Starting phenix.real_space_refine on Fri Mar 15 07:00:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ijz_9682/03_2024/6ijz_9682.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ijz_9682/03_2024/6ijz_9682.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ijz_9682/03_2024/6ijz_9682.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ijz_9682/03_2024/6ijz_9682.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ijz_9682/03_2024/6ijz_9682.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ijz_9682/03_2024/6ijz_9682.pdb" } resolution = 3.68 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= 0.001 sd= 0.014 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 50 5.16 5 C 7264 2.51 5 N 1778 2.21 5 O 1872 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 29": "NH1" <-> "NH2" Residue "A ARG 36": "NH1" <-> "NH2" Residue "A ARG 100": "NH1" <-> "NH2" Residue "A TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 197": "NH1" <-> "NH2" Residue "A ARG 198": "NH1" <-> "NH2" Residue "A ARG 207": "NH1" <-> "NH2" Residue "A ARG 675": "NH1" <-> "NH2" Residue "B ARG 29": "NH1" <-> "NH2" Residue "B ARG 36": "NH1" <-> "NH2" Residue "B ARG 100": "NH1" <-> "NH2" Residue "B TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 197": "NH1" <-> "NH2" Residue "B ARG 198": "NH1" <-> "NH2" Residue "B ARG 207": "NH1" <-> "NH2" Residue "B ARG 675": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10964 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5482 Classifications: {'peptide': 683} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'CIS': 1, 'PTRANS': 36, 'TRANS': 645} Chain breaks: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 3, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 5482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5482 Classifications: {'peptide': 683} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'CIS': 1, 'PTRANS': 36, 'TRANS': 645} Chain breaks: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 3, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 31 Time building chain proxies: 6.00, per 1000 atoms: 0.55 Number of scatterers: 10964 At special positions: 0 Unit cell: (95.411, 139.849, 108.481, 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 50 16.00 O 1872 8.00 N 1778 7.00 C 7264 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: 4.14 Conformation dependent library (CDL) restraints added in 1.9 seconds 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2636 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 2 sheets defined 69.2% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 3 through 30 removed outlier: 3.804A pdb=" N VAL A 9 " --> pdb=" O GLN A 5 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL A 20 " --> pdb=" O LEU A 16 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 39 Processing helix chain 'A' and resid 39 through 45 Processing helix chain 'A' and resid 77 through 81 removed outlier: 3.656A pdb=" N LYS A 81 " --> pdb=" O GLU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 91 Processing helix chain 'A' and resid 93 through 125 removed outlier: 3.744A pdb=" N VAL A 97 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR A 102 " --> pdb=" O TYR A 98 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) Proline residue: A 111 - end of helix removed outlier: 3.891A pdb=" N VAL A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A 121 " --> pdb=" O TRP A 117 " (cutoff:3.500A) Proline residue: A 122 - end of helix Processing helix chain 'A' and resid 158 through 193 removed outlier: 4.010A pdb=" N HIS A 162 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL A 164 " --> pdb=" O TRP A 160 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N TRP A 172 " --> pdb=" O ALA A 168 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS A 174 " --> pdb=" O THR A 170 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA A 185 " --> pdb=" O TYR A 181 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N MET A 187 " --> pdb=" O THR A 183 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 229 removed outlier: 4.040A pdb=" N LEU A 220 " --> pdb=" O SER A 216 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N VAL A 227 " --> pdb=" O HIS A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 267 removed outlier: 3.546A pdb=" N GLN A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR A 266 " --> pdb=" O TYR A 262 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA A 267 " --> pdb=" O GLN