Starting phenix.real_space_refine on Fri Aug 22 20:11:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w6t_37332/08_2025/8w6t_37332.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w6t_37332/08_2025/8w6t_37332.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w6t_37332/08_2025/8w6t_37332.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w6t_37332/08_2025/8w6t_37332.map" model { file = "/net/cci-nas-00/data/ceres_data/8w6t_37332/08_2025/8w6t_37332.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w6t_37332/08_2025/8w6t_37332.cif" } resolution = 3.0 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= -0.004 sd= 0.138 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: 4 Type Number sf(0) Gaussians S 53 5.16 5 C 5110 2.51 5 N 1158 2.21 5 O 1284 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7605 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3857 Classifications: {'peptide': 494} Link IDs: {'PTRANS': 30, 'TRANS': 463} Chain breaks: 3 Chain: "B" Number of atoms: 3748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3748 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 30, 'TRANS': 450} Chain breaks: 3 Time building chain proxies: 1.68, per 1000 atoms: 0.22 Number of scatterers: 7605 At special positions: 0 Unit cell: (92.395, 94.569, 107.613, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 53 16.00 O 1284 8.00 N 1158 7.00 C 5110 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: 0.39 Conformation dependent library (CDL) restraints added in 298.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1842 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 2 sheets defined 71.9% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 4 through 10 removed outlier: 3.791A pdb=" N LEU A 8 " --> pdb=" O PHE A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 22 removed outlier: 4.262A pdb=" N VAL A 16 " --> pdb=" O ARG A 12 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A 17 " --> pdb=" O PHE A 13 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A 21 " --> pdb=" O VAL A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 30 removed outlier: 3.719A pdb=" N ILE A 28 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 30 " --> pdb=" O LEU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 50 removed outlier: 3.660A pdb=" N TRP A 48 " --> pdb=" O VAL A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 59 Processing helix chain 'A' and resid 61 through 66 removed outlier: 3.528A pdb=" N LEU A 66 " --> pdb=" O PRO A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 78 Processing helix chain 'A' and resid 79 through 81 No H-bonds generated for 'chain 'A' and resid 79 through 81' Processing helix chain 'A' and resid 83 through 102 removed outlier: 3.878A pdb=" N LEU A 87 " --> pdb=" O LYS A 83 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 88 " --> pdb=" O ASP A 84 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N CYS A 94 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER A 98 " --> pdb=" O CYS A 94 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU A 100 " --> pdb=" O ALA A 96 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TRP A 102 " --> pdb=" O SER A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 117 removed outlier: 3.530A pdb=" N MET A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 135 removed outlier: 3.646A pdb=" N THR A 124 " --> pdb=" O PRO A 120 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU A 125 " --> pdb=" O ALA A 121 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY A 126 " --> pdb=" O TRP A 122 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N MET A 128 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE A 133 " --> pdb=" O SER A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 160 removed outlier: 3.797A pdb=" N MET A 146 " --> pdb=" O SER A 142 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N MET A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) Proline residue: A 149 - end of helix removed outlier: 3.691A pdb=" N ALA A 153 " --> pdb=" O PRO A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 246 removed outlier: 3.979A pdb=" N LYS A 238 " --> pdb=" O HIS A 234 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A 239 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR A 240 " --> pdb=" O THR A 236 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 251 Processing helix chain 'A' and resid 259 through 273 removed outlier: 3.824A pdb=" N LEU A 263 " --> pdb=" O THR A 259 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 309 Proline residue: A 290 - end of helix removed outlier: 3.791A pdb=" N ILE A 294 " --> pdb=" O PRO A 290 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE A 301 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY A 309 " --> pdb=" O TRP A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 339 removed outlier: 3.608A pdb=" N ALA A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU A 331 " --> pdb=" O LYS A 327 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A 332 " --> pdb=" O ALA A 328 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE A 333 " --> pdb=" O CYS A 329 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS A 339 " --> pdb=" O GLN A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 363 removed outlier: 3.681A pdb=" N ILE A 348 " --> pdb=" O ARG A 344 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL A 349 " --> pdb=" O