Starting phenix.real_space_refine on Sun Mar 24 21:28:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lsx_23508/03_2024/7lsx_23508.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lsx_23508/03_2024/7lsx_23508.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lsx_23508/03_2024/7lsx_23508.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lsx_23508/03_2024/7lsx_23508.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lsx_23508/03_2024/7lsx_23508.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lsx_23508/03_2024/7lsx_23508.pdb" } resolution = 3.61 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.051 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 S 79 5.16 5 C 14125 2.51 5 N 3717 2.21 5 O 4296 1.98 5 H 22176 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 44393 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 3850 Classifications: {'peptide': 245} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 234} Chain: "B" Number of atoms: 3791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 3791 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 12, 'TRANS': 234} Chain: "C" Number of atoms: 3676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 3676 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 5, 'TRANS': 228} Chain breaks: 1 Chain: "D" Number of atoms: 3700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 3700 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 10, 'TRANS': 224} Chain: "E" Number of atoms: 3827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 3827 Classifications: {'peptide': 249} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 244} Chain: "F" Number of atoms: 3614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 3614 Classifications: {'peptide': 234} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain: "G" Number of atoms: 3796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 3796 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 9, 'TRANS': 235} Chain: "H" Number of atoms: 1490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 1490 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain breaks: 1 Chain: "I" Number of atoms: 3131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 3131 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 4, 'TRANS': 202} Chain breaks: 3 Chain: "J" Number of atoms: 2740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 2740 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 6, 'TRANS': 169} Chain breaks: 2 Chain: "K" Number of atoms: 2937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 2937 Classifications: {'peptide': 182} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain breaks: 1 Chain: "O" Number of atoms: 3768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 3768 Classifications: {'peptide': 240} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 221} Chain breaks: 1 Chain: "P" Number of atoms: 4073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 4073 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 12, 'TRANS': 240} Chain breaks: 1 Time building chain proxies: 19.70, per 1000 atoms: 0.44 Number of scatterers: 44393 At special positions: 0 Unit cell: (150.52, 121.9, 139.92, 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 79 16.00 O 4296 8.00 N 3717 7.00 C 14125 6.00 H 22176 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 38.27 Conformation dependent library (CDL) restraints added in 4.6 seconds 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5274 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 22 sheets defined 42.2% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.30 Creating SS restraints... Processing helix chain 'A' and resid 11 through 15 Processing helix chain 'A' and resid 25 through 35 removed outlier: 3.719A pdb=" N THR A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 69 removed outlier: 3.589A pdb=" N THR A 68 " --> pdb=" O ASP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 109 Processing helix chain 'A' and resid 113 through 131 removed outlier: 3.732A pdb=" N TYR A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 190 removed outlier: 3.678A pdb=" N ILE A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 215 Processing helix chain 'A' and resid 219 through 221 No H-bonds generated for 'chain 'A' and resid 219 through 221' Processing helix chain 'A' and resid 237 through 251 Processing helix chain 'B' and resid 18 through 31 Processing helix chain 'B' and resid 57 through 61 Processing helix chain 'B' and resid 78 through 96 Processing helix chain 'B' and resid 97 through 102 Processing helix chain 'B' and resid 106 through 123 removed outlier: 3.537A pdb=" N ALA B 121 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN B 123 " --> pdb=" O GLN B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 179 Processing helix chain 'B' and