Starting phenix.real_space_refine on Fri Aug 22 19:23:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j14_61067/08_2025/9j14_61067.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j14_61067/08_2025/9j14_61067.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j14_61067/08_2025/9j14_61067.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j14_61067/08_2025/9j14_61067.map" model { file = "/net/cci-nas-00/data/ceres_data/9j14_61067/08_2025/9j14_61067.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j14_61067/08_2025/9j14_61067.cif" } resolution = 3.49 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= 0.001 sd= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 4686 2.51 5 N 1160 2.21 5 O 1318 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7218 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3593 Classifications: {'peptide': 485} Link IDs: {'PTRANS': 16, 'TRANS': 468} Chain: "B" Number of atoms: 3593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3593 Classifications: {'peptide': 485} Link IDs: {'PTRANS': 16, 'TRANS': 468} Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'ZEA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'ZEA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.45, per 1000 atoms: 0.20 Number of scatterers: 7218 At special positions: 0 Unit cell: (73.7, 115.5, 88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 1318 8.00 N 1160 7.00 C 4686 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 72 " - pdb=" SG CYS A 101 " distance=2.03 Simple disulfide: pdb=" SG CYS A 77 " - pdb=" SG CYS A 90 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 242 " distance=2.02 Simple disulfide: pdb=" SG CYS B 72 " - pdb=" SG CYS B 101 " distance=2.03 Simple disulfide: pdb=" SG CYS B 77 " - pdb=" SG CYS B 90 " distance=2.03 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 242 " distance=2.02 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: 0.47 Conformation dependent library (CDL) restraints added in 250.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1728 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 4 sheets defined 66.3% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 13 through 25 removed outlier: 3.506A pdb=" N HIS A 17 " --> pdb=" O ASP A 13 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 18 " --> pdb=" O MET A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 32 Processing helix chain 'A' and resid 39 through 55 Processing helix chain 'A' and resid 56 through 67 removed outlier: 3.568A pdb=" N VAL A 60 " --> pdb=" O TYR A 56 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA A 62 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP A 67 " --> pdb=" O ASN A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 77 removed outlier: 3.532A pdb=" N CYS A 77 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 91 removed outlier: 4.250A pdb=" N CYS A 90 " --> pdb=" O PRO A 86 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL A 91 " --> pdb=" O GLY A 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 86 through 91' Processing helix chain 'A' and resid 95 through 127 removed outlier: 3.693A pdb=" N VAL A 110 " --> pdb=" O LYS A 106 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLY A 120 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ALA A 123 " --> pdb=" O VAL A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 147 removed outlier: 4.104A pdb=" N TYR A 146 " --> pdb=" O ALA A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 179 removed outlier: 3.511A pdb=" N MET A 163 " --> pdb=" O TYR A 159 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU A 179 " --> pdb=" O ALA A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 186 Processing helix chain 'A' and resid 190 through 209 removed outlier: 3.658A pdb=" N ARG A 194 " --> pdb=" O PRO A 190 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 195 " --> pdb=" O GLN A 191 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 264 removed outlier: 3.542A pdb=" N TRP A 253 " --> pdb=" O SER A 249 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU