Starting phenix.real_space_refine on Wed Feb 4 18:40:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9tbd_55765/02_2026/9tbd_55765.cif Found real_map, /net/cci-nas-00/data/ceres_data/9tbd_55765/02_2026/9tbd_55765.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9tbd_55765/02_2026/9tbd_55765.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9tbd_55765/02_2026/9tbd_55765.map" model { file = "/net/cci-nas-00/data/ceres_data/9tbd_55765/02_2026/9tbd_55765.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9tbd_55765/02_2026/9tbd_55765.cif" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 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 7965 2.51 5 N 1755 2.21 5 O 2398 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12168 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2173 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 272, 2164 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 12, 'TRANS': 259} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 272, 2164 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 12, 'TRANS': 259} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 2221 Chain: "B" Number of atoms: 2173 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 272, 2164 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 12, 'TRANS': 259} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 272, 2164 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 12, 'TRANS': 259} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 2221 Chain: "C" Number of atoms: 2173 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 272, 2164 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 12, 'TRANS': 259} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 272, 2164 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 12, 'TRANS': 259} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 2221 Chain: "D" Number of atoms: 2173 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 272, 2164 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 12, 'TRANS': 259} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 272, 2164 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 12, 'TRANS': 259} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 2221 Chain: "E" Number of atoms: 2173 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 272, 2164 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 12, 'TRANS': 259} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 272, 2164 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 12, 'TRANS': 259} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 2221 Chain: "A" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 157 Unusual residues: {'LFA': 8, 'LMT': 2, 'RET': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 94 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 201 Unusual residues: {'LFA': 11, 'LMT': 2, 'RET': 1} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 110 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'LFA': 10, 'LMT': 2, 'RET': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 109 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 163 Unusual residues: {'LFA': 8, 'LMT': 2, 'RET': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 88 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 172 Unusual residues: {'LFA': 9, 'LMT': 2, 'RET': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 99 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 85 Classifications: {'water': 85} Link IDs: {None: 84} Chain: "B" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 90 Classifications: {'water': 90} Link IDs: {None: 89} Chain: "C" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Chain: "D" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 86 Classifications: {'water': 86} Link IDs: {None: 85} Chain: "E" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 85 Classifications: {'water': 85} Link IDs: {None: 84} Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N AGLN A 67 " occ=0.46 ... (16 atoms not shown) pdb=" NE2BGLN A 67 " occ=0.54 residue: pdb=" N AGLN B 67 " occ=0.46 ... (16 atoms not shown) pdb=" NE2BGLN B 67 " occ=0.54 residue: pdb=" N AGLN C 67 " occ=0.48 ... (16 atoms not shown) pdb=" NE2BGLN C 67 " occ=0.52 residue: pdb=" N AGLN D 67 " occ=0.45 ... (16 atoms not shown) pdb=" NE2BGLN D 67 " occ=0.55 residue: pdb=" N AGLN E 67 " occ=0.47 ... (16 atoms not shown) pdb=" NE2BGLN E 67 " occ=0.53 Time building chain proxies: 3.99, per 1000 atoms: 0.33 Number of scatterers: 12168 At special positions: 0 Unit cell: (90.75, 92.202, 83.49, 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 2398 8.00 N 1755 7.00 C 7965 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 804.6 milliseconds 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: 2550 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 5 sheets defined 84.6% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 3 through 8 removed outlier: 3.899A pdb=" N LEU A 8 " --> pdb=" O GLU A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 40 Processing helix chain 'A' and resid 41 through 43 No H-bonds generated for 'chain 'A' and resid 41 through 43' Processing helix chain 'A' and resid 47 through 75 removed outlier: 3.946A pdb=" N ALA A 51 " --> pdb=" O TYR A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 117 removed outlier: 3.765A pdb=" N MET A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASN A 101 " --> pdb=" O TYR A 97 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A 103 " --> pdb=" O TYR A 99 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ILE A 104 " --> pdb=" O MET A 100 " (cutoff:3.500A) Proline residue: A 107 - end of helix 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: 3.867A pdb=" N PHE A 164 " --> pdb=" O GLY A 160 " (cutoff:3.500A) removed outlier: 3.679A 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: 3.891A pdb=" N PHE 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: 3.680A pdb=" N VAL A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N PHE A 249 " --> pdb=" O SER A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 