Starting phenix.real_space_refine on Mon Jul 6 05:01:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uva_42613/07_2026/8uva_42613_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uva_42613/07_2026/8uva_42613.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uva_42613/07_2026/8uva_42613.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uva_42613/07_2026/8uva_42613.map" model { file = "/net/cci-nas-00/data/ceres_data/8uva_42613/07_2026/8uva_42613_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uva_42613/07_2026/8uva_42613_trim.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.288 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: 7 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 56 5.16 5 C 10456 2.51 5 N 2940 2.21 5 O 3184 1.98 5 H 16292 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32944 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 8162 Classifications: {'peptide': 535} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 501} Chain breaks: 1 Chain: "B" Number of atoms: 8162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 8162 Classifications: {'peptide': 535} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 501} Chain breaks: 1 Chain: "C" Number of atoms: 8162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 8162 Classifications: {'peptide': 535} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 501} Chain breaks: 1 Chain: "D" Number of atoms: 8162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 8162 Classifications: {'peptide': 535} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 501} Chain breaks: 1 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Classifications: {'peptide': 1} Modifications used: {'COO': 1, 'NH3': 1} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 54 Unusual residues: {' MG': 1, 'UTP': 1, 'XMW': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Classifications: {'peptide': 1} Modifications used: {'COO': 1, 'NH3': 1} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 54 Unusual residues: {' MG': 1, 'UTP': 1, 'XMW': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Classifications: {'peptide': 1} Modifications used: {'COO': 1, 'NH3': 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 54 Unusual residues: {' MG': 1, 'UTP': 1, 'XMW': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Classifications: {'peptide': 1} Modifications used: {'COO': 1, 'NH3': 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 54 Unusual residues: {' MG': 1, 'UTP': 1, 'XMW': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.93, per 1000 atoms: 0.15 Number of scatterers: 32944 At special positions: 0 Unit cell: (130.665, 135.723, 98.631, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 56 16.00 P 12 15.00 Mg 4 11.99 O 3184 8.00 N 2940 7.00 C 10456 6.00 H 16292 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 - 3.00 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: 3.22 Conformation dependent library (CDL) restraints added in 1.0 seconds 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3904 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 20 sheets defined 47.2% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 23 through 38 Processing helix chain 'A' and resid 54 through 58 removed outlier: 3.871A pdb=" N THR A 57 " --> pdb=" O ASP A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 64 Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.529A pdb=" N HIS A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 98 through 111 Processing helix chain 'A' and resid 123 through 136 removed outlier: 3.853A pdb=" N MET A 136 " --> pdb=" O ARG A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 161 No H-bonds generated for 'chain 'A' and resid 159 through 161' Processing helix chain 'A' and resid 162 through 177 Processing helix chain 'A' and resid 200 through 212 Processing helix chain 'A' and resid 229 through 241 Processing helix chain 'A' and resid 243 through 245 No H-bonds generated for 'chain 'A' and resid 243 through 245' Processing helix chain 'A' and resid 255 through 257 No H-bonds generated for 'chain 'A' and resid 255 through 257' Processing helix chain 'A' and resid 258 through 266 Processing helix chain 'A' and resid 267 through 277 Processing helix chain 'A' and resid 285 through 297 Processing helix chain 'A' and resid 314 through 316 No H-bonds generated for 'chain 'A' and resid 314 through 316' Processing helix chain 'A' and resid 317 through 330 removed outlier: 3.532A pdb=" N LYS A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 346 Processing helix chain 'A' and resid 347 through 355 Processing helix chain 'A' and resid 372 through 386 Processing helix chain 'A' and resid 393 through 407 Processing helix chain 'A' and resid 459 through 466 Processing helix chain 'A' and resid 484 through 489 Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 524 through 528 Processing helix chain 'A' and resid 535 through 552 Processing helix chain 'B' and resid 23 through 38 Processing helix chain 'B' and resid 54 through 58 removed outlier: 3.874A pdb=" N THR B 57 " --> pdb=" O ASP B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 64 Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.530A pdb=" N HIS B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 98 through 111 Processing helix chain 'B' and resid 123 through 136 removed outlier: 3.853A pdb=" N MET B 136 " --> pdb=" O ARG B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 161 No H-bonds generated for 'chain 'B' and resid 159 through 161' Processing helix chain 'B' and resid 162 through 177 Processing helix chain 'B' and resid 200 through 212 Processing helix chain 'B' and resid 229 through 241 Processing helix chain 'B' and resid 243 through 245 No H-bonds generated for 'chain 'B' and resid 243 through 245' Processing helix chain 'B' and resid 255 through 257 No H-bonds generated for 'chain 'B' and resid 255 through 257' Processing helix chain 'B' and resid 258 through 266 Processing helix chain 'B' and resid 267 through 277 Processing helix chain 'B' and resid 285 through 297 Processing helix chain 'B' and resid 314 through 316 No H-bonds generated for 'chain 'B' and resid 314 through 316' Processing helix chain 'B' and resid 317 through 330 removed outlier: 3.531A