Starting phenix.real_space_refine on Sun Aug 24 19:05:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8znr_60279/08_2025/8znr_60279_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8znr_60279/08_2025/8znr_60279.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8znr_60279/08_2025/8znr_60279_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8znr_60279/08_2025/8znr_60279_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8znr_60279/08_2025/8znr_60279.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8znr_60279/08_2025/8znr_60279.map" } resolution = 2.9 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= 0.002 sd= 0.033 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: 5 Type Number sf(0) Gaussians P 91 5.49 5 S 111 5.16 5 C 14086 2.51 5 N 3777 2.21 5 O 4540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 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: 22605 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2628 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 15, 'TRANS': 309} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2592 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 2621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2621 Classifications: {'peptide': 324} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 15, 'TRANS': 308} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2592 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1972 Classifications: {'peptide': 255} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 8, 'TRANS': 246} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 2235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2235 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 16, 'TRANS': 281} Chain breaks: 3 Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 4, 'HIS:plan': 1, 'GLU:plan': 8, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 74 Chain: "G" Number of atoms: 2593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2593 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 304} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "H" Number of atoms: 2368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2368 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 11, 'TRANS': 280} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 710 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain: "L" Number of atoms: 1203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1203 Classifications: {'RNA': 56} Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 11, 'rna3p_pur': 17, 'rna3p_pyr': 13} Link IDs: {'rna2p': 25, 'rna3p': 30} Chain breaks: 1 Chain: "M" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1091 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 5, 'TRANS': 149} Chain breaks: 3 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 160 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 4, 'HIS:plan': 4, 'GLU:plan': 1, 'TYR:plan': 3, 'GLN:plan1': 4} Unresolved non-hydrogen planarities: 85 Time building chain proxies: 4.10, per 1000 atoms: 0.18 Number of scatterers: 22605 At special positions: 0 Unit cell: (108.272, 144.632, 154.328, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 111 16.00 P 91 15.00 O 4540 8.00 N 3777 7.00 C 14086 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.51 Conformation dependent library (CDL) restraints added in 749.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 5134 Ramachandran restraints generated. 2567 Oldfield, 0 Emsley, 2567 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4968 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 36 sheets defined 27.8% alpha, 9.2% beta 19 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 2.49 Creating SS restraints... Processing helix chain 'A' and resid 63 through 71 removed outlier: 3.897A pdb=" N GLU A 68 " --> pdb=" O PRO A 64 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS A 69 " --> pdb=" O ASP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 106 removed outlier: 3.927A pdb=" N MET A 106 " --> pdb=" O LYS A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 128 removed outlier: 3.502A pdb=" N ARG A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 144 removed outlier: 3.580A pdb=" N ALA A 135 " --> pdb=" O PHE A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 201 removed outlier: 3.739A pdb=" N GLN A 195 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 259 removed outlier: 3.581A pdb=" N ILE A 254 " --> pdb=" O HIS A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 312 through 326 Processing helix chain 'B' and resid 36 through 40 removed outlier: 3.580A pdb=" N ARG B 40 " --> pdb=" O PHE B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 68 removed outlier: 3.960A pdb=" N GLU B 68 " --> pdb=" O PRO B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 104 No H-bonds generated for 'chain 'B' and resid 102 through 104' Processing helix chain 'B' and resid 111 through 129 removed outlier: 3.570A pdb=" N ARG B 115 " --> pdb=" O ASP B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 144 removed outlier: 3.588A pdb=" N ALA B 135 " --> pdb=" O PHE B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 186 through 202 removed outlier: 3.580A pdb=" N GLN B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 259 Processing helix chain 'B' and resid 296 through 302 Processing helix chain 'B' and resid 312 through 326 Processing helix chain 'C' and resid 63 through 71 removed outlier: 3.879A pdb=" N GLU C 68 " --> pdb=" O PRO C 64 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS C 69 " --> pdb=" O ASP C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 106 removed outlier: 3.736A pdb=" N SER C 105 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N MET C 106 " --> pdb=" O LYS C 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 102 through 106' Processing helix chain 'C' and resid 111 through 129 Processing helix chain 'C' and resid 131 through 144 Processing helix chain 'C' and resid 186 through 202 removed outlier: 3.710A pdb=" N GLN C 194 " --> pdb=" O ASN C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 259 Processing helix chain 'C' and resid 296 through 302 Processing helix chain 'C' and resid 312 through 326 Processing helix chain 'D' and resid 63 through 70 removed outlier: 3.854A pdb=" N LYS D 69 " --> pdb=" O ASP D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 129 Processing helix chain 'D' and resid 131 through 144 removed outlier: 3.655A