Starting phenix.real_space_refine on Sun Aug 4 02:26:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dny_30790/08_2024/7dny_30790.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dny_30790/08_2024/7dny_30790.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dny_30790/08_2024/7dny_30790.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dny_30790/08_2024/7dny_30790.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dny_30790/08_2024/7dny_30790.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dny_30790/08_2024/7dny_30790.cif" } resolution = 3.4 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= 0.009 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 34 5.16 5 C 5968 2.51 5 N 1557 2.21 5 O 1662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 359": "NH1" <-> "NH2" Residue "A ARG 365": "NH1" <-> "NH2" Residue "A PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 529": "OD1" <-> "OD2" Residue "A ARG 584": "NH1" <-> "NH2" Residue "A PHE 597": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 599": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 604": "OE1" <-> "OE2" Residue "A PHE 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 752": "OE1" <-> "OE2" Residue "A ASP 758": "OD1" <-> "OD2" Residue "B PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 365": "NH1" <-> "NH2" Residue "B GLU 433": "OE1" <-> "OE2" Residue "B ARG 435": "NH1" <-> "NH2" Residue "B GLU 446": "OE1" <-> "OE2" Residue "B TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 469": "OE1" <-> "OE2" Residue "B GLU 487": "OE1" <-> "OE2" Residue "B TYR 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 584": "NH1" <-> "NH2" Residue "B PHE 597": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 599": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 678": "OD1" <-> "OD2" Residue "B TYR 716": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 758": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 9221 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4482 Classifications: {'peptide': 571} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 12, 'TRANS': 558} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 4516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4516 Classifications: {'peptide': 575} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 13, 'TRANS': 561} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "A" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 153 Unusual residues: {'HT9': 1, 'Y01': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'Y01': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.91, per 1000 atoms: 0.64 Number of scatterers: 9221 At special positions: 0 Unit cell: (68.88, 101.68, 137.104, 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 34 16.00 O 1662 8.00 N 1557 7.00 C 5968 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: 4.31 Conformation dependent library (CDL) restraints added in 1.8 seconds 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2110 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 8 sheets defined 72.2% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 258 through 295 removed outlier: 3.717A pdb=" N GLN A 262 " --> pdb=" O SER A 258 " (cutoff:3.500A) Proline residue: A 283 - end of helix removed outlier: 3.600A pdb=" N GLU A 295 " --> pdb=" O ASN A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 317 removed outlier: 4.463A pdb=" N TRP A 304 " --> pdb=" O ASN A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 334 Processing helix chain 'A' and resid 334 through 355 removed outlier: 3.913A pdb=" N PHE A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 363 removed outlier: 3.605A pdb=" N GLY A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 390 removed outlier: 3.515A pdb=" N VAL A 369 " --> pdb=" O ARG A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 408 Processing helix chain 'A' and resid 410 through 459 removed outlier: 4.099A pdb=" N GLY A 414 " --> pdb=" O ASN A 410 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA A 453 " --> pdb=" O THR A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 467 Processing helix chain 'A' and resid 468 through 522 Processing helix chain 'A' and resid 526 through 570 removed outlier: 4.155A pdb=" N TYR A 530 " --> pdb=" O GLN A 526 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL A 531 " --> pdb=" O VAL A 527 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE A 538 " --> pdb=" O GLY A 534 " (cutoff:3.500A) Proline residue: A 543 - end of helix removed outlier: 4.064A pdb=" N TRP A 546 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY A 548 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N THR A 549 " --> pdb=" O ASN A 545 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N GLN A 555 " --> pdb=" O TYR A 551 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N THR A 556 " --> pdb=" O ARG A 552 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU A 570 " --> pdb=" O ASP A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 637 removed outlier: 4.062A pdb=" N LEU A 633 " --> pdb=" O LYS A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 664 removed outlier: 3.844A pdb=" N LEU A 662 " --> pdb=" O THR A 658 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER A 664 " --> pdb=" O ALA A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 688 removed outlier: 3.720A pdb=" N GLY A 687 " --> pdb=" O ASN A 683 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ARG