Starting phenix.real_space_refine on Sat Jul 4 16:47:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lc6_23269/07_2026/7lc6_23269_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lc6_23269/07_2026/7lc6_23269.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lc6_23269/07_2026/7lc6_23269.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lc6_23269/07_2026/7lc6_23269.map" model { file = "/net/cci-nas-00/data/ceres_data/7lc6_23269/07_2026/7lc6_23269_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lc6_23269/07_2026/7lc6_23269_trim.cif" } resolution = 3.7 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= 0.012 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: 8 Type Number sf(0) Gaussians K 1 8.98 5 P 1 5.49 5 Mg 1 5.21 5 S 60 5.16 5 C 6954 2.51 5 N 1814 2.21 5 O 1954 1.98 5 H 11106 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 21891 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 8445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 8445 Classifications: {'peptide': 557} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 25, 'TRANS': 531} Chain: "B" Number of atoms: 10166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 672, 10166 Classifications: {'peptide': 672} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 646} Chain: "C" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 2815 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 13, 'TRANS': 171} Chain: "D" Number of atoms: 402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 402 Classifications: {'peptide': 26} Link IDs: {'TRANS': 25} Chain: "A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Ad-hoc single atom residues: {' K': 1} Unusual residues: {'9Y0': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 12 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 3.89, per 1000 atoms: 0.18 Number of scatterers: 21891 At special positions: 0 Unit cell: (82.004, 105.742, 169.403, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) K 1 19.00 S 60 16.00 P 1 15.00 Mg 1 11.99 O 1954 8.00 N 1814 7.00 C 6954 6.00 H 11106 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.65 Conformation dependent library (CDL) restraints added in 490.1 milliseconds 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2620 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 8 sheets defined 63.7% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 1 through 31 removed outlier: 3.534A pdb=" N LEU A 7 " --> pdb=" O ALA A 3 " (cutoff:3.500A) Proline residue: A 22 - end of helix Processing helix chain 'A' and resid 41 through 51 Processing helix chain 'A' and resid 58 through 83 Processing helix chain 'A' and resid 98 through 111 Processing helix chain 'A' and resid 127 through 157 removed outlier: 3.699A pdb=" N THR A 134 " --> pdb=" O MET A 130 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N VAL A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN A 136 " --> pdb=" O GLY A 132 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA A 141 " --> pdb=" O ASN A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 176 Processing helix chain 'A' and resid 177 through 193 removed outlier: 4.200A pdb=" N VAL A 181 " --> pdb=" O VAL A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 229 Processing helix chain 'A' and resid 248 through 274 removed outlier: 4.938A pdb=" N ILE A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Proline residue: A 263 - end of helix removed outlier: 3.706A pdb=" N MET A 274 " --> pdb=" O PHE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 305 removed outlier: 4.156A pdb=" N GLY A 280 " --> pdb=" O ASP A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 313 removed outlier: 4.078A pdb=" N ALA A 311 " --> pdb=" O PRO A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 342 Processing helix chain 'A' and resid 350 through 354 Processing helix chain 'A' and resid 355 through 368 Proline residue: A 362 - end of helix Processing helix chain 'A' and resid 377 through 399 Processing helix chain 