TYR A 345 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N THR A 350 " --> pdb=" O GLN A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 377 removed outlier: 3.557A pdb=" N ALA A 374 " --> pdb=" O GLY A 371 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER A 377 " --> pdb=" O ALA A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 394 removed outlier: 3.689A pdb=" N VAL A 388 " --> pdb=" O THR A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 431 removed outlier: 3.706A pdb=" N SER A 429 " --> pdb=" O LYS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 453 removed outlier: 3.958A pdb=" N ALA A 436 " --> pdb=" O PRO A 432 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE A 437 " --> pdb=" O TRP A 433 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY A 453 " --> pdb=" O CYS A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 460 Processing helix chain 'A' and resid 469 through 485 removed outlier: 3.522A pdb=" N ILE A 474 " --> pdb=" O ALA A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 508 removed outlier: 3.529A pdb=" N ILE A 494 " --> pdb=" O ASN A 490 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR A 495 " --> pdb=" O PRO A 491 " (cutoff:3.500A) Proline residue: A 499 - end of helix Proline residue: A 503 - end of helix removed outlier: 3.919A pdb=" N GLU A 506 " --> pdb=" O SER A 502 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE A 508 " --> pdb=" O LEU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 522 removed outlier: 3.592A pdb=" N SER A 519 " --> pdb=" O ILE A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 539 removed outlier: 3.526A pdb=" N ILE A 538 " --> pdb=" O PRO A 534 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL A 539 " --> pdb=" O PRO A 535 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 534 through 539' Processing helix chain 'A' and resid 540 through 543 removed outlier: 3.846A pdb=" N GLY A 543 " --> pdb=" O PHE A 540 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 540 through 543' Processing helix chain 'A' and resid 546 through 569 removed outlier: 3.523A pdb=" N MET A 550 " --> pdb=" O LYS A 546 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLY A 556 " --> pdb=" O LYS A 552 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL A 557 " --> pdb=" O ALA A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 578 Processing helix chain 'B' and resid 13 through 18 removed outlier: 3.989A pdb=" N VAL B 17 " --> pdb=" O PHE B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 50 removed outlier: 3.863A pdb=" N THR B 40 " --> pdb=" O GLU B 36 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N PHE B 42 " --> pdb=" O ALA B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 60 Processing helix chain 'B' and resid 61 through 69 removed outlier: 3.803A pdb=" N LEU B 66 " --> pdb=" O PRO B 62 " (cutoff:3.500A) Proline residue: B 67 - end of helix Processing helix chain 'B' and resid 73 through 79 removed outlier: 3.749A pdb=" N SER B 79 " --> pdb=" O LYS B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'B' and resid 83 through 102 removed outlier: 4.225A pdb=" N LEU B 87 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU B 88 " --> pdb=" O ASP B 84 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N SER B 98 " --> pdb=" O CYS B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 135 removed outlier: 4.811A pdb=" N MET B 128 " --> pdb=" O THR B 124 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR B 131 " --> pdb=" O PHE B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 159 removed outlier: 3.627A pdb=" N ALA B 145 " --> pdb=" O THR B 141 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N MET B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Proline residue: B 149 - end of helix removed outlier: 3.702A pdb=" N ALA B 153 " --> pdb=" O PRO B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 251 removed outlier: 3.539A pdb=" N ILE B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA B 245 " --> pdb=" O CYS B 241 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR B 249 " --> pdb=" O ALA B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 258 removed outlier: 3.574A pdb=" N GLY B 258 " --> pdb=" O THR B 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 255 through 258' Processing helix chain 'B' and resid 259 through 271 removed outlier: 3.696A pdb=" N LEU B 263 " --> pdb=" O THR B 259 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR B 271 " --> pdb=" O GLU B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 308 removed outlier: 3.662A pdb=" N THR B 286 " --> pdb=" O GLY B 282 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N PHE B 287 " --> pdb=" O SER B 283 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER B 288 " --> pdb=" O TRP B 284 " (cutoff:3.500A) Proline residue: B 290 - end of helix removed outlier: 3.702A pdb=" N ILE B 294 " --> pdb=" O PRO B 290 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 296 " --> pdb=" O ALA B 292 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TRP B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE B 301 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP B 302 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE B 307 " --> pdb=" O LEU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 338 removed outlier: 3.735A pdb=" N ILE B 333 " --> pdb=" O CYS B 329 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS B 334 " --> pdb=" O ALA B 330 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLU B 336 " --> pdb=" O VAL B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 360 removed outlier: 3.660A pdb=" N THR B 350 " --> pdb=" O GLN B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 375 Processing helix chain 'B' and resid 385 through 394 removed outlier: 3.697A pdb=" N ALA B 389 " --> pdb=" O ASP B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 429 removed outlier: 3.525A pdb=" N SER B 429 " --> pdb=" O LYS B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 447 removed outlier: 3.909A pdb=" N ALA B 436 " --> pdb=" O PRO B 432 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE B 437 " --> pdb=" O TRP B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 462 removed outlier: 3.627A pdb=" N TRP B 457 " --> pdb=" O GLY B 453 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N GLY B 459 " --> pdb=" O SER B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 468 removed outlier: 3.531A pdb=" N SER B 467 " --> pdb=" O PRO B 464 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU B 468 " --> pdb=" O LEU B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 485 removed outlier: 3.584A pdb=" N ILE B 473 " --> pdb=" O PRO B 469 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE B 474 " --> pdb=" O ALA B 470 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL B 481 " --> pdb=" O SER B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 508 removed outlier: 3.747A pdb=" N ILE B 494 " --> pdb=" O ASN B 490 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N THR B 495 " --> pdb=" O PRO B 491 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE B 497 " --> pdb=" O THR B 493 " (cutoff:3.500A) Proline residue: B 499 - end of helix Proline residue: B 503 - end of helix removed outlier: 3.781A pdb=" N ILE B 508 " --> pdb=" O LEU B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 522 removed outlier: 3.736A pdb=" N ILE B 515 " --> pdb=" O ASN B 511 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE B 517 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Proline residue: B 518 - end of helix removed outlier: 3.505A pdb=" N LEU B 521 " --> pdb=" O ILE B 517 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N CYS B 522 " --> pdb=" O PRO B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 525 No H-bonds generated for 'chain 'B' and resid 523 through 525' Processing helix chain 'B' and resid 534 through 539 Processing helix chain 'B' and resid 546 through 567 removed outlier: 4.037A pdb=" N GLY B 556 " --> pdb=" O LYS B 552 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL B 557 " --> pdb=" O ALA B 553 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL B 560 " --> pdb=" O GLY B 556 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL B 565 " --> pdb=" O GLY B 561 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 400 through 403 removed outlier: 6.483A pdb=" N SER A 419 " --> pdb=" O ALA A 401 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 400 through 402 removed outlier: 6.909A pdb=" N SER B 419 " --> pdb=" O ALA B 401 " (cutoff:3.500A) 336 hydrogen bonds defined for protein. 990 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: 0.70 Time building geometry restraints manager: 0.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 1116 1.27 - 1.41: 1999 1.41 - 1.54: 4533 1.54 - 1.68: 94 1.68 - 1.81: 86 Bond restraints: 7828 Sorted by residual: bond pdb=" C PRO B 535 " pdb=" O PRO B 535 " ideal model delta sigma weight residual 1.235 1.144 0.091 1.30e-02 5.92e+03 4.89e+01 bond pdb=" C LEU B 528 " pdb=" O LEU B 528 " ideal model delta sigma weight residual 1.234 1.157 0.077 1.17e-02 7.31e+03 4.37e+01 bond pdb=" CA ASN B 536 " pdb=" CB ASN B 536 " ideal model delta sigma weight residual 1.530 1.439 0.090 1.64e-02 3.72e+03 3.03e+01 bond pdb=" CA ALA B 537 " pdb=" C ALA B 537 " ideal model delta sigma weight residual 1.526 1.576 -0.050 9.20e-03 1.18e+04 3.00e+01 bond pdb=" CG ASN B 536 " pdb=" OD1 ASN B 536 " ideal model delta sigma weight residual 1.231 1.141 0.090 1.90e-02 2.77e+03 2.27e+01 ... (remaining 7823 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.88: 10592 3.88 - 7.75: 102 7.75 - 11.63: 14 11.63 - 15.50: 0 15.50 - 19.38: 1 Bond angle restraints: 10709 Sorted by residual: angle pdb=" N LEU B 528 " pdb=" CA LEU B 528 " pdb=" C LEU B 528 " ideal model delta sigma weight residual 111.96 131.34 -19.38 1.41e+00 5.03e-01 1.89e+02 angle pdb=" CA ALA B 537 " pdb=" C ALA B 537 " pdb=" O ALA B 537 " ideal model delta sigma weight residual 120.71 113.79 6.92 1.10e+00 8.26e-01 3.96e+01 angle pdb=" N LEU B 125 " pdb=" CA LEU B 125 " pdb=" C LEU B 125 " ideal model delta sigma weight residual 113.18 105.91 7.27 1.33e+00 5.65e-01 2.99e+01 angle pdb=" C LEU B 253 " pdb=" N THR B 254 " pdb=" CA THR B 254 " ideal model delta sigma weight residual 121.54 131.75 -10.21 1.91e+00 2.74e-01 2.85e+01 angle pdb=" N TYR B 39 " pdb=" CA TYR B 39 " pdb=" C TYR B 39 " ideal model delta sigma weight residual 113.18 106.51 6.67 1.33e+00 5.65e-01 2.51e+01 ... (remaining 10704 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.51: 4039 15.51 - 31.02: 406 31.02 - 46.53: 80 46.53 - 62.04: 6 62.04 - 77.55: 4 Dihedral angle restraints: 4535 sinusoidal: 1697 harmonic: 2838 Sorted by residual: dihedral pdb=" N LEU B 528 " pdb=" C LEU B 528 " pdb=" CA LEU B 528 " pdb=" CB LEU B 528 " ideal model delta harmonic sigma weight residual 122.80 154.03 -31.23 0 2.50e+00 1.60e-01 1.56e+02 dihedral pdb=" C LEU B 528 " pdb=" N LEU B 528 " pdb=" CA LEU B 528 " pdb=" CB LEU B 528 " ideal model delta harmonic sigma weight residual -122.60 -153.26 30.66 0 2.50e+00 1.60e-01 1.50e+02 dihedral pdb=" CA VAL B 20 " pdb=" C VAL B 20 " pdb=" N LEU B 21 " pdb=" CA LEU B 21 " ideal model delta harmonic sigma weight residual 180.00 152.21 27.79 0 5.00e+00 4.00e-02 3.09e+01 ... (remaining 4532 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.275: 1289 0.275 - 0.551: 1 0.551 - 0.826: 0 0.826 - 1.102: 0 1.102 - 1.377: 1 Chirality restraints: 1291 Sorted by residual: chirality pdb=" CA LEU B 528 " pdb=" N LEU B 528 " pdb=" C LEU B 528 " pdb=" CB LEU B 528 " both_signs ideal model delta sigma weight residual False 2.51 1.13 1.38 2.00e-01 2.50e+01 4.74e+01 chirality pdb=" CA PRO B 535 " pdb=" N PRO B 535 " pdb=" C PRO B 535 " pdb=" CB PRO B 535 " both_signs ideal model delta sigma weight residual False 2.72 2.31 0.41 2.00e-01 2.50e+01 4.18e+00 chirality pdb=" CA ASN B 536 " pdb=" N ASN B 536 " pdb=" C ASN B 536 " pdb=" CB ASN B 536 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 1288 not shown) Planarity restraints: 1274 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 463 " 0.052 5.00e-02 4.00e+02 7.72e-02 9.53e+00 pdb=" N PRO B 464 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO B 464 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 464 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 53 " -0.047 5.00e-02 4.00e+02 7.16e-02 8.21e+00 pdb=" N PRO B 54 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO B 54 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 54 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 24 " -0.048 5.00e-02 4.00e+02 7.10e-02 8.06e+00 pdb=" N PRO A 25 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 25 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 25 " -0.040 5.00e-02 4.00e+02 ... (remaining 1271 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1624 2.78 - 3.31: 6750 3.31 - 3.84: 12276 3.84 - 4.37: 14932 4.37 - 4.90: 25544 Nonbonded interactions: 61126 Sorted by model distance: nonbonded pdb=" O PHE B 15 " pdb=" OG1 THR B 19 " model vdw 2.247 3.040 nonbonded pdb=" O PRO B 534 " pdb=" N ALA B 537 " model vdw 2.284 3.120 nonbonded pdb=" O ALA B 59 " pdb=" OH TYR B 81 " model vdw 2.293 3.040 nonbonded pdb=" N ASN B 536 " pdb=" OD1 ASN B 536 " model vdw 2.298 3.120 nonbonded pdb=" O PHE A 42 " pdb=" OG1 THR A 46 " model vdw 2.300 3.040 ... (remaining 61121 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 161 or resid 233 through 309 or resid 325 throug \ h 403 or resid 418 through 588)) selection = chain 'B' } 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: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.060 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.500 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 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:6.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 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 : 0.006 0.116 7828 Z= 0.303 Angle : 1.028 19.379 10709 Z= 0.589 Chirality : 0.065 1.377 1291 Planarity : 0.009 0.077 1274 Dihedral : 12.770 77.551 2693 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.26 % Favored : 93.64 % Rotamer: Outliers : 0.72 % Allowed : 5.74 % Favored : 93.54 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.55 (0.19), residues: 959 helix: -3.67 (0.12), residues: 638 sheet: None (None), residues: 0 loop : -3.26 (0.30), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 107 TYR 0.016 0.001 TYR A 514 PHE 0.025 0.002 PHE A 287 TRP 0.045 0.002 TRP A 48 HIS 0.005 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00575 ( 7828) covalent geometry : angle 1.02816 (10709) hydrogen bonds : bond 0.26246 ( 336) hydrogen bonds : angle 8.35870 ( 990) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 152 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: A 344 ARG cc_start: 0.7225 (ptt180) cc_final: 0.6817 (mmt180) REVERT: A 566 MET cc_start: 0.7882 (mmm) cc_final: 0.7674 (mmm) REVERT: A 576 MET cc_start: 0.7125 (mtp) cc_final: 0.6855 (ttm) REVERT: B 456 LYS cc_start: 0.7222 (ttmt) cc_final: 0.6990 (ttmm) REVERT: B 533 ASN cc_start: 0.6190 (t0) cc_final: 0.5500 (m110) REVERT: B 566 MET cc_start: 0.6575 (mmm) cc_final: 0.5731 (mmt) outliers start: 6 outliers final: 3 residues processed: 158 average time/residue: 0.4537 time to fit residues: 76.1775 Evaluate side-chains 105 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 102 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 536 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.1980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 HIS A 338 GLN B 86 HIS B 157 GLN B 234 HIS B 460 ASN B 490 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.164524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.138676 restraints weight = 9206.729| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.31 r_work: 0.3435 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7828 Z= 0.135 Angle : 0.653 6.754 10709 Z= 0.333 Chirality : 0.041 0.149 1291 Planarity : 0.007 0.058 1274 Dihedral : 5.720 35.037 1018 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.39 % Allowed : 13.88 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.34 (0.25), residues: 959 helix: -1.90 (0.18), residues: 659 sheet: None (None), residues: 0 loop : -2.58 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 12 TYR 0.012 0.001 TYR B 582 PHE 0.017 0.001 PHE B 15 TRP 0.032 0.002 TRP A 48 HIS 0.004 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 7828) covalent geometry : angle 0.65256 (10709) hydrogen bonds : bond 0.04213 ( 336) hydrogen bonds : angle 4.27386 ( 990) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.258 Fit side-chains REVERT: A 12 ARG cc_start: 0.8082 (ptm-80) cc_final: 0.7808 (ttp80) REVERT: A 65 MET cc_start: 0.9263 (ptt) cc_final: 0.8962 (ptm) REVERT: A 267 GLU cc_start: 0.7710 (pp20) cc_final: 0.7389 (pt0) REVERT: A 329 CYS cc_start: 0.8072 (m) cc_final: 0.7419 (t) REVERT: A 338 GLN cc_start: 0.7734 (mt0) cc_final: 0.7430 (tt0) REVERT: A 344 ARG cc_start: 0.7757 (ptt180) cc_final: 0.6809 (mmt180) REVERT: A 460 ASN cc_start: 0.7464 (m-40) cc_final: 0.6629 (t0) REVERT: A 566 MET cc_start: 0.7955 (mmm) cc_final: 0.7664 (mmm) REVERT: B 450 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7362 (tm-30) REVERT: B 566 MET cc_start: 0.6620 (mmm) cc_final: 0.5406 (mmt) outliers start: 20 outliers final: 9 residues processed: 132 average time/residue: 0.3899 time to fit residues: 55.3625 Evaluate side-chains 113 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 529 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 20 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 66 optimal weight: 6.9990 chunk 45 optimal weight: 0.4980 chunk 96 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 44 optimal weight: 0.0170 chunk 29 optimal weight: 3.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN ** B 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 ASN B 533 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.165142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.139443 restraints weight = 9077.221| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.28 r_work: 0.3443 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7828 Z= 0.112 Angle : 0.592 6.182 10709 Z= 0.299 Chirality : 0.040 0.148 1291 Planarity : 0.005 0.053 1274 Dihedral : 5.140 25.446 1014 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.47 % Allowed : 16.15 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.15 (0.27), residues: 959 helix: -0.98 (0.20), residues: 670 sheet: None (None), residues: 0 loop : -2.22 (0.37), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 12 TYR 0.008 0.001 TYR B 582 PHE 0.015 0.001 PHE B 15 TRP 0.022 0.001 TRP A 48 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 7828) covalent geometry : angle 0.59195 (10709) hydrogen bonds : bond 0.03289 ( 336) hydrogen bonds : angle 3.83580 ( 990) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 0.255 Fit side-chains REVERT: A 65 MET cc_start: 0.9203 (ptt) cc_final: 0.8970 (ptm) REVERT: A 99 ILE cc_start: 0.8779 (pt) cc_final: 0.8456 (mt) REVERT: A 329 CYS cc_start: 0.7944 (m) cc_final: 0.7253 (t) REVERT: A 344 ARG cc_start: 0.7715 (ptt180) cc_final: 0.6846 (mmt180) REVERT: A 357 MET cc_start: 0.9108 (OUTLIER) cc_final: 0.8891 (ttp) REVERT: A 416 PHE cc_start: 0.6754 (t80) cc_final: 0.6482 (t80) REVERT: A 460 ASN cc_start: 0.7464 (m-40) cc_final: 0.6682 (t0) REVERT: A 566 MET cc_start: 0.7966 (mmm) cc_final: 0.7739 (mmm) REVERT: B 338 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7918 (mp10) REVERT: B 450 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7239 (tm-30) REVERT: B 555 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7074 (pt) REVERT: B 566 MET cc_start: 0.6641 (mmm) cc_final: 0.5498 (mmp) outliers start: 29 outliers final: 12 residues processed: 126 average time/residue: 0.4520 time to fit residues: 60.7450 Evaluate side-chains 122 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 338 GLN Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 495 THR Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 555 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 48 optimal weight: 0.0570 chunk 70 optimal weight: 0.4980 chunk 84 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 4 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 38 optimal weight: 0.2980 chunk 71 optimal weight: 0.6980 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN B 105 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.165676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.141215 restraints weight = 9124.103| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.38 r_work: 0.3449 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7828 Z= 0.107 Angle : 0.579 5.978 10709 Z= 0.291 Chirality : 0.039 0.138 1291 Planarity : 0.005 0.056 1274 Dihedral : 4.814 25.502 1012 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.11 % Allowed : 16.75 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.28), residues: 959 helix: -0.45 (0.21), residues: 664 sheet: None (None), residues: 0 loop : -2.20 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 12 TYR 0.008 0.001 TYR B 337 PHE 0.016 0.001 PHE B 354 TRP 0.017 0.001 TRP A 48 HIS 0.002 0.000 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 7828) covalent geometry : angle 0.57860 (10709) hydrogen bonds : bond 0.02827 ( 336) hydrogen bonds : angle 3.68163 ( 990) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.283 Fit side-chains REVERT: A 65 MET cc_start: 0.9173 (ptt) cc_final: 0.8903 (ptm) REVERT: A 99 ILE cc_start: 0.8685 (pt) cc_final: 0.8476 (mt) REVERT: A 329 CYS cc_start: 0.8112 (m) cc_final: 0.7435 (t) REVERT: A 344 ARG cc_start: 0.7804 (ptt180) cc_final: 0.6872 (mmt180) REVERT: A 357 MET cc_start: 0.9097 (OUTLIER) cc_final: 0.8882 (ttp) REVERT: A 416 PHE cc_start: 0.6744 (t80) cc_final: 0.6479 (t80) REVERT: A 460 ASN cc_start: 0.7497 (m-40) cc_final: 0.6722 (t0) REVERT: A 566 MET cc_start: 0.7965 (mmm) cc_final: 0.7691 (mmm) REVERT: B 34 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6577 (mp0) REVERT: B 338 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7912 (mp10) REVERT: B 450 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7273 (tm-30) REVERT: B 555 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7131 (pt) REVERT: B 566 MET cc_start: 0.6606 (mmm) cc_final: 0.5417 (mmp) outliers start: 26 outliers final: 12 residues processed: 124 average time/residue: 0.4427 time to fit residues: 58.6297 Evaluate side-chains 118 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 338 GLN Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 495 THR Chi-restraints excluded: chain B residue 555 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 42 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 79 optimal weight: 0.5980 chunk 85 optimal weight: 0.6980 chunk 82 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 28 optimal weight: 0.1980 chunk 20 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.164506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.140133 restraints weight = 9028.363| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.32 r_work: 0.3445 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7828 Z= 0.112 Angle : 0.598 8.863 10709 Z= 0.298 Chirality : 0.040 0.137 1291 Planarity : 0.005 0.056 1274 Dihedral : 4.724 25.677 1012 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.11 % Allowed : 17.22 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.28), residues: 959 helix: -0.12 (0.21), residues: 664 sheet: None (None), residues: 0 loop : -2.24 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 12 TYR 0.013 0.001 TYR A 542 PHE 0.019 0.001 PHE B 354 TRP 0.017 0.001 TRP A 48 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 7828) covalent geometry : angle 0.59841 (10709) hydrogen bonds : bond 0.02919 ( 336) hydrogen bonds : angle 3.62818 ( 990) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 0.210 Fit side-chains REVERT: A 65 MET cc_start: 0.9130 (ptt) cc_final: 0.8892 (ptm) REVERT: A 338 GLN cc_start: 0.7890 (OUTLIER) cc_final: 0.7614 (tt0) REVERT: A 344 ARG cc_start: 0.7860 (ptt180) cc_final: 0.6973 (mmt180) REVERT: A 357 MET cc_start: 0.9078 (OUTLIER) cc_final: 0.8871 (ttp) REVERT: A 416 PHE cc_start: 0.6960 (t80) cc_final: 0.6659 (t80) REVERT: A 460 ASN cc_start: 0.7550 (m-40) cc_final: 0.6763 (t0) REVERT: A 550 MET cc_start: 0.8342 (OUTLIER) cc_final: 0.8134 (ttp) REVERT: A 566 MET cc_start: 0.8019 (mmm) cc_final: 0.7757 (mmm) REVERT: B 34 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.6755 (mp0) REVERT: B 338 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7924 (mp10) REVERT: B 450 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7248 (tm-30) REVERT: B 555 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7119 (pt) REVERT: B 566 MET cc_start: 0.6491 (mmm) cc_final: 0.5320 (mmp) outliers start: 26 outliers final: 13 residues processed: 118 average time/residue: 0.4033 time to fit residues: 50.8712 Evaluate side-chains 122 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 338 GLN Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 65 MET Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 338 GLN Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 495 THR Chi-restraints excluded: chain B residue 555 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 57 optimal weight: 0.6980 chunk 62 optimal weight: 0.0370 chunk 40 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN B 544 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.164414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.139956 restraints weight = 9067.210| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.31 r_work: 0.3446 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7828 Z= 0.111 Angle : 0.589 8.110 10709 Z= 0.293 Chirality : 0.040 0.136 1291 Planarity : 0.005 0.056 1274 Dihedral : 4.650 25.609 1012 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.11 % Allowed : 18.06 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.28), residues: 959 helix: 0.08 (0.21), residues: 659 sheet: None (None), residues: 0 loop : -2.22 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 12 TYR 0.011 0.001 TYR A 542 PHE 0.018 0.001 PHE B 354 TRP 0.016 0.001 TRP A 48 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 7828) covalent geometry : angle 0.58862 (10709) hydrogen bonds : bond 0.02840 ( 336) hydrogen bonds : angle 3.59068 ( 990) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 0.208 Fit side-chains REVERT: A 65 MET cc_start: 0.9125 (ptt) cc_final: 0.8882 (ptm) REVERT: A 329 CYS cc_start: 0.7833 (m) cc_final: 0.7454 (m) REVERT: A 344 ARG cc_start: 0.7829 (ptt180) cc_final: 0.6901 (mmt180) REVERT: A 357 MET cc_start: 0.9087 (OUTLIER) cc_final: 0.8874 (ttp) REVERT: A 416 PHE cc_start: 0.6873 (t80) cc_final: 0.6503 (t80) REVERT: A 460 ASN cc_start: 0.7500 (m-40) cc_final: 0.6777 (t0) REVERT: A 550 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.8150 (ttp) REVERT: A 566 MET cc_start: 0.8003 (mmm) cc_final: 0.7733 (mmm) REVERT: B 34 