Starting phenix.real_space_refine on Sat Jul 4 20:44:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tai_41136/07_2026/8tai_41136_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tai_41136/07_2026/8tai_41136.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tai_41136/07_2026/8tai_41136_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tai_41136/07_2026/8tai_41136_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tai_41136/07_2026/8tai_41136.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tai_41136/07_2026/8tai_41136.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.791 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: 6 Type Number sf(0) Gaussians Ca 3 9.91 5 S 71 5.16 5 C 7824 2.51 5 N 1906 2.21 5 O 2105 1.98 5 H 11607 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23516 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 11239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 705, 11239 Classifications: {'peptide': 705} Link IDs: {'PTRANS': 32, 'TRANS': 672} Chain breaks: 6 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'TYR:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 69 Chain: "B" Number of atoms: 12190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 12190 Classifications: {'peptide': 743} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 33, 'TRANS': 709} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 42 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 42 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.06, per 1000 atoms: 0.17 Number of scatterers: 23516 At special positions: 0 Unit cell: (135.079, 88.095, 119.977, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 3 19.99 S 71 16.00 O 2105 8.00 N 1906 7.00 C 7824 6.00 H 11607 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 372 " distance=2.04 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 365 " distance=2.04 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 807 " distance=2.03 Simple disulfide: pdb=" SG CYS A 352 " - pdb=" SG CYS A 356 " distance=2.03 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 601 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 372 " distance=2.03 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 365 " distance=2.03 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 807 " distance=2.03 Simple disulfide: pdb=" SG CYS B 352 " - pdb=" SG CYS B 356 " distance=2.03 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 601 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM23484 O5 NAG B 901 .*. O " rejected from bonding due to valence issues. Atom "HETATM23455 O5 NAG A 902 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 901 " - " ASN A 362 " " NAG A 902 " - " ASN A 785 " Time building additional restraints: 2.18 Conformation dependent library (CDL) restraints added in 603.0 milliseconds 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2758 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 6 sheets defined 63.5% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 92 through 108 Processing helix chain 'A' and resid 131 through 142 removed outlier: 3.700A pdb=" N MET A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 195 removed outlier: 5.732A pdb=" N ASN A 193 " --> pdb=" O SER A 190 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE A 195 " --> pdb=" O MET A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 220 Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 264 through 274 Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 284 through 292 Processing helix chain 'A' and resid 293 through 327 removed outlier: 3.972A pdb=" N LEU A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP A 327 " --> pdb=" O TYR A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 339 Processing helix chain 'A' and resid 364 through 375 removed outlier: 3.914A pdb=" N ILE A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE A 374 " --> pdb=" O LYS A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 408 removed outlier: 3.670A pdb=" N LEU A 380 " --> pdb=" O SER A 376 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL A 388 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N THR A 391 " --> pdb=" O GLY A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 486 Processing helix chain 'A' and resid 504 through 539 removed outlier: 3.875A pdb=" N THR A 526 " --> pdb=" O MET A 522 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE A 527 " --> pdb=" O ILE A 523 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU A 539 " --> pdb=" O ILE A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 573 removed outlier: 5.427A pdb=" N SER A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N CYS A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 638 removed outlier: 5.399A pdb=" N LEU A 627 " --> pdb=" O GLN A 623 " (cutoff:3.500A) Proline residue: A 628 - end of helix Processing helix chain 'A' and resid 648 through 656 removed outlier: 3.526A pdb=" N GLN A 652 " --> pdb=" O PRO A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 681 removed outlier: 4.103A pdb=" N PHE A 681 " --> pdb=" O PHE A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 710 removed outlier: 4.137A pdb=" N ARG A 701 " --> pdb=" O ILE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 747 removed outlier: 4.340A pdb=" N ILE A 728 " --> pdb=" O ALA A 724 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL A 738 " --> pdb=" O ILE A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 760 Processing helix chain 'A' and resid 775 through 781 Processing helix chain 'A' and resid 787 through 789 No H-bonds generated for 'chain 'A' and resid 787 through 789' Processing helix chain 'A' and resid 825 through 856 Processing helix chain 'A' and resid 861 through 870 removed outlier: 4.247A pdb=" N LYS A 865 " --> pdb=" O SER A 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 108 removed outlier: 3.626A pdb=" N ASN B 91 " --> pdb=" O LYS B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 142 Processing helix chain 'B' and resid 188 through 195 removed outlier: 3.641A pdb=" N MET B 192 " --> pdb=" O LYS B 189 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ASN B 193 " --> pdb=" O SER B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 204 removed outlier: 3.534A pdb=" N PHE B 204 " --> pdb=" O ARG B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 220 Processing helix chain 'B' and resid 232 through 239 removed outlier: 3.679A pdb=" N LEU B 236 " --> pdb=" O GLY B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 273 Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 284 through 293 Processing helix chain 'B' and resid 293 through 327 removed outlier: 3.928A pdb=" N TYR B 299 " --> pdb=" O LYS B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 339 Processing helix chain 'B' and resid 360 through 363 Processing helix chain 'B' and resid 364 through 375 Processing helix chain 'B' and resid 376 through 408 removed outlier: 3.745A pdb=" N LEU B 380 " --> pdb=" O SER B 376 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N THR B 391 " --> pdb=" O GLY B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 416 Processing helix chain 'B' and resid 456 through 488 removed outlier: 3.643A pdb=" N THR B 488 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 539 removed outlier: 3.944A pdb=" N THR B 526 " --> pdb=" O MET B 522 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE B 527 " --> pdb=" O ILE B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 573 removed outlier: 5.229A pdb=" N SER B 566 " --> pdb=" O ASN B 562 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N CYS B 567 " --> pdb=" O TYR B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 638 Proline residue: B 628 - end of helix Processing helix chain 'B' and resid 648 through 654 Processing helix