resid 184 through 200 removed outlier: 3.908A pdb=" N HIS B 190 " --> pdb=" O GLU B 186 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU B 198 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER B 199 " --> pdb=" O THR B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 222 Processing helix chain 'B' and resid 239 through 249 removed outlier: 3.861A pdb=" N ALA B 249 " --> pdb=" O ASP B 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 30 removed outlier: 3.694A pdb=" N SER C 30 " --> pdb=" O LEU C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 103 removed outlier: 3.726A pdb=" N ILE C 86 " --> pdb=" O ALA C 82 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 123 removed outlier: 3.650A pdb=" N THR C 123 " --> pdb=" O LYS C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 180 Processing helix chain 'C' and resid 185 through 201 removed outlier: 4.079A pdb=" N GLU C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 209 No H-bonds generated for 'chain 'C' and resid 207 through 209' Processing helix chain 'C' and resid 231 through 242 Processing helix chain 'D' and resid 17 through 28 removed outlier: 3.506A pdb=" N LYS D 28 " --> pdb=" O LEU D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 100 removed outlier: 3.555A pdb=" N ILE D 84 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 120 Processing helix chain 'D' and resid 167 through 179 removed outlier: 3.916A pdb=" N VAL D 171 " --> pdb=" O ASN D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 201 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 226 through 238 removed outlier: 4.019A pdb=" N ASN D 230 " --> pdb=" O SER D 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 34 removed outlier: 3.511A pdb=" N GLU E 25 " --> pdb=" O LEU E 21 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS E 32 " --> pdb=" O LEU E 28 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU E 33 " --> pdb=" O GLU E 29 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY E 34 " --> pdb=" O ALA E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 64 removed outlier: 4.198A pdb=" N ILE E 64 " --> pdb=" O SER E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 104 removed outlier: 3.694A pdb=" N ALA E 85 " --> pdb=" O LEU E 81 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 121 Processing helix chain 'E' and resid 122 through 124 No H-bonds generated for 'chain 'E' and resid 122 through 124' Processing helix chain 'E' and resid 175 through 187 Processing helix chain 'E' and resid 192 through 208 Processing helix chain 'E' and resid 232 through 247 Processing helix chain 'F' and resid 1 through 6 Processing helix chain 'F' and resid 19 through 28 Processing helix chain 'F' and resid 29 through 32 Processing helix chain 'F' and resid 77 through 99 Processing helix chain 'F' and resid 104 through 119 removed outlier: 3.662A pdb=" N LYS F 115 " --> pdb=" O LEU F 111 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASN F 119 " --> pdb=" O LYS F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 180 removed outlier: 4.546A pdb=" N ALA F 168 " --> pdb=" O ARG F 164 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ASP F 177 " --> pdb=" O GLU F 173 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N THR F 178 " --> pdb=" O ARG F 174 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE F 180 " --> pdb=" O LEU F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 183 No H-bonds generated for 'chain 'F' and resid 181 through 183' Processing helix chain 'F' and resid 185 through 199 removed outlier: 4.029A pdb=" N GLN F 199 " --> pdb=" O GLU F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 234 removed outlier: 4.038A pdb=" N LYS F 232 " --> pdb=" O ALA F 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 33 removed outlier: 3.637A pdb=" N GLU G 25 " --> pdb=" O ASN G 21 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU G 32 " --> pdb=" O VAL G 28 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASN G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 104 Processing helix chain 'G' and resid 108 through 124 removed outlier: 3.713A pdb=" N HIS G 123 " --> pdb=" O TYR G 119 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR G 124 " --> pdb=" O VAL G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 183 Processing helix chain 'G' and resid 188 through 204 removed outlier: 3.785A pdb=" N LYS G 194 " --> pdb=" O ARG G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 208 removed outlier: 4.073A pdb=" N LYS G 208 " --> pdb=" O GLU G 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 205 through 208' Processing helix chain 'G' and resid 233 through 244 Processing helix chain 'H' and resid 53 through 59 removed outlier: 4.360A pdb=" N ASN H 59 " --> pdb=" O SER H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 77 Processing helix