Starting phenix.real_space_refine on Sun Aug 24 06:55:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n17_24115/08_2025/7n17_24115.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n17_24115/08_2025/7n17_24115.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7n17_24115/08_2025/7n17_24115.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n17_24115/08_2025/7n17_24115.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7n17_24115/08_2025/7n17_24115.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n17_24115/08_2025/7n17_24115.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.100 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 96 5.16 5 C 11520 2.51 5 N 2872 2.21 5 O 3096 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 124 residue(s): 0.01s 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: 17596 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4270 Classifications: {'peptide': 517} Link IDs: {'PTRANS': 15, 'TRANS': 501} Chain: "B" Number of atoms: 4270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4270 Classifications: {'peptide': 517} Link IDs: {'PTRANS': 15, 'TRANS': 501} Chain: "A" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 129 Unusual residues: {'CPL': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 216 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'CPL:plan-3': 6, 'CPL:plan-4': 6, 'CPL:plan-1': 3, 'CPL:plan-2': 3} Unresolved non-hydrogen planarities: 68 Chain: "B" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 129 Unusual residues: {'CPL': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 216 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'CPL:plan-3': 6, 'CPL:plan-4': 6, 'CPL:plan-1': 3, 'CPL:plan-2': 3} Unresolved non-hydrogen planarities: 68 Restraints were copied for chains: C, D Time building chain proxies: 3.84, per 1000 atoms: 0.22 Number of scatterers: 17596 At special positions: 0 Unit cell: (130.31, 130.31, 136.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 P 12 15.00 O 3096 8.00 N 2872 7.00 C 11520 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 172 " distance=2.02 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 172 " distance=2.02 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 172 " distance=2.02 Simple disulfide: pdb=" SG CYS D 157 " - pdb=" SG CYS D 172 " 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: 1.01 Conformation dependent library (CDL) restraints added in 514.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3912 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 12 sheets defined 58.3% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 103 through 110 Processing helix chain 'A' and resid 118 through 145 removed outlier: 3.618A pdb=" N TYR A 122 " --> pdb=" O THR A 118 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ILE A 140 " --> pdb=" O LEU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 224 Processing helix chain 'A' and resid 236 through 247 Processing helix chain 'A' and resid 249 through 256 Processing helix chain 'A' and resid 260 through 265 Processing helix chain 'A' and resid 276 through 286 removed outlier: 4.172A pdb=" N ASN A 282 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG A 283 " --> pdb=" O ARG A 280 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG A 286 " --> pdb=" O ARG A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 299 Processing helix chain 'A' and resid 303 through 335 Processing helix chain 'A' and resid 358 through 375 Processing helix chain 'A' and resid 385 through 416 Processing helix chain 'A' and resid 418 through 438 Processing helix chain 'A' and resid 441 through 459 removed outlier: 3.707A pdb=" N LYS A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 471 Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.600A pdb=" N HIS A 484 " --> pdb=" O ALA A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 489 Processing helix chain 'A' and resid 498 through 507 Processing helix chain 'A' and resid 592 through 601 Processing helix chain 'A' and resid 602 through 619 removed outlier: 3.652A pdb=" N ARG A 606 " --> pdb=" O TYR A 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 110 Processing helix chain 'B' and resid 118 through 145 removed outlier: 3.617A pdb=" N TYR B 122 " --> pdb=" O THR B 118 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ILE B 140 " --> pdb=" O LEU B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 224 Processing helix chain 'B' and resid 236 through 247 Processing helix chain 'B' and resid 249 through 256 Processing helix chain 'B' and resid 260 through 265 Processing helix chain 'B' and resid 276 through 286 removed outlier: 4.172A pdb=" N ASN B 282 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG B 283 " --> pdb=" O ARG B 280 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG B 286 " --> pdb=" O ARG B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 299 Processing helix chain 'B' and resid 303 through 335 Processing helix chain 'B' and resid 358 through 375 Processing helix chain 'B' and resid 385 through 416 Processing helix chain 'B' and resid 418 through 438 Processing helix chain 'B' and resid 441 through 459 removed outlier: 3.707A pdb=" N LYS B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 471 Processing helix chain 'B' and resid 472 through 484 removed outlier: 3.600A pdb=" N HIS B 484 " --> pdb=" O ALA B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 489 Processing helix chain 'B' and resid 498 through 507 Processing helix chain 'B' and resid 592 through 601 Processing helix chain 'B' and resid 602 through 619 removed outlier: 3.652A pdb=" N ARG B 606 " --> pdb=" O TYR B 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 110 Processing helix chain 'C' and resid 118 through 145 removed outlier: 3.618A pdb=" N TYR C 122 " --> pdb=" O THR C 118 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ILE C 140 " --> pdb=" O LEU C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 224 Processing helix chain 'C' and resid 236 through 247 Processing helix chain 'C' and resid 249 through 256 Processing helix chain 'C' and resid 260 through 