Starting phenix.real_space_refine on Sun May 18 02:24:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rr4_19457/05_2025/8rr4_19457.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rr4_19457/05_2025/8rr4_19457.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rr4_19457/05_2025/8rr4_19457.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rr4_19457/05_2025/8rr4_19457.map" model { file = "/net/cci-nas-00/data/ceres_data/8rr4_19457/05_2025/8rr4_19457.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rr4_19457/05_2025/8rr4_19457.cif" } resolution = 3.2 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= 0.008 sd= 1.123 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 76 5.49 5 S 85 5.16 5 C 10175 2.51 5 N 2911 2.21 5 O 3290 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 16539 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "B" Number of atoms: 1811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1811 Classifications: {'peptide': 250} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 237} Chain breaks: 1 Chain: "C" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "D" Number of atoms: 1827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1827 Classifications: {'peptide': 252} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 239} Chain breaks: 1 Chain: "E" Number of atoms: 5265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 672, 5265 Classifications: {'peptide': 672} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 631} Chain breaks: 3 Chain: "F" Number of atoms: 2287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2287 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 8, 'TRANS': 267} Chain breaks: 1 Chain: "T" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1625 Classifications: {'RNA': 76} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 7, 'rna3p_pur': 31, 'rna3p_pyr': 27} Link IDs: {'rna2p': 18, 'rna3p': 57} Chain breaks: 2 Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Time building chain proxies: 9.43, per 1000 atoms: 0.57 Number of scatterers: 16539 At special positions: 0 Unit cell: (126.768, 108.42, 175.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 85 16.00 P 76 15.00 O 3290 8.00 N 2911 7.00 C 10175 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: 4.13 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 901 " pdb="ZN ZN E 901 " - pdb=" NE2 HIS E 551 " pdb="ZN ZN E 901 " - pdb=" NE2 HIS E 724 " pdb=" ZN E 902 " pdb="ZN ZN E 902 " - pdb=" NE2 HIS E 546 " pdb="ZN ZN E 902 " - pdb=" NE2 HIS E 644 " pdb="ZN ZN E 902 " - pdb=" ND1 HIS E 548 " 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3572 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 14 sheets defined 49.1% alpha, 13.8% beta 26 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 5.33 Creating SS restraints... Processing helix chain 'A' and resid 21 through 34 removed outlier: 3.527A pdb=" N ALA A 25 " --> pdb=" O GLY A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 45 Processing helix chain 'A' and resid 46 through 55 removed outlier: 4.086A pdb=" N GLN A 50 " --> pdb=" O GLY A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 83 Processing helix chain 'A' and resid 110 through 122 Processing helix chain 'A' and resid 122 through 137 removed outlier: 4.057A pdb=" N GLY A 134 " --> pdb=" O ARG A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 159 Processing helix chain 'A' and resid 165 through 187 removed outlier: 4.575A pdb=" N LEU A 180 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Proline residue: A 181 - end of helix Processing helix chain 'A' and resid 203 through 208 Processing helix chain 'A' and resid 210 through 221 removed outlier: 3.644A pdb=" N VAL A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 243 Processing helix chain 'B' and resid 21 through 34 removed outlier: 3.526A pdb=" N ALA B 25 " --> pdb=" O GLY B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 45 Processing helix chain 'B' and resid 46 through 55 removed outlier: 4.087A pdb=" N GLN B 50 " --> pdb=" O GLY B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 83 Processing helix chain 'B' and resid 110 through 122 Processing helix chain 'B' and resid 122 through 137 removed outlier: 4.057A pdb=" N GLY B 134 " --> pdb=" O ARG B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 159 Processing helix chain 'B' and resid 165 through 187 removed outlier: 4.575A pdb=" N LEU B 180 " --> pdb=" O VAL B 176 " (cutoff:3.500A) Proline residue: B 181 - end of helix Processing helix chain 'B' and resid 213 through 221 removed outlier: 3.644A pdb=" N VAL B 221 " --> pdb=" O LEU B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 243 Processing helix chain 'C' and resid 21 through 34 removed outlier: 3.526A pdb=" N ALA C 25 " --> pdb=" O GLY C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 45 Processing helix chain 'C' and resid 46 through 55 removed outlier: 4.086A pdb=" N GLN C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 83 Processing helix chain 'C' and resid 110 through 122 Processing helix chain 'C' and resid 122 through 137 removed outlier: 4.057A pdb=" N GLY C 134 " --> pdb=" O ARG C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 159 Processing helix chain 'C' and resid 165 through 187 removed outlier: 4.575A pdb=" N LEU C 180 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Proline residue: C 181 - end of helix Processing helix chain 'C' and resid 205 through 209 removed outlier: 3.644A pdb=" N LEU C 209 " --> pdb=" O LEU C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 221 removed outlier: 3.667A pdb=" N VAL C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 243 Processing helix chain 'D' and resid 21 through 34 removed outlier: 3.527A pdb=" N ALA D 25 " --> pdb=" O GLY D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 