'A' and resid 410 through 437 removed outlier: 3.753A pdb=" N THR A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) Proline residue: A 425 - end of helix Processing helix chain 'A' and resid 438 through 444 removed outlier: 3.615A pdb=" N ALA A 444 " --> pdb=" O ALA A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 465 removed outlier: 3.899A pdb=" N PHE A 453 " --> pdb=" O GLY A 449 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL A 456 " --> pdb=" O GLY A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 510 Proline residue: A 499 - end of helix removed outlier: 3.801A pdb=" N SER A 509 " --> pdb=" O GLY A 505 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS A 510 " --> pdb=" O SER A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 550 Proline residue: A 545 - end of helix Processing helix chain 'A' and resid 550 through 557 Processing helix chain 'B' and resid 12 through 24 Processing helix chain 'B' and resid 26 through 31 removed outlier: 3.884A pdb=" N TRP B 31 " --> pdb=" O PRO B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 55 Processing helix chain 'B' and resid 61 through 99 removed outlier: 3.573A pdb=" N SER B 65 " --> pdb=" O ASN B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 126 Processing helix chain 'B' and resid 155 through 160 removed outlier: 3.807A pdb=" N THR B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 210 Processing helix chain 'B' and resid 215 through 247 removed outlier: 3.570A pdb=" N LEU B 221 " --> pdb=" O ASN B 217 " (cutoff:3.500A) Proline residue: B 241 - end of helix removed outlier: 3.578A pdb=" N GLY B 246 " --> pdb=" O PHE B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 263 Processing helix chain 'B' and resid 265 through 284 removed outlier: 4.173A pdb=" N GLY B 269 " --> pdb=" O THR B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 299 Processing helix chain 'B' and resid 329 through 341 Processing helix chain 'B' and resid 346 through 360 Processing helix chain 'B' and resid 397 through 408 Processing helix chain 'B' and resid 414 through 426 Processing helix chain 'B' and resid 452 through 463 Processing helix chain 'B' and resid 474 through 486 Processing helix chain 'B' and resid 495 through 508 Processing helix chain 'B' and resid 522 through 529 Processing helix chain 'B' and resid 539 through 544 Processing helix chain 'B' and resid 555 through 595 removed outlier: 4.066A pdb=" N ILE B 559 " --> pdb=" O PRO B 555 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU B 560 " --> pdb=" O THR B 556 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE B 580 " --> pdb=" O THR B 576 " (cutoff:3.500A) Proline residue: B 592 - end of helix Processing helix chain 'B' and resid 599 through 605 removed outlier: 3.849A pdb=" N ASN B 603 " --> pdb=" O TYR B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 638 Proline residue: B 633 - end of helix removed outlier: 3.528A pdb=" N GLY B 638 " --> pdb=" O LEU B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 680 Proline residue: B 665 - end of helix Processing helix chain 'C' and resid 5 through 20 Processing helix chain 'C' and resid 20 through 34 removed outlier: 3.571A pdb=" N LEU C 24 " --> pdb=" O GLY C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 39 Processing helix chain 'C' and resid 91 through 109 removed outlier: 3.923A pdb=" N ASP C 95 " --> pdb=" O ASN C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 122 removed outlier: 3.772A pdb=" N VAL C 121 " --> pdb=" O PRO C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 140 removed outlier: 3.581A pdb=" N GLN C 140 " --> pdb=" O ALA C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 149 removed outlier: 3.636A pdb=" N VAL C 144 " --> pdb=" O GLN C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 162 Processing helix chain 'C' and resid 178 through 188 Processing helix chain 'D' and resid 3 through 25 Processing sheet with id=AA1, first strand: chain 'A' and resid 204 through 205 Processing sheet with