Starting phenix.real_space_refine on Thu Sep 26 17:12:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxz_21453/09_2024/6vxz_21453.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxz_21453/09_2024/6vxz_21453.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxz_21453/09_2024/6vxz_21453.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxz_21453/09_2024/6vxz_21453.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxz_21453/09_2024/6vxz_21453.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxz_21453/09_2024/6vxz_21453.cif" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 28 5.16 5 C 8876 2.51 5 N 2076 2.21 5 O 2332 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 13324 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3091 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 23, 'TRANS': 365} Chain breaks: 1 Chain: "A" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 240 Unusual residues: {'PGW': 6} Classifications: {'RNA': 1, 'undetermined': 6} Modifications used: {'rna3p': 1} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PGW:plan-3': 2} Unresolved non-hydrogen planarities: 4 Restraints were copied for chains: C, B, D Time building chain proxies: 6.78, per 1000 atoms: 0.51 Number of scatterers: 13324 At special positions: 0 Unit cell: (101.937, 101.937, 118.379, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 P 12 15.00 O 2332 8.00 N 2076 7.00 C 8876 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: 3.16 Conformation dependent library (CDL) restraints added in 1.6 seconds 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2952 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 8 sheets defined 67.4% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 10 through 36 Proline residue: A 31 - end of helix Processing helix chain 'A' and resid 43 through 62 removed outlier: 4.071A pdb=" N ASP A 47 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Proline residue: A 59 - end of helix removed outlier: 3.527A pdb=" N LEU A 62 " --> pdb=" O ILE A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 removed outlier: 3.619A pdb=" N LEU A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 98 Processing helix chain 'A' and resid 101 through 106 removed outlier: 3.911A pdb=" N LEU A 106 " --> pdb=" O SER A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 112 Processing helix chain 'A' and resid 113 through 126 removed outlier: 4.155A pdb=" N SER A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ARG A 124 " --> pdb=" O ARG A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 156 Processing helix chain 'A' and resid 165 through 182 removed outlier: 3.526A pdb=" N TYR A 170 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 171 " --> pdb=" O GLY A 167 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER A 172 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA A 173 " --> pdb=" O ARG A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 223 removed outlier: 3.838A pdb=" N LEU A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL A 214 " --> pdb=" O MET A 210 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 215 " --> pdb=" O TYR A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 246 removed outlier: 4.072A pdb=" N ARG A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS A 246 " --> pdb=" O PHE A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 268 removed outlier: 3.583A pdb=" N GLN A 253 " --> pdb=" O SER A 249 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR A 266 " --> pdb=" O TYR A 262 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 277 Processing helix chain 'A' and resid 280 through 292 Processing helix chain 'A' and resid 292 through 297 Processing helix chain 'A' and resid 307 through 315 removed outlier: 5.374A pdb=" N ARG A 311 " --> pdb=" O GLU A 307 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ASP A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LEU A 315 " --> pdb=" O ARG A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 395 through 403 removed outlier: 3.525A pdb=" N SER A 402 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG A 403 " --> pdb=" O ARG A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 412 removed outlier: 4.061A pdb=" N GLN A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 36 Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 43 through 62 removed outlier: 4.071A pdb=" N ASP B 47 " --> pdb=" O LEU B 43 " (cutoff:3.500A) Proline residue: B 59 - end of helix removed outlier: 3.527A pdb=" N LEU B 62 " --> pdb=" O ILE B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 removed outlier: 3.619A pdb=" N LEU B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 98 Processing helix chain 'B' and resid 101 through 106 removed outlier: 3.912A pdb=" N LEU B 106 " --> pdb=" O SER B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 112 Processing helix chain 'B' and resid 113 through 126 removed outlier: 4.155A pdb=" N SER B 117 