Starting phenix.real_space_refine on Sat Aug 23 05:18:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xlc_22239/08_2025/6xlc_22239.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xlc_22239/08_2025/6xlc_22239.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6xlc_22239/08_2025/6xlc_22239.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xlc_22239/08_2025/6xlc_22239.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6xlc_22239/08_2025/6xlc_22239.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xlc_22239/08_2025/6xlc_22239.map" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 18 5.16 5 C 6286 2.51 5 N 1620 2.21 5 O 1926 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 99 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: 9858 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4897 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 20, 'TRANS': 585} Chain breaks: 3 Chain: "B" Number of atoms: 4897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4897 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 20, 'TRANS': 585} Chain breaks: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.91, per 1000 atoms: 0.19 Number of scatterers: 9858 At special positions: 0 Unit cell: (98.487, 92.133, 131.316, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 18 16.00 P 6 15.00 Mg 2 11.99 O 1926 8.00 N 1620 7.00 C 6286 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: 0.79 Conformation dependent library (CDL) restraints added in 283.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2324 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 10 sheets defined 43.8% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 11 through 19 removed outlier: 4.074A pdb=" N SER A 17 " --> pdb=" O THR A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 52 removed outlier: 4.311A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N SER A 51 " --> pdb=" O TYR A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 57 Processing helix chain 'A' and resid 87 through 92 Processing helix chain 'A' and resid 99 through 107 Processing helix chain 'A' and resid 123 through 129 removed outlier: 3.566A pdb=" N LEU A 127 " --> pdb=" O PHE A 124 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE A 128 " --> pdb=" O TYR A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 185 removed outlier: 3.762A pdb=" N TYR A 184 " --> pdb=" O GLN A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 197 Processing helix chain 'A' and resid 276 through 280 Processing helix chain 'A' and resid 281 through 293 Processing helix chain 'A' and resid 384 through 405 removed outlier: 3.938A pdb=" N ILE A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 415 removed outlier: 3.547A pdb=" N PHE A 410 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 428 removed outlier: 3.502A pdb=" N ILE A 421 " --> pdb=" O PHE A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 437 removed outlier: 3.834A pdb=" N LYS A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 459 removed outlier: 3.650A pdb=" N ARG A 459 " --> pdb=" O ASP A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.594A pdb=" N VAL A 478 " --> pdb=" O SER A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 490 removed outlier: 3.833A pdb=" N LYS A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 510 removed outlier: 3.521A pdb=" N ALA A 505 " --> pdb=" O ILE A 501 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLN A 508 " --> pdb=" O TYR A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 541 removed outlier: 3.892A pdb=" N GLU A 535 " --> pdb=" O GLU A 531 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS A 541 " --> pdb=" O GLU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 555 Processing helix chain 'A' and resid 582 through 592 removed outlier: 3.634A pdb=" N GLU A 586 " --> pdb=" O SER A 582 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG A 587 " --> pdb=" O ALA A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 627 removed outlier: 3.712A pdb=" N LYS A 623 " --> pdb=" O LYS A 619 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG A 624 " --> pdb=" O GLU A 620 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL A 625 " --> pdb=" O LEU A 621 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP A 626 " --> pdb=" O LYS A 622 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU A 627 " --> pdb=" O LYS A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 651 removed outlier: 3.816A pdb=" N LYS A 636 " --> pdb=" O ASP A 632 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASP A 637 " --> pdb=" O LYS A 633 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU A 638 " --> pdb=" O THR A 634 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLY A 651 " --> pdb=" O LEU A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 672 removed outlier: 3.827A pdb=" N PHE A 660 " --> pdb=" O GLU A 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 22 removed outlier: 4.447A pdb=" N SER B 17 " --> pdb=" O THR B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 52 removed outlier: 4.376A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER B 51 " --> pdb=" O TYR B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 57 Processing helix chain 'B' and resid 87 through 92 Processing helix chain 'B' and resid 99 through 108 Processing helix chain 'B' and