A 254 " --> pdb=" O PRO A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 286 Processing helix chain 'A' and resid 298 through 309 Processing helix chain 'A' and resid 334 through 360 removed outlier: 4.101A pdb=" N GLY A 351 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 353 " --> pdb=" O THR A 349 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N TYR A 354 " --> pdb=" O THR A 350 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU A 358 " --> pdb=" O TYR A 354 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ILE A 359 " --> pdb=" O THR A 355 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY A 360 " --> pdb=" O MET A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 381 Processing helix chain 'A' and resid 382 through 387 Processing helix chain 'A' and resid 399 through 406 removed outlier: 3.872A pdb=" N LEU A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 422 removed outlier: 3.522A pdb=" N ALA A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 432 removed outlier: 3.954A pdb=" N ASN A 432 " --> pdb=" O PRO A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 437 Processing helix chain 'A' and resid 438 through 451 Processing helix chain 'A' and resid 452 through 456 removed outlier: 3.551A pdb=" N ILE A 456 " --> pdb=" O VAL A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 478 removed outlier: 3.884A pdb=" N THR A 466 " --> pdb=" O LYS A 462 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET A 474 " --> pdb=" O THR A 470 " (cutoff:3.500A) Proline residue: A 475 - end of helix Processing helix chain 'A' and resid 479 through 495 removed outlier: 4.046A pdb=" N GLY A 483 " --> pdb=" O SER A 479 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A 484 " --> pdb=" O ILE A 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 25 removed outlier: 3.526A pdb=" N LEU B 18 " --> pdb=" O MET B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 32 Processing helix chain 'B' and resid 39 through 55 Processing helix chain 'B' and resid 56 through 67 removed outlier: 3.569A pdb=" N VAL B 60 " --> pdb=" O TYR B 56 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA B 62 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP B 67 " --> pdb=" O ASN B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 77 removed outlier: 3.531A pdb=" N CYS B 77 " --> pdb=" O ILE B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 91 removed outlier: 4.251A pdb=" N CYS B 90 " --> pdb=" O PRO B 86 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL B 91 " --> pdb=" O GLY B 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 86 through 91' Processing helix chain 'B' and resid 95 through 127 removed outlier: 3.693A pdb=" N VAL B 110 " --> pdb=" O LYS B 106 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL B 111 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLY B 120 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ALA B 123 " --> pdb=" O VAL B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 147 removed outlier: 4.104A pdb=" N TYR B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 179 removed outlier: 3.511A pdb=" N MET B 163 " --> pdb=" O TYR B 159 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU B 179 " --> pdb=" O ALA B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 186 Processing helix chain 'B' and resid 190 through 209 removed outlier: 3.658A pdb=" N ARG B 194 " --> pdb=" O PRO B 190 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU B 195 " --> pdb=" O GLN B 191 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY B 202 " --> pdb=" O ALA B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 264 removed outlier: 3.542A pdb=" N TRP B 253 " --> pdb=" O SER B 249 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU B 254 " --> pdb=" O PRO B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 286 Processing helix chain 'B' and resid 298 through 309 Processing helix chain 'B' and resid 334 through 360 removed outlier: 4.101A pdb=" N GLY B 351 " --> pdb=" O LEU B 347 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU B 353 " --> pdb=" O THR B 349 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N TYR B 354 " --> pdb=" O THR B 350 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU B 358 " --> pdb=" O TYR B 354 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE B 359 " --> pdb=" O THR B 355 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY B 360 " --> pdb=" O MET B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 381 Processing helix chain 'B' and resid 382 through 387 Processing helix chain 'B' and resid 399 through 406 removed outlier: 3.873A pdb=" N LEU B 403 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 422 removed outlier: 3.522A pdb=" N ALA B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 432 removed outlier: 3.954A pdb=" N ASN B 432 " --> pdb=" O PRO B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 437 Processing helix chain 'B' and resid 438 through 451 Processing helix chain 'B' and resid 452 through 456 removed outlier: 3.552A pdb=" N ILE B 456 " --> pdb=" O VAL B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 478 removed outlier: 3.885A pdb=" N THR B 466 " --> pdb=" O LYS B 462 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET B 474 " --> pdb=" O THR B 470 " (cutoff:3.500A) Proline residue: B 475 - end of helix Processing helix chain 'B' and resid 479 through 495 removed outlier: 4.045A pdb=" N GLY B 483 " --> pdb=" O SER B 479 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE B 484 " --> pdb=" O ILE B 480 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 134 through 135 removed outlier: 4.131A pdb=" N ALA A 135 " --> pdb=" O ALA A 394 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A 394 " --> pdb=" O ALA A 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 219 through 221 Processing sheet with id=AA3, first strand: chain 'B' and resid 134 through 135 removed outlier: 4.133A pdb=" N ALA B 135 " --> pdb=" O ALA B 394 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA B 394 " --> pdb=" O ALA B 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 219 through 221 380 hydrogen bonds defined for protein. 1122 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: 0.74 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1193 1.33 - 1.45: 1917 1.45 - 1.57: 4164 1.57 - 1.69: 0 1.69 - 1.81: 92 Bond restraints: 7366 Sorted by residual: bond pdb=" C4 ZEA A 601 " pdb=" C5 ZEA A 601 " ideal model delta sigma weight residual 1.387 1.456 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C4 ZEA B 601 " pdb=" C5 ZEA B 601 " ideal model delta sigma weight residual 1.387 1.455 -0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C5 ZEA B 601 " pdb=" C6 ZEA B 601 " ideal model delta sigma weight residual 1.410 1.468 -0.058 2.00e-02 2.50e+03 8.39e+00 bond pdb=" C5 ZEA A 601 " pdb=" C6 ZEA A 601 " ideal model delta sigma weight residual 1.410 1.468 -0.058 2.00e-02 2.50e+03 8.39e+00 bond pdb=" C PHE B 396 " pdb=" O PHE B 396 " ideal model delta sigma weight residual 1.236 1.204 0.032 1.21e-02 6.83e+03 6.89e+00 ... (remaining 7361 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.11: 9893 3.11 - 6.21: 89 6.21 - 9.32: 20 9.32 - 12.43: 2 12.43 - 15.54: 2 Bond angle restraints: 10006 Sorted by residual: angle pdb=" N GLU A 234 " pdb=" CA GLU A 234 " pdb=" C GLU A 234 " ideal model delta sigma weight residual 109.59 94.05 15.54 1.47e+00 4.63e-01 1.12e+02 angle pdb=" N GLU B 234 " pdb=" CA GLU B 234 " pdb=" C GLU B 234 " ideal model delta sigma weight residual 109.59 94.08 15.51 1.47e+00 4.63e-01 1.11e+02 angle pdb=" N THR B 235 " pdb=" CA THR B 235 " pdb=" CB THR B 235 " ideal model delta sigma weight residual 110.77 122.89 -12.12 1.63e+00 3.76e-01 5.53e+01 angle pdb=" N THR A 235 " pdb=" CA THR A 235 " pdb=" CB THR A 235 " ideal model delta sigma weight residual 110.77 122.81 -12.04 1.63e+00 3.76e-01 5.46e+01 angle pdb=" N THR A 235 " pdb=" CA THR A 235 " pdb=" C THR A 235 " ideal model delta sigma weight residual 108.26 99.58 8.68 1.66e+00 3.63e-01 2.74e+01 ... (remaining 10001 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 