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ARG B 124 " --> pdb=" O ARG B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 156 Processing helix chain 'B' and resid 165 through 182 removed outlier: 3.526A pdb=" N TYR B 170 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU B 171 " --> pdb=" O GLY B 167 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER B 172 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA B 173 " --> pdb=" O ARG B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 223 removed outlier: 3.838A pdb=" N LEU B 213 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL B 214 " --> pdb=" O MET B 210 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE B 215 " --> pdb=" O TYR B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 246 removed outlier: 4.073A pdb=" N ARG B 233 " --> pdb=" O LYS B 229 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR B 245 " --> pdb=" O ALA B 241 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS B 246 " --> pdb=" O PHE B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 268 removed outlier: 3.583A pdb=" N GLN B 253 " --> pdb=" O SER B 249 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR B 266 " --> pdb=" O TYR B 262 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG B 267 " --> pdb=" O LEU B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 277 Processing helix chain 'B' and resid 280 through 292 Processing helix chain 'B' and resid 292 through 297 Processing helix chain 'B' and resid 307 through 315 removed outlier: 5.374A pdb=" N ARG B 311 " --> pdb=" O GLU B 307 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ASP B 312 " --> pdb=" O GLU B 308 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LEU B 315 " --> pdb=" O ARG B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 395 through 403 removed outlier: 3.525A pdb=" N SER B 402 " --> pdb=" O ASP B 398 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG B 403 " --> pdb=" O ARG B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 412 removed outlier: 4.061A pdb=" N GLN B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 36 Proline residue: C 31 - end of helix Processing helix chain 'C' and resid 43 through 62 removed outlier: 4.071A pdb=" N ASP C 47 " --> pdb=" O LEU C 43 " (cutoff:3.500A) Proline residue: C 59 - end of helix removed outlier: 3.528A pdb=" N LEU C 62 " --> pdb=" O ILE C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.619A pdb=" N LEU C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 98 Processing helix chain 'C' and resid 101 through 106 removed outlier: 3.911A pdb=" N LEU C 106 " --> pdb=" O SER C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 112 Processing helix chain 'C' and resid 113 through 126 removed outlier: 4.155A pdb=" N SER C 117 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ARG C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 156 Processing helix chain 'C' and resid 165 through 182 removed outlier: 3.527A pdb=" N TYR C 170 " --> pdb=" O ALA C 166 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU C 171 " --> pdb=" O GLY C 167 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER C 172 " --> pdb=" O THR C 168 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA C 173 " --> pdb=" O ARG C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 223 removed outlier: 3.838A pdb=" N LEU C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL C 214 " --> pdb=" O MET C 210 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE C 215 " --> pdb=" O TYR C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 246 removed outlier: 4.073A pdb=" N ARG C 233 " --> pdb=" O LYS C 229 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS C 246 " --> pdb=" O PHE C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 268 removed outlier: 3.583A pdb=" N GLN C 253 " --> pdb=" O SER C 249 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR C 266 " --> pdb=" O TYR C 262 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 277 Processing helix chain 'C' and resid 280 through 292 Processing helix chain 'C' and resid 292 through 297 Processing helix chain 'C' and resid 307 through 315 removed outlier: 5.374A pdb=" N ARG C 311 " --> pdb=" O GLU C 307 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ASP C 312 " --> pdb=" O GLU C 308 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LEU C 315 " --> pdb=" O ARG C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 395 through 403 removed outlier: 3.526A pdb=" N SER C 402 " --> pdb=" O ASP C 398 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG C 403 " --> pdb=" O ARG C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 412 removed outlier: 4.061A pdb=" N GLN C 412 " --> pdb=" O ALA C 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 36 Proline residue: D 31 - end of helix Processing helix chain 'D' and resid 43 through 62 removed outlier: 4.071A pdb=" N ASP D 47 " --> pdb=" O LEU D 43 " (cutoff:3.500A) Proline residue: D 59 - end of helix removed outlier: 