272 Processing helix chain 'B' and resid 3 through 8 removed outlier: 3.887A pdb=" N LEU B 8 " --> pdb=" O GLU B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 40 Processing helix chain 'B' and resid 41 through 43 No H-bonds generated for 'chain 'B' and resid 41 through 43' Processing helix chain 'B' and resid 47 through 75 removed outlier: 3.919A pdb=" N ALA B 51 " --> pdb=" O TYR B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 117 removed outlier: 3.753A pdb=" N MET B 100 " --> pdb=" O GLY B 96 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASN B 101 " --> pdb=" O TYR B 97 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 103 " --> pdb=" O TYR B 99 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ILE B 104 " --> pdb=" O MET B 100 " (cutoff:3.500A) Proline residue: B 107 - end of helix 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: 3.909A pdb=" N PHE B 164 " --> pdb=" O GLY B 160 " (cutoff:3.500A) removed outlier: 3.684A 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: 3.922A pdb=" N PHE 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: 4.603A pdb=" N PHE B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 272 Processing helix chain 'C' and resid 3 through 8 removed outlier: 3.875A pdb=" N LEU C 8 " --> pdb=" O GLU C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 40 Processing helix chain 'C' and resid 41 through 43 No H-bonds generated for 'chain 'C' and resid 41 through 43' Processing helix chain 'C' and resid 47 through 75 removed outlier: 3.921A pdb=" N ALA C 51 " --> pdb=" O TYR C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 117 removed outlier: 3.617A pdb=" N MET C 100 " --> pdb=" O GLY C 96 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASN C 101 " --> pdb=" O TYR C 97 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C 103 " --> pdb=" O TYR C 99 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ILE C 104 " --> pdb=" O MET C 100 " (cutoff:3.500A) Proline residue: C 107 - end of helix 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: 3.910A pdb=" N PHE C 164 " --> pdb=" O GLY C 160 " (cutoff:3.500A) removed outlier: 3.674A 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: 3.880A pdb=" N PHE 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: 4.638A pdb=" N PHE C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 272 Processing helix chain 'D' and resid 3 through 8 removed outlier: 3.894A pdb=" N LEU D 8 " --> pdb=" O GLU D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 40 Processing helix chain 'D' and resid 41 through 43 No H-bonds generated for 'chain 'D' and resid 41 through 43' Processing helix chain 'D' and resid 47 through 75 removed outlier: 3.941A pdb=" N ALA D 51 " --> pdb=" O TYR D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 117 removed outlier: 3.793A pdb=" N MET D 100 " --> pdb=" O GLY D 96 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ASN D 101 " --> pdb=" O TYR D 97 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU D 103 " --> pdb=" O TYR D 99 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE D 104 " --> pdb=" O MET D 100 " (cutoff:3.500A) Proline residue: D 107 - end of helix 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: 3.901A pdb=" N PHE D 164 " --> pdb=" O GLY D 160 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TRP D 165 " --> pdb=" O ALA D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 213 Processing helix chain 'D' and resid 213 through 225 removed outlier: 3.953A pdb=" N PHE D 217 " --> pdb=" O SER D 213 " (cutoff:3.500A) Proline residue: D 222 - end of helix Processing helix chain 'D' and resid 227 through 264 removed outlier: 4.461A pdb=" N PHE D 249 " --> pdb=" O SER D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 272 Processing helix chain 'E' and resid 3 through 8 removed outlier: 3.871A pdb=" N LEU E 8 " --> pdb=" O GLU E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 40 Processing helix chain 'E' and resid 41 through 43 No H-bonds generated for 'chain 'E' and resid 41 through 43' Processing helix chain 'E' and resid 47 through 75 removed outlier: 3.977A pdb=" N ALA E 51 " --> pdb=" O TYR E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 117 removed outlier: 3.659A pdb=" N MET E 100 " --> pdb=" O GLY E 96 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASN E 101 " --> pdb=" O TYR E 97 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU E 103 " --> pdb=" O TYR E 99 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE E 104 " --> pdb=" O MET E 100 " (cutoff:3.500A) Proline residue: E 107 - end of helix 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: 3.904A pdb=" N PHE E 164 " --> pdb=" O GLY E 160 " (cutoff:3.500A) removed outlier: 3.658A 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: 3.914A pdb=" N PHE 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: 4.628A pdb=" N PHE E 249 " --> pdb=" O SER E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 272 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 79 869 hydrogen bonds defined for protein. 2567 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.34 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3262 1.34 - 1.46: 2680 1.46 - 1.58: 6012 1.58 - 1.70: 0 1.70 - 1.82: 90 Bond restraints: 12044 Sorted by residual: bond pdb=" C14 RET A 311 " pdb=" C15 RET A 311 " ideal model delta sigma weight residual 1.448 1.492 -0.044 2.00e-02 2.50e+03 4.76e+00 bond pdb=" C14 RET E 312 " pdb=" C15 RET E 312 " ideal model delta sigma weight residual 1.448 1.491 -0.043 2.00e-02 2.50e+03 4.52e+00 bond pdb=" C14 RET D 311 " pdb=" C15 RET D 311 " ideal model delta sigma weight residual 1.448 1.489 -0.041 2.00e-02 2.50e+03 4.21e+00 bond pdb=" C14 RET C 311 " pdb=" C15 RET C 311 " ideal model delta sigma weight residual 1.448 1.487 -0.039 2.00e-02 2.50e+03 3.82e+00 bond pdb=" C14 RET B 313 " pdb=" C15 RET B 313 " ideal model delta sigma weight residual 1.448 1.487 -0.039 2.00e-02 2.50e+03 3.80e+00 ... (remaining 12039 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 15457 