Starting phenix.real_space_refine on Sat Aug 23 09:21:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r0p_18800/08_2025/8r0p_18800.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r0p_18800/08_2025/8r0p_18800.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r0p_18800/08_2025/8r0p_18800.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r0p_18800/08_2025/8r0p_18800.map" model { file = "/net/cci-nas-00/data/ceres_data/8r0p_18800/08_2025/8r0p_18800.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r0p_18800/08_2025/8r0p_18800.cif" } resolution = 2.44 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= 0.048 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 30 5.16 5 C 7379 2.51 5 N 1735 2.21 5 O 2010 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11154 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2109 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 9, 'TRANS': 272} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 2109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2109 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 9, 'TRANS': 272} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "C" Number of atoms: 2109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2109 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 9, 'TRANS': 272} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "D" Number of atoms: 2109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2109 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 9, 'TRANS': 272} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "E" Number of atoms: 2109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2109 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 9, 'TRANS': 272} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "A" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 90 Unusual residues: {'LFA': 7, 'RET': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 71 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 89 Unusual residues: {'LFA': 7, 'RET': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 72 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 93 Unusual residues: {'LFA': 7, 'RET': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 70 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 91 Unusual residues: {'LFA': 7, 'RET': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 70 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 91 Unusual residues: {'LFA': 7, 'RET': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 70 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Time building chain proxies: 2.29, per 1000 atoms: 0.21 Number of scatterers: 11154 At special positions: 0 Unit cell: (95.304, 92.796, 85.272, 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 30 16.00 O 2010 8.00 N 1735 7.00 C 7379 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: 0.97 Conformation dependent library (CDL) restraints added in 544.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2600 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 10 sheets defined 81.6% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 8 through 12 removed outlier: 3.573A pdb=" N ALA A 12 " --> pdb=" O PRO A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 43 Processing helix chain 'A' and resid 44 through 47 removed outlier: 3.731A pdb=" N VAL A 47 " --> pdb=" O ARG A 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 44 through 47' Processing helix chain 'A' and resid 48 through 50 No H-bonds generated for 'chain 'A' and resid 48 through 50' Processing helix chain 'A' and resid 51 through 78 removed outlier: 3.734A pdb=" N VAL A 55 " --> pdb=" O TYR A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 118 removed outlier: 3.946A pdb=" N PHE A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ARG A 100 " --> pdb=" O ILE A 96 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TYR A 101 " --> pdb=" O PHE A 97 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL A 106 " --> pdb=" O ILE A 102 " (cutoff:3.500A) Proline residue: A 109 - end of helix removed outlier: 3.580A pdb=" N VAL A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 150 Processing helix chain 'A' and resid 151 through 155 Processing helix chain 'A' and resid 156 through 186 removed outlier: 3.511A pdb=" N LEU A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 189 No H-bonds generated for 'chain 'A' and resid 187 through 189' Processing helix chain 'A' and resid 190 through 207 removed outlier: 4.161A pdb=" N GLY A 207 " --> pdb=" O VAL A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 217 through 220 Processing helix chain 'A' and resid 223 through 243 Processing helix chain 'A' and resid 247 through 263 Processing helix chain 'B' and resid 8 through 12 removed outlier: 3.574A pdb=" N ALA B 12 " --> pdb=" O PRO B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 43 Processing helix chain 'B' and resid 44 through 47 removed outlier: 3.728A pdb=" N VAL B 47 " --> pdb=" O ARG B 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 44 through 47' Processing helix chain 