chain 'B' and resid 664 through 681 removed outlier: 3.906A pdb=" N PHE B 681 " --> pdb=" O PHE B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 710 removed outlier: 4.361A pdb=" N ARG B 701 " --> pdb=" O ILE B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 747 removed outlier: 3.992A pdb=" N ILE B 728 " --> pdb=" O ALA B 724 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL B 737 " --> pdb=" O ALA B 733 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL B 738 " --> pdb=" O ILE B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 760 Processing helix chain 'B' and resid 775 through 781 Processing helix chain 'B' and resid 787 through 789 No H-bonds generated for 'chain 'B' and resid 787 through 789' Processing helix chain 'B' and resid 825 through 857 Processing helix chain 'B' and resid 861 through 868 Processing sheet with id=AA1, first strand: chain 'A' and resid 113 through 116 removed outlier: 3.571A pdb=" N ALA A 244 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 348 removed outlier: 3.682A pdb=" N TRP A 359 " --> pdb=" O MET A 348 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 784 through 785 Processing sheet with id=AA4, first strand: chain 'B' and resid 114 through 116 removed outlier: 3.578A pdb=" N PHE B 246 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA B 244 " --> pdb=" O VAL B 76 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 221 through 225 removed outlier: 4.207A pdb=" N GLN B 223 " --> pdb=" O LYS B 230 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS B 230 " --> pdb=" O GLN B 223 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET B 225 " --> pdb=" O VAL B 228 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 782 through 785 removed outlier: 3.535A pdb=" N TYR B 809 " --> pdb=" O SER B 782 " (cutoff:3.500A) 694 hydrogen bonds defined for protein. 2031 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: 5.43 Time building geometry restraints manager: 3.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 11595 1.03 - 1.23: 266 1.23 - 1.43: 5068 1.43 - 1.63: 6802 1.63 - 1.83: 112 Bond restraints: 23843 Sorted by residual: bond pdb=" N PHE B 52 " pdb=" H1 PHE B 52 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" CG1 ILE B 472 " pdb=" CD1 ILE B 472 " ideal model delta sigma weight residual 1.513 1.443 0.070 3.90e-02 6.57e+02 3.18e+00 bond pdb=" CG MET A 309 " pdb=" SD MET A 309 " ideal model delta sigma weight residual 1.803 1.764 0.039 2.50e-02 1.60e+03 2.38e+00 bond pdb=" C1 NAG A 901 " pdb=" O5 NAG A 901 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.57e+00 bond pdb=" C1 NAG B 901 " pdb=" O5 NAG B 901 " ideal model delta sigma weight residual 1.406 1.429 -0.023 2.00e-02 2.50e+03 1.35e+00 ... (remaining 23838 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.16: 42921 7.16 - 14.33: 3 14.33 - 21.49: 0 21.49 - 28.66: 0 28.66 - 35.82: 24 Bond angle restraints: 42948 Sorted by residual: angle pdb=" N ILE B 141 " pdb=" CA ILE B 141 " pdb=" HA ILE B 141 " ideal model delta sigma weight residual 110.00 74.18 35.82 3.00e+00 1.11e-01 1.43e+02 angle pdb=" CB GLN A 94 " pdb=" CA GLN A 94 " pdb=" HA GLN A 94 " ideal model delta sigma weight residual 109.00 73.21 35.79 3.00e+00 1.11e-01 1.42e+02 angle pdb=" C ARG A 235 " pdb=" CA ARG A 235 " pdb=" HA ARG A 235 " ideal model delta sigma weight residual 109.00 73.68 35.32 3.00e+00 1.11e-01 1.39e+02 angle pdb=" CB PHE B 215 " pdb=" CA PHE B 215 " pdb=" HA PHE B 215 " ideal model delta sigma weight residual 109.00 73.72 35.28 3.00e+00 1.11e-01 1.38e+02 angle pdb=" N ASP A 286 " pdb=" CA ASP A 286 " pdb=" HA ASP A 286 " ideal model delta sigma weight residual 110.00 74.87 35.13 3.00e+00 1.11e-01 1.37e+02 ... (remaining 42943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 10289 17.99 - 35.98: 864 35.98 - 53.97: 212 53.97 - 71.96: 47 71.96 - 89.95: 10 Dihedral angle restraints: 11422 sinusoidal: 6018 harmonic: 