pdb=" N ALA D 135 " --> pdb=" O PHE D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 186 through 202 removed outlier: 3.829A pdb=" N GLN D 194 " --> pdb=" O ASN D 190 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN D 195 " --> pdb=" O GLU D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 260 removed outlier: 3.523A pdb=" N THR D 260 " --> pdb=" O ASN D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 302 Processing helix chain 'D' and resid 312 through 326 Processing helix chain 'E' and resid 27 through 43 removed outlier: 3.713A pdb=" N PHE E 31 " --> pdb=" O ALA E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 126 removed outlier: 3.603A pdb=" N CYS E 121 " --> pdb=" O ASP E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 168 Processing helix chain 'E' and resid 173 through 185 Processing helix chain 'F' and resid 102 through 106 Processing helix chain 'F' and resid 166 through 179 removed outlier: 3.671A pdb=" N ASN F 170 " --> pdb=" O SER F 166 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG F 179 " --> pdb=" O ASP F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 199 removed outlier: 3.932A pdb=" N GLY F 199 " --> pdb=" O ALA F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 217 through 221 Processing helix chain 'F' and resid 238 through 242 removed outlier: 3.637A pdb=" N LEU F 242 " --> pdb=" O ILE F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 266 removed outlier: 4.015A pdb=" N LEU F 258 " --> pdb=" O ALA F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 277 Processing helix chain 'F' and resid 282 through 291 Processing helix chain 'F' and resid 325 through 335 Processing helix chain 'G' and resid 39 through 43 removed outlier: 3.794A pdb=" N PHE G 43 " --> pdb=" O ARG G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 70 removed outlier: 3.697A pdb=" N LYS G 69 " --> pdb=" O LYS G 66 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU G 70 " --> pdb=" O LEU G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 129 Processing helix chain 'G' and resid 131 through 144 removed outlier: 3.516A pdb=" N ALA G 135 " --> pdb=" O PHE G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 186 through 201 Processing helix chain 'G' and resid 250 through 259 Processing helix chain 'G' and resid 296 through 305 Processing helix chain 'G' and resid 312 through 326 Processing helix chain 'H' and resid 36 through 43 removed outlier: 3.774A pdb=" N ARG H 40 " --> pdb=" O PHE H 37 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N HIS H 41 " --> pdb=" O LEU H 38 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE H 43 " --> pdb=" O ARG H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 129 Processing helix chain 'H' and resid 131 through 144 Processing helix chain 'H' and resid 186 through 202 Processing helix chain 'H' and resid 250 through 259 removed outlier: 3.549A pdb=" N ILE H 254 " --> pdb=" O HIS H 250 " (cutoff:3.500A) Processing helix chain 'H' and resid 300 through 305 Processing helix chain 'H' and resid 312 through 326 removed outlier: 4.004A pdb=" N TYR H 318 " --> pdb=" O GLU H 314 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ILE H 324 " --> pdb=" O MET H 320 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG H 325 " --> pdb=" O ALA H 321 " (cutoff:3.500A) Processing helix chain 'M' and resid 15 through 23 Processing helix chain 'M' and resid 23 through 33 removed outlier: 3.551A pdb=" N VAL M 27 " --> pdb=" O ASP M 23 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL M 33 " --> pdb=" O HIS M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 71 Processing helix chain 'M' and resid 130 through 139 removed outlier: 3.763A pdb=" N LYS M 134 " --> pdb=" O HIS M 130 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N GLN M 137 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ILE M 138 " --> pdb=" O LYS M 134 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE M 139 " --> pdb=" O ASN M 135 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 removed outlier: 4.009A pdb=" N SER A 108 " --> pdb=" O SER A 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 25 through 27 current: chain 'A' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 45 through 46 current: chain 'A' and resid 167 through 168 No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 57 removed outlier: 4.109A pdb=" N CYS A 82 " --> pdb=" O VAL A 223 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 242 through 243 Processing sheet with id=AA5, first strand: chain 'A' and resid 260 through 262 Processing sheet with id=AA6, first strand: chain 'B' and resid 106 through 109 Processing sheet with id=AA7, first strand: chain 'B' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 25 through 27 current: chain 'B' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 45 through 46 current: chain 'B' and resid 167 through 168 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 167 through 168 current: chain 'B' and resid 246 through 249 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 50 through 51 Processing sheet with id=AA9, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AB1, first strand: chain 'B' and resid 260 through 262 Processing sheet with id=AB2, first strand: chain 'C' and resid 108 through 109 removed outlier: 3.804A pdb=" N SER C 108 " --> pdb=" O SER C 20 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 25 through 27 current: chain 'C' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 45 through 46 current: chain 'C' and resid 167 through 168 No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 50 through 57 removed outlier: 4.089A pdb=" N CYS C 82 " --> pdb=" O VAL C 223 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 242 through 243 Processing sheet with id=AB6, first strand: chain 'C' and resid 282 through 283 removed outlier: 3.846A pdb=" N ALA C 283 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE C 288 " --> pdb=" O ALA C 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 20 through 21 Processing sheet with id=AB8, first strand: chain 'D' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 25 through 27 current: chain 'D' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 45 through 46 current: chain 'D' and resid 172 through 173 No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 49 through 57 removed outlier: 3.554A pdb=" N ASN D 75 " --> pdb=" O ALA D 56 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N