'B' and resid 48 through 50 No H-bonds generated for 'chain 'B' and resid 48 through 50' Processing helix chain 'B' and resid 51 through 78 removed outlier: 3.734A pdb=" N VAL B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 118 removed outlier: 3.931A pdb=" N PHE B 97 " --> pdb=" O ALA B 93 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ARG B 100 " --> pdb=" O ILE B 96 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR B 101 " --> pdb=" O PHE B 97 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL B 106 " --> pdb=" O ILE B 102 " (cutoff:3.500A) Proline residue: B 109 - end of helix removed outlier: 3.580A pdb=" N VAL B 118 " --> pdb=" O GLU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 150 Processing helix chain 'B' and resid 151 through 155 Processing helix chain 'B' and resid 156 through 186 removed outlier: 3.514A pdb=" N LEU B 186 " --> pdb=" O VAL B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 189 No H-bonds generated for 'chain 'B' and resid 187 through 189' Processing helix chain 'B' and resid 190 through 207 removed outlier: 4.165A pdb=" N GLY B 207 " --> pdb=" O VAL B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 216 removed outlier: 3.555A pdb=" N PHE B 216 " --> pdb=" O PRO B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 220 Processing helix chain 'B' and resid 223 through 243 Processing helix chain 'B' and resid 247 through 263 Processing helix chain 'C' and resid 8 through 12 removed outlier: 3.575A pdb=" N ALA C 12 " --> pdb=" O PRO C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 43 Processing helix chain 'C' and resid 44 through 47 removed outlier: 3.730A pdb=" N VAL C 47 " --> pdb=" O ARG C 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 44 through 47' Processing helix chain 'C' and resid 48 through 50 No H-bonds generated for 'chain 'C' and resid 48 through 50' Processing helix chain 'C' and resid 51 through 78 removed outlier: 3.733A pdb=" N VAL C 55 " --> pdb=" O TYR C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 118 removed outlier: 3.825A pdb=" N PHE C 97 " --> pdb=" O ALA C 93 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ARG C 100 " --> pdb=" O ILE C 96 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR C 101 " --> pdb=" O PHE C 97 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL C 106 " --> pdb=" O ILE C 102 " (cutoff:3.500A) Proline residue: C 109 - end of helix removed outlier: 3.580A pdb=" N VAL C 118 " --> pdb=" O GLU C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 150 Processing helix chain 'C' and resid 151 through 155 Processing helix chain 'C' and resid 156 through 186 removed outlier: 3.513A pdb=" N LEU C 186 " --> pdb=" O VAL C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 189 No H-bonds generated for 'chain 'C' and resid 187 through 189' Processing helix chain 'C' and resid 190 through 207 removed outlier: 4.162A pdb=" N GLY C 207 " --> pdb=" O VAL C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 216 Processing helix chain 'C' and resid 217 through 220 Processing helix chain 'C' and resid 223 through 243 Processing helix chain 'C' and resid 247 through 263 Processing helix chain 'D' and resid 8 through 12 removed outlier: 3.574A pdb=" N ALA D 12 " --> pdb=" O PRO D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 43 Processing helix chain 'D' and resid 44 through 47 removed outlier: 3.731A pdb=" N VAL D 47 " --> pdb=" O ARG D 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 44 through 47' Processing helix chain 'D' and resid 48 through 50 No H-bonds generated for 'chain 'D' and resid 48 through 50' Processing helix chain 'D' and resid 51 through 78 removed outlier: 3.733A pdb=" N VAL D 55 " --> pdb=" O TYR D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 118 removed outlier: 3.829A pdb=" N PHE D 97 " --> pdb=" O ALA D 93 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ARG D 100 " --> pdb=" O ILE D 96 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TYR D 101 " --> pdb=" O PHE D 97 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL D 106 " --> pdb=" O ILE D 102 " (cutoff:3.500A) Proline residue: D 109 - end of helix removed outlier: 3.580A pdb=" N VAL D 118 " --> pdb=" O GLU D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 150 Processing helix chain 'D' and resid 151 through 155 Processing helix chain 'D' and resid 156 through 186 removed outlier: 3.512A pdb=" N LEU D 186 " --> pdb=" O VAL D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 189 No H-bonds generated for 'chain 'D' and resid 187 through 189' Processing helix chain 'D' and resid 190 through 207 removed outlier: 4.166A pdb=" N GLY D 207 " --> pdb=" O VAL D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 216 removed outlier: 3.563A pdb=" N PHE D 216 " --> pdb=" O PRO D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 220 Processing helix chain 'D' and resid 223 through 243 Processing helix chain 'D' and resid 247 through 263 Processing helix chain 'E' and resid 8 through 12 removed outlier: 3.574A pdb=" N ALA E 12 " --> pdb=" O PRO