chain 'H' and resid 78 through 95 removed outlier: 3.641A pdb=" N THR H 94 " --> pdb=" O ILE H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 111 removed outlier: 3.679A pdb=" N ASP H 108 " --> pdb=" O SER H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 123 Processing helix chain 'H' and resid 137 through 147 Processing helix chain 'I' and resid 8 through 18 Processing helix chain 'I' and resid 77 through 100 Processing helix chain 'I' and resid 104 through 119 removed outlier: 3.628A pdb=" N ALA I 108 " --> pdb=" O ARG I 104 " (cutoff:3.500A) Processing helix chain 'I' and resid 144 through 146 No H-bonds generated for 'chain 'I' and resid 144 through 146' Processing helix chain 'I' and resid 159 through 171 removed outlier: 3.752A pdb=" N ALA I 163 " --> pdb=" O GLY I 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 176 through 190 Processing helix chain 'J' and resid 56 through 79 Processing helix chain 'J' and resid 83 through 97 Processing helix chain 'J' and resid 142 through 152 Processing helix chain 'J' and resid 159 through 173 Processing helix chain 'K' and resid 51 through 72 Processing helix chain 'K' and resid 76 through 92 Processing helix chain 'K' and resid 93 through 95 No H-bonds generated for 'chain 'K' and resid 93 through 95' Processing helix chain 'K' and resid 134 through 138 removed outlier: 3.837A pdb=" N PHE K 138 " --> pdb=" O TYR K 135 " (cutoff:3.500A) Processing helix chain 'K' and resid 140 through 148 removed outlier: 4.758A pdb=" N HIS K 146 " --> pdb=" O SER K 142 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 172 Processing helix chain 'O' and resid 39 through 47 removed outlier: 3.559A pdb=" N LEU O 42 " --> pdb=" O PRO O 39 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASP O 43 " --> pdb=" O GLN O 40 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL O 44 " --> pdb=" O ASP O 41 " (cutoff:3.500A) Proline residue: O 45 - end of helix No H-bonds generated for 'chain 'O' and resid 39 through 47' Processing helix chain 'O' and resid 55 through 61 Proline residue: O 59 - end of helix Processing helix chain 'O' and resid 143 through 159 removed outlier: 3.938A pdb=" N GLY O 147 " --> pdb=" O SER O 143 " (cutoff:3.500A) Processing helix chain 'O' and resid 194 through 206 Processing helix chain 'O' and resid 231 through 247 removed outlier: 4.291A pdb=" N GLN O 244 " --> pdb=" O ASP O 240 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TRP O 245 " --> pdb=" O LEU O 241 " (cutoff:3.500A) Processing helix chain 'O' and resid 249 through 263 Processing helix chain 'O' and resid 270 through 275 Processing helix chain 'P' and resid 10 through 12 No H-bonds generated for 'chain 'P' and resid 10 through 12' Processing helix chain 'P' and resid 13 through 26 Processing helix chain 'P' and resid 91 through 93 No H-bonds generated for 'chain 'P' and resid 91 through 93' Processing helix chain 'P' and resid 94 through 102 removed outlier: 3.659A pdb=" N ILE P 99 " --> pdb=" O LEU P 95 " (cutoff:3.500A) Processing helix chain 'P' and resid 102 through 110 Processing helix chain 'P' and resid 126 through 130 removed outlier: 3.864A pdb=" N VAL P 130 " --> pdb=" O GLU P 127 " (cutoff:3.500A) Processing helix chain 'P' and resid 148 through 156 Processing helix chain 'P' and resid 182 through 193 removed outlier: 4.312A pdb=" N PHE P 186 " --> pdb=" O ASP P 182 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS P 187 " --> pdb=" O GLN P 183 " (cutoff:3.500A) Processing helix chain 'P' and resid 217 through 231 Processing helix chain 'P' and resid 238 through 242 removed outlier: 4.520A pdb=" N VAL P 241 " --> pdb=" O PRO P 238 " (cutoff:3.500A) Processing helix chain 'P' and resid 246 through 254 removed outlier: 4.355A pdb=" N TYR P 253 " --> pdb=" O GLN P 250 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 168 through 171 Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 74 removed outlier: 3.848A pdb=" N ILE A 154 " --> pdb=" O TYR A 166 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 161 through 164 Processing sheet with id=AA4, first strand: chain 'B' and resid 65 through 68 removed outlier: 6.507A pdb=" N ILE B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 224 through 225 Processing sheet with id=AA6, first strand: chain 'C' and resid 162 through 165 Processing sheet with id=AA7, first strand: chain 'C' and resid 66 through 70 removed outlier: 6.015A pdb=" N LEU C 66 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL C 77 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N LYS C 68 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL C 75 " --> pdb=" O LYS C 68 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN C 70 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY C 139 " --> pdb=" O GLN C 147 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN C 147 " --> pdb=" O GLY C 139 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU C 148 " --> pdb=" O TRP C 160 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 161 through 164 Processing sheet with id=AA9, first strand: chain 'D' and resid 65 through 68 removed outlier: 6.267A pdb=" N VAL D 71 " --> pdb=" O ILE D 67 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 169 through 172 removed outlier: 3.664A pdb=" N VAL E 46 " --> pdb=" O ILE E 222 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN E 218 " --> pdb=" O VAL E 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 67 through 69 removed outlier: 3.538A pdb=" N ASP E 148 " --> pdb=" O GLY E 152 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 158 through 161 Processing sheet with id=AB4, first strand: chain 'F' and resid 63 through 67 removed outlier: 6.579A pdb=" N MET F 70 " --> pdb=" O CYS F 66 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU F 132 " --> pdb=" O PHE F 147 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 162 through 165 removed outlier: 3.626A pdb=" N SER G 37 " --> pdb=" O THR G 165 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY G 45 " --> pdb=" O CYS G 42 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL G 50 " --> pdb=" O GLU G 215 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 68 through 71 removed outlier: 6.401A pdb=" N ILE G 74 " --> pdb=" O VAL G 70 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 63 through 67 removed outlier: 6.433A pdb=" N ILE I 70 " --> pdb=" O ILE I 66 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 243 through 246 removed outlier: 3.863A pdb=" N CYS J 20 " --> pdb=" O GLY J 17 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 43 through 46 Processing sheet with id=AC1, first strand: chain 'K' and resid 130 through 133 removed outlier: 3.929A pdb=" N ILE K 4 " --> pdb=" O HIS K 133 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N VAL K 181 " --> pdb=" O VAL K 192 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP K 185 " --> pdb=" O GLY K 188 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 35 through 39 removed outlier: 6.268A pdb=" N THR K 42 " --> pdb=" O LEU K 38 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN K 101 " --> pdb=" O ALA K 47 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'O' and resid 35 through 37 removed outlier: 6.635A pdb=" N ILE O 124 " --> pdb=" O ILE O 71 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLU O 73 " --> pdb=" O PHE O 122 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N PHE O 122 " --> pdb=" O GLU O 73 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LYS O 75 " --> pdb=" O PHE O 120 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N PHE O 120 " --> pdb=" O LYS O 75 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N THR O 77 " --> pdb=" O TYR O 118 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N TYR O 118 " --> pdb=" O THR O 77 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N SER O 134 " --> pdb=" O PRO O 123 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE O 52 " --> pdb=" O ILE O 166 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ILE O 165 " --> pdb=" O LYS O 215 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N LEU O 217 " --> pdb=" O ILE O 165 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL O 167 " --> pdb=" O LEU O 217 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N ALA O 219 " --> pdb=" O VAL O 167 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N GLY O 169 " --> pdb=" O ALA O 219 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'P' and resid 30 through 35 removed outlier: 7.105A pdb=" N VAL P 72 " --> pdb=" O LEU P 33 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ALA P 35 " --> pdb=" O LEU P 70 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N LEU P 70 " --> pdb=" O ALA P 35 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU P 71 " --> pdb=" O GLN P 84 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N CYS P 3 " --> pdb=" O PHE P 81 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N ILE P 83 " --> pdb=" O CYS P 3 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL P 5 " --> pdb=" O ILE P 83 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N GLN P 85 " --> pdb=" O VAL P 5 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU P 4 " --> pdb=" O CYS P 116 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N TRP P 118 " --> pdb=" O LEU P 4 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU P 6 " --> pdb=" O TRP P 118 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N SER P 120 " --> pdb=" O LEU P 6 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ILE P 115 " --> pdb=" O LYS P 206 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N CYS P 208 " --> pdb=" O ILE P 115 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE P 117 " --> pdb=" O CYS P 208 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N CYS P 210 " --> pdb=" O ILE P 117 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ASP P 119 " --> pdb=" O CYS P 210 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ALA P 212 " --> pdb=" O ASP P 119 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N LEU P 121 " --> pdb=" O ALA P 212 " (cutoff:3.500A) 1159 hydrogen bonds defined for protein. 