Starting phenix.real_space_refine on Sun Aug 24 01:01:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k9t_62198/08_2025/9k9t_62198.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k9t_62198/08_2025/9k9t_62198.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k9t_62198/08_2025/9k9t_62198.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k9t_62198/08_2025/9k9t_62198.map" model { file = "/net/cci-nas-00/data/ceres_data/9k9t_62198/08_2025/9k9t_62198.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k9t_62198/08_2025/9k9t_62198.cif" } resolution = 2.96 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= 0.003 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2154 atoms to isotropic. 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 43 5.49 5 S 70 5.16 5 C 8933 2.51 5 N 2351 2.21 5 O 2742 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 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: 14139 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 8106 Classifications: {'peptide': 990} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 952} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 409 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "P" Number of atoms: 473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 473 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "C" Number of atoms: 3389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3389 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 10, 'TRANS': 405} Chain breaks: 1 Chain: "B" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1762 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 2} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 204} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 3.03, per 1000 atoms: 0.21 Number of scatterers: 14139 At special positions: 0 Unit cell: (110.5, 126.65, 141.95, 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 70 16.00 P 43 15.00 O 2742 8.00 N 2351 7.00 C 8933 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 1.20 Conformation dependent library (CDL) restraints added in 493.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3110 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 18 sheets defined 39.8% alpha, 19.3% beta 12 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 44 through 48 Processing helix chain 'A' and resid 108 through 118 Processing helix chain 'A' and resid 128 through 130 No H-bonds generated for 'chain 'A' and resid 128 through 130' Processing helix chain 'A' and resid 144 through 149 removed outlier: 3.538A pdb=" N PHE A 149 " --> pdb=" O PRO A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 220 Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.667A pdb=" N GLU A 229 " --> pdb=" O SER A 226 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N MET A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 226 through 230' Processing helix chain 'A' and resid 240 through 253 Processing helix chain 'A' and resid 267 through 280 Processing helix chain 'A' and resid 330 through 339 Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 380 through 390 removed outlier: 3.529A pdb=" N THR A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 446 removed outlier: 3.889A pdb=" N ASP A 446 " --> pdb=" O GLN A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 474 removed outlier: 3.735A pdb=" N CYS A 466 " --> pdb=" O ASP A 462 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN A 467 " --> pdb=" O ALA A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 487 Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.896A pdb=" N VAL A 493 " --> pdb=" O GLN A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 502 removed outlier: 3.639A pdb=" N ILE A 501 " --> pdb=" O ARG A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 514 Processing helix chain 'A' and resid 552 through 562 Processing helix chain 'A' and resid 564 through 566 No H-bonds generated for 'chain 'A' and resid 564 through 566' Processing helix chain 'A' and resid 576 through 591 Processing helix chain 'A' and resid 622 through 643 removed outlier: 3.833A pdb=" N GLN A 643 " --> pdb=" O LYS A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 665 Processing helix chain 'A' and resid 666 through 672 removed outlier: 3.663A pdb=" N GLY A 672 " --> pdb=" O TYR A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 703 Processing helix chain 'A' and resid 763 through 782 Processing helix chain 'A' and resid 837 through 855 removed outlier: 3.782A pdb=" N SER A 855 " --> pdb=" O SER A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 883 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.500A pdb=" N MET A 891 " --> pdb=" O GLU A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 918 removed outlier: 4.185A pdb=" N TYR A 909 " --> pdb=" O ASN A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 949 removed outlier: 3.718A pdb=" N THR A 949 " --> pdb=" O ASN A 946 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 946 through 949' Processing helix chain 'A' and resid 967 through 982 removed outlier: 4.489A pdb=" N TYR A 971 " --> pdb=" O PHE A 967 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 982 " --> pdb=" O GLU A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 997 Processing helix chain 'C' and resid 3 through 19 removed outlier: 3.632A pdb=" N LEU C 7 " --> pdb=" O SER C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 