265 Processing helix chain 'C' and resid 276 through 286 removed outlier: 4.172A pdb=" N ASN C 282 " --> pdb=" O LEU C 279 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG C 283 " --> pdb=" O ARG C 280 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG C 286 " --> pdb=" O ARG C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 299 Processing helix chain 'C' and resid 303 through 335 Processing helix chain 'C' and resid 358 through 375 Processing helix chain 'C' and resid 385 through 416 Processing helix chain 'C' and resid 418 through 438 Processing helix chain 'C' and resid 441 through 459 removed outlier: 3.707A pdb=" N LYS C 459 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 471 Processing helix chain 'C' and resid 472 through 484 removed outlier: 3.601A pdb=" N HIS C 484 " --> pdb=" O ALA C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 489 Processing helix chain 'C' and resid 498 through 507 Processing helix chain 'C' and resid 592 through 601 Processing helix chain 'C' and resid 602 through 619 removed outlier: 3.652A pdb=" N ARG C 606 " --> pdb=" O TYR C 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 110 Processing helix chain 'D' and resid 118 through 145 removed outlier: 3.618A pdb=" N TYR D 122 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ILE D 140 " --> pdb=" O LEU D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 224 Processing helix chain 'D' and resid 236 through 247 Processing helix chain 'D' and resid 249 through 256 Processing helix chain 'D' and resid 260 through 265 Processing helix chain 'D' and resid 276 through 286 removed outlier: 4.172A pdb=" N ASN D 282 " --> pdb=" O LEU D 279 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG D 283 " --> pdb=" O ARG D 280 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG D 286 " --> pdb=" O ARG D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 299 Processing helix chain 'D' and resid 303 through 335 Processing helix chain 'D' and resid 358 through 375 Processing helix chain 'D' and resid 385 through 416 Processing helix chain 'D' and resid 418 through 438 Processing helix chain 'D' and resid 441 through 459 removed outlier: 3.707A pdb=" N LYS D 459 " --> pdb=" O LEU D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 471 Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.599A pdb=" N HIS D 484 " --> pdb=" O ALA D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 489 Processing helix chain 'D' and resid 498 through 507 Processing helix chain 'D' and resid 592 through 601 Processing helix chain 'D' and resid 602 through 619 removed outlier: 3.652A pdb=" N ARG D 606 " --> pdb=" O TYR D 602 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 166 through 171 removed outlier: 3.692A pdb=" N SER A 166 " --> pdb=" O ASN A 161 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN A 161 " --> pdb=" O SER A 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 511 through 514 removed outlier: 6.714A pdb=" N ASP A 586 " --> pdb=" O LYS A 534 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 519 through 521 removed outlier: 6.659A pdb=" N VAL A 579 " --> pdb=" O ILE A 520 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASN A 578 " --> pdb=" O VAL A 541 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL A 541 " --> pdb=" O ASN A 578 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 166 through 171 removed outlier: 3.693A pdb=" N SER B 166 " --> pdb=" O ASN B 161 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN B 161 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 511 through 514 removed outlier: 6.714A pdb=" N ASP B 586 " --> pdb=" O LYS B 534 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 519 through 521 removed outlier: 6.659A pdb=" N VAL B 579 " --> pdb=" O ILE B 520 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASN B 578 " --> pdb=" O VAL B 541 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL B 541 " --> pdb=" O ASN B 578 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 166 through 171 removed outlier: 3.692A pdb=" N SER C 166 " --> pdb=" O ASN C 161 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN C 161 " --> pdb=" O SER C 166 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 511 through 514 removed outlier: 6.713A pdb=" N ASP C 586 " --> pdb=" O LYS C 534 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 519 through 521 removed outlier: 6.658A pdb=" N VAL C 579 " --> pdb=" O ILE C 520 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASN C 578 " --> pdb=" O VAL C 541 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL C 541 " --> pdb=" O ASN C 578 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 166 through 171 removed outlier: 3.693A pdb=" N SER D 166 " --> pdb=" O ASN D 161 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN D 161 " --> pdb=" O SER D 166 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 511 through 514 removed outlier: 6.715A pdb=" N ASP D 586 " --> pdb=" O LYS D 534 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 519 through 521 removed outlier: 6.659A pdb=" N VAL D 579 " --> pdb=" O ILE D 520 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASN D 578 " --> pdb=" O VAL D 541 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL D 541 " --> pdb=" O ASN D 578 " (cutoff:3.500A) 969 hydrogen bonds defined for protein. 