3267 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: 17.05 Time building geometry restraints manager: 39.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 22142 1.03 - 1.23: 36 1.23 - 1.42: 9383 1.42 - 1.61: 13123 1.61 - 1.81: 124 Bond restraints: 44808 Sorted by residual: bond pdb=" N ASP A 212 " pdb=" H ASP A 212 " ideal model delta sigma weight residual 0.860 0.913 -0.053 2.00e-02 2.50e+03 6.97e+00 bond pdb=" N GLY A 215 " pdb=" H GLY A 215 " ideal model delta sigma weight residual 0.860 0.911 -0.051 2.00e-02 2.50e+03 6.50e+00 bond pdb=" N THR A 216 " pdb=" H THR A 216 " ideal model delta sigma weight residual 0.860 0.911 -0.051 2.00e-02 2.50e+03 6.40e+00 bond pdb=" N ALA A 213 " pdb=" CA ALA A 213 " ideal model delta sigma weight residual 1.457 1.486 -0.028 1.17e-02 7.31e+03 5.82e+00 bond pdb=" CA ALA A 213 " pdb=" CB ALA A 213 " ideal model delta sigma weight residual 1.537 1.497 0.040 1.76e-02 3.23e+03 5.12e+00 ... (remaining 44803 not shown) Histogram of bond angle deviations from ideal: 74.19 - 86.16: 3 86.16 - 98.13: 0 98.13 - 110.10: 42149 110.10 - 122.07: 31693 122.07 - 134.04: 7201 Bond angle restraints: 81046 Sorted by residual: angle pdb=" C ALA P 69 " pdb=" CA ALA P 69 " pdb=" HA ALA P 69 " ideal model delta sigma weight residual 109.00 74.19 34.81 3.00e+00 1.11e-01 1.35e+02 angle pdb=" N ALA P 69 " pdb=" CA ALA P 69 " pdb=" HA ALA P 69 " ideal model delta sigma weight residual 110.00 75.39 34.61 3.00e+00 1.11e-01 1.33e+02 angle pdb=" CB ALA P 69 " pdb=" CA ALA P 69 " pdb=" HA ALA P 69 " ideal model delta sigma weight residual 109.00 75.21 33.79 3.00e+00 1.11e-01 1.27e+02 angle pdb=" N LEU A 214 " pdb=" CA LEU A 214 " pdb=" C LEU A 214 " ideal model delta sigma weight residual 111.28 103.03 8.25 1.09e+00 8.42e-01 5.73e+01 angle pdb=" CA THR A 216 " pdb=" C THR A 216 " pdb=" O THR A 216 " ideal model delta sigma weight residual 120.36 116.04 4.32 1.08e+00 8.57e-01 1.60e+01 ... (remaining 81041 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 19424 17.96 - 35.91: 1195 35.91 - 53.87: 319 53.87 - 71.83: 96 71.83 - 89.79: 21 Dihedral angle restraints: 21055 sinusoidal: 11493 harmonic: 9562 Sorted by residual: dihedral pdb=" CA PHE I 37 " pdb=" C PHE I 37 " pdb=" N ASN I 38 " pdb=" CA ASN I 38 " ideal model delta harmonic sigma weight residual -180.00 -159.99 -20.01 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA ASP P 260 " pdb=" C ASP P 260 " pdb=" N LYS P 261 " pdb=" CA LYS P 261 " ideal model delta harmonic sigma weight residual 180.00 160.08 19.92 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA ASN G 21 " pdb=" C ASN G 21 " pdb=" N PHE G 22 " pdb=" CA PHE G 22 " ideal model delta harmonic sigma weight residual -180.00 -160.17 -19.83 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 21052 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 3110 0.067 - 0.135: 351 0.135 - 0.202: 6 0.202 - 0.269: 0 0.269 - 0.336: 1 Chirality restraints: 3468 Sorted by residual: chirality pdb=" CA ALA P 69 " pdb=" N ALA P 69 " pdb=" C ALA P 69 " pdb=" CB ALA P 69 " both_signs ideal model delta sigma weight residual False 2.48 2.15 0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CA LEU A 214 " pdb=" N LEU A 214 " pdb=" C LEU A 214 " pdb=" CB LEU A 214 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.08e-01 chirality pdb=" CA ILE I 32 " pdb=" N ILE I 32 " pdb=" C ILE I 32 " pdb=" CB ILE I 32 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.32e-01 ... (remaining 3465 not shown) Planarity restraints: 6640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 211 " 0.012 2.00e-02 2.50e+03 2.32e-02 5.39e+00 pdb=" C ILE A 211 " -0.040 2.00e-02 2.50e+03 pdb=" O ILE A 211 " 0.015 2.00e-02 2.50e+03 pdb=" N ASP A 212 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE J 7 " -0.010 2.00e-02 2.50e+03 1.85e-02 3.41e+00 pdb=" N ASN J 8 " 0.032 2.00e-02 2.50e+03 pdb=" CA ASN J 8 " -0.008 2.00e-02 2.50e+03 pdb=" H ASN J 8 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG O 252 " -0.131 9.50e-02 1.11e+02 4.45e-02 3.30e+00 pdb=" NE ARG O 252 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG O 252 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG O 252 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG O 252 " 0.003 2.00e-02 2.50e+03 pdb="HH11 ARG O 252 " 0.003 2.00e-02 2.50e+03 pdb="HH12 ARG O 252 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG O 252 " -0.010 2.00e-02 