3.527A pdb=" N LEU D 62 " --> pdb=" O ILE D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 removed outlier: 3.620A pdb=" N LEU D 89 " --> pdb=" O LEU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 98 Processing helix chain 'D' and resid 101 through 106 removed outlier: 3.911A pdb=" N LEU D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 112 Processing helix chain 'D' and resid 113 through 126 removed outlier: 4.155A pdb=" N SER D 117 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ARG D 124 " --> pdb=" O ARG D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 156 Processing helix chain 'D' and resid 165 through 182 removed outlier: 3.526A pdb=" N TYR D 170 " --> pdb=" O ALA D 166 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU D 171 " --> pdb=" O GLY D 167 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER D 172 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA D 173 " --> pdb=" O ARG D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 223 removed outlier: 3.838A pdb=" N LEU D 213 " --> pdb=" O ALA D 209 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL D 214 " --> pdb=" O MET D 210 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE D 215 " --> pdb=" O TYR D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 246 removed outlier: 4.073A pdb=" N ARG D 233 " --> pdb=" O LYS D 229 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR D 245 " --> pdb=" O ALA D 241 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS D 246 " --> pdb=" O PHE D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 268 removed outlier: 3.583A pdb=" N GLN D 253 " --> pdb=" O SER D 249 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR D 266 " --> pdb=" O TYR D 262 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG D 267 " --> pdb=" O LEU D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 277 Processing helix chain 'D' and resid 280 through 292 Processing helix chain 'D' and resid 292 through 297 Processing helix chain 'D' and resid 307 through 315 removed outlier: 5.374A pdb=" N ARG D 311 " --> pdb=" O GLU D 307 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ASP D 312 " --> pdb=" O GLU D 308 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LEU D 315 " --> pdb=" O ARG D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 395 through 403 removed outlier: 3.526A pdb=" N SER D 402 " --> pdb=" O ASP D 398 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG D 403 " --> pdb=" O ARG D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 412 removed outlier: 4.061A pdb=" N GLN D 412 " --> pdb=" O ALA D 408 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 318 through 319 removed outlier: 3.668A pdb=" N VAL A 338 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 327 through 329 removed outlier: 7.027A pdb=" N TYR A 327 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ALA A 383 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE A 329 " --> pdb=" O VAL A 381 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 318 through 319 removed outlier: 3.669A pdb=" N VAL B 338 " --> pdb=" O LEU B 392 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 327 through 329 removed outlier: 7.027A pdb=" N TYR B 327 " --> pdb=" O ALA B 383 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ALA B 383 " --> pdb=" O TYR B 327 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE B 329 " --> pdb=" O VAL B 381 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 318 through 319 removed outlier: 3.669A pdb=" N VAL C 338 " --> pdb=" O LEU C 392 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 327 through 329 removed outlier: 7.028A pdb=" N TYR C 327 " --> pdb=" O ALA C 383 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ALA C 383 " --> pdb=" O TYR C 327 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE C 329 " --> pdb=" O VAL C 381 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 318 through 319 removed outlier: 3.668A pdb=" N VAL D 338 " --> pdb=" O LEU D 392 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 327 through 329 removed outlier: 7.027A pdb=" N TYR D 327 " --> pdb=" O ALA D 383 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ALA D 383 " --> pdb=" O TYR D 327 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE D 329 " --> pdb=" O VAL D 381 " (cutoff:3.500A) 680 hydrogen bonds defined for protein. 1956 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.76 Time building geometry restraints manager: 3.