A 688 " --> pdb=" O ILE A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 703 Processing helix chain 'A' and resid 705 through 712 Processing helix chain 'A' and resid 714 through 718 removed outlier: 3.590A pdb=" N ARG A 717 " --> pdb=" O GLU A 714 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR A 718 " --> pdb=" O GLY A 715 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 714 through 718' Processing helix chain 'A' and resid 728 through 744 Processing helix chain 'A' and resid 758 through 773 Processing helix chain 'A' and resid 785 through 790 Processing helix chain 'A' and resid 807 through 815 Processing helix chain 'A' and resid 816 through 827 Processing helix chain 'B' and resid 258 through 295 removed outlier: 4.546A pdb=" N VAL B 280 " --> pdb=" O ARG B 276 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU B 281 " --> pdb=" O ALA B 277 " (cutoff:3.500A) Proline residue: B 283 - end of helix Processing helix chain 'B' and resid 298 through 316 removed outlier: 3.969A pdb=" N TRP B 304 " --> pdb=" O ASN B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 356 removed outlier: 4.515A pdb=" N ARG B 336 " --> pdb=" O PHE B 332 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL B 337 " --> pdb=" O LEU B 333 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N PHE B 340 " --> pdb=" O ARG B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 362 removed outlier: 3.620A pdb=" N HIS B 361 " --> pdb=" O SER B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 408 removed outlier: 4.487A pdb=" N ILE B 372 " --> pdb=" O GLU B 368 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ILE B 392 " --> pdb=" O VAL B 388 " (cutoff:3.500A) Proline residue: B 393 - end of helix Processing helix chain 'B' and resid 410 through 459 removed outlier: 3.545A pdb=" N GLY B 414 " --> pdb=" O ASN B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 466 Processing helix chain 'B' and resid 468 through 522 removed outlier: 4.196A pdb=" N LYS B 489 " --> pdb=" O GLY B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 542 removed outlier: 3.669A pdb=" N TYR B 530 " --> pdb=" O GLN B 526 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE B 538 " --> pdb=" O GLY B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 553 Processing helix chain 'B' and resid 553 through 570 removed outlier: 4.207A pdb=" N ASN B 557 " --> pdb=" O MET B 553 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU B 562 " --> pdb=" O PHE B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 637 Processing helix chain 'B' and resid 658 through 666 Processing helix chain 'B' and resid 680 through 685 Processing helix chain 'B' and resid 686 through 688 No H-bonds generated for 'chain 'B' and resid 686 through 688' Processing helix chain 'B' and resid 692 through 704 Processing helix chain 'B' and resid 705 through 712 Processing helix chain 'B' and resid 714 through 718 removed outlier: 3.730A pdb=" N ARG B 717 " --> pdb=" O GLU B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 744 Processing helix chain 'B' and resid 758 through 774 removed outlier: 3.759A pdb=" N ALA B 764 " --> pdb=" O SER B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 790 removed outlier: 3.553A pdb=" N ASN B 790 " --> pdb=" O SER B 786 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 815 Processing helix chain 'B' and resid 816 through 827 Processing sheet with id=AA1, first strand: chain 'A' and resid 606 through 607 removed outlier: 3.515A pdb=" N PHE A 597 " --> pdb=" O LEU A 606 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE A 611 " --> pdb=" O PHE A 592 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 606 through 607 removed outlier: 3.515A pdb=" N PHE A 597 " --> pdb=" O LEU A 606 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N PHE A 592 " --> pdb=" O ARG A 648 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ARG A 648 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ASN A 594 " --> pdb=" O CYS A 646 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N CYS A 646 " --> pdb=" O ASN A 594 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 619 through 621 removed outlier: 6.900A pdb=" N LEU A 619 " --> pdb=" O VAL A 780 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL A 781 " --> pdb=" O LEU A 750 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 666 through 667 Processing sheet with id=AA5, first strand: chain 'A' and resid 795 through 798 removed outlier: 6.958A pdb=" N VAL A 796 " --> pdb=" O VAL A 803 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 595 through 597 removed outlier: 3.672A pdb=" N VAL B 595 " --> pdb=" O VAL B 609 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N PHE B 597 " --> pdb=" O GLN B 607 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N GLN B 607 " --> pdb=" O PHE B 597 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 619 through 620 Processing sheet with id=AA8, first strand: chain 'B' and resid 796 through 798 removed outlier: 7.321A pdb=" N VAL B 796 " --> pdb=" O VAL B 803 " (cutoff:3.500A) 615 hydrogen bonds defined for protein. 1818 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: 2.54 Time building geometry restraints manager: 4.