2811 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.30 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2672 1.30 - 1.43: 5063 1.43 - 1.56: 10069 1.56 - 1.68: 32 1.68 - 1.81: 156 Bond restraints: 17992 Sorted by residual: bond pdb=" C11 CPL C1806 " pdb=" O3 CPL C1806 " ideal model delta sigma weight residual 1.327 1.399 -0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C11 CPL A 805 " pdb=" O3 CPL A 805 " ideal model delta sigma weight residual 1.327 1.399 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C11 CPL B1806 " pdb=" O3 CPL B1806 " ideal model delta sigma weight residual 1.327 1.399 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C31 CPL D1801 " pdb=" O2 CPL D1801 " ideal model delta sigma weight residual 1.332 1.404 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C31 CPL B1801 " pdb=" O2 CPL B1801 " ideal model delta sigma weight residual 1.332 1.404 -0.072 2.00e-02 2.50e+03 1.28e+01 ... (remaining 17987 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.86: 23749 3.86 - 7.71: 479 7.71 - 11.57: 52 11.57 - 15.42: 8 15.42 - 19.28: 12 Bond angle restraints: 24300 Sorted by residual: angle pdb=" O3P CPL C1801 " pdb=" P CPL C1801 " pdb=" O4P CPL C1801 " ideal model delta sigma weight residual 93.29 112.57 -19.28 3.00e+00 1.11e-01 4.13e+01 angle pdb=" O3P CPL B1801 " pdb=" P CPL B1801 " pdb=" O4P CPL B1801 " ideal model delta sigma weight residual 93.29 112.57 -19.28 3.00e+00 1.11e-01 4.13e+01 angle pdb=" O3P CPL D1801 " pdb=" P CPL D1801 " pdb=" O4P CPL D1801 " ideal model delta sigma weight residual 93.29 112.56 -19.27 3.00e+00 1.11e-01 4.13e+01 angle pdb=" O3P CPL A 806 " pdb=" P CPL A 806 " pdb=" O4P CPL A 806 " ideal model delta sigma weight residual 93.29 112.53 -19.24 3.00e+00 1.11e-01 4.11e+01 angle pdb=" O3P CPL C1806 " pdb=" P CPL C1806 " pdb=" O4P CPL C1806 " ideal model delta sigma weight residual 93.29 109.99 -16.70 3.00e+00 1.11e-01 3.10e+01 ... (remaining 24295 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.39: 10384 35.39 - 70.77: 300 70.77 - 106.16: 40 106.16 - 141.54: 8 141.54 - 176.93: 8 Dihedral angle restraints: 10740 sinusoidal: 4640 harmonic: 6100 Sorted by residual: dihedral pdb=" CA LYS C 469 " pdb=" C LYS C 469 " pdb=" N VAL C 470 " pdb=" CA VAL C 470 " ideal model delta harmonic sigma weight residual 180.00 -155.08 -24.92 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA LYS D 469 " pdb=" C LYS D 469 " pdb=" N VAL D 470 " pdb=" CA VAL D 470 " ideal model delta harmonic sigma weight residual -180.00 -155.11 -24.89 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA LYS B 469 " pdb=" C LYS B 469 " pdb=" N VAL B 470 " pdb=" CA VAL B 470 " ideal model delta harmonic sigma weight residual -180.00 -155.13 -24.87 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 10737 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1926 0.060 - 0.121: 553 0.121 - 0.181: 99 0.181 - 0.241: 54 0.241 - 0.302: 12 Chirality restraints: 2644 Sorted by residual: chirality pdb=" CA PHE A 403 " pdb=" N PHE A 403 " pdb=" C PHE A 403 " pdb=" CB PHE A 403 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CA PHE C 403 " pdb=" N PHE C 403 " pdb=" C PHE C 403 " pdb=" CB PHE C 403 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CA PHE D 403 " pdb=" N PHE D 403 " pdb=" C PHE D 403 " pdb=" CB PHE D 403 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.22e+00 ... (remaining 2641 not shown) Planarity restraints: 2960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 150 " -0.051 5.00e-02 4.00e+02 7.72e-02 9.54e+00 pdb=" N PRO C 151 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO C 151 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 151 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 150 " 0.051 5.00e-02 4.00e+02 7.69e-02 9.47e+00 pdb=" N PRO A 151 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 151 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 151 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 150 " -0.051 5.00e-02 4.00e+02 7.69e-02 9.47e+00 pdb=" N PRO D 151 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO D 151 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 151 " -0.043 5.00e-02 4.00e+02 ... (remaining 2957 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.86: 6170 2.86 - 3.37: 15520 3.37 - 3.88: 29624 3.88 - 4.39: 33379 4.39 - 4.90: 57961 Nonbonded interactions: 142654 Sorted by model distance: nonbonded pdb=" OH TYR C 112 " pdb=" OE1 GLN C 114 " model vdw 2.355 3.040 nonbonded pdb=" OH TYR A 112 " pdb=" OE1 GLN A 114 " model vdw 2.355 3.040 nonbonded pdb=" OH TYR D 112 " pdb=" OE1 GLN D 114 " model vdw 2.356 3.040 nonbonded pdb=" OH TYR B 112 " pdb=" OE1 GLN B 114 " model vdw 2.356 3.040 nonbonded pdb=" O ASP D 453 " pdb=" OG1 THR D 457 " model vdw 2.368 3.040 ... (remaining 142649 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 103 through 619 or (resid 801 and (name C1 or name C11 or \ name C12 or name C13 or name C14 or name C2 or name C3 or name C31 or name C32 o \ r name C33 or name C34 or name C4 or name C5 or name O11 or name O1P or name O2 \ or name O2P or name O3 or name O31 or name O3P or name O4P or name P )) or (resi \ d 802 through 803 and (name C12 or name C13 or name C14 or name C15 or name C16 \ or name C17 or name C18 or name C19)) or (resid 804 through 805 and (name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C1 \ 9 or name C20 or name C21 or name C22 or name C23)) or (resid 806 and (name C1 o \ r name C11 or name C12 or name C13 or name C14 or name C2 or name C3 or name C31 \ or name C32 or name C33 or name C34 or name O11 or name O1P or name O2 or name \ O2P or name O3 or name O31 or name O3P or name O4P or name P )))) selection = (chain 'B' and (resid 103 through 1801 or (resid 1802 through 1803 and (name C12 \ or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name \ C19)) or (resid 1804 through 1805 and (name C12 or name C13 or name C14 or name \ C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C21 or \ name C22 or name C23)) or (resid 1806 and (name C1 or name C11 or name C12 or na \ me C13 or name C14 or name C2 or name C3 or name C31 or name C32 or name C33 or \ name C34 or name O11 or name O1P or name O2 or name O2P or name O3 or name O31 o \ r name O3P or name O4P or name P )))) selection = (chain 'C' and (resid 103 through 1801 or (resid 1802 through 1803 and (name C12 \ or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name \ C19)) or (resid 1804 through 1805 and (name C12 or name C13 or name C14 or name \ C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C21 or \ name C22 or name C23)) or (resid 1806 and (name C1 or name C11 or name C12 or na \ me C13 or name C14 or name C2 or name C3 or name C31 or name C32 or name C33 or \ name C34 or name O11 or name O1P or name O2 or name O2P or name O3 or name O31 o \ r name O3P or name O4P or name P )))) selection = (chain 'D' and (resid 103 through 1801 or (resid 