5404 Sorted by residual: dihedral pdb=" CB CYS A 338 " pdb=" SG CYS A 338 " pdb=" SG CYS A 365 " pdb=" CB CYS A 365 " ideal model delta sinusoidal sigma weight residual -86.00 -175.95 89.95 1 1.00e+01 1.00e-02 9.59e+01 dihedral pdb=" CB CYS A 352 " pdb=" SG CYS A 352 " pdb=" SG CYS A 356 " pdb=" CB CYS A 356 " ideal model delta sinusoidal sigma weight residual -86.00 -146.29 60.29 1 1.00e+01 1.00e-02 4.84e+01 dihedral pdb=" CB CYS B 352 " pdb=" SG CYS B 352 " pdb=" SG CYS B 356 " pdb=" CB CYS B 356 " ideal model delta sinusoidal sigma weight residual -86.00 -138.27 52.27 1 1.00e+01 1.00e-02 3.73e+01 ... (remaining 11419 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.309: 1812 0.309 - 0.618: 8 0.618 - 0.927: 0 0.927 - 1.236: 0 1.236 - 1.545: 1 Chirality restraints: 1821 Sorted by residual: chirality pdb=" C4 NAG A 901 " pdb=" C3 NAG A 901 " pdb=" C5 NAG A 901 " pdb=" O4 NAG A 901 " both_signs ideal model delta sigma weight residual False -2.53 -0.99 -1.55 2.00e-01 2.50e+01 5.97e+01 chirality pdb=" C1 NAG A 902 " pdb=" ND2 ASN A 785 " pdb=" C2 NAG A 902 " pdb=" O5 NAG A 902 " both_signs ideal model delta sigma weight residual False -2.40 -2.99 0.59 2.00e-01 2.50e+01 8.83e+00 chirality pdb=" CA CYS A 356 " pdb=" N CYS A 356 " pdb=" C CYS A 356 " pdb=" CB CYS A 356 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.24e+00 ... (remaining 1818 not shown) Planarity restraints: 3437 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 785 " -0.230 2.00e-02 2.50e+03 2.26e-01 6.37e+02 pdb=" CG ASN A 785 " 0.075 2.00e-02 2.50e+03 pdb=" OD1 ASN A 785 " 0.064 2.00e-02 2.50e+03 pdb=" ND2 ASN A 785 " 0.352 2.00e-02 2.50e+03 pdb=" C1 NAG A 902 " -0.262 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS A 349 " 0.039 5.00e-02 4.00e+02 5.96e-02 5.68e+00 pdb=" N PRO A 350 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 350 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 350 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 796 " 0.039 5.00e-02 4.00e+02 5.96e-02 5.68e+00 pdb=" N PRO B 797 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 797 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 797 " 0.033 5.00e-02 4.00e+02 ... (remaining 3434 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1548 2.20 - 2.80: 46822 2.80 - 3.40: 64549 3.40 - 4.00: 80569 4.00 - 4.60: 125381 Nonbonded interactions: 318869 Sorted by model distance: nonbonded pdb=" O SER A 278 " pdb="HH21 ARG A 701 " model vdw 1.598 2.450 nonbonded pdb=" HA ARG B 235 " pdb=" HB3 ARG B 235 " model vdw 1.602 1.952 nonbonded pdb=" HA PHE B 215 " pdb=" HB3 PHE B 215 " model vdw 1.608 1.952 nonbonded pdb=" ND2 ASN B 362 " pdb=" O5 NAG B 901 " model vdw 1.625 2.950 nonbonded pdb=" HA ASP A 286 " pdb=" HB2 ASP A 286 " model vdw 1.630 1.952 ... (remaining 318864 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 59 through 868 or resid 901 through 902 or resid 904)) selection = (chain 'B' and (resid 59 through 82 or resid 91 through 93 or (resid 94 through \ 97 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 98 or (resid 99 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 100 or (resid 101 through 107 and (name N or na \ me CA or name C or name O or name CB or name H or name HA )) or resid 108 throug \ h 115 or (resid 116 through 126 and (name N or name CA or name C or name O or na \ me CB or name H or name HA )) or resid 127 through 128 or (resid 129 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 130 \ through 134 or (resid 135 through 137 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 138 through 140 or (resid 141 and ( \ name N or name CA or name C or name O or name CB or name H or name HA )) or resi \ d 142 or (resid 143 and (name N or name CA or name C or name O or name CB or nam \ e H or name HA )) or resid 144 through 147 or resid 185 through 222 or resid 232 \ through 235 or (resid 236 through 239 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 