CYS D 82 " --> pdb=" O VAL D 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 242 through 243 Processing sheet with id=AC2, first strand: chain 'E' and resid 1 through 16 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 1 through 16 current: chain 'E' and resid 100 through 113 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 100 through 113 current: chain 'E' and resid 214 through 228 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 214 through 228 current: chain 'E' and resid 248 through 252 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 248 through 252 current: chain 'F' and resid 157 through 163 No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'E' and resid 22 through 24 Processing sheet with id=AC4, first strand: chain 'E' and resid 65 through 67 Processing sheet with id=AC5, first strand: chain 'F' and resid 35 through 37 Processing sheet with id=AC6, first strand: chain 'F' and resid 39 through 40 Processing sheet with id=AC7, first strand: chain 'F' and resid 245 through 246 removed outlier: 3.751A pdb=" N CYS F 249 " --> pdb=" O ASP F 246 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 301 through 304 removed outlier: 3.560A pdb=" N LEU F 323 " --> pdb=" O GLU F 302 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 106 through 108 removed outlier: 3.548A pdb=" N SER G 108 " --> pdb=" O SER G 20 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 25 through 27 current: chain 'G' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 45 through 46 current: chain 'G' and resid 167 through 168 No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'G' and resid 50 through 54 removed outlier: 4.151A pdb=" N CYS G 82 " --> pdb=" O VAL G 223 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 242 through 243 Processing sheet with id=AD4, first strand: chain 'G' and resid 282 through 283 removed outlier: 3.940A pdb=" N ALA G 283 " --> pdb=" O ILE G 288 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ILE G 288 " --> pdb=" O ALA G 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'H' and resid 106 through 109 removed outlier: 3.608A pdb=" N GLY H 327 " --> pdb=" O PHE H 21 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 25 through 27 current: chain 'H' and resid 90 through 99 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 90 through 99 current: chain 'H' and resid 167 through 168 No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'M' and resid 2 through 8 removed outlier: 3.626A pdb=" N VAL M 60 " --> pdb=" O GLN M 4 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'M' and resid 98 through 99 Processing sheet with id=AD9, first strand: chain 'M' and resid 143 through 144 518 hydrogen bonds defined for protein. 1446 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 50 hydrogen bonds 100 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 3.51 Time building geometry restraints manager: 1.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5232 1.33 - 1.45: 5582 1.45 - 1.58: 12102 1.58 - 1.70: 180 1.70 - 1.82: 176 Bond restraints: 23272 Sorted by residual: bond pdb=" C MET G 328 " pdb=" N PHE G 329 " ideal model delta sigma weight residual 1.332 1.208 0.125 1.40e-02 5.10e+03 7.94e+01 bond pdb=" C ILE M 20 " pdb=" N SER M 21 " ideal model delta sigma weight residual 1.334 1.435 -0.101 1.38e-02 5.25e+03 5.36e+01 bond pdb=" C GLY G 327 " pdb=" N MET G 328 " ideal model delta sigma weight residual 1.331 1.216 0.115 1.65e-02 3.67e+03 4.83e+01 bond pdb=" C SER D 251 " pdb=" N GLN D 252 " ideal model delta sigma weight residual 1.335 1.425 -0.090 1.38e-02 5.25e+03 4.22e+01 bond pdb=" C THR G 270 " pdb=" N TYR G 271 " ideal model delta sigma weight residual 1.331 1.435 -0.104 1.65e-02 3.67e+03 3.98e+01 ... (remaining 23267 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 30106 2.35 - 4.71: 1511 4.71 - 7.06: 231 7.06 - 9.42: 49 9.42 - 11.77: 9 Bond angle restraints: 31906 Sorted by residual: angle pdb=" N ILE F 132 " pdb=" CA ILE F 132 " pdb=" C ILE F 132 " ideal model delta sigma weight residual 112.17 104.66 7.51 9.50e-01 1.11e+00 6.26e+01 angle pdb=" C3' C L 50 " pdb=" O3' C L 50 " pdb=" P G L 51 " ideal model delta sigma weight residual 120.20 109.52 10.68 1.50e+00 4.44e-01 5.07e+01 angle pdb=" N ASP B 36 " pdb=" CA ASP B 36 " pdb=" C ASP B 36 " ideal model delta sigma weight residual 109.40 98.89 10.51 1.63e+00 3.76e-01 4.16e+01 angle pdb=" C3' G L 51 " pdb=" O3' G L 51 " pdb=" P G L 52 " ideal model delta sigma weight residual 120.20 110.96 9.24 1.50e+00 4.44e-01 3.80e+01 angle pdb=" N ILE G 261 " pdb=" CA ILE G 261 " pdb=" C ILE G 261 " ideal model delta sigma weight residual 113.10 107.27 5.83 9.70e-01 1.06e+00 3.61e+01 ... (remaining 31901 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.07: 13420 34.07 - 68.15: 572 68.15 - 102.22: 41 102.22 - 136.29: 0 136.29 - 170.36: 10 Dihedral angle restraints: 14043 sinusoidal: 6364 harmonic: 7679 Sorted by residual: dihedral pdb=" C5' G L 51 " pdb=" C4' G L 51 " pdb=" C3' G L 51 " pdb=" O3' G L 51 " ideal model delta sinusoidal sigma weight residual 82.00 138.25 -56.25 1 8.00e+00 1.56e-02 6.67e+01 dihedral pdb=" O4' C L 6 " pdb=" C1' C L 6 " pdb=" N1 C L 6 " pdb=" C2 C L 6 " ideal model delta sinusoidal sigma weight residual -128.00 42.36 -170.36 1 1.70e+01 3.46e-03 6.60e+01 dihedral pdb=" O4' C L 24 " pdb=" C1' C L 24 " pdb=" N1 C L 24 " pdb=" C2 C L 24 " ideal model delta sinusoidal sigma weight residual -128.00 37.26 -165.26 1 1.70e+01 3.46e-03 6.53e+01 ... (remaining 14040 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 3291 0.116 - 0.231: 263 0.231 - 0.347: 12 0.347 - 0.463: 15 0.463 - 0.578: 4 Chirality restraints: 3585 Sorted by residual: chirality pdb=" P U L 46 " pdb=" OP1 U L 46 " pdb=" OP2 U L 46 " pdb=" O5' U L 46 " both_signs ideal model delta sigma weight residual True 2.41 -2.99 -0.58 2.00e-01 2.50e+01 8.36e+00 chirality pdb=" P DT I -2 " pdb=" OP1 DT I -2 " pdb=" OP2 DT I -2 " pdb=" O5' DT I -2 " both_signs ideal model delta sigma weight residual True 2.35 -2.85 -0.50 2.00e-01 2.50e+01 6.32e+00 chirality pdb=" P DC I 5 " pdb=" OP1 DC I 5 " pdb=" OP2 DC I 5 " pdb=" O5' DC I 5 " both_signs ideal model delta sigma weight residual True 2.35 -2.81 -0.47 2.00e-01 2.50e+01 5.49e+00 ... (remaining 3582 not shown) Planarity restraints: 3777 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE F 31 " -0.021 2.00e-02 2.50e+03 4.18e-02 1.74e+01 pdb=" C ILE F 31 " 0.072 2.00e-02 2.50e+03 