Starting phenix.real_space_refine on Mon Dec 11 13:39:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h69_34497/12_2023/8h69_34497.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h69_34497/12_2023/8h69_34497.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h69_34497/12_2023/8h69_34497.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h69_34497/12_2023/8h69_34497.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h69_34497/12_2023/8h69_34497.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h69_34497/12_2023/8h69_34497.pdb" } resolution = 3.7 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= 0.002 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 36 5.49 5 S 128 5.16 5 C 11214 2.51 5 N 3150 2.21 5 O 3500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 57": "NH1" <-> "NH2" Residue "A ARG 82": "NH1" <-> "NH2" Residue "A ARG 116": "NH1" <-> "NH2" Residue "A ARG 185": "NH1" <-> "NH2" Residue "A ARG 196": "NH1" <-> "NH2" Residue "A ARG 204": "NH1" <-> "NH2" Residue "A ARG 230": "NH1" <-> "NH2" Residue "A ARG 256": "NH1" <-> "NH2" Residue "A ARG 266": "NH1" <-> "NH2" Residue "A ARG 269": "NH1" <-> "NH2" Residue "A ARG 279": "NH1" <-> "NH2" Residue "A ARG 361": "NH1" <-> "NH2" Residue "A ARG 391": "NH1" <-> "NH2" Residue "A ARG 401": "NH1" <-> "NH2" Residue "A ARG 495": "NH1" <-> "NH2" Residue "A ARG 559": "NH1" <-> "NH2" Residue "B ARG 187": "NH1" <-> "NH2" Residue "B ARG 189": "NH1" <-> "NH2" Residue "B ARG 211": "NH1" <-> "NH2" Residue "B ARG 215": "NH1" <-> "NH2" Residue "B ARG 287": "NH1" <-> "NH2" Residue "B ARG 327": "NH1" <-> "NH2" Residue "B ARG 386": "NH1" <-> "NH2" Residue "B ARG 430": "NH1" <-> "NH2" Residue "B TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 465": "NH1" <-> "NH2" Residue "B ARG 486": "NH1" <-> "NH2" Residue "B ARG 584": "NH1" <-> "NH2" Residue "B ARG 706": "NH1" <-> "NH2" Residue "B ARG 723": "NH1" <-> "NH2" Residue "B ARG 734": "NH1" <-> "NH2" Residue "B ARG 754": "NH1" <-> "NH2" Residue "C ARG 3": "NH1" <-> "NH2" Residue "C ARG 8": "NH1" <-> "NH2" Residue "C ARG 15": "NH1" <-> "NH2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "C ARG 70": "NH1" <-> "NH2" Residue "C ARG 136": "NH1" <-> "NH2" Residue "C ARG 143": "NH1" <-> "NH2" Residue "C ARG 251": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 18028 Number of models: 1 Model: "" Number of chains: 5 Chain: "3" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 369 Classifications: {'RNA': 18} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 4, 'rna3p_pur': 4, 'rna3p_pyr': 9} Link IDs: {'rna2p': 5, 'rna3p': 12} Chain: "5" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 411 Classifications: {'RNA': 19} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 10, 'rna3p_pyr': 6} Link IDs: {'rna2p': 3, 'rna3p': 15} Chain: "A" Number of atoms: 5790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 716, 5790 Classifications: {'peptide': 716} Link IDs: {'PTRANS': 33, 'TRANS': 682} Chain: "B" Number of atoms: 6022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 754, 6022 Classifications: {'peptide': 754} Link IDs: {'PTRANS': 32, 'TRANS': 721} Chain: "C" Number of atoms: 5436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5436 Classifications: {'peptide': 683} Link IDs: {'PTRANS': 27, 'TRANS': 655} Time building chain proxies: 11.36, per 1000 atoms: 0.63 Number of scatterers: 18028 At special positions: 0 Unit cell: (136.24, 123.76, 116.48, 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 128 16.00 P 36 15.00 O 3500 8.00 N 3150 7.00 C 11214 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.85 Conformation dependent library (CDL) restraints added in 3.6 seconds 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4058 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 22 sheets defined 42.3% alpha, 11.5% beta 8 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 6.95 Creating SS restraints... Processing helix chain 'A' and resid 1 through 8 Processing helix chain 'A' and resid 10 through 22 removed outlier: 3.653A pdb=" N LEU A 16 " --> pdb=" O MET A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 48 removed outlier: 3.817A pdb=" N CYS A 39 " --> pdb=" O PHE A 35 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 98 removed outlier: 3.600A pdb=" N TRP A 88 " --> pdb=" O ARG A 84 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 134 removed outlier: 3.998A pdb=" N TYR A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LEU A 132 " --> pdb=" O HIS A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 160 removed outlier: 4.014A pdb=" N ALA A 159 " --> pdb=" O ALA A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 186 removed outlier: 3.864A pdb=" N GLY A 186 " --> pdb=" O MET A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 234 removed outlier: 4.059A pdb=" N