.8595 (tpt-90) cc_final: 0.8137 (tpt-90) REVERT: D 97 TYR cc_start: 0.8742 (OUTLIER) cc_final: 0.6980 (t80) REVERT: D 149 GLU cc_start: 0.9136 (pt0) cc_final: 0.8877 (pt0) REVERT: D 162 GLU cc_start: 0.7832 (pm20) cc_final: 0.7485 (pm20) REVERT: D 259 ARG cc_start: 0.8565 (tpt-90) cc_final: 0.8225 (tpt-90) REVERT: E 97 TYR cc_start: 0.8734 (OUTLIER) cc_final: 0.6831 (t80) REVERT: E 184 ASN cc_start: 0.8233 (t0) cc_final: 0.7602 (m110) outliers start: 29 outliers final: 17 residues processed: 162 average time/residue: 1.6382 time to fit residues: 283.2205 Evaluate side-chains 161 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 140 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 200 ARG Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain B residue 97 TYR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 97 TYR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 97 TYR Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 152 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 73 optimal weight: 0.0070 chunk 109 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 chunk 60 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 ASN ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11762 Z= 0.159 Angle : 0.551 9.548 15896 Z= 0.274 Chirality : 0.037 0.140 1735 Planarity : 0.005 0.031 1905 Dihedral : 11.022 68.100 2213 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.76 % Allowed : 12.50 % Favored : 85.74 % 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: 2.01 (0.23), residues: 1335 helix: 1.51 (0.16), residues: 985 sheet: 0.62 (0.78), residues: 50 loop : 1.17 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 13 HIS 0.001 0.001 HIS B 20 PHE 0.011 0.001 PHE B 164 TYR 0.012 0.001 TYR A 219 ARG 0.003 0.000 ARG A 259 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 142 time to evaluate : 1.492 Fit side-chains REVERT: A 97 TYR cc_start: 0.8700 (OUTLIER) cc_final: 0.6959 (t80) REVERT: A 184 ASN cc_start: 0.8324 (t0) cc_final: 0.7614 (m110) REVERT: A 200 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.8163 (mtt180) REVERT: B 149 GLU cc_start: 0.8995 (pt0) cc_final: 0.8792 (pt0) REVERT: C 184 ASN cc_start: 0.8324 (t0) cc_final: 0.7708 (m110) REVERT: C 259 ARG cc_start: 0.8590 (tpt-90) cc_final: 0.8170 (tpt-90) REVERT: D 149 GLU cc_start: 0.9122 (pt0) cc_final: 0.8862 (pt0) REVERT: D 162 GLU cc_start: 0.7756 (pm20) cc_final: 0.7420 (pm20) REVERT: D 259 ARG cc_start: 0.8584 (tpt-90) cc_final: 0.8262 (tpt-90) REVERT: E 259 ARG cc_start: 0.8556 (tpt90) cc_final: 0.8177 (tpt-90) outliers start: 19 outliers final: 11 residues processed: 156 average time/residue: 1.7292 time to fit residues: 287.5605 Evaluate side-chains 158 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 145 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 200 ARG Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain B residue 97 TYR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain E residue 152 VAL 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 77 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 118 optimal weight: 0.6980 chunk 124 optimal weight: 3.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 ASN ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 ASN E 184 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 11762 Z= 0.233 Angle : 0.599 10.300 15896 Z= 0.298 Chirality : 0.040 0.146 1735 Planarity : 0.006 0.030 1905 Dihedral : 11.339 71.473 2204 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.04 % Allowed : 11.85 % Favored : 86.11 % 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: 1.88 (0.22), residues: 1335 helix: 1.41 (0.16), residues: 985 sheet: 0.72 (0.76), residues: 50 loop : 1.15 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 13 HIS 0.002 0.001 HIS C 20 PHE 0.014 0.002 PHE B 164 TYR 0.014 0.002 TYR C 97 ARG 0.004 0.000 ARG A 259 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 137 time to evaluate : 1.346 Fit side-chains REVERT: A 97 TYR cc_start: 0.8801 (OUTLIER) cc_final: 0.6904 (t80) REVERT: A 184 ASN cc_start: 0.8353 (t0) cc_final: 0.7646 (m-40) REVERT: A 200 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.8146 (mtt180) REVERT: C 184 ASN cc_start: 0.8328 (t0) cc_final: 0.7724 (m110) REVERT: C 259 ARG cc_start: 0.8608 (tpt-90) cc_final: 0.8181 (tpt-90) REVERT: D 97 TYR cc_start: 0.8811 (OUTLIER) cc_final: 0.7030 (t80) REVERT: D 162 GLU cc_start: 0.7803 (pm20) cc_final: 0.7437 (pm20) REVERT: D 184 ASN cc_start: 0.8216 (t0) cc_final: 0.7635 (m110) REVERT: D 259 ARG cc_start: 0.8566 (tpt-90) cc_final: 0.8245 (tpt-90) REVERT: E 97 TYR cc_start: 0.8807 (OUTLIER) cc_final: 0.6833 (t80) REVERT: E 184 ASN cc_start: 0.8266 (t0) cc_final: 0.7667 (m-40) outliers start: 22 outliers final: 15 residues processed: 157 average time/residue: 1.7589 time to fit residues: 294.3448 Evaluate side-chains 165 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 146 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 200 ARG Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain B residue 97 TYR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 97 TYR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain E residue 97 TYR Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 258 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 109 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 ASN ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11762 Z= 0.166 Angle : 0.557 9.631 15896 Z= 0.278 Chirality : 0.038 0.140 1735 Planarity : 0.005 0.030 1905 Dihedral : 10.799 