2.50e+03 pdb="HH22 ARG O 252 " 0.008 2.00e-02 2.50e+03 ... (remaining 6637 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 1670 2.17 - 2.77: 89237 2.77 - 3.38: 126234 3.38 - 3.99: 164107 3.99 - 4.60: 257261 Nonbonded interactions: 638509 Sorted by model distance: nonbonded pdb=" OE2 GLU G 51 " pdb=" HD1 HIS G 204 " model vdw 1.557 1.850 nonbonded pdb=" HD1 HIS B 94 " pdb=" OG SER I 90 " model vdw 1.563 1.850 nonbonded pdb=" H LYS C 231 " pdb=" OE2 GLU C 234 " model vdw 1.585 1.850 nonbonded pdb=" HH TYR G 126 " pdb=" OE2 GLU H 87 " model vdw 1.593 1.850 nonbonded pdb=" OE2 GLU G 32 " pdb="HH12 ARG G 169 " model vdw 1.595 1.850 ... (remaining 638504 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.670 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: 0.730 Extract box with map and model: 12.730 Check model and map are aligned: 0.690 Set scattering table: 0.480 Process input model: 138.230 Find NCS groups from input model: 1.250 Set up NCS constraints: 0.110 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: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 160.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 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 : 0.003 0.051 22632 Z= 0.186 Angle : 0.553 8.250 30616 Z= 0.318 Chirality : 0.041 0.336 3468 Planarity : 0.003 0.059 3932 Dihedral : 12.740 89.786 8369 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.87 % 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: 0.77 (0.16), residues: 2792 helix: 1.51 (0.17), residues: 1002 sheet: 0.12 (0.20), residues: 608 loop : -0.01 (0.19), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 159 HIS 0.006 0.001 HIS A 209 PHE 0.024 0.001 PHE J 44 TYR 0.023 0.001 TYR K 135 ARG 0.011 0.000 ARG O 252 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 3.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.7747 (m-80) cc_final: 0.7522 (m-80) REVERT: B 57 MET cc_start: 0.8191 (mtm) cc_final: 0.7811 (mtm) REVERT: B 119 GLN cc_start: 0.8971 (tm-30) cc_final: 0.8691 (tm-30) REVERT: C 122 TYR cc_start: 0.8119 (m-10) cc_final: 0.7815 (m-10) REVERT: E 206 GLN cc_start: 0.9516 (tp-100) cc_final: 0.8932 (tp-100) REVERT: H 70 GLU cc_start: 0.8539 (tp30) cc_final: 0.7894 (tp30) REVERT: O 8 ASP cc_start: 0.7638 (m-30) cc_final: 0.7317 (p0) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.7433 time to fit residues: 252.5773 Evaluate side-chains 172 residues out of total 2431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 4.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 234 optimal weight: 1.9990 chunk 210 optimal weight: 0.9980 chunk 116 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 217 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 chunk 252 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 118 GLN I 64 HIS J 89 GLN K 63 ASN K 78 GLN ** K 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.0867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22632 Z= 0.286 Angle : 0.561 8.243 30616 Z= 0.308 Chirality : 0.043 0.330 3468 Planarity : 0.004 0.048 3932 Dihedral : 4.897 22.512 3057 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.49 % Allowed : 4.20 % Favored : 95.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.87 % 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: 0.58 (0.16), residues: 2792 helix: 1.43 (0.16), residues: 1023 sheet: 0.01 (0.20), residues: 621 loop : -0.25 (0.19), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 218 HIS 0.012 0.001 HIS H 139 PHE 0.019 0.001 PHE J 44 TYR 0.020 0.001 TYR J 96 ARG 0.004 0.000 ARG C 9 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 174 time to evaluate : 3.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ASP cc_start: 0.7659 (t0) cc_final: 0.7447 (m-30) REVERT: B 119 GLN cc_start: 0.8973 (tm-30) cc_final: 0.8688 (tm-30) REVERT: H 70 GLU cc_start: 0.8568 (tp30) cc_final: 0.7938 (tp30) REVERT: H 86 MET cc_start: 0.8689 (ttm) cc_final: 0.8450 (ttm) REVERT: K 127 GLU cc_start: 0.7138 (tm-30) cc_final: 0.6533 (tm-30) REVERT: O 8 ASP cc_start: 0.7722 (m-30) cc_final: 0.7191 (p0) outliers start: 12 outliers final: 9 residues processed: 181 average time/residue: 0.7489 time to fit residues: 215.7341 Evaluate side-chains 169 residues out of total 2431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 160 time to evaluate : 3.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain G residue 181 ASP Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain O residue 168 ILE Chi-restraints excluded: chain O residue 172 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 140 optimal weight: 0.0670 chunk 78 optimal weight: 3.9990 chunk 210 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 chunk 69 optimal weight: 0.2980 chunk 252 optimal weight: 4.9990 chunk 273 optimal weight: 5.9990 chunk 225 optimal weight: 3.9990 chunk 250 optimal weight: 7.9990 chunk 86 optimal weight: 4.9990 chunk 202 optimal weight: 3.9990 overall best weight: 2.0724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN D 231 GLN ** K 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 46 GLN ** O 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22632 Z= 0.290 Angle : 0.543 6.736 30616 Z= 0.295 Chirality : 0.042 0.336 3468 Planarity : 0.004 0.050 3932 Dihedral : 4.866 21.756 3057 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.58 % Allowed : 6.13 % Favored : 93.