240 or (resid 241 and (name N or n \ ame CA or name C or name O or name CB or name H or name HA )) or resid 242 throu \ gh 423 or resid 457 through 487 or resid 503 through 589 or (resid 590 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 59 \ 1 through 638 or resid 645 through 660 or (resid 661 and (name N or name CA or n \ ame C or name O or name CB or name H or name HA )) or resid 662 through 777 or ( \ resid 778 and (name N or name CA or name C or name O or name CB or name CG or na \ me OD1 or name ND2 or name H or name HA or name HB2 or name HB3)) or resid 779 t \ hrough 784 or (resid 785 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name ND2 or name H or name HA or name HB2 or name HB3)) \ or resid 786 through 857 or (resid 858 and (name N or name CA or name C or name \ O or name CB or name CG or name CD )) or (resid 859 and (name N or name CA or n \ ame C or name O or name CB or name CG or name OD1 or name OD2)) or resid 860 thr \ ough 868 or resid 902 through 903 or resid 905)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 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: 0.160 Extract box with map and model: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.540 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 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 : 0.004 0.328 12248 Z= 0.205 Angle : 0.689 50.568 16633 Z= 0.337 Chirality : 0.059 1.545 1821 Planarity : 0.004 0.060 2064 Dihedral : 13.720 89.498 4503 Min Nonbonded Distance : 1.625 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.22), residues: 1426 helix: 2.26 (0.17), residues: 822 sheet: -0.83 (0.78), residues: 58 loop : -1.16 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 98 TYR 0.015 0.001 TYR A 306 PHE 0.015 0.001 PHE B 73 TRP 0.023 0.001 TRP B 132 HIS 0.004 0.001 HIS B 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (12236) covalent geometry : angle 0.55833 / 0.31 (16607) SS BOND : bond 0.00256 / 0.16 ( 10) SS BOND : angle 1.87441 / 1.07 ( 20) hydrogen bonds : bond 0.12224 / 8.38 ( 694) hydrogen bonds : angle 5.11064 / 3.79 ( 2031) link_NAG-ASN : bond 0.23200 / 16.57 ( 2) link_NAG-ASN : angle 21.00944 / 6.81 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 184 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.643 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 396 PHE cc_start: 0.7208 (m-10) cc_final: 0.6822 (m-10) REVERT: A 479 LEU cc_start: 0.9037 (mt) cc_final: 0.8786 (mt) REVERT: B 235 ARG cc_start: 0.7989 (ttm-80) cc_final: 0.7402 (ttm110) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.2136 time to fit residues: 59.8638 Evaluate side-chains 160 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 30.0000 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 351 GLN B 104 ASN B 621 ASN B 652 GLN ** B 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.212122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.156870 restraints weight = 42244.307| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.77 r_work: 0.3541 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12248 Z= 0.124 Angle : 0.531 7.894 16633 Z= 0.288 Chirality : 0.045 0.411 1821 Planarity : 0.005 0.054 2064 Dihedral : 5.503 53.241 1722 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.03 % Allowed : 5.40 % Favored : 93.57 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.22), residues: 1426 helix: 2.23 (0.17), residues: 837 sheet: -0.75 (0.70), residues: 64 loop : -1.22 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 98 TYR 0.013 0.001 TYR B 138 PHE 0.015 0.001 PHE A 461 TRP 0.011 0.001 TRP B 132 HIS 0.003 0.001 HIS B 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (12236) covalent geometry : angle 0.52632 / 0.29 (16607) SS BOND : bond 0.00251 / 0.17 ( 10) SS BOND : angle 1.05409 / 0.52 ( 20) hydrogen bonds : bond 0.04950 / 3.39 ( 694) hydrogen bonds : angle 4.54143 / 3.41 ( 2031) link_NAG-ASN : bond 0.00619 / 0.44 ( 2) link_NAG-ASN : angle 3.38200 / 1.60 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 183 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 170 time to evaluate : 0.660 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: A 479 LEU cc_start: 0.9286 (mt) cc_final: 0.9029 (mt) REVERT: B 143 HIS cc_start: 0.7447 (m170) cc_final: 0.7206 (m-70) REVERT: B 235 ARG cc_start: 0.8175 (ttm-80) cc_final: 0.7615 (ttm110) outliers start: 13 outliers final: 10 residues processed: 174 average time/residue: 0.2170 time to fit residues: 57.2250 Evaluate side-chains 169 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 159 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 624 GLU Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 717 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 24 optimal weight: 4.9990 chunk 125 optimal weight: 0.0370 chunk 87 optimal weight: 0.5980 chunk 123 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 overall best weight: 1.2862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 621 ASN B 730 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.207343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.144863 restraints weight = 40712.015| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.52 r_work: 0.3590 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12248 Z= 0.128 Angle : 0.508 7.938 16633 Z= 0.276 Chirality : 0.045 0.417 1821 Planarity : 0.004 0.054 2064 Dihedral : 5.131 54.437 1722 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.35 % Allowed : 6.43 % Favored : 92.22 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.22), residues: 1426 helix: 2.30 (0.17), residues: 832 sheet: -0.88 (0.69), residues: 64 loop : -1.21 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 98 TYR 0.012 0.001 TYR B 77 PHE 0.013 0.001 PHE A 461 TRP 0.011 0.001 TRP B 132 HIS 0.003 0.001 HIS B 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (12236) covalent geometry : angle 0.50459 / 0.28 (16607) SS BOND : bond 0.00148 / 0.10 ( 10) SS BOND : angle 0.73707 / 0.38 ( 20) hydrogen bonds : bond 0.04757 / 3.24 ( 694) hydrogen bonds : angle 4.33515 / 3.23 ( 2031) link_NAG-ASN : bond 0.00098 / 0.07 ( 2) link_NAG-ASN : angle 3.06911 / 1.52 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 180 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 163 time to evaluate : 0.612 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: A 753 ARG cc_start: 0.8578 (ptp90) cc_final: 0.7641 (ptp90) REVERT: B 235 ARG cc_start: 0.8178 (ttm-80) cc_final: 0.7624 (ttm110) outliers start: 17 outliers final: 13 residues processed: 171 average time/residue: 0.2172 time to fit residues: 55.8776 Evaluate side-chains 168 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 155 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 624 GLU Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 717 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 142 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 89 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 2 optimal weight: 0.0470 chunk 30 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN B 620 ASN B 621 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.207172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.144619 restraints weight = 40676.694| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.52 r_work: 0.3591 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3456 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12248 Z= 0.122 Angle : 0.500 7.942 16633 Z= 0.270 Chirality : 0.044 0.417 1821 Planarity : 0.004 0.054 2064 Dihedral : 4.831 55.911 1722 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.43 % Allowed : 6.90 % Favored : 91.67 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.22), residues: 1426 helix: 2.38 (0.17), residues: 831 sheet: -1.32 (0.63), residues: 74 loop : -1.22 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 