3681 17.54 - 35.09: 479 35.09 - 52.63: 106 52.63 - 70.18: 12 70.18 - 87.72: 8 Dihedral angle restraints: 4286 sinusoidal: 1558 harmonic: 2728 Sorted by residual: dihedral pdb=" CA ILE A 144 " pdb=" C ILE A 144 " pdb=" N ALA A 145 " pdb=" CA ALA A 145 " ideal model delta harmonic sigma weight residual 180.00 151.75 28.25 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CA ILE B 144 " pdb=" C ILE B 144 " pdb=" N ALA B 145 " pdb=" CA ALA B 145 " ideal model delta harmonic sigma weight residual 180.00 151.82 28.18 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA PHE B 420 " pdb=" C PHE B 420 " pdb=" N LEU B 421 " pdb=" CA LEU B 421 " ideal model delta harmonic sigma weight residual 180.00 162.88 17.12 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 4283 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 858 0.043 - 0.086: 274 0.086 - 0.129: 59 0.129 - 0.172: 9 0.172 - 0.214: 4 Chirality restraints: 1204 Sorted by residual: chirality pdb=" CA GLU B 234 " pdb=" N GLU B 234 " pdb=" C GLU B 234 " pdb=" CB GLU B 234 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA GLU A 234 " pdb=" N GLU A 234 " pdb=" C GLU A 234 " pdb=" CB GLU A 234 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA THR A 71 " pdb=" N THR A 71 " pdb=" C THR A 71 " pdb=" CB THR A 71 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.54e-01 ... (remaining 1201 not shown) Planarity restraints: 1232 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 439 " 0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO A 440 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 440 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 440 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 439 " -0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO B 440 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 440 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 440 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 144 " 0.007 2.00e-02 2.50e+03 1.49e-02 2.23e+00 pdb=" C ILE A 144 " -0.026 2.00e-02 2.50e+03 pdb=" O ILE A 144 " 0.010 2.00e-02 2.50e+03 pdb=" N ALA A 145 " 0.009 2.00e-02 2.50e+03 ... (remaining 1229 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.32: 11 2.32 - 2.96: 3592 2.96 - 3.61: 10586 3.61 - 4.25: 14875 4.25 - 4.90: 26011 Nonbonded interactions: 55075 Sorted by model distance: nonbonded pdb=" CE MET A 450 " pdb=" CH2 TRP B 458 " model vdw 1.674 3.760 nonbonded pdb=" CH2 TRP A 458 " pdb=" CE MET B 450 " model vdw 1.683 3.760 nonbonded pdb=" CE MET A 450 " pdb=" CZ3 TRP B 458 " model vdw 2.133 3.760 nonbonded pdb=" CZ3 TRP A 458 " pdb=" CE MET B 450 " model vdw 2.143 3.760 nonbonded pdb=" O SER A 68 " pdb=" OG SER A 68 " model vdw 2.251 3.040 ... (remaining 55070 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 5.870 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 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 0.069 7372 Z= 0.192 Angle : 0.812 15.537 10018 Z= 0.452 Chirality : 0.044 0.214 1204 Planarity : 0.004 0.040 1232 Dihedral : 16.002 87.724 2540 Min Nonbonded Distance : 1.674 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.87 % Favored : 89.13 % Rotamer: Outliers : 0.26 % Allowed : 27.02 % Favored : 72.72 % 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 aren not related in a simple way. whole: -0.73 (0.27), residues: 966 helix: 0.85 (0.23), residues: 572 sheet: None (None), residues: 0 loop : -2.62 (0.27), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 104 TYR 0.008 0.001 TYR B 143 PHE 0.024 0.001 PHE B 295 TRP 0.003 0.001 TRP A 286 HIS 0.003 0.001 HIS A 17 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 7366) covalent geometry : angle 0.81043 (10006) SS BOND : bond 0.00378 ( 6) SS BOND : angle 1.71785 ( 12) hydrogen bonds : bond 0.16226 ( 380) hydrogen bonds : angle 5.33571 ( 1122) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 159 time to evaluate : 0.250 Fit side-chains REVERT: A 16 LYS cc_start: 0.8466 (tttm) cc_final: 0.7905 (mmmt) REVERT: A 152 ARG cc_start: 0.8507 (mtt180) cc_final: 0.8016 (mtt-85) REVERT: A 184 LYS