45 Processing helix chain 'D' and resid 46 through 55 removed outlier: 4.087A pdb=" N GLN D 50 " --> pdb=" O GLY D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 83 Processing helix chain 'D' and resid 110 through 122 Processing helix chain 'D' and resid 122 through 137 removed outlier: 4.057A pdb=" N GLY D 134 " --> pdb=" O ARG D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 159 Processing helix chain 'D' and resid 165 through 187 removed outlier: 4.574A pdb=" N LEU D 180 " --> pdb=" O VAL D 176 " (cutoff:3.500A) Proline residue: D 181 - end of helix Processing helix chain 'D' and resid 212 through 221 removed outlier: 3.644A pdb=" N VAL D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 243 Processing helix chain 'E' and resid 90 through 98 Processing helix chain 'E' and resid 114 through 119 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'E' and resid 143 through 152 removed outlier: 3.531A pdb=" N LYS E 152 " --> pdb=" O LEU E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 261 Processing helix chain 'E' and resid 270 through 279 removed outlier: 3.690A pdb=" N ILE E 274 " --> pdb=" O ALA E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 288 Processing helix chain 'E' and resid 292 through 296 Processing helix chain 'E' and resid 313 through 315 No H-bonds generated for 'chain 'E' and resid 313 through 315' Processing helix chain 'E' and resid 316 through 323 Processing helix chain 'E' and resid 323 through 331 removed outlier: 3.721A pdb=" N GLN E 327 " --> pdb=" O ASN E 323 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR E 329 " --> pdb=" O THR E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 350 Processing helix chain 'E' and resid 351 through 360 Processing helix chain 'E' and resid 379 through 391 Processing helix chain 'E' and resid 442 through 452 removed outlier: 3.532A pdb=" N PHE E 446 " --> pdb=" O ASN E 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 467 removed outlier: 4.065A pdb=" N ALA E 467 " --> pdb=" O TYR E 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 519 through 529 Processing helix chain 'E' and resid 531 through 538 Processing helix chain 'E' and resid 554 through 570 Processing helix chain 'E' and resid 582 through 595 removed outlier: 4.169A pdb=" N ALA E 586 " --> pdb=" O ASN E 582 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TRP E 587 " --> pdb=" O GLN E 583 " (cutoff:3.500A) Processing helix chain 'E' and resid 598 through 600 No H-bonds generated for 'chain 'E' and resid 598 through 600' Processing helix chain 'E' and resid 608 through 611 Processing helix chain 'E' and resid 618 through 633 Processing helix chain 'E' and resid 670 through 677 removed outlier: 3.956A pdb=" N VAL E 674 " --> pdb=" O CYS E 670 " (cutoff:3.500A) Processing helix chain 'E' and resid 690 through 692 No H-bonds generated for 'chain 'E' and resid 690 through 692' Processing helix chain 'E' and resid 693 through 700 Processing helix chain 'E' and resid 704 through 716 Processing helix chain 'E' and resid 755 through 757 No H-bonds generated for 'chain 'E' and resid 755 through 757' Processing helix chain 'E' and resid 758 through 763 removed outlier: 4.343A pdb=" N LYS E 762 " --> pdb=" O PRO E 758 " (cutoff:3.500A) Processing helix chain 'E' and resid 763 through 771 Processing helix chain 'E' and resid 771 through 792 removed outlier: 3.533A pdb=" N ILE E 775 " --> pdb=" O PHE E 771 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 105 removed outlier: 3.588A pdb=" N TRP F 101 " --> pdb=" O PHE F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 122 Processing helix chain 'F' and resid 125 through 154 removed outlier: 3.736A pdb=" N ILE F 148 " --> pdb=" O LYS F 144 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS F 149 " --> pdb=" O ALA F 145 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS F 150 " --> pdb=" O ARG F 146 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU F 151 " --> pdb=" O GLN F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 202 removed outlier: 3.522A pdb=" N ASN F 186 " --> pdb=" O LEU F 182 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN F 200 " --> pdb=" O ALA F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 213 removed outlier: 4.478A pdb=" N ASN F 213 " --> pdb=" O ALA F 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 210 through 213' Processing helix chain 'F' and resid 216 through 237 Processing helix chain 'F' and resid 252 through 263 Processing helix chain 'F' and resid 264 through 268 removed outlier: 3.577A pdb=" N ASP F 267 " --> pdb=" O GLU F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 283 through 285 No H-bonds generated for 'chain 'F' and resid 283 through 285' Processing helix chain 'F' and resid 320 through 329 removed outlier: 3.676A pdb=" N LEU F 329 " --> pdb=" O LYS F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 341 removed outlier: 3.671A pdb=" N TYR F 341 " --> pdb=" O PRO F 337 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 337 through 341' Processing helix chain 'F' and resid 352 through 365 Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 374 through 376 No H-bonds generated for 'chain 'F' and resid 374 through 376' Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 62 removed outlier: 6.911A pdb=" N ALA A 37 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ALA A 61 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU A 39 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ALA A 88 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N THR A 153 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ASN A 90 " --> pdb=" O THR A 153 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 102 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 6.911A pdb=" N ALA B 37 