pdb=" N LYS B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 346 Processing helix chain 'B' and resid 347 through 355 Processing helix chain 'B' and resid 372 through 386 Processing helix chain 'B' and resid 393 through 407 Processing helix chain 'B' and resid 459 through 466 Processing helix chain 'B' and resid 484 through 489 Processing helix chain 'B' and resid 490 through 492 No H-bonds generated for 'chain 'B' and resid 490 through 492' Processing helix chain 'B' and resid 524 through 528 Processing helix chain 'B' and resid 535 through 552 Processing helix chain 'C' and resid 23 through 38 Processing helix chain 'C' and resid 54 through 58 removed outlier: 3.869A pdb=" N THR C 57 " --> pdb=" O ASP C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 64 Processing helix chain 'C' and resid 77 through 87 removed outlier: 3.529A pdb=" N HIS C 81 " --> pdb=" O LEU C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 93 No H-bonds generated for 'chain 'C' and resid 91 through 93' Processing helix chain 'C' and resid 98 through 111 Processing helix chain 'C' and resid 123 through 136 removed outlier: 3.851A pdb=" N MET C 136 " --> pdb=" O ARG C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 161 No H-bonds generated for 'chain 'C' and resid 159 through 161' Processing helix chain 'C' and resid 162 through 177 Processing helix chain 'C' and resid 200 through 212 Processing helix chain 'C' and resid 229 through 241 Processing helix chain 'C' and resid 243 through 245 No H-bonds generated for 'chain 'C' and resid 243 through 245' Processing helix chain 'C' and resid 255 through 257 No H-bonds generated for 'chain 'C' and resid 255 through 257' Processing helix chain 'C' and resid 258 through 266 Processing helix chain 'C' and resid 267 through 277 Processing helix chain 'C' and resid 285 through 297 Processing helix chain 'C' and resid 314 through 316 No H-bonds generated for 'chain 'C' and resid 314 through 316' Processing helix chain 'C' and resid 317 through 330 removed outlier: 3.532A pdb=" N LYS C 330 " --> pdb=" O ALA C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 346 Processing helix chain 'C' and resid 347 through 355 Processing helix chain 'C' and resid 372 through 386 Processing helix chain 'C' and resid 393 through 407 Processing helix chain 'C' and resid 459 through 466 Processing helix chain 'C' and resid 484 through 489 Processing helix chain 'C' and resid 490 through 492 No H-bonds generated for 'chain 'C' and resid 490 through 492' Processing helix chain 'C' and resid 524 through 528 Processing helix chain 'C' and resid 535 through 552 Processing helix chain 'D' and resid 23 through 38 Processing helix chain 'D' and resid 54 through 58 removed outlier: 3.870A pdb=" N THR D 57 " --> pdb=" O ASP D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 64 Processing helix chain 'D' and resid 77 through 87 removed outlier: 3.529A pdb=" N HIS D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'D' and resid 98 through 111 Processing helix chain 'D' and resid 123 through 136 removed outlier: 3.853A pdb=" N MET D 136 " --> pdb=" O ARG D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 161 No H-bonds generated for 'chain 'D' and resid 159 through 161' Processing helix chain 'D' and resid 162 through 177 Processing helix chain 'D' and resid 200 through 212 Processing helix chain 'D' and resid 229 through 241 Processing helix chain 'D' and resid 243 through 245 No H-bonds generated for 'chain 'D' and resid 243 through 245' Processing helix chain 'D' and resid 255 through 257 No H-bonds generated for 'chain 'D' and resid 255 through 257' Processing helix chain 'D' and resid 258 through 266 Processing helix chain 'D' and resid 267 through 277 Processing helix chain 'D' and resid 285 through 297 Processing helix chain 'D' and resid 314 through 316 No H-bonds generated for 'chain 'D' and resid 314 through 316' Processing helix chain 'D' and resid 317 through 330 removed outlier: 3.529A pdb=" N LYS D 330 " --> pdb=" O ALA D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 346 Processing helix chain 'D' and resid 347 through 355 Processing helix chain 'D' and resid 372 through 386 Processing helix chain 'D' and resid 393 through 407 Processing helix chain 'D' and resid 459 through 466 Processing helix chain 'D' and resid 484 through 489 Processing helix chain 'D' and resid 490 through 492 No H-bonds generated for 'chain 'D' and resid 490 through 492' Processing helix chain 'D' and resid 524 through 528 Processing helix chain 'D' and resid 535 through 552 Processing sheet with id=AA1, first strand: chain 'A' and resid 95 through 97 removed outlier: 6.574A pdb=" N LYS A 10 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N THR A 151 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU A 12 " --> pdb=" O THR A 151 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ILE A 153 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL A 14 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N HIS A 11 " --> pdb=" O PHE A 182 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU A 184 " --> pdb=" O HIS A 11 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N PHE A 13 " --> pdb=" O LEU A 184 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N VAL A 186 " --> pdb=" O PHE A 13 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N SER A 15 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N LEU A 188 " --> pdb=" O SER A 15 " (cutoff:3.500A) removed outlier: 9.119A pdb=" N ALA A 219 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N PHE A 183 " --> pdb=" O ALA A 219 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ILE A 221 " --> pdb=" O PHE A 183 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N HIS A 185 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ARG A 223 " --> pdb=" O HIS A 185 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N SER A 187 " --> pdb=" O ARG A 223 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU A 220 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N THR A 250 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LEU A 222 " --> pdb=" O THR A 250 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 68 Processing sheet with id=AA3, first strand: chain 'A' and resid 191 through 