cc_start: 0.6743 (ttpt) cc_final: 0.6042 (tmtt) REVERT: A 331 LYS cc_start: 0.7062 (mtpp) cc_final: 0.6861 (ptpp) REVERT: A 346 LEU cc_start: 0.8841 (tp) cc_final: 0.8632 (tp) REVERT: A 371 GLU cc_start: 0.7323 (tp30) cc_final: 0.6759 (pt0) REVERT: A 435 ARG cc_start: 0.8291 (ttp80) cc_final: 0.8026 (ptt-90) REVERT: A 448 MET cc_start: 0.7979 (mmm) cc_final: 0.7760 (mmp) REVERT: B 16 LYS cc_start: 0.8462 (tttm) cc_final: 0.7906 (mmmt) REVERT: B 152 ARG cc_start: 0.8526 (mtt180) cc_final: 0.8042 (mtt-85) REVERT: B 184 LYS cc_start: 0.6694 (ttpt) cc_final: 0.5991 (tmtt) REVERT: B 331 LYS cc_start: 0.7011 (mtpp) cc_final: 0.6810 (ptpp) REVERT: B 346 LEU cc_start: 0.8850 (tp) cc_final: 0.8637 (tp) REVERT: B 371 GLU cc_start: 0.7315 (tp30) cc_final: 0.6765 (pt0) REVERT: B 435 ARG cc_start: 0.8392 (ttp80) cc_final: 0.8131 (ptt-90) REVERT: B 448 MET cc_start: 0.8021 (mmm) cc_final: 0.7814 (mmp) outliers start: 2 outliers final: 0 residues processed: 161 average time/residue: 0.0678 time to fit residues: 14.5696 Evaluate side-chains 123 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.0670 chunk 62 optimal weight: 0.0980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN A 211 GLN B 95 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.180932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.149345 restraints weight = 9340.596| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.48 r_work: 0.3494 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7372 Z= 0.120 Angle : 0.596 6.451 10018 Z= 0.313 Chirality : 0.042 0.163 1204 Planarity : 0.004 0.042 1232 Dihedral : 4.823 29.246 1030 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 6.01 % Allowed : 22.19 % Favored : 71.80 % 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 aren not related in a simple way. whole: -0.45 (0.27), residues: 966 helix: 1.12 (0.22), residues: 568 sheet: None (None), residues: 0 loop : -2.54 (0.27), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 288 TYR 0.011 0.001 TYR A 143 PHE 0.007 0.001 PHE B 51 TRP 0.008 0.001 TRP B 458 HIS 0.003 0.001 HIS B 17 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 7366) covalent geometry : angle 0.59265 (10006) SS BOND : bond 0.00089 ( 6) SS BOND : angle 2.00199 ( 12) hydrogen bonds : bond 0.03740 ( 380) hydrogen bonds : angle 4.07722 ( 1122) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 142 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 LYS cc_start: 0.8365 (tttm) cc_final: 0.7882 (mmmt) REVERT: A 33 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7246 (mt) REVERT: A 104 ARG cc_start: 0.7324 (ttp-110) cc_final: 0.6913 (mtm180) REVERT: A 124 MET cc_start: 0.8622 (tpt) cc_final: 0.8080 (tpp) REVERT: A 152 ARG cc_start: 0.8733 (mtt180) cc_final: 0.8339 (mtt-85) REVERT: A 171 CYS cc_start: 0.8454 (m) cc_final: 0.8003 (t) REVERT: A 184 LYS cc_start: 0.6909 (ttpt) cc_final: 0.5820 (tmtt) REVERT: A 234 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7049 (tp30) REVERT: A 330 ARG cc_start: 0.4776 (mpt180) cc_final: 0.3389 (tmm160) REVERT: A 356 MET cc_start: 0.6824 (OUTLIER) cc_final: 0.6276 (tpt) REVERT: A 371 GLU cc_start: 0.7016 (tp30) cc_final: 0.6669 (pt0) REVERT: A 435 ARG cc_start: 0.8566 (ttp80) cc_final: 0.8255 (ptt-90) REVERT: A 448 MET cc_start: 0.8611 (mmm) cc_final: 0.8142 (mmp) REVERT: A 450 MET cc_start: 0.8833 (ttp) cc_final: 0.8615 (tmm) REVERT: A 460 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7789 (mt-10) REVERT: B 16 LYS cc_start: 0.8387 (tttm) cc_final: 0.7893 (mmmt) REVERT: B 33 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7270 (mt) REVERT: B 104 ARG cc_start: 0.7315 (ttp-110) cc_final: 0.6901 (mtm180) REVERT: B 124 MET cc_start: 0.8623 (tpt) cc_final: 0.8077 (tpp) REVERT: B 152 ARG cc_start: 0.8675 (mtt180) cc_final: 0.8274 (mtt-85) REVERT: B 171 CYS cc_start: 0.8472 (m) cc_final: 0.8007 (t) REVERT: B 184 LYS cc_start: 0.6904 (ttpt) cc_final: 0.5801 (tmtt) REVERT: B 226 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8684 (mt) REVERT: B 234 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7053 (tp30) REVERT: B 330 ARG cc_start: 0.4778 (mpt180) cc_final: 0.3363 (tmm160) REVERT: B 356 MET cc_start: 0.6850 (OUTLIER) cc_final: 0.6198 (tpt) REVERT: B 371 GLU cc_start: 0.7028 (tp30) cc_final: 0.6775 (pt0) REVERT: B 448 MET cc_start: 0.8596 (mmm) cc_final: 0.8122 (mmp) REVERT: B 450 MET cc_start: 0.8792 (ttp) cc_final: 0.8584 (tmm) REVERT: B 460 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7785 (mt-10) outliers start: 46 outliers final: 18 residues processed: 178 average time/residue: 0.0733 time to fit residues: 16.8898 Evaluate side-chains 147 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 492 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 21 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 86 optimal weight: 0.0170 chunk 83 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 34 optimal weight: 0.0030 chunk 54 optimal weight: 0.0070 overall best weight: 0.3648 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.182574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.151053 restraints weight = 9238.385| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.43 r_work: 0.3347 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7372 Z= 0.105 Angle : 0.565 6.009 10018 Z= 0.294 Chirality : 0.041 0.196 1204 Planarity : 0.004 0.043 1232 Dihedral : 4.563 30.271 1030 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.94 % Favored : 90.06 % Rotamer: Outliers : 5.35 % Allowed : 21.80 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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 aren not related in a simple way. whole: -0.20 (0.27), residues: 966 helix: 1.33 (0.22), residues: 568 sheet: None (None), residues: 0 loop : -2.44 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 182 TYR 0.008 0.001 TYR B 143 PHE 0.009 0.001 PHE B 368 TRP 0.003 0.001 TRP A 253 HIS 0.003 0.001 HIS B 17 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 7366) covalent geometry : angle 0.56263 (10006) SS BOND : bond 0.00166 ( 6) SS BOND : angle 1.72536 ( 12) hydrogen bonds : bond 0.03124 ( 380) hydrogen bonds : angle 3.98802 ( 1122) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 128 time to evaluate : 0.203 Fit side-chains REVERT: A 16 LYS cc_start: 0.8341 (tttm) cc_final: 0.7790 (mmmt) REVERT: A 104 ARG cc_start: 0.7461 (ttp-110) cc_final: 0.7015 (mtm180) REVERT: A 124 MET cc_start: 0.8670 (tpt) cc_final: 0.8133 (tpp) REVERT: A 152 ARG cc_start: 0.8754 (mtt180) cc_final: 0.8368 (mtt-85) REVERT: A 171 CYS cc_start: 0.8635 (m) cc_final: 0.8154 (t) REVERT: A 179 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7405 (pp) REVERT: A 184 LYS cc_start: 0.6791 (ttpt) cc_final: 0.5632 (tmtt) REVERT: A 234 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7188 (tp30) REVERT: A 330 ARG cc_start: 0.4590 (mpt180) cc_final: 0.3110 (ttp-170) REVERT: A 450 MET cc_start: 0.9119 (OUTLIER) cc_final: 0.8860 (tmm) REVERT: B 16 LYS cc_start: 0.8332 (tttm) cc_final: 0.7790 (mmmt) REVERT: B 104 ARG cc_start: 0.7446 (ttp-110) cc_final: 0.6998 (mtm180) REVERT: B 124 MET cc_start: 0.8669 (tpt) cc_final: 0.8120 (tpp) REVERT: B 152 ARG cc_start: 0.8739 (mtt180) cc_final: 0.8364 (mtt-85) REVERT: B 171 CYS cc_start: 0.8618 (m) cc_final: 0.8126 (t) REVERT: B 179 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7382 (pp) REVERT: B 234 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7215 (tp30) REVERT: B 330 ARG cc_start: 0.4488 (mpt180) cc_final: 0.3106 (ttp-170) REVERT: B 356 MET cc_start: 0.6582 (OUTLIER) cc_final: 0.5826 (tpt) REVERT: B 448 MET cc_start: 0.8759 (mmm) cc_final: 0.8546 (mmm) REVERT: B 450 MET cc_start: 0.9105 (OUTLIER) cc_final: 0.8858 (tmm) outliers start: 41 outliers final: 12 residues processed: 154 average time/residue: 0.0716 time to fit residues: 14.9274 Evaluate side-chains 130 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 450 MET Chi-restraints excluded: chain B residue 492 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 19 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 44 optimal weight: 0.4980 chunk 75 optimal weight: 0.7980 chunk 28 optimal weight: 