pdb=" O ILE F 31 " -0.027 2.00e-02 2.50e+03 pdb=" N ASP F 32 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE M 20 " -0.017 2.00e-02 2.50e+03 3.50e-02 1.22e+01 pdb=" C ILE M 20 " 0.060 2.00e-02 2.50e+03 pdb=" O ILE M 20 " -0.024 2.00e-02 2.50e+03 pdb=" N SER M 21 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 288 " 0.017 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" C ILE A 288 " -0.059 2.00e-02 2.50e+03 pdb=" O ILE A 288 " 0.022 2.00e-02 2.50e+03 pdb=" N PRO A 289 " 0.020 2.00e-02 2.50e+03 ... (remaining 3774 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2039 2.74 - 3.28: 20464 3.28 - 3.82: 37854 3.82 - 4.36: 48921 4.36 - 4.90: 79353 Nonbonded interactions: 188631 Sorted by model distance: nonbonded pdb=" O ILE E 235 " pdb=" N SER E 237 " model vdw 2.197 3.120 nonbonded pdb=" O LEU G 55 " pdb=" O2' A L 29 " model vdw 2.199 3.040 nonbonded pdb=" OH TYR D 265 " pdb=" O PHE D 273 " model vdw 2.229 3.040 nonbonded pdb=" OG1 THR G 35 " pdb=" OG1 THR G 90 " model vdw 2.239 3.040 nonbonded pdb=" O PHE D 21 " pdb=" O2' A L 15 " model vdw 2.265 3.040 ... (remaining 188626 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 12 through 37 or (resid 38 and (name N or name CA or name \ C or name O or name CB )) or resid 39 through 51 or resid 79 through 231 or resi \ d 237 or (resid 238 and (name N or name CA or name C or name O or name CB )) or \ resid 239 through 287 or (resid 288 and (name N or name CA or name C or name O o \ r name CB )) or resid 289 through 305 or (resid 306 through 307 and (name N or n \ ame CA or name C or name O or name CB )) or resid 308 through 332)) selection = (chain 'B' and (resid 12 through 37 or (resid 38 and (name N or name CA or name \ C or name O or name CB )) or resid 39 through 51 or resid 79 through 231 or resi \ d 237 or (resid 238 and (name N or name CA or name C or name O or name CB )) or \ resid 239 through 287 or (resid 288 and (name N or name CA or name C or name O o \ r name CB )) or resid 289 through 305 or (resid 306 through 307 and (name N or n \ ame CA or name C or name O or name CB )) or resid 308 through 332)) selection = (chain 'C' and (resid 12 through 37 or (resid 38 and (name N or name CA or name \ C or name O or name CB )) or resid 39 through 51 or resid 79 through 231 or resi \ d 237 or (resid 238 and (name N or name CA or name C or name O or name CB )) or \ resid 239 through 287 or (resid 288 and (name N or name CA or name C or name O o \ r name CB )) or resid 289 through 305 or (resid 306 through 307 and (name N or n \ ame CA or name C or name O or name CB )) or resid 308 through 332)) selection = (chain 'D' and (resid 12 through 37 or (resid 38 and (name N or name CA or name \ C or name O or name CB )) or resid 39 through 51 or resid 79 through 231 or resi \ d 237 or (resid 238 and (name N or name CA or name C or name O or name CB )) or \ resid 239 through 287 or (resid 288 and (name N or name CA or name C or name O o \ r name CB )) or resid 289 through 305 or (resid 306 through 307 and (name N or n \ ame CA or name C or name O or name CB )) or resid 308 through 332)) selection = (chain 'G' and (resid 12 or (resid 13 and (name N or name CA or name C or name O \ or name CB )) or resid 14 through 37 or (resid 38 and (name N or name CA or nam \ e C or name O or name CB )) or resid 39 through 51 or resid 79 through 231 or re \ sid 237 or (resid 238 and (name N or name CA or name C or name O or name CB )) o \ r resid 239 through 287 or (resid 288 and (name N or name CA or name C or name O \ or name CB )) or resid 289 through 305 or (resid 306 through 307 and (name N or \ name CA or name C or name O or name CB )) or resid 308 through 332)) selection = (chain 'H' and (resid 12 through 231 or resid 237 through 306 or (resid 307 and \ (name N or name CA or name C or name O or name CB )) or resid 308 through 332)) } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.030 Find NCS groups from input model: 0.390 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:9.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 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 : 0.007 0.125 23272 Z= 0.368 Angle : 1.172 11.770 31906 Z= 0.691 Chirality : 0.070 0.578 3585 Planarity : 0.010 0.096 3777 Dihedral : 18.216 170.363 9075 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.58 % Favored : 92.99 % Rotamer: Outliers : 1.40 % Allowed : 18.99 % Favored : 79.61 % 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: -3.03 (0.14), residues: 2567 helix: -2.02 (0.16), residues: 692 sheet: -0.21 (0.25), residues: 412 loop : -2.66 (0.13), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG E 162 TYR 0.039 0.003 TYR M 46 PHE 0.048 0.004 PHE H 37 TRP 0.042 0.003 TRP G 149 HIS 0.019 0.003 HIS E 203 Details of bonding type rmsd covalent geometry : bond 0.00677 (23272) covalent geometry : angle 1.17217 (31906) hydrogen bonds : bond 0.18841 ( 568) hydrogen bonds : angle 8.08238 ( 1546) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5134 Ramachandran restraints generated. 2567 Oldfield, 0 Emsley, 2567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5134 Ramachandran restraints generated. 2567 Oldfield, 0 Emsley, 2567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 770 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.7438 (m-30) cc_final: 0.7237 (m-30) REVERT: A 216 LYS cc_start: 0.8156 (tttt) cc_final: 0.7827 (tttp) REVERT: A 278 GLU cc_start: 0.7317 (mm-30) cc_final: 0.7094 (mm-30) REVERT: A 303 ARG cc_start: 0.8424 (mtp180) cc_final: 0.8223 (mtp180) REVERT: A 334 GLU cc_start: 0.7412 (mp0) cc_final: 0.7155 (mp0) REVERT: B 39 LYS cc_start: 0.8209 (mttt) cc_final: 0.7974 (mtpp) REVERT: B 72 MET cc_start: 0.7709 (mmm) cc_final: 0.7450 (mmm) REVERT: B 239 LYS cc_start: 0.8398 (mttt) cc_final: 0.8177 (mtmm) REVERT: B 262 ASP cc_start: 0.8428 (t0) cc_final: 0.8157 (t0) REVERT: B 278 GLU cc_start: 0.7157 (mt-10) cc_final: 0.6829 (mt-10) REVERT: B 303 ARG cc_start: 0.8172 (ttp80) cc_final: 0.7888 (ttp80) REVERT: B 331 LYS cc_start: 0.8401 (tptm) cc_final: 0.8197 (tptp) REVERT: C 52 LYS cc_start: 0.8359 (ttmt) cc_final: 0.8051 (ttpp) REVERT: C 166 ASP cc_start: 0.6931 (t0) cc_final: 0.6710 (t0) REVERT: C 183 VAL cc_start: 0.8854 (m) cc_final: 0.8599 (p) REVERT: C 184 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7359 (mm-30) REVERT: C 200 PHE cc_start: 0.8648 (m-10) cc_final: 0.8444 (m-10) REVERT: C 216 LYS cc_start: 0.7935 (tttt) cc_final: 0.7690 (ttpp) REVERT: C 224 TYR cc_start: 0.8445 (m-80) cc_final: 0.8091 (m-80) REVERT: C 262 ASP cc_start: 0.8424 (t0) cc_final: 0.7794 (t0) REVERT: C 303 ARG cc_start: 0.8282 (ttp80) cc_final: 0.7747 (ttt90) REVERT: D 66 LYS cc_start: 0.8505 (ttpt) cc_final: 0.8120 (ttmm) REVERT: D 69 LYS cc_start: 0.8609 (mtmt) cc_final: 0.8373 (mtmm) REVERT: D 172 PHE cc_start: 0.8419 (m-10) cc_final: 0.8080 (m-80) REVERT: D 204 ARG cc_start: 0.8243 (mtp85) cc_final: 0.7999 (mtp85) REVERT: D 222 GLU cc_start: 0.7611 (tt0) cc_final: 0.7371 (tt0) REVERT: D 228 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7300 (mt-10) REVERT: E 102 ASP cc_start: 0.7319 (t0) cc_final: 0.7102 (t0) REVERT: E 104 ASN cc_start: 0.7963 (t0) cc_final: 0.7737 (t160) REVERT: E 112 GLU cc_start: 0.6815 (mt-10) cc_final: 0.6575 (mt-10) REVERT: E 209 ASP cc_start: 0.7917 (t0) cc_final: 0.7705 (t0) REVERT: F 27 LEU cc_start: 0.7818 (mp) cc_final: 0.7389 (tm) REVERT: F 45 GLU cc_start: 0.7315 (tp30) cc_final: 0.6653 (tp30) REVERT: F 68 ASP cc_start: 0.7047 (t0) cc_final: 0.6704 (t70) REVERT: F 172 GLU cc_start: 0.7607 (tp30) cc_final: 0.7402 (tp30) REVERT: F 176 ARG cc_start: 0.7724 (mtt180) cc_final: 0.7489 (mtt180) REVERT: F 177 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8079 (mp) REVERT: F 230 LYS cc_start: 0.8429 (mttt) cc_final: 0.7613 (mttt) REVERT: F 266 LYS cc_start: 0.7496 (mmmm) cc_final: 0.6664 (mmmm) REVERT: F 309 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8419 (mt) REVERT: F 322 MET cc_start: 0.5412 (tpp) cc_final: 0.5074 (tpp) REVERT: G 94 ASP cc_start: 0.8250 (m-30) cc_final: 0.7943 (m-30) REVERT: G 125 TYR cc_start: 0.8192 (t80) cc_final: 0.7877 (t80) REVERT: G 166 ASP cc_start: 0.6894 (t0) cc_final: 0.6619 (t0) REVERT: G 174 SER cc_start: 0.8690 (m) cc_final: 0.8382 (t) REVERT: G 271 TYR cc_start: 0.7819 (OUTLIER) cc_final: 0.7106 (m-80) REVERT: G 288 ILE cc_start: 0.8052 (mm) cc_final: 0.7695 (mm) REVERT: G 307 LYS cc_start: 0.8390 (mtpp) cc_final: 0.8135 (mttp) REVERT: H 47 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8357 (tt) REVERT: H 105 SER cc_start: 0.8605 (t) cc_final: 0.8353 (t) REVERT: H 156 GLU cc_start: 0.6590 (OUTLIER) cc_final: 0.6200 (pt0) REVERT: H 161 ILE cc_start: 0.8174 (mt) cc_final: 0.7862 (tp) REVERT: H 181 THR cc_start: 0.8466 (p) cc_final: 0.8145 (t) REVERT: H 217 ILE cc_start: 0.8825 (pt) cc_final: 0.8440 (pp) REVERT: H 228 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7391 (mt-10) REVERT: M 34 GLU cc_start: 0.7618 (tm-30) cc_final: 0.7357 (tm-30) REVERT: M 39 PHE cc_start: 0.6515 (m-10) cc_final: 0.6248 (m-10) REVERT: M 58 ILE cc_start: 0.7055 (tt) cc_final: 0.6790 (pt) REVERT: M 101 ARG cc_start: 0.8042 (tpt-90) cc_final: 0.7092 (tmt170) outliers start: 31 outliers final: 8 residues processed: 782 average time/residue: 0.6021 time to fit residues: 536.3805 Evaluate side-chains 720 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 707 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain D residue 252 GLN Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 320 MET Chi-restraints excluded: chain G residue 271 TYR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 156 GLU Chi-restraints excluded: chain M residue 19 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.6980 chunk 111 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 HIS B 77 GLN B 80 GLN B 195 GLN B 208 ASN B 250 HIS D 252 GLN E 11 ASN E 16 ASN E 20 ASN E 43 ASN E 52 ASN ** E 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 ASN E 203 HIS F 34 ASN ** F 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 144 ASN F 149 GLN F 206 ASN F 270 ASN G 26 ASN ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN G 77 GLN G 186 ASN ** H 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN H 256 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.119791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.105701 restraints weight = 32972.001| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.77 r_work: 0.3288 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.164 23272 Z= 0.260 Angle : 0.680 11.849 31906 Z= 0.366 Chirality : 0.047 0.299 3585 Planarity : 0.006 0.056 3777 Dihedral : 18.413 175.158 4108 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.35 % Favored : 93.42 % Rotamer: Outliers : 4.55 % Allowed : 18.77 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.23 (0.15), residues: 2567 helix: -0.85 (0.18), residues: 712 sheet: 0.21 (0.25), residues: 437 loop : -2.49 (0.14), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 162 TYR 0.019 0.002 TYR G 271 PHE 0.017 0.002 PHE A 172 TRP 0.010 0.002 TRP D 264 HIS 0.007 0.001 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00598 (23272) covalent geometry : angle 0.68015 (31906) hydrogen bonds : bond 0.04977 ( 568) hydrogen bonds : angle 5.59593 ( 1546) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5134 Ramachandran restraints generated. 2567 Oldfield, 0 Emsley, 2567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5134 Ramachandran restraints generated. 2567 Oldfield, 0 Emsley, 2567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 807 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 706 time to evaluate : 0.738 Fit side-chains revert: symmetry clash REVERT: A 23 ARG cc_start: 0.8455 (ttm110) cc_final: 0.8171 (mtm-85) REVERT: A 77 GLN cc_start: 0.7890 (mm-40) cc_final: 0.7495 (mm110) REVERT: A 334 GLU cc_start: 0.7578 (mp0) cc_final: 0.7334 (mp0) REVERT: B 20 SER cc_start: 0.8138 (OUTLIER) cc_final: 0.7932 (p) REVERT: B 39 LYS cc_start: 0.8288 (mttt) cc_final: 0.7977 (mtpp) REVERT: B 72 MET cc_start: 0.8023 (mmm) cc_final: 0.7718 (mmm) REVERT: B 83 THR cc_start: 0.8681 (p) cc_final: 0.8450 (m) REVERT: B 156 GLU cc_start: 0.7405 (mp0) cc_final: 0.7082 (mp0) REVERT: B 278 GLU cc_start: 0.7455 (mt-10) cc_final: 0.7152 (mt-10) REVERT: B 290 PHE cc_start: 0.8759 (m-10) cc_final: 0.8552 (m-80) REVERT: B 304 MET cc_start: 0.8524 (ttm) cc_final: 0.8305 (ttp) REVERT: B 331 LYS cc_start: 0.8601 (tptm) cc_final: 0.8374 (tptp) REVERT: C 52 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.7969 (ptmt) REVERT: C 85 SER cc_start: 0.8326 (t) cc_final: 0.8071 (p) REVERT: C 166 ASP cc_start: 0.7299 (t0) cc_final: 0.6947 (t0) REVERT: C 183 VAL cc_start: 0.8876 (m) cc_final: 0.8646 (p) REVERT: C 206 TYR cc_start: 0.7586 (p90) cc_final: 0.7233 (p90) REVERT: C 239 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8255 (mtmm) REVERT: D 15 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.7389 (mtp-110) REVERT: D 172 PHE cc_start: 0.8462 (m-10) cc_final: 0.8253 (m-80) REVERT: D 204 ARG cc_start: 0.8348 (mtp85) cc_final: 0.8124 (mtp85) REVERT: D 278 GLU cc_start: 0.7664 (mp0) cc_final: 0.7393 (mp0) REVERT: D 307 LYS cc_start: 0.8758 (mtpp) cc_final: 0.8513 (mttp) REVERT: D 309 GLU cc_start: 0.7865 (tt0) cc_final: 0.7618 (tt0) REVERT: E 209 ASP cc_start: 0.8118 (t0) cc_final: 0.7874 (t0) REVERT: F 27 LEU cc_start: 0.7668 (mp) cc_final: 0.7455 (tm) REVERT: F 45 GLU cc_start: 0.7801 (tp30) cc_final: 0.7286 (tp30) REVERT: F 61 ASP cc_start: 0.7190 (t0) cc_final: 0.6814 (t0) REVERT: F 63 ASN cc_start: 0.8419 (m-40) cc_final: 0.8178 (m110) REVERT: F 172 GLU cc_start: 0.7913 (tp30) cc_final: 0.7680 (tp30) REVERT: F 205 LYS cc_start: 0.8841 (mtpt) cc_final: 0.8618 (ptpt) REVERT: F 220 LEU cc_start: 0.8434 (mt) cc_final: 0.8230 (mt) REVERT: F 230 LYS cc_start: 0.8548 (mttt) cc_final: 0.8226 (mttt) REVERT: F 236 ASP cc_start: 0.7002 (m-30) cc_final: 0.6687 (m-30) REVERT: F 237 ILE cc_start: 0.7991 (pt) cc_final: 0.7539 (pp) REVERT: F 247 ASN cc_start: 0.8233 (m-40) cc_final: 0.7760 (t0) REVERT: F 266 LYS cc_start: 0.7502 (mmmm) cc_final: 0.6894 (mmmm) REVERT: F 272 ARG cc_start: 0.7532 (mmt90) cc_final: 0.7165 (mmt90) REVERT: F 277 ARG cc_start: 0.8233 (mtt90) cc_final: 0.7542 (mtt90) REVERT: F 322 MET cc_start: 0.5511 (tpp) cc_final: 0.5145 (tpp) REVERT: G 288 ILE cc_start: 0.7865 (mm) cc_final: 0.7495 (mm) REVERT: G 307 LYS cc_start: 0.8674 (mtpp) cc_final: 0.8398 (mttp) REVERT: H 105 SER cc_start: 0.8736 (t) cc_final: 0.8439 (t) REVERT: H 129 ASP cc_start: 0.7305 (p0) cc_final: 0.6962 (p0) REVERT: H 140 ASN cc_start: 0.8154 (m-40) cc_final: 0.7723 (m-40) REVERT: H 151 ASN cc_start: 0.8475 (m-40) cc_final: 0.8139 (m110) REVERT: H 216 LYS cc_start: 0.8369 (ttpp) cc_final: 0.7896 (ttpp) REVERT: H 217 ILE cc_start: 0.8834 (pt) cc_final: 0.8580 (pp) REVERT: M 58 ILE cc_start: 0.7204 (tt) cc_final: 0.6813 (pt) outliers start: 101 outliers final: 47 residues processed: 754 average time/residue: 0.6086 time to fit residues: 521.7846 Evaluate side-chains 723 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 672 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 239 LYS Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain D residue 15 ARG Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain F residue 137 SER Chi-restraints excluded: chain F residue 229 ASP Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain G residue 62 MET Chi-restraints excluded: chain G residue 161 ILE Chi-restraints excluded: chain G residue 184 GLU Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 286 ILE Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 167 LYS Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 300 LEU Chi-restraints excluded: chain H residue 307 LYS Chi-restraints excluded: chain H residue 322 ILE Chi-restraints excluded: chain M residue 19 ILE Chi-restraints excluded: chain M residue 102 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 152 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 chunk 189 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 258 optimal weight: 8.9990 chunk 244 optimal weight: 2.9990 chunk 263 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 169 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 chunk 150 optimal weight: 0.8980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 ASN ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 GLN B 208 ASN B 256 ASN B 308 ASN D 18 ASN D 252 GLN E 43 ASN ** E 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN E 203 HIS F 35 HIS ** F 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 51 ASN F 82 ASN ** F 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 26 ASN G 186 ASN ** H 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.118701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.104530 restraints weight = 32942.700| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.78 r_work: 0.3271 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 23272 Z= 0.253 Angle : 0.640 9.680 31906 Z= 0.341 Chirality : 0.046 0.280 3585 Planarity : 0.005 0.050 3777 Dihedral : 18.114 174.663 4083 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.65 % Favored : 94.27 % Rotamer: Outliers : 4.50 % Allowed : 19.62 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.77 (0.15), residues: 2567 helix: -0.23 (0.19), residues: 706 sheet: 0.54 (0.26), residues: 409 loop : -2.29 (0.14), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 284 TYR 0.025 0.002 TYR G 271 PHE 0.021 0.002 PHE H 37 TRP 0.011 0.002 TRP G 33 HIS 0.009 0.002 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00581 (23272) covalent geometry : angle 0.63976 (31906) hydrogen bonds : bond 0.04669 ( 568) hydrogen bonds : angle 5.18509 ( 1546) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5134 Ramachandran restraints generated. 2567 Oldfield, 0 Emsley, 2567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5134 Ramachandran restraints generated. 2567 Oldfield, 0 Emsley, 2567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 681 time to evaluate : 0.559 Fit side-chains revert: symmetry clash REVERT: A 23 ARG cc_start: 0.8479 (ttm110) cc_final: 0.8190 (mtm-85) REVERT: A 39 LYS cc_start: 0.8809 (ptpp) cc_final: 0.8507 (ptmm) REVERT: A 40 ARG cc_start: 0.8699 (ptt-90) cc_final: 0.8464 (ptt-90) REVERT: A 89 ASP cc_start: 0.8292 (p0) cc_final: 0.8033 (p0) REVERT: A 244 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7438 (mp0) REVERT: A 334 GLU cc_start: 0.7562 (mp0) cc_final: 0.7311 (mp0) REVERT: B 39 LYS cc_start: 0.8333 (mttt) cc_final: 0.8007 (mtpp) REVERT: B 72 MET cc_start: 0.8036 (mmm) cc_final: 0.7751 (mmm) REVERT: B 83 THR cc_start: 0.8681 (p) cc_final: 0.8449 (m) REVERT: B 156 GLU cc_start: 0.7256 (mp0) cc_final: 0.6926 (mp0) REVERT: B 163 THR cc_start: 0.8856 (OUTLIER) cc_final: 0.8533 (p) REVERT: B 278 GLU cc_start: 0.7448 (mt-10) cc_final: 0.7164 (mt-10) REVERT: B 331 LYS cc_start: 0.8698 (tptm) cc_final: 0.8454 (tptp) REVERT: C 17 GLU cc_start: 0.7738 (tt0) cc_final: 0.7461 (tt0) REVERT: C 52 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8073 (ptmt) REVERT: C 85 SER cc_start: 0.8448 (t) cc_final: 0.8240 (p) REVERT: C 86 THR cc_start: 0.8643 (m) cc_final: 0.8394 (p) REVERT: C 166 ASP cc_start: 0.7401 (t0) cc_final: 0.7023 (t0) REVERT: C 183 VAL cc_start: 0.8899 (m) cc_final: 0.8691 (p) REVERT: C 206 TYR cc_start: 0.7759 (p90) cc_final: 