E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 43 Processing helix chain 'E' and resid 44 through 47 removed outlier: 3.731A pdb=" N VAL E 47 " --> pdb=" O ARG E 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 44 through 47' Processing helix chain 'E' and resid 48 through 50 No H-bonds generated for 'chain 'E' and resid 48 through 50' Processing helix chain 'E' and resid 51 through 78 removed outlier: 3.734A pdb=" N VAL E 55 " --> pdb=" O TYR E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 118 removed outlier: 3.949A pdb=" N PHE E 97 " --> pdb=" O ALA E 93 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ARG E 100 " --> pdb=" O ILE E 96 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TYR E 101 " --> pdb=" O PHE E 97 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL E 106 " --> pdb=" O ILE E 102 " (cutoff:3.500A) Proline residue: E 109 - end of helix removed outlier: 3.581A pdb=" N VAL E 118 " --> pdb=" O GLU E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 150 Processing helix chain 'E' and resid 151 through 155 Processing helix chain 'E' and resid 156 through 186 removed outlier: 3.515A pdb=" N LEU E 186 " --> pdb=" O VAL E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 189 No H-bonds generated for 'chain 'E' and resid 187 through 189' Processing helix chain 'E' and resid 190 through 207 removed outlier: 4.163A pdb=" N GLY E 207 " --> pdb=" O VAL E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 216 Processing helix chain 'E' and resid 217 through 220 Processing helix chain 'E' and resid 223 through 243 Processing helix chain 'E' and resid 247 through 263 Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 82 Processing sheet with id=AA2, first strand: chain 'A' and resid 272 through 274 removed outlier: 6.446A pdb=" N ILE A 272 " --> pdb=" O GLN A 279 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 80 through 82 Processing sheet with id=AA4, first strand: chain 'B' and resid 272 through 274 removed outlier: 6.445A pdb=" N ILE B 272 " --> pdb=" O GLN B 279 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 80 through 82 Processing sheet with id=AA6, first strand: chain 'C' and resid 272 through 274 removed outlier: 6.447A pdb=" N ILE C 272 " --> pdb=" O GLN C 279 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 80 through 82 Processing sheet with id=AA8, first strand: chain 'D' and resid 272 through 274 removed outlier: 6.448A pdb=" N ILE D 272 " --> pdb=" O GLN D 279 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 80 through 82 Processing sheet with id=AB1, first strand: chain 'E' and resid 272 through 274 removed outlier: 6.446A pdb=" N ILE E 272 " --> pdb=" O GLN E 279 " (cutoff:3.500A) 838 hydrogen bonds defined for protein. 2439 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: 1.65 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 1602 1.30 - 1.43: 2918 1.43 - 1.56: 6633 1.56 - 1.70: 0 1.70 - 1.83: 45 Bond restraints: 11198 Sorted by residual: bond pdb=" C PRO B 218 " pdb=" O PRO B 218 " ideal model delta sigma weight residual 1.237 1.166 0.072 1.32e-02 5.74e+03 2.95e+01 bond pdb=" C PRO A 218 " pdb=" O PRO A 218 " ideal model delta sigma weight residual 1.237 1.166 0.071 1.32e-02 5.74e+03 2.92e+01 bond pdb=" C PRO D 218 " pdb=" O PRO D 218 " ideal model delta sigma weight residual 1.238 1.163 0.075 1.42e-02 4.96e+03 2.80e+01 bond pdb=" C PRO E 218 " pdb=" O PRO E 218 " ideal model delta sigma weight residual 1.238 1.163 0.075 1.42e-02 4.96e+03 2.80e+01 bond pdb=" C PRO C 218 " pdb=" O PRO C 218 " ideal model delta sigma weight residual 1.238 1.165 0.073 1.42e-02 4.96e+03 2.65e+01 ... (remaining 11193 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 13435 2.62 - 5.23: 1568 5.23 - 7.85: 182 7.85 - 10.47: 17 10.47 - 13.09: 10 Bond angle restraints: 15212 Sorted by residual: angle pdb=" C PRO D 218 " pdb=" CA PRO D 218 " pdb=" CB PRO D 218 " ideal model delta sigma weight residual 111.62 124.71 -13.09 1.46e+00 4.69e-01 8.03e+01 angle pdb=" C PRO C 218 " pdb=" CA PRO C 218 " pdb=" CB PRO C 218 " ideal model delta sigma weight residual 111.62 124.58 -12.96 1.46e+00 4.69e-01 7.88e+01 angle pdb=" C PRO E 218 " pdb=" CA PRO E 218 " pdb=" CB PRO E 218 " ideal model delta sigma weight residual 111.62 123.82 -12.20 1.46e+00 4.69e-01 6.98e+01 angle pdb=" C PRO B 218 " pdb=" CA PRO B 218 " pdb=" CB PRO B 218 " ideal model delta sigma weight residual 111.85 123.45 -11.60 1.42e+00 4.96e-01 6.67e+01 angle pdb=" CA ASN B 90 " pdb=" CB ASN B 90 " pdb=" CG ASN B 90 " ideal model delta sigma weight residual 112.60 120.42 -7.82 1.00e+00 1.00e+00 6.11e+01 ... (remaining 15207 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.84: 5479 12.84 - 25.68: 726 25.68 - 38.53: 168 38.53 - 51.37: 62 51.37 - 64.21: 32 Dihedral angle restraints: 6467 sinusoidal: 2422 harmonic: 4045 Sorted by residual: dihedral pdb=" C PHE C 220 " pdb=" N PHE C 220 " pdb=" CA PHE C 220 " pdb=" CB PHE C 220 " ideal model delta harmonic sigma weight residual -122.60 -134.52 11.92 0 2.50e+00 1.60e-01 2.27e+01 dihedral pdb=" C PRO C 218 " pdb=" N PRO C 218 " pdb=" CA PRO C 218 " pdb=" CB PRO C 218 " ideal model delta harmonic sigma weight residual -120.70 -131.45 10.75 0 2.50e+00 1.60e-01 1.85e+01 dihedral pdb=" CA ILE E 149 " pdb=" C ILE E 149 " pdb=" N VAL E 150 " pdb=" CA VAL E 150 " ideal model delta harmonic sigma weight residual -180.00 -159.16 -20.84 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 6464 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1279 0.073 - 0.147: 505 0.147 - 0.220: 65 0.220 - 0.293: 22 0.293 - 0.367: 4 Chirality restraints: 1875 Sorted by residual: chirality pdb=" CA PRO C 218 " pdb=" N PRO C 218 " pdb=" C PRO C 218 " pdb=" CB PRO C 218 " both_signs ideal model delta sigma weight residual False 2.72 2.35 0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CA PRO D 218 " pdb=" N PRO D 218 " pdb=" C PRO D 218 " pdb=" CB PRO D 218 " both_signs ideal model delta sigma weight residual False 2.72 2.39 0.33 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CA PRO E 218 " pdb=" N PRO E 218 " pdb=" C PRO E 218 " pdb=" CB PRO E 218 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.30 2.00e-01 2.50e+01 2.32e+00 ... (remaining 1872 not shown) Planarity restraints: 1815 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 100 " -0.416 9.50e-02 1.11e+02 1.87e-01 2.39e+01 pdb=" NE ARG E 100 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG E 100 " 0.033 2.00e-02 2.50e+03 pdb=" NH1 ARG E 100 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG E 100 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 RET B 408 " -0.052 2.00e-02 2.50e+03 4.81e-02 2.32e+01 pdb=" C11 RET B 408 " 0.061 2.00e-02 2.50e+03 pdb=" C12 RET B 408 " 0.033 2.00e-02 2.50e+03 pdb=" C13 RET B 408 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 RET C 408 " -0.052 2.00e-02 2.50e+03 4.80e-02 2.31e+01 pdb=" C11 RET C 408 " 0.061 2.00e-02 2.50e+03 pdb=" C12 RET C 408 " 0.033 2.00e-02 2.50e+03 pdb=" C13 RET C 408 " -0.042 2.00e-02 2.50e+03 ... (remaining 1812 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 652 2.69 - 3.24: 11578 3.24 - 3.79: 19507 3.79 - 4.35: 27088 4.35 - 4.90: 42749 Nonbonded interactions: 101574 Sorted by model distance: nonbonded pdb=" NE2 HIS A 19 " pdb=" O HOH A 501 " model vdw 2.132 3.120 nonbonded pdb=" NE2 HIS E 19 " pdb=" O HOH E 501 " model vdw 2.205 3.120 nonbonded pdb=" O THR D 83 " pdb=" N GLY D 85 " model vdw 2.311 3.120 nonbonded pdb=" O THR C 83 " pdb=" N GLY C 85 " model vdw 2.314 3.120 nonbonded pdb=" O THR E 83 " pdb=" N GLY E 85 " model vdw 2.315 3.120 ... (remaining 101569 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 5 through 401 or (resid 402 and (name C10 or name C11)) or \ (resid 404 and (name C12 or name C13 or name C14 or name C15 or name C16 or nam \ e C17 or name C18 or name C19 or name C20)) or resid 408)) selection = (chain 'B' and (resid 5 through 401 or (resid 402 and (name C10 or name C11)) or \ resid 404 or resid 408)) selection = (chain 'C' and (resid 5 through 401 or (resid 402 and (name C10 or name C11)) or \ (resid 404 and (name C10 or name C2 or name C3 or name C4 or name C5 or name C6 \ or name C7 or name C8 or name C9 )) or resid 408)) selection = (chain 'D' and (resid 5 through 401 or (resid 402 and (name C10 or name C11)) or \ (resid 404 and (name C11 or name C2 or name C3 or name C4 or name C5 or name C6 \ or name C7 or name C8 or name C9 )) or resid 408)) selection = (chain 'E' and (resid 5 through 401 or (resid 402 and (name C10 or name C11)) or \ (resid 404 and (name C12 or name C13 or name C14 or name C15 or name C16 or nam \ e C17 or name C18 or name C19 or name C20)) or resid 408)) } 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=1.00 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: 3.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.360 Find NCS groups from input model: 0.230 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:6.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 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 : 0.012 0.092 11203 Z= 0.817 Angle : 1.747 13.087 15212 Z= 1.187 Chirality : 0.078 0.367 1875 Planarity : 0.017 0.187 1815 Dihedral : 13.760 64.208 3867 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 6.64 % Allowed : 7.36 % Favored : 86.00 % Cbeta Deviations : 0.46 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.40 (0.18), residues: 1400 helix: -2.32 (0.13), residues: 980 sheet: None (None), residues: 0 loop : -1.50 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.004 ARG E 100 TYR 0.051 0.012 TYR E 24 PHE 0.054 0.010 PHE B 220 TRP 0.035 0.008 TRP A 273 HIS 0.020 0.007 HIS C 19 Details of bonding type rmsd covalent geometry : bond 0.01204 (11198) covalent geometry : angle 1.74734 (15212) hydrogen bonds : bond 0.18290 ( 838) hydrogen bonds : angle 7.73038 ( 2439) Misc. bond : bond 0.03325 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 116 time to evaluate : 0.302 Fit side-chains REVERT: A 20 GLN cc_start: 0.8318 (tp40) cc_final: 0.7989 (tp-100) REVERT: A 61 MET cc_start: 0.8301 (ttm) cc_final: 0.7797 (ttp) REVERT: A 111 LEU cc_start: 0.8097 (tt) cc_final: 0.7327 (mt) REVERT: B 20 GLN cc_start: 0.8409 (tp40) cc_final: 0.8073 (tp-100) REVERT: C 5 ASN cc_start: 0.6432 (OUTLIER) cc_final: 0.6157 (t0) REVERT: D 5 ASN cc_start: 0.6032 (OUTLIER) cc_final: 0.5800 (t0) REVERT: D 61 MET cc_start: 0.8306 (ttm) cc_final: 0.7815 (ttp) REVERT: D 111 LEU cc_start: 0.8186 (tt) cc_final: 0.7416 (mt) REVERT: E 20 GLN cc_start: 0.8372 (tp40) cc_final: 0.8076 (mm110) outliers start: 73 outliers final: 39 residues processed: 172 average time/residue: 0.4188 time to fit residues: 78.4851 Evaluate side-chains 145 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 104 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 218 PRO Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 218 PRO Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 5 ASN Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 218 PRO Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 5 ASN Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 249 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.2980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 0.0970 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN C 5 ASN C 90 ASN C 153 ASN D 5 ASN E 153 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.121927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.102108 restraints weight = 10080.616| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.51 r_work: 0.3024 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11203 Z= 0.136 Angle : 0.602 8.366 15212 Z= 0.311 Chirality : 0.041 0.124 1875 Planarity : 0.005 0.048 1815 Dihedral : 9.608 57.579 1866 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.64 % Allowed : 9.27 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.21), residues: 1400 helix: 1.18 (0.15), residues: 1030 sheet: None (None), residues: 0 loop : -0.81 (0.28), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 100 TYR 0.012 0.002 TYR B 69 PHE 0.025 0.002 PHE C 160 TRP 0.015 0.001 TRP A 163 HIS 0.010 0.003 HIS E 194 Details of bonding type rmsd covalent geometry : bond 0.00294 (11198) covalent geometry : angle 0.60160 (15212) hydrogen bonds : bond 0.04651 ( 838) hydrogen bonds : angle 4.09294 ( 2439) Misc. bond : bond 0.00009 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 128 time to evaluate : 0.254 Fit side-chains REVERT: A 39 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.6720 (ttt-90) REVERT: A 61 MET cc_start: 0.8019 (ttm) cc_final: 0.7265 (ttp) REVERT: A 111 LEU cc_start: 0.7707 (tt) cc_final: 0.6702 (mt) REVERT: B 39 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.6663 (ttt-90) REVERT: B 270 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7684 (pt0) REVERT: D 61 MET cc_start: 0.7974 (ttm) cc_final: 0.7594 (ttm) REVERT: E 5 ASN cc_start: 0.5766 (OUTLIER) cc_final: 0.5481 (t0) REVERT: E 114 GLU cc_start: 0.7860 (tt0) cc_final: 0.7315 (tt0) REVERT: E 162 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7348 (tp) outliers start: 40 outliers final: 22 residues processed: 158 average time/residue: 0.5332 time to fit residues: 90.9005 Evaluate side-chains 139 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 112 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 5 ASN Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 249 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 48 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 104 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 111 optimal weight: 0.0030 chunk 73 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN A 194 HIS B 194 HIS D 194 HIS E 20 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.125518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.109452 restraints weight = 10347.395| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.02 r_work: 0.3118 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 11203 Z= 0.195 Angle : 0.629 8.166 15212 Z= 0.326 Chirality : 0.044 0.129 1875 Planarity : 0.005 0.046 1815 Dihedral : 9.693 57.666 1832 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 4.36 % Allowed : 11.18 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.89 (0.22), residues: 1400 helix: 1.91 (0.16), residues: 1030 sheet: None (None), residues: 0 loop : -0.61 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 44 TYR 0.016 0.002 TYR E 69 PHE 0.023 0.002 PHE C 160 TRP 0.014 0.002 TRP A 163 HIS 0.011 0.003 HIS E 194 Details of bonding type rmsd covalent geometry : bond 0.00470 (11198) covalent geometry : angle 0.62924 (15212) hydrogen bonds : bond 0.05160 ( 838) hydrogen bonds : angle 4.02498 ( 2439) Misc. bond : bond 0.00035 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 107 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: B 5 ASN cc_start: 0.6725 (OUTLIER) cc_final: 0.6423 (t0) REVERT: B 39 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7277 (ttm170) REVERT: B 162 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7904 (tp) REVERT: D 162 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7836 (tp) REVERT: E 5 ASN cc_start: 0.6514 (OUTLIER) cc_final: 0.6306 (t0) REVERT: E 162 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7828 (tp) outliers start: 48 outliers final: 31 residues processed: 136 average time/residue: 0.5885 time to fit residues: 86.2078 Evaluate side-chains 141 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 104 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 5 ASN Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 249 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 110 optimal weight: 0.4980 chunk 70 optimal weight: 0.3980 chunk 87 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 126 optimal weight: 0.5980 chunk 121 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 HIS ** B 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 HIS D 194 HIS E 194 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.121948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.102241 restraints weight = 10414.521| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.54 r_work: 0.3033 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11203 Z= 0.125 Angle : 0.531 7.054 15212 Z= 0.274 Chirality : 0.040 0.121 1875 Planarity : 0.004 0.042 1815 Dihedral : 8.528 59.097 1831 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.91 % Allowed : 11.36 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.57 (0.22), residues: 1400 helix: 2.44 (0.16), residues: 1030 sheet: None (None), residues: 0 loop : -0.45 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 44 TYR 0.011 0.002 TYR C 69 PHE 0.020 0.002 PHE D 160 TRP 0.011 0.001 TRP B 163 HIS 0.011 0.003 HIS A 194 Details of bonding type rmsd covalent geometry : bond 0.00280 (11198) covalent geometry : angle 0.53096 (15212) hydrogen bonds : bond 0.04101 ( 838) hydrogen bonds : angle 3.79982 ( 2439) Misc. bond : bond 0.00011 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 115 time to evaluate : 0.458 Fit side-chains REVERT: B 5 ASN cc_start: 0.5993 (OUTLIER) cc_final: 0.5747 (t0) REVERT: B 162 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7350 (tp) REVERT: E 162 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7389 (tp) outliers start: 43 outliers final: 25 residues processed: 143 average time/residue: 0.5650 time to fit residues: 86.5348 Evaluate side-chains 139 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 249 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 99 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 130 optimal weight: 0.0870 chunk 110 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 HIS B 194 HIS C 194 HIS D 194 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.120480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.101006 restraints weight = 10276.934| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.50 r_work: 0.3014 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11203 Z= 0.150 Angle : 0.557 7.689 15212 Z= 0.289 Chirality : 0.042 0.126 1875 Planarity : 0.005 0.041 1815 Dihedral : 8.675 59.053 1831 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 4.00 % Allowed : 11.45 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.56 (0.22), residues: 1400 helix: 2.40 (0.16), residues: 1035 sheet: None (None), residues: 0 loop : -0.39 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 44 TYR 0.014 0.002 TYR A 69 PHE 0.020 0.002 PHE C 160 TRP 0.011 0.001 TRP C 163 HIS 0.012 0.003 HIS A 194 Details of bonding type rmsd covalent geometry : bond 0.00351 (11198) covalent geometry : angle 0.55739 (15212) hydrogen bonds : bond 0.04501 ( 838) hydrogen bonds : angle 3.85712 ( 2439) Misc. bond : bond 0.00026 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 112 time to evaluate : 0.295 Fit side-chains REVERT: B 162 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7531 (tp) REVERT: D 162 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7518 (tp) REVERT: E 162 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7364 (tp) outliers start: 44 outliers final: 30 residues processed: 140 average time/residue: 0.5581 time to fit residues: 83.9754 Evaluate side-chains 143 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 110 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 249 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 36 optimal weight: 0.0670 chunk 128 optimal weight: 3.9990 chunk 117 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 0.3980 chunk 38 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 HIS B 194 HIS C 194 HIS D 194 HIS E 194 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.121333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.101699 restraints weight = 10351.246| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.53 r_work: 0.3024 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11203 Z= 0.136 Angle : 0.537 7.564 15212 Z= 0.278 Chirality : 0.041 0.122 1875 Planarity : 0.005 0.041 1815 Dihedral : 8.415 58.512 1831 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.45 % Allowed : 10.91 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.69 (0.22), residues: 1400 helix: 2.50 (0.16), residues: 1035 sheet: None (None), residues: 0 loop : -0.36 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 44 TYR 0.012 