0.0040 chunk 1 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 64 optimal weight: 0.0370 overall best weight: 0.3670 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.183028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.151100 restraints weight = 9470.023| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.48 r_work: 0.3551 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7372 Z= 0.107 Angle : 0.566 5.820 10018 Z= 0.296 Chirality : 0.041 0.233 1204 Planarity : 0.004 0.043 1232 Dihedral : 4.514 29.855 1030 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % Rotamer: Outliers : 5.87 % Allowed : 21.15 % Favored : 72.98 % 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 aren not related in a simple way. whole: -0.15 (0.27), residues: 966 helix: 1.40 (0.22), residues: 568 sheet: None (None), residues: 0 loop : -2.47 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 182 TYR 0.009 0.001 TYR A 343 PHE 0.010 0.001 PHE B 368 TRP 0.003 0.001 TRP B 253 HIS 0.003 0.001 HIS A 17 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 7366) covalent geometry : angle 0.56200 (10006) SS BOND : bond 0.00509 ( 6) SS BOND : angle 2.06344 ( 12) hydrogen bonds : bond 0.02896 ( 380) hydrogen bonds : angle 3.94828 ( 1122) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 116 time to evaluate : 0.174 Fit side-chains REVERT: A 16 LYS cc_start: 0.8279 (tttm) cc_final: 0.7854 (mmmt) REVERT: A 76 ASP cc_start: 0.8125 (m-30) cc_final: 0.7882 (t0) REVERT: A 124 MET cc_start: 0.8563 (tpt) cc_final: 0.8038 (tpp) REVERT: A 152 ARG cc_start: 0.8688 (mtt180) cc_final: 0.8227 (mtt-85) REVERT: A 171 CYS cc_start: 0.8467 (m) cc_final: 0.8036 (t) REVERT: A 179 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7378 (pp) REVERT: A 330 ARG cc_start: 0.4411 (mpt180) cc_final: 0.3278 (ttp-170) REVERT: A 448 MET cc_start: 0.8471 (mmm) cc_final: 0.8112 (mmp) REVERT: A 450 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.8624 (tmm) REVERT: B 16 LYS cc_start: 0.8283 (tttm) cc_final: 0.7864 (mmmt) REVERT: B 33 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7200 (mt) REVERT: B 76 ASP cc_start: 0.8133 (m-30) cc_final: 0.7896 (t0) REVERT: B 124 MET cc_start: 0.8553 (tpt) cc_final: 0.8028 (tpp) REVERT: B 152 ARG cc_start: 0.8660 (mtt180) cc_final: 0.8198 (mtt-85) REVERT: B 171 CYS cc_start: 0.8482 (m) cc_final: 0.8039 (t) REVERT: B 179 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7360 (pp) REVERT: B 330 ARG cc_start: 0.4345 (mpt180) cc_final: 0.3245 (ttp-170) REVERT: B 450 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8628 (tmm) outliers start: 45 outliers final: 24 residues processed: 149 average time/residue: 0.0657 time to fit residues: 13.2448 Evaluate side-chains 138 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 450 MET Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 492 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 1 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.177598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.145987 restraints weight = 9502.480| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.46 r_work: 0.3485 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7372 Z= 0.121 Angle : 0.587 6.131 10018 Z= 0.308 Chirality : 0.042 0.251 1204 Planarity : 0.004 0.042 1232 Dihedral : 4.618 30.191 1030 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.18 % Favored : 88.82 % Rotamer: Outliers : 6.27 % Allowed : 20.63 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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 aren not related in a simple way. whole: -0.07 (0.28), residues: 966 helix: 1.53 (0.23), residues: 566 sheet: None (None), residues: 0 loop : -2.55 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 182 TYR 0.010 0.001 TYR A 343 PHE 0.008 0.001 PHE B 368 TRP 0.003 0.001 TRP B 286 HIS 0.003 0.001 HIS A 17 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 7366) covalent geometry : angle 0.58225 (10006) SS BOND : bond 0.00226 ( 6) SS BOND : angle 2.15084 ( 12) hydrogen bonds : bond 0.03495 ( 380) hydrogen bonds : angle 