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1549 1.32 - 1.45: 2494 1.45 - 1.57: 5313 1.57 - 1.70: 1 1.70 - 1.82: 56 Bond restraints: 9413 Sorted by residual: bond pdb=" N ILE A 747 " pdb=" CA ILE A 747 " ideal model delta sigma weight residual 1.456 1.496 -0.039 1.14e-02 7.69e+03 1.19e+01 bond pdb=" N THR B 320 " pdb=" CA THR B 320 " ideal model delta sigma weight residual 1.456 1.496 -0.039 1.23e-02 6.61e+03 1.03e+01 bond pdb=" N VAL B 527 " pdb=" CA VAL B 527 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.00e+01 bond pdb=" N ILE B 705 " pdb=" CA ILE B 705 " ideal model delta sigma weight residual 1.459 1.498 -0.040 1.25e-02 6.40e+03 1.00e+01 bond pdb=" N ALA A 744 " pdb=" CA ALA A 744 " ideal model delta sigma weight residual 1.457 1.485 -0.029 9.10e-03 1.21e+04 9.84e+00 ... (remaining 9408 not shown) Histogram of bond angle deviations from ideal: 94.60 - 102.52: 41 102.52 - 110.44: 2320 110.44 - 118.36: 5139 118.36 - 126.28: 5175 126.28 - 134.20: 132 Bond angle restraints: 12807 Sorted by residual: angle pdb=" CA GLY B 324 " pdb=" C GLY B 324 " pdb=" O GLY B 324 " ideal model delta sigma weight residual 122.37 118.09 4.28 7.30e-01 1.88e+00 3.43e+01 angle pdb=" C THR B 320 " pdb=" CA THR B 320 " pdb=" CB THR B 320 " ideal model delta sigma weight residual 110.06 117.37 -7.31 1.44e+00 4.82e-01 2.58e+01 angle pdb=" CB ARG A 452 " pdb=" CG ARG A 452 " pdb=" CD ARG A 452 " ideal model delta sigma weight residual 111.30 122.91 -11.61 2.30e+00 1.89e-01 2.55e+01 angle pdb=" N PHE B 409 " pdb=" CA PHE B 409 " pdb=" C PHE B 409 " ideal model delta sigma weight residual 109.18 102.13 7.05 1.42e+00 4.96e-01 2.47e+01 angle pdb=" CB MET A 442 " pdb=" CG MET A 442 " pdb=" SD MET A 442 " ideal model delta sigma weight residual 112.70 97.81 14.89 3.00e+00 1.11e-01 2.46e+01 ... (remaining 12802 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 5107 17.66 - 35.32: 542 35.32 - 52.98: 97 52.98 - 70.63: 23 70.63 - 88.29: 12 Dihedral angle restraints: 5781 sinusoidal: 2487 harmonic: 3294 Sorted by residual: dihedral pdb=" CA ARG A 814 " pdb=" C ARG A 814 " pdb=" N GLY A 815 " pdb=" CA GLY A 815 " ideal model delta harmonic sigma weight residual 180.00 153.69 26.31 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA GLU A 591 " pdb=" C GLU A 591 " pdb=" N PHE A 592 " pdb=" CA PHE A 592 " ideal model delta harmonic sigma weight residual 180.00 154.23 25.77 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA LEU A 353 " pdb=" C LEU A 353 " pdb=" N HIS A 354 " pdb=" CA HIS A 354 " ideal model delta harmonic sigma weight residual 180.00 155.07 24.93 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 5778 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1188 0.083 - 0.166: 254 0.166 - 0.249: 37 0.249 - 0.332: 7 0.332 - 0.416: 2 Chirality restraints: 1488 Sorted by residual: chirality pdb=" CB VAL B 696 " pdb=" CA VAL B 696 " pdb=" CG1 VAL B 696 " pdb=" CG2 VAL B 696 " both_signs ideal model delta sigma weight residual False -2.63 -2.21 -0.42 2.00e-01 2.50e+01 4.32e+00 chirality pdb=" CG LEU B 769 " pdb=" CB LEU B 769 " pdb=" CD1 LEU B 769 " pdb=" CD2 LEU B 769 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" CB VAL A 388 " pdb=" CA VAL A 388 " pdb=" CG1 VAL A 388 " pdb=" CG2 VAL A 388 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.66e+00 ... (remaining 1485 not shown) Planarity restraints: 1592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 HT9 A 904 " -0.065 2.00e-02 2.50e+03 1.85e-01 7.71e+02 pdb=" C11 HT9 A 904 " 0.080 2.00e-02 2.50e+03 pdb=" C12 HT9 A 904 " -0.045 2.00e-02 2.50e+03 pdb=" C13 HT9 A 904 " 0.062 2.00e-02 2.50e+03 pdb=" C14 HT9 A 904 " -0.262 2.00e-02 2.50e+03 pdb=" C20 HT9 A 904 " 0.144 2.00e-02 2.50e+03 pdb=" C21 HT9 A 904 " 0.313 2.00e-02 2.50e+03 pdb=" C35 HT9 A 904 " -0.312 2.00e-02 2.50e+03 pdb=" N3 HT9 A 904 " 0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 299 " -0.037 2.00e-02 2.50e+03 3.06e-02 2.34e+01 pdb=" CG TRP A 299 " 0.078 2.00e-02 2.50e+03 pdb=" CD1 TRP A 299 " -0.039 2.00e-02 2.50e+03 pdb=" CD2 TRP A 299 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 299 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 299 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 299 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 299 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 299 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 299 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET B 542 " 0.060 5.00e-02 4.00e+02 9.03e-02 1.31e+01 pdb=" N PRO B 543 " -0.156 5.00e-02 4.00e+02 pdb=" CA PRO B 543 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 543 " 0.050 5.00e-02 4.00e+02 ... (remaining 1589 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 963 2.74 - 3.28: 9759 3.28 - 3.82: 16047 3.82 - 4.36: 18156 4.36 - 4.90: 29758 Nonbonded interactions: 74683 Sorted by model distance: nonbonded pdb=" O THR B 428 " pdb=" OG1 THR B 432 " model vdw 2.203 3.040 nonbonded pdb=" O ILE A 402 " pdb=" OG SER A 406 " model vdw 2.260 3.040 nonbonded pdb=" OG1 THR A 449 " pdb=" NH2 ARG A 452 " model vdw 2.303 3.120 nonbonded pdb=" OD1 ASN A 459 " pdb=" OG1 THR A 462 " model vdw 2.305 3.040 nonbonded pdb=" OE1 GLN B 701 " pdb=" OH TYR B 716 " model vdw 2.308 3.040 ... (remaining 74678 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 258 through 357 or (resid 358 through 359 and (name N or n \ ame CA or name C or name O or name CB )) or resid 360 through 463 or (resid 464 \ through 468 and (name N or name CA or name C or name O or name CB )) or resid 46 \ 9 through 828 or resid 901 through 902)) selection = (chain 'B' and (resid 258 through 465 or (resid 466 through 468 and (name N or n \ ame CA or