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.6734 (mp0) REVERT: B 338 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7871 (mp10) REVERT: B 450 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7174 (tm-30) REVERT: B 555 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7116 (pt) REVERT: B 566 MET cc_start: 0.6443 (mmm) cc_final: 0.5192 (mmp) outliers start: 26 outliers final: 12 residues processed: 121 average time/residue: 0.4285 time to fit residues: 55.6149 Evaluate side-chains 120 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 65 MET Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 338 GLN Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 495 THR Chi-restraints excluded: chain B residue 555 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 28 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 73 optimal weight: 0.0980 chunk 39 optimal weight: 0.0000 chunk 69 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN B 533 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.165688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.141111 restraints weight = 9046.548| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.40 r_work: 0.3448 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7828 Z= 0.103 Angle : 0.572 7.388 10709 Z= 0.285 Chirality : 0.039 0.134 1291 Planarity : 0.005 0.054 1274 Dihedral : 4.502 25.387 1012 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.51 % Allowed : 18.66 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.28), residues: 959 helix: 0.29 (0.21), residues: 660 sheet: None (None), residues: 0 loop : -2.19 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 11 TYR 0.009 0.001 TYR A 542 PHE 0.017 0.001 PHE B 354 TRP 0.015 0.001 TRP A 48 HIS 0.003 0.000 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 7828) covalent geometry : angle 0.57188 (10709) hydrogen bonds : bond 0.02622 ( 336) hydrogen bonds : angle 3.53930 ( 990) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.206 Fit side-chains REVERT: A 65 MET cc_start: 0.9086 (ptt) cc_final: 0.8864 (ptm) REVERT: A 329 CYS cc_start: 0.7871 (m) cc_final: 0.7231 (m) REVERT: A 344 ARG cc_start: 0.7849 (ptt180) cc_final: 0.6903 (mmt180) REVERT: A 357 MET cc_start: 0.9063 (OUTLIER) cc_final: 0.8859 (ttp) REVERT: A 416 PHE cc_start: 0.6818 (t80) cc_final: 0.6426 (t80) REVERT: A 566 MET cc_start: 0.7997 (mmm) cc_final: 0.7747 (mmm) REVERT: B 57 VAL cc_start: 0.8732 (t) cc_final: 0.8437 (t) REVERT: B 338 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7816 (mp10) REVERT: B 450 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7149 (tm-30) REVERT: B 555 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7157 (pt) REVERT: B 566 MET cc_start: 0.6510 (mmm) cc_final: 0.5330 (mmp) outliers start: 21 outliers final: 10 residues processed: 119 average time/residue: 0.4500 time to fit residues: 57.0077 Evaluate side-chains 118 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 338 GLN Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 495 THR Chi-restraints excluded: chain B residue 555 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 4 optimal weight: 3.9990 chunk 64 optimal weight: 0.0470 chunk 88 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 28 optimal weight: 0.0070 chunk 20 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 90 optimal weight: 0.3980 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN B 533 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.164249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.140636 restraints weight = 9154.777| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.26 r_work: 0.3471 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7828 Z= 0.107 Angle : 0.580 8.009 10709 Z= 0.290 Chirality : 0.039 0.133 1291 Planarity : 0.005 0.054 1274 Dihedral : 4.455 24.916 1012 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.91 % Allowed : 20.57 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.28), residues: 959 helix: 0.44 (0.21), residues: 660 sheet: None (None), residues: 0 loop : -2.34 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 11 TYR 0.012 0.001 TYR B 542 PHE 0.019 0.001 PHE B 354 TRP 0.015 0.001 TRP A 48 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 7828) covalent geometry : angle 0.57955 (10709) hydrogen bonds : bond 0.02696 ( 336) hydrogen bonds : angle 3.51525 ( 990) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.217 Fit side-chains REVERT: A 65 MET cc_start: 0.9074 (ptt) cc_final: 0.8842 (ptm) REVERT: A 100 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7827 (tt0) REVERT: A 329 CYS cc_start: 0.7858 (m) cc_final: 0.7223 (m) REVERT: A 344 ARG cc_start: 0.7826 (ptt180) cc_final: 0.6909 (mmt180) REVERT: A 357 MET cc_start: 0.9061 (OUTLIER) cc_final: 0.8845 (ttp) REVERT: A 460 ASN cc_start: 0.7465 (m-40) cc_final: 0.6784 (t0) REVERT: A 566 MET cc_start: 0.7997 (mmm) cc_final: 0.7747 (mmm) REVERT: B 57 VAL cc_start: 0.8686 (t) cc_final: 0.8426 (t) REVERT: B 114 MET cc_start: 0.7038 (ptm) cc_final: 0.6787 (ppp) REVERT: B 338 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7812 (mp10) REVERT: B 450 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7147 (tm-30) REVERT: B 555 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7146 (pt) REVERT: B 566 MET cc_start: 0.6509 (mmm) cc_final: 0.5325 (mmp) outliers start: 16 outliers final: 10 residues processed: 120 average time/residue: 0.4288 time