ASP A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 249 removed outlier: 3.570A pdb=" N GLN A 248 " --> pdb=" O GLY A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 313 removed outlier: 3.643A pdb=" N ILE A 308 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS A 309 " --> pdb=" O TYR A 305 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N CYS A 310 " --> pdb=" O ASP A 306 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET A 311 " --> pdb=" O ALA A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 345 removed outlier: 4.083A pdb=" N TYR A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 348 No H-bonds generated for 'chain 'A' and resid 346 through 348' Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.762A pdb=" N TRP A 368 " --> pdb=" O SER A 364 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA A 369 " --> pdb=" O GLN A 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 364 through 369' Processing helix chain 'A' and resid 405 through 416 removed outlier: 3.629A pdb=" N SER A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 445 Processing helix chain 'A' and resid 446 through 449 Processing helix chain 'A' and resid 454 through 476 removed outlier: 3.553A pdb=" N TYR A 458 " --> pdb=" O ARG A 454 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR A 464 " --> pdb=" O MET A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 533 removed outlier: 3.549A pdb=" N GLU A 533 " --> pdb=" O PRO A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 582 No H-bonds generated for 'chain 'A' and resid 580 through 582' Processing helix chain 'A' and resid 583 through 598 removed outlier: 4.040A pdb=" N GLN A 591 " --> pdb=" O GLN A 587 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ILE A 592 " --> pdb=" O SER A 588 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE A 596 " --> pdb=" O ILE A 592 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU A 597 " --> pdb=" O GLU A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 604 removed outlier: 3.730A pdb=" N LYS A 603 " --> pdb=" O GLU A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 612 removed outlier: 3.722A pdb=" N PHE A 611 " --> pdb=" O MET A 607 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N PHE A 612 " --> pdb=" O THR A 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 607 through 612' Processing helix chain 'A' and resid 632 through 650 removed outlier: 3.774A pdb=" N ARG A 638 " --> pdb=" O GLY A 634 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 641 " --> pdb=" O CYS A 637 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER A 648 " --> pdb=" O SER A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 660 removed outlier: 3.882A pdb=" N GLU A 656 " --> pdb=" O SER A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 674 removed outlier: 4.347A pdb=" N ILE A 668 " --> pdb=" O LYS A 664 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL A 669 " --> pdb=" O LEU A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 691 Processing helix chain 'A' and resid 699 through 712 removed outlier: 3.624A pdb=" N SER A 705 " --> pdb=" O LEU A 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 11 removed outlier: 3.882A pdb=" N PHE B 9 " --> pdb=" O THR B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 22 removed outlier: 3.516A pdb=" N THR B 20 " --> pdb=" O ALA B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 50 removed outlier: 3.568A pdb=" N THR B 42 " --> pdb=" O TYR B 38 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ARG B 45 " --> pdb=" O ASP B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 94 removed outlier: 4.209A pdb=" N GLU B 90 " --> pdb=" O ASP B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 99 removed outlier: 3.506A pdb=" N SER B 98 " --> pdb=" O PHE B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 114 removed outlier: 3.678A pdb=" N ASN B 105 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU B 108 " --> pdb=" O GLU B 104 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU B 109 " --> pdb=" O ASN B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 153 removed outlier: 3.718A pdb=" N LEU B 143 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N GLU B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE B 150 " --> pdb=" O THR B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 173 removed outlier: 3.705A pdb=" N VAL B 170 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N MET B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 222 removed outlier: 3.671A pdb=" N ARG B 220 " --> pdb=" O SER B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 266 removed outlier: 4.075A pdb=" N ARG B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLY B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N PHE