3.98821 ( 1122) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 126 time to evaluate : 0.231 Fit side-chains REVERT: A 16 LYS cc_start: 0.8372 (tttm) cc_final: 0.7880 (mmmt) REVERT: A 33 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7324 (mt) REVERT: A 124 MET cc_start: 0.8665 (tpt) cc_final: 0.8128 (tpp) REVERT: A 179 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7523 (pp) REVERT: A 182 ARG cc_start: 0.7480 (ttp80) cc_final: 0.7257 (ttp80) REVERT: A 184 LYS cc_start: 0.6857 (ttpt) cc_final: 0.5674 (tmtt) REVERT: A 330 ARG cc_start: 0.4614 (mpt180) cc_final: 0.3184 (ttp-170) REVERT: A 448 MET cc_start: 0.8639 (mmm) cc_final: 0.8249 (mmp) REVERT: A 450 MET cc_start: 0.9076 (OUTLIER) cc_final: 0.8367 (tmm) REVERT: B 16 LYS cc_start: 0.8373 (tttm) cc_final: 0.7883 (mmmt) REVERT: B 33 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7336 (mt) REVERT: B 124 MET cc_start: 0.8636 (tpt) cc_final: 0.8104 (tpp) REVERT: B 152 ARG cc_start: 0.8744 (mtt180) cc_final: 0.8331 (mtt-85) REVERT: B 179 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7512 (pp) REVERT: B 182 ARG cc_start: 0.7465 (ttp80) cc_final: 0.7210 (ttp80) REVERT: B 330 ARG cc_start: 0.4553 (mpt180) cc_final: 0.3127 (ttp-170) REVERT: B 448 MET cc_start: 0.8696 (mmm) cc_final: 0.8311 (mmp) REVERT: B 450 MET cc_start: 0.9104 (OUTLIER) cc_final: 0.8381 (tmm) outliers start: 48 outliers final: 32 residues processed: 161 average time/residue: 0.0595 time to fit residues: 13.4398 Evaluate side-chains 148 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 110 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 450 MET Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 492 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.2908 > 50: distance: 23 - 46: 12.512 distance: 32 - 54: 5.384 distance: 36 - 60: 11.180 distance: 42 - 46: 12.838 distance: 43 - 71: 15.372 distance: 46 - 47: 12.138 distance: 47 - 48: 9.652 distance: 47 - 50: 6.310 distance: 48 - 49: 15.668 distance: 48 - 54: 6.967 distance: 49 - 78: 24.769 distance: 50 - 51: 8.371 distance: 50 - 52: 6.823 distance: 51 - 53: 8.479 distance: 54 - 55: 7.721 distance: 55 - 56: 7.911 distance: 55 - 58: 20.077 distance: 56 - 57: 8.292 distance: 56 - 60: 10.841 distance: 57 - 87: 12.408 distance: 60 - 61: 6.450 distance: 61 - 62: 10.816 distance: 61 - 64: 5.162 distance: 62 - 63: 10.205 distance: 62 - 71: 10.404 distance: 63 - 96: 21.163 distance: 64 - 65: 15.844 distance: 65 - 66: 8.658 distance: 66 - 67: 10.413 distance: 67 - 68: 7.564 distance: 68 - 69: 5.858 distance: 68 - 70: 5.793 distance: 71 - 72: 11.229 distance: 72 - 73: 9.199 distance: 72 - 75: 3.738 distance: 73 - 74: 11.751 distance: 73 - 78: 8.274 distance: 74 - 104: 41.938 distance: 75 - 76: 15.707 distance: 75 - 77: 20.512 distance: 78 - 79: 13.106 distance: 79 - 80: 7.774 distance: 79 - 82: 5.822 distance: 80 - 81: 14.471 distance: 80 - 87: 4.699 distance: 82 - 83: 6.035 distance: 83 - 84: 3.205 distance: 84 - 85: 5.492 distance: 85 - 86: 3.364 distance: 87 - 88: 9.838 distance: 88 - 89: 13.846 distance: 88 - 91: 10.457 distance: 89 - 90: 13.574 distance: 89 - 96: 6.427 distance: 91 - 92: 11.692 distance: 93 - 94: 7.347 distance: 94 - 95: 10.401 distance: 96 - 97: 7.441 distance: 97 - 98: 15.745 distance: 97 - 100: 11.926 distance: 99 - 126: 24.672 distance: 100 - 101: 18.813 distance: 101 - 102: 13.144 distance: 101 - 103: 13.438 distance: 104 - 105: 17.752 distance: 105 - 106: 19.778 distance: 105 - 108: 30.011 distance: 106 - 107: 16.239 distance: 106 - 112: 26.270 distance: 107 - 131: 27.269 distance: 108 - 109: 5.110 distance: 109 - 110: 12.770 distance: 109 - 111: 17.629 distance: 112 - 113: 9.225 distance: 113 - 114: 10.403 distance: 113 - 116: 9.057 distance: 114 - 115: 5.142 distance: 114 - 119: 17.786 distance: 115 - 138: 23.323 distance: 116 - 117: 9.908 distance: 116 - 118: 8.655 distance: 119 - 120: 13.466 distance: 120 - 121: 8.366 distance: 120 - 123: 15.444 distance: 121 - 122: 7.304 distance: 121 - 126: 12.316 distance: 122 - 143: 6.735 distance: 123 - 124: 10.018 distance: 123 - 125: 10.336