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2108 1.32 - 1.44: 3371 1.44 - 1.57: 8045 1.57 - 1.69: 20 1.69 - 1.81: 52 Bond restraints: 13596 Sorted by residual: bond pdb=" C5 CMP B 501 " pdb=" C6 CMP B 501 " ideal model delta sigma weight residual 1.490 1.404 0.086 2.00e-02 2.50e+03 1.87e+01 bond pdb=" C5 CMP A 501 " pdb=" C6 CMP A 501 " ideal model delta sigma weight residual 1.490 1.404 0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C5 CMP D 501 " pdb=" C6 CMP D 501 " ideal model delta sigma weight residual 1.490 1.404 0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C8 CMP D 501 " pdb=" N9 CMP D 501 " ideal model delta sigma weight residual 1.337 1.422 -0.085 2.00e-02 2.50e+03 1.83e+01 bond pdb=" C8 CMP C 501 " pdb=" N9 CMP C 501 " ideal model delta sigma weight residual 1.337 1.422 -0.085 2.00e-02 2.50e+03 1.81e+01 ... (remaining 13591 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 17222 2.10 - 4.21: 873 4.21 - 6.31: 171 6.31 - 8.42: 22 8.42 - 10.52: 16 Bond angle restraints: 18304 Sorted by residual: angle pdb=" N GLU D 395 " pdb=" CA GLU D 395 " pdb=" C GLU D 395 " ideal model delta sigma weight residual 111.14 105.04 6.10 1.08e+00 8.57e-01 3.19e+01 angle pdb=" N GLU C 395 " pdb=" CA GLU C 395 " pdb=" C GLU C 395 " ideal model delta sigma weight residual 111.14 105.04 6.10 1.08e+00 8.57e-01 3.19e+01 angle pdb=" N GLU A 395 " pdb=" CA GLU A 395 " pdb=" C GLU A 395 " ideal model delta sigma weight residual 111.14 105.06 6.08 1.08e+00 8.57e-01 3.17e+01 angle pdb=" N GLU B 395 " pdb=" CA GLU B 395 " pdb=" C GLU B 395 " ideal model delta sigma weight residual 111.14 105.09 6.05 1.08e+00 8.57e-01 3.14e+01 angle pdb=" C ASP B 393 " pdb=" N LYS B 394 " pdb=" CA LYS B 394 " ideal model delta sigma weight residual 121.54 132.01 -10.47 1.91e+00 2.74e-01 3.01e+01 ... (remaining 18299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.43: 7872 34.43 - 68.85: 428 68.85 - 103.28: 56 103.28 - 137.70: 12 137.70 - 172.13: 32 Dihedral angle restraints: 8400 sinusoidal: 3824 harmonic: 4576 Sorted by residual: dihedral pdb=" C5' CMP D 501 " pdb=" O5' CMP D 501 " pdb=" P CMP D 501 " pdb=" O1P CMP D 501 " ideal model delta sinusoidal sigma weight residual 60.00 168.08 -108.08 1 2.00e+01 2.50e-03 3.15e+01 dihedral pdb=" C5' CMP B 501 " pdb=" O5' CMP B 501 " pdb=" P CMP B 501 " pdb=" O1P CMP B 501 " ideal model delta sinusoidal sigma weight residual 60.00 168.07 -108.07 1 2.00e+01 2.50e-03 3.14e+01 dihedral pdb=" C5' CMP A 501 " pdb=" O5' CMP A 501 " pdb=" P CMP A 501 " pdb=" O1P CMP A 501 " ideal model delta sinusoidal sigma weight residual 60.00 168.04 -108.04 1 2.00e+01 2.50e-03 3.14e+01 ... (remaining 8397 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1613 0.063 - 0.126: 412 0.126 - 0.188: 49 0.188 - 0.251: 14 0.251 - 0.314: 4 Chirality restraints: 2092 Sorted by residual: chirality pdb=" CA ALA B 408 " pdb=" N ALA B 408 " pdb=" C ALA B 408 " pdb=" CB ALA B 408 " both_signs ideal model delta sigma weight residual False 2.48 2.17 0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CA ALA A 408 " pdb=" N ALA A 408 " pdb=" C ALA A 408 " pdb=" CB ALA A 408 " both_signs ideal model delta sigma weight residual False 2.48 2.17 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CA ALA C 408 " pdb=" N ALA C 408 " pdb=" C ALA C 408 " pdb=" CB ALA C 408 " both_signs ideal model delta sigma weight residual False 2.48 2.17 0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 2089 not shown) Planarity restraints: 2196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C06 PGW A 502 " 0.076 2.00e-02 2.50e+03 1.50e-01 2.26e+02 pdb=" C10 PGW A 502 " -0.199 2.00e-02 2.50e+03 pdb=" C8 PGW A 502 " -0.076 2.00e-02 2.50e+03 pdb=" C9 PGW A 502 " 0.199 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW B 502 " -0.076 2.00e-02 2.50e+03 1.50e-01 2.26e+02 pdb=" C10 PGW B 502 " 0.198 2.00e-02 2.50e+03 pdb=" C8 PGW B 502 " 0.076 2.00e-02 2.50e+03 pdb=" C9 PGW B 502 " -0.198 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW D 502 " 0.076 2.00e-02 2.50e+03 1.50e-01 2.26e+02 pdb=" C10 PGW D 502 " -0.198 2.00e-02 2.50e+03 pdb=" C8 PGW D 502 " -0.076 2.00e-02 2.50e+03 pdb=" C9 PGW D 502 " 0.198 2.00e-02 2.50e+03 ... (remaining 2193 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 100 2.55 - 3.14: 10756 3.14 - 3.72: 18817 3.72 - 4.31: 26624 4.31 - 4.90: 45936 Nonbonded interactions: 102233 Sorted by model distance: nonbonded pdb=" O THR A 182 " pdb=" OG1 THR A 183 " model vdw 1.959 3.040 nonbonded pdb=" O THR D 182 " pdb=" OG1 THR D 183 " model vdw 1.959 3.040 nonbonded pdb=" O THR C 182 " pdb=" OG1 THR C 183 " model vdw 1.959 3.040 nonbonded pdb=" O THR B 182 " pdb=" OG1 THR B 183 " model vdw 1.959 3.040 nonbonded pdb=" ND1 HIS A 149 " pdb=" OH TYR A 170 " model vdw 2.260 3.120 ... (remaining 102228 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 0.010 Normalize map: mean=0, sd=1: 0.930 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: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 29.320 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 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 : 0.011 0.086 13596 Z= 0.706 Angle : 1.068 10.523 18304 Z= 0.563 Chirality : 0.057 0.314 2092 Planarity : 0.008 0.150 2196 Dihedral : 23.657 172.130 5448 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 2.40 % Allowed : 17.72 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.97 (0.19), residues: 1540 helix: -2.12 (0.14), residues: 1032 sheet: -3.22 (0.43), residues: 120 loop : -3.24 (0.26), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 18 HIS 0.003 0.001 HIS B 232 PHE 0.011 0.001 PHE A 397 TYR 0.014 0.001 TYR D 175 ARG 0.003 0.001 ARG D 399 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 146 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 LEU cc_start: 0.4769 (OUTLIER) cc_final: 0.4314 (pt) REVERT: A 393 ASP cc_start: 0.6847 (OUTLIER) cc_final: 0.6186 (t0) REVERT: B 301 LEU cc_start: 0.4761 (OUTLIER) cc_final: 0.4302 (pt) REVERT: B 393 ASP cc_start: 0.7024 (OUTLIER) cc_final: 0.6223 (t0) REVERT: C 301 LEU cc_start: 0.4806 (OUTLIER) cc_final: 0.4340 (pt) REVERT: C 329 ILE cc_start: 0.9037 (mt) cc_final: 0.8834 (mt) REVERT: C 393 ASP cc_start: 0.7051 (OUTLIER) cc_final: 0.6229 (t0) REVERT: D 301 LEU cc_start: 0.4770 (OUTLIER) cc_final: 0.4306 (pt) REVERT: D 393 ASP cc_start: 0.6854 (OUTLIER) cc_final: 0.6196 (t0) outliers start: 32 outliers final: 13 residues processed: 178 average time/residue: 0.2654 time to fit residues: 67.5305 Evaluate side-chains 125 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 104 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 307 GLU Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 307 GLU Chi-restraints excluded: chain D residue 393 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 119 optimal weight: 4.9990 chunk 46 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 138 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13596 Z= 0.219 Angle : 0.697 9.178 18304 Z= 0.328 Chirality : 0.044 0.191 2092 Planarity : 0.005 0.047 2196 Dihedral : 25.418 165.737 2562 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.15 % Allowed : 18.69 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.22), residues: 1540 helix: -0.15 (0.17), residues: 1008 sheet: -1.88 (0.47), residues: 112 loop : -2.64 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 155 HIS 0.002 0.001 HIS C 281 PHE 0.005 0.001 PHE B 40 TYR 0.013 0.001 TYR A 25 ARG 0.003 0.000 ARG D 382 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 119 time to evaluate : 1.700 Fit side-chains REVERT: A 329 ILE cc_start: 0.8955 (mt) cc_final: 0.8708 (mt) REVERT: B 329 ILE cc_start: 0.8954 (mt) cc_final: 0.8708 (mt) REVERT: D 329 ILE cc_start: 0.8955 (mt) cc_final: 0.8707 (mt) outliers start: 42 outliers final: 11 residues processed: 156 average time/residue: 0.3111 time to fit residues: 67.4883 Evaluate side-chains 115 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 104 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain C residue 124 ARG Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 124 ARG Chi-restraints excluded: chain D residue 295 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 114 optimal weight: 10.0000 chunk 93 optimal weight: 0.9990 chunk 38 optimal weight: 10.0000 chunk 138 optimal weight: 0.7980 chunk 149 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 13596 Z= 0.298 Angle : 0.704 8.404 18304 Z= 0.336 Chirality : 0.045 0.206 2092 Planarity : 0.005 0.050 2196 Dihedral : 23.516 171.624 2516 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 4.05 % Allowed : 18.84 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.22), residues: 1540 helix: 0.33 (0.18), residues: 1008 sheet: -1.79 (0.46), residues: 116 loop : -2.09 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 155 HIS 0.003 0.001 HIS C 281 PHE 0.009 0.001 PHE B 397 TYR 0.014 0.001 TYR D 175 ARG 0.005 0.000 ARG C 111 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 110 time to evaluate : 1.410 Fit side-chains REVERT: A 230 LEU cc_start: 0.8759 (mm) cc_final: 0.8470 (mt) REVERT: A 329 ILE cc_start: 0.9100 (mt) cc_final: 0.8865 (mt) REVERT: B 230 LEU cc_start: 0.8767 (mm) cc_final: 0.8473 (mt) REVERT: B 329 ILE cc_start: 0.9104 (mt) cc_final: 0.8878 (mt) REVERT: C 230 LEU cc_start: 0.8761 (mm) cc_final: 0.8471 (mt) REVERT: C 329 ILE cc_start: 0.9069 (mt) cc_final: 0.8858 (mt) REVERT: D 230 LEU cc_start: 0.8755 (mm) cc_final: 0.8470 (mt) REVERT: D 329 ILE cc_start: 0.9103 (mt) cc_final: 0.8869 (mt) REVERT: D 369 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.7746 (mtm) outliers start: 54 outliers final: 28 residues processed: 157 average time/residue: 0.2365 time to fit residues: 55.3198 Evaluate side-chains 132 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 103 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 369 MET Chi-restraints excluded: chain D residue 389 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 138 optimal weight: 0.2980 chunk 146 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13596 Z= 0.162 Angle : 0.634 9.990 18304 Z= 0.295 Chirality : 0.042 0.183 2092 Planarity : 0.005 0.060 2196 Dihedral : 21.787 177.293 2516 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.40 % Allowed : 20.80 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.23), residues: 1540 helix: 0.68 (0.18), residues: 1008 sheet: -1.49 (0.44), residues: 116 loop : -1.58 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 155 HIS 0.001 0.000 HIS D 