B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS B 263 " --> pdb=" O ALA B 259 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS B 265 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 285 removed outlier: 3.666A pdb=" N LYS B 278 " --> pdb=" O GLY B 274 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL B 285 " --> pdb=" O LYS B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 291 removed outlier: 3.503A pdb=" N THR B 291 " --> pdb=" O LYS B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 325 Processing helix chain 'B' and resid 330 through 337 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 371 through 375 removed outlier: 3.650A pdb=" N ALA B 374 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 381 Processing helix chain 'B' and resid 382 through 391 removed outlier: 3.760A pdb=" N LYS B 387 " --> pdb=" O GLU B 383 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU B 390 " --> pdb=" O ARG B 386 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS B 391 " --> pdb=" O LYS B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 394 No H-bonds generated for 'chain 'B' and resid 392 through 394' Processing helix chain 'B' and resid 415 through 427 removed outlier: 3.780A pdb=" N LEU B 424 " --> pdb=" O GLY B 420 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY B 427 " --> pdb=" O ILE B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 455 through 471 removed outlier: 3.613A pdb=" N ASP B 464 " --> pdb=" O GLN B 460 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG B 465 " --> pdb=" O ALA B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 474 No H-bonds generated for 'chain 'B' and resid 472 through 474' Processing helix chain 'B' and resid 525 through 534 removed outlier: 3.546A pdb=" N ILE B 530 " --> pdb=" O GLY B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 559 removed outlier: 3.647A pdb=" N LYS B 553 " --> pdb=" O GLN B 549 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR B 557 " --> pdb=" O LYS B 553 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR B 558 " --> pdb=" O ASP B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 583 removed outlier: 3.766A pdb=" N LYS B 577 " --> pdb=" O SER B 573 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS B 578 " --> pdb=" O PHE B 574 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU B 579 " --> pdb=" O GLU B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 589 removed outlier: 3.919A pdb=" N GLY B 588 " --> pdb=" O SER B 585 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU B 589 " --> pdb=" O LYS B 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 585 through 589' Processing helix chain 'B' and resid 590 through 594 removed outlier: 3.658A pdb=" N ASP B 593 " --> pdb=" O LEU B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 612 Processing helix chain 'B' and resid 617 through 625 removed outlier: 4.307A pdb=" N GLN B 621 " --> pdb=" O ASP B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 676 removed outlier: 3.502A pdb=" N ASN B 676 " --> pdb=" O SER B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 683 removed outlier: 3.652A pdb=" N ILE B 682 " --> pdb=" O GLN B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 697 Processing helix chain 'B' and resid 701 through 705 removed outlier: 4.059A pdb=" N SER B 704 " --> pdb=" O PRO B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 731 removed outlier: 3.848A pdb=" N VAL B 719 " --> pdb=" O VAL B 715 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG B 721 " --> pdb=" O ALA B 717 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE B 724 " --> pdb=" O SER B 720 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG B 727 " --> pdb=" O ARG B 723 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE B 728 " --> pdb=" O ILE B 724 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP B 729 " --> pdb=" O ASP B 725 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 752 removed outlier: 3.541A pdb=" N GLU B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE B 746 " --> pdb=" O GLU B 742 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N CYS B 747 " --> pdb=" O ILE B 743 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER B 748 " --> pdb=" O MET B 744 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR B 749 " --> pdb=" O LYS B 745 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 10 removed outlier: 4.407A pdb=" N GLU C 6 " --> pdb=" O GLU C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 32 Processing helix chain 'C' and resid 42 through 51 removed outlier: 3.594A pdb=" N ARG C 46 " --> pdb=" O ASN C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 67 Processing helix chain 'C' and resid 92 through 103 removed outlier: 4.179A pdb=" N VAL C 96 " --> pdb=" O SER C 92 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG C 101 " --> pdb=" O THR C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 115 removed outlier: 3.525A pdb=" N TYR C 115 " --> pdb=" O TYR C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 127 removed outlier: 3.635A pdb=" N PHE C 119 " --> pdb=" O TYR C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 168 removed outlier: 3.756A pdb=" N PHE C 168 " --> pdb=" O MET C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 172 removed outlier: 3.673A pdb=" N VAL C 172 " --> pdb=" O PRO C 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 169 through 172' Processing helix chain 'C' and resid 181 through 197 removed outlier: 3.870A pdb=" N ILE C 185 " --> pdb=" O SER C 181 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU C 191 " --> pdb=" O LYS C 187 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU C 192 " --> pdb=" O GLU C 188 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU C 193 " --> pdb=" O LYS C 189 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLN C 194 " --> pdb=" O LYS C 190 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS C 197 " --> pdb=" O LEU C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 208 removed outlier: 3.569A pdb=" N LEU C 207 " --> pdb=" O VAL C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 273 removed outlier: 4.049A pdb=" N ILE C 261 " --> pdb=" O GLN C 257 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA C 262 " --> pdb=" O SER C 258 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE C 266 " --> pdb=" O ALA C 262 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG C 269 " --> pdb=" O ASN C 265 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL C 272 " --> pdb=" O ARG C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 283 removed outlier: 3.691A pdb=" N LEU C 280 " --> pdb=" O PRO C 276 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N LEU C 281 " --> pdb=" O LEU C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 286 No H-bonds generated for 'chain 'C' and resid 284 through 286' Processing helix chain 'C' and resid 294 through 298 Processing helix chain 'C' and resid 305 through 315 removed outlier: 3.894A pdb=" N MET C 315 " --> pdb=" O CYS C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 405 Processing helix chain 'C' and resid 407 through 412 Processing helix chain 'C' and resid 429 through 441 removed outlier: 3.662A pdb=" N ARG C 436 " --> pdb=" O HIS C 432 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE C 438 " --> pdb=" O LEU C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 449 Processing helix chain 'C' and resid 536 through 541 Processing helix chain 'C' and resid 541 through 556 removed outlier: 3.551A pdb=" N LEU C 546 " --> pdb=" O PRO C 542 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR C 550 " --> pdb=" O LEU C 546 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE C 554 " --> pdb=" O TYR C 550 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG C 555 " --> pdb=" O GLN C 551 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN C 556 " --> pdb=" O TRP C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 566 removed outlier: 3.877A pdb=" N ILE C 562 " --> pdb=" O GLU C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 573 Processing helix chain 'C' and resid 579 through 583 removed outlier: 3.593A pdb=" N SER C 582 " --> pdb=" O SER C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 607 removed outlier: 3.598A pdb=" N THR C 598 " --> pdb=" O GLY C 594 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU C 607 " --> pdb=" O MET C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 619 removed outlier: 3.762A pdb=" N ILE C 616 " --> pdb=" O THR C 612 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU C 619 " --> pdb=" O ILE C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 624 removed outlier: 3.883A pdb=" N ALA C 623 " --> pdb=" O PRO C 620 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA C 624 " --> pdb=" O PHE C 621 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 620 through 624' Processing helix chain 'C' and resid 677 through 682 Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.209A pdb=" N PHE A 117 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N HIS A 146 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N GLU A 119 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N PHE A 148 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N GLY A 121 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 290 through 293 removed outlier: 5.007A pdb=" N LEU A 500 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N SER A 487 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY A 502 " --> pdb=" O MET A 485 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN A 481 " --> pdb=" O LYS A 506 