A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 310 removed outlier: 5.250A pdb=" N ALA A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER A 306 " --> pdb=" O SER A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 337 removed outlier: 3.562A pdb=" N ALA A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 370 through 389 removed outlier: 3.595A pdb=" N ARG A 374 " --> pdb=" O SER A 370 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL A 380 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE A 382 " --> pdb=" O MET A 378 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE A 387 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 401 removed outlier: 3.508A pdb=" N ILE A 393 " --> pdb=" O PHE A 389 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL A 396 " --> pdb=" O PRO A 392 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 399 " --> pdb=" O PHE A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 Processing helix chain 'A' and resid 420 through 428 Processing helix chain 'A' and resid 428 through 438 Processing helix chain 'A' and resid 440 through 452 removed outlier: 3.961A pdb=" N GLU A 452 " --> pdb=" O MET A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 475 removed outlier: 4.215A pdb=" N ARG A 462 " --> pdb=" O SER A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 489 removed outlier: 3.822A pdb=" N ALA A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA A 486 " --> pdb=" O ILE A 482 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N PHE A 487 " --> pdb=" O ALA A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 496 removed outlier: 3.609A pdb=" N GLN A 496 " --> pdb=" O SER A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 512 removed outlier: 3.739A pdb=" N ILE A 505 " --> pdb=" O ILE A 501 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 509 " --> pdb=" O ILE A 505 " (cutoff:3.500A) Proline residue: A 510 - end of helix Processing helix chain 'A' and resid 513 through 523 Processing helix chain 'A' and resid 524 through 530 Processing helix chain 'A' and resid 534 through 547 removed outlier: 4.112A pdb=" N MET A 540 " --> pdb=" O LYS A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 560 removed outlier: 3.514A pdb=" N ALA A 558 " --> pdb=" O ARG A 555 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N MET A 559 " --> pdb=" O GLU A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 583 removed outlier: 3.848A pdb=" N ILE A 573 " --> pdb=" O GLY A 569 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN A 574 " --> pdb=" O GLU A 570 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR A 583 " --> pdb=" O LEU A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 612 removed outlier: 3.948A pdb=" N ILE A 603 " --> pdb=" O ALA A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 647 removed outlier: 3.773A pdb=" N GLY A 629 " --> pdb=" O PRO A 625 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY A 644 " --> pdb=" O LEU A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 655 removed outlier: 3.838A pdb=" N ALA A 654 " --> pdb=" O ALA A 651 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA A 655 " --> pdb=" O ALA A 652 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 651 through 655' Processing helix chain 'A' and resid 659 through 676 removed outlier: 3.852A pdb=" N VAL A 663 " --> pdb=" O ILE A 659 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE A 666 " --> pdb=" O PRO A 662 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY A 674 " --> pdb=" O HIS A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 680 Processing helix chain 'A' and resid 684 through 699 removed outlier: 3.636A pdb=" N ASP A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 709 removed outlier: 3.582A pdb=" N GLN A 709 " --> pdb=" O LYS A 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 30 removed outlier: 3.804A pdb=" N VAL B 9 " --> pdb=" O GLN B 5 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL B 20 " --> pdb=" O LEU B 16 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU B 30 " --> pdb=" O ALA B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 39 Processing helix chain 'B' and resid 39 through 45 Processing helix chain 'B' and resid 77 through 81 removed outlier: 3.656A pdb=" N LYS B 81 " --> pdb=" O GLU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 91 Processing helix chain 'B' and resid 93 through 125 removed outlier: 3.744A pdb=" N VAL B 97 