192 Processing sheet with id=AA4, first strand: chain 'A' and resid 334 through 341 removed outlier: 6.318A pdb=" N VAL A 302 " --> pdb=" O GLU A 336 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N CYS A 338 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE A 304 " --> pdb=" O CYS A 338 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL A 340 " --> pdb=" O ILE A 304 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N LEU A 306 " --> pdb=" O VAL A 340 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL A 361 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N LEU A 392 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE A 363 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLY A 497 " --> pdb=" O GLU A 506 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL A 508 " --> pdb=" O PHE A 495 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N PHE A 495 " --> pdb=" O VAL A 508 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 413 through 414 removed outlier: 6.722A pdb=" N ASN A 413 " --> pdb=" O ILE A 426 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 95 through 97 removed outlier: 6.650A pdb=" N THR B 43 " --> pdb=" O ILE B 150 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N GLU B 152 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLN B 45 " --> pdb=" O GLU B 152 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LYS B 10 " --> pdb=" O VAL B 149 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N THR B 151 " --> pdb=" O LYS B 10 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU B 12 " --> pdb=" O THR B 151 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ILE B 153 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL B 14 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N HIS B 11 " --> pdb=" O PHE B 182 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N LEU B 184 " --> pdb=" O HIS B 11 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N PHE B 13 " --> pdb=" O LEU B 184 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N VAL B 186 " --> pdb=" O PHE B 13 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N SER B 15 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 8.804A pdb=" N LEU B 188 " --> pdb=" O SER B 15 " (cutoff:3.500A) removed outlier: 9.121A pdb=" N ALA B 219 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N PHE B 183 " --> pdb=" O ALA B 219 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE B 221 " --> pdb=" O PHE B 183 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N HIS B 185 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N ARG B 223 " --> pdb=" O HIS B 185 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N SER B 187 " --> pdb=" O ARG B 223 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU B 220 " --> pdb=" O ILE B 248 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N THR B 250 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU B 222 " --> pdb=" O THR B 250 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 67 through 68 Processing sheet with id=AA8, first strand: chain 'B' and resid 191 through 192 Processing sheet with id=AA9, first strand: chain 'B' and resid 334 through 341 removed outlier: 6.320A pdb=" N VAL B 302 " --> pdb=" O GLU B 336 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N CYS B 338 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ILE B 304 " --> pdb=" O CYS B 338 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL B 340 " --> pdb=" O ILE B 304 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N LEU B 306 " --> pdb=" O VAL B 340 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL B 361 " --> pdb=" O LEU B 390 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N LEU B 392 " --> pdb=" O VAL B 361 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE B 363 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLY B 497 " --> pdb=" O GLU B 506 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL B 508 " --> pdb=" O PHE B 495 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N PHE B 495 " --> pdb=" O VAL B 508 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 413 through 414 removed outlier: 6.717A pdb=" N ASN B 413 " --> pdb=" O ILE B 426 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 95 through 97 removed outlier: 6.650A pdb=" N THR C 43 " --> pdb=" O ILE C 150 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N GLU C 152 " --> pdb=" O THR C 43 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLN C 45 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LYS C 10 " --> pdb=" O VAL C 149 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N THR C 151 " --> pdb=" O LYS C 10 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU C 12 " --> pdb=" O THR C 151 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ILE C 153 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL C 14 " --> pdb=" O ILE C 153 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N HIS C 11 " --> pdb=" O PHE C 182 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N LEU C 184 " --> pdb=" O HIS C 11 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N PHE C 13 " --> pdb=" O LEU C 184 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL C 186 " --> pdb=" O PHE C 13 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N SER C 15 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N LEU C 188 " --> pdb=" O SER C 15 " (cutoff:3.500A) removed outlier: 9.120A pdb=" N ALA C 219 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N PHE C 183 " --> pdb=" O ALA C 219 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE C 221 " --> pdb=" O PHE C 183 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N HIS C 185 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N ARG C 223 " --> pdb=" O HIS C 185 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N SER C 187 " --> pdb=" O ARG C 223 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU C 220 " --> pdb=" O ILE C 248 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N THR C 250 " --> pdb=" O LEU C 220 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LEU C 222 " --> pdb=" O THR C 250 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 67 through 68 Processing sheet with id=AB4, first strand: chain 'C' and resid 191 through 192 