0.002 TYR B 69 PHE 0.019 0.002 PHE C 160 TRP 0.010 0.001 TRP B 163 HIS 0.011 0.003 HIS E 194 Details of bonding type rmsd covalent geometry : bond 0.00315 (11198) covalent geometry : angle 0.53746 (15212) hydrogen bonds : bond 0.04259 ( 838) hydrogen bonds : angle 3.81158 ( 2439) Misc. bond : bond 0.00021 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 109 time to evaluate : 0.579 Fit side-chains REVERT: B 162 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7464 (tp) REVERT: D 162 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7501 (tp) REVERT: E 162 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7410 (tp) outliers start: 49 outliers final: 34 residues processed: 138 average time/residue: 0.5802 time to fit residues: 86.2784 Evaluate side-chains 145 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 108 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 249 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 24 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 chunk 131 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 HIS B 194 HIS C 194 HIS D 194 HIS E 194 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.121280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.101666 restraints weight = 10319.647| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.53 r_work: 0.3023 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11203 Z= 0.137 Angle : 0.537 7.603 15212 Z= 0.277 Chirality : 0.041 0.124 1875 Planarity : 0.005 0.040 1815 Dihedral : 8.358 58.081 1831 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.36 % Allowed : 11.27 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.69 (0.22), residues: 1400 helix: 2.50 (0.16), residues: 1035 sheet: None (None), residues: 0 loop : -0.35 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 44 TYR 0.013 0.002 TYR A 69 PHE 0.019 0.002 PHE C 160 TRP 0.012 0.001 TRP A 163 HIS 0.011 0.003 HIS E 194 Details of bonding type rmsd covalent geometry : bond 0.00316 (11198) covalent geometry : angle 0.53688 (15212) hydrogen bonds : bond 0.04280 ( 838) hydrogen bonds : angle 3.80242 ( 2439) Misc. bond : bond 0.00023 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 106 time to evaluate : 0.444 Fit side-chains REVERT: B 162 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7470 (tp) REVERT: D 162 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7499 (tp) REVERT: D 209 VAL cc_start: 0.7767 (OUTLIER) cc_final: 0.7492 (p) REVERT: E 162 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7411 (tp) outliers start: 48 outliers final: 35 residues processed: 137 average time/residue: 0.6012 time to fit residues: 88.7703 Evaluate side-chains 145 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 106 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 249 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 52 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 106 optimal weight: 0.5980 chunk 103 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 HIS B 194 HIS C 194 HIS D 194 HIS E 194 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.121934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.102297 restraints weight = 10340.534| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.53 r_work: 0.3032 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11203 Z= 0.130 Angle : 0.527 7.621 15212 Z= 0.271 Chirality : 0.040 0.122 1875 Planarity : 0.005 0.040 1815 Dihedral : 8.151 59.023 1831 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.00 % Allowed : 11.73 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.80 (0.22), residues: 1400 helix: 2.55 (0.16), residues: 1040 sheet: None (None), residues: 0 loop : -0.25 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 44 TYR 0.012 0.002 TYR B 69 PHE 0.018 0.002 PHE D 160 TRP 0.011 0.001 TRP A 163 HIS 0.011 0.003 HIS D 194 Details of bonding type rmsd covalent geometry : bond 0.00296 (11198) covalent geometry : angle 0.52686 (15212) hydrogen bonds : bond 0.04135 ( 838) hydrogen bonds : angle 3.75958 ( 2439) Misc. bond : bond 0.00022 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 107 time to evaluate : 0.314 Fit side-chains REVERT: A 209 VAL cc_start: 0.7639 (OUTLIER) cc_final: 0.7325 (p) REVERT: B 162 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7405 (tp) REVERT: D 162 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7497 (tp) REVERT: D 209 VAL cc_start: 0.7733 (OUTLIER) cc_final: 0.7472 (p) REVERT: E 162 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7400 (tp) outliers start: 44 outliers final: 32 residues processed: 137 average time/residue: 0.5492 time to fit residues: 80.8492 Evaluate side-chains 144 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 107 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 249 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 88 optimal weight: 2.9990 chunk 82 optimal weight: 0.3980 chunk 17 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 HIS B 194 HIS C 194 HIS D 194 HIS E 194 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.121664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.102077 