1.55 - 3.10: 622 3.10 - 4.65: 143 4.65 - 6.20: 30 6.20 - 7.75: 6 Bond angle restraints: 16258 Sorted by residual: angle pdb=" C ASN D 95 " pdb=" N GLY D 96 " pdb=" CA GLY D 96 " ideal model delta sigma weight residual 121.34 127.44 -6.10 2.32e+00 1.86e-01 6.91e+00 angle pdb=" CA ARG C 127 " pdb=" CB ARG C 127 " pdb=" CG ARG C 127 " ideal model delta sigma weight residual 114.10 108.86 5.24 2.00e+00 2.50e-01 6.87e+00 angle pdb=" CB MET A 108 " pdb=" CG MET A 108 " pdb=" SD MET A 108 " ideal model delta sigma weight residual 112.70 120.45 -7.75 3.00e+00 1.11e-01 6.67e+00 angle pdb=" CA GLU C 149 " pdb=" CB GLU C 149 " pdb=" CG GLU C 149 " ideal model delta sigma weight residual 114.10 119.24 -5.14 2.00e+00 2.50e-01 6.60e+00 angle pdb=" N TYR E 97 " pdb=" CA TYR E 97 " pdb=" CB TYR E 97 " ideal model delta sigma weight residual 110.14 106.09 4.05 1.58e+00 4.01e-01 6.59e+00 ... (remaining 16253 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 6449 17.88 - 35.77: 642 35.77 - 53.65: 145 53.65 - 71.53: 37 71.53 - 89.42: 19 Dihedral angle restraints: 7292 sinusoidal: 3317 harmonic: 3975 Sorted by residual: dihedral pdb=" CD ARG C 41 " pdb=" NE ARG C 41 " pdb=" CZ ARG C 41 " pdb=" NH1 ARG C 41 " ideal model delta sinusoidal sigma weight residual 0.00 78.63 -78.63 1 1.00e+01 1.00e-02 7.71e+01 dihedral pdb=" CD ARG B 41 " pdb=" NE ARG B 41 " pdb=" CZ ARG B 41 " pdb=" NH1 ARG B 41 " ideal model delta sinusoidal sigma weight residual 0.00 -73.29 73.29 1 1.00e+01 1.00e-02 6.84e+01 dihedral pdb=" CD ARG A 41 " pdb=" NE ARG A 41 " pdb=" CZ ARG A 41 " pdb=" NH1 ARG A 41 " ideal model delta sinusoidal sigma weight residual 0.00 71.34 -71.34 1 1.00e+01 1.00e-02 6.53e+01 ... (remaining 7289 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1115 0.035 - 0.070: 413 0.070 - 0.106: 203 0.106 - 0.141: 54 0.141 - 0.176: 5 Chirality restraints: 1790 Sorted by residual: 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 2.33 0.18 2.00e-01 2.50e+01 7.73e-01 chirality pdb=" CG LEU E 65 " pdb=" CB LEU E 65 " pdb=" CD1 LEU E 65 " pdb=" CD2 LEU E 65 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.80e-01 chirality pdb=" CA PRO D 45 " pdb=" N PRO D 45 " pdb=" C PRO D 45 " pdb=" CB PRO D 45 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.40e-01 ... (remaining 1787 not shown) Planarity restraints: 1940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 41 " 0.938 9.50e-02 1.11e+02 4.21e-01 1.17e+02 pdb=" NE ARG C 41 " -0.076 2.00e-02 2.50e+03 pdb=" CZ ARG C 41 " 0.043 2.00e-02 2.50e+03 pdb=" NH1 ARG C 41 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG C 41 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 41 " 0.888 9.50e-02 1.11e+02 3.99e-01 1.09e+02 pdb=" NE ARG B 41 " -0.076 2.00e-02 2.50e+03 pdb=" CZ ARG B 41 " 0.051 2.00e-02 2.50e+03 pdb=" NH1 ARG B 41 " -0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG B 41 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 41 " -0.873 9.50e-02 1.11e+02 3.93e-01 1.05e+02 pdb=" NE ARG A 41 " 0.074 2.00e-02 2.50e+03 pdb=" CZ ARG A 41 " -0.048 2.00e-02 2.50e+03 pdb=" NH1 ARG A 41 " 0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG A 41 " -0.002 2.00e-02 2.50e+03 ... (remaining 1937 not shown) Histogram of nonbonded interaction distances: 2.56 - 3.03: 8020 3.03 - 3.50: 14084 3.50 - 3.97: 24209 3.97 - 4.43: 28551 4.43 - 4.90: 41651 Nonbonded interactions: 116515 Sorted by model distance: nonbonded pdb=" O LEU D 70 " pdb=" OE1 GLU D 74 " model vdw 2.563 3.040 nonbonded pdb=" OH TYR C 47 " pdb=" OE2 GLU C 264 " model vdw 2.597 3.040 nonbonded pdb=" N ILE C 4 " pdb=" OE2 GLU C 149 " model vdw 2.604 3.120 nonbonded pdb=" OE1 GLN E 255 " pdb=" O2' LMT E 311 " model vdw 2.610 3.040 nonbonded pdb=" OE1 GLN C 255 " pdb=" O2' LMT C 310 " model vdw 2.610 3.040 ... (remaining 116510 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 272 or (resid 301 and (na \ me C8 or name C9 )) or resid 306)) selection = (chain 'B' and (resid 1 through 66 or resid 68 through 272 or (resid 301 and (na \ me C8 or name C9 )) or (resid 306 and (name C1 or name C2 or name C3 or name C4 \ or name C5 )))) selection = (chain 'C' and (resid 1 through 66 or resid 68 through 272 or (resid 301 and (na \ me C8 or name C9 )) or (resid 306 and (name C1 or name C2 or name C3 or name C4 \ or name C5 )))) selection = (chain 'D' and (resid 1 through 66 or resid 68 through 272 or (resid 301 and (na \ me C8 or name C9 )) or (resid 306 and (name C1 or name C2 or name C3 or name C4 \ or name C5 )))) selection = (chain 'E' and (resid 1 through 66 or resid 68 through 272 or (resid 301 and (na \ me C8 or name C9 )) or (resid 306 and (name C1 or name C2 or name C3 or name C4 \ or name C5 )))) } 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=0.45 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: 17.820 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 14.390 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 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:10.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 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 : 0.004 0.044 12049 Z= 0.205 Angle : 0.764 7.749 16258 Z= 0.421 Chirality : 0.046 0.176 1790 Planarity : 0.024 0.421 1940 Dihedral : 15.357 89.416 4742 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.08 % Allowed : 9.95 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.21), residues: 1360 helix: 1.10 (0.14), residues: 1050 sheet: None (None), residues: 0 loop : 0.41 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.061 0.008 ARG B 41 TYR 0.024 0.002 TYR D 238 PHE 0.024 0.002 PHE B 22 TRP 0.016 0.002 TRP D 72 HIS 0.003 0.001 HIS E 20 Details of bonding type rmsd covalent geometry : bond 0.00377 (12044) covalent geometry : angle 0.76364 (16258) hydrogen bonds : bond 0.08114 ( 869) hydrogen bonds : angle 4.82502 ( 2567) Misc. bond : bond 0.03042 ( 5) *********************** 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 151 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.468 Fit side-chains REVERT: A 41 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7955 (mmt-90) REVERT: A 159 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7766 (mm-30) REVERT: A 267 GLU cc_start: 0.7942 (tp30) cc_final: 0.7666 (tp30) REVERT: B 70 LEU cc_start: 0.9150 (mt) cc_final: 0.8932 (tp) REVERT: B 196 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7757 (tp30) REVERT: C 41 ARG cc_start: 0.8472 (mmm160) cc_final: 0.8253 (mmt-90) REVERT: D 41 ARG cc_start: 0.8567 (mmt180) cc_final: 0.8044 (mmt-90) REVERT: D 70 LEU cc_start: 0.9093 (mt) cc_final: 0.8888 (tp) REVERT: D 159 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7103 (mp0) REVERT: D 267 GLU cc_start: 0.7936 (tp30) cc_final: 0.7693 (tp30) REVERT: E 267 GLU cc_start: 0.7898 (tp30) cc_final: 0.7528 (tp30) outliers start: 20 outliers final: 14 residues processed: 148 average time/residue: 0.8664 time to fit residues: 136.2714 Evaluate side-chains 146 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 122 THR 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 196 GLU Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 152 VAL 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 159 GLU 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=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.0670 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 GLN B C 184 ASN ** D 67 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.124146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.101995 restraints weight = 26375.600| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 1.15 r_work: 0.2829 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2697 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2697 r_free = 0.2697 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2697 r_free = 0.2697 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2697 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.0545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12049 Z= 0.165 Angle : 0.642 7.286 16258 Z= 0.336 Chirality : 0.041 0.153 1790 Planarity : 0.006 0.062 1940 Dihedral : 10.155 59.775 2476 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.08 % Allowed : 10.23 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.30 (0.21), residues: 1360 helix: 2.54 (0.15), residues: 1015 sheet: None (None), residues: 0 loop : 1.22 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 41 TYR 0.020 0.002 TYR D 238 PHE 0.015 0.002 PHE B 22 TRP 0.011 0.002 TRP E 128 HIS 0.002 0.001 HIS C 20 Details of bonding type rmsd covalent geometry : bond 0.00331 (12044) covalent geometry : angle 0.64152 (16258) hydrogen bonds : bond 0.06296 ( 869) hydrogen bonds : angle 4.54871 ( 2567) Misc. bond : bond 0.00012 ( 5) *********************** 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 152 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.469 Fit side-chains REVERT: A 41 ARG cc_start: 0.8053 (mmm160) cc_final: 0.7776 (mmp80) REVERT: A 70 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8905 (tp) REVERT: A 97 TYR cc_start: 0.8779 (OUTLIER) cc_final: 0.7196 (m-80) REVERT: A 267 GLU cc_start: 0.7893 (tp30) cc_final: 0.7657 (tp30) REVERT: B 70 LEU cc_start: 0.9134 (mt) cc_final: 0.8933 (tp) REVERT: B 97 TYR cc_start: 0.8868 (OUTLIER) cc_final: 0.7896 (m-80) REVERT: B 196 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7642 (tp30) REVERT: C 97 TYR cc_start: 0.8824 (OUTLIER) cc_final: 0.7787 (m-80) REVERT: D 41 ARG cc_start: 0.8559 (mmt180) cc_final: 0.8290 (mmt180) REVERT: D 97 TYR cc_start: 0.8831 (OUTLIER) cc_final: 0.7807 (m-80) REVERT: D 159 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7077 (mp0) REVERT: D 267 GLU cc_start: 0.7902 (tp30) cc_final: 0.7634 (tp30) REVERT: E 97 TYR cc_start: 0.8819 (OUTLIER) cc_final: 0.7805 (m-80) REVERT: E 267 GLU cc_start: 0.7812 (tp30) cc_final: 0.7470 (tp30) outliers start: 21 outliers final: 7 residues processed: 148 average time/residue: 0.8595 time to fit residues: 135.0471 Evaluate side-chains 141 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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 123 GLU Chi-restraints excluded: chain B residue 97 TYR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain D residue 97 TYR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain E residue 97 TYR Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 149 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 1 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 19 optimal weight: 0.0470 chunk 45 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 82 GLN C 184 ASN ** D 67 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN 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 = 0.3394 r_free = 0.3394 target = 0.124443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.102516 restraints weight = 25393.854| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 1.12 r_work: 0.2847 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2710 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2710 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.0662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12049 Z= 0.156 Angle : 0.617 7.436 16258 Z= 0.321 Chirality : 0.040 0.152 1790 Planarity : 0.005 0.036 1940 Dihedral : 9.822 59.611 2468 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.63 % Allowed : 10.68 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.55 (0.21), residues: 1360 helix: 2.73 (0.15), residues: 1015 sheet: None (None), residues: 0 loop : 1.32 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 125 TYR 0.015 0.002 TYR D 238 PHE 0.015 0.002 PHE B 164 TRP 0.011 0.002 TRP A 128 HIS 0.003 0.002 HIS A 20 Details of bonding type rmsd covalent geometry : bond 0.00312 (12044) covalent geometry : angle 0.61654 (16258) hydrogen bonds : bond 0.06073 ( 869) hydrogen bonds : angle 4.46659 ( 2567) Misc. bond : bond 0.00042 ( 5) *********************** 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 150 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.447 Fit side-chains REVERT: A 41 ARG cc_start: 0.8106 (mmm160) cc_final: 0.7855 (mmp80) REVERT: A 70 