Processing sheet with id=AB5, first strand: chain 'C' and resid 334 through 341 removed outlier: 6.317A pdb=" N VAL C 302 " --> pdb=" O GLU C 336 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N CYS C 338 " --> pdb=" O VAL C 302 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ILE C 304 " --> pdb=" O CYS C 338 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL C 340 " --> pdb=" O ILE C 304 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LEU C 306 " --> pdb=" O VAL C 340 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL C 361 " --> pdb=" O LEU C 390 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N LEU C 392 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE C 363 " --> pdb=" O LEU C 392 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLY C 497 " --> pdb=" O GLU C 506 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL C 508 " --> pdb=" O PHE C 495 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N PHE C 495 " --> pdb=" O VAL C 508 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 413 through 414 removed outlier: 6.716A pdb=" N ASN C 413 " --> pdb=" O ILE C 426 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 95 through 97 removed outlier: 6.648A pdb=" N THR D 43 " --> pdb=" O ILE D 150 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N GLU D 152 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLN D 45 " --> pdb=" O GLU D 152 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LYS D 10 " --> pdb=" O VAL D 149 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N THR D 151 " --> pdb=" O LYS D 10 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU D 12 " --> pdb=" O THR D 151 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N ILE D 153 " --> pdb=" O LEU D 12 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL D 14 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N HIS D 11 " --> pdb=" O PHE D 182 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N LEU D 184 " --> pdb=" O HIS D 11 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N PHE D 13 " --> pdb=" O LEU D 184 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N VAL D 186 " --> pdb=" O PHE D 13 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N SER D 15 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 8.804A pdb=" N LEU D 188 " --> pdb=" O SER D 15 " (cutoff:3.500A) removed outlier: 9.119A pdb=" N ALA D 219 " --> pdb=" O VAL D 181 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N PHE D 183 " --> pdb=" O ALA D 219 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE D 221 " --> pdb=" O PHE D 183 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N HIS D 185 " --> pdb=" O ILE D 221 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N ARG D 223 " --> pdb=" O HIS D 185 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N SER D 187 " --> pdb=" O ARG D 223 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU D 220 " --> pdb=" O ILE D 248 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N THR D 250 " --> pdb=" O LEU D 220 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LEU D 222 " --> pdb=" O THR D 250 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 67 through 68 Processing sheet with id=AB9, first strand: chain 'D' and resid 191 through 192 Processing sheet with id=AC1, first strand: chain 'D' and resid 334 through 341 removed outlier: 6.319A pdb=" N VAL D 302 " --> pdb=" O GLU D 336 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N CYS D 338 " --> pdb=" O VAL D 302 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ILE D 304 " --> pdb=" O CYS D 338 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL D 340 " --> pdb=" O ILE D 304 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N LEU D 306 " --> pdb=" O VAL D 340 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL D 361 " --> pdb=" O LEU D 390 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N LEU D 392 " --> pdb=" O VAL D 361 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE D 363 " --> pdb=" O LEU D 392 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLY D 497 " --> pdb=" O GLU D 506 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL D 508 " --> pdb=" O PHE D 495 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N PHE D 495 " --> pdb=" O VAL D 508 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 413 through 414 removed outlier: 6.708A pdb=" N ASN D 413 " --> pdb=" O ILE D 426 " (cutoff:3.500A) 717 hydrogen bonds defined for protein. 2043 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: 7.48 Time building geometry restraints manager: 4.06 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: 16268 1.03 - 1.23: 128 1.23 - 1.42: 6927 1.42 - 1.62: 9885 1.62 - 1.82: 108 Bond restraints: 33316 Sorted by residual: bond pdb=" C6 UTP A 603 " pdb=" N1 UTP A 603 " ideal model delta sigma weight residual 1.369 1.581 -0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C6 UTP C 602 " pdb=" N1 UTP C 602 " ideal model delta sigma weight residual 1.369 1.580 -0.211 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C6 UTP D 602 " pdb=" N1 UTP D 602 " ideal model delta sigma weight residual 1.369 1.580 -0.211 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C6 UTP B 603 " pdb=" N1 UTP B 603 " ideal model delta sigma weight residual 1.369 1.579 -0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C12 XMW D 604 " pdb=" C13 XMW D 604 " ideal model delta sigma weight residual 1.374 1.518 -0.144 2.00e-02 2.50e+03 5.21e+01 ... (remaining 33311 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.24: 60063 4.24 - 8.48: 125 8.48 - 12.73: 44 12.73 - 16.97: 4 16.97 - 21.21: 8 Bond angle restraints: 60244 Sorted by residual: angle pdb=" O1A UTP A 603 " pdb=" PA UTP A 603 " pdb=" O2A UTP A 603 " ideal model delta sigma weight residual 121.55 100.34 21.21 3.00e+00 1.11e-01 5.00e+01 angle pdb=" O1A UTP B 603 " pdb=" PA UTP B 603 " pdb=" O2A UTP B 603 " ideal model delta sigma weight residual 121.55 100.49 21.06 3.00e+00 1.11e-01 4.93e+01 angle pdb=" O1A UTP D 602 " pdb=" PA UTP D 602 " pdb=" O2A UTP D 602 " ideal model delta sigma weight residual 121.55 100.50 21.05 3.00e+00 1.11e-01 4.92e+01 angle pdb=" O1A UTP C 602 " pdb=" PA UTP C 602 " pdb=" O2A UTP C 602 " ideal model delta sigma weight residual 121.55 100.73 