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ALA B 61 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU B 39 " --> pdb=" O ALA B 61 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ALA B 88 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N THR B 153 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ASN B 90 " --> pdb=" O THR B 153 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 101 through 102 Processing sheet with id=AA5, first strand: chain 'C' and resid 58 through 62 removed outlier: 6.911A pdb=" N ALA C 37 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ALA C 61 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU C 39 " --> pdb=" O ALA C 61 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ALA C 88 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N THR C 153 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ASN C 90 " --> pdb=" O THR C 153 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 Processing sheet with id=AA7, first strand: chain 'D' and resid 58 through 62 removed outlier: 6.910A pdb=" N ALA D 37 " --> pdb=" O VAL D 59 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ALA D 61 " --> pdb=" O ALA D 37 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU D 39 " --> pdb=" O ALA D 61 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ALA D 88 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N THR D 153 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ASN D 90 " --> pdb=" O THR D 153 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 101 through 102 Processing sheet with id=AA9, first strand: chain 'E' and resid 162 through 167 removed outlier: 3.538A pdb=" N GLY E 140 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASP E 106 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N SER E 139 " --> pdb=" O ASP E 106 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILE E 108 " --> pdb=" O SER E 139 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ARG E 82 " --> pdb=" O ASN E 107 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N PHE E 109 " --> pdb=" O ARG E 82 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU E 84 " --> pdb=" O PHE E 109 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE E 85 " --> pdb=" O LEU E 74 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER E 67 " --> pdb=" O GLY E 71 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ALA E 73 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ALA E 65 " --> pdb=" O ALA E 73 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N TYR E 75 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL E 63 " --> pdb=" O TYR E 75 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N PHE E 77 " --> pdb=" O GLN E 61 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N GLN E 61 " --> pdb=" O PHE E 77 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 173 through 174 removed outlier: 3.846A pdb=" N TYR E 173 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N VAL E 241 " --> pdb=" O GLU E 310 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N GLU E 310 " --> pdb=" O VAL E 241 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU E 339 " --> pdb=" O ALA E 305 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 602 through 606 removed outlier: 6.186A pdb=" N LEU E 576 " --> pdb=" O SER E 603 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE E 605 " --> pdb=" O LEU E 576 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N VAL E 578 " --> pdb=" O ILE E 605 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU E 577 " --> pdb=" O ALA E 540 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N SER E 511 " --> pdb=" O ALA E 540 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL E 542 " --> pdb=" O SER E 511 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU E 513 " --> pdb=" O VAL E 542 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR E 510 " --> pdb=" O ILE E 506 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE E 506 " --> pdb=" O THR E 510 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N THR E 502 " --> pdb=" O LEU E 514 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ALA E 501 " --> pdb=" O LEU E 486 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N MET E 750 " --> pdb=" O PHE E 485 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 634 through 638 removed outlier: 6.863A pdb=" N VAL E 654 " --> pdb=" O GLU E 635 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N PHE E 637 " --> pdb=" O ALA E 652 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ALA E 652 " --> pdb=" O PHE E 637 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LYS E 660 " --> pdb=" O LEU E 682 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ILE E 684 " --> pdb=" O LYS E 660 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL E 662 " --> pdb=" O ILE E 684 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N GLU E 686 " --> pdb=" O VAL E 662 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LEU E 683 " --> pdb=" O MET E 721 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ASN E 723 " --> pdb=" O LEU E 683 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N HIS E 685 " --> pdb=" O ASN E 723 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 272 through 273 removed outlier: 6.508A pdb=" N LEU F 205 " --> pdb=" O TYR F 244 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N CYS F 246 " --> pdb=" O LEU F 205 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N PHE F 207 " --> pdb=" O CYS F 246 " (cutoff:3.500A) removed outlier: 8.772A pdb=" N ILE F 309 " --> pdb=" O PRO F 204 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL F 206 " --> pdb=" O ILE F 309 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N GLY F 310 " --> pdb=" O LEU F 290 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA F 332 " --> pdb=" O ILE F 287 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 342 through 344 removed outlier: 4.436A pdb=" N GLY F 383 " --> pdb=" O GLN F 343 " (cutoff:3.500A) 711 hydrogen bonds defined for protein. 