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N PHE A 480 " --> pdb=" O MET A 360 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LYS A 358 " --> pdb=" O LEU A 482 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 290 through 293 removed outlier: 3.560A pdb=" N VAL A 557 " --> pdb=" O LEU A 550 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG A 559 " --> pdb=" O MET A 548 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N MET A 548 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU A 563 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N GLU A 544 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL A 565 " --> pdb=" O VAL A 542 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N VAL A 542 " --> pdb=" O VAL A 565 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 377 through 378 removed outlier: 3.588A pdb=" N ARG B 365 " --> pdb=" O GLU A 377 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU B 364 " --> pdb=" O SER B 359 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N TYR B 355 " --> pdb=" O ILE B 368 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 420 through 421 Processing sheet with id=AA6, first strand: chain 'A' and resid 627 through 631 removed outlier: 6.691A pdb=" N GLY A 627 " --> pdb=" O GLU A 623 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLU A 623 " --> pdb=" O GLY A 627 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N GLU A 629 " --> pdb=" O ILE A 621 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AA8, first strand: chain 'B' and resid 181 through 183 removed outlier: 3.637A pdb=" N GLN B 210 " --> pdb=" O ILE B 181 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 186 through 192 removed outlier: 3.619A pdb=" N THR B 204 " --> pdb=" O ARG B 187 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN B 202 " --> pdb=" O ARG B 189 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 242 through 243 removed outlier: 6.930A pdb=" N LEU B 224 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 437 through 442 Processing sheet with id=AB3, first strand: chain 'B' and resid 489 through 490 removed outlier: 3.621A pdb=" N PHE B 490 " --> pdb=" O TYR B 497 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 643 through 644 removed outlier: 3.683A pdb=" N ALA B 643 " --> pdb=" O MET B 655 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 667 through 668 removed outlier: 4.339A pdb=" N ILE B 667 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N MET C 90 " --> pdb=" O SER C 79 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 129 through 134 removed outlier: 4.448A pdb=" N MET C 243 " --> pdb=" O GLY C 131 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N VAL C 133 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLU C 241 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 141 through 147 removed outlier: 3.679A pdb=" N ILE C 141 " --> pdb=" O VAL C 220 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 292 through 293 removed outlier: 3.593A pdb=" N ILE C 292 " --> pdb=" O ILE C 289 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 329 through 335 removed outlier: 6.965A pdb=" N GLU C 362 " --> pdb=" O THR C 333 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N THR C 371 " --> pdb=" O VAL C 386 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N VAL C 386 " --> pdb=" O THR C 371 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE C 373 " --> pdb=" O LEU C 384 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU C 384 " --> pdb=" O ILE C 373 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ARG C 375 " --> pdb=" O ILE C 382 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N ARG C 479 " --> pdb=" O ILE C 382 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N LEU C 384 " --> pdb=" O ARG C 479 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N SER C 481 " --> pdb=" O LEU C 384 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL C 386 " --> pdb=" O SER C 481 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N VAL C 478 " --> pdb=" O ILE C 463 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ILE C 463 " --> pdb=" O VAL C 478 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER C 470 " --> pdb=" O GLY C 462 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 341 through 345 Processing sheet with id=AC2, first strand: chain 'C' and resid 451 through 453 Processing sheet with id=AC3, first strand: chain 'C' and resid 636 through 639 removed outlier: 3.530A pdb=" N LEU C 636 " --> pdb=" O ILE C 647 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 656 through 659 removed outlier: 3.565A pdb=" N ASN C 659 " --> pdb=" O ARG C 664 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG C 664 " --> pdb=" O ASN C 659 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU C 665 " --> pdb=" O ALA C 672 " (cutoff:3.500A) 561 hydrogen bonds defined for protein. 