281 PHE 0.007 0.001 PHE D 36 TYR 0.009 0.001 TYR A 259 ARG 0.005 0.000 ARG C 311 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 129 time to evaluate : 1.424 Fit side-chains REVERT: A 22 VAL cc_start: 0.8298 (OUTLIER) cc_final: 0.8079 (t) REVERT: A 230 LEU cc_start: 0.8737 (mm) cc_final: 0.8518 (mt) REVERT: A 329 ILE cc_start: 0.9090 (mt) cc_final: 0.8867 (mt) REVERT: A 362 GLU cc_start: 0.7700 (pt0) cc_final: 0.7444 (tt0) REVERT: A 373 LEU cc_start: 0.6426 (OUTLIER) cc_final: 0.6215 (mt) REVERT: B 22 VAL cc_start: 0.8298 (OUTLIER) cc_final: 0.8079 (t) REVERT: B 230 LEU cc_start: 0.8740 (mm) cc_final: 0.8522 (mt) REVERT: B 329 ILE cc_start: 0.9100 (mt) cc_final: 0.8874 (mt) REVERT: B 362 GLU cc_start: 0.7704 (pt0) cc_final: 0.7449 (tt0) REVERT: B 373 LEU cc_start: 0.6405 (OUTLIER) cc_final: 0.6203 (mt) REVERT: C 22 VAL cc_start: 0.8311 (OUTLIER) cc_final: 0.8084 (t) REVERT: C 230 LEU cc_start: 0.8742 (mm) cc_final: 0.8472 (mt) REVERT: C 362 GLU cc_start: 0.7640 (pt0) cc_final: 0.7380 (tt0) REVERT: D 22 VAL cc_start: 0.8298 (OUTLIER) cc_final: 0.8071 (t) REVERT: D 230 LEU cc_start: 0.8741 (mm) cc_final: 0.8519 (mt) REVERT: D 329 ILE cc_start: 0.9086 (mt) cc_final: 0.8864 (mt) REVERT: D 362 GLU cc_start: 0.7694 (pt0) cc_final: 0.7443 (tt0) REVERT: D 373 LEU cc_start: 0.6406 (OUTLIER) cc_final: 0.6202 (mt) outliers start: 32 outliers final: 8 residues processed: 157 average time/residue: 0.2595 time to fit residues: 59.4064 Evaluate side-chains 126 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 111 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 389 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 2.9990 chunk 83 optimal weight: 0.0770 chunk 2 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 60 optimal weight: 0.0980 chunk 125 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 131 optimal weight: 0.6980 chunk 37 optimal weight: 6.9990 overall best weight: 0.5540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13596 Z= 0.157 Angle : 0.615 9.910 18304 Z= 0.287 Chirality : 0.041 0.161 2092 Planarity : 0.005 0.054 2196 Dihedral : 19.987 173.724 2516 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.23 % Allowed : 21.55 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.23), residues: 1540 helix: 0.86 (0.18), residues: 1012 sheet: -1.25 (0.49), residues: 96 loop : -1.27 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 155 HIS 0.001 0.000 HIS C 281 PHE 0.007 0.001 PHE B 36 TYR 0.009 0.001 TYR A 175 ARG 0.006 0.000 ARG B 311 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 120 time to evaluate : 1.427 Fit side-chains REVERT: A 22 VAL cc_start: 0.8319 (OUTLIER) cc_final: 0.8103 (t) REVERT: A 230 LEU cc_start: 0.8744 (mm) cc_final: 0.8482 (mt) REVERT: A 329 ILE cc_start: 0.9088 (mt) cc_final: 0.8871 (mt) REVERT: A 362 GLU cc_start: 0.7618 (pt0) cc_final: 0.7413 (tt0) REVERT: A 373 LEU cc_start: 0.6509 (OUTLIER) cc_final: 0.6227 (mt) REVERT: B 22 VAL cc_start: 0.8319 (OUTLIER) cc_final: 0.8102 (t) REVERT: B 230 LEU cc_start: 0.8750 (mm) cc_final: 0.8488 (mt) REVERT: B 329 ILE cc_start: 0.9091 (mt) cc_final: 0.8890 (mt) REVERT: B 362 GLU cc_start: 0.7649 (pt0) cc_final: 0.7404 (tt0) REVERT: B 373 LEU cc_start: 0.6489 (OUTLIER) cc_final: 0.6210 (mt) REVERT: C 22 VAL cc_start: 0.8317 (OUTLIER) cc_final: 0.8103 (t) REVERT: C 230 LEU cc_start: 0.8751 (mm) cc_final: 0.8489 (mt) REVERT: C 362 GLU cc_start: 0.7655 (pt0) cc_final: 0.7381 (tt0) REVERT: C 369 MET cc_start: 0.8133 (mmt) cc_final: 0.7914 (mtt) REVERT: D 230 LEU cc_start: 0.8751 (mm) cc_final: 0.8488 (mt) REVERT: D 329 ILE cc_start: 0.9085 (mt) cc_final: 0.8874 (mt) REVERT: D 362 GLU cc_start: 0.7643 (pt0) cc_final: 0.7397 (tt0) REVERT: D 373 LEU cc_start: 0.6466 (OUTLIER) cc_final: 0.6183 (mt) outliers start: 43 outliers final: 24 residues processed: 159 average time/residue: 0.2506 time to fit residues: 58.4559 Evaluate side-chains 133 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 103 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 124 ARG Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 124 ARG Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 389 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 68 optimal weight: 0.0060 chunk 12 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13596 Z= 0.214 Angle : 0.635 9.326 18304 Z= 0.298 Chirality : 0.042 0.157 2092 Planarity : 0.005 0.055 2196 Dihedral : 19.577 165.685 2516 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.75 % Allowed : 21.32 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.23), residues: 1540 helix: 0.88 (0.18), residues: 1008 sheet: -1.29 (0.45), residues: 116 loop : -1.11 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 155 HIS 0.002 0.000 HIS A 281 PHE 0.007 0.001 PHE C 36 TYR 0.011 0.001 TYR D 175 ARG 0.005 0.000 ARG B 311 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 109 time to evaluate : 1.525 Fit side-chains REVERT: A 22 VAL cc_start: 0.8357 (OUTLIER) cc_final: 0.8145 (t) REVERT: A 230 LEU