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TYR B 102 " --> pdb=" O TYR B 98 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) Proline residue: B 111 - end of helix removed outlier: 3.891A pdb=" N VAL B 119 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL B 121 " --> pdb=" O TRP B 117 " (cutoff:3.500A) Proline residue: B 122 - end of helix Processing helix chain 'B' and resid 158 through 193 removed outlier: 4.009A pdb=" N HIS B 162 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL B 164 " --> pdb=" O TRP B 160 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N TRP B 172 " --> pdb=" O ALA B 168 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS B 174 " --> pdb=" O THR B 170 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR B 181 " --> pdb=" O LEU B 177 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA B 185 " --> pdb=" O TYR B 181 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N MET B 187 " --> pdb=" O THR B 183 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 229 removed outlier: 4.040A pdb=" N LEU B 220 " --> pdb=" O SER B 216 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL B 227 " --> pdb=" O HIS B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 267 removed outlier: 3.546A pdb=" N GLN B 263 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR B 266 " --> pdb=" O TYR B 262 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA B 267 " --> pdb=" O GLN B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 310 removed outlier: 5.250A pdb=" N ALA B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER B 306 " --> pdb=" O SER B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 337 removed outlier: 3.561A pdb=" N ALA B 333 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 369 No H-bonds generated for 'chain 'B' and resid 367 through 369' Processing helix chain 'B' and resid 370 through 389 removed outlier: 3.596A pdb=" N ARG B 374 " --> pdb=" O SER B 370 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL B 380 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE B 382 " --> pdb=" O MET B 378 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE B 387 " --> pdb=" O PHE B 383 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE B 389 " --> pdb=" O LEU B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 401 removed outlier: 3.508A pdb=" N ILE B 393 " --> pdb=" O PHE B 389 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL B 396 " --> pdb=" O PRO B 392 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU B 399 " --> pdb=" O PHE B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 407 Processing helix chain 'B' and resid 420 through 428 Processing helix chain 'B' and resid 428 through 438 Processing helix chain 'B' and resid 440 through 452 removed outlier: 3.961A pdb=" N GLU B 452 " --> pdb=" O MET B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 475 removed outlier: 4.215A pdb=" N ARG B 462 " --> pdb=" O SER B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 489 removed outlier: 3.822A pdb=" N ALA B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA B 486 " --> pdb=" O ILE B 482 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N PHE B 487 " --> pdb=" O ALA B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 496 removed outlier: 3.608A pdb=" N GLN B 496 " --> pdb=" O SER B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 512 removed outlier: 3.739A pdb=" N ILE B 505 " --> pdb=" O ILE B 501 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE B 509 " --> pdb=" O ILE B 505 " (cutoff:3.500A) Proline residue: B 510 - end of helix Processing helix chain 'B' and resid 513 through 523 Processing helix chain 'B' and resid 524 through 530 Processing helix chain 'B' and resid 534 through 547 removed outlier: 4.112A pdb=" N MET B 540 " --> pdb=" O LYS B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 560 removed outlier: 3.514A pdb=" N ALA B 558 " --> pdb=" O ARG B 555 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N MET B 559 " --> pdb=" O GLU B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 583 removed outlier: 3.848A pdb=" N ILE B 573 " --> pdb=" O GLY B 569 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN B 574 " --> pdb=" O GLU B 570 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR B 583 " --> pdb=" O LEU B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 612 removed outlier: 3.947A pdb=" N ILE B 603 " --> pdb=" O ALA B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 647 removed