id=AA2, first strand: chain 'A' and resid 403 through 404 Processing sheet with id=AA3, first strand: chain 'B' and resid 119 through 121 removed outlier: 4.019A pdb=" N ARG B 107 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N VAL B 188 " --> pdb=" O ILE B 147 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE B 147 " --> pdb=" O VAL B 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 165 through 167 removed outlier: 3.910A pdb=" N ARG B 181 " --> pdb=" O ASP B 154 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 466 through 470 removed outlier: 5.789A pdb=" N LEU B 304 " --> pdb=" O VAL B 468 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ILE B 470 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU B 306 " --> pdb=" O ILE B 470 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL B 303 " --> pdb=" O ALA B 514 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N THR B 516 " --> pdb=" O VAL B 303 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU B 305 " --> pdb=" O THR B 516 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL B 513 " --> pdb=" O VAL B 531 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N VAL B 533 " --> pdb=" O VAL B 513 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N MET B 515 " --> pdb=" O VAL B 533 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 323 through 324 removed outlier: 6.631A pdb=" N VAL B 433 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL B 442 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LEU B 431 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ALA B 444 " --> pdb=" O THR B 429 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N THR B 429 " --> pdb=" O ALA B 444 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 42 through 45 removed outlier: 6.964A pdb=" N ILE C 43 " --> pdb=" O ARG C 50 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 131 through 132 removed outlier: 3.552A pdb=" N ILE C 132 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL C 175 " --> pdb=" O GLN C 164 " (cutoff:3.500A) 673 hydrogen bonds defined for protein. 1974 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: 5.11 Time building geometry restraints manager: 3.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 11094 1.02 - 1.22: 17 1.22 - 1.42: 4344 1.42 - 1.62: 6518 1.62 - 1.82: 110 Bond restraints: 22083 Sorted by residual: bond pdb=" C13 9Y0 A 602 " pdb=" C14 9Y0 A 602 " ideal model delta sigma weight residual 1.333 1.545 -0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" ND2 ASN B 624 " pdb="HD22 ASN B 624 " ideal model delta sigma weight residual 0.860 0.977 -0.117 2.00e-02 2.50e+03 3.41e+01 bond pdb=" ND2 ASN B 624 " pdb="HD21 ASN B 624 " ideal model delta sigma weight residual 0.860 0.976 -0.116 2.00e-02 2.50e+03 3.38e+01 bond pdb=" C5 9Y0 A 602 " pdb=" O5 9Y0 A 602 " ideal model delta sigma weight residual 1.326 1.421 -0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" C21 9Y0 A 602 " pdb=" O7 9Y0 A 602 " ideal model delta sigma weight residual 1.330 1.419 -0.089 2.00e-02 2.50e+03 2.00e+01 ... (remaining 22078 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.27: 39975 5.27 - 10.54: 84 10.54 - 15.82: 7 15.82 - 21.09: 0 21.09 - 26.36: 1 Bond angle restraints: 40067 Sorted by residual: angle pdb=" C11 9Y0 A 602 " pdb=" C12 9Y0 A 602 " pdb=" C13 9Y0 A 602 " ideal model delta sigma weight residual 111.77 85.41 26.36 3.00e+00 1.11e-01 7.72e+01 angle pdb=" C12 9Y0 A 602 " pdb=" C13 9Y0 A 602 " pdb=" C14 9Y0 A 602 " ideal model delta sigma weight residual 127.16 112.84 14.32 3.00e+00 1.11e-01 2.28e+01 angle pdb=" CD1 ILE C 141 " pdb=" CG1 ILE C 141 " pdb="HG13 ILE C 141 " ideal model delta sigma weight residual 108.00 94.49 13.51 3.00e+00 1.11e-01 2.03e+01 angle pdb=" CB ILE C 141 " pdb=" CG1 ILE C 141 " pdb=" CD1 ILE C 141 " ideal model delta sigma weight residual 113.80 122.90 -9.10 2.10e+00 2.27e-01 1.88e+01 angle pdb=" N ASN A 32 " pdb=" CA ASN A 32 " pdb=" C ASN A 32 " ideal model delta sigma weight residual 