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.87 % 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: 0.38 (0.16), residues: 2792 helix: 1.35 (0.16), residues: 1032 sheet: -0.26 (0.20), residues: 638 loop : -0.36 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 218 HIS 0.012 0.001 HIS H 139 PHE 0.018 0.001 PHE J 44 TYR 0.022 0.001 TYR B 82 ARG 0.003 0.000 ARG A 14 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 164 time to evaluate : 4.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 119 GLN cc_start: 0.9006 (tm-30) cc_final: 0.8726 (tm-30) REVERT: C 9 ARG cc_start: 0.7947 (mtm-85) cc_final: 0.7444 (mtt90) REVERT: F 146 GLU cc_start: 0.6886 (tt0) cc_final: 0.6631 (tt0) REVERT: H 70 GLU cc_start: 0.8608 (tp30) cc_final: 0.8006 (tp30) REVERT: H 86 MET cc_start: 0.8666 (ttm) cc_final: 0.8425 (ttm) REVERT: I 93 GLU cc_start: 0.8685 (tp30) cc_final: 0.8199 (tm-30) REVERT: K 49 GLU cc_start: 0.8087 (pm20) cc_final: 0.7710 (pm20) REVERT: O 8 ASP cc_start: 0.7813 (m-30) cc_final: 0.7170 (p0) outliers start: 14 outliers final: 11 residues processed: 170 average time/residue: 0.7850 time to fit residues: 217.0890 Evaluate side-chains 164 residues out of total 2431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 153 time to evaluate : 3.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain G residue 181 ASP Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain O residue 168 ILE Chi-restraints excluded: chain O residue 172 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 249 optimal weight: 3.9990 chunk 190 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 120 optimal weight: 0.5980 chunk 169 optimal weight: 1.9990 chunk 253 optimal weight: 0.5980 chunk 268 optimal weight: 10.0000 chunk 132 optimal weight: 0.8980 chunk 240 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22632 Z= 0.211 Angle : 0.509 7.128 30616 Z= 0.274 Chirality : 0.041 0.332 3468 Planarity : 0.004 0.047 3932 Dihedral : 4.689 20.373 3057 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.70 % Allowed : 6.83 % Favored : 92.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.87 % 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: 0.51 (0.16), residues: 2792 helix: 1.50 (0.16), residues: 1033 sheet: -0.26 (0.20), residues: 639 loop : -0.28 (0.19), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 218 HIS 0.010 0.001 HIS H 139 PHE 0.016 0.001 PHE F 179 TYR 0.017 0.001 TYR C 122 ARG 0.003 0.000 ARG A 14 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 168 time to evaluate : 4.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 119 GLN cc_start: 0.8994 (tm-30) cc_final: 0.8692 (tm-30) REVERT: C 9 ARG cc_start: 0.7873 (mtm-85) cc_final: 0.7416 (mtt90) REVERT: H 70 GLU cc_start: 0.8579 (tp30) cc_final: 0.7942 (tp30) REVERT: H 86 MET cc_start: 0.8641 (ttm) cc_final: 0.8386 (ttm) REVERT: I 93 GLU cc_start: 0.8710 (tp30) cc_final: 0.8059 (tm-30) REVERT: I 168 GLU cc_start: 0.7717 (pm20) cc_final: 0.7280 (pm20) REVERT: I 207 MET cc_start: 0.7772 (mpp) cc_final: 0.7511 (mpp) REVERT: K 127 GLU cc_start: 0.7146 (tm-30) cc_final: 0.6495 (tm-30) REVERT: O 8 ASP cc_start: 0.7836 (m-30) cc_final: 0.7117 (p0) outliers start: 17 outliers final: 13 residues processed: 176 average time/residue: 0.7494 time to fit residues: 211.3031 Evaluate side-chains 168 residues out of total 2431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 155 time to evaluate : 3.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 163 TYR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain G residue 181 ASP Chi-restraints excluded: chain J residue 193 ASP Chi-restraints excluded: chain O residue 168 ILE Chi-restraints excluded: chain O residue 172 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 223 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 200 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 229 optimal weight: 0.5980 chunk 185 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 137 optimal weight: 3.9990 chunk 241 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS E 168 ASN ** K 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 22632 Z= 0.328 Angle : 0.546 7.129 30616 Z= 0.297 Chirality : 0.042 0.338 3468 Planarity : 0.004 0.050 3932 Dihedral : 4.784 21.642 3057 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.03 % Allowed : 7.86 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.87 % 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: 0.29 (0.16), residues: 2792 helix: 1.37 (0.16), residues: 1033 sheet: -0.39 (0.20), residues: 635 loop : -0.46 (0.19), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 218 HIS 0.007 0.001 HIS H 106 PHE 0.014 0.001 PHE F 147 TYR 0.019 0.001 TYR J 96 ARG 0.003 0.000 ARG P 259 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 152 time to evaluate : 3.