outlier: 3.773A pdb=" N GLY B 629 " --> pdb=" O PRO B 625 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY B 644 " --> pdb=" O LEU B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 655 removed outlier: 3.837A pdb=" N ALA B 654 " --> pdb=" O ALA B 651 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA B 655 " --> pdb=" O ALA B 652 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 651 through 655' Processing helix chain 'B' and resid 659 through 676 removed outlier: 3.852A pdb=" N VAL B 663 " --> pdb=" O ILE B 659 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE B 666 " --> pdb=" O PRO B 662 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY B 674 " --> pdb=" O HIS B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 680 Processing helix chain 'B' and resid 684 through 699 removed outlier: 3.636A pdb=" N ASP B 692 " --> pdb=" O ALA B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 709 removed outlier: 3.581A pdb=" N GLN B 709 " --> pdb=" O LYS B 705 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 203 through 205 removed outlier: 4.859A pdb=" N VAL A 239 " --> pdb=" O MET A 320 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 203 through 205 removed outlier: 4.860A pdb=" N VAL B 239 " --> pdb=" O MET B 320 " (cutoff:3.500A) 557 hydrogen bonds defined for protein. 1653 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: 2.75 Time building geometry restraints manager: 4.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3027 1.33 - 1.45: 2070 1.45 - 1.57: 6083 1.57 - 1.69: 0 1.69 - 1.81: 92 Bond restraints: 11272 Sorted by residual: bond pdb=" CB TRP A 624 " pdb=" CG TRP A 624 " ideal model delta sigma weight residual 1.498 1.404 0.094 3.10e-02 1.04e+03 9.10e+00 bond pdb=" CB TRP B 624 " pdb=" CG TRP B 624 " ideal model delta sigma weight residual 1.498 1.405 0.093 3.10e-02 1.04e+03 9.04e+00 bond pdb=" CB PRO B 111 " pdb=" CG PRO B 111 " ideal model delta sigma weight residual 1.492 1.398 0.094 5.00e-02 4.00e+02 3.54e+00 bond pdb=" CB PRO A 111 " pdb=" CG PRO A 111 " ideal model delta sigma weight residual 1.492 1.398 0.094 5.00e-02 4.00e+02 3.54e+00 bond pdb=" CB TRP B 172 " pdb=" CG TRP B 172 " ideal model delta sigma weight residual 1.498 1.443 0.055 3.10e-02 1.04e+03 3.15e+00 ... (remaining 11267 not shown) Histogram of bond angle deviations from ideal: 98.52 - 105.64: 302 105.64 - 112.77: 5738 112.77 - 119.89: 4337 119.89 - 127.02: 4797 127.02 - 134.14: 174 Bond angle restraints: 15348 Sorted by residual: angle pdb=" C SER B 619 " pdb=" N ALA B 620 " pdb=" CA ALA B 620 " ideal model delta sigma weight residual 121.70 133.31 -11.61 1.80e+00 3.09e-01 4.16e+01 angle pdb=" C SER A 619 " pdb=" N ALA A 620 " pdb=" CA ALA A 620 " ideal model delta sigma weight residual 121.70 133.31 -11.61 1.80e+00 3.09e-01 4.16e+01 angle pdb=" C VAL A 206 " pdb=" N ARG A 207 " pdb=" CA ARG A 207 " ideal model delta sigma weight residual 121.54 130.94 -9.40 1.91e+00 2.74e-01 2.42e+01 angle pdb=" C VAL B 206 " pdb=" N ARG B 207 " pdb=" CA ARG B 207 " ideal model delta sigma weight residual 121.54 130.89 -9.35 1.91e+00 2.74e-01 2.40e+01 angle pdb=" CA TRP B 624 " pdb=" CB TRP B 624 " pdb=" CG TRP B 624 " ideal model delta sigma weight residual 113.60 104.68 8.92 1.90e+00 2.77e-01 2.20e+01 ... (remaining 15343 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.25: 5910 12.25 - 24.50: 580 24.50 - 36.75: 120 36.75 - 49.00: 32 49.00 - 61.25: 4 Dihedral angle restraints: 6646 sinusoidal: 2596 harmonic: 4050 Sorted by residual: dihedral pdb=" CA GLN B 135 " pdb=" C GLN B 135 " pdb=" N LEU B 136 " pdb=" CA LEU B 136 " ideal model delta harmonic sigma weight residual -180.00 -131.79 -48.21 0 5.00e+00 4.00e-02 9.29e+01 dihedral pdb=" CA GLN A 135 " pdb=" C GLN A 135 " pdb=" N LEU A 136 " pdb=" CA LEU A 136 " ideal model delta harmonic sigma weight residual -180.00 -131.83 -48.17 0 5.00e+00 4.00e-02 9.28e+01 dihedral pdb=" CA LYS A 134 " pdb=" C LYS A 134 " pdb=" N GLN A 135 " pdb=" CA GLN A 135 " ideal model delta harmonic sigma weight residual 180.00 148.87 31.13 0 5.00e+00 4.00e-02 3.88e+01 ... (remaining 6643 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1371 0.073 - 0.146: 326 0.146 - 0.218: 34 0.218 - 0.291: 11 0.291 - 0.364: 2 Chirality restraints: 1744 Sorted by residual: chirality pdb=" CB VAL A 206 " pdb=" CA VAL A 206 " pdb=" CG1 VAL A 206 " pdb=" CG2 VAL A 206 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CB VAL B 206 " pdb=" CA VAL B 206 " pdb=" CG1 