20.82 3.00e+00 1.11e-01 4.82e+01 angle pdb=" O1B UTP A 603 " pdb=" PB UTP A 603 " pdb=" O2B UTP A 603 " ideal model delta sigma weight residual 119.49 102.04 17.45 3.00e+00 1.11e-01 3.38e+01 ... (remaining 60239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.43: 14064 16.43 - 32.85: 893 32.85 - 49.28: 328 49.28 - 65.70: 459 65.70 - 82.13: 40 Dihedral angle restraints: 15784 sinusoidal: 8784 harmonic: 7000 Sorted by residual: dihedral pdb=" CA PRO C 123 " pdb=" C PRO C 123 " pdb=" N HIS C 124 " pdb=" CA HIS C 124 " ideal model delta harmonic sigma weight residual -180.00 -152.87 -27.13 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA PRO A 123 " pdb=" C PRO A 123 " pdb=" N HIS A 124 " pdb=" CA HIS A 124 " ideal model delta harmonic sigma weight residual -180.00 -152.91 -27.09 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA PRO D 123 " pdb=" C PRO D 123 " pdb=" N HIS D 124 " pdb=" CA HIS D 124 " ideal model delta harmonic sigma weight residual -180.00 -152.93 -27.07 0 5.00e+00 4.00e-02 2.93e+01 ... (remaining 15781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1414 0.035 - 0.070: 742 0.070 - 0.104: 324 0.104 - 0.139: 111 0.139 - 0.174: 17 Chirality restraints: 2608 Sorted by residual: chirality pdb=" C3' UTP A 603 " pdb=" C2' UTP A 603 " pdb=" C4' UTP A 603 " pdb=" O3' UTP A 603 " both_signs ideal model delta sigma weight residual False -2.69 -2.51 -0.17 2.00e-01 2.50e+01 7.57e-01 chirality pdb=" C3' UTP C 602 " pdb=" C2' UTP C 602 " pdb=" C4' UTP C 602 " pdb=" O3' UTP C 602 " both_signs ideal model delta sigma weight residual False -2.69 -2.51 -0.17 2.00e-01 2.50e+01 7.54e-01 chirality pdb=" C3' UTP D 602 " pdb=" C2' UTP D 602 " pdb=" C4' UTP D 602 " pdb=" O3' UTP D 602 " both_signs ideal model delta sigma weight residual False -2.69 -2.52 -0.17 2.00e-01 2.50e+01 7.47e-01 ... (remaining 2605 not shown) Planarity restraints: 5040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS C 476 " -0.004 2.00e-02 2.50e+03 2.72e-02 1.67e+01 pdb=" CG HIS C 476 " 0.016 2.00e-02 2.50e+03 pdb=" ND1 HIS C 476 " 0.049 2.00e-02 2.50e+03 pdb=" CD2 HIS C 476 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 HIS C 476 " 0.029 2.00e-02 2.50e+03 pdb=" NE2 HIS C 476 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 HIS C 476 " -0.045 2.00e-02 2.50e+03 pdb=" HD2 HIS C 476 " -0.024 2.00e-02 2.50e+03 pdb=" HE1 HIS C 476 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS D 476 " 0.004 2.00e-02 2.50e+03 2.71e-02 1.65e+01 pdb=" CG HIS D 476 " -0.016 2.00e-02 2.50e+03 pdb=" ND1 HIS D 476 " -0.049 2.00e-02 2.50e+03 pdb=" CD2 HIS D 476 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 HIS D 476 " -0.028 2.00e-02 2.50e+03 pdb=" NE2 HIS D 476 " 0.002 2.00e-02 2.50e+03 pdb=" HD1 HIS D 476 " 0.045 2.00e-02 2.50e+03 pdb=" HD2 HIS D 476 " 0.023 2.00e-02 2.50e+03 pdb=" HE1 HIS D 476 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 476 " -0.003 2.00e-02 2.50e+03 2.71e-02 1.65e+01 pdb=" CG HIS A 476 " 0.015 2.00e-02 2.50e+03 pdb=" ND1 HIS A 476 " 0.049 2.00e-02 2.50e+03 pdb=" CD2 HIS A 476 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 HIS A 476 " 0.028 2.00e-02 2.50e+03 pdb=" NE2 HIS A 476 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 HIS A 476 " -0.045 2.00e-02 2.50e+03 pdb=" HD2 HIS A 476 " -0.024 2.00e-02 2.50e+03 pdb=" HE1 HIS A 476 " -0.024 2.00e-02 2.50e+03 ... (remaining 5037 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.12: 885 2.12 - 2.74: 58636 2.74 - 3.36: 94709 3.36 - 3.98: 125627 3.98 - 4.60: 198017 Nonbonded interactions: 477874 Sorted by model distance: nonbonded pdb=" HG1 THR D 69 " pdb=" OD1 ASP D 71 " model vdw 1.495 2.450 nonbonded pdb=" HG1 THR B 69 " pdb=" OD1 ASP B 71 " model vdw 1.495 2.450 nonbonded pdb=" HG1 THR C 69 " pdb=" OD1 ASP C 71 " model vdw 1.496 2.450 nonbonded pdb=" HG1 THR A 69 " pdb=" OD1 ASP A 71 " model vdw 1.496 2.450 nonbonded pdb="HH22 ARG C 223 " pdb=" OD1 ASP C 252 " model vdw 1.575 2.450 ... (remaining 477869 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: 0.04 Found NCS groups: ncs_group { reference = (chain 'A' and resid 5 through 601) selection = (chain 'B' and resid 5 through 601) selection = (chain 'C' and resid 5 through 601) selection = (chain 'D' and resid 5 through 601) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.220 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 29.500 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 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 : 0.010 0.212 17024 Z= 0.455 Angle : 1.062 21.211 23196 Z= 0.503 Chirality : 0.051 0.174 2608 Planarity : 0.009 0.080 3040 Dihedral : 12.842 82.130 6356 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.38 % Allowed : 1.88 % Favored : 97.74 % Rotamer: Outliers : 0.46 % Allowed : 1.60 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.16), residues: 2124 helix: -0.25 (0.16), residues: 844 sheet: 1.08 (0.25), residues: 348 loop : 0.11 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.042 0.003 ARG C 173 TYR 0.035 0.006 TYR A 50 PHE 0.022 0.003 PHE C 182 TRP 0.014 0.003 TRP C 288 HIS 0.008 0.003 HIS B 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00971 / 0.45 (17024) covalent geometry : angle 1.06180 / 0.50 (23196) hydrogen bonds : bond 0.12735 / 8.30 ( 717) hydrogen bonds : angle 6.68197 / 4.88 ( 2043) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 345 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 THR cc_start: 0.8739 (t) cc_final: 0.8505 (p) REVERT: A 322 GLU cc_start: 0.7035 (mm-30) cc_final: 0.6753 (mm-30) REVERT: A 332 ARG cc_start: 0.7412 (mtt-85) cc_final: 0.7155 (mtt-85) REVERT: A 334 LYS cc_start: 0.8200 (tttt) cc_final: 0.7981 (tttm) REVERT: A 402 GLU cc_start: 0.6701 (tm-30) cc_final: 0.6374 (tm-30) REVERT: B 43 THR cc_start: 0.8787 (t) cc_final: 0.8559 (p) REVERT: B 334 LYS cc_start: 0.8190 (tttt) cc_final: 0.7963 (tttm) REVERT: B 402 GLU cc_start: 0.6657 (tm-30) cc_final: 0.6329 (tm-30) REVERT: B 482 ASN cc_start: 0.7819 (m-40) cc_final: 0.7368 (m-40) REVERT: C 43 THR cc_start: 0.8732 (t) cc_final: 0.8510 (p) REVERT: C 322 GLU cc_start: 0.7036 (mm-30) cc_final: 0.6752 (mm-30) REVERT: C 334 LYS cc_start: 0.8182 (tttt) cc_final: 0.7957 (tttm) REVERT: C 402 GLU cc_start: 0.6730 (tm-30) cc_final: 0.6377 (tm-30) REVERT: C 482 ASN cc_start: 0.7816 (m-40) cc_final: 0.7381 (m-40) REVERT: D 43 THR cc_start: 0.8737 (t) cc_final: 0.8506 (p) REVERT: D 322 GLU cc_start: 0.7033 (mm-30) cc_final: 0.6747 (mm-30) REVERT: D 334 LYS cc_start: 0.8181 (tttt) cc_final: 0.7954 (tttm) REVERT: D 402 GLU cc_start: 0.6710 (tm-30) cc_final: 0.6360 (tm-30) REVERT: D 482 ASN cc_start: 0.7813 (m-40) cc_final: 0.7362 (m-40) outliers start: 8 outliers final: 4 residues processed: 353 average time/residue: 1.1982 time to fit residues: 471.7888 Evaluate side-chains 265 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 261 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain D residue 450 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.150451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.117745 restraints weight = 58174.968| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.03 r_work: 0.3179 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17024 Z= 0.156 Angle : 0.612 10.770 23196 Z= 0.304 Chirality : 0.044 0.149 2608 Planarity : 0.005 0.058 3040 Dihedral : 7.492 52.751 2540 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.32 % Favored : 98.49 % Rotamer: Outliers : 1.08 % Allowed : 9.13 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.17), residues: 2124 helix: 1.06 (0.17), residues: 856 sheet: 0.86 (0.25), residues: 348 loop : 0.12 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 370 TYR 0.011 0.002 TYR B 50 PHE 0.010 0.002 PHE B 61 TRP 0.005 0.001 TRP A 288 HIS 0.005 0.001 HIS B 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (17024) covalent geometry : angle 0.61201 / 0.30 (23196) hydrogen bonds : bond 0.04616 / 3.12 ( 717) hydrogen bonds : angle 5.58270 / 4.08 ( 2043) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 264 time to evaluate : 0.845 Fit side-chains revert: symmetry clash REVERT: A 43 THR cc_start: 0.8886 (t) cc_final: 0.8520 (p) REVERT: A 322 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7120 (mm-30) REVERT: A 332 ARG cc_start: 0.7807 (mtt-85) cc_final: 0.7548 (mtt-85) REVERT: A 334 LYS cc_start: 0.8333 (tttt) cc_final: 0.8074 (tttm) REVERT: A 402 GLU cc_start: 0.6755 (tm-30) cc_final: 0.6205 (tm-30) REVERT: B 43 THR cc_start: 0.8882 (t) cc_final: 0.8556 (p) REVERT: B 334 LYS cc_start: 0.8318 (tttt) cc_final: 0.8059 (tttm) REVERT: B 402 GLU cc_start: 0.6797 (tm-30) cc_final: 0.6226 (tm-30) REVERT: C 43 THR cc_start: 0.8884 (t) cc_final: 0.8553 (p) REVERT: C 117 ASP cc_start: 0.8558 (m-30) cc_final: 0.8292 (t0) REVERT: C 322 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7185 (mm-30) REVERT: C 334 LYS cc_start: 0.8327 (tttt) cc_final: 0.8072 (tttm) REVERT: C 402 GLU cc_start: 0.6792 (tm-30) cc_final: 0.6204 (tm-30) REVERT: D 43 THR cc_start: 0.8881 (t) cc_final: 0.8557 (p) REVERT: D 117 ASP cc_start: 0.8547 (m-30) cc_final: 0.8293 (t0) REVERT: D 322 GLU cc_start: 0.7510 (mm-30) cc_final: 0.7125 (mm-30) REVERT: D 334 LYS cc_start: 0.8322 (tttt) cc_final: 0.8060 (tttm) REVERT: D 370 ARG cc_start: 0.7868 (mtm110) cc_final: 0.7665 (mpp80) REVERT: D 402 GLU cc_start: 0.6732 (tm-30) cc_final: 0.6153 (tm-30) outliers start: 19 outliers final: 10 residues processed: 268 average time/residue: 1.1496 time to fit residues: 348.8609 Evaluate side-chains 247 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 237 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain C residue 446 MET Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 446 MET Chi-restraints excluded: chain D residue 508 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 127 optimal weight: 1.9990 chunk 111 optimal weight: 0.5980 chunk 207 optimal weight: 0.0050 chunk 63 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 150 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 ASN B 95 ASN C 95 ASN D 95 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.149879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.117350 restraints weight = 58258.533| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.02 r_work: 0.3177 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17024 Z= 0.121 Angle : 0.530 8.028 23196 Z= 0.261 Chirality : 0.043 0.141 2608 Planarity : 0.005 0.046 3040 Dihedral : 7.178 55.099 2536 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.02 % Favored : 97.79 % Rotamer: Outliers : 1.54 % Allowed : 9.93 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.18), residues: 2124 helix: 1.65 (0.18), residues: 860 sheet: 0.51 (0.25), residues: 356 loop : 0.01 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 370 TYR 0.011 0.001 TYR B 50 PHE 0.007 0.001 PHE B 417 TRP 0.004 0.001 TRP D 288 HIS 0.007 0.001 HIS A 503 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 (17024) covalent geometry : angle 0.53048 / 0.26 (23196) hydrogen bonds : bond 0.03869 / 2.63 ( 717) hydrogen bonds : angle 4.98362 / 3.64 ( 2043) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 244 time to evaluate : 0.840 Fit side-chains REVERT: A 43 THR cc_start: 0.8849 (t) cc_final: 0.8466 (p) REVERT: A 211 ARG cc_start: 0.8088 (ttm-80) cc_final: 0.7842 (ttm110) REVERT: A 332 ARG cc_start: 0.7829 (mtt-85) cc_final: 0.7574 (mtt-85) REVERT: A 334 LYS cc_start: 0.8352 (tttt) cc_final: 0.8113 (tttm) REVERT: B 43 THR cc_start: 0.8878 (t) cc_final: 0.8553 (p) REVERT: B 211 ARG cc_start: 0.8095 (ttm-80) cc_final: 0.7850 (ttm110) REVERT: B 334 LYS cc_start: 0.8316 (tttt) cc_final: 0.8081 (tttm) REVERT: C 43 THR cc_start: 0.8879 (t) cc_final: 0.8566 (p) REVERT: C 117 ASP cc_start: 0.8484 (m-30) cc_final: 0.8250 (t0) REVERT: C 334 LYS cc_start: 0.8358 (tttt) cc_final: 0.8122 (tttm) REVERT: D 43 THR cc_start: 0.8879 (t) cc_final: 0.8567 (p) REVERT: D 117 ASP cc_start: 0.8504 (m-30) cc_final: 0.8283 (t0) REVERT: D 211 ARG cc_start: 0.8098 (ttm-80) cc_final: 0.7858 (ttm110) REVERT: D 322 GLU cc_start: 0.7553 (mm-30) cc_final: 0.7235 (mm-30) REVERT: D 334 LYS cc_start: 0.8327 (tttt) cc_final: 0.8083 (tttm) outliers start: 27 outliers final: 13 residues processed: 252 average time/residue: 1.2040 time to fit residues: 342.2463 Evaluate side-chains 237 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 224 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 399 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 12 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 131 optimal weight: 0.1980 chunk 203 