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 119 GLN cc_start: 0.9008 (tm-30) cc_final: 0.8694 (tm-30) REVERT: C 9 ARG cc_start: 0.7955 (mtm-85) cc_final: 0.7476 (mtt90) REVERT: H 70 GLU cc_start: 0.8614 (tp30) cc_final: 0.8012 (tp30) REVERT: I 93 GLU cc_start: 0.8731 (tp30) cc_final: 0.8054 (tm-30) REVERT: K 127 GLU cc_start: 0.7141 (tm-30) cc_final: 0.6580 (tm-30) REVERT: O 8 ASP cc_start: 0.7751 (m-30) cc_final: 0.7030 (p0) outliers start: 25 outliers final: 17 residues processed: 166 average time/residue: 0.7597 time to fit residues: 201.9742 Evaluate side-chains 166 residues out of total 2431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 149 time to evaluate : 3.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 163 TYR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain G residue 181 ASP Chi-restraints excluded: chain J residue 59 ASP Chi-restraints excluded: chain J residue 193 ASP Chi-restraints excluded: chain O residue 168 ILE Chi-restraints excluded: chain O residue 172 ASP Chi-restraints excluded: chain P residue 124 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.6403 > 50: distance: 83 - 90: 5.899 distance: 84 - 85: 10.585 distance: 84 - 87: 5.525 distance: 84 - 91: 4.260 distance: 85 - 86: 8.778 distance: 85 - 97: 15.972 distance: 87 - 88: 3.467 distance: 88 - 93: 3.581 distance: 97 - 98: 11.591 distance: 97 - 103: 3.957 distance: 98 - 99: 21.491 distance: 98 - 101: 7.720 distance: 98 - 104: 20.568 distance: 99 - 100: 37.630 distance: 99 - 108: 35.516 distance: 101 - 102: 10.561 distance: 101 - 105: 9.107 distance: 101 - 106: 19.115 distance: 102 - 107: 6.667 distance: 108 - 116: 25.733 distance: 109 - 110: 46.543 distance: 109 - 112: 3.082 distance: 109 - 117: 27.307 distance: 110 - 111: 44.013 distance: 110 - 127: 47.733 distance: 112 - 113: 28.386 distance: 112 - 114: 12.799 distance: 112 - 118: 25.057 distance: 113 - 115: 8.692 distance: 113 - 119: 20.278 distance: 113 - 120: 25.251 distance: 114 - 121: 9.899 distance: 114 - 122: 16.041 distance: 114 - 123: 11.320 distance: 115 - 124: 14.811 distance: 115 - 125: 14.680 distance: 115 - 126: 15.576 distance: 127 - 128: 19.388 distance: 127 - 131: 47.577 distance: 128 - 129: 15.844 distance: 128 - 132: 36.847 distance: 128 - 133: 42.151 distance: 129 - 130: 31.556 distance: 129 - 134: 15.662 distance: 134 - 135: 21.953 distance: 134 - 141: 11.916 distance: 135 - 136: 30.310 distance: 135 - 138: 11.725 distance: 135 - 142: 36.102 distance: 136 - 137: 58.686 distance: 136 - 148: 48.327 distance: 138 - 139: 48.898 distance: 138 - 140: 13.949 distance: 138 - 143: 44.500 distance: 139 - 144: 40.336 distance: 140 - 145: 32.331 distance: 140 - 146: 17.863 distance: 140 - 147: 18.565 distance: 148 - 149: 39.919 distance: 148 - 152: 40.532 distance: 149 - 150: 41.428 distance: 149 - 153: 59.834 distance: 149 - 154: 26.596 distance: 150 - 151: 49.004 distance: 150 - 155: 47.601 distance: 155 - 156: 40.856 distance: 155 - 167: 44.730 distance: 156 - 157: 44.822 distance: 156 - 159: 40.781 distance: 156 - 168: 21.501 distance: 157 - 158: 27.982 distance: 157 - 176: 15.164 distance: 159 - 160: 35.923 distance: 159 - 169: 39.402 distance: 159 - 170: 42.771 distance: 160 - 161: 9.126 distance: 160 - 162: 18.059 distance: 161 - 163: 18.933 distance: 161 - 171: 15.690 distance: 162 - 164: 21.454 distance: 162 - 172: 34.168 distance: 163 - 165: 18.844 distance: 163 - 173: 11.386 distance: 164 - 165: 16.357 distance: 164 - 174: 14.270 distance: 165 - 166: 8.337 distance: 166 - 175: 6.784 distance: 176 - 177: 10.328 distance: 176 - 184: 37.826 distance: 177 - 178: 46.093 distance: 177 - 180: 11.405 distance: 177 - 185: 37.526 distance: 178 - 179: 16.596 distance: 178 - 188: 14.282 distance: 180 - 181: 16.583 distance: 180 - 186: 38.781 distance: 180 - 187: 21.914 distance: 181 - 182: 29.352 distance: 181 - 183: 22.834 distance: 188 - 189: 34.121 distance: 188 - 196: 41.965 distance: 189 - 190: 15.175 distance: 189 - 192: 30.068 distance: 189 - 197: 27.061 distance: 190 - 191: 52.017 distance: 190 - 207: 33.099 distance: 192 - 193: 38.725 distance: 192 - 198: 30.683 distance: 192 - 199: 49.474 distance: 193 - 194: 13.084 distance: 193 - 195: 16.654 distance: 193 - 200: 19.161 distance: 194 - 201: 6.726 distance: 194 - 202: 9.063 distance: 194 - 203: 8.141 distance: 195 - 204: 13.461 distance: 195 - 205: 12.633 distance: 195 - 206: 18.215