2025 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 62 hydrogen bonds 108 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 5.99 Time building geometry restraints manager: 4.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2650 1.32 - 1.44: 4571 1.44 - 1.56: 9488 1.56 - 1.69: 149 1.69 - 1.81: 135 Bond restraints: 16993 Sorted by residual: bond pdb=" C PRO C 198 " pdb=" O PRO C 198 " ideal model delta sigma weight residual 1.234 1.193 0.040 1.14e-02 7.69e+03 1.25e+01 bond pdb=" CA SER C 208 " pdb=" CB SER C 208 " ideal model delta sigma weight residual 1.536 1.488 0.049 1.46e-02 4.69e+03 1.11e+01 bond pdb=" N PRO C 198 " pdb=" CA PRO C 198 " ideal model delta sigma weight residual 1.466 1.432 0.034 1.19e-02 7.06e+03 8.18e+00 bond pdb=" N LYS E 129 " pdb=" CA LYS E 129 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.17e-02 7.31e+03 7.07e+00 bond pdb=" O5' A T 66 " pdb=" C5' A T 66 " ideal model delta sigma weight residual 1.420 1.459 -0.039 1.50e-02 4.44e+03 6.61e+00 ... (remaining 16988 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 22927 1.82 - 3.65: 355 3.65 - 5.47: 75 5.47 - 7.30: 17 7.30 - 9.12: 3 Bond angle restraints: 23377 Sorted by residual: angle pdb=" N ALA F 93 " pdb=" CA ALA F 93 " pdb=" C ALA F 93 " ideal model delta sigma weight residual 112.38 103.26 9.12 1.22e+00 6.72e-01 5.59e+01 angle pdb=" CA HIS F 381 " pdb=" CB HIS F 381 " pdb=" CG HIS F 381 " ideal model delta sigma weight residual 113.80 120.30 -6.50 1.00e+00 1.00e+00 4.22e+01 angle pdb=" N LYS F 380 " pdb=" CA LYS F 380 " pdb=" C LYS F 380 " ideal model delta sigma weight residual 114.62 109.07 5.55 1.14e+00 7.69e-01 2.37e+01 angle pdb=" C PRO F 337 " pdb=" CA PRO F 337 " pdb=" CB PRO F 337 " ideal model delta sigma weight residual 112.89 107.15 5.74 1.31e+00 5.83e-01 1.92e+01 angle pdb=" N SER C 208 " pdb=" CA SER C 208 " pdb=" C SER C 208 " ideal model delta sigma weight residual 114.39 108.70 5.69 1.45e+00 4.76e-01 1.54e+01 ... (remaining 23372 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.65: 9524 24.65 - 49.31: 613 49.31 - 73.96: 182 73.96 - 98.61: 30 98.61 - 123.27: 2 Dihedral angle restraints: 10351 sinusoidal: 4794 harmonic: 5557 Sorted by residual: dihedral pdb=" O4' C T 64 " pdb=" C2' C T 64 " pdb=" C1' C T 64 " pdb=" C3' C T 64 " ideal model delta sinusoidal sigma weight residual 25.00 -8.35 33.35 1 8.00e+00 1.56e-02 2.47e+01 dihedral pdb=" C5' C T 65 " pdb=" C4' C T 65 " pdb=" C3' C T 65 " pdb=" O3' C T 65 " ideal model delta sinusoidal sigma weight residual 147.00 113.88 33.12 1 8.00e+00 1.56e-02 2.44e+01 dihedral pdb=" C4' C T 64 " pdb=" O4' C T 64 " pdb=" C1' C T 64 " pdb=" C2' C T 64 " ideal model delta sinusoidal sigma weight residual 3.00 -28.22 31.22 1 8.00e+00 1.56e-02 2.17e+01 ... (remaining 10348 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2549 0.093 - 0.186: 186 0.186 - 0.279: 4 0.279 - 0.373: 0 0.373 - 0.466: 8 Chirality restraints: 2747 Sorted by residual: chirality pdb=" P C T 65 " pdb=" OP1 C T 65 " pdb=" OP2 C T 65 " pdb=" O5' C T 65 " both_signs ideal model delta sigma weight residual True 2.41 -2.88 -0.47 2.00e-01 2.50e+01 5.42e+00 chirality pdb=" P A T 63 " pdb=" OP1 A T 63 " pdb=" OP2 A T 63 " pdb=" O5' A T 63 " both_signs ideal model delta sigma weight residual True 2.41 -2.88 -0.47 2.00e-01 2.50e+01 5.41e+00 chirality pdb=" P G T 67 " pdb=" OP1 G T 67 " pdb=" OP2 G T 67 " pdb=" O5' G T 67 " both_signs ideal model delta sigma weight residual True 2.41 -2.87 -0.46 2.00e-01 2.50e+01 5.20e+00 ... (remaining 2744 not shown) Planarity restraints: 2756 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 379 " 0.389 9.50e-02 1.11e+02 1.74e-01 1.86e+01 pdb=" NE ARG F 379 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG F 379 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG F 379 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG F 379 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 95 " -0.274 9.50e-02 1.11e+02 1.23e-01 9.25e+00 pdb=" NE ARG F 95 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG F 95 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG F 95 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG F 95 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 378 " 0.015 2.00e-02 2.50e+03 3.01e-02 9.08e+00 pdb=" C LYS F 378 " -0.052 2.00e-02 2.50e+03 pdb=" O LYS F 378 " 0.020 2.00e-02 2.50e+03 pdb=" N ARG F 379 " 0.018 2.00e-02 2.50e+03 ... (remaining 2753 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 122 2.55 - 3.14: 12727 3.14 - 3.73: 26990 3.73 - 4.31: 36648 4.31 - 4.90: 60379 Nonbonded interactions: 136866 Sorted by model distance: nonbonded pdb=" O ALA E 549 " pdb=" OD1 ASN E 550 " model vdw 1.967 3.040 nonbonded pdb=" OD2 ASP E 666 " pdb="ZN ZN E 901 " model vdw 2.083 2.230 nonbonded pdb=" OD2 ASP E 666 " pdb="ZN ZN E 902 " model vdw 2.089 2.230 nonbonded pdb=" OD1 ASP A 41 " pdb=" N LEU A 42 " model vdw 2.173 3.120 nonbonded pdb=" OD1 ASP D 41 " pdb=" N LEU D 42 " model vdw 2.174 3.120 ... (remaining 136861 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 7 through 206 or resid 212 through 261)) selection = chain 'B' selection = (chain 'C' and (resid 7 through 206 or resid 212 through 261)) selection = (chain 'D' and (resid 7 through 206 or resid 212 through 261)) } 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=0.87 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 4.