Starting phenix.real_space_refine on Tue Jun 10 00:06:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r0p_18800/06_2025/8r0p_18800.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r0p_18800/06_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_18800/06_2025/8r0p_18800.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r0p_18800/06_2025/8r0p_18800.map" model { file = "/net/cci-nas-00/data/ceres_data/8r0p_18800/06_2025/8r0p_18800.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r0p_18800/06_2025/8r0p_18800.cif" } resolution = 2.44 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.048 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'ASP: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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'ASP: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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'ASP: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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'ASP: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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'ASP: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: 7.86, per 1000 atoms: 0.70 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: 2.89 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.06 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: 3.63 Time building geometry restraints manager: 3.42 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 286 or resid 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 na \ me C16 or name C17 or name C18 or name C19 or name C20)) or resid 408)) selection = (chain 'B' and (resid 5 through 286 or resid 401 or (resid 402 and (name C10 or \ name C11)) or resid 404 or resid 408)) selection = (chain 'C' and (resid 5 through 286 or resid 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 286 or resid 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 286 or resid 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 na \ me C16 or name 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: 2.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 29.050 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 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:15.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.850 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (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 TRP 0.035 0.008 TRP A 273 HIS 0.020 0.007 HIS C 19 PHE 0.054 0.010 PHE B 220 TYR 0.051 0.012 TYR E 24 ARG 0.028 0.004 ARG E 100 Details of bonding type rmsd hydrogen bonds : bond 0.18290 ( 838) hydrogen bonds : angle 7.73038 ( 2439) covalent geometry : bond 0.01204 (11198) covalent geometry : angle 1.74734 (15212) 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 : 1.217 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: 1.1041 time to fit residues: 207.7002 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 : 1.162 ------------------------------------------------------------------------------- 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 118 optimal weight: 0.9980 chunk 106 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 109 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 127 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN ** A 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 ASN C 90 ASN C 153 ASN ** C 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 5 ASN ** D 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 153 ASN ** E 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.121472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.101882 restraints weight = 10029.792| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.48 r_work: 0.3022 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11203 Z= 0.144 Angle : 0.610 8.621 15212 Z= 0.316 Chirality : 0.041 0.123 1875 Planarity : 0.005 0.050 1815 Dihedral : 9.717 58.916 1866 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.64 % Allowed : 9.18 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.21), residues: 1400 helix: 1.20 (0.15), residues: 1025 sheet: None (None), residues: 0 loop : -0.93 (0.28), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 163 HIS 0.010 0.003 HIS E 194 PHE 0.026 0.002 PHE B 160 TYR 0.012 0.002 TYR B 69 ARG 0.003 0.000 ARG B 100 Details of bonding type rmsd hydrogen bonds : bond 0.04723 ( 838) hydrogen bonds : angle 4.09312 ( 2439) covalent geometry : bond 0.00317 (11198) covalent geometry : angle 0.61011 (15212) Misc. bond : bond 0.00002 ( 