name C or name O or name CB )) or resid 469 through 523 or (resid 524 \ and (name N or name CA or name C or name O or name CB )) or resid 525 or (resid \ 526 and (name N or name CA or name C or name O or name CB )) or resid 527 throug \ h 828 or resid 901 through 902)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 29.300 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 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 0.104 9413 Z= 0.583 Angle : 1.248 14.894 12807 Z= 0.742 Chirality : 0.071 0.416 1488 Planarity : 0.008 0.185 1592 Dihedral : 15.292 88.293 3671 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.04 % Allowed : 1.46 % Favored : 97.49 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.22), residues: 1142 helix: -0.53 (0.17), residues: 769 sheet: -2.07 (0.64), residues: 53 loop : -2.49 (0.28), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.078 0.005 TRP A 299 HIS 0.007 0.001 HIS B 352 PHE 0.051 0.004 PHE A 405 TYR 0.042 0.004 TYR A 465 ARG 0.023 0.001 ARG A 452 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 153 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 478 GLU cc_start: 0.8635 (tm-30) cc_final: 0.8188 (tm-30) REVERT: A 758 ASP cc_start: 0.8140 (m-30) cc_final: 0.7680 (t0) REVERT: B 309 TYR cc_start: 0.7549 (t80) cc_final: 0.7217 (t80) REVERT: B 370 LEU cc_start: 0.9107 (tp) cc_final: 0.8906 (tp) REVERT: B 422 SER cc_start: 0.7976 (m) cc_final: 0.7592 (p) REVERT: B 466 TYR cc_start: 0.7597 (m-80) cc_final: 0.7279 (m-80) REVERT: B 646 CYS cc_start: 0.8053 (m) cc_final: 0.7827 (m) REVERT: B 822 TRP cc_start: 0.8610 (t-100) cc_final: 0.8290 (t-100) outliers start: 10 outliers final: 2 residues processed: 161 average time/residue: 0.2749 time to fit residues: 60.7041 Evaluate side-chains 113 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 111 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 748 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 46 optimal weight: 20.0000 chunk 89 optimal weight: 30.0000 chunk 34 optimal weight: 20.0000 chunk 54 optimal weight: 20.0000 chunk 66 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 ASN ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9413 Z= 0.241 Angle : 0.682 8.172 12807 Z= 0.361 Chirality : 0.042 0.150 1488 Planarity : 0.005 0.071 1592 Dihedral : 8.300 59.987 1641 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.15 % Allowed : 11.49 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.24), residues: 1142 helix: 0.42 (0.18), residues: 777 sheet: -2.05 (0.67), residues: 53 loop : -2.29 (0.30), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 434 HIS 0.009 0.001 HIS A 354 PHE 0.027 0.002 PHE A 418 TYR 0.023 0.002 TYR A 483 ARG 0.008 0.001 ARG A 452 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 140 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 TYR cc_start: 0.7818 (t80) cc_final: 0.6857 (t80) REVERT: A 386 TYR cc_start: 0.8356 (t80) cc_final: 0.7940 (t80) REVERT: A 388 VAL cc_start: 0.8460 (p) cc_final: 0.8232 (p) REVERT: A 478 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8205 (tm-30) REVERT: A 561 MET cc_start: 0.7115 (tmm) cc_final: 0.6851 (tmm) REVERT: A 758 ASP cc_start: 0.8097 (m-30) cc_final: 0.7657 (t0) REVERT: B 272 MET cc_start: 0.8038 (tmm) cc_final: 0.7800 (tmm) REVERT: B 309 TYR cc_start: 0.7399 (t80) cc_final: 0.7127 (t80) REVERT: B 370 LEU cc_start: 0.9153 (tp) cc_final: 0.8950 (tp) REVERT: B 466 TYR cc_start: 0.7621 (m-80) cc_final: 0.7328 (m-80) REVERT: B 503 LEU cc_start: 0.8669 (tp) cc_final: 0.8402 (tp) REVERT: B 646 CYS cc_start: 0.7971 (m) cc_final: 0.7762 (m) REVERT: B 822 TRP cc_start: 0.8626 (t-100) cc_final: 0.8322 (t-100) outliers start: 11 outliers final: 7 residues processed: 147 average time/residue: 0.2211 time to fit residues: 45.0332 Evaluate side-chains 125 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 118 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 551 TYR Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 748 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 112 optimal weight: 40.0000 chunk 92 optimal weight: 8.9990 chunk 102 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 83 optimal weight: 0.5980 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS A 445 GLN ** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 GLN A 659 GLN ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 539 GLN ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9413 Z= 0.238 Angle : 0.634 6.461 12807 Z= 0.332 Chirality : 0.042 0.224 1488 Planarity : 0.004 0.057 1592 Dihedral : 7.581 58.188 1641 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.78 % Allowed : 16.09 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.24), residues: 1142 helix: 0.86 (0.18), residues: 769 sheet: -2.02 (0.67), residues: 53 loop : -2.09 (0.31), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 434 HIS 0.012 0.001 HIS A 665 PHE 0.028 0.002 PHE A 418 TYR 0.034 0.002 TYR A 465 ARG 0.006 0.000 ARG A 452 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 123 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 TYR cc_start: 0.8387 (t80) cc_final: 0.8036 (t80) REVERT: A 388 VAL cc_start: 0.8457 (p) cc_final: 0.8226 (p) REVERT: A 445 GLN cc_start: 0.7429 (OUTLIER) cc_final: 0.6632 (tm-30) REVERT: A 478 GLU cc_start: 0.8635 (tm-30) cc_final: 0.8233 (tm-30) REVERT: A 483 TYR cc_start: 0.8730 (t80) cc_final: 0.8270 (t80) REVERT: A 518 TYR cc_start: 0.7926 (t80) cc_final: 0.7362 (t80) REVERT: A 561 MET cc_start: 0.7105 (tmm) cc_final: 0.6761 (tmm) REVERT: B 272 MET cc_start: 0.8089 (tmm) cc_final: 0.7855 (tmm) REVERT: B 275 GLU cc_start: 0.8304 (tm-30) cc_final: 0.8004 (tm-30) REVERT: B 309 TYR cc_start: 0.7557 (t80) cc_final: 0.7188 (t80) REVERT: B 370 LEU cc_start: 0.9165 (tp) cc_final: 0.8953 (tp) REVERT: B 466 TYR cc_start: 0.7669 (m-80) cc_final: 0.7405 (m-80) REVERT: B 503 LEU cc_start: 0.8692 (tp) cc_final: 0.8422 (tp) REVERT: B 646 CYS cc_start: 0.7973 (m) cc_final: 0.7762 (m) REVERT: B 656 GLN cc_start: 0.8594 (pp30) cc_final: 0.8018 (mp10) REVERT: B 697 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6614 (tt0) REVERT: B 822 TRP cc_start: 0.8618 (t-100) cc_final: 0.8315 (t-100) outliers start: 17 outliers final: 7 residues processed: 137 average time/residue: 0.2147 time to fit residues: 41.2685 Evaluate side-chains 121 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 112 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 445 GLN Chi-restraints excluded: chain A residue 551 TYR Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain B residue 409 PHE Chi-restraints excluded: chain B residue 434 TRP Chi-restraints excluded: chain B residue 566 ASP Chi-restraints excluded: chain B residue 697 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 11 optimal weight: 0.3980 chunk 49 optimal weight: 7.9990 chunk 69 optimal weight: 10.0000 chunk 104 optimal weight: 9.9990 chunk 110 optimal weight: 0.8980 chunk 54 optimal weight: 0.0770 chunk 98 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 overall best weight: 1.0740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS A 498 ASN B 354 HIS B 502 ASN ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9413 Z= 0.184 Angle : 0.601 9.698 12807 Z= 0.312 Chirality : 0.041 0.208 1488 Planarity : 0.004 0.050 1592 Dihedral : 6.956 58.568 1639 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.19 % Allowed : 18.08 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.25), residues: 1142 helix: 1.17 (0.19), residues: 767 sheet: -1.93 (0.67), residues: 53 loop : -2.03 (0.31), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 434 HIS 0.006 0.001 HIS A 665 PHE 0.018 0.001 PHE A 418 TYR 0.023 0.002 TYR A 465 ARG 0.005 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 130 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 TYR cc_start: 0.8348 (t80) cc_final: 0.8036 (t80) REVERT: A 388 VAL cc_start: 0.8463 (p) cc_final: 0.8231 (p) REVERT: A 478 GLU cc_start: 0.8656 (tm-30) cc_final: 0.8274 (tm-30) REVERT: A 518 TYR cc_start: 0.7884 (t80) cc_final: 0.7318 (t80) REVERT: A 561 MET cc_start: 0.7049 (tmm) cc_final: 0.6763 (tmm) REVERT: A 758 ASP cc_start: 0.8032 (m-30) cc_final: 0.7635 (t0) REVERT: B 309 TYR cc_start: 0.7473 (t80) cc_final: 0.7115 (t80) REVERT: B 370 LEU cc_start: 0.9172 (tp) cc_final: 0.8964 (tp) REVERT: B 466 TYR cc_start: 0.7638 (m-80) cc_final: 0.7403 (m-80) REVERT: B 502 ASN cc_start: 0.8816 (OUTLIER) cc_final: 0.8603 (m-40) REVERT: B 503 LEU cc_start: 0.8672 (tp) cc_final: 0.8410 (tp) REVERT: B 541 TYR cc_start: 0.7862 (m-10) cc_final: 0.7283 (m-10) REVERT: B 646 CYS cc_start: 0.7969 (m) cc_final: 0.7765 (m) REVERT: B 656 GLN cc_start: 0.8541 (pp30) cc_final: 0.7957 (mp10) REVERT: B 697 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6713 (tt0) REVERT: B 822 TRP cc_start: 0.8610 (t-100) cc_final: 0.8302 (t-100) outliers start: 21 outliers final: 12 residues processed: 143 average time/residue: 0.2323 time to fit residues: 45.5234 Evaluate side-chains 133 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 119 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 551 TYR Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain B residue 434 TRP Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 502 ASN Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 566 ASP Chi-restraints excluded: chain B residue 697 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 45 optimal weight: 6.9990 chunk 94 optimal weight: 0.2980 chunk 76 optimal weight: 3.9990 chunk 0 optimal weight: 0.7980 chunk 56 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS A 354 HIS A 498 ASN ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9413 Z= 0.174 Angle : 0.608 13.977 12807 Z= 0.310 Chirality : 0.040 0.149 1488 Planarity : 0.004 0.048 1592 Dihedral : 6.703 59.863 1639 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.51 % Allowed : 19.64 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.25), residues: 1142 helix: 1.39 (0.19), residues: 766 sheet: -1.87 (0.67), residues: 53 loop : -2.04 (0.31), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 360 HIS 0.004 0.001 HIS A 665 PHE 0.015 0.001 PHE A 418 TYR 0.024 0.001 TYR A 465 ARG 0.006 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 128 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 TYR cc_start: 0.8330 (t80) cc_final: 0.8080 (t80) REVERT: A 388 VAL cc_start: 0.8438 (p) cc_final: 0.8204 (p) REVERT: A 442 MET cc_start: 0.7142 (tpp) cc_final: 0.6823 (tpp) REVERT: A 478 GLU cc_start: 0.8635 (tm-30) cc_final: 0.8278 (tm-30) REVERT: A 518 TYR cc_start: 0.7847 (t80) cc_final: 0.7304 (t80) REVERT: A 561 MET cc_start: 0.6990 (tmm) cc_final: 0.6757 (tmm) REVERT: B 271 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8187 (mt) REVERT: B 275 GLU cc_start: 0.8264 (tm-30) cc_final: 0.8010 (tm-30) REVERT: B 309 TYR cc_start: 0.7400 (t80) cc_final: 0.7085 (t80) REVERT: B 370 LEU cc_start: 0.9163 (tp) cc_final: 0.8957 (tp) REVERT: B 466 TYR cc_start: 0.7678 (m-80) cc_final: 0.7442 (m-80) REVERT: B 503 LEU cc_start: 0.8661 (tp) cc_final: 0.8404 (tp) REVERT: B 541 TYR cc_start: 0.7786 (m-10) cc_final: 0.7340 (m-10) REVERT: B 656 GLN cc_start: 0.8520 (pp30) cc_final: 0.7932 (mp10) REVERT: B 697 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.6719 (tt0) REVERT: B 766 GLN cc_start: 0.9281 (OUTLIER) cc_final: 0.9039 (mp10) REVERT: B 822 TRP cc_start: 0.8604 (t-100) cc_final: 0.8285 (t-100) outliers start: 24 outliers final: 12 residues processed: 146 average time/residue: 0.2343 time to fit residues: 46.8324 Evaluate side-chains 141 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 126 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain B residue 409 PHE Chi-restraints excluded: chain B residue 434 TRP Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 566 ASP Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 766 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 110 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 51 optimal weight: 20.0000 chunk 9 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 HIS ** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 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 : 0.007 0.070 9413 Z= 0.451 Angle : 0.765 11.714 12807 Z= 0.387 Chirality : 0.047 0.328 1488 Planarity : 0.004 0.041 1592 Dihedral : 7.364 55.415 1639 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.82 % Allowed : 21.11 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.24), residues: 1142 helix: 0.92 (0.18), residues: 766 sheet: -2.03 (0.64), residues: 53 loop : -1.97 (0.31), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 360 HIS 0.004 0.001 HIS A 665 PHE 0.042 0.003 PHE A 418 TYR 0.022 0.003 TYR A 465 ARG 0.009 0.001 ARG A 452 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 119 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 TYR cc_start: 0.7832 (t80) cc_final: 0.7363 (t80) REVERT: A 445 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.7072 (tm-30) REVERT: A 478 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8250 (tm-30) REVERT: A 496 LEU cc_start: 0.9305 (tp) cc_final: 0.9070 (tt) REVERT: A 518 TYR cc_start: 0.7993 (t80) cc_final: 0.7416 (t80) REVERT: A 561 MET cc_start: 0.7105 (tmm) cc_final: 0.6730 (tmm) REVERT: A 758 ASP cc_start: 0.8057 (m-30) cc_final: 0.7688 (t0) REVERT: B 309 TYR cc_start: 0.7709 (t80) cc_final: 0.7297 (t80) REVERT: B 370 LEU cc_start: 0.9198 (tp) cc_final: 0.8984 (tp) REVERT: B 466 TYR cc_start: 0.7677 (m-80) cc_final: 0.7474 (m-80) REVERT: B 503 LEU cc_start: 0.8723 (tp) cc_final: 0.8167 (tt) REVERT: B 697 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6793 (tt0) REVERT: B 822 TRP cc_start: 0.8596 (t-100) cc_final: 0.8272 (t-100) outliers start: 27 outliers final: 20 residues processed: 140 average time/residue: 0.2443 time to fit residues: 46.7715 Evaluate side-chains 138 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 116 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 445 GLN Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 409 PHE Chi-restraints excluded: chain B residue 434 TRP Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 566 ASP Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 766 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 92 optimal weight: 8.9990 chunk 61 optimal weight: 0.7980 chunk 109 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 HIS A 498 ASN ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9413 Z= 0.209 Angle : 0.659 15.579 12807 Z= 0.331 Chirality : 0.041 0.165 1488 Planarity : 0.004 0.047 1592 Dihedral : 6.823 54.858 1639 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.03 % Allowed : 21.94 % Favored : 75.03 % 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: 0.34 (0.24), residues: 1142 helix: 1.27 (0.18), residues: 767 sheet: -1.76 (0.67), residues: 53 loop : -1.99 (0.31), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 360 HIS 0.003 0.001 HIS A 665 PHE 0.017 0.001 PHE A 418 TYR 0.033 0.002 TYR A 465 ARG 0.007 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 130 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 VAL cc_start: 0.8499 (OUTLIER) cc_final: 0.8263 (p) REVERT: A 445 GLN cc_start: 0.7536 (OUTLIER) cc_final: 0.6998 (tm-30) REVERT: A 452 ARG cc_start: 0.7729 (tmm-80) cc_final: 0.7155 (tmm-80) REVERT: A 478 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8257 (tm-30) REVERT: A 518 TYR cc_start: 0.7895 (t80) cc_final: 0.7328 (t80) REVERT: A 561 MET cc_start: 0.7076 (tmm) cc_final: 0.6794 (tmm) REVERT: A 758 ASP cc_start: 0.8033 (m-30) cc_final: 0.7667 (t0) REVERT: B 275 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7771 (tm-30) REVERT: B 309 TYR cc_start: 0.7541 (t80) cc_final: 0.7153 (t80) REVERT: B 370 LEU cc_start: 0.9169 (tp) cc_final: 0.8964 (tp) REVERT: B 466 TYR cc_start: 0.7654 (m-80) cc_final: 0.7450 (m-80) REVERT: B 503 LEU cc_start: 0.8684 (tp) cc_final: 0.8424 (tp) REVERT: B 672 ASP cc_start: 0.8898 (m-30) cc_final: 0.7728 (p0) REVERT: B 697 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6688 (tt0) REVERT: B 822 TRP cc_start: 0.8555 (t-100) cc_final: 0.8228 (t-100) outliers start: 29 outliers final: 13 residues processed: 152 average time/residue: 0.2335 time to fit residues: 48.9546 Evaluate side-chains 133 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 117 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 445 GLN Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 551 TYR Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain B residue 409 PHE Chi-restraints excluded: chain B residue 434 TRP Chi-restraints excluded: chain B residue 566 ASP Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 766 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.0370 chunk 65 optimal weight: 3.9990 chunk 33 optimal weight: 20.0000 chunk 21 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 54 optimal weight: 30.0000 chunk 10 optimal weight: 10.0000 chunk 86 optimal weight: 0.9990 chunk 99 optimal weight: 8.9990 chunk 105 optimal weight: 6.9990 overall best weight: 1.