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.650 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 42.980 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.060 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 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 : 0.005 0.261 16998 Z= 0.228 Angle : 0.571 9.124 23377 Z= 0.336 Chirality : 0.048 0.466 2747 Planarity : 0.005 0.174 2756 Dihedral : 17.639 123.267 6779 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.43 % Favored : 97.52 % Rotamer: Outliers : 0.50 % Allowed : 12.22 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % 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: 1.22 (0.20), residues: 1936 helix: 1.78 (0.18), residues: 805 sheet: 0.72 (0.31), residues: 358 loop : -0.10 (0.24), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 344 HIS 0.015 0.001 HIS F 381 PHE 0.013 0.001 PHE F 179 TYR 0.009 0.001 TYR F 341 ARG 0.003 0.000 ARG E 630 Details of bonding type rmsd hydrogen bonds : bond 0.22300 ( 773) hydrogen bonds : angle 7.01491 ( 2133) metal coordination : bond 0.25447 ( 5) covalent geometry : bond 0.00284 (16993) covalent geometry : angle 0.57135 (23377) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 188 time to evaluate : 1.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8452 (tttp) cc_final: 0.7392 (tttp) REVERT: B 259 MET cc_start: 0.8778 (mmm) cc_final: 0.8480 (mmp) REVERT: C 194 MET cc_start: 0.8172 (mmt) cc_final: 0.7914 (mmt) REVERT: E 145 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8849 (tm-30) REVERT: E 668 MET cc_start: 0.7935 (mtp) cc_final: 0.7428 (mtp) REVERT: E 715 MET cc_start: 0.8417 (ttp) cc_final: 0.8066 (ttm) outliers start: 8 outliers final: 3 residues processed: 196 average time/residue: 0.3299 time to fit residues: 93.6503 Evaluate side-chains 112 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 109 time to evaluate : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain E residue 129 LYS Chi-restraints excluded: chain F residue 278 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 169 optimal weight: 5.9990 chunk 152 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 102 optimal weight: 8.9990 chunk 81 optimal weight: 3.9990 chunk 157 optimal weight: 0.7980 chunk 60 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 117 optimal weight: 30.0000 chunk 182 optimal weight: 0.8980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 117 ASN E 418 GLN F 111 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.066764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.047502 restraints weight = 57207.369| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 2.88 r_work: 0.2673 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2678 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2678 r_free = 0.2678 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2678 r_free = 0.2678 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2678 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 16998 Z= 0.219 Angle : 0.578 7.851 23377 Z= 0.298 Chirality : 0.042 0.180 2747 Planarity : 0.004 0.050 2756 Dihedral : 15.694 123.745 3256 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.43 % Favored : 97.52 % Rotamer: Outliers : 1.83 % Allowed : 12.60 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % 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: 1.29 (0.20), residues: 1936 helix: 2.00 (0.18), residues: 845 sheet: 0.42 (0.29), residues: 360 loop : -0.20 (0.25), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 587 HIS 0.010 0.001 HIS E 546 PHE 0.012 0.001 PHE E 521 TYR 0.011 0.001 TYR E 463 ARG 0.005 0.000 ARG E 431 Details of bonding type rmsd hydrogen bonds : bond 0.05209 ( 773) hydrogen bonds : angle 4.95397 ( 2133) metal coordination : bond 0.00984 ( 5) covalent geometry : bond 0.00486 (16993) covalent geometry : angle 0.57769 (23377) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 1.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 41 ASP cc_start: 0.8060 (t70) cc_final: 0.7747 (t0) REVERT: B 135 GLU cc_start: 0.8973 (mm-30) cc_final: 0.8753 (tp30) REVERT: B 259 MET cc_start: 0.9251 (mmm) cc_final: 0.8893 (mmp) REVERT: C 64 ASP cc_start: 0.8429 (t0) cc_final: 0.8095 (t0) REVERT: C 259 MET cc_start: 0.9239 (mmm) cc_final: 0.8924 (mmm) REVERT: D 160 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7519 (pm20) REVERT: E 422 LEU cc_start: 0.9606 (OUTLIER) cc_final: 0.9397 (mm) REVERT: E 668 MET cc_start: 0.8739 (mtp) cc_final: 0.8509 (mtp) REVERT: F 129 LYS cc_start: 0.8655 (mtmt) cc_final: 0.8384 (mttt) outliers start: 29 outliers final: 13 residues processed: 133 average time/residue: 0.2644 time to fit residues: 55.7720 Evaluate side-chains 117 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 286 HIS Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 492 ILE Chi-restraints excluded: chain E residue 507 SER Chi-restraints excluded: chain E residue 546 HIS Chi-restraints excluded: chain E residue 693 LEU Chi-restraints excluded: chain F residue 111 HIS Chi-restraints excluded: chain F residue 343 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 115 optimal weight: 6.9990 chunk 104 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 160 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 61 GLN ** E 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.066719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.047557 restraints weight = 56609.480| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 2.83 r_work: 0.2676 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2681 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2681 r_free = 0.2681 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2681 r_free = 0.2681 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2681 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16998 Z= 0.162 Angle : 0.520 7.951 23377 Z= 0.263 Chirality : 0.041 0.158 2747 Planarity : 0.004 0.049 2756 Dihedral : 15.607 122.495 3246 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.17 % Favored : 97.78 % Rotamer: Outliers : 1.58 % Allowed : 13.04 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % 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: 1.29 (0.20), residues: 1936 helix: 2.10 (0.18), residues: 846 sheet: 0.23 (0.29), residues: 362 loop : -0.26 (0.25), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 587 HIS 0.010 0.001 HIS F 111 PHE 0.013 0.001 PHE E 521 TYR 0.009 0.001 TYR E 463 ARG 0.004 0.000 ARG E 431 Details of bonding type rmsd hydrogen bonds : bond 0.04537 ( 773) hydrogen bonds : angle 4.61087 ( 2133) metal coordination : bond 0.00388 ( 5) covalent geometry : bond 0.00364 (16993) covalent geometry : angle 0.51964 (23377) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 1.