to fit residues: 55.0969 Evaluate side-chains 117 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 338 GLN Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 495 THR Chi-restraints excluded: chain B residue 555 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 55 optimal weight: 0.0270 chunk 28 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 50 optimal weight: 0.0670 chunk 49 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN B 533 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.165222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.140742 restraints weight = 9047.532| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.32 r_work: 0.3439 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7828 Z= 0.108 Angle : 0.580 9.159 10709 Z= 0.290 Chirality : 0.039 0.133 1291 Planarity : 0.005 0.053 1274 Dihedral : 4.411 24.949 1012 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.91 % Allowed : 20.93 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.29), residues: 959 helix: 0.56 (0.21), residues: 659 sheet: None (None), residues: 0 loop : -2.34 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 12 TYR 0.007 0.001 TYR A 514 PHE 0.019 0.001 PHE B 354 TRP 0.015 0.001 TRP A 48 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 7828) covalent geometry : angle 0.58020 (10709) hydrogen bonds : bond 0.02684 ( 336) hydrogen bonds : angle 3.50357 ( 990) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.222 Fit side-chains REVERT: A 65 MET cc_start: 0.9090 (ptt) cc_final: 0.8877 (ptm) REVERT: A 329 CYS cc_start: 0.7917 (m) cc_final: 0.7275 (m) REVERT: A 338 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7637 (tt0) REVERT: A 344 ARG cc_start: 0.7827 (ptt180) cc_final: 0.6905 (mmt180) REVERT: A 357 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.8864 (ttp) REVERT: A 460 ASN cc_start: 0.7484 (m-40) cc_final: 0.6783 (t0) REVERT: A 566 MET cc_start: 0.7984 (mmm) cc_final: 0.7741 (mmm) REVERT: B 57 VAL cc_start: 0.8697 (t) cc_final: 0.8436 (t) REVERT: B 338 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7849 (mp10) REVERT: B 450 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7269 (tm-30) REVERT: B 555 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7212 (pt) REVERT: B 566 MET cc_start: 0.6522 (mmm) cc_final: 0.5327 (mmp) outliers start: 16 outliers final: 10 residues processed: 118 average time/residue: 0.4262 time to fit residues: 53.8789 Evaluate side-chains 115 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 338 GLN Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 338 GLN Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 495 THR Chi-restraints excluded: chain B residue 555 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.4359 > 50: distance: 66 - 106: 29.309 distance: 77 - 78: 12.138 distance: 78 - 79: 6.628 distance: 78 - 81: 11.736 distance: 79 - 80: 18.930 distance: 79 - 86: 10.619 distance: 81 - 82: 8.193 distance: 82 - 83: 12.859 distance: 83 - 84: 4.741 distance: 84 - 85: 6.413 distance: 86 - 87: 6.070 distance: 87 - 88: 16.504 distance: 87 - 90: 4.900 distance: 88 - 89: 7.358 distance: 88 - 95: 6.576 distance: 89 - 121: 51.493 distance: 90 - 91: 10.714 distance: 91 - 92: 10.871 distance: 92 - 93: 20.409 distance: 92 - 94: 13.183 distance: 95 - 96: 4.073 distance: 96 - 97: 6.092 distance: 96 - 99: 4.349 distance: 97 - 98: 3.640 distance: 97 - 106: 6.841 distance: 98 - 132: 13.434 distance: 99 - 100: 3.761 distance: 100 - 101: 3.926 distance: 100 - 102: 9.754 distance: 101 - 103: 4.195 distance: 102 - 104: 5.883 distance: 103 - 105: 12.962 distance: 104 - 105: 11.072 distance: 106 - 107: 25.127 distance: 107 - 108: 25.811 distance: 107 - 110: 22.903 distance: 108 - 109: 39.700 distance: 108 - 115: 17.362 distance: 110 - 111: 22.737 distance: 111 - 112: 9.175 distance: 112 - 113: 21.206 distance: 112 - 114: 13.853 distance: 115 - 116: 18.595 distance: 116 - 117: 48.193 distance: 116 - 119: 41.724 distance: 117 - 118: 24.395 distance: 117 - 121: 46.792 distance: 119 - 120: 8.547 distance: 121 - 122: 13.912 distance: 122 - 123: 27.168 distance: 122 - 125: 8.780 distance: 123 - 124: 19.823 distance: 123 - 132: 9.641 distance: 125 - 126: 16.941 distance: 126 - 127: 10.871 distance: 126 - 128: 16.841 distance: 127 - 129: 6.902 distance: 128 - 130: 8.132 distance: 129 - 131: 13.088 distance: 130 - 131: 13.538 distance: 132 - 133: 14.200 distance: 133 - 134: 9.309 distance: 133 - 136: 13.912 distance: 134 - 135: 16.611 distance: 134 - 140: 12.349 distance: 136 - 137: 7.035 distance: 137 - 138: 18.413 distance: 138 - 139: 12.201 distance: 140 - 141: 4.465 distance: 140 - 146: 6.062 distance: 141 - 142: 7.726 distance: 141 - 144: 5.989 distance: 142 - 147: 5.507 distance: 144 - 145: 6.481 distance: 145 - 146: 3.751 distance: 147 - 148: 8.410 distance: 148 - 149: 14.117 distance: 148 - 151: 5.444 distance: 149 - 150: 8.645 distance: 149 - 161: 4.271 distance: 151 - 152: 18.224 distance: 152 - 153: 10.557 distance: 152 - 154: 3.786 distance: 153 - 155: 8.271 distance: 154 - 156: 10.926 distance: 154 - 157: 11.986 distance: 155 - 156: 10.032 distance: 156 - 158: 6.061 distance: 157 - 159: 3.262 distance: 158 - 160: 13.622 distance: 159 - 160: 12.571 distance: 161 - 162: 16.421 distance: 162 - 163: 21.066 distance: 162 - 165: 5.349 distance: 163 - 164: 3.429 distance: 163 - 169: 8.694 distance: 164 - 189: 12.680 distance: 165 - 166: 21.400 distance: 166 - 167: 10.463