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8888 (tp) REVERT: A 97 TYR cc_start: 0.8775 (OUTLIER) cc_final: 0.7214 (m-80) REVERT: A 267 GLU cc_start: 0.7896 (tp30) cc_final: 0.7680 (tp30) REVERT: B 70 LEU cc_start: 0.9138 (mt) cc_final: 0.8929 (tp) REVERT: B 97 TYR cc_start: 0.8855 (OUTLIER) cc_final: 0.7875 (m-80) REVERT: B 196 GLU cc_start: 0.7898 (tp30) cc_final: 0.7634 (tp30) REVERT: C 97 TYR cc_start: 0.8820 (OUTLIER) cc_final: 0.7652 (m-80) REVERT: D 41 ARG cc_start: 0.8484 (mmt180) cc_final: 0.8220 (mmt180) REVERT: D 97 TYR cc_start: 0.8823 (OUTLIER) cc_final: 0.7817 (m-80) REVERT: D 159 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7080 (mp0) REVERT: E 70 LEU cc_start: 0.9094 (mt) cc_final: 0.8882 (tp) REVERT: E 97 TYR cc_start: 0.8832 (OUTLIER) cc_final: 0.7834 (m-80) REVERT: E 267 GLU cc_start: 0.7790 (tp30) cc_final: 0.7457 (tp30) outliers start: 16 outliers final: 6 residues processed: 147 average time/residue: 0.7796 time to fit residues: 121.6516 Evaluate side-chains 142 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 129 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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 97 TYR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 97 TYR Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 97 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 57 optimal weight: 2.9990 chunk 75 optimal weight: 0.1980 chunk 131 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 97 optimal weight: 0.2980 chunk 80 optimal weight: 0.4980 chunk 90 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 82 GLN C 184 ASN ** D 67 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN 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 = 0.3407 r_free = 0.3407 target = 0.125462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.103798 restraints weight = 31830.609| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 1.24 r_work: 0.2860 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2723 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2723 r_free = 0.2723 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2723 r_free = 0.2723 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2723 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.0742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12049 Z= 0.144 Angle : 0.594 7.815 16258 Z= 0.307 Chirality : 0.039 0.145 1790 Planarity : 0.004 0.034 1940 Dihedral : 9.494 59.435 2463 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.63 % Allowed : 11.40 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.40 (0.21), residues: 1360 helix: 2.66 (0.15), residues: 1045 sheet: None (None), residues: 0 loop : 0.90 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 41 TYR 0.013 0.001 TYR D 238 PHE 0.015 0.002 PHE B 164 TRP 0.010 0.001 TRP A 128 HIS 0.003 0.001 HIS C 20 Details of bonding type rmsd covalent geometry : bond 0.00284 (12044) covalent geometry : angle 0.59374 (16258) hydrogen bonds : bond 0.05775 ( 869) hydrogen bonds : angle 4.39408 ( 2567) Misc. bond : bond 0.00032 ( 5) *********************** 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 149 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.440 Fit side-chains REVERT: A 41 ARG cc_start: 0.8147 (mmm160) cc_final: 0.7885 (mmp80) REVERT: A 70 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8944 (tp) REVERT: A 97 TYR cc_start: 0.8737 (OUTLIER) cc_final: 0.7168 (m-80) REVERT: B 70 LEU cc_start: 0.9144 (mt) cc_final: 0.8937 (tp) REVERT: B 97 TYR cc_start: 0.8835 (OUTLIER) cc_final: 0.7835 (m-80) REVERT: B 196 GLU cc_start: 0.7880 (tp30) cc_final: 0.7666 (tp30) REVERT: C 97 TYR cc_start: 0.8795 (OUTLIER) cc_final: 0.7615 (m-80) REVERT: D 41 ARG cc_start: 0.8497 (mmt180) cc_final: 0.8238 (mmt180) REVERT: D 97 TYR cc_start: 0.8812 (OUTLIER) cc_final: 0.7765 (m-80) REVERT: D 159 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7117 (mp0) REVERT: E 97 TYR cc_start: 0.8813 (OUTLIER) cc_final: 0.7783 (m-80) REVERT: E 267 GLU cc_start: 0.7828 (tp30) cc_final: 0.7532 (tp30) outliers start: 16 outliers final: 7 residues processed: 144 average time/residue: 0.8748 time to fit residues: 133.7266 Evaluate side-chains 141 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 0.458 ------------------------------------------------------------------------------- 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 123 GLU Chi-restraints excluded: chain B residue 82 GLN 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 152 VAL Chi-restraints excluded: chain D residue 97 TYR Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 97 TYR Chi-restraints excluded: chain E residue 149 GLU Chi-restraints excluded: chain E residue 152 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 41 optimal weight: 0.2980 chunk 53 optimal weight: 0.6980 chunk 19 optimal weight: 0.0870 chunk 1 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 82 GLN ** D 67 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN D 184 ASN E 184 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.125190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.104283 restraints weight = 34314.046| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 1.23 r_work: 0.2876 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2724 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2724 r_free = 0.2724 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2724 r_free = 0.2724 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2724 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.0770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12049 Z= 0.148 Angle : 0.600 7.949 16258 Z= 0.310 Chirality : 0.039 0.148 1790 Planarity : 0.004 0.036 1940 Dihedral : 9.401 59.184 2460 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.72 % Allowed : 11.76 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.66 (0.21), residues: 1360 helix: 2.81 (0.15), residues: 1015 sheet: None (None), residues: 0 loop : 1.33 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 41 TYR 0.012 0.002 TYR D 238 PHE 0.014 0.002 PHE B 164 TRP 0.010 0.001 