112.59 107.49 5.10 1.22e+00 6.72e-01 1.75e+01 ... (remaining 40062 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.91: 9918 28.91 - 57.83: 379 57.83 - 86.74: 39 86.74 - 115.65: 4 115.65 - 144.57: 5 Dihedral angle restraints: 10345 sinusoidal: 5701 harmonic: 4644 Sorted by residual: dihedral pdb=" C23 9Y0 A 602 " pdb=" C21 9Y0 A 602 " pdb=" C22 9Y0 A 602 " pdb=" O7 9Y0 A 602 " ideal model delta sinusoidal sigma weight residual 181.02 36.45 144.57 1 3.00e+01 1.11e-03 1.94e+01 dihedral pdb=" C23 9Y0 A 602 " pdb=" C21 9Y0 A 602 " pdb=" C22 9Y0 A 602 " pdb=" O6 9Y0 A 602 " ideal model delta sinusoidal sigma weight residual 0.61 -143.51 144.12 1 3.00e+01 1.11e-03 1.93e+01 dihedral pdb=" C3 9Y0 A 602 " pdb=" O1 9Y0 A 602 " pdb=" P 9Y0 A 602 " pdb=" O3 9Y0 A 602 " ideal model delta sinusoidal sigma weight residual 291.93 150.21 141.72 1 3.00e+01 1.11e-03 1.90e+01 ... (remaining 10342 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1323 0.060 - 0.120: 395 0.120 - 0.180: 65 0.180 - 0.240: 11 0.240 - 0.300: 4 Chirality restraints: 1798 Sorted by residual: chirality pdb=" CG LEU B 225 " pdb=" CB LEU B 225 " pdb=" CD1 LEU B 225 " pdb=" CD2 LEU B 225 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CB ILE A 148 " pdb=" CA ILE A 148 " pdb=" CG1 ILE A 148 " pdb=" CG2 ILE A 148 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CA THR A 424 " pdb=" N THR A 424 " pdb=" C THR A 424 " pdb=" CB THR A 424 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 1795 not shown) Planarity restraints: 3264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 624 " -0.313 2.00e-02 2.50e+03 3.84e-01 2.21e+03 pdb=" CG ASN B 624 " 0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN B 624 " 0.303 2.00e-02 2.50e+03 pdb=" ND2 ASN B 624 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN B 624 " -0.595 2.00e-02 2.50e+03 pdb="HD22 ASN B 624 " 0.581 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 9Y0 A 602 " 0.039 2.00e-02 2.50e+03 3.09e-01 9.57e+02 pdb=" C13 9Y0 A 602 " 0.203 2.00e-02 2.50e+03 pdb=" C14 9Y0 A 602 " -0.515 2.00e-02 2.50e+03 pdb=" C15 9Y0 A 602 " 0.274 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 86 " 0.048 2.00e-02 2.50e+03 8.93e-02 1.20e+02 pdb=" CG ASN C 86 " -0.096 2.00e-02 2.50e+03 pdb=" OD1 ASN C 86 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN C 86 " 0.152 2.00e-02 2.50e+03 pdb="HD21 ASN C 86 " 0.022 2.00e-02 2.50e+03 pdb="HD22 ASN C 86 " -0.112 2.00e-02 2.50e+03 ... (remaining 3261 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.33: 6078 2.33 - 3.03: 62479 3.03 - 3.73: 79473 3.73 - 4.44: 122643 4.44 - 5.14: 191216 Nonbonded interactions: 461889 Sorted by model distance: nonbonded pdb=" O ASP B 329 " pdb=" H THR B 332 " model vdw 1.626 2.450 nonbonded pdb=" HZ1 LYS B 499 " pdb=" OD2 ASP B 522 " model vdw 1.644 2.450 nonbonded pdb=" OE1 GLN B 601 " pdb=" H GLN B 601 " model vdw 1.651 2.450 nonbonded pdb=" O ARG C 68 " pdb=" HH TYR C 77 " model vdw 1.667 2.450 nonbonded pdb=" OE2 GLU A 121 " pdb=" HG SER C 82 " model vdw 1.670 2.450 ... (remaining 461884 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.590 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: 0.170 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 21.300 Find NCS groups from input model: 0.060 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 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 : 0.010 0.212 10977 Z= 0.439 Angle : 1.124 26.360 14930 Z= 0.623 Chirality : 0.058 0.300 1798 Planarity : 0.011 0.309 1891 Dihedral : 12.510 144.567 3923 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 1.51 % Allowed : 5.15 % Favored : 93.35 % 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: -2.96 (0.18), residues: 1432 helix: -1.05 (0.15), residues: 857 sheet: -3.62 (0.38), residues: 97 loop : -3.13 (0.22), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 107 TYR 0.035 0.004 TYR C 22 PHE 0.036 0.005 PHE A 392 TRP 0.027 0.003 TRP A 176 HIS 0.009 0.002 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00986 / 