42 Processing helix chain 'C' and resid 107 through 121 removed outlier: 4.057A pdb=" N ARG C 111 " --> pdb=" O PRO C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 159 removed outlier: 4.095A pdb=" N PHE C 152 " --> pdb=" O PRO C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 189 Processing helix chain 'C' and resid 249 through 257 Processing helix chain 'C' and resid 285 through 298 removed outlier: 4.132A pdb=" N VAL C 289 " --> pdb=" O THR C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 323 Processing helix chain 'C' and resid 330 through 341 Processing helix chain 'C' and resid 344 through 351 Processing helix chain 'C' and resid 353 through 361 removed outlier: 3.666A pdb=" N LEU C 361 " --> pdb=" O SER C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 373 Processing helix chain 'C' and resid 392 through 396 Processing helix chain 'C' and resid 397 through 425 removed outlier: 4.575A pdb=" N ASN C 408 " --> pdb=" O TYR C 404 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N GLN C 409 " --> pdb=" O GLY C 405 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER C 412 " --> pdb=" O ASN C 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 18 No H-bonds generated for 'chain 'B' and resid 16 through 18' Processing helix chain 'B' and resid 19 through 31 removed outlier: 4.044A pdb=" N SER B 24 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N GLN B 25 " --> pdb=" O PRO B 21 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU B 26 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL B 27 " --> pdb=" O MET B 23 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLU B 28 " --> pdb=" O SER B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 38 Processing helix chain 'B' and resid 45 through 49 removed outlier: 4.199A pdb=" N PHE B 49 " --> pdb=" O PRO B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 55 Processing helix chain 'B' and resid 86 through 101 Processing helix chain 'B' and resid 133 through 150 removed outlier: 5.610A pdb=" N LYS B 139 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ILE B 140 " --> pdb=" O TYR B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 205 removed outlier: 4.244A pdb=" N ILE B 197 " --> pdb=" O ARG B 193 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP B 205 " --> pdb=" O LEU B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 214 No H-bonds generated for 'chain 'B' and resid 212 through 214' Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 134 removed outlier: 8.282A pdb=" N TYR A 140 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N PHE A 31 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N CYS A 142 " --> pdb=" O PHE A 31 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ARG A 33 " --> pdb=" O CYS A 142 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N PHE A 17 " --> pdb=" O GLU A 10 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N GLU A 10 " --> pdb=" O PHE A 17 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N TYR A 19 " --> pdb=" O TRP A 8 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N TRP A 8 " --> pdb=" O TYR A 19 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LYS A 21 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N CYS A 124 " --> pdb=" O ILE A 153 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 43 removed outlier: 6.161A pdb=" N SER A 84 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ARG A 64 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALA A 86 " --> pdb=" O LYS A 62 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LYS A 62 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N MET A 88 " --> pdb=" O MET A 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 72 through 73 removed outlier: 6.704A pdb=" N SER A 73 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU A 568 " --> pdb=" O ASP A 616 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASP A 616 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY A 570 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU A 611 " --> pdb=" O CYS A 601 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 222 through 223 removed outlier: 6.303A pdb=" N LEU A 222 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N VAL A 237 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N THR A 201 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N CYS A 239 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N ILE A 203 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N SER A 184 " --> pdb=" O ASN A 204 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU A 163 " --> pdb=" O VAL A 260 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 285 through 287 Processing sheet with id=AA6, first strand: chain 'A' and resid 300 through 302 Processing sheet with id=AA7, first strand: chain 'A' and resid 355 through 360 removed outlier: 6.990A pdb=" N MET A 357 " --> pdb=" O ASP A 373 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ASP A 373 " --> pdb=" O MET A 357 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG A 407 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N SER A 420 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL A 405 " --> pdb=" O SER A 420 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 733 through 734 removed outlier: 5.469A pdb=" N SER A 747 " --> pdb=" O GLU A 758 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLU A 758 " --> pdb=" O SER A 747 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N TYR A 749 " --> pdb=" O PHE A 756 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL A 545 " --> pdb=" O VAL A 794 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N VAL A 794 " --> pdb=" O VAL A 545 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE A 547 " --> pdb=" O GLU A 792 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LEU A 798 " --> pdb=" O THR A 807 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N THR A 807 " --> pdb=" O LEU A 798 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 892 through 895 Processing sheet with id=AB1, first strand: chain 'A' and resid 892 through 895 Processing sheet with id=AB2, first strand: chain 'C' and resid 70 through 71 removed outlier: 3.745A pdb=" N THR C 174 " --> pdb=" O ILE C 71 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 166 through 169 removed outlier: 3.897A pdb=" N GLN C 208 " --> pdb=" O TYR C 199 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 95 through 96 removed outlier: 8.144A pdb=" N ARG C 128 " --> pdb=" O GLU C 139 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU C 139 " --> pdb=" O ARG C 128 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL C 130 " --> pdb=" O ILE C 137 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ILE C 137 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU C 132 " --> pdb=" O ARG C 135 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 233 through 239 removed outlier: 4.009A pdb=" N SER C 222 " --> pdb=" O ILE C 238 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS C 214 " --> pdb=" O LYS C 268 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 375 through 380 removed outlier: 6.758A pdb=" N ARG C 376 " --> pdb=" O PHE C 387 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N PHE C 387 " --> pdb=" O ARG C 376 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LYS C 378 " --> pdb=" O VAL C 385 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 3 through 5 Processing sheet with id=AB8, first strand: chain 'B' and resid 115 through 120 removed outlier: 6.540A pdb=" N GLY B 115 " --> pdb=" O LYS B 60 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE B 117 " --> pdb=" O VAL B 62 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 107 through 108 578 hydrogen bonds defined for protein. 1641 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 28 hydrogen bonds 56 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 32 stacking parallelities Total time for adding SS restraints: 2.80 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3682 1.33 - 1.45: 2859 1.45 - 1.57: 7800 1.57 - 1.69: 84 1.69 - 1.81: 107 Bond restraints: 14532 Sorted by residual: bond pdb=" N TYR A 74 " pdb=" CA TYR A 74 " ideal model delta sigma weight residual 1.456 1.493 -0.036 1.22e-02 6.72e+03 8.82e+00 bond pdb=" N ASP A 77 " pdb=" CA ASP A 77 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.27e-02 6.20e+03 5.35e+00 bond pdb=" N LEU A 76 " pdb=" CA LEU A 76 " ideal model delta sigma weight residual 1.458 1.484 -0.027 1.25e-02 6.40e+03 4.55e+00 bond pdb=" N ASN A 860 " pdb=" CA ASN A 860 " ideal model delta sigma weight residual 1.457 1.481 -0.023 1.29e-02 6.01e+03 3.25e+00 bond pdb=" C TYR A 74 " pdb=" O TYR A 74 " ideal model delta sigma weight residual 1.236 1.214 0.021 1.38e-02 5.25e+03 2.37e+00 ... (remaining 14527 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 19450 2.17 - 4.34: 330 4.34 - 6.51: 32 6.51 - 8.68: 6 8.68 - 10.84: 4 Bond angle restraints: 19822 Sorted by residual: angle pdb=" C GLU A 852 " pdb=" N MET A 853 " pdb=" CA MET A 853 " ideal model delta sigma weight residual 122.38 113.28 9.10 1.81e+00 3.05e-01 2.53e+01 angle pdb=" N MET A 853 " pdb=" CA MET A 853 " pdb=" CB MET A 853 " ideal model delta sigma weight residual 110.44 116.09 -5.65 1.53e+00 4.27e-01 1.37e+01 angle pdb=" CB MET A 357 " pdb=" CG MET A 357 " pdb=" SD MET A 357 " ideal model delta sigma weight residual 112.70 123.54 -10.84 3.00e+00 1.11e-01 1.31e+01 angle pdb=" C ASP A 77 " pdb=" N ILE A 78 " pdb=" CA ILE A 78 " ideal model delta sigma weight residual 123.19 118.96 4.23 1.24e+00 6.50e-01 1.16e+01 angle pdb=" CA LEU A 76 " pdb=" C LEU A 76 " pdb=" O LEU A 76 " ideal model delta sigma weight residual 120.32 117.00 3.32 1.02e+00 9.61e-01 1.06e+01 ... (remaining 19817 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.93: 8178 27.93 - 55.86: 457 55.86 - 83.79: 30 83.79 - 111.71: 2 111.71 - 139.64: 1 Dihedral angle restraints: 8668 sinusoidal: 3848 harmonic: 4820 Sorted by residual: dihedral pdb=" CA ARG C 135 " pdb=" C ARG C 135 " pdb=" N TRP C 136 " pdb=" CA TRP C 136 " ideal model delta harmonic sigma weight residual 180.00 -151.64 -28.36 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA THR A 209 " pdb=" C THR A 209 " pdb=" N GLU A 210 " pdb=" CA GLU A 210 " ideal model delta harmonic sigma weight residual 180.00 -154.70 -25.30 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA ARG A 832 " pdb=" C ARG A 832 " pdb=" N ARG A 833 " pdb=" CA ARG A 833 " ideal model delta harmonic sigma weight residual -180.00 -156.23 -23.77 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 8665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1908 0.066 - 0.132: 274 0.132 - 0.198: 11 0.198 - 0.264: 3 0.264 - 0.329: 1 Chirality restraints: 2197 Sorted by residual: chirality