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 164 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 124 time to evaluate : 1.111 Fit side-chains REVERT: A 39 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.6795 (ttt-90) REVERT: A 61 MET cc_start: 0.8073 (ttm) cc_final: 0.7399 (ttp) REVERT: A 111 LEU cc_start: 0.7749 (tt) cc_final: 0.6747 (mt) REVERT: B 39 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.6699 (ttt-90) REVERT: D 61 MET cc_start: 0.7929 (ttm) cc_final: 0.7555 (ttm) REVERT: E 5 ASN cc_start: 0.5822 (OUTLIER) cc_final: 0.5534 (t0) REVERT: E 114 GLU cc_start: 0.7870 (tt0) cc_final: 0.7424 (tt0) REVERT: E 162 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7387 (tp) outliers start: 40 outliers final: 22 residues processed: 154 average time/residue: 1.2162 time to fit residues: 202.4502 Evaluate side-chains 137 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 1.215 ------------------------------------------------------------------------------- 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 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 12 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 120 optimal weight: 0.0970 chunk 122 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 HIS D 194 HIS E 20 GLN E 194 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.120427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.100814 restraints weight = 10326.803| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.52 r_work: 0.3012 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11203 Z= 0.147 Angle : 0.573 7.774 15212 Z= 0.296 Chirality : 0.041 0.124 1875 Planarity : 0.004 0.044 1815 Dihedral : 9.053 55.780 1832 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.64 % Allowed : 11.27 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.22), residues: 1400 helix: 2.16 (0.16), residues: 1030 sheet: None (None), residues: 0 loop : -0.54 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 163 HIS 0.011 0.003 HIS E 194 PHE 0.022 0.002 PHE C 160 TYR 0.013 0.002 TYR A 69 ARG 0.008 0.001 ARG D 44 Details of bonding type rmsd hydrogen bonds : bond 0.04555 ( 838) hydrogen bonds : angle 3.90492 ( 2439) covalent geometry : bond 0.00340 (11198) covalent geometry : angle 0.57324 (15212) Misc. bond : bond 0.00016 ( 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 151 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 111 time to evaluate : 1.113 Fit side-chains REVERT: A 39 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7819 (tmm160) REVERT: A 270 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7693 (pt0) REVERT: B 5 ASN cc_start: 0.5966 (OUTLIER) cc_final: 0.5698 (t0) REVERT: B 249 THR cc_start: 0.7977 (OUTLIER) cc_final: 0.7720 (m) REVERT: C 256 ARG cc_start: 0.8148 (mmm160) cc_final: 0.7896 (mmm160) REVERT: D 61 MET cc_start: 0.7983 (ttm) cc_final: 0.7558 (ttm) REVERT: D 162 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7492 (tp) REVERT: E 5 ASN cc_start: 0.5831 (OUTLIER) cc_final: 0.5616 (t0) REVERT: E 114 GLU cc_start: 0.7822 (tt0) cc_final: 0.7442 (tt0) REVERT: E 162 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7322 (tp) outliers start: 40 outliers final: 25 residues processed: 138 average time/residue: 1.4656 time to fit residues: 217.6256 Evaluate side-chains 138 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 106 time to evaluate : 1.250 ------------------------------------------------------------------------------- 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 A residue 270 GLU Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 71 LEU 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 13 THR 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 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 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 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 46 optimal weight: 0.7980 chunk 55 optimal weight: 0.0370 chunk 60 optimal weight: 0.0070 chunk 35 optimal weight: 4.9990 chunk 71 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 111 optimal weight: 0.0040 chunk 1 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 overall best weight: 0.2888 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.125577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.106398 restraints weight = 10250.908| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.49 r_work: 0.3095 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11203 Z= 0.100 Angle : 0.493 6.854 15212 Z= 0.252 Chirality : 0.039 0.121 1875 Planarity : 0.004 0.039 1815 Dihedral : 7.649 57.645 1832 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.00 % Allowed : 11.91 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.96 (0.22), residues: 1400 helix: 2.66 (0.16), residues: 1040 sheet: None (None), residues: 0 loop : -0.20 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 163 HIS 0.011 0.002 HIS C 194 PHE 0.017 0.001 PHE D 160 TYR 0.008 0.001 TYR D 69 ARG 0.008 0.000 ARG C 44 Details of bonding type rmsd hydrogen bonds : bond 0.03491 ( 838) hydrogen bonds : angle 3.65862 ( 2439) covalent geometry : bond 0.00207 (11198) covalent geometry : angle 0.49349 (15212) Misc. bond : bond 0.00007 ( 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 155 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 1.235 Fit side-chains REVERT: A 71 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7547 (mt) REVERT: A 209 VAL cc_start: 0.7433 (OUTLIER) cc_final: 0.7171 (p) REVERT: A 249 THR cc_start: 0.7950 (OUTLIER) cc_final: 0.7640 (m) REVERT: B 114 GLU cc_start: 0.7553 (tt0) cc_final: 0.7124 (tt0) REVERT: B 249 THR cc_start: 0.7988 (OUTLIER) cc_final: 0.7638 (m) REVERT: D 61 MET cc_start: 0.7954 (ttm) cc_final: 0.7509 (ttm) REVERT: E 71 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7446 (mt) REVERT: E 114 GLU cc_start: 0.7725 (tt0) cc_final: 0.7349 (tt0) REVERT: E 162 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7442 (tp) outliers start: 33 outliers final: 17 residues processed: 144 average time/residue: 1.4648 time to fit residues: 225.6475 Evaluate side-chains 144 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 71 LEU 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 42 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 249 THR 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 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 196 MET Chi-restraints excluded: chain E residue 226 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 24 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 131 optimal weight: 0.6980 chunk 138 optimal weight: 0.2980 chunk 73 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 129 ASN B 194 HIS C 194 HIS D 194 HIS E 194 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.122189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.102572 restraints weight = 10221.361| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.52 r_work: 0.3038 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2276 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 : 0.524 5.163 15212 Z= 0.271 Chirality : 0.041 0.125 1875 Planarity : 0.004 0.038 1815 Dihedral : 7.929 59.701 1824 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 4.18 % Allowed : 10.36 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.88 (0.22), residues: 1400 helix: 2.60 (0.16), residues: 1040 sheet: None (None), residues: 0 loop : -0.21 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 163 HIS 0.011 0.003 HIS E 194 PHE 0.019 0.002 PHE C 160 TYR 0.013 0.002 TYR B 69 ARG 0.009 0.001 ARG C 44 Details of bonding type rmsd hydrogen bonds : bond 0.04160 ( 838) hydrogen bonds : angle 3.77906 ( 2439) covalent geometry : bond 0.00298 (11198) covalent geometry : angle 0.52354 (15212) Misc. bond : bond 0.00009 ( 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 161 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 115 time to evaluate : 1.131 Fit side-chains REVERT: A 209 VAL cc_start: 0.7626 (OUTLIER) cc_final: 0.7345 (p) REVERT: A 243 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7588 (tm) REVERT: B 162 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7447 (tp) REVERT: B 249 THR cc_start: 0.7964 (OUTLIER) cc_final: 0.7718 (m) REVERT: D 61 MET cc_start: 0.7963 (ttm) cc_final: 0.7547 (ttm) REVERT: E 114 GLU cc_start: 0.7772 (tt0) cc_final: 0.7458 (tt0) REVERT: E 162 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7396 (tp) REVERT: E 209 VAL cc_start: 0.7490 (OUTLIER) cc_final: 0.7236 (p) outliers start: 46 outliers final: 21 residues processed: 139 average time/residue: 1.3480 time to fit residues: 201.4950 Evaluate side-chains 142 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 1.421 ------------------------------------------------------------------------------- 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 162 LEU Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 249 THR 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 188 THR 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 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 249 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 