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 135 GLU cc_start: 0.9014 (mm-30) cc_final: 0.8788 (tp30) REVERT: B 259 MET cc_start: 0.9238 (mmm) cc_final: 0.8983 (mmp) REVERT: C 64 ASP cc_start: 0.8506 (t0) cc_final: 0.8298 (t0) REVERT: C 259 MET cc_start: 0.9229 (mmm) cc_final: 0.8938 (mmm) REVERT: D 160 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7698 (pm20) REVERT: E 416 MET cc_start: 0.9052 (ppp) cc_final: 0.8448 (ppp) REVERT: E 668 MET cc_start: 0.8741 (mtp) cc_final: 0.8524 (mtp) REVERT: F 129 LYS cc_start: 0.8597 (mtmt) cc_final: 0.8325 (mttt) outliers start: 25 outliers final: 11 residues processed: 127 average time/residue: 0.2640 time to fit residues: 53.4669 Evaluate side-chains 111 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 492 ILE Chi-restraints excluded: chain E residue 546 HIS Chi-restraints excluded: chain E residue 547 LEU Chi-restraints excluded: chain E residue 691 ASP Chi-restraints excluded: chain F residue 117 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 159 optimal weight: 7.9990 chunk 137 optimal weight: 4.9990 chunk 163 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 109 optimal weight: 6.9990 chunk 144 optimal weight: 0.8980 chunk 154 optimal weight: 6.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 111 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.064845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.045524 restraints weight = 57289.681| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 2.85 r_work: 0.2615 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2621 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2621 r_free = 0.2621 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2621 r_free = 0.2621 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2621 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 16998 Z= 0.278 Angle : 0.602 9.142 23377 Z= 0.304 Chirality : 0.043 0.143 2747 Planarity : 0.004 0.049 2756 Dihedral : 15.675 124.355 3246 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.00 % Favored : 96.95 % Rotamer: Outliers : 2.21 % Allowed : 14.11 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % 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: 1.02 (0.20), residues: 1936 helix: 1.93 (0.18), residues: 853 sheet: 0.03 (0.28), residues: 356 loop : -0.45 (0.24), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 587 HIS 0.006 0.001 HIS F 111 PHE 0.013 0.001 PHE F 97 TYR 0.011 0.001 TYR E 729 ARG 0.004 0.000 ARG E 675 Details of bonding type rmsd hydrogen bonds : bond 0.05001 ( 773) hydrogen bonds : angle 4.73233 ( 2133) metal coordination : bond 0.00519 ( 5) covalent geometry : bond 0.00629 (16993) covalent geometry : angle 0.60206 (23377) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 106 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 ASP cc_start: 0.9252 (m-30) cc_final: 0.8960 (m-30) REVERT: B 135 GLU cc_start: 0.9036 (mm-30) cc_final: 0.8695 (tp30) REVERT: B 259 MET cc_start: 0.9260 (mmm) cc_final: 0.9034 (mmp) REVERT: C 259 MET cc_start: 0.9312 (mmm) cc_final: 0.9082 (mmm) REVERT: D 160 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.7950 (pm20) REVERT: E 416 MET cc_start: 0.9128 (ppp) cc_final: 0.8369 (ppp) REVERT: F 97 PHE cc_start: 0.9051 (m-10) cc_final: 0.8780 (m-10) REVERT: F 129 LYS cc_start: 0.8601 (mtmt) cc_final: 0.8350 (mttt) outliers start: 35 outliers final: 18 residues processed: 132 average time/residue: 0.2437 time to fit residues: 51.5934 Evaluate side-chains 117 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 1.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 286 HIS Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 507 SER Chi-restraints excluded: chain E residue 546 HIS Chi-restraints excluded: chain E residue 691 ASP Chi-restraints excluded: chain E residue 693 LEU Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain F residue 111 HIS Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 122 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 60 optimal weight: 0.7980 chunk 176 optimal weight: 2.9990 chunk 135 optimal weight: 10.0000 chunk 132 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 154 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 162 optimal weight: 0.0970 chunk 25 optimal weight: 4.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 98 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.066709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.047520 restraints weight = 57312.234| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 2.85 r_work: 0.2674 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2680 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2680 r_free = 0.2680 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2680 r_free = 0.2680 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2680 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16998 Z= 0.101 Angle : 0.501 7.927 23377 Z= 0.252 Chirality : 0.040 0.140 2747 Planarity : 0.004 0.048 2756 Dihedral : 15.597 121.067 3246 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.01 % Favored : 97.93 % Rotamer: Outliers : 1.32 % Allowed : 15.37 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % 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: 1.25 (0.20), residues: 1936 helix: 2.15 (0.18), residues: 853 sheet: 0.18 (0.28), residues: 366 loop : -0.39 (0.25), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 115 HIS 0.009 0.001 HIS F 111 PHE 0.015 0.001 PHE E 735 TYR 0.009 0.001 TYR E 729 ARG 0.005 0.000 ARG E 781 Details of bonding type rmsd hydrogen bonds : bond 0.03749 ( 773) hydrogen bonds : angle 4.34440 ( 2133) metal coordination : bond 0.00114 ( 5) covalent geometry : bond 0.00218 (16993) covalent geometry : angle 0.50098 (23377) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 1.