0.44 (10977) covalent geometry : angle 1.12418 / 0.62 (14930) hydrogen bonds : bond 0.13335 / 8.82 ( 673) hydrogen bonds : angle 6.53817 / 4.71 ( 1974) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 175 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ASN cc_start: 0.8322 (OUTLIER) cc_final: 0.7860 (t0) REVERT: A 321 GLU cc_start: 0.7800 (tp30) cc_final: 0.7295 (tm-30) REVERT: B 190 GLU cc_start: 0.7016 (tt0) cc_final: 0.6370 (tp30) REVERT: B 192 SER cc_start: 0.7970 (t) cc_final: 0.7450 (m) REVERT: B 350 ARG cc_start: 0.8421 (mtm-85) cc_final: 0.7633 (mmm160) REVERT: C 48 THR cc_start: 0.6938 (p) cc_final: 0.6504 (p) REVERT: C 111 ASP cc_start: 0.7698 (m-30) cc_final: 0.7314 (t0) outliers start: 17 outliers final: 5 residues processed: 190 average time/residue: 0.2819 time to fit residues: 72.5088 Evaluate side-chains 105 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ASN Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 453 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 GLN ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 ASN B 316 ASN B 390 ASN B 582 ASN C 58 ASN C 135 GLN C 164 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.116273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.092598 restraints weight = 91323.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.094127 restraints weight = 38724.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.094734 restraints weight = 23888.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.094828 restraints weight = 19322.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.095050 restraints weight = 19025.080| |-----------------------------------------------------------------------------| r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10977 Z= 0.148 Angle : 0.610 6.745 14930 Z= 0.321 Chirality : 0.039 0.153 1798 Planarity : 0.005 0.070 1891 Dihedral : 11.517 163.615 1571 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.80 % Allowed : 8.52 % Favored : 90.68 % 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: -1.62 (0.20), residues: 1432 helix: 0.06 (0.16), residues: 866 sheet: -3.34 (0.45), residues: 81 loop : -2.69 (0.24), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 504 TYR 0.027 0.001 TYR A 381 PHE 0.013 0.001 PHE A 354 TRP 0.012 0.001 TRP A 364 HIS 0.004 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.15 (10977) covalent geometry : angle 0.61044 / 0.32 (14930) hydrogen bonds : bond 0.06062 / 4.14 ( 673) hydrogen bonds : angle 5.12009 / 3.71 ( 1974) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 116 time to evaluate : 0.592 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: symmetry clash revert: symmetry clash REVERT: B 191 CYS cc_start: 0.6654 (m) cc_final: 0.6184 (t) REVERT: B 279 MET cc_start: 0.5987 (mmp) cc_final: 0.5733 (mmp) REVERT: B 350 ARG cc_start: 0.8292 (mtm-85) cc_final: 0.7759 (mmm160) outliers start: 9 outliers final: 8 residues processed: 123 average time/residue: 0.2525 time to fit residues: 44.3752 Evaluate side-chains 105 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 516 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 100 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 109 optimal weight: 5.9990 chunk 5 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 110 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 ASN C 86 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.114522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.091018 restraints weight = 90552.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.092262 restraints weight = 43894.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.092509 restraints weight = 26078.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.092556 restraints weight = 23432.