1560 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 18 hydrogen bonds 36 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 6.22 Time building geometry restraints manager: 7.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4003 1.33 - 1.45: 4105 1.45 - 1.57: 10050 1.57 - 1.69: 71 1.69 - 1.81: 224 Bond restraints: 18453 Sorted by residual: bond pdb=" CA PHE A 205 " pdb=" CB PHE A 205 " ideal model delta sigma weight residual 1.525 1.472 0.053 1.47e-02 4.63e+03 1.29e+01 bond pdb=" N ASN B 314 " pdb=" CA ASN B 314 " ideal model delta sigma weight residual 1.457 1.407 0.050 1.41e-02 5.03e+03 1.26e+01 bond pdb=" N ASN C 429 " pdb=" CA ASN C 429 " ideal model delta sigma weight residual 1.453 1.493 -0.040 1.18e-02 7.18e+03 1.15e+01 bond pdb=" N ARG C 427 " pdb=" CA ARG C 427 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.29e-02 6.01e+03 8.45e+00 bond pdb=" N ARG C 423 " pdb=" CA ARG C 423 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.82e+00 ... (remaining 18448 not shown) Histogram of bond angle deviations from ideal: 98.14 - 105.34: 577 105.34 - 112.54: 9239 112.54 - 119.74: 6773 119.74 - 126.94: 8167 126.94 - 134.14: 302 Bond angle restraints: 25058 Sorted by residual: angle pdb=" N VAL B 286 " pdb=" CA VAL B 286 " pdb=" C VAL B 286 " ideal model delta sigma weight residual 113.16 103.05 10.11 1.49e+00 4.50e-01 4.60e+01 angle pdb=" N ALA C 587 " pdb=" CA ALA C 587 " pdb=" C ALA C 587 " ideal model delta sigma weight residual 112.23 104.58 7.65 1.26e+00 6.30e-01 3.69e+01 angle pdb=" C HIS A 297 " pdb=" N GLU A 298 " pdb=" CA GLU A 298 " ideal model delta sigma weight residual 121.54 132.09 -10.55 1.91e+00 2.74e-01 3.05e+01 angle pdb=" N LEU B 271 " pdb=" CA LEU B 271 " pdb=" C LEU B 271 " ideal model delta sigma weight residual 113.16 120.52 -7.36 1.42e+00 4.96e-01 2.68e+01 angle pdb=" N VAL C 421 " pdb=" CA VAL C 421 " pdb=" C VAL C 421 " ideal model delta sigma weight residual 109.34 98.77 10.57 2.08e+00 2.31e-01 2.58e+01 ... (remaining 25053 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 10531 17.69 - 35.37: 597 35.37 - 53.06: 126 53.06 - 70.75: 40 70.75 - 88.43: 13 Dihedral angle restraints: 11307 sinusoidal: 5040 harmonic: 6267 Sorted by residual: dihedral pdb=" CA CYS C 239 " pdb=" C CYS C 239 " pdb=" N TRP C 240 " pdb=" CA TRP C 240 " ideal model delta harmonic sigma weight residual -180.00 -150.90 -29.10 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA GLN B 545 " pdb=" C GLN B 545 " pdb=" N MET B 546 " pdb=" CA MET B 546 " ideal model delta harmonic sigma weight residual 180.00 151.22 28.78 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA LYS C 197 " pdb=" C LYS C 197 " pdb=" N ILE C 198 " pdb=" CA ILE C 198 " ideal model delta harmonic sigma weight residual 180.00 151.29 28.71 0 5.00e+00 4.00e-02 3.30e+01 ... (remaining 11304 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1906 0.057 - 0.113: 698 0.113 - 0.170: 154 0.170 - 0.226: 24 0.226 - 0.283: 8 Chirality restraints: 2790 Sorted by residual: chirality pdb=" CA LEU B 224 " pdb=" N LEU B 224 " pdb=" C LEU B 224 " pdb=" CB LEU B 224 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CB ILE B 450 " pdb=" CA ILE B 450 " pdb=" CG1 ILE B 450 " pdb=" CG2 ILE B 450 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CG LEU B 604 " pdb=" CB LEU B 604 " pdb=" CD1 LEU B 604 " pdb=" CD2 LEU B 604 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 2787 not shown) Planarity restraints: 3100 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 633 " 0.035 2.00e-02 2.50e+03 2.86e-02 1.44e+01 pdb=" CG PHE C 633 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE C 633 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE C 633 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE C 633 " 0.024 2.00e-02 2.50e+03 pdb=" CE2 PHE C 633 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 633 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 537 " 0.013 2.00e-02 2.50e+03 1.88e-02 8.87e+00 pdb=" CG TRP A 537 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP A 537 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP A 537 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 537 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 537 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 537 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 537 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 537 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A 537 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 344 " 0.020 2.00e-02 2.50e+03 2.18e-02 8.35e+00 pdb=" CG PHE B 344 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE B 344 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE B 344 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE B 344 