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 GLU cc_start: 0.7755 (tm-30) cc_final: 0.7531 (tp30) REVERT: B 70 ASP cc_start: 0.9247 (m-30) cc_final: 0.8949 (m-30) REVERT: B 160 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8448 (mt-10) REVERT: C 64 ASP cc_start: 0.8473 (t0) cc_final: 0.8218 (t0) REVERT: C 194 MET cc_start: 0.9225 (mmm) cc_final: 0.8898 (mmt) REVERT: E 416 MET cc_start: 0.9112 (ppp) cc_final: 0.8439 (ppp) REVERT: F 129 LYS cc_start: 0.8651 (mtmt) cc_final: 0.8368 (mttt) outliers start: 21 outliers final: 14 residues processed: 128 average time/residue: 0.2504 time to fit residues: 52.1184 Evaluate side-chains 118 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 507 SER Chi-restraints excluded: chain E residue 546 HIS Chi-restraints excluded: chain E residue 628 LEU Chi-restraints excluded: chain E residue 691 ASP Chi-restraints excluded: chain E residue 693 LEU Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 122 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 50 optimal weight: 7.9990 chunk 84 optimal weight: 3.9990 chunk 170 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 200 optimal weight: 20.0000 chunk 110 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 154 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.065893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.046717 restraints weight = 57246.663| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 2.81 r_work: 0.2653 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2658 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2658 r_free = 0.2658 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2658 r_free = 0.2658 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2658 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16998 Z= 0.160 Angle : 0.527 7.848 23377 Z= 0.263 Chirality : 0.040 0.135 2747 Planarity : 0.004 0.047 2756 Dihedral : 15.523 118.812 3246 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.48 % Favored : 97.47 % Rotamer: Outliers : 1.64 % Allowed : 15.69 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % 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: 1.24 (0.20), residues: 1936 helix: 2.19 (0.18), residues: 855 sheet: 0.13 (0.28), residues: 366 loop : -0.44 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 115 HIS 0.004 0.001 HIS E 546 PHE 0.012 0.001 PHE E 521 TYR 0.009 0.001 TYR E 729 ARG 0.002 0.000 ARG E 104 Details of bonding type rmsd hydrogen bonds : bond 0.04030 ( 773) hydrogen bonds : angle 4.33332 ( 2133) metal coordination : bond 0.00266 ( 5) covalent geometry : bond 0.00363 (16993) covalent geometry : angle 0.52732 (23377) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 1.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.9050 (t70) cc_final: 0.8689 (t0) REVERT: A 211 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7577 (tp30) REVERT: B 70 ASP cc_start: 0.9253 (m-30) cc_final: 0.8961 (m-30) REVERT: B 160 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8533 (mt-10) REVERT: E 262 MET cc_start: 0.8801 (ppp) cc_final: 0.8107 (ppp) REVERT: E 416 MET cc_start: 0.9125 (ppp) cc_final: 0.8520 (ppp) REVERT: F 129 LYS cc_start: 0.8654 (mtmt) cc_final: 0.8385 (mttt) outliers start: 26 outliers final: 18 residues processed: 129 average time/residue: 0.2416 time to fit residues: 50.3800 Evaluate side-chains 118 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 507 SER Chi-restraints excluded: chain E residue 546 HIS Chi-restraints excluded: chain E residue 628 LEU Chi-restraints excluded: chain E residue 691 ASP Chi-restraints excluded: chain E residue 693 LEU Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 122 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 167 optimal weight: 6.9990 chunk 113 optimal weight: 10.0000 chunk 147 optimal weight: 0.9980 chunk 48 optimal weight: 0.0870 chunk 129 optimal weight: 2.9990 chunk 162 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.066310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.047165 restraints weight = 56996.798| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 2.86 r_work: 0.2662 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2666 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2666 r_free = 0.2666 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2666 r_free = 0.2666 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2666 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16998 Z= 0.136 Angle : 0.525 8.706 23377 Z= 0.261 Chirality : 0.040 0.163 2747 Planarity : 0.004 0.047 2756 Dihedral : 15.455 116.560 3246 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.27 % Favored : 97.68 % Rotamer: Outliers : 1.20 % Allowed : 16.57 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % 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: 1.27 (0.20), residues: 1936 helix: 2.20 (0.18), residues: 856 sheet: 0.19 (0.28), residues: 366 loop : -0.46 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 433 HIS 0.004 0.000 HIS E 546 PHE 0.012 0.001 PHE E 521 TYR 0.011 0.001 TYR F 214 ARG 0.002 0.000 ARG A 130 Details of bonding type rmsd hydrogen bonds : bond 0.03721 ( 773) hydrogen bonds : angle 4.23775 ( 2133) metal coordination : bond 0.00185 ( 5) covalent geometry : bond 0.00308 (16993) covalent geometry : angle 0.52453 (23377) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 1.