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.092928 restraints weight = 21473.508| |-----------------------------------------------------------------------------| r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10977 Z= 0.154 Angle : 0.566 6.346 14930 Z= 0.299 Chirality : 0.038 0.178 1798 Planarity : 0.004 0.057 1891 Dihedral : 10.605 167.522 1567 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.24 % Allowed : 9.32 % Favored : 89.44 % 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: -1.05 (0.21), residues: 1432 helix: 0.52 (0.16), residues: 869 sheet: -3.15 (0.46), residues: 82 loop : -2.50 (0.25), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 363 TYR 0.024 0.001 TYR A 381 PHE 0.011 0.001 PHE A 244 TRP 0.009 0.001 TRP A 176 HIS 0.003 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (10977) covalent geometry : angle 0.56602 / 0.30 (14930) hydrogen bonds : bond 0.05423 / 3.71 ( 673) hydrogen bonds : angle 4.84398 / 3.52 ( 1974) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.546 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: B 279 MET cc_start: 0.5880 (mmp) cc_final: 0.5582 (mmp) REVERT: B 350 ARG cc_start: 0.8258 (mtm-85) cc_final: 0.7771 (mmm160) REVERT: B 535 MET cc_start: 0.8295 (pmm) cc_final: 0.7849 (pmm) outliers start: 14 outliers final: 9 residues processed: 109 average time/residue: 0.2397 time to fit residues: 37.4511 Evaluate side-chains 103 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain D residue 15 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 13 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 97 optimal weight: 8.9990 chunk 115 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 135 optimal weight: 0.4980 chunk 49 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 GLN C 86 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.113042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.088916 restraints weight = 90495.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.090910 restraints weight = 38752.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.090943 restraints weight = 25013.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.091010 restraints weight = 20500.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.091175 restraints weight = 20539.873| |-----------------------------------------------------------------------------| r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10977 Z= 0.160 Angle : 0.559 7.071 14930 Z= 0.293 Chirality : 0.038 0.142 1798 Planarity : 0.004 0.046 1891 Dihedral : 9.454 116.428 1565 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.42 % Allowed : 9.85 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.21), residues: 1432 helix: 0.86 (0.17), residues: 870 sheet: -2.48 (0.51), residues: 77 loop : -2.44 (0.25), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 363 TYR 0.024 0.002 TYR A 381 PHE 0.015 0.001 PHE A 260 TRP 0.008 0.001 TRP A 176 HIS 0.005 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (10977) covalent geometry : angle 0.55875 / 0.29 (14930) hydrogen bonds : bond 0.05080 / 3.49 ( 673) hydrogen bonds : angle 4.66902 / 3.39 ( 1974) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.644 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 279 MET cc_start: 0.5931 (mmp) cc_final: 0.5627 (mmp) REVERT: B 350 ARG cc_start: 0.8296 (mtm-85) cc_final: 0.7948 (mmm160) REVERT: B 535 MET cc_start: 0.8349 (pmm) cc_final: 0.7968 (pmm) outliers start: 16 outliers final: 13 residues processed: 111 average time/residue: 0.2538 time to fit residues: 39.9057 Evaluate side-chains 105 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain D residue 15 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 120 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 121 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 ASN B 248 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.112540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.087403 restraints weight = 89939.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.089918 restraints weight = 35920.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.091272 restraints weight = 20571.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.091771 restraints weight = 15336.