restraints weight = 10217.138| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.52 r_work: 0.3029 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11203 Z= 0.134 Angle : 0.534 8.210 15212 Z= 0.274 Chirality : 0.041 0.123 1875 Planarity : 0.004 0.040 1815 Dihedral : 8.134 59.530 1829 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.27 % Allowed : 11.27 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.79 (0.22), residues: 1400 helix: 2.53 (0.16), residues: 1040 sheet: None (None), residues: 0 loop : -0.24 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 44 TYR 0.012 0.002 TYR A 69 PHE 0.019 0.002 PHE C 160 TRP 0.011 0.001 TRP A 163 HIS 0.012 0.003 HIS D 194 Details of bonding type rmsd covalent geometry : bond 0.00307 (11198) covalent geometry : angle 0.53375 (15212) hydrogen bonds : bond 0.04213 ( 838) hydrogen bonds : angle 3.76484 ( 2439) Misc. bond : bond 0.00024 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 107 time to evaluate : 0.406 Fit side-chains REVERT: B 162 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7391 (tp) REVERT: C 71 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7378 (mt) REVERT: D 162 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7504 (tp) REVERT: D 209 VAL cc_start: 0.7749 (OUTLIER) cc_final: 0.7480 (p) REVERT: E 162 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7404 (tp) outliers start: 47 outliers final: 34 residues processed: 138 average time/residue: 0.5947 time to fit residues: 88.3296 Evaluate side-chains 146 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 107 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 196 MET Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 249 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 46 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 106 optimal weight: 0.5980 chunk 83 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 127 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 HIS B 194 HIS C 194 HIS D 194 HIS E 194 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.121803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.102527 restraints weight = 10428.811| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.51 r_work: 0.3038 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11203 Z= 0.127 Angle : 0.526 8.446 15212 Z= 0.269 Chirality : 0.040 0.122 1875 Planarity : 0.004 0.040 1815 Dihedral : 7.970 59.988 1829 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.00 % Allowed : 11.64 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.83 (0.22), residues: 1400 helix: 2.53 (0.16), residues: 1045 sheet: None (None), residues: 0 loop : -0.15 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 44 TYR 0.012 0.002 TYR A 69 PHE 0.018 0.002 PHE D 160 TRP 0.011 0.001 TRP A 163 HIS 0.012 0.003 HIS D 194 Details of bonding type rmsd covalent geometry : bond 0.00288 (11198) covalent geometry : angle 0.52588 (15212) hydrogen bonds : bond 0.04080 ( 838) hydrogen bonds : angle 3.73536 ( 2439) Misc. bond : bond 0.00021 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 108 time to evaluate : 0.373 Fit side-chains REVERT: A 209 VAL cc_start: 0.7641 (OUTLIER) cc_final: 0.7338 (p) REVERT: B 162 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7410 (tp) REVERT: D 162 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7508 (tp) REVERT: D 209 VAL cc_start: 0.7761 (OUTLIER) cc_final: 0.7490 (p) REVERT: E 162 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7431 (tp) outliers start: 44 outliers final: 31 residues processed: 138 average time/residue: 0.5458 time to fit residues: 80.9446 Evaluate side-chains 143 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 107 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 196 MET Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 249 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 HIS B 194 HIS C 194 HIS D 194 HIS E 194 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.120294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.100845 restraints weight = 10397.588| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.51 r_work: 0.3012 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11203 Z= 0.162 Angle : 0.567 8.575 15212 Z= 0.291 Chirality : 0.042 0.127 1875 Planarity : 0.005 0.040 1815 Dihedral : 8.399 59.974 1827 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.91 % Allowed : 11.64 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.60 (0.22), residues: 1400 helix: 2.41 (0.16), residues: 1035 sheet: None (None), residues: 0 loop : -0.31 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 44 TYR 0.014 0.002 TYR B 69 PHE 0.020 0.002 PHE C 160 TRP 0.012 0.002 TRP A 163 HIS 0.012 0.003 HIS B 194 Details of bonding type rmsd covalent geometry : bond 0.00386 (11198) covalent geometry : angle 0.56702 (15212) hydrogen bonds : bond 0.04593 ( 838) hydrogen bonds : angle 3.83297 ( 2439) Misc. bond : bond 0.00041 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3292.88 seconds wall clock time: 56 minutes 51.99 seconds (3411.99 seconds total)