cc_start: 0.8809 (mm) cc_final: 0.8594 (mt) REVERT: A 329 ILE cc_start: 0.9112 (mt) cc_final: 0.8902 (mt) REVERT: A 373 LEU cc_start: 0.6532 (OUTLIER) cc_final: 0.6205 (mt) REVERT: B 22 VAL cc_start: 0.8361 (OUTLIER) cc_final: 0.8143 (t) REVERT: B 230 LEU cc_start: 0.8808 (mm) cc_final: 0.8594 (mt) REVERT: B 329 ILE cc_start: 0.9114 (mt) cc_final: 0.8906 (mt) REVERT: B 373 LEU cc_start: 0.6503 (OUTLIER) cc_final: 0.6184 (mt) REVERT: C 22 VAL cc_start: 0.8360 (OUTLIER) cc_final: 0.8146 (t) REVERT: C 230 LEU cc_start: 0.8807 (mm) cc_final: 0.8596 (mt) REVERT: C 369 MET cc_start: 0.8177 (mmt) cc_final: 0.7935 (mtt) REVERT: D 230 LEU cc_start: 0.8811 (mm) cc_final: 0.8594 (mt) REVERT: D 329 ILE cc_start: 0.9100 (mt) cc_final: 0.8882 (mt) REVERT: D 373 LEU cc_start: 0.6462 (OUTLIER) cc_final: 0.6170 (mt) outliers start: 50 outliers final: 25 residues processed: 155 average time/residue: 0.2319 time to fit residues: 54.2553 Evaluate side-chains 130 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 99 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 124 ARG Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 124 ARG Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 389 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 83 optimal weight: 0.0870 chunk 107 optimal weight: 6.9990 chunk 123 optimal weight: 7.9990 chunk 82 optimal weight: 8.9990 chunk 146 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 89 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 90 optimal weight: 0.0010 overall best weight: 0.4964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13596 Z= 0.153 Angle : 0.610 9.893 18304 Z= 0.284 Chirality : 0.040 0.155 2092 Planarity : 0.005 0.057 2196 Dihedral : 18.386 149.936 2516 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.93 % Allowed : 21.47 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.23), residues: 1540 helix: 1.03 (0.18), residues: 1012 sheet: -1.26 (0.51), residues: 96 loop : -0.86 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 15 HIS 0.001 0.000 HIS B 281 PHE 0.006 0.001 PHE C 36 TYR 0.009 0.001 TYR B 259 ARG 0.005 0.000 ARG B 311 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 119 time to evaluate : 1.686 Fit side-chains REVERT: A 22 VAL cc_start: 0.8318 (OUTLIER) cc_final: 0.8114 (t) REVERT: A 329 ILE cc_start: 0.9114 (mt) cc_final: 0.8911 (mt) REVERT: A 369 MET cc_start: 0.8089 (mmt) cc_final: 0.7864 (mtt) REVERT: A 373 LEU cc_start: 0.6399 (OUTLIER) cc_final: 0.6121 (mt) REVERT: B 329 ILE cc_start: 0.9116 (mt) cc_final: 0.8913 (mt) REVERT: B 369 MET cc_start: 0.8090 (mmt) cc_final: 0.7862 (mtt) REVERT: B 373 LEU cc_start: 0.6391 (OUTLIER) cc_final: 0.6116 (mt) REVERT: C 369 MET cc_start: 0.8243 (mmt) cc_final: 0.7928 (mtt) REVERT: D 329 ILE cc_start: 0.9104 (mt) cc_final: 0.8903 (mt) REVERT: D 373 LEU cc_start: 0.6355 (OUTLIER) cc_final: 0.6104 (mt) outliers start: 39 outliers final: 22 residues processed: 154 average time/residue: 0.2389 time to fit residues: 54.9185 Evaluate side-chains 134 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 108 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 124 ARG Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 124 ARG Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 389 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 44 optimal weight: 0.0970 chunk 28 optimal weight: 0.7980 chunk 93 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 72 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13596 Z= 0.173 Angle : 0.620 9.249 18304 Z= 0.288 Chirality : 0.041 0.158 2092 Planarity : 0.005 0.057 2196 Dihedral : 18.072 144.778 2516 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.40 % Allowed : 22.30 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.23), residues: 1540 helix: 1.11 (0.18), residues: 996 sheet: -1.23 (0.51), residues: 96 loop : -0.57 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 18 HIS 0.002 0.000 HIS A 281 PHE 0.006 0.001 PHE C 36 TYR 0.010 0.001 TYR A 175 ARG 0.004 0.000 ARG D 311 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 119 time to evaluate : 1.433 Fit side-chains REVERT: A 22 VAL cc_start: 0.8320 (OUTLIER) cc_final: 0.8110 (t) REVERT: A 369 MET cc_start: 0.8130 (mmt) cc_final: 0.7839 (mtt) REVERT: A 373 LEU cc_start: 0.6366 (OUTLIER) cc_final: 0.6141 (mt) REVERT: B 369 MET cc_start: 0.8095 (mmt) cc_final: 0.7825 (mtt) REVERT: B 373 LEU cc_start: 0.6367 (OUTLIER) cc_final: 0.6099 (mt) REVERT: C 369 MET cc_start: 0.8234 (mmt) cc_final: 0.7875 (mtt) REVERT: D 373 LEU cc_start: 0.6332 (OUTLIER) cc_final: 0.6129 (mt) outliers start: 32 outliers final: 23 residues processed: 147 average time/residue: 0.2631 time to fit residues: 56.1912 Evaluate side-chains 132 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 105 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 124 ARG Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 124 ARG Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 389 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.7980 