1802 through 1803 and (name C12 \ or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name \ C19)) or (resid 1804 through 1805 and (name C12 or name C13 or name C14 or name \ C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C21 or \ name C22 or name C23)) or (resid 1806 and (name C1 or name C11 or name C12 or na \ me C13 or name C14 or name C2 or name C3 or name C31 or name C32 or name C33 or \ name C34 or name O11 or name O1P or name O2 or name O2P or name O3 or name O31 o \ r name O3P or name O4P or name P )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.700 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: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.150 Find NCS groups from input model: 0.350 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.103 17996 Z= 0.407 Angle : 1.325 19.278 24308 Z= 0.649 Chirality : 0.065 0.302 2644 Planarity : 0.009 0.077 2960 Dihedral : 18.631 176.927 6816 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.28 % Allowed : 6.62 % Favored : 92.09 % Cbeta Deviations : 0.20 % 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: -4.58 (0.12), residues: 2060 helix: -3.59 (0.08), residues: 1204 sheet: -1.96 (0.32), residues: 192 loop : -1.70 (0.18), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 614 TYR 0.029 0.003 TYR D 363 PHE 0.019 0.003 PHE D 328 TRP 0.027 0.003 TRP D 266 HIS 0.006 0.002 HIS C 199 Details of bonding type rmsd covalent geometry : bond 0.00943 (17992) covalent geometry : angle 1.32481 (24300) SS BOND : bond 0.00880 ( 4) SS BOND : angle 1.06060 ( 8) hydrogen bonds : bond 0.17260 ( 969) hydrogen bonds : angle 7.42289 ( 2811) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 296 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: A 112 TYR cc_start: 0.8466 (t80) cc_final: 0.7997 (t80) REVERT: A 270 TYR cc_start: 0.7490 (m-80) cc_final: 0.7161 (m-80) REVERT: A 397 MET cc_start: 0.7596 (mmm) cc_final: 0.7249 (mtm) REVERT: A 426 ASN cc_start: 0.8321 (m110) cc_final: 0.7894 (m110) REVERT: A 478 GLU cc_start: 0.8256 (tp30) cc_final: 0.7925 (tp30) REVERT: A 537 ARG cc_start: 0.7976 (ttm-80) cc_final: 0.7636 (ttm110) REVERT: B 112 TYR cc_start: 0.8455 (t80) cc_final: 0.7934 (t80) REVERT: B 270 TYR cc_start: 0.7479 (m-80) cc_final: 0.7158 (m-80) REVERT: B 397 MET cc_start: 0.7596 (mmm) cc_final: 0.7214 (mtm) REVERT: B 426 ASN cc_start: 0.8310 (m110) cc_final: 0.7934 (m110) REVERT: B 478 GLU cc_start: 0.8233 (tp30) cc_final: 0.7889 (tp30) REVERT: B 537 ARG cc_start: 0.8005 (ttm-80) cc_final: 0.7264 (ttm110) REVERT: C 112 TYR cc_start: 0.8454 (t80) cc_final: 0.7957 (t80) REVERT: C 270 TYR cc_start: 0.7506 (m-80) cc_final: 0.7180 (m-80) REVERT: C 397 MET cc_start: 0.7598 (mmm) cc_final: 0.7238 (mtm) REVERT: C 426 ASN cc_start: 0.8259 (m110) cc_final: 0.7884 (m110) REVERT: C 478 GLU cc_start: 0.8212 (tp30) cc_final: 0.7873 (tp30) REVERT: C 537 ARG cc_start: 0.7961 (ttm-80) cc_final: 0.7274 (ttm110) REVERT: D 270 TYR cc_start: 0.7511 (m-80) cc_final: 0.7182 (m-80) REVERT: D 397 MET cc_start: 0.7554 (mmm) cc_final: 0.7207 (mtm) REVERT: D 426 ASN cc_start: 0.8324 (m110) cc_final: 0.7917 (m110) REVERT: D 478 GLU cc_start: 0.8232 (tp30) cc_final: 0.7905 (tp30) REVERT: D 537 ARG cc_start: 0.7933 (ttm-80) cc_final: 0.7606 (ttm110) REVERT: D 558 PHE cc_start: 0.8292 (p90) cc_final: 0.7988 (p90) outliers start: 24 outliers final: 4 residues processed: 316 average time/residue: 0.1251 time to fit residues: 58.7269 Evaluate side-chains 221 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 217 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 205 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.0670 chunk 200 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 GLN A 426 ASN A 578 ASN B 426 ASN B 482 GLN B 578 ASN C 426 ASN C 578 ASN D 246 GLN D 425 GLN D 482 GLN D 578 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.175504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.132258 restraints weight = 20153.329| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 3.25 r_work: 0.3102 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17996 Z= 0.113 Angle : 0.541 7.236 24308 Z= 0.283 Chirality : 0.040 0.154 2644 Planarity : 0.005 0.038 2960 Dihedral : 15.568 172.363 2728 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.53 % Allowed : 8.87 % Favored : 90.60 % 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: -1.33 (0.16), residues: 2060 helix: -0.66 (0.13), residues: 1188 sheet: -0.77 (0.36), residues: 184 loop : -1.01 (0.20), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 280 TYR 0.012 0.001 TYR D 363 PHE 0.018 0.001 PHE B 558 TRP 0.016 0.001 TRP A 329 HIS 0.001 0.000 HIS B 199 Details of bonding type rmsd covalent geometry : bond 0.00241 (17992) covalent geometry : angle 0.54055 (24300) SS BOND : bond 0.00039 ( 4) SS BOND : angle 0.82083 ( 8) hydrogen bonds : bond 0.04207 ( 969) hydrogen bonds : angle 4.68683 ( 2811) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 257 time to evaluate : 0.507 Fit side-chains REVERT: A 262 TYR cc_start: 0.8815 (m-80) cc_final: 0.8525 (m-80) REVERT: A 270 TYR cc_start: 0.7947 (m-80) cc_final: 0.7659 (m-80) REVERT: A 426 ASN cc_start: 0.8157 (m-40) cc_final: 0.7733 (m110) REVERT: A 478 GLU cc_start: 0.8138 (tp30) cc_final: 0.7784 (tp30) REVERT: A 481 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.8016 (mmm) REVERT: A 537 ARG cc_start: 0.8202 (ttm-80) cc_final: 0.7859 (ttm110) REVERT: A 588 PHE cc_start: 0.8528 (m-80) cc_final: 0.8228 (m-10) REVERT: B 262 TYR cc_start: 0.8800 (m-80) cc_final: 0.8516 (m-80) REVERT: B 270 TYR cc_start: 0.7943 (m-80) cc_final: 0.7666 (m-80) REVERT: B 426 ASN cc_start: 0.8190 (m-40) cc_final: 0.7753 (m110) REVERT: B 478 GLU cc_start: 0.8212 (tp30) cc_final: 0.7886 (tp30) REVERT: B 485 PHE cc_start: 0.8250 (t80) cc_final: 0.7851 (t80) REVERT: B 510 GLN cc_start: 0.8023 (pt0) cc_final: 0.7713 (mt0) REVERT: B 537 ARG cc_start: 0.8194 (ttm-80) cc_final: 0.7863 (ttm110) REVERT: B 588 PHE cc_start: 0.8492 (m-80) cc_final: 0.8250 (m-10) REVERT: C 262 TYR cc_start: 0.8798 (m-80) cc_final: 0.8514 (m-80) REVERT: C 270 TYR cc_start: 0.7935 (m-80) cc_final: 0.7665 (m-80) REVERT: C 426 ASN cc_start: 0.8079 (m-40) cc_final: 0.7663 (m110) REVERT: C 478 GLU cc_start: 0.8165 (tp30) cc_final: 0.7798 (tp30) REVERT: C 481 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.8035 (mmm) REVERT: C 529 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7461 (mt-10) REVERT: C 535 ARG cc_start: 0.8194 (ttp-110) cc_final: 0.7431 (ttp80) REVERT: C 537 ARG cc_start: 0.8204 (ttm-80) cc_final: 0.7900 (ttm110) REVERT: C 588 PHE cc_start: 0.8448 (m-80) cc_final: 0.8079 (m-10) REVERT: D 270 TYR cc_start: 0.7947 (m-80) cc_final: 0.7657 (m-80) REVERT: D 426 ASN cc_start: 0.8277 (m110) cc_final: 0.7861 (m110) REVERT: D 478 GLU cc_start: 0.8203 (tp30) cc_final: 0.7838 (tp30) REVERT: D 535 ARG cc_start: 0.8231 (ttp-110) cc_final: 0.7564 (ttp80) REVERT: D 537 ARG cc_start: 0.8228 (ttm-80) cc_final: 0.7856 (ttm110) outliers start: 10 outliers final: 2 residues processed: 264 average time/residue: 0.1134 time to fit residues: 46.2453 Evaluate side-chains 221 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 217 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 481 MET Chi-restraints excluded: chain C residue 481 MET Chi-restraints excluded: chain D residue 382 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 159 optimal weight: 3.9990 chunk 178 optimal weight: 0.7980 chunk 185 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 40 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 164 optimal weight: 0.7980 chunk 165 optimal weight: 4.9990 chunk 146 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 GLN B 425 GLN B 482 GLN C 425 GLN C 460 GLN D 426 ASN D 482 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.173093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.111878 restraints weight = 20360.851| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.96 r_work: 0.3147 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 17996 Z= 0.145 Angle : 0.527 7.482 24308 Z= 0.271 Chirality : 0.041 0.151 2644 Planarity : 0.004 0.037 2960 Dihedral : 13.777 159.316 2724 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.91 % Allowed : 11.49 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.04 (0.18), residues: 2060 helix: 0.48 (0.15), residues: 1184 sheet: -0.12 (0.38), residues: 160 loop : -0.69 (0.21), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 280 TYR 0.015 0.001 TYR B 363 PHE 0.023 0.002 PHE C 558 TRP 0.012 0.001 TRP D 329 HIS 0.002 0.001 HIS C 321 Details of bonding type rmsd covalent geometry : bond 0.00339 (17992) covalent geometry : angle 0.52693 (24300) SS BOND : bond 0.00033 ( 4) SS BOND : angle 0.77871 ( 8) hydrogen bonds : bond 0.04038 ( 969) hydrogen bonds : angle 4.28923 ( 2811) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 225 time to evaluate : 0.666 Fit side-chains REVERT: A 270 TYR cc_start: 0.8078 (m-80) cc_final: 0.7782 (m-80) REVERT: A 416 ASN cc_start: 0.8828 (t0) cc_final: 0.8615 (t0) REVERT: A 426 ASN cc_start: 0.8223 (m-40) cc_final: 0.7794 (m110) REVERT: A 436 GLU cc_start: 0.8024 (tp30) cc_final: 0.7741 (tp30) REVERT: A 478 GLU cc_start: 0.8195 (tp30) cc_final: 0.7792 (tp30) REVERT: A 481 MET cc_start: 0.8419 (mmt) cc_final: 0.8051 (mmm) REVERT: A 537 ARG cc_start: 0.8304 (ttm-80) cc_final: 0.7999 (ttm110) REVERT: A 588 PHE cc_start: 0.8591 (m-80) cc_final: 0.8275 (m-10) REVERT: B 270 TYR cc_start: 0.8036 (m-80) cc_final: 0.7733 (m-80) REVERT: B 426 ASN cc_start: 0.8261 (m-40) cc_final: 0.7817 (m110) REVERT: B 436 GLU cc_start: 0.8042 (tp30) cc_final: 0.7823 (tp30) REVERT: B 453 ASP cc_start: 0.7658 (m-30) cc_final: 0.7208 (m-30) REVERT: B 478 GLU cc_start: 0.8249 (tp30) cc_final: 0.7872 (tp30) REVERT: B 485 PHE cc_start: 0.8255 (t80) cc_final: 0.7830 (t80) REVERT: B 535 ARG cc_start: 0.8247 (ttp-110) cc_final: 0.7471 (ttp80) REVERT: B 537 ARG cc_start: 0.8343 (ttm-80) cc_final: 0.8038 (ttm110) REVERT: C 262 TYR cc_start: 0.8780 (m-80) cc_final: 0.8568 (m-80) REVERT: C 270 TYR cc_start: 0.8060 (m-80) cc_final: 0.7763 (m-80) REVERT: C 426 ASN cc_start: 0.8207 (m-40) cc_final: 0.7769 (m110) REVERT: C 453 ASP cc_start: 0.7652 (m-30) cc_final: 0.7221 (m-30) REVERT: C 478 GLU cc_start: 0.8173 (tp30) cc_final: 0.7946 (tp30) REVERT: C 481 MET cc_start: 0.8449 (mmt) cc_final: 0.8096 (mmm) REVERT: C 535 ARG cc_start: 0.8249 (ttp-110) cc_final: 0.7520 (ttp80) REVERT: C 537 ARG cc_start: 0.8362 (ttm-80) cc_final: 0.7935 (ttm110) REVERT: C 588 PHE cc_start: 0.8552 (m-80) cc_final: 0.8222 (m-10) REVERT: D 191 ASP cc_start: 0.8995 (p0) cc_final: 0.8773 (p0) REVERT: D 262 TYR cc_start: 0.8869 (m-80) cc_final: 0.8619 (m-80) REVERT: D 270 TYR cc_start: 0.8052 (m-80) cc_final: 0.7747 (m-80) REVERT: D 426 ASN cc_start: 0.8311 (m-40) cc_final: 0.7885 (m110) REVERT: D 478 GLU cc_start: 0.8244 (tp30) cc_final: 0.7863 (tp30) REVERT: D 529 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7571 (mt-10) REVERT: D 535 ARG cc_start: 0.8259 (ttp-110) cc_final: 0.7584 (ttp80) outliers start: 17 outliers final: 8 residues processed: 239 average time/residue: 0.1298 time to fit residues: 46.2089 Evaluate side-chains 216 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 208 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 460 GLN Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 382 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 198 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 chunk 67 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 160 optimal weight: 0.0050 chunk 195 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 GLN ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.173483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.112917 restraints weight = 20445.076| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.90 r_work: 0.3165 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17996 Z= 0.135 Angle : 0.506 7.251 24308 Z= 0.260 Chirality : 0.041 0.152 2644 Planarity : 0.003 0.037 2960 Dihedral : 12.847 146.882 2724 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.23 % Allowed : 11.43 % Favored : 87.34 % 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: 0.43 (0.18), residues: 2060 helix: 0.84 (0.15), residues: 