pdb=" CB ILE C 313 " pdb=" CA ILE C 313 " pdb=" CG1 ILE C 313 " pdb=" CG2 ILE C 313 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CB VAL A 365 " pdb=" CA VAL A 365 " pdb=" CG1 VAL A 365 " pdb=" CG2 VAL A 365 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CG LEU C 131 " pdb=" CB LEU C 131 " pdb=" CD1 LEU C 131 " pdb=" CD2 LEU C 131 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 2194 not shown) Planarity restraints: 2370 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 73 " 0.020 2.00e-02 2.50e+03 3.96e-02 1.57e+01 pdb=" C SER A 73 " -0.069 2.00e-02 2.50e+03 pdb=" O SER A 73 " 0.025 2.00e-02 2.50e+03 pdb=" N TYR A 74 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 231 " 0.014 2.00e-02 2.50e+03 2.88e-02 8.32e+00 pdb=" C ASN C 231 " -0.050 2.00e-02 2.50e+03 pdb=" O ASN C 231 " 0.019 2.00e-02 2.50e+03 pdb=" N ILE C 232 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 592 " -0.045 5.00e-02 4.00e+02 6.80e-02 7.41e+00 pdb=" N PRO A 593 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 593 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 593 " -0.037 5.00e-02 4.00e+02 ... (remaining 2367 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2393 2.77 - 3.30: 13429 3.30 - 3.83: 23232 3.83 - 4.37: 26467 4.37 - 4.90: 44455 Nonbonded interactions: 109976 Sorted by model distance: nonbonded pdb=" O ASN A 181 " pdb=" OH TYR A 271 " model vdw 2.236 3.040 nonbonded pdb=" O TYR A 909 " pdb=" OG1 THR A 912 " model vdw 2.242 3.040 nonbonded pdb=" OE2 GLU C 97 " pdb=" N GLY C 101 " model vdw 2.258 3.120 nonbonded pdb=" NE ARG C 227 " pdb=" O GLY C 229 " model vdw 2.262 3.120 nonbonded pdb=" O ASP C 72 " pdb=" OH TYR C 76 " model vdw 2.271 3.040 ... (remaining 109971 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.390 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 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 : 0.003 0.071 14532 Z= 0.157 Angle : 0.684 10.844 19822 Z= 0.383 Chirality : 0.045 0.329 2197 Planarity : 0.005 0.068 2370 Dihedral : 15.457 139.642 5558 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.22 % Favored : 95.66 % Rotamer: Outliers : 0.27 % Allowed : 0.53 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.22 (0.21), residues: 1612 helix: 0.89 (0.22), residues: 564 sheet: 0.34 (0.29), residues: 301 loop : -1.15 (0.22), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 693 TYR 0.019 0.001 TYR A 74 PHE 0.023 0.002 PHE B 49 TRP 0.028 0.001 TRP C 136 HIS 0.004 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00322 (14532) covalent geometry : angle 0.68401 (19822) hydrogen bonds : bond 0.15773 ( 602) hydrogen bonds : angle 6.35494 ( 1697) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 384 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7338 (p0) cc_final: 0.7093 (p0) REVERT: A 230 MET cc_start: 0.7460 (tmm) cc_final: 0.6387 (tmt) REVERT: A 413 ASN cc_start: 0.8264 (p0) cc_final: 0.7945 (p0) REVERT: A 577 ARG cc_start: 0.7889 (mtt180) cc_final: 0.7626 (mtt180) REVERT: A 794 VAL cc_start: 0.8075 (t) cc_final: 0.7704 (p) REVERT: A 878 SER cc_start: 0.9206 (t) cc_final: 0.8908 (p) REVERT: A 965 ARG cc_start: 0.7295 (ppt170) cc_final: 0.6868 (ppt170) REVERT: A 966 ILE cc_start: 0.8574 (mt) cc_final: 0.8095 (mt) REVERT: C 95 MET cc_start: 0.4864 (tpt) cc_final: 0.4051 (tmt) REVERT: C 154 LEU cc_start: 0.8663 (pp) cc_final: 0.8460 (pp) REVERT: C 181 TYR cc_start: 0.8433 (t80) cc_final: 0.8193 (t80) REVERT: C 251 ASP cc_start: 0.8468 (m-30) cc_final: 0.7850 (m-30) REVERT: C 252 HIS cc_start: 0.7698 (t-170) cc_final: 0.6909 (t-170) REVERT: C 264 VAL cc_start: 0.7218 (p) cc_final: 0.6595 (t) REVERT: C 300 ASP cc_start: 0.7974 (p0) cc_final: 0.7719 (t0) REVERT: C 323 LEU cc_start: 0.8298 (mm) cc_final: 0.7732 (mm) REVERT: C 367 ASP cc_start: 0.7585 (m-30) cc_final: 0.7348 (m-30) REVERT: C 371 LEU cc_start: 0.8221 (tt) cc_final: 0.7929 (tm) REVERT: B 60 LYS cc_start: 0.8622 (mmtp) cc_final: 0.8420 (mmtp) REVERT: B 114 ASP cc_start: 0.7938 (p0) cc_final: 0.7735 (p0) REVERT: B 155 LEU cc_start: 0.8306 (tp) cc_final: 0.8084 (tp) outliers start: 4 outliers final: 3 residues processed: 385 average time/residue: 0.6054 time to fit residues: 254.8166 Evaluate side-chains 335 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 332 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 334 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.0030 chunk 122 optimal weight: 0.0870 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 overall best weight: 0.9772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN A 524 GLN ** A 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.156462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.119770 restraints weight = 29351.875| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 3.02 r_work: 0.3527 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14532 Z= 0.160 Angle : 0.646 12.515 19822 Z= 0.344 Chirality : 0.044 0.199 2197 Planarity : 0.004 0.056 2370 Dihedral : 14.699 151.546 2271 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.91 % Favored : 95.97 % Rotamer: Outliers : 2.40 % Allowed : 13.14 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 (0.21), residues: 1612 helix: 1.13 (0.23), residues: 568 sheet: 0.31 (0.29), residues: 299 loop : -1.07 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 692 TYR 0.017 0.001 TYR C 199 PHE 0.021 0.001 PHE A 992 TRP 0.024 0.002 TRP C 136 