chunk 136 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 chunk 123 optimal weight: 6.9990 chunk 129 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 144 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13596 Z= 0.188 Angle : 0.634 9.468 18304 Z= 0.296 Chirality : 0.041 0.166 2092 Planarity : 0.005 0.060 2196 Dihedral : 17.959 143.380 2516 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.10 % Allowed : 23.80 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.23), residues: 1540 helix: 1.18 (0.18), residues: 996 sheet: -1.27 (0.52), residues: 96 loop : -0.51 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 155 HIS 0.002 0.000 HIS C 281 PHE 0.006 0.001 PHE D 36 TYR 0.010 0.001 TYR D 175 ARG 0.004 0.000 ARG B 311 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 111 time to evaluate : 1.442 Fit side-chains REVERT: A 22 VAL cc_start: 0.8326 (OUTLIER) cc_final: 0.8115 (t) REVERT: A 369 MET cc_start: 0.8123 (mmt) cc_final: 0.7852 (mtt) REVERT: A 373 LEU cc_start: 0.6325 (OUTLIER) cc_final: 0.6122 (mt) REVERT: B 369 MET cc_start: 0.8119 (mmt) cc_final: 0.7880 (mtt) REVERT: C 369 MET cc_start: 0.8226 (mmt) cc_final: 0.7887 (mtt) outliers start: 28 outliers final: 21 residues processed: 134 average time/residue: 0.2568 time to fit residues: 50.5128 Evaluate side-chains 130 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 107 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 124 ARG Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 124 ARG Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 389 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 100 optimal weight: 0.1980 chunk 151 optimal weight: 4.9990 chunk 139 optimal weight: 0.0010 chunk 120 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 128 optimal weight: 0.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13596 Z= 0.165 Angle : 0.626 9.169 18304 Z= 0.292 Chirality : 0.041 0.157 2092 Planarity : 0.005 0.062 2196 Dihedral : 17.508 140.512 2516 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.18 % Allowed : 23.50 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.23), residues: 1540 helix: 1.33 (0.18), residues: 996 sheet: -1.25 (0.53), residues: 96 loop : -0.41 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 15 HIS 0.001 0.000 HIS D 281 PHE 0.007 0.001 PHE A 36 TYR 0.009 0.001 TYR A 175 ARG 0.006 0.000 ARG A 311 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 118 time to evaluate : 1.393 Fit side-chains REVERT: A 369 MET cc_start: 0.8104 (mmt) cc_final: 0.7860 (mtt) REVERT: B 369 MET cc_start: 0.8210 (mmt) cc_final: 0.7870 (mtt) REVERT: C 356 ARG cc_start: 0.7134 (ptt180) cc_final: 0.6856 (ptt180) REVERT: C 369 MET cc_start: 0.8219 (mmt) cc_final: 0.7834 (mtt) REVERT: D 369 MET cc_start: 0.8325 (mmm) cc_final: 0.7757 (mtm) outliers start: 29 outliers final: 21 residues processed: 142 average time/residue: 0.2734 time to fit residues: 56.7326 Evaluate side-chains 127 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 106 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 124 ARG Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 389 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.1852 > 50: distance: 8 - 18: 33.745 distance: 18 - 19: 37.335 distance: 19 - 20: 52.820 distance: 20 - 21: 50.011 distance: 20 - 22: 40.400 distance: 22 - 28: 14.356 distance: 23 - 24: 15.320 distance: 23 - 26: 42.038 distance: 24 - 25: 24.175 distance: 24 - 29: 43.108 distance: 26 - 27: 28.708 distance: 27 - 28: 36.856 distance: 29 - 30: 7.039 distance: 30 - 31: 6.754 distance: 31 - 33: 22.913 distance: 33 - 34: 19.792 distance: 34 - 35: 9.928 distance: 34 - 37: 10.838 distance: 35 - 36: 31.626 distance: 35 - 42: 11.620 distance: 38 - 39: 11.985 distance: 39 - 40: 9.245 distance: 39 - 41: 14.512 distance: 42 - 43: 28.855 distance: 43 - 46: 53.407 distance: 44 - 45: 37.981 distance: 44 - 54: 42.447 distance: 46 - 47: 36.976 distance: 47 - 48: 21.326 distance: 47 - 49: 39.963 distance: 48 - 50: 18.093 distance: 49 - 51: 5.675 distance: 50 - 52: 31.776 distance: 51 - 52: 54.332 distance: 52 - 53: 8.501 distance: 54 - 55: 35.350 distance: 55 - 56: 30.763 distance: 55 - 58: 44.832 distance: 56 - 57: 22.215 distance: 56 - 62: 26.256 distance: 58 - 59: 36.681 distance: 58 - 60: 41.651 distance: 59 - 61: 15.090 distance: 62 - 63: 21.581 distance: 63 - 64: 39.601 distance: 63 - 66: 56.213 distance: 64 - 65: 39.066 distance: 64 - 70: 40.388 distance: 65 - 145: 35.222 distance: 66 - 67: 36.607 distance: 66 - 68: 47.626 distance: 67 - 69: 64.151 distance: 70 - 71: 24.237 distance: 71 - 72: 29.683 distance: 71 - 74: 42.429 distance: 72 - 81: 70.186 distance: 74 - 75: 35.150 distance: 75 - 76: 8.073 distance: 76 - 77: 17.843 distance: 77 - 78: 9.386 distance: 78 - 79: 15.414 distance: 78 - 80: 8.698 distance: 82 - 85: 40.406 distance: 83 - 84: 43.981 distance: 83 - 86: 37.242 distance: 86 - 87: 55.550 distance: 87 - 88: 41.085 distance: 88 - 89: 13.573 distance: 88 - 90: 29.846