1208 sheet: 0.13 (0.37), residues: 160 loop : -0.50 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 438 TYR 0.014 0.001 TYR B 363 PHE 0.016 0.001 PHE C 558 TRP 0.010 0.001 TRP C 329 HIS 0.001 0.000 HIS B 321 Details of bonding type rmsd covalent geometry : bond 0.00313 (17992) covalent geometry : angle 0.50608 (24300) SS BOND : bond 0.00075 ( 4) SS BOND : angle 0.73017 ( 8) hydrogen bonds : bond 0.03815 ( 969) hydrogen bonds : angle 4.09211 ( 2811) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 226 time to evaluate : 0.747 Fit side-chains REVERT: A 191 ASP cc_start: 0.8981 (p0) cc_final: 0.8778 (p0) REVERT: A 262 TYR cc_start: 0.8889 (m-80) cc_final: 0.8550 (m-80) REVERT: A 270 TYR cc_start: 0.8064 (m-80) cc_final: 0.7785 (m-80) REVERT: A 426 ASN cc_start: 0.8215 (m-40) cc_final: 0.7783 (m110) REVERT: A 436 GLU cc_start: 0.7990 (tp30) cc_final: 0.7678 (tp30) REVERT: A 478 GLU cc_start: 0.8164 (tp30) cc_final: 0.7766 (tp30) REVERT: A 481 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.8083 (mmm) REVERT: A 537 ARG cc_start: 0.8308 (ttm-80) cc_final: 0.7919 (ttm110) REVERT: B 262 TYR cc_start: 0.8881 (m-80) cc_final: 0.8554 (m-80) REVERT: B 270 TYR cc_start: 0.8017 (m-80) cc_final: 0.7746 (t80) REVERT: B 426 ASN cc_start: 0.8228 (m-40) cc_final: 0.7795 (m110) REVERT: B 436 GLU cc_start: 0.7982 (tp30) cc_final: 0.7731 (tp30) REVERT: B 453 ASP cc_start: 0.7648 (m-30) cc_final: 0.7092 (m-30) REVERT: B 478 GLU cc_start: 0.8207 (tp30) cc_final: 0.7837 (tp30) REVERT: B 481 MET cc_start: 0.8452 (mmt) cc_final: 0.8125 (mmm) REVERT: B 485 PHE cc_start: 0.8254 (t80) cc_final: 0.7826 (t80) REVERT: B 535 ARG cc_start: 0.8244 (ttp-110) cc_final: 0.7518 (ttp80) REVERT: B 537 ARG cc_start: 0.8331 (ttm-80) cc_final: 0.7939 (ttm110) REVERT: B 554 GLU cc_start: 0.8375 (tm-30) cc_final: 0.8173 (tm-30) REVERT: C 191 ASP cc_start: 0.8997 (p0) cc_final: 0.8791 (p0) REVERT: C 270 TYR cc_start: 0.7997 (m-80) cc_final: 0.7703 (m-80) REVERT: C 426 ASN cc_start: 0.8178 (m-40) cc_final: 0.7757 (m110) REVERT: C 453 ASP cc_start: 0.7646 (m-30) cc_final: 0.7107 (m-30) REVERT: C 478 GLU cc_start: 0.8170 (tp30) cc_final: 0.7941 (tp30) REVERT: C 481 MET cc_start: 0.8421 (mmt) cc_final: 0.8085 (mmm) REVERT: C 537 ARG cc_start: 0.8330 (ttm-80) cc_final: 0.7929 (ttm110) REVERT: C 554 GLU cc_start: 0.8384 (tm-30) cc_final: 0.8160 (tm-30) REVERT: C 588 PHE cc_start: 0.8552 (m-80) cc_final: 0.8222 (m-10) REVERT: C 589 VAL cc_start: 0.8893 (t) cc_final: 0.8666 (m) REVERT: D 191 ASP cc_start: 0.8984 (p0) cc_final: 0.8770 (p0) REVERT: D 262 TYR cc_start: 0.8797 (m-80) cc_final: 0.8538 (m-80) REVERT: D 270 TYR cc_start: 0.8040 (m-80) cc_final: 0.7758 (m-80) REVERT: D 423 GLU cc_start: 0.8458 (tp30) cc_final: 0.8199 (tp30) REVERT: D 426 ASN cc_start: 0.8293 (m-40) cc_final: 0.7865 (m110) REVERT: D 478 GLU cc_start: 0.8215 (tp30) cc_final: 0.7839 (tp30) REVERT: D 481 MET cc_start: 0.8377 (mmt) cc_final: 0.8026 (mmm) REVERT: D 485 PHE cc_start: 0.8126 (t80) cc_final: 0.7758 (t80) REVERT: D 537 ARG cc_start: 0.8281 (ttm-80) cc_final: 0.7918 (ttm110) outliers start: 23 outliers final: 13 residues processed: 242 average time/residue: 0.1490 time to fit residues: 54.6474 Evaluate side-chains 217 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 203 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 481 MET Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 382 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 153 optimal weight: 20.0000 chunk 79 optimal weight: 1.9990 chunk 90 optimal weight: 20.0000 chunk 91 optimal weight: 4.9990 chunk 201 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 113 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 134 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 GLN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.171133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.126459 restraints weight = 20299.094| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 3.60 r_work: 0.2986 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17996 Z= 0.171 Angle : 0.532 7.481 24308 Z= 0.275 Chirality : 0.041 0.150 2644 Planarity : 0.004 0.037 2960 Dihedral : 12.413 134.637 2724 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.39 % Allowed : 11.65 % Favored : 86.97 % 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: 0.57 (0.18), residues: 2060 helix: 0.94 (0.15), residues: 1204 sheet: 0.22 (0.37), residues: 160 loop : -0.42 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 580 TYR 0.014 0.001 TYR B 363 PHE 0.016 0.002 PHE C 328 TRP 0.010 0.001 TRP A 329 HIS 0.002 0.001 HIS C 321 Details of bonding type rmsd covalent geometry : bond 0.00407 (17992) covalent geometry : angle 0.53153 (24300) SS BOND : bond 0.00031 ( 4) SS BOND : angle 0.70319 ( 8) hydrogen bonds : bond 0.03989 ( 969) hydrogen bonds : angle 4.08875 ( 2811) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 212 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 262 TYR cc_start: 0.8804 (m-80) cc_final: 0.8573 (m-80) REVERT: A 270 TYR cc_start: 0.8046 (m-80) cc_final: 0.7781 (m-80) REVERT: A 423 GLU cc_start: 0.8442 (tp30) cc_final: 0.8177 (tp30) REVERT: A 426 ASN cc_start: 0.8267 (m-40) cc_final: 0.7831 (m110) REVERT: A 436 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7665 (tp30) REVERT: A 478 GLU cc_start: 0.8201 (tp30) cc_final: 0.7800 (tp30) REVERT: A 481 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.8065 (mmm) REVERT: A 537 ARG cc_start: 0.8287 (ttm-80) cc_final: 0.7818 (ttm110) REVERT: B 262 TYR cc_start: 0.8791 (m-80) cc_final: 0.8562 (m-80) REVERT: B 270 TYR cc_start: 0.8018 (m-80) cc_final: 0.7785 (t80) REVERT: B 423 GLU cc_start: 0.8436 (tp30) cc_final: 0.8161 (tp30) REVERT: B 426 ASN cc_start: 0.8312 (m-40) cc_final: 0.7913 (m110) REVERT: B 436 GLU cc_start: 0.8017 (tp30) cc_final: 0.7718 (tp30) REVERT: B 478 GLU cc_start: 0.8260 (tp30) cc_final: 0.7872 (tp30) REVERT: B 485 PHE cc_start: 0.8210 (t80) cc_final: 0.7778 (t80) REVERT: B 535 ARG cc_start: 0.8268 (ttp-110) cc_final: 0.7830 (ttp80) REVERT: B 537 ARG cc_start: 0.8343 (ttm-80) cc_final: 0.7912 (ttm110) REVERT: B 554 GLU cc_start: 