TRP A 128 HIS 0.002 0.001 HIS C 20 Details of bonding type rmsd covalent geometry : bond 0.00295 (12044) covalent geometry : angle 0.59974 (16258) hydrogen bonds : bond 0.05862 ( 869) hydrogen bonds : angle 4.40099 ( 2567) Misc. bond : bond 0.00040 ( 5) *********************** 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 149 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 0.427 Fit side-chains revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8150 (mmm160) cc_final: 0.7905 (mmp80) REVERT: A 70 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8940 (tp) REVERT: A 97 TYR cc_start: 0.8749 (OUTLIER) cc_final: 0.7337 (m-80) REVERT: B 70 LEU cc_start: 0.9140 (mt) cc_final: 0.8935 (tp) REVERT: B 97 TYR cc_start: 0.8848 (OUTLIER) cc_final: 0.7859 (m-80) REVERT: C 97 TYR cc_start: 0.8817 (OUTLIER) cc_final: 0.7655 (m-80) REVERT: D 41 ARG cc_start: 0.8455 (mmt180) cc_final: 0.8201 (mmt180) REVERT: D 97 TYR cc_start: 0.8823 (OUTLIER) cc_final: 0.7815 (m-80) REVERT: D 159 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7139 (mp0) REVERT: E 70 LEU cc_start: 0.9107 (mt) cc_final: 0.8894 (tp) REVERT: E 97 TYR cc_start: 0.8833 (OUTLIER) cc_final: 0.7819 (m-80) REVERT: E 221 MET cc_start: 0.8622 (mmm) cc_final: 0.8416 (mmm) REVERT: E 267 GLU cc_start: 0.7828 (tp30) cc_final: 0.7538 (tp30) outliers start: 17 outliers final: 7 residues processed: 145 average time/residue: 0.8396 time to fit residues: 129.2117 Evaluate side-chains 140 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 97 TYR 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 152 VAL Chi-restraints excluded: chain D residue 97 TYR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 97 TYR Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 149 GLU 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 132 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 35 optimal weight: 0.0050 chunk 116 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 overall best weight: 1.2598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 82 GLN B 73 ASN ** D 67 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN D 184 ASN E 82 GLN E 184 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.115011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.092208 restraints weight = 28232.925| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 1.09 r_work: 0.2803 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2659 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2659 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.0860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12049 Z= 0.202 Angle : 0.675 8.128 16258 Z= 0.354 Chirality : 0.043 0.170 1790 Planarity : 0.005 0.042 1940 Dihedral : 10.026 59.168 2460 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.81 % Allowed : 11.31 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.38 (0.21), residues: 1360 helix: 2.63 (0.15), residues: 1010 sheet: None (None), residues: 0 loop : 1.18 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 98 TYR 0.015 0.002 TYR B 10 PHE 0.018 0.003 PHE B 7 TRP 0.011 0.002 TRP A 128 HIS 0.002 0.001 HIS C 20 Details of bonding type rmsd covalent geometry : bond 0.00424 (12044) covalent geometry : angle 0.67465 (16258) hydrogen bonds : bond 0.06872 ( 869) hydrogen bonds : angle 4.63019 ( 2567) Misc. bond : bond 0.00090 ( 5) *********************** 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 148 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8273 (mmm160) cc_final: 0.7966 (mmp80) REVERT: A 70 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8995 (tp) REVERT: A 97 TYR cc_start: 0.8829 (OUTLIER) cc_final: 0.7435 (m-80) REVERT: B 97 TYR cc_start: 0.8894 (OUTLIER) cc_final: 0.7947 (m-80) REVERT: C 97 TYR cc_start: 0.8868 (OUTLIER) cc_final: 0.7890 (m-80) REVERT: D 97 TYR cc_start: 0.8868 (OUTLIER) cc_final: 0.7694 (m-80) REVERT: D 159 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7161 (mp0) REVERT: E 97 TYR cc_start: 0.8875 (OUTLIER) cc_final: 0.8055 (m-80) REVERT: E 267 GLU cc_start: 0.7984 (tp30) cc_final: 0.7685 (tp30) outliers start: 18 outliers final: 9 residues processed: 146 average time/residue: 0.7036 time to fit residues: 109.2025 Evaluate side-chains 143 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.420 ------------------------------------------------------------------------------- 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 97 TYR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 97 TYR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 97 TYR Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 149 GLU 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 97 optimal weight: 0.9990 chunk 120 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 109 optimal weight: 0.0980 chunk 53 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN B A 82 GLN C 184 ASN ** D 67 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN D 184 ASN E 82 GLN E 184 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.118663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.096886 restraints weight = 29743.793| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.17 r_work: 0.2836 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2693 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2693 r_free = 0.2693 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2693 r_free = 0.2693 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2693 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.0811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12049 Z= 0.154 Angle : 0.610 8.320 16258 Z= 0.316 Chirality : 0.040 0.151 1790 Planarity : 0.004 0.035 1940 Dihedral : 9.634 59.479 2460 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.72 % Allowed : 11.40 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.58 (0.21), residues: 1360 helix: 2.75 (0.15), residues: 1015 sheet: None (None), residues: 0 loop : 1.31 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 41 TYR 0.011 0.002 TYR D 143 PHE 0.014 0.002 PHE B 164 TRP 0.010 0.001 TRP A 128 HIS 0.003 0.001 