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 HIS A 498 ASN B 354 HIS ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9413 Z= 0.206 Angle : 0.681 15.531 12807 Z= 0.338 Chirality : 0.042 0.163 1488 Planarity : 0.004 0.052 1592 Dihedral : 6.604 54.404 1639 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.40 % Allowed : 22.57 % Favored : 75.03 % 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: 0.47 (0.25), residues: 1142 helix: 1.37 (0.18), residues: 766 sheet: -1.53 (0.70), residues: 52 loop : -1.96 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 360 HIS 0.004 0.001 HIS B 354 PHE 0.018 0.001 PHE A 418 TYR 0.036 0.002 TYR A 465 ARG 0.008 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 128 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 VAL cc_start: 0.8494 (OUTLIER) cc_final: 0.8264 (p) REVERT: A 445 GLN cc_start: 0.7502 (OUTLIER) cc_final: 0.6931 (tm-30) REVERT: A 452 ARG cc_start: 0.7752 (tmm-80) cc_final: 0.7277 (tmm-80) REVERT: A 478 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8272 (tm-30) REVERT: A 518 TYR cc_start: 0.7874 (t80) cc_final: 0.7323 (t80) REVERT: A 561 MET cc_start: 0.7028 (tmm) cc_final: 0.6733 (tmm) REVERT: B 275 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7611 (tm-30) REVERT: B 309 TYR cc_start: 0.7527 (t80) cc_final: 0.7166 (t80) REVERT: B 371 ARG cc_start: 0.8922 (tmm-80) cc_final: 0.8603 (ttp80) REVERT: B 672 ASP cc_start: 0.8894 (m-30) cc_final: 0.7757 (p0) REVERT: B 697 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6677 (tt0) REVERT: B 739 ARG cc_start: 0.7771 (ttp-170) cc_final: 0.7334 (mtt-85) REVERT: B 822 TRP cc_start: 0.8550 (t-100) cc_final: 0.8217 (t-100) outliers start: 23 outliers final: 14 residues processed: 145 average time/residue: 0.2374 time to fit residues: 46.5127 Evaluate side-chains 139 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 122 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 445 GLN Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 551 TYR Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 409 PHE Chi-restraints excluded: chain B residue 434 TRP Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain B residue 566 ASP Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 766 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 20.0000 chunk 102 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 chunk 44 optimal weight: 10.0000 chunk 80 optimal weight: 0.8980 chunk 31 optimal weight: 8.9990 chunk 92 optimal weight: 20.0000 chunk 67 optimal weight: 0.9990 chunk 108 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 HIS A 498 ASN B 354 HIS ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 683 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9413 Z= 0.262 Angle : 0.733 14.927 12807 Z= 0.357 Chirality : 0.043 0.179 1488 Planarity : 0.004 0.051 1592 Dihedral : 6.677 54.368 1639 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.51 % Allowed : 22.99 % Favored : 74.50 % 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: 0.35 (0.24), residues: 1142 helix: 1.26 (0.18), residues: 766 sheet: -1.67 (0.69), residues: 52 loop : -1.93 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 360 HIS 0.004 0.001 HIS B 354 PHE 0.024 0.002 PHE A 418 TYR 0.025 0.002 TYR A 550 ARG 0.008 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 124 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 VAL cc_start: 0.8478 (OUTLIER) cc_final: 0.8258 (p) REVERT: A 445 GLN cc_start: 0.7531 (OUTLIER) cc_final: 0.6931 (tm-30) REVERT: A 452 ARG cc_start: 0.7785 (tmm-80) cc_final: 0.7383 (tmm-80) REVERT: A 478 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8270 (tm-30) REVERT: A 509 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8543 (tt) REVERT: A 518 TYR cc_start: 0.7898 (t80) cc_final: 0.7330 (t80) REVERT: A 550 TYR cc_start: 0.8135 (m-80) cc_final: 0.7690 (m-10) REVERT: A 561 MET cc_start: 0.7068 (tmm) cc_final: 0.6829 (tmm) REVERT: A 565 PHE cc_start: 0.5077 (OUTLIER) cc_final: 0.3711 (m-80) REVERT: A 758 ASP cc_start: 0.8050 (m-30) cc_final: 0.7685 (t0) REVERT: B 309 TYR cc_start: 0.7583 (t80) cc_final: 0.7194 (t80) REVERT: B 371 ARG cc_start: 0.8911 (tmm-80) cc_final: 0.8584 (ttp80) REVERT: B 672 ASP cc_start: 0.8866 (m-30) cc_final: 0.7733 (p0) REVERT: B 697 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6662 (tt0) REVERT: B 822 TRP cc_start: 0.8534 (t-100) cc_final: 0.8183 (t-100) outliers start: 24 outliers final: 14 residues processed: 143 average time/residue: 0.2376 time to fit residues: 45.7488 Evaluate side-chains 138 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 119 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 445 GLN Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 551 TYR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain B residue 409 PHE Chi-restraints excluded: chain B residue 434 TRP Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain B residue 566 ASP Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 766 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 113 optimal weight: 7.9990 chunk 104 optimal weight: 0.0670 chunk 90 optimal weight: 30.0000 chunk 9 optimal weight: 0.0170 chunk 69 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 chunk 96 optimal weight: 40.0000 chunk 27 optimal weight: 0.7980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN A 352 HIS B 354 HIS B 443 ASN B 459 ASN ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 733 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9413 Z= 0.185 Angle : 0.722 16.324 12807 Z= 0.347 Chirality : 0.041 0.169 1488 Planarity : 0.004 0.051 1592 Dihedral : 6.349 56.349 1639 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.09 % Allowed : 23.30 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.25), residues: 1142 helix: 1.47 (0.19), residues: 767 sheet: -1.45 (0.71), residues: 52 loop : -1.97 (0.31), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 360 HIS 0.004 0.001 HIS B 354 PHE 0.015 0.001 PHE B 676 TYR 0.042 0.002 TYR A 465 ARG 0.008 0.000 ARG A 439 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 141 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 TYR cc_start: 0.8122 (t80) cc_final: 0.7699 (t80) REVERT: A 388 VAL cc_start: 0.8438 (OUTLIER) cc_final: 0.8195 (p) REVERT: A 413 PHE cc_start: 0.6938 (m-80) cc_final: 0.6671 (m-80) REVERT: A 439 ARG cc_start: 0.9181 (mmm160) cc_final: 0.8945 (mmm160) REVERT: A 445 GLN cc_start: 0.7467 (OUTLIER) cc_final: 0.6865 (tm-30) REVERT: A 452 ARG cc_start: 0.7745 (tmm-80) cc_final: 0.7388 (tmm-80) REVERT: A 478 GLU cc_start: 0.8634 (tm-30) cc_final: 0.8285 (tm-30) REVERT: A 518 TYR cc_start: 0.7859 (t80) cc_final: 0.7291 (t80) REVERT: A 565 PHE cc_start: 0.5060 (OUTLIER) cc_final: 0.3592 (m-80) REVERT: A 758 ASP cc_start: 0.8046 (m-30) cc_final: 0.7674 (t0) REVERT: B 275 GLU cc_start: 0.8262 (tm-30) cc_final: 0.7773 (tm-30) REVERT: B 309 TYR cc_start: 0.7447 (t80) cc_final: 0.6958 (t80) REVERT: B 371 ARG cc_start: 0.8877 (tmm-80) cc_final: 0.8545 (ttp80) REVERT: B 466 TYR cc_start: 0.7479 (m-80) cc_final: 0.7269 (m-80) REVERT: B 576 ASP cc_start: 0.8119 (t0) cc_final: 0.7917 (t0) REVERT: B 672 ASP cc_start: 0.8837 (m-30) cc_final: 0.7767 (p0) REVERT: B 739 ARG cc_start: 0.7808 (ttp-170) cc_final: 0.7370 (mtt-85) REVERT: B 822 TRP cc_start: 0.8519 (t-100) cc_final: 0.8169 (t-100) outliers start: 20 outliers final: 11 residues processed: 154 average time/residue: 0.2401 time to fit residues: 50.4428 Evaluate side-chains 149 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 135 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 445 GLN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain B residue 409 PHE Chi-restraints excluded: chain B residue 434 TRP Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 566 ASP Chi-restraints excluded: chain B residue 766 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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: 50.6202 > 50: distance: 4 - 9: 3.537 distance: 11 - 12: 5.917 distance: 11 - 17: 10.514 distance: 13 - 14: 11.328 distance: 14 - 15: 4.351 distance: 14 - 16: 15.435 distance: 17 - 18: 4.527 distance: 18 - 19: 5.335 distance: 19 - 20: 8.450 distance: 19 - 28: 11.235 distance: 21 - 22: 3.860 distance: 22 - 23: 3.230 distance: 23 - 24: 6.315 distance: 24 - 25: 7.407 distance: 25 - 26: 7.045 distance: 25 - 27: 4.266 distance: 28 - 29: 5.582 distance: 29 - 30: 6.383 distance: 29 - 32: 11.907 distance: 30 - 31: 18.143 distance: 30 - 39: 15.571 distance: 32 - 33: 10.680 distance: 33 - 34: 14.097 distance: 33 - 35: 23.867 distance: 34 - 36: 9.127 distance: 35 - 37: 8.173 distance: 36 - 38: 18.381 distance: 37 - 38: 18.821 distance: 39 - 40: 16.037 distance: 40 - 41: 8.423 distance: 40 - 43: 18.491 distance: 41 - 42: 13.204 distance: 41 - 48: 21.470 distance: 43 - 44: 13.181 distance: 44 - 45: 12.402 distance: 45 - 46: 20.020 distance: 45 - 47: 16.053 distance: 48 - 49: 20.889 distance: 49 - 50: 21.156 distance: 49 - 52: 10.440 distance: 50 - 51: 18.792 distance: 50 - 57: 7.789 distance: 52 - 53: 11.846 distance: 53 - 54: 13.851 distance: 54 - 55: 19.706 distance: 55 - 56: 19.918 distance: 57 - 58: 10.306 distance: 58 - 59: 15.137 distance: 59 - 60: 6.857 distance: 59 - 61: 6.373 distance: 61 - 62: 5.138 distance: 62 - 63: 9.951 distance: 62 - 65: 7.632 distance: 63 - 64: 7.672 distance: 63 - 72: 24.714 distance: 65 - 66: 4.164 distance: 66 - 67: 6.154 distance: 67 - 68: 8.130 distance: 68 - 69: 3.592 distance: 69 - 70: 4.788 distance: 69 - 71: 6.461 distance: 72 - 73: 12.738 distance: 73 - 74: 11.351 distance: 73 - 76: 13.814 distance: 74 - 75: 5.539 distance: 74 - 80: 12.049 distance: 76 - 77: 8.852 distance: 76 - 78: 7.218 distance: 77 - 79: 5.871 distance: 80 - 81: 5.187 distance: 81 - 82: 18.895 distance: 81 - 84: 13.956 distance: 82 - 83: 15.920 distance: 82 - 89: 4.605 distance: 84 - 85: 5.124 distance: 85 - 86: 16.963 distance: 86 - 87: 7.493 distance: 86 - 88: 25.922 distance: 89 - 90: 13.243 distance: 90 - 91: 8.443 distance: 90 - 93: 9.273 distance: 91 - 92: 5.352 distance: 91 - 100: 12.540 distance: 93 - 94: 7.022 distance: 94 - 95: 7.028 distance: 94 - 96: 8.607 distance: 95 - 97: 9.734 distance: 96 - 98: 8.612 distance: 97 - 99: 8.992 distance: 98 - 99: 6.001