289 TYR 0.011 0.001 TYR B 138 PHE 0.012 0.001 PHE B 675 TRP 0.009 0.001 TRP B 132 HIS 0.003 0.001 HIS B 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (12236) covalent geometry : angle 0.49657 / 0.27 (16607) SS BOND : bond 0.00104 / 0.07 ( 10) SS BOND : angle 0.59620 / 0.31 ( 20) hydrogen bonds : bond 0.04536 / 3.10 ( 694) hydrogen bonds : angle 4.22118 / 3.14 ( 2031) link_NAG-ASN : bond 0.00110 / 0.08 ( 2) link_NAG-ASN : angle 2.86672 / 1.47 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 180 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 0.519 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: B 104 ASN cc_start: 0.7801 (m-40) cc_final: 0.7384 (m-40) REVERT: B 221 LYS cc_start: 0.8357 (ptmt) cc_final: 0.7681 (ttpt) REVERT: B 235 ARG cc_start: 0.8254 (ttm-80) cc_final: 0.7679 (ttm110) outliers start: 18 outliers final: 15 residues processed: 170 average time/residue: 0.1940 time to fit residues: 49.4788 Evaluate side-chains 170 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 624 GLU Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 717 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 51 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 47 optimal weight: 20.0000 chunk 91 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 620 ASN B 730 GLN B 785 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.200854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.136845 restraints weight = 40672.950| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.49 r_work: 0.3495 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 12248 Z= 0.290 Angle : 0.610 7.469 16633 Z= 0.338 Chirality : 0.049 0.429 1821 Planarity : 0.005 0.051 2064 Dihedral : 5.174 55.338 1722 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.21 % Favored : 95.72 % Rotamer: Outliers : 1.43 % Allowed : 8.57 % Favored : 90.00 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.22), residues: 1426 helix: 1.84 (0.17), residues: 826 sheet: -1.73 (0.61), residues: 75 loop : -1.46 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 753 TYR 0.014 0.002 TYR B 291 PHE 0.026 0.002 PHE B 675 TRP 0.018 0.002 TRP B 132 HIS 0.006 0.002 HIS B 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00679 / 0.29 (12236) covalent geometry : angle 0.60771 / 0.34 (16607) SS BOND : bond 0.00262 / 0.14 ( 10) SS BOND : angle 1.02996 / 0.67 ( 20) hydrogen bonds : bond 0.05815 / 3.96 ( 694) hydrogen bonds : angle 4.52791 / 3.35 ( 2031) link_NAG-ASN : bond 0.00169 / 0.11 ( 2) link_NAG-ASN : angle 2.68415 / 1.41 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 176 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 158 time to evaluate : 0.524 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: B 104 ASN cc_start: 0.7800 (m-40) cc_final: 0.7551 (m110) REVERT: B 235 ARG cc_start: 0.8286 (ttm-80) cc_final: 0.7696 (ttm110) outliers start: 18 outliers final: 17 residues processed: 166 average time/residue: 0.1999 time to fit residues: 49.8178 Evaluate side-chains 170 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 624 GLU Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 714 MET Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 717 GLU Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 805 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.9613 > 50: distance: 197 - 212: 8.765 distance: 212 - 213: 19.998 distance: 212 - 223: 20.697 distance: 213 - 214: 24.289 distance: 213 - 216: 8.973 distance: 213 - 224: 9.124 distance: 214 - 215: 12.242 distance: 214 - 232: 29.784 distance: 216 - 217: 12.108 distance: 216 - 225: 20.098 distance: 216 - 226: 24.598 distance: 217 - 218: 12.578 distance: 217 - 219: 6.518 distance: 218 - 220: 4.319 distance: 218 - 227: 5.025 distance: 219 - 221: 4.689 distance: 219 - 228: 5.663 distance: 220 - 222: 10.799 distance: 220 - 229: 4.824 distance: 221 - 222: 6.661 distance: 221 - 230: 7.024 distance: 232 - 233: 8.290 distance: 232 - 240: 21.550 distance: 233 - 234: 7.302 distance: 233 - 236: 3.043 distance: 233 - 241: 3.387 distance: 234 - 235: 7.489 distance: 234 - 246: 10.714 distance: 235 - 284: 10.005 distance: 236 - 237: 8.998 distance: 236 - 242: 11.141 distance: 236 - 243: 3.840 distance: 237 - 238: 12.006 distance: 237 - 239: 12.885 distance: 239 - 244: 5.114 distance: 246 - 247: 9.120 distance: 246 - 252: 18.447 distance: 247 - 248: 6.829 distance: 247 - 250: 9.646 distance: 247 - 253: 9.410 distance: 248 - 260: 4.720 distance: 249 - 308: 15.935 distance: 250 - 251: 12.006 distance: 250 - 254: 3.772 distance: 250 - 255: 10.089 distance: 251 - 252: 9.910 distance: 251 - 256: 12.643 distance: 251 - 257: 12.757 distance: 252 - 258: 10.870 distance: 252 - 259: 4.148 distance: 260 - 261: 5.144 distance: 260 - 265: 13.534 distance: 261 - 262: 4.989 distance: 261 - 264: 6.007 distance: 261 - 266: 10.015 distance: 262 - 263: 8.067 distance: 262 - 270: 3.529 distance: 263 - 319: 22.806 distance: 264 - 267: 9.263 distance: 264 - 268: 10.005 distance: 264 - 269: 3.064 distance: 270 - 271: 3.349 distance: 271 - 272: 7.139 distance: 271 - 274: 6.208 distance: 271 - 278: 4.368 distance: 272 - 273: 5.607 distance: 272 - 284: 8.490 distance: 273 - 343: 9.819 distance: 274 - 275: 4.999 distance: 274 - 276: 10.780 distance: 274 - 279: 7.592 distance: 276 - 281: 9.912 distance: 276 - 282: 5.241 distance: 276 - 283: 8.991 distance: 284 - 285: 3.347 distance: 284 - 295: 20.747 distance: 285 - 286: 6.998 distance: 285 - 288: 8.400 distance: 285 - 296: 7.321 distance: 286 - 287: 14.217 distance: 286 - 308: 7.049 distance: 287 - 362: 12.604 distance: 288 - 289: 13.413 distance: 288 - 297: 10.814 distance: 288 - 298: 9.068 distance: 289 - 290: 5.190 distance: 289 - 300: 10.098 distance: 290 - 291: 7.412 distance: 290 - 301: 7.571 distance: 291 - 292: 5.070 distance: 291 - 303: 11.749 distance: 292 - 293: 10.298 distance: 292 - 294: 9.092 distance: 293 - 304: 5.434 distance: 294 - 306: 7.156 distance: 294 - 307: 3.199 distance: 308 - 309: 4.472 distance: 308 - 314: 7.506 distance: 309 - 310: 5.793 distance: 309 - 312: 12.560 distance: 309 - 315: 10.294 distance: 310 - 311: 9.610 distance: 310 - 319: 8.198 distance: 311 - 378: 10.721 distance: 312 - 313: 5.133 distance: 312 - 316: 11.621 distance: 312 - 317: 12.184 distance: 313 - 318: 20.889 distance: 319 - 320: 7.798 distance: 319 - 330: 7.266 distance: 320 - 321: 4.159 distance: 320 - 323: 8.661 distance: 320 - 331: 6.762 distance: 321 - 322: 10.323 distance: 321 - 343: 10.505 distance: 322 - 390: 23.263 distance: 323 - 333: 3.450 distance: 324 - 325: 8.142 distance: 324 - 334: 14.514 distance: 324 - 335: 11.038 distance: 325 - 326: 5.282 distance: 325 - 336: 7.029 distance: 325 - 337: 7.348 distance: 326 - 327: 4.698 distance: 326 - 338: 7.045 distance: 327 - 328: 5.242 distance: 327 - 329: 8.977 distance: 328 - 339: 5.734 distance: 328 - 340: 4.893 distance: 329 - 341: 3.689 distance: 329 - 342: 4.416 distance: 343 - 344: 6.186 distance: 343 - 351: 5.084 distance: 344 - 345: 6.986 distance: 344 - 347: 3.174 distance: 344 - 352: 7.166 distance: 345 - 346: 11.788 distance: 345 - 362: 11.409 distance: 346 - 402: 20.126 distance: 347 - 348: 4.525 distance: 347 - 349: 10.958 distance: 347 - 353: 6.341 distance: 348 - 350: 11.295 distance: 348 - 355: 11.686 distance: 349 - 356: 27.728 distance: 349 - 357: 16.804 distance: 349 - 358: 19.564 distance: 350 - 360: 6.460 distance: 350 - 361: 9.264 distance: 362 - 369: 9.880 distance: 363 - 364: 3.278 distance: 363 - 366: 3.470 distance: 363 - 370: 3.667 distance: 364 - 365: 7.198 distance: 364 - 378: 3.997 distance: 365 - 420: 8.875 distance: 366 - 367: 6.325 distance: 366 - 368: 4.384 distance: 366 - 371: 5.938 distance: 367 - 372: 3.290 distance: 367 - 373: 6.333 distance: 367 - 374: 7.832 distance: 368 - 375: 7.514 distance: 368 - 376: 3.080 distance: 368 - 377: 8.273