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE B 344 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 344 " 0.010 2.00e-02 2.50e+03 ... (remaining 3097 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 126 2.51 - 3.11: 12856 3.11 - 3.71: 28482 3.71 - 4.30: 41001 4.30 - 4.90: 64994 Nonbonded interactions: 147459 Sorted by model distance: nonbonded pdb=" O ASN C 425 " pdb=" O GLN C 426 " model vdw 1.917 3.040 nonbonded pdb=" OG SER C 273 " pdb=" OE1 GLU C 578 " model vdw 2.196 2.440 nonbonded pdb=" N GLN C 426 " pdb=" OE1 GLN C 426 " model vdw 2.197 2.520 nonbonded pdb=" O SER B 293 " pdb=" OG SER C 643 " model vdw 2.208 2.440 nonbonded pdb=" OG1 THR C 129 " pdb=" OG1 THR C 245 " model vdw 2.259 2.440 ... (remaining 147454 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 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: 4.400 Check model and map are aligned: 0.430 Set scattering table: 0.220 Process input model: 56.930 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 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 : 0.009 0.082 18453 Z= 0.585 Angle : 1.121 10.572 25058 Z= 0.630 Chirality : 0.061 0.283 2790 Planarity : 0.007 0.060 3100 Dihedral : 12.537 88.432 7249 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.45 % Favored : 92.36 % Rotamer: Outliers : 1.52 % Allowed : 3.98 % Favored : 94.50 % 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: -4.98 (0.14), residues: 2147 helix: -4.07 (0.09), residues: 819 sheet: -2.19 (0.33), residues: 214 loop : -2.92 (0.16), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.004 TRP A 537 HIS 0.008 0.002 HIS A 326 PHE 0.060 0.004 PHE C 633 TYR 0.044 0.004 TYR B 30 ARG 0.017 0.001 ARG B 249 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 1909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 533 time to evaluate : 1.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 4 residues processed: 550 average time/residue: 0.3656 time to fit residues: 286.2769 Evaluate side-chains 325 residues out of total 1909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 321 time to evaluate : 1.948 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1721 time to fit residues: 3.9868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 10.0000 chunk 163 optimal weight: 10.0000 chunk 90 optimal weight: 0.9990 chunk 55 optimal weight: 0.3980 chunk 110 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 169 optimal weight: 9.9990 chunk 65 optimal weight: 0.0770 chunk 102 optimal weight: 7.9990 chunk 126 optimal weight: 0.8980 chunk 196 optimal weight: 50.0000 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 ASN A 670 GLN B 58 ASN B 153 ASN B 186 GLN B 284 ASN B 292 ASN B 306 ASN B 310 ASN B 329 GLN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 649 HIS C 110 HIS C 134 HIS C 182 GLN ** C 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 18453 Z= 0.206 Angle : 0.691 11.239 25058 Z= 0.360 Chirality : 0.044 0.284 2790 Planarity : 0.005 0.056 3100 Dihedral : 11.313 83.845 2857 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.62 % Allowed : 12.78 % Favored : 84.60 % 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: -3.77 (0.15), residues: 2147 helix: -2.56 (0.14), residues: 844 sheet: -2.18 (0.31), residues: 235 loop : -2.48 (0.17), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 537 HIS 0.011 0.001 HIS C 110 PHE 0.040 0.002 PHE C 595 TYR 0.018 0.002 TYR C 205 ARG 0.010 0.001 ARG B 563 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 392 time to evaluate : 2.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 23 residues processed: 417 average time/residue: 0.3144 time to fit residues: 195.3210 Evaluate side-chains 336 residues out of total 1909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 313 time to evaluate : 1.916 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1708 time to fit residues: 10.1368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 109 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 163 optimal weight: 10.0000 chunk 133 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 196 optimal weight: 0.5980 chunk 212 optimal weight: 0.0470 chunk 175 optimal weight: 8.9990 chunk 194 optimal weight: 8.9990 chunk 66 optimal weight: 0.5980 chunk 157 optimal weight: 0.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 HIS ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 569 GLN B 676 ASN ** C 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18453 Z= 0.187 Angle : 0.650 11.345 25058 Z= 0.335 Chirality : 0.043 0.214 2790 Planarity : 0.004 0.044 3100 Dihedral : 10.992 81.602 2857 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 1.83 % Allowed : 15.14 % Favored : 83.03 % 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: -3.08 (0.16), residues: 2147 helix: -1.81 (0.16), residues: 858 sheet: -2.08 (0.31), residues: 243 loop : -2.18 (0.18), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 537 HIS 0.004 0.001 HIS A 510 PHE 0.026 0.002 PHE B 103 TYR 0.024 0.001 TYR B 689 ARG 0.008 0.001 ARG C 604 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 351 time to evaluate : 1.