0.8353 (tm-30) cc_final: 0.8139 (tm-30) REVERT: C 262 TYR cc_start: 0.8870 (m-80) cc_final: 0.8539 (m-80) REVERT: C 270 TYR cc_start: 0.8028 (m-80) cc_final: 0.7784 (t80) REVERT: C 423 GLU cc_start: 0.8438 (tp30) cc_final: 0.8182 (tp30) REVERT: C 426 ASN cc_start: 0.8226 (m-40) cc_final: 0.7805 (m110) REVERT: C 478 GLU cc_start: 0.8224 (tp30) cc_final: 0.7816 (tp30) REVERT: C 481 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.8025 (mmm) REVERT: C 537 ARG cc_start: 0.8298 (ttm-80) cc_final: 0.7825 (ttm110) REVERT: C 554 GLU cc_start: 0.8371 (tm-30) cc_final: 0.8142 (tm-30) REVERT: C 588 PHE cc_start: 0.8578 (m-80) cc_final: 0.8293 (m-10) REVERT: C 589 VAL cc_start: 0.8893 (t) cc_final: 0.8682 (m) REVERT: D 191 ASP cc_start: 0.8980 (p0) cc_final: 0.8778 (p0) REVERT: D 262 TYR cc_start: 0.8773 (m-80) cc_final: 0.8516 (m-80) REVERT: D 270 TYR cc_start: 0.8049 (m-80) cc_final: 0.7781 (m-80) REVERT: D 423 GLU cc_start: 0.8467 (tp30) cc_final: 0.8205 (tp30) REVERT: D 426 ASN cc_start: 0.8307 (m-40) cc_final: 0.7884 (m110) REVERT: D 478 GLU cc_start: 0.8259 (tp30) cc_final: 0.7868 (tp30) REVERT: D 535 ARG cc_start: 0.8336 (ttp80) cc_final: 0.7969 (ttp80) REVERT: D 537 ARG cc_start: 0.8315 (ttm-80) cc_final: 0.7861 (ttm110) outliers start: 26 outliers final: 18 residues processed: 226 average time/residue: 0.1408 time to fit residues: 48.9322 Evaluate side-chains 226 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 205 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 436 GLU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 481 MET Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 481 MET Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 382 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 108 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 51 optimal weight: 20.0000 chunk 55 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 199 HIS ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 HIS ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 GLN ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.172489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.111523 restraints weight = 20317.422| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.92 r_work: 0.3140 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17996 Z= 0.140 Angle : 0.506 8.823 24308 Z= 0.261 Chirality : 0.040 0.145 2644 Planarity : 0.003 0.037 2960 Dihedral : 11.384 111.031 2724 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.23 % Allowed : 12.93 % Favored : 85.84 % 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 aren not related in a simple way. whole: 0.79 (0.19), residues: 2060 helix: 1.09 (0.15), residues: 1204 sheet: 0.48 (0.37), residues: 160 loop : -0.33 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 580 TYR 0.014 0.001 TYR B 363 PHE 0.014 0.001 PHE C 328 TRP 0.010 0.001 TRP C 124 HIS 0.001 0.001 HIS D 321 Details of bonding type rmsd covalent geometry : bond 0.00327 (17992) covalent geometry : angle 0.50587 (24300) SS BOND : bond 0.00041 ( 4) SS BOND : angle 0.66659 ( 8) hydrogen bonds : bond 0.03745 ( 969) hydrogen bonds : angle 3.98493 ( 2811) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 206 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 270 TYR cc_start: 0.8057 (m-80) cc_final: 0.7731 (t80) REVERT: A 423 GLU cc_start: 0.8486 (tp30) cc_final: 0.8222 (tp30) REVERT: A 426 ASN cc_start: 0.8234 (m-40) cc_final: 0.7797 (m110) REVERT: A 436 GLU cc_start: 0.8013 (tp30) cc_final: 0.7667 (tp30) REVERT: A 478 GLU cc_start: 0.8184 (tp30) cc_final: 0.7773 (tp30) REVERT: A 481 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.8088 (mmm) REVERT: A 537 ARG cc_start: 0.8295 (ttm-80) cc_final: 0.7848 (ttm110) REVERT: A 586 ASP cc_start: 0.8684 (m-30) cc_final: 0.8276 (m-30) REVERT: B 270 TYR cc_start: 0.8013 (m-80) cc_final: 0.7726 (t80) REVERT: B 423 GLU cc_start: 0.8437 (tp30) cc_final: 0.8182 (tp30) REVERT: B 426 ASN cc_start: 0.8271 (m-40) cc_final: 0.7889 (m110) REVERT: B 436 GLU cc_start: 0.7971 (tp30) cc_final: 0.7683 (tp30) REVERT: B 478 GLU cc_start: 0.8212 (tp30) cc_final: 0.7843 (tp30) REVERT: B 485 PHE cc_start: 0.8201 (t80) cc_final: 0.7787 (t80) REVERT: B 535 ARG cc_start: 0.8292 (ttp-110) cc_final: 0.7888 (ttp80) REVERT: B 537 ARG cc_start: 0.8337 (ttm-80) cc_final: 0.7869 (ttm110) REVERT: C 270 TYR cc_start: 0.8014 (m-80) cc_final: 0.7740 (t80) REVERT: C 423 GLU cc_start: 0.8452 (tp30) cc_final: 0.8197 (tp30) REVERT: C 426 ASN cc_start: 0.8189 (m-40) cc_final: 0.7761 (m110) REVERT: C 436 GLU cc_start: 0.7971 (tp30) cc_final: 0.7739 (tp30) REVERT: C 478 GLU cc_start: 0.8191 (tp30) cc_final: 0.7775 (tp30) REVERT: C 481 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.8081 (mmm) REVERT: C 537 ARG cc_start: 0.8267 (ttm-80) cc_final: 0.7821 (ttm110) REVERT: C 586 ASP cc_start: 0.8645 (m-30) cc_final: 0.8283 (m-30) REVERT: C 588 PHE cc_start: 0.8519 (m-80) cc_final: 0.8234 (m-10) REVERT: D 270 TYR cc_start: 0.8028 (m-80) cc_final: 0.7687 (t80) REVERT: D 423 GLU cc_start: 0.8495 (tp30) cc_final: 0.8243 (tp30) REVERT: D 426 ASN cc_start: 0.8251 (m-40) cc_final: 0.7825 (m110) REVERT: D 478 GLU cc_start: 0.8225 (tp30) cc_final: 0.7852 (tp30) REVERT: D 485 PHE cc_start: 0.8127 (t80) cc_final: 0.7765 (t80) REVERT: D 535 ARG cc_start: 0.8262 (ttp80) cc_final: 0.7935 (ttp80) REVERT: D 537 ARG cc_start: 0.8328 (ttm-80) cc_final: 0.7876 (ttm110) outliers start: 23 outliers final: 13 residues processed: 223 average time/residue: 0.1347 time to fit residues: 46.8135 Evaluate side-chains 213 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 198 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 481 MET Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 481 MET Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 493 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 20 optimal weight: 0.9990 chunk 146 optimal weight: 9.9990 chunk 111 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 185 optimal weight: 4.9990 chunk 172 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 159 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 ASN ** 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 = 0.3988 r_free = 0.3988 target = 0.170324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.112081 restraints weight = 20365.244| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.25 r_work: 0.3086 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 17996 Z= 0.191 Angle : 0.555 8.598 24308 Z= 0.284 Chirality : 0.042 0.160 2644 Planarity : 0.003 0.037 2960 Dihedral : 10.372 57.740 2724 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.60 % Allowed : 12.87 % Favored : 85.52 % 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: 0.69 (0.19), residues: 2060 helix: 1.05 (0.15), residues: 1204 sheet: 0.30 (0.37), residues: 168 loop : -0.40 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 580 TYR 0.014 0.001 TYR B 363 PHE 0.016 0.002 PHE C 328 TRP 0.010 0.001 TRP B 596 HIS 0.004 0.001 HIS B 199 Details of bonding type rmsd covalent geometry : bond 0.00458 (17992) covalent geometry : angle 0.55534 (24300) SS BOND : bond 0.00014 ( 4) SS BOND : angle 0.69037 ( 8) hydrogen bonds : bond 0.04059 ( 969) hydrogen bonds : angle 4.05846 ( 2811) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 201 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 423 GLU cc_start: 0.8531 (tp30) cc_final: 0.8261 (tp30) REVERT: A 426 ASN cc_start: 0.8361 (m-40) cc_final: 0.7966 (m110) REVERT: A 436 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7699 (tp30) REVERT: A 478 GLU cc_start: 0.8211 (tp30) cc_final: 0.7810 (tp30) REVERT: A 481 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.8067 (mmm) REVERT: A 537 ARG cc_start: 0.8350 (ttm-80) cc_final: 0.7821 (ttm110) REVERT: A 586 ASP cc_start: 0.8710 (m-30) cc_final: 0.8280 (m-30) REVERT: B 270 TYR cc_start: 0.8080 (m-80) cc_final: 0.7796 (t80) REVERT: B 423 GLU cc_start: 0.8500 (tp30) cc_final: 0.8230 (tp30) REVERT: B 426 ASN cc_start: 0.8376 (m-40) cc_final: 0.7974 (m110) REVERT: B 436 GLU cc_start: 0.8038 (tp30) cc_final: 0.7748 (tp30) REVERT: B 478 GLU cc_start: 0.8264 (tp30) cc_final: 0.7889 (tp30) REVERT: B 485 PHE cc_start: 0.8193 (t80) cc_final: 0.7783 (t80) REVERT: B 535 ARG cc_start: 0.8348 (ttp-110) cc_final: 0.8006 (ttp80) REVERT: B 537 ARG cc_start: 0.8352 (ttm-80) cc_final: 0.7852 (ttm110) REVERT: C 423 GLU cc_start: 0.8513 (tp30) cc_final: 0.8253 (tp30) REVERT: C 426 ASN cc_start: 0.8356 (m-40) cc_final: 0.7967 (m110) REVERT: C 438 ARG cc_start: 0.7716 (mpt180) cc_final: 0.7351 (mpt180) REVERT: C 478 GLU cc_start: 0.8248 (tp30) cc_final: 0.7835 (tp30) REVERT: C 481 MET cc_start: 0.8379 (OUTLIER) cc_final: 0.8046 (mmm) REVERT: C 537 ARG cc_start: 0.8342 (ttm-80) cc_final: 0.7841 (ttm110) REVERT: C 586 ASP cc_start: 0.8626 (m-30) cc_final: 0.8214 (m-30) REVERT: D 262 TYR cc_start: 0.8874 (m-80) cc_final: 0.8609 (m-80) REVERT: D 423 GLU cc_start: 0.8550 (tp30) cc_final: 0.8275 (tp30) REVERT: D 426 ASN cc_start: 0.8342 (m-40) cc_final: 0.7908 (m110) REVERT: D 478 GLU cc_start: 0.8306 (tp30) cc_final: 0.7927 (tp30) REVERT: D 535 ARG cc_start: 0.8347 (ttp80) cc_final: 0.7887 (ttp80) REVERT: D 537 ARG cc_start: 0.8342 (ttm-80) cc_final: 0.7842 (ttm110) outliers start: 30 outliers final: 21 residues processed: 219 average time/residue: 0.1375 time to fit residues: 47.2665 Evaluate side-chains 221 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 197 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 436 GLU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 481 MET Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 481 MET Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 557 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- 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: 52.5769 > 50: distance: 11 - 112: 22.456 distance: 14 - 109: 9.146 distance: 26 - 93: 27.926 distance: 29 - 90: 14.081 distance: 62 - 66: 11.897 distance: 66 - 67: 11.561 distance: 67 - 68: 20.445 distance: 67 - 70: 19.262 distance: 68 - 69: 20.940 distance: 68 - 75: 16.729 distance: 70 - 71: 26.696 distance: 71 - 72: 7.413 distance: 72 - 74: 15.697 distance: 75 - 76: 16.858 distance: 76 - 77: 32.722 distance: 76 - 79: 10.903 distance: 77 - 78: 22.493 distance: 77 - 83: 18.243 distance: 79 - 80: 10.116 distance: 80 - 81: 33.130 distance: 81 - 82: 19.965 distance: 83 - 84: 9.561 distance: 83 - 89: 17.532 distance: 84 - 85: 7.685 distance: 84 - 87: 10.492 distance: 85 - 86: 18.284 distance: 85 - 90: 19.020 distance: 87 - 88: 23.215 distance: 88 - 89: 17.606 distance: 90 - 91: 7.167 distance: 91 - 92: 8.024 distance: 91 - 94: 10.574 distance: 92 - 93: 19.691 distance: 92 - 97: 8.939 distance: 94 - 95: 15.122 distance: 94 - 96: 15.169 distance: 97 - 98: 13.894 distance: 98 - 99: 8.647 distance: 98 - 101: 10.897 distance: 99 - 100: 5.260 distance: 99 - 109: 11.335 distance: 101 - 102: 5.515 distance: 102 - 103: 9.814 distance: 102 - 104: 10.125 distance: 103 - 105: 10.045 distance: 104 - 106: 14.102 distance: 105 - 107: 9.205 distance: 106 - 107: 14.535 distance: 107 - 108: 20.666 distance: 109 - 110: 12.306 distance: 110 - 111: 6.522 distance: 110 - 113: 7.998 distance: 111 - 112: 23.655 distance: 111 - 115: 9.659 distance: 113 - 114: 15.191 distance: 115 - 116: 8.520 distance: 116 - 117: 16.125 distance: 116 - 119: 18.692 distance: 117 - 118: 24.120 distance: 117 - 124: 11.437 distance: 119 - 120: 43.530 distance: 120 - 121: 15.744 distance: 121 - 122: 13.827 distance: 121 - 123: 28.701 distance: 124 - 125: 4.082 distance: 125 - 126: 44.692 distance: 125 - 128: 11.796 distance: 126 - 127: 38.608 distance: 126 - 136: 41.676 distance: 128 - 129: 10.083 distance: 129 - 130: 15.844 distance: 130 - 132: 18.368 distance: 131 - 133: 14.910 distance: 132 - 134: 15.404 distance: 133 - 134: 23.169 distance: 134 - 135: 10.532 distance: 136 - 137: 31.306 distance: 136 - 142: 20.159 distance: 137 - 138: 15.031 distance: 137 - 140: 18.039 distance: 138 - 139: 20.658 distance: 138 - 143: 11.124 distance: 140 - 141: 20.820 distance: 141 - 142: 4.681 distance: 143 - 144: 13.313 distance: 144 - 145: 10.280 distance: 144 - 147: 11.483 distance: 145 - 146: 23.333 distance: 145 - 151: 6.934 distance: 147 - 148: 8.093 distance: 148 - 149: 20.400 distance: 148 - 150: 13.892