0.7300 (p90) REVERT: C 224 TYR cc_start: 0.8606 (m-80) cc_final: 0.8327 (m-80) REVERT: C 239 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8275 (mtmm) REVERT: D 15 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.7381 (mtp-110) REVERT: D 70 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7208 (mt-10) REVERT: D 72 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.7888 (mtp) REVERT: D 148 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7715 (mt) REVERT: D 204 ARG cc_start: 0.8374 (mtp85) cc_final: 0.8094 (mtp180) REVERT: D 307 LYS cc_start: 0.8715 (mtpp) cc_final: 0.8477 (mttp) REVERT: D 309 GLU cc_start: 0.7882 (tt0) cc_final: 0.7653 (tt0) REVERT: E 52 ASN cc_start: 0.8101 (m-40) cc_final: 0.7901 (m110) REVERT: E 209 ASP cc_start: 0.8136 (t0) cc_final: 0.7836 (t0) REVERT: F 27 LEU cc_start: 0.7721 (mp) cc_final: 0.7503 (tm) REVERT: F 45 GLU cc_start: 0.7820 (tp30) cc_final: 0.7265 (tp30) REVERT: F 61 ASP cc_start: 0.7201 (t0) cc_final: 0.6862 (t0) REVERT: F 63 ASN cc_start: 0.8437 (m-40) cc_final: 0.8163 (m110) REVERT: F 68 ASP cc_start: 0.7408 (t0) cc_final: 0.7115 (t0) REVERT: F 132 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7852 (mt) REVERT: F 172 GLU cc_start: 0.8037 (tp30) cc_final: 0.7777 (mm-30) REVERT: F 230 LYS cc_start: 0.8643 (mttt) cc_final: 0.8275 (mttt) REVERT: F 236 ASP cc_start: 0.7107 (m-30) cc_final: 0.6786 (m-30) REVERT: F 237 ILE cc_start: 0.8062 (pt) cc_final: 0.7586 (pp) REVERT: F 247 ASN cc_start: 0.8266 (m-40) cc_final: 0.7765 (t0) REVERT: F 266 LYS cc_start: 0.7450 (mmmm) cc_final: 0.6854 (mmmm) REVERT: F 272 ARG cc_start: 0.7606 (mmt90) cc_final: 0.7093 (mmt90) REVERT: F 277 ARG cc_start: 0.8163 (mtt90) cc_final: 0.7263 (mtt90) REVERT: F 322 MET cc_start: 0.5708 (tpp) cc_final: 0.5385 (tpp) REVERT: G 273 PHE cc_start: 0.8369 (p90) cc_final: 0.8129 (p90) REVERT: G 288 ILE cc_start: 0.8134 (mm) cc_final: 0.7699 (mm) REVERT: G 307 LYS cc_start: 0.8693 (mtpp) cc_final: 0.8430 (mttp) REVERT: H 105 SER cc_start: 0.8713 (t) cc_final: 0.8382 (t) REVERT: H 146 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7810 (ttp-170) REVERT: H 173 ASN cc_start: 0.8190 (t0) cc_final: 0.7942 (t0) REVERT: H 216 LYS cc_start: 0.8383 (ttpp) cc_final: 0.7917 (ttpp) REVERT: H 217 ILE cc_start: 0.8901 (pt) cc_final: 0.8596 (pp) REVERT: H 226 SER cc_start: 0.8577 (p) cc_final: 0.8267 (m) REVERT: H 255 ASN cc_start: 0.7756 (m-40) cc_final: 0.7518 (m-40) outliers start: 100 outliers final: 54 residues processed: 724 average time/residue: 0.5636 time to fit residues: 464.3113 Evaluate side-chains 717 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 655 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 239 LYS Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain D residue 15 ARG Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain F residue 132 ILE Chi-restraints excluded: chain F residue 229 ASP Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 320 MET Chi-restraints excluded: chain G residue 18 ASN Chi-restraints excluded: chain G residue 34 GLN Chi-restraints excluded: chain G residue 62 MET Chi-restraints excluded: chain G residue 159 GLU Chi-restraints excluded: chain G residue 184 GLU Chi-restraints excluded: chain G residue 205 GLU Chi-restraints excluded: chain G residue 286 ILE Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 146 ARG Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 222 GLU Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain H residue 299 LYS Chi-restraints excluded: chain H residue 300 LEU Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 58 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 27 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 117 optimal weight: 0.3980 chunk 191 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 260 optimal weight: 5.9990 chunk 213 optimal weight: 3.9990 chunk 251 optimal weight: 5.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN A 208 ASN B 308 ASN D 252 GLN E 43 ASN ** E 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 HIS F 145 GLN G 26 ASN H 18 ASN H 26 ASN H 178 ASN H 279 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.119127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.105040 restraints weight = 32881.041| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.77 r_work: 0.3281 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 23272 Z= 0.208 Angle : 0.602 10.387 31906 Z= 0.319 Chirality : 0.044 0.270 3585 Planarity : 0.005 0.052 3777 Dihedral : 17.999 175.938 4081 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.38 % Favored : 94.55 % Rotamer: Outliers : 4.77 % Allowed : 20.61 % Favored : 74.62 % 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: -1.43 (0.16), residues: 2567 helix: 0.21 (0.20), residues: 701 sheet: 0.43 (0.26), residues: 425 loop : -2.08 (0.14), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 103 TYR 0.018 0.001 TYR A 271 PHE 0.030 0.002 PHE H 37 TRP 0.010 0.001 TRP G 33 HIS 0.008 0.001 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00479 (23272) covalent geometry : angle 0.60199 (31906) hydrogen bonds : bond 0.04124 ( 568) hydrogen bonds : angle 4.96957 ( 1546) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5134 Ramachandran restraints generated. 2567 Oldfield, 0 Emsley, 2567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5134 Ramachandran restraints generated. 2567 Oldfield, 0 Emsley, 2567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 677 time to evaluate : 0.898 Fit side-chains REVERT: A 23 ARG cc_start: 0.8457 (ttm110) cc_final: 0.8165 (ttp-110) REVERT: A 129 ASP cc_start: 0.7277 (t0) cc_final: 0.7054 (t0) REVERT: A 334 GLU cc_start: 0.7554 (mp0) cc_final: 0.7300 (mp0) REVERT: B 39 LYS cc_start: 0.8346 (mttt) cc_final: 0.8029 (mtpp) REVERT: B 72 MET cc_start: 0.8025 (mmm) cc_final: 0.7776 (mmm) REVERT: B 83 THR cc_start: 0.8667 (p) cc_final: 0.8434 (m) REVERT: B 103 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8281 (mtmt) REVERT: B 156 GLU cc_start: 0.7205 (mp0) cc_final: 0.6922 (mp0) REVERT: B 163 THR cc_start: 0.8849 (OUTLIER) cc_final: 0.8535 (p) REVERT: B 278 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7169 (mt-10) REVERT: B 331 LYS cc_start: 0.8692 (tptm) cc_final: 0.8439 (tptp) REVERT: C 17 GLU cc_start: 0.7744 (tt0) cc_final: 0.7505 (tt0) REVERT: C 20 SER cc_start: 0.8296 (p) cc_final: 0.8089 (p) REVERT: C 52 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8055 (ptmt) REVERT: C 66 