0.4980 chunk 69 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 131 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 HIS 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 = 0.3389 r_free = 0.3389 target = 0.121969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.102305 restraints weight = 10270.063| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.53 r_work: 0.3032 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11203 Z= 0.132 Angle : 0.526 5.162 15212 Z= 0.272 Chirality : 0.041 0.123 1875 Planarity : 0.004 0.039 1815 Dihedral : 8.016 59.429 1824 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.00 % Allowed : 10.64 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.87 (0.22), residues: 1400 helix: 2.59 (0.16), residues: 1040 sheet: None (None), residues: 0 loop : -0.20 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 163 HIS 0.011 0.003 HIS E 194 PHE 0.019 0.002 PHE B 160 TYR 0.012 0.002 TYR B 69 ARG 0.009 0.001 ARG C 44 Details of bonding type rmsd hydrogen bonds : bond 0.04175 ( 838) hydrogen bonds : angle 3.78041 ( 2439) covalent geometry : bond 0.00301 (11198) covalent geometry : angle 0.52620 (15212) Misc. bond : bond 0.00015 ( 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 154 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 110 time to evaluate : 1.109 Fit side-chains REVERT: A 209 VAL cc_start: 0.7642 (OUTLIER) cc_final: 0.7334 (p) REVERT: A 243 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7604 (tm) REVERT: B 162 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7449 (tp) REVERT: B 249 THR cc_start: 0.7919 (OUTLIER) cc_final: 0.7649 (m) REVERT: D 162 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7483 (tp) REVERT: E 114 GLU cc_start: 0.7782 (tt0) cc_final: 0.7365 (tt0) REVERT: E 162 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7395 (tp) outliers start: 44 outliers final: 25 residues processed: 136 average time/residue: 1.3661 time to fit residues: 200.2988 Evaluate side-chains 141 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 110 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 249 THR Chi-restraints excluded: chain B residue 270 GLU 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 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 249 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 105 optimal weight: 0.0770 chunk 25 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 74 optimal weight: 0.2980 chunk 40 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 77 optimal weight: 0.2980 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.124710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.105029 restraints weight = 10337.883| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.54 r_work: 0.3070 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11203 Z= 0.105 Angle : 0.492 5.420 15212 Z= 0.252 Chirality : 0.039 0.127 1875 Planarity : 0.004 0.038 1815 Dihedral : 7.425 59.595 1824 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.82 % Allowed : 11.00 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.19 (0.22), residues: 1400 helix: 2.95 (0.16), residues: 1020 sheet: None (None), residues: 0 loop : -0.32 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 163 HIS 0.011 0.002 HIS E 194 PHE 0.018 0.001 PHE D 160 TYR 0.010 0.001 TYR B 24 ARG 0.009 0.000 ARG C 44 Details of bonding type rmsd hydrogen bonds : bond 0.03656 ( 838) hydrogen bonds : angle 3.65817 ( 2439) covalent geometry : bond 0.00223 (11198) covalent geometry : angle 0.49186 (15212) Misc. bond : bond 0.00004 ( 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 159 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 117 time to evaluate : 1.211 Fit side-chains REVERT: A 209 VAL cc_start: 0.7555 (OUTLIER) cc_final: 0.7272 (p) REVERT: A 243 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7560 (tm) REVERT: B 162 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7351 (tp) REVERT: B 249 THR cc_start: 0.7908 (OUTLIER) cc_final: 0.7637 (m) REVERT: C 209 VAL cc_start: 0.7336 (OUTLIER) cc_final: 0.7111 (p) REVERT: E 114 GLU cc_start: 0.7781 (tt0) cc_final: 0.7385 (tt0) REVERT: E 162 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7446 (tp) REVERT: E 209 VAL cc_start: 0.7397 (OUTLIER) cc_final: 0.7135 (p) outliers start: 42 outliers final: 21 residues processed: 141 average time/residue: 1.4412 time to fit residues: 217.9983 Evaluate side-chains 138 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 226 LEU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 