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 469 GLN C 469 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.147494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.115040 restraints weight = 58572.355| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.02 r_work: 0.3144 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 17024 Z= 0.192 Angle : 0.578 9.591 23196 Z= 0.285 Chirality : 0.045 0.144 2608 Planarity : 0.005 0.076 3040 Dihedral : 7.060 51.549 2536 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.64 % Favored : 97.18 % Rotamer: Outliers : 1.54 % Allowed : 9.82 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.17), residues: 2124 helix: 1.46 (0.18), residues: 860 sheet: 0.32 (0.25), residues: 356 loop : -0.11 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 370 TYR 0.016 0.001 TYR C 50 PHE 0.010 0.002 PHE D 367 TRP 0.004 0.001 TRP D 288 HIS 0.006 0.001 HIS B 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.19 (17024) covalent geometry : angle 0.57806 / 0.28 (23196) hydrogen bonds : bond 0.04262 / 2.89 ( 717) hydrogen bonds : angle 4.95056 / 3.61 ( 2043) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 224 time to evaluate : 0.719 Fit side-chains revert: symmetry clash REVERT: A 211 ARG cc_start: 0.8206 (ttm-80) cc_final: 0.7972 (ttm110) REVERT: A 239 MET cc_start: 0.7780 (OUTLIER) cc_final: 0.7065 (mtp) REVERT: A 332 ARG cc_start: 0.7909 (mtt-85) cc_final: 0.7671 (mtt-85) REVERT: A 334 LYS cc_start: 0.8368 (tttt) cc_final: 0.8125 (tttm) REVERT: B 43 THR cc_start: 0.8931 (t) cc_final: 0.8584 (p) REVERT: B 211 ARG cc_start: 0.8225 (ttm-80) cc_final: 0.7989 (ttm110) REVERT: B 334 LYS cc_start: 0.8353 (tttt) cc_final: 0.8099 (tttm) REVERT: C 43 THR cc_start: 0.8934 (t) cc_final: 0.8594 (p) REVERT: C 117 ASP cc_start: 0.8564 (m-30) cc_final: 0.8325 (t0) REVERT: C 239 MET cc_start: 0.7757 (OUTLIER) cc_final: 0.7036 (mtp) REVERT: C 334 LYS cc_start: 0.8374 (tttt) cc_final: 0.8132 (tttm) REVERT: D 43 THR cc_start: 0.8936 (t) cc_final: 0.8597 (p) REVERT: D 117 ASP cc_start: 0.8553 (m-30) cc_final: 0.8312 (t0) REVERT: D 211 ARG cc_start: 0.8234 (ttm-80) cc_final: 0.8005 (ttm110) REVERT: D 322 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7382 (mm-30) REVERT: D 334 LYS cc_start: 0.8345 (tttt) cc_final: 0.8090 (tttm) outliers start: 27 outliers final: 18 residues processed: 233 average time/residue: 1.2429 time to fit residues: 325.8501 Evaluate side-chains 237 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 217 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 446 MET Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 446 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 80 optimal weight: 0.0980 chunk 136 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 159 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 157 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 205 optimal weight: 3.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 466 GLN B 469 GLN C 469 GLN D 466 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.152023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.119645 restraints weight = 57584.173| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.99 r_work: 0.3018 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17024 Z= 0.147 Angle : 0.536 8.808 23196 Z= 0.262 Chirality : 0.043 0.141 2608 Planarity : 0.005 0.043 3040 Dihedral : 6.945 50.948 2536 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.45 % Favored : 97.36 % Rotamer: Outliers : 1.54 % Allowed : 9.13 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.18), residues: 2124 helix: 1.60 (0.18), residues: 864 sheet: 0.23 (0.24), residues: 356 loop : -0.11 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 131 TYR 0.012 0.001 TYR B 50 PHE 0.009 0.001 PHE A 61 TRP 0.003 0.001 TRP B 288 HIS 0.004 0.001 HIS D 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (17024) covalent geometry : angle 0.53573 / 0.26 (23196) hydrogen bonds : bond 0.03853 / 2.61 ( 717) hydrogen bonds : angle 4.79588 / 3.50 ( 2043) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 239 time to evaluate : 0.841 Fit side-chains REVERT: A 211 ARG cc_start: 0.8163 (ttm-80) cc_final: 0.7858 (ttm110) REVERT: A 239 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.6987 (mtp) REVERT: A 332 ARG cc_start: 0.7834 (mtt-85) cc_final: 0.7417 (mtt-85) REVERT: A 334 LYS cc_start: 0.8379 (tttt) cc_final: 0.8131 (tttm) REVERT: B 43 THR cc_start: 0.8918 (t) cc_final: 0.8520 (p) REVERT: B 211 ARG cc_start: 0.8157 (ttm-80) cc_final: 0.7847 (ttm110) REVERT: B 239 MET cc_start: 0.7710 (OUTLIER) cc_final: 0.7001 (mtp) REVERT: B 334 LYS cc_start: 0.8347 (tttt) cc_final: 0.8096 (tttm) REVERT: C 43 THR cc_start: 0.8924 (t) cc_final: 0.8530 (p) REVERT: C 117 ASP cc_start: 0.8613 (m-30) cc_final: 0.8374 (t0) REVERT: C 239 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.6964 (mtp) REVERT: C 334 LYS cc_start: 0.8351 (tttt) cc_final: 0.8109 (tttm) REVERT: D 43 THR cc_start: 0.8927 (t) cc_final: 0.8536 (p) REVERT: D 117 ASP cc_start: 0.8589 (m-30) cc_final: 0.8359 (t0) REVERT: D 180 ASP cc_start: 0.8780 (m-30) cc_final: 0.8562 (m-30) REVERT: D 211 ARG cc_start: 0.8176 (ttm-80) cc_final: 0.7871 (ttm110) REVERT: D 239 MET cc_start: 0.7722 (OUTLIER) cc_final: 0.7007 (mtp) REVERT: D 334 LYS cc_start: 0.8345 (tttt) cc_final: 0.8094 (tttm) REVERT: D 482 ASN cc_start: 0.7958 (m-40) cc_final: 0.7749 (m-40) outliers start: 27 outliers final: 17 residues processed: 245 average time/residue: 1.1645 time to fit residues: 322.2335 Evaluate side-chains 244 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 223 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain C residue 446 MET Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 446 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 53 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 167 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 466 GLN B 469 GLN C 466 GLN C 469 GLN D 469 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.151790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.119403 restraints weight = 57510.553| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.00 r_work: 0.3029 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17024 Z= 0.150 Angle : 0.539 8.896 23196 Z= 0.264 