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.091955 restraints weight = 13686.004| |-----------------------------------------------------------------------------| r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10977 Z= 0.148 Angle : 0.543 7.229 14930 Z= 0.283 Chirality : 0.038 0.139 1798 Planarity : 0.004 0.042 1891 Dihedral : 8.841 115.007 1565 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.33 % Allowed : 10.38 % Favored : 88.29 % 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: -0.31 (0.22), residues: 1432 helix: 1.08 (0.17), residues: 874 sheet: -2.23 (0.53), residues: 77 loop : -2.31 (0.26), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 363 TYR 0.022 0.001 TYR A 381 PHE 0.015 0.001 PHE A 260 TRP 0.008 0.001 TRP A 176 HIS 0.003 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (10977) covalent geometry : angle 0.54251 / 0.28 (14930) hydrogen bonds : bond 0.04790 / 3.29 ( 673) hydrogen bonds : angle 4.54596 / 3.30 ( 1974) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.611 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: A 321 GLU cc_start: 0.7508 (tp30) cc_final: 0.7189 (tm-30) REVERT: B 74 ILE cc_start: 0.9395 (OUTLIER) cc_final: 0.9182 (tt) REVERT: B 78 PHE cc_start: 0.7611 (m-10) cc_final: 0.7389 (m-10) REVERT: B 279 MET cc_start: 0.6048 (mmp) cc_final: 0.5673 (mmt) REVERT: B 535 MET cc_start: 0.8281 (pmm) cc_final: 0.7898 (pmm) REVERT: C 75 MET cc_start: 0.6712 (ptm) cc_final: 0.6355 (ptm) outliers start: 15 outliers final: 12 residues processed: 107 average time/residue: 0.2202 time to fit residues: 34.2967 Evaluate side-chains 101 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain D residue 15 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 52 optimal weight: 0.6980 chunk 120 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 78 optimal weight: 4.9990 chunk 139 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.110739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.086721 restraints weight = 91735.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.088228 restraints weight = 38984.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.088639 restraints weight = 25616.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.088869 restraints weight = 21706.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.089025 restraints weight = 20190.214| |-----------------------------------------------------------------------------| r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10977 Z= 0.138 Angle : 0.531 7.796 14930 Z= 0.276 Chirality : 0.038 0.139 1798 Planarity : 0.004 0.044 1891 Dihedral : 8.675 113.833 1565 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.42 % Allowed : 10.74 % Favored : 87.84 % 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: -0.10 (0.22), residues: 1432 helix: 1.25 (0.17), residues: 874 sheet: -2.07 (0.56), residues: 77 loop : -2.25 (0.26), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 363 TYR 0.022 0.001 TYR A 381 PHE 0.012 0.001 PHE A 490 TRP 0.007 0.001 TRP A 176 HIS 0.002 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (10977) covalent geometry : angle 0.53125 / 0.28 (14930) hydrogen bonds : bond 0.04625 / 3.17 ( 673) hydrogen bonds : angle 4.45436 / 3.23 ( 1974) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.577 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: A 321 GLU cc_start: 0.7500 (tp30) cc_final: 0.7178 (tm-30) REVERT: A 327 PHE cc_start: 0.8642 (OUTLIER) cc_final: 0.7988 (p90) REVERT: B 279 MET cc_start: 0.5875 (mmp) cc_final: 0.5568 (mmt) REVERT: B 535 MET cc_start: 0.8244 (pmm) cc_final: 0.7858 (pmm) REVERT: C 75 MET cc_start: 0.6791 (ptm) cc_final: 0.6405 (ptm) outliers start: 16 outliers final: 13 residues processed: 102 average time/residue: 0.2216 time to fit residues: 33.0879 Evaluate side-chains 100 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain D residue 15 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- 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: 