249 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 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 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 249 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 29 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 HIS 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 = 0.3383 r_free = 0.3383 target = 0.121470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.101796 restraints weight = 10333.222| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.53 r_work: 0.3026 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2302 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= 0.142 Angle : 0.539 5.436 15212 Z= 0.277 Chirality : 0.041 0.126 1875 Planarity : 0.005 0.045 1815 Dihedral : 7.949 59.792 1822 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.73 % Allowed : 11.00 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.88 (0.22), residues: 1400 helix: 2.63 (0.16), residues: 1035 sheet: None (None), residues: 0 loop : -0.25 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 163 HIS 0.011 0.003 HIS C 194 PHE 0.020 0.002 PHE A 160 TYR 0.013 0.002 TYR B 69 ARG 0.010 0.001 ARG C 44 Details of bonding type rmsd hydrogen bonds : bond 0.04324 ( 838) hydrogen bonds : angle 3.77550 ( 2439) covalent geometry : bond 0.00331 (11198) covalent geometry : angle 0.53865 (15212) Misc. bond : bond 0.00026 ( 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 147 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 106 time to evaluate : 1.222 Fit side-chains REVERT: A 209 VAL cc_start: 0.7716 (OUTLIER) cc_final: 0.7401 (p) REVERT: A 243 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7622 (tm) REVERT: B 162 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7445 (tp) REVERT: B 249 THR cc_start: 0.7889 (OUTLIER) cc_final: 0.7628 (m) REVERT: D 162 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7475 (tp) REVERT: E 114 GLU cc_start: 0.7821 (tt0) cc_final: 0.7429 (tt0) REVERT: E 162 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7405 (tp) outliers start: 41 outliers final: 24 residues processed: 132 average time/residue: 1.2898 time to fit residues: 184.0589 Evaluate side-chains 135 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 188 THR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 226 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 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 249 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.6196 > 50: distance: 62 - 65: 8.220 distance: 65 - 66: 22.367 distance: 66 - 67: 7.617 distance: 67 - 68: 12.328 distance: 67 - 69: 20.582 distance: 69 - 70: 3.929 distance: 70 - 71: 11.667 distance: 70 - 73: 5.019 distance: 71 - 72: 17.310 distance: 71 - 77: 3.539 distance: 74 - 75: 3.981 distance: 74 - 76: 3.788 distance: 77 - 78: 8.637 distance: 78 - 79: 8.212 distance: 78 - 81: 8.828 distance: 79 - 80: 15.935 distance: 79 - 85: 10.080 distance: 82 - 83: 3.179 distance: 82 - 84: 9.658 distance: 85 - 86: 8.263 distance: 86 - 87: 9.273 distance: 86 - 89: 14.119 distance: 87 - 88: 28.448 distance: 87 - 92: 15.347 distance: 89 - 90: 25.680 distance: 89 - 91: 8.049 distance: 92 - 93: 6.381 distance: 93 - 94: 9.530 distance: 93 - 96: 10.073 distance: 94 - 95: 21.842 distance: 94 - 102: 29.706 distance: 96 - 97: 15.556 distance: 97 - 98: 14.040 distance: 97 - 99: 11.390 distance: 98 - 100: 14.572 distance: 99 - 101: 13.486 distance: 100 - 101: 10.820 distance: 102 - 103: 7.413 distance: 102 - 108: 8.658 distance: 103 - 104: 20.312 distance: 103 - 106: 30.313 distance: 104 - 105: 19.084 distance: 104 - 109: 16.260 distance: 106 - 107: 8.943 distance: 107 - 108: 29.147 distance: 109 - 110: 3.849 distance: 110 - 111: 13.801 distance: 110 - 113: 13.519 distance: 111 - 112: 12.116 distance: 111 - 118: 4.386 distance: 113 - 114: 25.832 distance: 114 - 115: 12.873 distance: 115 - 116: 11.588 distance: 115 - 117: 9.364 distance: 118 - 119: 10.299 distance: 119 - 120: 9.755 distance: 119 - 122: 13.025 distance: 120 - 121: 9.932 distance: 120 - 124: 9.266 distance: 122 - 123: 20.306 distance: 124 - 125: 11.280 distance: 125 - 126: 13.212 distance: 125 - 128: 13.309 distance: 126 - 127: 14.751 distance: 126 - 132: 11.009 distance: 127 - 172: 21.289 distance: 128 - 129: 7.103 distance: 128 - 130: 16.554 distance: 129 - 131: 18.853 distance: 132 - 133: 11.412 distance: 133 - 134: 9.818 distance: 133 - 136: 6.142 distance: 134 - 135: 15.151 distance: 134 - 146: 7.432 distance: 138 - 140: 5.272 distance: 139 - 141: 4.619 distance: 144 - 145: 4.657