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.9061 (t70) cc_final: 0.8707 (t0) REVERT: B 70 ASP cc_start: 0.9257 (m-30) cc_final: 0.8952 (m-30) REVERT: B 160 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8485 (mt-10) REVERT: E 416 MET cc_start: 0.9145 (ppp) cc_final: 0.8524 (ppp) REVERT: F 129 LYS cc_start: 0.8657 (mtmt) cc_final: 0.8400 (mttt) outliers start: 19 outliers final: 17 residues processed: 119 average time/residue: 0.2523 time to fit residues: 49.2717 Evaluate side-chains 120 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 507 SER Chi-restraints excluded: chain E residue 546 HIS Chi-restraints excluded: chain E residue 628 LEU Chi-restraints excluded: chain E residue 691 ASP Chi-restraints excluded: chain E residue 693 LEU Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 122 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 139 optimal weight: 0.9980 chunk 169 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 116 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 165 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.066502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.047409 restraints weight = 56862.772| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 2.83 r_work: 0.2668 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2673 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2673 r_free = 0.2673 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2673 r_free = 0.2673 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2673 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16998 Z= 0.126 Angle : 0.522 8.555 23377 Z= 0.260 Chirality : 0.040 0.149 2747 Planarity : 0.004 0.046 2756 Dihedral : 15.367 114.112 3246 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.38 % Favored : 97.57 % Rotamer: Outliers : 1.39 % Allowed : 16.45 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % 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: 1.31 (0.20), residues: 1936 helix: 2.25 (0.18), residues: 856 sheet: 0.22 (0.28), residues: 366 loop : -0.45 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 433 HIS 0.004 0.000 HIS E 546 PHE 0.012 0.001 PHE E 521 TYR 0.006 0.001 TYR E 729 ARG 0.003 0.000 ARG C 252 Details of bonding type rmsd hydrogen bonds : bond 0.03626 ( 773) hydrogen bonds : angle 4.17753 ( 2133) metal coordination : bond 0.00165 ( 5) covalent geometry : bond 0.00284 (16993) covalent geometry : angle 0.52213 (23377) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 1.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.9048 (t70) cc_final: 0.8690 (t0) REVERT: B 70 ASP cc_start: 0.9264 (m-30) cc_final: 0.8967 (m-30) REVERT: B 160 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8463 (mt-10) REVERT: B 217 LEU cc_start: 0.8691 (mt) cc_final: 0.8456 (mt) REVERT: D 160 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8103 (pm20) REVERT: E 343 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.8279 (mtm) REVERT: E 416 MET cc_start: 0.9143 (ppp) cc_final: 0.8531 (ppp) REVERT: F 129 LYS cc_start: 0.8641 (mtmt) cc_final: 0.8383 (mttt) outliers start: 22 outliers final: 16 residues processed: 124 average time/residue: 0.2570 time to fit residues: 51.6076 Evaluate side-chains 125 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 343 MET Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 507 SER Chi-restraints excluded: chain E residue 546 HIS Chi-restraints excluded: chain E residue 628 LEU Chi-restraints excluded: chain E residue 691 ASP Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain F residue 117 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.5086 > 50: distance: 65 - 92: 6.391 distance: 68 - 73: 4.264 distance: 69 - 99: 11.650 distance: 74 - 77: 4.643 distance: 75 - 76: 4.191 distance: 76 - 107: 6.308 distance: 77 - 78: 3.076 distance: 78 - 79: 4.640 distance: 78 - 80: 4.895 distance: 79 - 81: 4.383 distance: 81 - 83: 7.748 distance: 82 - 83: 3.749 distance: 84 - 85: 5.286 distance: 85 - 86: 3.268 distance: 86 - 87: 4.498 distance: 87 - 118: 9.345 distance: 89 - 90: 4.838 distance: 89 - 91: 6.983 distance: 92 - 93: 5.530 distance: 93 - 94: 5.310 distance: 93 - 96: 4.870 distance: 94 - 95: 8.903 distance: 94 - 99: 7.320 distance: 95 - 126: 6.193 distance: 96 - 97: 6.680 distance: 96 - 98: 8.241 distance: 99 - 100: 3.959 distance: 100 - 101: 7.272 distance: 101 - 102: 7.309 distance: 101 - 107: 4.859 distance: 102 - 133: 15.152 distance: 103 - 104: 7.618 distance: 103 - 105: 10.055 distance: 104 - 106: 4.787 distance: 107 - 108: 3.179 distance: 109 - 110: 8.103 distance: 109 - 118: 4.269 distance: 112 - 113: 5.916 distance: 114 - 115: 7.794 distance: 115 - 116: 13.415 distance: 115 - 117: 6.508 distance: 119 - 120: 3.436 distance: 119 - 122: 4.833 distance: 120 - 121: 5.061 distance: 121 - 142: 6.926 distance: 122 - 123: 10.050 distance: 123 - 124: 6.244 distance: 123 - 125: 14.341 distance: 126 - 127: 6.138 distance: 127 - 130: 8.657 distance: 128 - 129: 7.462 distance: 128 - 133: 9.474 distance: 129 - 151: 7.276 distance: 130 - 131: 8.215 distance: 130 - 132: 9.862 distance: 133 - 134: 7.587 distance: 134 - 135: 12.239 distance: 134 - 137: 7.731 distance: 135 - 136: 25.893 distance: 135 - 138: 18.502 distance: 136 - 159: 22.119 distance: 138 - 139: 10.083 distance: 139 - 140: 32.413 distance: 140 - 141: 20.968 distance: 140 - 142: 10.911 distance: 142 - 143: 9.178 distance: 143 - 144: 7.064 distance: 143 - 146: 4.030 distance: 144 - 145: 8.204 distance: 146 - 147: 9.937 distance: 147 - 148: 4.268 distance: 148 - 149: 5.200 distance: 148 - 150: 9.212