HIS 0.005 0.001 HIS A 839 Details of bonding type rmsd covalent geometry : bond 0.00370 (14532) covalent geometry : angle 0.64622 (19822) hydrogen bonds : bond 0.04767 ( 602) hydrogen bonds : angle 4.74242 ( 1697) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 351 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.7926 (mppt) REVERT: A 105 ASP cc_start: 0.8110 (p0) cc_final: 0.7821 (p0) REVERT: A 144 ASP cc_start: 0.8243 (t0) cc_final: 0.7746 (t0) REVERT: A 413 ASN cc_start: 0.8584 (p0) cc_final: 0.8158 (p0) REVERT: A 430 LYS cc_start: 0.8078 (ptmt) cc_final: 0.7865 (ptpp) REVERT: A 446 ASP cc_start: 0.7964 (p0) cc_final: 0.7742 (p0) REVERT: A 577 ARG cc_start: 0.8459 (mtt180) cc_final: 0.7770 (mpp80) REVERT: A 742 ARG cc_start: 0.6221 (tpp-160) cc_final: 0.5964 (tpp-160) REVERT: A 794 VAL cc_start: 0.8156 (t) cc_final: 0.7784 (p) REVERT: A 834 ASP cc_start: 0.7416 (t0) cc_final: 0.7214 (t0) REVERT: A 842 MET cc_start: 0.8058 (tpp) cc_final: 0.7794 (tpp) REVERT: A 895 MET cc_start: 0.7836 (tmt) cc_final: 0.7334 (tmm) REVERT: A 965 ARG cc_start: 0.7734 (ppt170) cc_final: 0.7526 (ppt170) REVERT: C 95 MET cc_start: 0.4979 (tpt) cc_final: 0.4416 (tmt) REVERT: C 367 ASP cc_start: 0.8100 (m-30) cc_final: 0.7855 (m-30) REVERT: C 378 LYS cc_start: 0.8284 (ttpp) cc_final: 0.7948 (ttpp) REVERT: C 379 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8692 (pt) REVERT: C 380 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7717 (tm-30) REVERT: B 153 SER cc_start: 0.8864 (m) cc_final: 0.8525 (t) outliers start: 36 outliers final: 14 residues processed: 362 average time/residue: 0.6618 time to fit residues: 261.1303 Evaluate side-chains 346 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 330 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 812 SER Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 85 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 90 optimal weight: 3.9990 chunk 114 optimal weight: 20.0000 chunk 140 optimal weight: 4.9990 chunk 110 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 88 optimal weight: 9.9990 chunk 75 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 841 ASN C 133 ASN B 199 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.151593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.115046 restraints weight = 28949.761| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.97 r_work: 0.3448 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 14532 Z= 0.290 Angle : 0.721 9.219 19822 Z= 0.385 Chirality : 0.048 0.183 2197 Planarity : 0.005 0.059 2370 Dihedral : 14.767 148.570 2265 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.78 % Favored : 95.10 % Rotamer: Outliers : 4.07 % Allowed : 16.14 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.38 (0.20), residues: 1612 helix: 0.76 (0.22), residues: 575 sheet: 0.13 (0.29), residues: 308 loop : -1.22 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 255 TYR 0.023 0.002 TYR C 363 PHE 0.026 0.002 PHE B 29 TRP 0.019 0.003 TRP B 212 HIS 0.008 0.002 HIS A 839 Details of bonding type rmsd covalent geometry : bond 0.00685 (14532) covalent geometry : angle 0.72119 (19822) hydrogen bonds : bond 0.06050 ( 602) hydrogen bonds : angle 4.84387 ( 1697) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 346 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.8287 (p0) cc_final: 0.7755 (OUTLIER) REVERT: A 144 ASP cc_start: 0.8404 (t0) cc_final: 0.7864 (t0) REVERT: A 230 MET cc_start: 0.7777 (tmm) cc_final: 0.5906 (tmt) REVERT: A 413 ASN cc_start: 0.8590 (p0) cc_final: 0.8128 (p0) REVERT: A 427 ASP cc_start: 0.7781 (m-30) cc_final: 0.7120 (t0) REVERT: A 471 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8281 (mt-10) REVERT: A 794 VAL cc_start: 0.8204 (t) cc_final: 0.7854 (p) REVERT: A 834 ASP cc_start: 0.7615 (t0) cc_final: 0.7405 (t0) REVERT: C 95 MET cc_start: 0.5274 (tpt) cc_final: 0.4120 (tmt) REVERT: C 181 TYR cc_start: 0.8649 (t80) cc_final: 0.8415 (t80) REVERT: C 264 VAL cc_start: 0.7282 (p) cc_final: 0.6968 (t) REVERT: C 299 ARG cc_start: 0.7843 (mmp80) cc_final: 0.7345 (mmp80) REVERT: C 359 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7780 (mm-30) REVERT: C 367 ASP cc_start: 0.8182 (m-30) cc_final: 0.7964 (m-30) REVERT: C 379 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8773 (pt) REVERT: C 401 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8221 (mt-10) REVERT: B 29 PHE cc_start: 0.8148 (OUTLIER) cc_final: 0.7943 (m-80) REVERT: B 114 ASP cc_start: 0.8123 (p0) cc_final: 0.7911 (p0) REVERT: B 153 SER cc_start: 0.8956 (m) cc_final: 0.8604 (t) REVERT: B 203 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7844 (mm-30) outliers start: 61 outliers final: 28 residues processed: 367 average time/residue: 0.6717 time to fit residues: 269.0912 Evaluate side-chains 359 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 329 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 812 SER Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 964 GLN Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 421 LYS Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 152 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 147 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 102 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 112 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 124 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 351 GLN B 