LYS cc_start: 0.8141 (mtpt) cc_final: 0.7893 (mtpp) REVERT: C 72 MET cc_start: 0.8022 (mmm) cc_final: 0.7751 (mmm) REVERT: C 85 SER cc_start: 0.8388 (t) cc_final: 0.8151 (p) REVERT: C 86 THR cc_start: 0.8622 (OUTLIER) cc_final: 0.8256 (p) REVERT: C 166 ASP cc_start: 0.7425 (t0) cc_final: 0.7039 (t0) REVERT: C 181 THR cc_start: 0.8744 (m) cc_final: 0.8509 (p) REVERT: C 183 VAL cc_start: 0.8886 (m) cc_final: 0.8684 (p) REVERT: C 206 TYR cc_start: 0.7781 (p90) cc_final: 0.7334 (p90) REVERT: C 224 TYR cc_start: 0.8612 (m-80) cc_final: 0.8339 (m-80) REVERT: C 239 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8287 (mtmm) REVERT: D 15 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.7335 (mtp-110) REVERT: D 69 LYS cc_start: 0.8798 (mtmt) cc_final: 0.8591 (mtmm) REVERT: D 70 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7261 (mt-10) REVERT: D 72 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.8009 (mtp) REVERT: D 148 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7717 (mt) REVERT: D 204 ARG cc_start: 0.8332 (mtp85) cc_final: 0.8076 (mtp85) REVERT: D 278 GLU cc_start: 0.7582 (mp0) cc_final: 0.7190 (mt-10) REVERT: D 309 GLU cc_start: 0.7892 (tt0) cc_final: 0.7646 (tt0) REVERT: E 209 ASP cc_start: 0.8124 (t0) cc_final: 0.7767 (t0) REVERT: F 27 LEU cc_start: 0.7693 (mp) cc_final: 0.7490 (tm) REVERT: F 45 GLU cc_start: 0.7804 (tp30) cc_final: 0.7232 (tp30) REVERT: F 61 ASP cc_start: 0.7178 (t0) cc_final: 0.6893 (t0) REVERT: F 63 ASN cc_start: 0.8421 (m-40) cc_final: 0.8135 (m110) REVERT: F 68 ASP cc_start: 0.7400 (t0) cc_final: 0.7087 (t0) REVERT: F 172 GLU cc_start: 0.8098 (tp30) cc_final: 0.7860 (mm-30) REVERT: F 175 ASP cc_start: 0.7756 (t0) cc_final: 0.7362 (t0) REVERT: F 230 LYS cc_start: 0.8649 (mttt) cc_final: 0.8270 (mttt) REVERT: F 236 ASP cc_start: 0.7151 (m-30) cc_final: 0.6814 (m-30) REVERT: F 237 ILE cc_start: 0.8096 (pt) cc_final: 0.7628 (pp) REVERT: F 247 ASN cc_start: 0.8279 (m-40) cc_final: 0.7780 (t0) REVERT: F 266 LYS cc_start: 0.7495 (mmmm) cc_final: 0.6896 (mmmm) REVERT: F 272 ARG cc_start: 0.7652 (mmt90) cc_final: 0.7090 (mmt90) REVERT: F 276 LEU cc_start: 0.8413 (mt) cc_final: 0.7978 (mm) REVERT: F 277 ARG cc_start: 0.8132 (mtt90) cc_final: 0.7231 (mtt90) REVERT: F 322 MET cc_start: 0.5757 (tpp) cc_final: 0.5433 (tpp) REVERT: G 166 ASP cc_start: 0.7273 (t0) cc_final: 0.6946 (t0) REVERT: G 304 MET cc_start: 0.8170 (ttp) cc_final: 0.7961 (ttm) REVERT: G 307 LYS cc_start: 0.8689 (mtpp) cc_final: 0.8457 (mttp) REVERT: H 26 ASN cc_start: 0.8204 (m-40) cc_final: 0.7963 (m-40) REVERT: H 105 SER cc_start: 0.8680 (t) cc_final: 0.8337 (t) REVERT: H 146 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7341 (ttp-110) REVERT: H 151 ASN cc_start: 0.8499 (m-40) cc_final: 0.8247 (m110) REVERT: H 156 GLU cc_start: 0.6712 (OUTLIER) cc_final: 0.6307 (pt0) REVERT: H 216 LYS cc_start: 0.8352 (ttpp) cc_final: 0.7931 (ttpp) REVERT: H 217 ILE cc_start: 0.8914 (pt) cc_final: 0.8695 (pp) REVERT: H 320 MET cc_start: 0.8320 (mpp) cc_final: 0.7949 (mpp) REVERT: M 8 ILE cc_start: 0.7181 (OUTLIER) cc_final: 0.6548 (pp) outliers start: 106 outliers final: 64 residues processed: 721 average time/residue: 0.5927 time to fit residues: 485.9758 Evaluate side-chains 742 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 667 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 239 LYS Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain D residue 15 ARG Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain E residue 89 LYS Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain F residue 137 SER Chi-restraints excluded: chain F residue 229 ASP Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 320 MET Chi-restraints excluded: chain G residue 34 GLN Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 62 MET Chi-restraints excluded: chain G residue 68 GLU Chi-restraints excluded: chain G residue 159 GLU Chi-restraints excluded: chain G residue 184 GLU Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 205 GLU Chi-restraints excluded: chain G residue 286 ILE Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 144 ASN Chi-restraints excluded: chain H residue 146 ARG Chi-restraints excluded: chain H residue 156 GLU Chi-restraints excluded: chain H residue 167 LYS Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 184 GLU Chi-restraints excluded: chain H residue 222 GLU Chi-restraints excluded: chain H residue 299 LYS Chi-restraints excluded: chain H residue 300 LEU Chi-restraints excluded: chain H residue 307 LYS Chi-restraints excluded: chain H residue 322 ILE Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 58 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 65.9022 > 50: distance: 132 - 159: 19.894 distance: 135 - 156: 14.052 distance: 143 - 144: 7.896 distance: 144 - 147: 3.826 distance: 145 - 146: 26.362 distance: 145 - 152: 25.622 distance: 147 - 148: 6.667 distance: 148 - 149: 7.363 distance: 149 - 150: 7.522 distance: 149 - 151: 7.306 distance: 152 - 153: 17.182 distance: 153 - 154: 11.364 distance: 154 - 155: 11.316 distance: 154 - 156: 25.479 distance: 156 - 157: 9.667 distance: 157 - 160: 10.928 distance: 158 - 159: 3.208 distance: 160 - 161: 11.866 distance: 162 - 163: 10.883 distance: 163 - 164: 9.630 distance: 163 - 166: 6.003 distance: 164 - 165: 18.275 distance: 164 - 167: 11.125 distance: 167 - 168: 10.344 distance: 168 - 169: 6.123 distance: 169 - 170: 5.421 distance: 169 - 171: 5.789 distance: 171 - 172: 5.477 distance: 172 - 173: 5.890 distance: 172 - 175: 5.589 distance: 173 - 174: 3.555 distance: 173 - 179: 3.943 distance: 175 - 176: 6.267 distance: 176 - 177: 6.241 distance: 177 - 178: 7.344 distance: 179 - 180: 4.788 distance: 180 - 183: 9.894 distance: 181 - 182: 6.419 distance: 182 - 213: 7.742 distance: 183 - 184: 6.530 distance: 184 - 185: 4.345 distance: 184 - 186: 9.078 distance: 185 - 187: 8.125 distance: 186 - 188: 5.526 distance: 187 - 188: 7.705 distance: 190 - 191: 3.966 distance: 191 - 192: 6.335 distance: 192 - 221: 9.995 distance: 193 - 194: 4.441 distance: 195 - 196: 4.939 distance: 196 - 199: 5.356 distance: 197 - 198: 3.774 distance: 197 - 204: 4.218 distance: 198 - 229: 3.744 distance: 199 - 200: 5.911 distance: 201 - 203: 6.590 distance: 205 - 206: 3.985 distance: 205 - 208: 5.678 distance: 206 - 207: 3.095 distance: 206 - 213: 5.103 distance: 207 - 234: 3.603 distance: 208 - 209: 9.971 distance: 209 - 210: 14.718 distance: 210 - 211: 14.926 distance: 211 - 212: 12.277