68.950 2202 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.76 % Allowed : 12.50 % Favored : 85.74 % 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: 1.97 (0.23), residues: 1335 helix: 1.49 (0.16), residues: 985 sheet: 0.64 (0.77), residues: 50 loop : 1.15 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 13 HIS 0.001 0.001 HIS B 20 PHE 0.012 0.001 PHE B 164 TYR 0.011 0.001 TYR A 219 ARG 0.004 0.000 ARG A 259 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 145 time to evaluate : 2.756 Fit side-chains REVERT: A 97 TYR cc_start: 0.8727 (OUTLIER) cc_final: 0.6895 (t80) REVERT: A 184 ASN cc_start: 0.8308 (t0) cc_final: 0.7607 (m110) REVERT: A 200 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8155 (mtt180) REVERT: B 149 GLU cc_start: 0.9016 (pt0) cc_final: 0.8772 (pt0) REVERT: C 184 ASN cc_start: 0.8332 (t0) cc_final: 0.7734 (m110) REVERT: C 259 ARG cc_start: 0.8594 (tpt-90) cc_final: 0.8184 (tpt-90) REVERT: D 97 TYR cc_start: 0.8741 (OUTLIER) cc_final: 0.7071 (t80) REVERT: D 149 GLU cc_start: 0.9123 (pt0) cc_final: 0.8878 (pt0) REVERT: D 162 GLU cc_start: 0.7762 (pm20) cc_final: 0.7418 (pm20) REVERT: D 184 ASN cc_start: 0.8211 (t0) cc_final: 0.7616 (m110) REVERT: D 259 ARG cc_start: 0.8571 (tpt-90) cc_final: 0.8261 (tpt-90) REVERT: E 97 TYR cc_start: 0.8744 (OUTLIER) cc_final: 0.6894 (t80) REVERT: E 184 ASN cc_start: 0.8241 (t0) cc_final: 0.7617 (m110) outliers start: 19 outliers final: 11 residues processed: 158 average time/residue: 1.7231 time to fit residues: 289.3537 Evaluate side-chains 156 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 141 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 200 ARG Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain B residue 97 TYR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 97 TYR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain E residue 97 TYR Chi-restraints excluded: chain E residue 152 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 89 optimal weight: 0.1980 chunk 134 optimal weight: 0.5980 chunk 123 optimal weight: 0.4980 chunk 107 optimal weight: 0.9980 chunk 11 optimal weight: 0.0170 chunk 82 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 85 optimal weight: 0.6980 overall best weight: 0.3818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN B 184 ASN ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 11762 Z= 0.139 Angle : 0.530 9.094 15896 Z= 0.262 Chirality : 0.036 0.135 1735 Planarity : 0.005 0.029 1905 Dihedral : 10.029 67.058 2202 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.20 % Allowed : 13.33 % Favored : 85.46 % 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: 2.10 (0.22), residues: 1335 helix: 1.58 (0.16), residues: 990 sheet: None (None), residues: 0 loop : 1.12 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 13 HIS 0.001 0.001 HIS B 20 PHE 0.011 0.001 PHE B 164 TYR 0.014 0.001 TYR C 219 ARG 0.003 0.000 ARG A 259 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 154 time to evaluate : 1.288 Fit side-chains REVERT: A 200 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.8156 (mtt180) REVERT: B 149 GLU cc_start: 0.8938 (pt0) cc_final: 0.8719 (pt0) REVERT: C 259 ARG cc_start: 0.8580 (tpt-90) cc_final: 0.8180 (tpt-90) REVERT: D 97 TYR cc_start: 0.8663 (OUTLIER) cc_final: 0.7158 (t80) REVERT: D 162 GLU cc_start: 0.7646 (pm20) cc_final: 0.7279 (pm20) REVERT: D 259 ARG cc_start: 0.8567 (tpt-90) cc_final: 0.8267 (tpt-90) REVERT: E 97 TYR cc_start: 0.8635 (OUTLIER) cc_final: 0.7013 (t80) REVERT: E 259 ARG cc_start: 0.8547 (tpt90) cc_final: 0.8120 (tpt-90) outliers start: 13 outliers final: 7 residues processed: 164 average time/residue: 1.5974 time to fit residues: 279.9557 Evaluate side-chains 160 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 150 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 200 ARG Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain D residue 97 TYR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain E residue 97 TYR Chi-restraints excluded: chain E residue 152 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 15 optimal weight: 0.0010 chunk 29 optimal weight: 4.9990 chunk 107 optimal weight: 0.4980 chunk 44 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 0.0870 chunk 94 optimal weight: 0.7980 overall best weight: 0.4564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 ASN B 184 ASN ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 ASN D 184 ASN E 184 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.101155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.089471 restraints weight = 12381.909| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 0.92 r_work: 0.2822 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2710 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2710 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 11762 Z= 0.143 Angle : 0.535 10.377 15896 Z= 0.264 Chirality : 0.037 0.148 1735 Planarity : 0.005 0.029 1905 Dihedral : 9.937 69.278 2202 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.02 % Allowed : 13.52 % Favored : 85.46 % 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: 2.11 (0.22), residues: 1335 helix: 1.58 (0.16), residues: 990 sheet: None (None), residues: 0 loop : 1.15 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 13 HIS 0.002 0.001 HIS C 20 PHE 0.011 0.001 PHE B 164 TYR 0.012 0.001 TYR A 219 ARG 0.004 0.000 ARG A 259 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4692.69 seconds wall clock time: 84 minutes 51.74 seconds (5091.74 seconds total)