VAL B 206 " pdb=" CG2 VAL B 206 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.27e+00 chirality pdb=" CA TYR A 613 " pdb=" N TYR A 613 " pdb=" C TYR A 613 " pdb=" CB TYR A 613 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 1741 not shown) Planarity restraints: 1914 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 233 " 0.016 2.00e-02 2.50e+03 3.20e-02 1.03e+01 pdb=" C TYR B 233 " -0.055 2.00e-02 2.50e+03 pdb=" O TYR B 233 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU B 234 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 233 " -0.016 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C TYR A 233 " 0.055 2.00e-02 2.50e+03 pdb=" O TYR A 233 " -0.020 2.00e-02 2.50e+03 pdb=" N LEU A 234 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 612 " 0.014 2.00e-02 2.50e+03 3.01e-02 9.03e+00 pdb=" C VAL A 612 " -0.052 2.00e-02 2.50e+03 pdb=" O VAL A 612 " 0.020 2.00e-02 2.50e+03 pdb=" N TYR A 613 " 0.018 2.00e-02 2.50e+03 ... (remaining 1911 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 52 2.58 - 3.16: 8901 3.16 - 3.74: 16886 3.74 - 4.32: 22900 4.32 - 4.90: 37417 Nonbonded interactions: 86156 Sorted by model distance: nonbonded pdb=" O VAL B 612 " pdb=" CD1 TYR B 613 " model vdw 2.000 3.340 nonbonded pdb=" O VAL A 612 " pdb=" CD1 TYR A 613 " model vdw 2.001 3.340 nonbonded pdb=" OG SER A 216 " pdb=" OE1 GLU A 219 " model vdw 2.242 2.440 nonbonded pdb=" OG SER B 216 " pdb=" OE1 GLU B 219 " model vdw 2.242 2.440 nonbonded pdb=" O PHE B 420 " pdb=" OG SER B 423 " model vdw 2.314 2.440 ... (remaining 86151 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' 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 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: 0.440 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: 2.380 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 30.230 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 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 : 0.008 0.094 11272 Z= 0.486 Angle : 1.110 11.610 15348 Z= 0.589 Chirality : 0.064 0.364 1744 Planarity : 0.009 0.068 1914 Dihedral : 10.644 61.249 4010 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.93 % Favored : 88.77 % Rotamer: Outliers : 0.69 % Allowed : 3.45 % Favored : 95.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 2.78 % Twisted General : 0.31 % 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: -5.03 (0.17), residues: 1354 helix: -2.86 (0.13), residues: 860 sheet: -3.31 (1.09), residues: 20 loop : -4.03 (0.23), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.004 TRP A 525 HIS 0.009 0.002 HIS A 162 PHE 0.029 0.003 PHE A 21 TYR 0.048 0.003 TYR A 181 ARG 0.007 0.001 ARG A 630 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 376 time to evaluate : 1.222 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: A 14 ASN cc_start: 0.7948 (m-40) cc_final: 0.7405 (m110) REVERT: A 165 MET cc_start: 0.8984 (mmm) cc_final: 0.8551 (mpp) REVERT: A 370 SER cc_start: 0.9131 (p) cc_final: 0.8818 (t) REVERT: A 397 GLN cc_start: 0.8925 (mp10) cc_final: 0.8443 (mp10) REVERT: A 415 ILE cc_start: 0.7030 (mm) cc_final: 0.6711 (mm) REVERT: A 428 PHE cc_start: 0.9116 (t80) cc_final: 0.8820 (t80) REVERT: A 446 MET cc_start: 0.8927 (tpt) cc_final: 0.8697 (tpp) REVERT: A 512 LYS cc_start: 0.9126 (tttp) cc_final: 0.8792 (ttmm) REVERT: A 521 MET cc_start: 0.7940 (mmt) cc_final: 0.7468 (mmt) REVERT: A 574 GLN cc_start: 0.8580 (mt0) cc_final: 0.8362 (mt0) REVERT: A 581 LEU cc_start: 0.8919 (mt) cc_final: 0.8698 (mt) REVERT: A 589 MET cc_start: 0.8154 (mmm) cc_final: 0.7795 (mmm) REVERT: A 612 VAL cc_start: 0.8839 (t) cc_final: 0.8499 (p) REVERT: A 682 ARG cc_start: 0.8161 (mtm180) cc_final: 0.7957 (mtm-85) REVERT: A 709 GLN cc_start: 0.8693 (tm-30) cc_final: 0.8245 (tm-30) REVERT: A 712 TYR cc_start: 0.8591 (m-80) cc_final: 0.8236 (m-80) REVERT: B 14 ASN cc_start: 0.7948 (m-40) cc_final: 0.7390 (m110) REVERT: B 165 MET cc_start: 0.8986 (mmm) cc_final: 0.8565 (mpp) REVERT: B 303 LYS cc_start: 0.7984 (mttt) cc_final: 0.7779 (mttt) REVERT: B 378 MET cc_start: 0.8575 (mmt) cc_final: 0.8103 (mmt) REVERT: B 397 GLN cc_start: 0.8824 (mp10) cc_final: 0.8383 (mp10) REVERT: B 446 MET cc_start: 0.8921 (tpt) cc_final: 0.8698 (tpt) REVERT: B 448 MET cc_start: 0.8808 (ttt) cc_final: 0.8244 (ttt) REVERT: B 459 SER cc_start: 0.8685 (m) cc_final: 0.8211 (t) REVERT: B 521 MET cc_start: 0.7893 (mmt) cc_final: 0.7396 (mmt) REVERT: B 589 MET cc_start: 0.8254 (mmm) cc_final: 0.7968 (mmm) REVERT: B 645 LEU cc_start: 0.8316 (mt) cc_final: 0.8105 (mm) REVERT: B 690 MET cc_start: 0.8038 (ttm) cc_final: 0.7739 (ttm) REVERT: B 709 GLN cc_start: 0.8686 (tm-30) cc_final: 0.8441 (tm-30) REVERT: B 712 TYR cc_start: 0.8704 (m-80) cc_final: 0.8406 (m-80) outliers start: 8 outliers final: 6 residues processed: 379 average time/residue: 0.2228 time to fit residues: 118.8645 Evaluate side-chains 268 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 262 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 531 GLU Chi-restraints excluded: chain B residue 533 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 123 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN A 232 HIS ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 257 ASN A 489 GLN A 607 HIS A 608 GLN B 151 ASN B 232 HIS ** B 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 ASN B 489 GLN B 495 ASN B 567 ASN B 607 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11272 Z= 0.218 Angle : 0.708 8.742 15348 Z= 0.369 Chirality : 0.045 0.179 1744 Planarity : 0.006 0.057 1914 Dihedral : 7.119 49.506 1478 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.97 % Favored : 89.96 % Rotamer: Outliers : 3.53 % Allowed : 10.60 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.42 (0.20), residues: 1354 helix: -1.41 (0.16), residues: 868 sheet: -3.59 (0.96), residues: 30 loop : -3.77 (0.24), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 624 HIS 0.006 0.001 HIS A 379 PHE 0.019 0.001 PHE B 428 TYR 0.020 0.002 TYR A 181 ARG 0.008 0.000 ARG A 698 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 314 time to evaluate : 1.305 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: A 36 ARG cc_start: 0.8228 (tpp-160) cc_final: 0.7733 (mmt180) REVERT: A 200 ASP cc_start: 0.8127 (t0) cc_final: 0.7801 (t0) REVERT: A 257 ASN cc_start: 0.8757 (m110) cc_final: 0.8468 (m110) REVERT: A 370 SER cc_start: 0.8981 (p) cc_final: 0.8725 (t) REVERT: A 415 ILE cc_start: 0.6948 (mm) cc_final: 0.6701 (mm) REVERT: A 436 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8676 (mm) REVERT: A 446 MET cc_start: 0.9083 (tpt) cc_final: 0.8598 (tpp) REVERT: A 488 GLU cc_start: 0.8498 (mt-10) cc_final: 0.7900 (mt-10) REVERT: A 540 MET cc_start: 0.7393 (mmm) cc_final: 0.7165 (mmm) REVERT: A 613 TYR cc_start: 0.9156 (OUTLIER) cc_final: 0.7018 (m-10) REVERT: A 682 ARG cc_start: 0.8117 (mtm180) cc_final: 0.7890 (mtm-85) REVERT: B 36 ARG cc_start: 0.8298 (tpp-160) cc_final: 0.7775 (mmt-90) REVERT: B 103 TRP cc_start: 0.7763 (t-100) cc_final: 0.7441 (t-100) REVERT: B 182 GLU cc_start: 0.8264 (tt0) cc_final: 0.8025 (tt0) REVERT: B 257 ASN cc_start: 0.8722 (m110) cc_final: 0.8466 (m110) REVERT: B 415 ILE cc_start: 0.6699 (mm) cc_final: 0.6393 (mm) REVERT: B 422 LYS cc_start: 0.8752 (ttpt) cc_final: 0.8272 (ttpt) REVERT: B 446 MET cc_start: 0.9032 (tpt) cc_final: 0.8528 (tpp) REVERT: B 459 SER cc_start: 0.8608 (m) cc_final: 0.8244 (t) REVERT: B 488 GLU cc_start: 0.8478 (mt-10) cc_final: 0.7941 (mt-10) REVERT: B 540 MET cc_start: 0.7386 (mmm) cc_final: 0.7184 (mmm) REVERT: B 690 MET cc_start: 0.7953 (ttm) cc_final: 0.7743 (ttm) outliers start: 41 outliers final: 28 residues processed: 337 average time/residue: 0.2137 time to fit residues: 102.5997 Evaluate side-chains 292 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 262 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 613 TYR Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 384 PHE Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 531 GLU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 613 TYR Chi-restraints excluded: chain B residue 670 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 133 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 567 ASN ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 GLN A 710 ASN B 151 ASN B 567 ASN B 710 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11272 Z= 0.194 Angle : 0.655 8.548 15348 Z= 0.341 Chirality : 0.044 0.175 1744 Planarity : 0.005 0.058 1914 Dihedral : 6.718 51.878 1478 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.97 % Favored : 89.88 % Rotamer: Outliers : 3.97 % Allowed : 14.05 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.58 (0.22), residues: 1354 helix: -0.73 (0.17), residues: 892 sheet: -3.16 (1.07), residues: 30 loop : -3.62 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 525 HIS 0.005 0.001 HIS A 628 PHE 0.022 0.001 PHE B 428 TYR 0.018 0.002 TYR A 468 ARG 0.005 0.000 ARG A 463 