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.153982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.117366 restraints weight = 29241.308| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 3.02 r_work: 0.3495 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14532 Z= 0.149 Angle : 0.656 12.704 19822 Z= 0.344 Chirality : 0.044 0.423 2197 Planarity : 0.004 0.052 2370 Dihedral : 14.720 149.423 2265 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.72 % Favored : 96.15 % Rotamer: Outliers : 3.47 % Allowed : 19.35 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.13 (0.21), residues: 1612 helix: 1.00 (0.22), residues: 578 sheet: 0.19 (0.29), residues: 308 loop : -1.08 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 407 TYR 0.020 0.001 TYR C 307 PHE 0.027 0.002 PHE B 29 TRP 0.021 0.002 TRP B 212 HIS 0.004 0.001 HIS B 16 Details of bonding type rmsd covalent geometry : bond 0.00350 (14532) covalent geometry : angle 0.65630 (19822) hydrogen bonds : bond 0.04467 ( 602) hydrogen bonds : angle 4.53332 ( 1697) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 343 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.8194 (p0) cc_final: 0.7677 (OUTLIER) REVERT: A 144 ASP cc_start: 0.8341 (t0) cc_final: 0.7739 (t0) REVERT: A 283 LYS cc_start: 0.8831 (mmtp) cc_final: 0.8559 (mptt) REVERT: A 339 GLU cc_start: 0.8188 (tp30) cc_final: 0.7809 (tp30) REVERT: A 413 ASN cc_start: 0.8520 (p0) cc_final: 0.8062 (p0) REVERT: A 427 ASP cc_start: 0.7710 (m-30) cc_final: 0.7176 (t70) REVERT: A 573 VAL cc_start: 0.8726 (m) cc_final: 0.8475 (t) REVERT: A 742 ARG cc_start: 0.6375 (tpp-160) cc_final: 0.6110 (tpp-160) REVERT: A 794 VAL cc_start: 0.8170 (t) cc_final: 0.7805 (p) REVERT: A 834 ASP cc_start: 0.7552 (t0) cc_final: 0.7223 (t0) REVERT: A 859 MET cc_start: 0.6227 (OUTLIER) cc_final: 0.5781 (mmp) REVERT: A 895 MET cc_start: 0.7884 (tmt) cc_final: 0.7390 (tmm) REVERT: C 95 MET cc_start: 0.5416 (tpt) cc_final: 0.4668 (tmt) REVERT: C 154 LEU cc_start: 0.8885 (tm) cc_final: 0.8249 (pp) REVERT: C 179 GLU cc_start: 0.8788 (tm-30) cc_final: 0.8204 (mp0) REVERT: C 181 TYR cc_start: 0.8660 (t80) cc_final: 0.8432 (t80) REVERT: C 299 ARG cc_start: 0.7781 (mmp80) cc_final: 0.7316 (mmp80) REVERT: C 367 ASP cc_start: 0.8101 (m-30) cc_final: 0.7886 (m-30) REVERT: C 379 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8714 (pt) REVERT: C 401 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8176 (mt-10) REVERT: B 29 PHE cc_start: 0.8148 (OUTLIER) cc_final: 0.7940 (m-80) REVERT: B 153 SER cc_start: 0.8905 (m) cc_final: 0.8537 (t) REVERT: B 155 LEU cc_start: 0.8364 (tp) cc_final: 0.8039 (tm) REVERT: B 156 TYR cc_start: 0.7945 (t80) cc_final: 0.7696 (t80) REVERT: B 203 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7790 (mm-30) REVERT: B 206 ASN cc_start: 0.8456 (p0) cc_final: 0.8249 (p0) outliers start: 52 outliers final: 28 residues processed: 365 average time/residue: 0.7032 time to fit residues: 278.4569 Evaluate side-chains 360 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 330 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 812 SER Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 421 LYS Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 152 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 73 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 24 optimal weight: 0.6980 chunk 77 optimal weight: 0.0870 chunk 63 optimal weight: 2.9990 chunk 114 optimal weight: 10.0000 chunk 129 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 116 optimal weight: 20.0000 chunk 93 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 overall best weight: 1.5564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 841 ASN ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.151980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.115309 restraints weight = 29249.618| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 3.01 r_work: 0.3463 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 14532 Z= 0.209 Angle : 0.691 12.230 19822 Z= 0.364 Chirality : 0.045 0.174 2197 Planarity : 0.005 0.053 2370 Dihedral : 14.768 149.339 2265 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.53 % Favored : 95.35 % Rotamer: Outliers : 4.27 % Allowed : 20.48 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.21 (0.21), residues: 1612 helix: 0.97 (0.22), residues: 571 sheet: 0.15 (0.29), residues: 308 loop : -1.15 (0.22), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 255 TYR 0.022 0.001 TYR C 307 PHE 0.025 0.002 PHE B 29 TRP 0.022 0.002 TRP B 212 HIS 0.006 0.001 HIS B 16 Details of bonding type rmsd covalent geometry : bond 0.00495 (14532) covalent geometry : angle 0.69075 (19822) hydrogen bonds : bond 0.05115 ( 602) hydrogen bonds : angle 4.63475 ( 1697) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 346 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.8269 (p0) cc_final: 0.7728 (OUTLIER) REVERT: A 144 ASP cc_start: 0.8382 (t0) cc_final: 0.7768 (t0) REVERT: A 174 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8679 (ptpt) REVERT: A 283 LYS cc_start: 0.8874 (mmtp) cc_final: 0.8608 (mptp) REVERT: A 413 ASN cc_start: 0.8528 (p0) cc_final: 0.8069 (p0) REVERT: A 427 ASP cc_start: 0.7768 (m-30) cc_final: 0.7226 (t70) REVERT: A 577 ARG cc_start: 0.8472 (mtt180) cc_final: 0.7984 (mpt-90) REVERT: A 794 VAL cc_start: 0.8188 (t) cc_final: 0.7845 (p) REVERT: A 822 GLU cc_start: 0.7165 (tm-30) cc_final: 0.6913 (tm-30) REVERT: A 834 ASP cc_start: 0.7609 (t0) cc_final: 0.7263 (t0) REVERT: A 859 MET cc_start: 0.6286 (OUTLIER) cc_final: 0.6057 (mmp) REVERT: A 895 MET cc_start: 0.7897 (tmt) cc_final: 0.7430 (tmm) REVERT: C 95 MET cc_start: 0.5516 (tpt) cc_final: 0.4741 (tmt) REVERT: C 154 LEU cc_start: 0.8859 (tm) cc_final: 0.8318 (pp) REVERT: C 181 TYR cc_start: 0.8602 (OUTLIER) cc_final: 0.8392 (t80) REVERT: C 299 ARG cc_start: 0.7755 (mmp80) cc_final: 0.7295 (mmp80) REVERT: C 375 MET cc_start: 0.7757 (pmm) cc_final: 0.7544 (pmm) REVERT: C 379 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8779 (pt) REVERT: C 380 GLU cc_start: 0.8436 (tp30) cc_final: 0.8173 (tm-30) REVERT: B 80 GLU cc_start: 0.6681 (tm-30) cc_final: 0.6388 (tm-30) REVERT: B 114 ASP cc_start: 0.8143 (p0) cc_final: 0.7878 (p0) REVERT: B 146 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7957 (mt0) REVERT: B 155 LEU cc_start: 0.8376 (tp) cc_final: 0.8051 (tm) REVERT: B 206 ASN cc_start: 0.8484 (p0) cc_final: 0.8268 (p0) outliers start: 64 outliers final: 37 residues processed: 373 average time/residue: 0.6761 time to fit residues: 274.2430 Evaluate side-chains 375 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 334 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 812 SER Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain A residue 878 SER Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 963 ASN Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 181 TYR Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 374 ASN Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 421 LYS Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 152 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 82 optimal weight: 0.9990 chunk 162 optimal weight: 0.0970 chunk 152 optimal weight: 0.9980 chunk 131 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.153715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.117273 restraints weight = 29019.354| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 3.00 r_work: 0.3498 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14532 Z= 0.145 Angle : 0.676 12.571 19822 Z= 0.352 Chirality : 0.044 0.246 2197 Planarity : 0.005 0.053 2370 Dihedral : 14.758 151.560 2265 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.03 % Favored : 95.84 % Rotamer: Outliers : 4.00 % Allowed : 21.48 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.08 (0.21), residues: 1612 helix: 1.11 (0.22), residues: 572 sheet: 0.22 (0.29), residues: 310 loop : -1.10 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 255 TYR 0.028 0.001 TYR C 307 PHE 0.038 0.002 PHE B 29 TRP 0.033 0.002 TRP B 212 HIS 0.004 0.001 HIS B 16 Details of bonding type rmsd covalent geometry : bond 0.00339 (14532) covalent geometry : angle 0.67623 (19822) hydrogen bonds : bond 0.04300 ( 602) hydrogen bonds : angle 4.48023 ( 1697) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 345 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.8203 (p0) cc_final: 0.7668 (OUTLIER) REVERT: A 144 ASP cc_start: 0.8348 (t0) cc_final: 0.7706 (t0) REVERT: A 283 LYS cc_start: 0.8878 (mmtp) cc_final: 0.8567 (mptp) REVERT: A 413 ASN cc_start: 0.8536 (p0) cc_final: 0.8064 (p0) REVERT: A 427 ASP cc_start: 0.7804 (m-30) cc_final: 0.7221 (t70) REVERT: A 445 LYS cc_start: 0.8577 (tppp) cc_final: 0.8351 (tppt) REVERT: A 577 ARG cc_start: 0.8337 (mtt180) cc_final: 0.7847 (mpt-90) REVERT: A 794 VAL cc_start: 0.8076 (t) cc_final: 0.7704 (p) REVERT: A 834 ASP cc_start: 0.7591 (t0) cc_final: 0.7186 (t0) REVERT: A 859 MET cc_start: 0.6364 (OUTLIER) cc_final: 0.6156 (mmp) REVERT: A 891 MET cc_start: 0.8775 (ttm) cc_final: 0.8469 (ttp) REVERT: A 895 MET cc_start: 0.7936 (tmt) cc_final: 0.7417 (tmm) REVERT: A 985 ASN cc_start: 0.7830 (t0) cc_final: 0.6683 (m-40) REVERT: C 95 MET cc_start: 0.5485 (tpt) cc_final: 0.4763 (tmt) REVERT: C 154 LEU cc_start: 0.8831 (tm) cc_final: 0.8311 (pp) REVERT: C 179 GLU cc_start: 0.8762 (tm-30) cc_final: 0.8203 (mp0) REVERT: C 299 ARG cc_start: 0.7788 (mmp80) cc_final: 0.7309 (mmp80) REVERT: C 375 MET cc_start: 0.7741 (pmm) cc_final: 0.7459 (pmm) REVERT: C 380 GLU cc_start: 0.8355 (tp30) cc_final: 0.8113 (tm-30) REVERT: B 25 GLN cc_start: 0.8065 (tm-30) cc_final: 0.7862 (tm130) REVERT: B 114 ASP cc_start: 0.8101 (p0) cc_final: 0.7827 (p0) REVERT: B 146 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7895 (mt0) REVERT: B 155 LEU cc_start: 0.8356 (tp) cc_final: 0.8037 (tm) REVERT: B 206 ASN cc_start: 0.8441 (p0) cc_final: 0.8233 (p0) outliers start: 60 outliers final: 36 residues processed: 374 average time/residue: 0.6795 time to fit residues: 276.9351 Evaluate side-chains 367 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 330 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 812 SER Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 421 LYS Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 152 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 33 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 105 optimal weight: 20.0000 chunk 120 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.150140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.113593 restraints weight = 29123.812| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.98 r_work: 0.3435 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 14532 Z= 0.280 Angle : 0.771 14.721 19822 Z= 0.405 Chirality : 0.048 0.401 2197 Planarity : 0.006 0.072 2370 Dihedral : 14.927 150.908 2265 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.15 % Favored : 94.73 % Rotamer: Outliers : 4.34 % Allowed : 22.21 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.34 (0.21), residues: 1612 helix: 0.89 (0.22), residues: 570 sheet: -0.01 (0.28), residues: 330 loop : -1.23 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C 255 TYR 0.029 0.002 TYR C 307 PHE 0.033 0.003 PHE A 880 TRP 0.022 0.002 TRP B 212 HIS 0.007 0.002 HIS B 16 Details of bonding type rmsd covalent geometry : bond 0.00673 (14532) covalent geometry : angle 0.77072 (19822) hydrogen bonds : bond 0.05824 ( 602) hydrogen bonds : angle 4.82281 ( 1697) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 335 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.8298 (p0) cc_final: 0.7779 (OUTLIER) REVERT: A 144 ASP cc_start: 0.8427 (t0) cc_final: 0.7808 (t0) REVERT: A 174 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8754 (ptpt) REVERT: A 283 LYS cc_start: 0.8871 (mmtp) cc_final: 0.8540 (mptp) REVERT: A 413 ASN cc_start: 0.8567 (p0) cc_final: 0.8086 (p0) REVERT: A 427 ASP cc_start: 0.7874 (m-30) cc_final: 0.7258 (t70) REVERT: A 445 LYS cc_start: 0.8577 (tppp) cc_final: 0.8243 (tppt) REVERT: A 446 ASP cc_start: 0.7848 (p0) cc_final: 0.7570 (p0) REVERT: A 577 ARG cc_start: 0.8418 (mtt180) cc_final: 0.7961 (mpt-90) REVERT: A 794 VAL cc_start: 0.8190 (t) cc_final: 0.7874 (p) REVERT: A 804 LYS cc_start: 0.8522 (mmmm) cc_final: 0.8295 (mmmt) REVERT: A 822 GLU cc_start: 0.7274 (tm-30) cc_final: 0.6840 (tm-30) REVERT: A 832 ARG cc_start: 0.8082 (ttp80) cc_final: 0.7495 (ttp80) REVERT: A 834 ASP cc_start: 0.7634 (t0) cc_final: 0.7298 (t0) REVERT: A 859 MET cc_start: 0.6354 (OUTLIER) cc_final: 0.6069 (mmp) REVERT: A 895 MET cc_start: 0.7988 (tmt) cc_final: 0.7565 (tmm) REVERT: C 154 LEU cc_start: 0.8866 (tm) cc_final: 0.8336 (pp) REVERT: C 179 GLU cc_start: 0.8815 (tm-30) cc_final: 0.8256 (mp0) REVERT: C 299 ARG cc_start: 0.7796 (mmp80) cc_final: 0.7354 (mmp80) REVERT: C 374 ASN cc_start: 0.7777 (OUTLIER) cc_final: 0.7424 (OUTLIER) REVERT: C 375 MET cc_start: 0.7808 (pmm) cc_final: 0.7531 (pmm) REVERT: C 380 GLU cc_start: 0.8391 (tp30) cc_final: 0.8172 (tm-30) REVERT: B 23 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7076 (ttp) REVERT: B 114 ASP cc_start: 0.8012 (p0) cc_final: 0.7748 (p0) REVERT: B 155 LEU cc_start: 0.8357 (tp) cc_final: 0.8045 (tm) outliers start: 65 outliers final: 43 residues processed: 369 average time/residue: 0.6732 time to fit residues: 270.3262 Evaluate side-chains 366 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 321 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 812 SER Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 963 ASN Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 243 LYS Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 374 ASN Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 421 LYS Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 201 LEU 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: 62.0379 > 50: distance: 19 - 108: 30.885 distance: 27 - 111: 35.755 distance: 30 - 123: 37.450 distance: 39 - 126: 24.442 distance: 55 - 76: 13.740 distance: 71 - 76: 11.244 distance: 76 - 77: 15.347 distance: 77 - 78: 8.600 distance: 77 - 80: 27.470 distance: 78 - 79: 8.646 distance: 78 - 85: 8.402 distance: 80 - 81: 17.841 distance: 81 - 82: 38.895 distance: 82 - 83: 18.637 distance: 83 - 84: 39.911 distance: 85 - 86: 11.761 distance: 86 - 87: 28.720 distance: 86 - 89: 18.836 distance: 87 - 88: 20.922 distance: 87 - 95: 18.510 distance: 89 - 90: 13.857 distance: 90 - 91: 17.441 distance: 90 - 92: 13.655 distance: 91 - 93: 33.890 distance: 92 - 94: 34.095 distance: 93 - 94: 14.676 distance: 95 - 96: 25.016 distance: 96 - 97: 19.317 distance: 96 - 99: 17.877 distance: 97 - 98: 40.604 distance: 97 - 102: 24.378 distance: 99 - 100: 27.295 distance: 99 - 101: 52.729 distance: 102 - 103: 17.831 distance: 103 - 104: 9.867 distance: 103 - 106: 32.904 distance: 104 - 105: 27.491 distance: 104 - 108: 21.881 distance: 106 - 107: 48.101 distance: 108 - 109: 23.612 distance: 109 - 110: 29.280 distance: 109 - 112: 18.351 distance: 110 - 111: 22.355 distance: 110 - 115: 24.062 distance: 112 - 113: 22.145 distance: 112 - 114: 24.264 distance: 115 - 116: 21.011 distance: 115 - 183: 30.855 distance: 116 - 117: 22.940 distance: 116 - 119: 41.783 distance: 117 - 118: 28.761 distance: 117 - 123: 23.504 distance: 118 - 193: 26.968 distance: 119 - 120: 22.843 distance: 120 - 121: 42.493 distance: 120 - 122: 54.116 distance: 123 - 124: 8.994 distance: 124 - 125: 34.290 distance: 124 - 127: 28.395 distance: 125 - 126: 29.169 distance: 125 - 135: 20.939 distance: 127 - 128: 25.418 distance: 128 - 129: 18.767 distance: 128 - 130: 24.832 distance: 129 - 131: 33.454 distance: 130 - 132: 27.789 distance: 131 - 133: 23.863 distance: 132 - 133: 18.068 distance: 133 - 134: 17.433 distance: 135 - 136: 47.096 distance: 135 - 196: 31.184 distance: 136 - 137: 40.490 distance: 136 - 139: 42.623 distance: 137 - 141: 42.956 distance: 139 - 140: 57.365 distance: 141 - 142: 17.569 distance: 142 - 143: 8.100 distance: 142 - 145: 4.113 distance: 143 - 144: 40.105 distance: 143 - 149: 40.269 distance: 145 - 146: 6.396 distance: 146 - 148: 3.110 distance: 149 - 150: 56.244 distance: 150 - 151: 40.617 distance: 151 - 152: 40.980 distance: 151 - 153: 30.829