HIS D 20 Details of bonding type rmsd covalent geometry : bond 0.00309 (12044) covalent geometry : angle 0.60978 (16258) hydrogen bonds : bond 0.05997 ( 869) hydrogen bonds : angle 4.43458 ( 2567) Misc. bond : bond 0.00045 ( 5) *********************** 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 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.458 Fit side-chains REVERT: A 41 ARG cc_start: 0.8293 (mmm160) cc_final: 0.8049 (mmm-85) REVERT: A 97 TYR cc_start: 0.8742 (OUTLIER) cc_final: 0.7129 (m-80) REVERT: A 234 ARG cc_start: 0.9321 (OUTLIER) cc_final: 0.8131 (ttt180) REVERT: B 97 TYR cc_start: 0.8841 (OUTLIER) cc_final: 0.7823 (m-80) REVERT: C 97 TYR cc_start: 0.8822 (OUTLIER) cc_final: 0.7650 (m-80) REVERT: D 97 TYR cc_start: 0.8808 (OUTLIER) cc_final: 0.7583 (m-80) REVERT: E 97 TYR cc_start: 0.8813 (OUTLIER) cc_final: 0.7790 (m-80) REVERT: E 267 GLU cc_start: 0.7961 (tp30) cc_final: 0.7700 (tp30) outliers start: 18 outliers final: 9 residues processed: 147 average time/residue: 0.8050 time to fit residues: 125.7633 Evaluate side-chains 144 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 234 ARG 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 122 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 97 TYR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain E residue 97 TYR Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 149 GLU 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 63 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 119 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** D 67 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN D 184 ASN E 82 GLN E 184 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.116300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.093777 restraints weight = 27202.634| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 1.07 r_work: 0.2808 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2685 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2685 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.0855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12049 Z= 0.177 Angle : 0.646 8.616 16258 Z= 0.337 Chirality : 0.041 0.160 1790 Planarity : 0.005 0.036 1940 Dihedral : 9.726 59.641 2457 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.54 % Allowed : 11.76 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.46 (0.21), residues: 1360 helix: 2.70 (0.15), residues: 1010 sheet: None (None), residues: 0 loop : 1.17 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 98 TYR 0.013 0.002 TYR D 219 PHE 0.015 0.002 PHE B 7 TRP 0.011 0.002 TRP A 128 HIS 0.002 0.001 HIS C 20 Details of bonding type rmsd covalent geometry : bond 0.00365 (12044) covalent geometry : angle 0.64610 (16258) hydrogen bonds : bond 0.06469 ( 869) hydrogen bonds : angle 4.53549 ( 2567) Misc. bond : bond 0.00066 ( 5) *********************** 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 148 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.416 Fit side-chains REVERT: A 41 ARG cc_start: 0.8215 (mmm160) cc_final: 0.7937 (mmm-85) REVERT: A 97 TYR cc_start: 0.8785 (OUTLIER) cc_final: 0.7362 (m-80) REVERT: A 234 ARG cc_start: 0.9330 (OUTLIER) cc_final: 0.8099 (ttt180) REVERT: B 97 TYR cc_start: 0.8864 (OUTLIER) cc_final: 0.7898 (m-80) REVERT: C 97 TYR cc_start: 0.8846 (OUTLIER) cc_final: 0.7842 (m-80) REVERT: C 267 GLU cc_start: 0.7898 (tp30) cc_final: 0.7365 (tm-30) REVERT: D 97 TYR cc_start: 0.8841 (OUTLIER) cc_final: 0.7665 (m-80) REVERT: E 70 LEU cc_start: 0.9074 (mt) cc_final: 0.8364 (tp) REVERT: E 74 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8116 (mp0) REVERT: E 97 TYR cc_start: 0.8847 (OUTLIER) cc_final: 0.7864 (m-80) REVERT: E 267 GLU cc_start: 0.7915 (tp30) cc_final: 0.7644 (tp30) outliers start: 16 outliers final: 9 residues processed: 147 average time/residue: 0.8704 time to fit residues: 135.7456 Evaluate side-chains 145 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 234 ARG 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 122 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 97 TYR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 97 TYR Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 149 GLU Chi-restraints excluded: chain E residue 152 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 134 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 97 optimal weight: 0.4980 chunk 69 optimal weight: 0.0270 chunk 39 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 overall best weight: 0.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN C 184 ASN ** D 67 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN D 184 ASN E 82 GLN E 184 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.117986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.096131 restraints weight = 29542.113| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 1.14 r_work: 0.2851 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2697 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2697 r_free = 0.2697 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2697 r_free = 0.2697 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2697 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.0821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12049 Z= 0.154 Angle : 0.616 8.699 16258 Z= 0.318 Chirality : 0.040 0.150 1790 Planarity : 0.004 0.036 1940 Dihedral : 9.485 59.891 2457 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.63 % Allowed : 11.58 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.58 (0.21), residues: 1360 helix: 2.76 (0.15), residues: 1015 sheet: None (None), residues: 0 loop : 1.28 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 234 TYR 0.011 0.002 TYR D 143 PHE 0.014 0.002 PHE B 164 TRP 0.010 0.001 TRP A 128 HIS 0.002 0.001 HIS C 20 Details of bonding type rmsd covalent geometry : bond 0.00309 (12044) covalent geometry : angle 0.61605 (16258) hydrogen bonds : bond 0.05997 ( 869) hydrogen bonds : angle 4.43701 ( 2567) Misc. bond : bond 0.00041 ( 5) *********************** 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 