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 286 time to evaluate : 1.208 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 REVERT: A 36 ARG cc_start: 0.8297 (tpp-160) cc_final: 0.7625 (tpp80) REVERT: A 78 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7586 (tm-30) REVERT: A 129 THR cc_start: 0.7391 (p) cc_final: 0.7185 (p) REVERT: A 182 GLU cc_start: 0.8319 (tt0) cc_final: 0.7991 (tt0) REVERT: A 257 ASN cc_start: 0.8743 (m110) cc_final: 0.8455 (m110) REVERT: A 303 LYS cc_start: 0.9150 (tptp) cc_final: 0.8811 (tptp) REVERT: A 307 LYS cc_start: 0.8390 (mttt) cc_final: 0.8140 (mttt) REVERT: A 370 SER cc_start: 0.8942 (p) cc_final: 0.8645 (t) REVERT: A 415 ILE cc_start: 0.6680 (mm) cc_final: 0.6287 (mm) REVERT: A 421 MET cc_start: 0.8500 (mmt) cc_final: 0.8257 (mmt) REVERT: A 446 MET cc_start: 0.9097 (tpt) cc_final: 0.8555 (tpp) REVERT: A 459 SER cc_start: 0.8633 (m) cc_final: 0.8284 (t) REVERT: A 525 TRP cc_start: 0.7739 (t-100) cc_final: 0.7343 (t-100) REVERT: A 531 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8079 (tm-30) REVERT: A 540 MET cc_start: 0.7318 (mmm) cc_final: 0.7107 (mmm) REVERT: A 613 TYR cc_start: 0.9129 (OUTLIER) cc_final: 0.6863 (m-10) REVERT: A 661 LEU cc_start: 0.8670 (mt) cc_final: 0.8466 (mt) REVERT: A 682 ARG cc_start: 0.8055 (mtm180) cc_final: 0.7823 (mtm-85) REVERT: A 698 ARG cc_start: 0.8493 (ttm-80) cc_final: 0.8276 (ttm110) REVERT: B 36 ARG cc_start: 0.8336 (tpp-160) cc_final: 0.8106 (tpp-160) REVERT: B 78 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7574 (tm-30) REVERT: B 103 TRP cc_start: 0.7792 (t-100) cc_final: 0.7568 (t-100) REVERT: B 182 GLU cc_start: 0.8182 (tt0) cc_final: 0.7899 (tt0) REVERT: B 257 ASN cc_start: 0.8694 (m110) cc_final: 0.8473 (m110) REVERT: B 415 ILE cc_start: 0.6577 (mm) cc_final: 0.6118 (mm) REVERT: B 446 MET cc_start: 0.9062 (tpt) cc_final: 0.8560 (tpp) REVERT: B 459 SER cc_start: 0.8617 (m) cc_final: 0.8275 (t) REVERT: B 540 MET cc_start: 0.7458 (mmm) cc_final: 0.7221 (mmm) REVERT: B 608 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.7876 (mm-40) REVERT: B 613 TYR cc_start: 0.9047 (OUTLIER) cc_final: 0.7052 (m-10) REVERT: B 702 LEU cc_start: 0.6349 (OUTLIER) cc_final: 0.6002 (mm) outliers start: 46 outliers final: 31 residues processed: 311 average time/residue: 0.2168 time to fit residues: 97.0076 Evaluate side-chains 297 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 261 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 384 PHE Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 613 TYR Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 531 GLU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 608 GLN Chi-restraints excluded: chain B residue 613 TYR Chi-restraints excluded: chain B residue 670 HIS Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain B residue 702 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 0.5980 chunk 93 optimal weight: 0.0370 chunk 64 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 109 optimal weight: 0.7980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 397 GLN A 574 GLN ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 615 GLN B 151 ASN B 397 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11272 Z= 0.176 Angle : 0.635 8.634 15348 Z= 0.325 Chirality : 0.043 0.163 1744 Planarity : 0.005 0.047 1914 Dihedral : 6.335 55.514 1476 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.90 % Favored : 89.96 % Rotamer: Outliers : 4.22 % Allowed : 15.86 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.23), residues: 1354 helix: -0.14 (0.18), residues: 884 sheet: -3.08 (1.06), residues: 30 loop : -3.39 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 525 HIS 0.005 0.001 HIS A 628 PHE 0.025 0.001 PHE A 428 TYR 0.015 0.002 TYR A 468 ARG 0.005 0.000 ARG A 463 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 278 time to evaluate : 1.312 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: A 36 ARG cc_start: 0.8352 (tpp-160) cc_final: 0.7519 (tpp80) REVERT: A 78 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7608 (tm-30) REVERT: A 129 THR cc_start: 0.7184 (p) cc_final: 0.6974 (p) REVERT: A 182 GLU cc_start: 0.8256 (tt0) cc_final: 0.7979 (tt0) REVERT: A 190 GLN cc_start: 0.8261 (tp40) cc_final: 0.7955 (tp40) REVERT: A 257 ASN cc_start: 0.8690 (m110) cc_final: 0.8448 (m110) REVERT: A 370 SER cc_start: 0.8884 (p) cc_final: 0.8620 (t) REVERT: A 415 ILE cc_start: 0.6783 (mm) cc_final: 0.6362 (mm) REVERT: A 421 MET cc_start: 0.8576 (mmt) cc_final: 0.8263 (mmt) REVERT: A 446 MET cc_start: 0.9113 (tpt) cc_final: 0.8595 (tpp) REVERT: A 459 SER cc_start: 0.8597 (m) cc_final: 0.8263 (t) REVERT: A 488 GLU cc_start: 0.8373 (mt-10) cc_final: 0.7796 (mt-10) REVERT: A 521 MET cc_start: 0.9022 (mmm) cc_final: 0.8603 (mmm) REVERT: A 531 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8158 (tm-30) REVERT: A 540 MET cc_start: 0.7410 (mmm) cc_final: 0.7193 (mmm) REVERT: A 570 GLU cc_start: 0.9195 (tm-30) cc_final: 0.8673 (tm-30) REVERT: A 613 TYR cc_start: 0.9031 (OUTLIER) cc_final: 0.7003 (m-10) REVERT: A 682 ARG cc_start: 0.8136 (mtm180) cc_final: 0.7871 (mtm-85) REVERT: A 702 LEU cc_start: 0.6575 (OUTLIER) cc_final: 0.6330 (mm) REVERT: B 14 ASN cc_start: 0.7691 (m110) cc_final: 0.7444 (m110) REVERT: B 36 ARG cc_start: 0.8362 (tpp-160) cc_final: 0.7581 (tpp80) REVERT: B 78 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7522 (tm-30) REVERT: B 182 GLU cc_start: 0.8250 (tt0) cc_final: 0.7984 (tt0) REVERT: B 190 GLN cc_start: 0.8293 (tp40) cc_final: 0.7987 (tp40) REVERT: B 299 ASP cc_start: 0.7006 (m-30) cc_final: 0.6716 (t0) REVERT: B 422 LYS cc_start: 0.8625 (ttpp) cc_final: 0.8125 (ttpt) REVERT: B 446 MET cc_start: 0.9072 (tpt) cc_final: 0.8584 (tpp) REVERT: B 459 SER cc_start: 0.8600 (m) cc_final: 0.8251 (t) REVERT: B 488 GLU cc_start: 0.8350 (mt-10) cc_final: 0.7717 (mt-10) REVERT: B 540 MET cc_start: 0.7470 (mmm) cc_final: 0.7211 (mmm) REVERT: B 608 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.7901 (mm-40) REVERT: B 613 TYR cc_start: 0.8997 (OUTLIER) cc_final: 0.7030 (m-10) REVERT: B 649 LYS cc_start: 0.8771 (mmtt) cc_final: 0.8482 (mttp) outliers start: 49 outliers final: 28 residues processed: 310 average time/residue: 0.1975 time to fit residues: 89.7377 Evaluate side-chains 289 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 256 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 384 PHE Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 613 TYR Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 384 PHE Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 608 GLN Chi-restraints excluded: chain B residue 613 TYR Chi-restraints excluded: chain B residue 670 HIS Chi-restraints excluded: chain B residue 699 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 70.3384 > 50: distance: 9 - 12: 4.239 distance: 10 - 37: 15.167 distance: 12 - 13: 10.562 distance: 13 - 14: 7.152 distance: 13 - 16: 17.535 distance: 14 - 15: 9.744 distance: 15 - 42: 5.794 distance: 17 - 18: 14.765 distance: 17 - 19: 12.209 distance: 20 - 21: 18.942 distance: 21 - 22: 9.325 distance: 21 - 24: 4.241 distance: 22 - 23: 10.124 distance: 22 - 29: 5.715 distance: 23 - 50: 36.367 distance: 24 - 25: 25.207 distance: 25 - 26: 16.064 distance: 26 - 27: 28.718 distance: 27 - 28: 13.748 distance: 30 - 31: 4.860 distance: 30 - 33: 4.025 distance: 31 - 32: 7.463 distance: 32 - 58: 47.242 distance: 33 - 34: 14.677 distance: 34 - 35: 11.238 distance: 34 - 36: 10.635 distance: 38 - 39: 7.649 distance: 38 - 41: 4.606 distance: 39 - 40: 6.963 distance: 40 - 65: 17.923 distance: 42 - 43: 15.710 distance: 43 - 44: 17.197 distance: 43 - 46: 13.738 distance: 44 - 45: 11.687 distance: 44 - 50: 9.417 distance: 45 - 74: 22.591 distance: 46 - 47: 13.992 distance: 47 - 48: 10.627 distance: 47 - 49: 4.882 distance: 50 - 51: 4.520 distance: 51 - 52: 15.558 distance: 51 - 54: 5.554 distance: 52 - 53: 13.949 distance: 52 - 58: 26.127 distance: 53 - 83: 24.562 distance: 54 - 55: 9.512 distance: 55 - 56: 8.701 distance: 55 - 57: 9.203 distance: 58 - 59: 39.441 distance: 59 - 60: 20.443 distance: 59 - 62: 21.049 distance: 60 - 61: 8.845 distance: 60 - 65: 7.783 distance: 61 - 92: 18.977 distance: 62 - 63: 4.883 distance: 62 - 64: 29.863 distance: 65 - 66: 9.966 distance: 66 - 67: 9.891 distance: 66 - 69: 13.358 distance: 67 - 68: 8.779 distance: 67 - 74: 11.509 distance: 68 - 98: 26.078 distance: 69 - 70: 23.299 distance: 70 - 71: 11.701 distance: 71 - 72: 12.420 distance: 72 - 73: 3.291 distance: 74 - 75: 3.314 distance: 75 - 76: 6.415 distance: 75 - 78: 10.663 distance: 76 - 77: 8.072 distance: 76 - 83: 4.818 distance: 77 - 106: 13.554 distance: 78 - 79: 12.930 distance: 79 - 80: 11.063 distance: 80 - 81: 24.302 distance: 81 - 82: 14.044 distance: 83 - 84: 8.138 distance: 84 - 85: 4.895 distance: 84 - 87: 10.483 distance: 85 - 86: 9.125 distance: 86 - 114: 9.341 distance: 87 - 88: 12.554 distance: 88 - 89: 10.742 distance: 89 - 90: 10.919 distance: 90 - 91: 4.696