67.6226 > 50: distance: 207 - 219: 7.936 distance: 219 - 220: 27.736 distance: 219 - 224: 13.412 distance: 220 - 221: 8.949 distance: 220 - 223: 19.839 distance: 220 - 225: 13.340 distance: 221 - 222: 25.229 distance: 221 - 229: 8.627 distance: 223 - 226: 30.832 distance: 223 - 227: 22.261 distance: 223 - 228: 3.846 distance: 229 - 230: 31.865 distance: 229 - 238: 26.571 distance: 230 - 231: 18.983 distance: 230 - 233: 43.413 distance: 230 - 239: 24.474 distance: 231 - 232: 17.706 distance: 233 - 234: 35.487 distance: 233 - 240: 27.479 distance: 233 - 241: 36.223 distance: 234 - 235: 9.202 distance: 234 - 242: 7.299 distance: 234 - 243: 6.844 distance: 235 - 236: 5.342 distance: 235 - 237: 7.377 distance: 244 - 245: 7.796 distance: 244 - 252: 29.530 distance: 245 - 246: 21.167 distance: 245 - 248: 34.743 distance: 245 - 253: 13.516 distance: 246 - 247: 29.862 distance: 246 - 261: 26.154 distance: 248 - 249: 26.819 distance: 248 - 254: 34.307 distance: 248 - 255: 30.190 distance: 249 - 250: 5.317 distance: 249 - 256: 9.073 distance: 249 - 257: 6.904 distance: 250 - 251: 21.922 distance: 251 - 258: 11.324 distance: 251 - 259: 7.658 distance: 251 - 260: 6.800 distance: 261 - 262: 25.152 distance: 261 - 267: 19.492 distance: 262 - 263: 27.317 distance: 262 - 265: 17.985 distance: 262 - 268: 10.816 distance: 263 - 264: 13.668 distance: 263 - 275: 48.519 distance: 265 - 266: 13.269 distance: 265 - 269: 10.966 distance: 265 - 270: 14.241 distance: 266 - 267: 9.558 distance: 266 - 271: 3.863 distance: 266 - 272: 16.742 distance: 267 - 273: 20.669 distance: 267 - 274: 32.889 distance: 275 - 276: 16.960 distance: 275 - 287: 14.226 distance: 276 - 277: 14.099 distance: 276 - 279: 29.004 distance: 276 - 288: 19.081 distance: 277 - 278: 38.866 distance: 277 - 296: 15.291 distance: 279 - 289: 22.773 distance: 279 - 290: 7.758 distance: 280 - 281: 14.883 distance: 280 - 282: 9.325 distance: 281 - 283: 7.111 distance: 281 - 291: 4.800 distance: 282 - 284: 9.128 distance: 282 - 292: 4.463 distance: 283 - 285: 3.040 distance: 283 - 293: 5.018 distance: 284 - 285: 6.139 distance: 285 - 286: 6.361 distance: 286 - 295: 3.846 distance: 296 - 297: 8.910 distance: 296 - 304: 11.303 distance: 297 - 298: 30.322 distance: 297 - 300: 27.213 distance: 297 - 305: 16.234 distance: 298 - 299: 22.140 distance: 298 - 310: 21.476 distance: 300 - 301: 24.129 distance: 300 - 306: 29.910 distance: 300 - 307: 24.793 distance: 301 - 302: 12.477 distance: 301 - 303: 11.499 distance: 303 - 308: 10.248 distance: 303 - 309: 8.326 distance: 310 - 311: 16.593 distance: 310 - 316: 20.003 distance: 311 - 312: 12.585 distance: 311 - 314: 8.278 distance: 311 - 317: 19.923 distance: 312 - 313: 16.754 distance: 312 - 324: 33.279 distance: 314 - 315: 43.557 distance: 314 - 318: 30.629 distance: 314 - 319: 15.778 distance: 315 - 316: 11.480 distance: 315 - 320: 22.000 distance: 315 - 321: 22.253 distance: 316 - 322: 13.452 distance: 316 - 323: 20.541 distance: 324 - 325: 7.148 distance: 324 - 333: 16.113 distance: 325 - 326: 18.483 distance: 325 - 328: 29.016 distance: 325 - 334: 12.467 distance: 326 - 327: 31.354 distance: 326 - 341: 9.283 distance: 328 - 329: 16.386 distance: 328 - 335: 23.523 distance: 328 - 336: 17.801 distance: 329 - 330: 11.153 distance: 329 - 337: 15.268 distance: 329 - 338: 19.748 distance: 330 - 331: 10.076 distance: 330 - 332: 10.062 distance: 332 - 339: 10.036 distance: 332 - 340: 15.480 distance: 341 - 342: 38.554 distance: 341 - 346: 24.535 distance: 342 - 343: 18.117 distance: 342 - 345: 25.162 distance: 342 - 347: 31.228 distance: 343 - 344: 12.644 distance: 343 - 351: 19.022 distance: 345 - 348: 7.036 distance: 345 - 349: 6.206 distance: 345 - 350: 21.029 distance: 351 - 352: 15.657 distance: 351 - 357: 16.017 distance: 352 - 353: 7.228 distance: 352 - 355: 41.167 distance: 352 - 358: 29.843 distance: 353 - 354: 16.398 distance: 353 - 362: 21.820 distance: 355 - 356: 33.344 distance: 355 - 359: 25.299 distance: 355 - 360: 17.835 distance: 356 - 361: 43.321