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.444 Fit side-chains REVERT: A 97 TYR cc_start: 0.8741 (OUTLIER) cc_final: 0.7152 (m-80) REVERT: A 234 ARG cc_start: 0.9323 (OUTLIER) cc_final: 0.8137 (ttt180) REVERT: B 97 TYR cc_start: 0.8843 (OUTLIER) cc_final: 0.7837 (m-80) REVERT: C 97 TYR cc_start: 0.8822 (OUTLIER) cc_final: 0.7660 (m-80) REVERT: C 267 GLU cc_start: 0.7918 (tp30) cc_final: 0.7415 (tm-30) REVERT: D 97 TYR cc_start: 0.8812 (OUTLIER) cc_final: 0.7598 (m-80) REVERT: E 70 LEU cc_start: 0.9097 (mt) cc_final: 0.8445 (tp) REVERT: E 74 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8196 (mp0) REVERT: E 97 TYR cc_start: 0.8813 (OUTLIER) cc_final: 0.7785 (m-80) REVERT: E 267 GLU cc_start: 0.7971 (tp30) cc_final: 0.7717 (tp30) outliers start: 17 outliers final: 10 residues processed: 146 average time/residue: 0.8227 time to fit residues: 127.6466 Evaluate side-chains 146 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 234 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 C residue 97 TYR Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 97 TYR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 97 TYR Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 149 GLU 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 133 optimal weight: 0.5980 chunk 47 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 106 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** D 67 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN D 184 ASN E 82 GLN E 184 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.117970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.095704 restraints weight = 26832.014| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 1.06 r_work: 0.2819 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2693 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2693 r_free = 0.2693 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2693 r_free = 0.2693 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2693 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.0852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12049 Z= 0.168 Angle : 0.637 8.809 16258 Z= 0.330 Chirality : 0.040 0.156 1790 Planarity : 0.004 0.037 1940 Dihedral : 9.571 59.800 2457 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.72 % Allowed : 11.58 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.50 (0.21), residues: 1360 helix: 2.74 (0.15), residues: 1010 sheet: None (None), residues: 0 loop : 1.16 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 41 TYR 0.012 0.002 TYR D 219 PHE 0.014 0.002 PHE D 12 TRP 0.010 0.002 TRP A 128 HIS 0.002 0.001 HIS D 20 Details of bonding type rmsd covalent geometry : bond 0.00345 (12044) covalent geometry : angle 0.63702 (16258) hydrogen bonds : bond 0.06291 ( 869) hydrogen bonds : angle 4.49565 ( 2567) Misc. bond : bond 0.00056 ( 5) ********************** 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 149 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 0.429 Fit side-chains REVERT: A 97 TYR cc_start: 0.8766 (OUTLIER) cc_final: 0.7353 (m-80) REVERT: A 234 ARG cc_start: 0.9329 (OUTLIER) cc_final: 0.8109 (ttt180) REVERT: B 97 TYR cc_start: 0.8847 (OUTLIER) cc_final: 0.7875 (m-80) REVERT: C 97 TYR cc_start: 0.8835 (OUTLIER) cc_final: 0.7824 (m-80) REVERT: C 267 GLU cc_start: 0.7855 (tp30) cc_final: 0.7335 (tm-30) REVERT: D 97 TYR cc_start: 0.8828 (OUTLIER) cc_final: 0.7647 (m-80) REVERT: E 70 LEU cc_start: 0.9068 (mt) cc_final: 0.8356 (tp) REVERT: E 74 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8088 (mp0) REVERT: E 97 TYR cc_start: 0.8828 (OUTLIER) cc_final: 0.7833 (m-80) REVERT: E 267 GLU cc_start: 0.7913 (tp30) cc_final: 0.7644 (tp30) outliers start: 18 outliers final: 10 residues processed: 148 average time/residue: 0.7334 time to fit residues: 115.3603 Evaluate side-chains 146 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 234 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 C residue 97 TYR Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 97 TYR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 97 TYR Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 149 GLU 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: 0.5980 chunk 55 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 chunk 17 optimal weight: 0.6980 chunk 83 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 102 optimal weight: 0.0010 chunk 31 optimal weight: 0.8980 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN C 184 ASN ** D 67 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN D 184 ASN E 82 GLN E 184 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.117712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.095353 restraints weight = 28136.622| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 1.18 r_work: 0.2840 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2720 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2720 r_free = 0.2720 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2720 r_free = 0.2720 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2720 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.0837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12049 Z= 0.152 Angle : 0.616 9.108 16258 Z= 0.317 Chirality : 0.040 0.149 1790 Planarity : 0.004 0.037 1940 Dihedral : 9.369 59.595 2457 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.72 % Allowed : 11.58 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.59 (0.21), residues: 1360 helix: 2.77 (0.15), residues: 1015 sheet: None (None), residues: 0 loop : 1.27 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 41 TYR 0.011 0.002 TYR D 143 PHE 0.014 0.002 PHE B 164 TRP 0.010 0.001 TRP A 128 HIS 0.002 0.001 HIS C 20 Details of bonding type rmsd covalent geometry : bond 0.00305 (12044) covalent geometry : angle 0.61604 (16258) hydrogen bonds : bond 0.05938 ( 869) hydrogen bonds : angle 4.42333 ( 2567) Misc. bond : bond 0.00040 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5446.97 seconds wall clock time: 93 minutes 45.52 seconds (5625.52 seconds total)