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 17 residues processed: 369 average time/residue: 0.3360 time to fit residues: 181.5833 Evaluate side-chains 313 residues out of total 1909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 296 time to evaluate : 2.123 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1840 time to fit residues: 8.5344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 10.0000 chunk 147 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 chunk 93 optimal weight: 8.9990 chunk 131 optimal weight: 4.9990 chunk 197 optimal weight: 8.9990 chunk 208 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 186 optimal weight: 30.0000 chunk 56 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 670 GLN B 136 ASN ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 ASN B 292 ASN ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 ASN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 GLN B 641 ASN B 690 GLN ** C 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 ASN ** C 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.4727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 18453 Z= 0.475 Angle : 0.810 13.424 25058 Z= 0.416 Chirality : 0.049 0.285 2790 Planarity : 0.005 0.078 3100 Dihedral : 11.368 80.560 2857 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 20.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 3.40 % Allowed : 16.08 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -3.04 (0.17), residues: 2147 helix: -1.74 (0.16), residues: 854 sheet: -2.12 (0.30), residues: 252 loop : -2.16 (0.18), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 537 HIS 0.008 0.002 HIS A 146 PHE 0.025 0.003 PHE C 595 TYR 0.023 0.002 TYR B 689 ARG 0.008 0.001 ARG C 3 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 311 time to evaluate : 2.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 42 residues processed: 352 average time/residue: 0.3175 time to fit residues: 168.2830 Evaluate side-chains 316 residues out of total 1909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 274 time to evaluate : 2.216 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.1838 time to fit residues: 17.0730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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: 70.6544 > 50: distance: 41 - 48: 32.134 distance: 48 - 49: 53.713 distance: 49 - 50: 58.013 distance: 49 - 52: 9.673 distance: 50 - 51: 24.122 distance: 50 - 59: 4.023 distance: 52 - 53: 58.129 distance: 53 - 54: 12.994 distance: 54 - 55: 46.731 distance: 55 - 56: 17.475 distance: 56 - 57: 9.171 distance: 56 - 58: 5.918 distance: 59 - 60: 42.246 distance: 60 - 61: 56.771 distance: 60 - 63: 44.004 distance: 61 - 67: 40.299 distance: 63 - 64: 48.801 distance: 64 - 65: 22.197 distance: 64 - 66: 27.491 distance: 67 - 68: 39.926 distance: 68 - 69: 38.953 distance: 68 - 71: 3.189 distance: 69 - 76: 55.530 distance: 71 - 72: 22.322 distance: 72 - 73: 29.167 distance: 73 - 74: 26.869 distance: 73 - 75: 7.456 distance: 76 - 77: 28.343 distance: 77 - 78: 43.852 distance: 77 - 80: 27.580 distance: 78 - 79: 51.505 distance: 78 - 85: 50.291 distance: 80 - 81: 15.423 distance: 81 - 82: 23.047 distance: 82 - 83: 12.431 distance: 82 - 84: 22.598 distance: 86 - 87: 23.145 distance: 87 - 88: 55.371 distance: 87 - 89: 14.101 distance: 89 - 90: 10.819 distance: 90 - 93: 38.173 distance: 91 - 98: 55.358 distance: 93 - 94: 44.024 distance: 94 - 95: 13.700 distance: 95 - 96: 43.673 distance: 95 - 97: 43.720 distance: 98 - 99: 36.823 distance: 99 - 100: 22.656 distance: 99 - 102: 24.178 distance: 100 - 101: 25.410 distance: 100 - 105: 51.239 distance: 102 - 103: 34.871 distance: 102 - 104: 24.802 distance: 105 - 106: 15.213 distance: 106 - 107: 42.477 distance: 106 - 109: 27.679 distance: 107 - 108: 8.184 distance: 109 - 110: 18.277 distance: 110 - 111: 28.835 distance: 110 - 112: 28.924 distance: 113 - 114: 50.723 distance: 114 - 115: 15.843 distance: 114 - 117: 38.488 distance: 115 - 116: 3.856 distance: 115 - 127: 41.999 distance: 117 - 118: 21.592 distance: 118 - 119: 15.520 distance: 118 - 120: 5.898 distance: 119 - 121: 14.354 distance: 120 - 122: 13.864 distance: 120 - 123: 5.181 distance: 121 - 122: 13.838 distance: 122 - 124: 16.300 distance: 123 - 125: 15.677 distance: 124 - 126: 16.959 distance: 125 - 126: 18.213 distance: 127 - 128: 40.290 distance: 127 - 156: 37.367 distance: 128 - 129: 27.149 distance: 128 - 131: 41.201 distance: 129 - 130: 30.678 distance: 129 - 133: 20.310 distance: 131 - 132: 54.272