Chirality : 0.043 0.141 2608 Planarity : 0.005 0.088 3040 Dihedral : 6.906 50.777 2536 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.73 % Favored : 97.08 % Rotamer: Outliers : 1.37 % Allowed : 10.05 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.18), residues: 2124 helix: 1.61 (0.18), residues: 864 sheet: 0.23 (0.24), residues: 356 loop : -0.16 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 370 TYR 0.013 0.001 TYR C 50 PHE 0.008 0.001 PHE A 61 TRP 0.003 0.001 TRP D 285 HIS 0.004 0.001 HIS C 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.15 (17024) covalent geometry : angle 0.53901 / 0.26 (23196) hydrogen bonds : bond 0.03827 / 2.59 ( 717) hydrogen bonds : angle 4.74381 / 3.46 ( 2043) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 248 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 ARG cc_start: 0.8173 (ttm-80) cc_final: 0.7879 (ttm110) REVERT: A 239 MET cc_start: 0.7705 (OUTLIER) cc_final: 0.6991 (mtp) REVERT: A 332 ARG cc_start: 0.7857 (mtt-85) cc_final: 0.7403 (mtt-85) REVERT: A 334 LYS cc_start: 0.8354 (tttt) cc_final: 0.8104 (tttm) REVERT: B 43 THR cc_start: 0.8937 (t) cc_final: 0.8548 (p) REVERT: B 211 ARG cc_start: 0.8182 (ttm-80) cc_final: 0.7879 (ttm110) REVERT: B 239 MET cc_start: 0.7753 (OUTLIER) cc_final: 0.7049 (mtp) REVERT: B 334 LYS cc_start: 0.8345 (tttt) cc_final: 0.8089 (tttm) REVERT: C 43 THR cc_start: 0.8952 (t) cc_final: 0.8565 (p) REVERT: C 239 MET cc_start: 0.7680 (OUTLIER) cc_final: 0.6969 (mtp) REVERT: C 334 LYS cc_start: 0.8350 (tttt) cc_final: 0.8108 (tttm) REVERT: D 43 THR cc_start: 0.8947 (t) cc_final: 0.8563 (p) REVERT: D 211 ARG cc_start: 0.8196 (ttm-80) cc_final: 0.7897 (ttm110) REVERT: D 239 MET cc_start: 0.7745 (OUTLIER) cc_final: 0.7030 (mtp) REVERT: D 300 GLU cc_start: 0.7729 (pt0) cc_final: 0.7520 (pt0) REVERT: D 334 LYS cc_start: 0.8347 (tttt) cc_final: 0.8097 (tttm) REVERT: D 482 ASN cc_start: 0.7923 (m-40) cc_final: 0.7682 (m-40) outliers start: 24 outliers final: 14 residues processed: 254 average time/residue: 1.1301 time to fit residues: 323.7628 Evaluate side-chains 238 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 220 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 446 MET Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 446 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.2371 > 50: distance: 429 - 434: 15.394 distance: 434 - 435: 9.097 distance: 434 - 442: 19.368 distance: 435 - 436: 41.557 distance: 435 - 438: 13.311 distance: 435 - 443: 15.340 distance: 436 - 437: 27.260 distance: 436 - 448: 34.639 distance: 438 - 439: 8.293 distance: 438 - 444: 15.036 distance: 438 - 445: 23.627 distance: 439 - 440: 3.546 distance: 441 - 446: 5.704 distance: 441 - 447: 5.355 distance: 448 - 449: 12.265 distance: 448 - 459: 17.518 distance: 449 - 450: 42.809 distance: 449 - 452: 8.079 distance: 449 - 460: 30.126 distance: 450 - 451: 16.567 distance: 450 - 472: 20.574 distance: 452 - 453: 28.285 distance: 452 - 461: 30.249 distance: 452 - 462: 10.985 distance: 453 - 454: 8.491 distance: 453 - 463: 15.990 distance: 453 - 464: 9.495 distance: 454 - 455: 3.484 distance: 454 - 465: 5.835 distance: 454 - 466: 4.557 distance: 455 - 467: 3.661 distance: 456 - 458: 3.139 distance: 472 - 473: 6.844 distance: 472 - 478: 7.187 distance: 473 - 474: 10.177 distance: 473 - 476: 4.774 distance: 473 - 479: 13.092 distance: 474 - 475: 17.778 distance: 474 - 486: 6.068 distance: 476 - 477: 9.697 distance: 476 - 480: 10.723 distance: 476 - 481: 10.064 distance: 477 - 478: 3.668 distance: 477 - 482: 10.591 distance: 478 - 484: 4.550 distance: 478 - 485: 7.142 distance: 486 - 487: 7.524 distance: 486 - 494: 4.008 distance: 487 - 488: 9.774 distance: 487 - 490: 3.514 distance: 487 - 495: 5.827 distance: 488 - 489: 14.807 distance: 488 - 498: 14.672 distance: 490 - 491: 8.693 distance: 490 - 496: 6.746 distance: 490 - 497: 7.357 distance: 491 - 492: 7.587 distance: 491 - 493: 4.747 distance: 498 - 499: 3.640 distance: 498 - 505: 12.043 distance: 499 - 500: 18.753 distance: 499 - 502: 6.697 distance: 499 - 506: 4.441 distance: 500 - 501: 21.337 distance: 500 - 514: 25.328 distance: 502 - 503: 10.441 distance: 502 - 504: 9.917 distance: 502 - 507: 8.093 distance: 503 - 508: 8.363 distance: 503 - 509: 7.855 distance: 504 - 511: 10.106 distance: 504 - 512: 6.919 distance: 504 - 513: 11.624 distance: 514 - 515: 13.209 distance: 514 - 521: 11.488 distance: 515 - 516: 14.349 distance: 515 - 518: 8.582 distance: 515 - 522: 12.928 distance: 516 - 517: 13.075 distance: 516 - 530: 5.547 distance: 518 - 519: 10.801 distance: 518 - 520: 3.997 distance: 519 - 524: 3.724 distance: 519 - 526: 9.744 distance: 520 - 527: 3.709 distance: 520 - 528: 3.458 distance: 520 - 529: 6.597 distance: 530 - 531: 15.070 distance: 530 - 538: 5.429 distance: 531 - 532: 18.590 distance: 531 - 534: 5.620 distance: 531 - 539: 21.795 distance: 532 - 533: 17.898 distance: 532 - 549: 17.651 distance: 534 - 535: 7.259 distance: 534 - 536: 10.251 distance: 534 - 540: 14.352 distance: 535 - 537: 4.598 distance: 535 - 541: 17.663 distance: 535 - 542: 20.971 distance: 536 - 543: 22.151 distance: 536 - 544: 9.152 distance: 536 - 545: 11.752 distance: 537 - 546: 7.770 distance: 537 - 547: 4.027 distance: 537 - 548: 6.412 distance: 549 - 550: 11.823 distance: 549 - 556: 10.835 distance: 550 - 551: 9.401 distance: 550 - 553: 8.828 distance: 550 - 557: 9.431 distance: 551 - 552: 8.841 distance: 551 - 563: 5.839 distance: 553 - 554: 19.270 distance: 553 - 555: 10.914 distance: 553 - 558: 23.107 distance: 554 - 559: 16.409 distance: 555 - 560: 14.750 distance: 555 - 561: 11.916 distance: 555 - 562: 20.512 distance: 563 - 564: 7.945 distance: 563 - 572: 18.126 distance: 564 - 565: 4.681 distance: 564 - 567: 4.547 distance: 564 - 573: 8.357 distance: 565 - 566: 8.070 distance: 565 - 578: 6.433 distance: 567 - 568: 5.788 distance: 567 - 574: 4.167 distance: 567 - 575: 5.296 distance: 568 - 569: 3.461 distance: 568 - 577: 3.095 distance: 578 - 579: 5.907 distance: 578 - 586: 6.353 distance: 579 - 580: 5.409 distance: 579 - 582: 3.855 distance: 579 - 587: 6.747 distance: 580 - 581: 11.477 distance: 580 - 597: 4.236 distance: 582 - 583: 3.838 distance: 583 - 589: 3.661 distance: 583 - 590: 5.080 distance: 584 - 591: 5.464 distance: 584 - 592: 4.646