resid 122 through 129 removed outlier: 3.521A pdb=" N LEU B 127 " --> pdb=" O PHE B 124 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE B 128 " --> pdb=" O TYR B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 185 removed outlier: 3.664A pdb=" N TYR B 184 " --> pdb=" O GLN B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 198 Processing helix chain 'B' and resid 281 through 293 Processing helix chain 'B' and resid 383 through 405 removed outlier: 3.625A pdb=" N VAL B 387 " --> pdb=" O LYS B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 417 Processing helix chain 'B' and resid 417 through 427 Processing helix chain 'B' and resid 431 through 437 removed outlier: 3.790A pdb=" N LYS B 437 " --> pdb=" O ALA B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 459 removed outlier: 3.603A pdb=" N THR B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG B 459 " --> pdb=" O ASP B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 480 removed outlier: 3.536A pdb=" N VAL B 478 " --> pdb=" O SER B 474 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LYS B 480 " --> pdb=" O LYS B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 490 removed outlier: 3.519A pdb=" N LYS B 490 " --> pdb=" O ALA B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 510 removed outlier: 3.553A pdb=" N ALA B 505 " --> pdb=" O ILE B 501 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLN B 508 " --> pdb=" O TYR B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 541 Processing helix chain 'B' and resid 543 through 555 Processing helix chain 'B' and resid 582 through 590 removed outlier: 3.823A pdb=" N ARG B 587 " --> pdb=" O ALA B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 627 removed outlier: 3.573A pdb=" N LYS B 623 " --> pdb=" O LYS B 619 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG B 624 " --> pdb=" O GLU B 620 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL B 625 " --> pdb=" O LEU B 621 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP B 626 " --> pdb=" O LYS B 622 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU B 627 " --> pdb=" O LYS B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 651 removed outlier: 3.630A pdb=" N LYS B 636 " --> pdb=" O ASP B 632 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP B 637 " --> pdb=" O LYS B 633 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU B 638 " --> pdb=" O THR B 634 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY B 651 " --> pdb=" O LEU B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 672 removed outlier: 3.967A pdb=" N PHE B 660 " --> pdb=" O GLU B 656 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 removed outlier: 3.548A pdb=" N GLU A 4 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG B 133 " --> pdb=" O PHE B 176 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG B 174 " --> pdb=" O GLN B 135 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ILE B 64 " --> pdb=" O GLN B 206 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N LEU B 208 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ILE B 66 " --> pdb=" O LEU B 208 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 9 through 10 removed outlier: 6.475A pdb=" N GLN A 9 " --> pdb=" O ILE B 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 262 through 265 removed outlier: 6.058A pdb=" N ILE A 64 " --> pdb=" O GLN A 206 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N LEU A 208 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ILE A 66 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR A 67 " --> pdb=" O GLU A 76 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU A 76 " --> pdb=" O THR A 67 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ARG A 133 " --> pdb=" O PHE A 176 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU B 4 " --> pdb=" O VAL A 158 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 95 through 96 Processing sheet with id=AA5, first strand: chain 'A' and resid 301 through 307 removed outlier: 3.512A pdb=" N TYR A 301 " --> pdb=" O ILE A 319 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N THR A 347 " --> pdb=" O LEU A 339 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL A 341 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N PHE A 345 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 442 through 443 removed outlier: 4.048A pdb=" N ASN A 442 " --> pdb=" O PHE A 496 " (cutoff:3.500A) removed outlier: 8.844A pdb=" N LEU A 495 " --> pdb=" O ASN A 466 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N TYR A 468 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N LEU A 497 " --> pdb=" O TYR A 468 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE A 470 " --> pdb=" O LEU A 497 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ILE A 467 " --> pdb=" O VAL A 518 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 561 through 563 removed outlier: 3.524A pdb=" N ILE A 611 " --> pdb=" O VAL A 562 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 301 through 307 removed outlier: 3.515A pdb=" N VAL B 364 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N LEU B 339 " --> pdb=" O ILE B 346 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 442 through 443 removed outlier: 3.885A pdb=" N ASN B 442 " --> pdb=" O PHE B 496 " (cutoff:3.500A) removed outlier: 8.834A pdb=" N LEU B 495 " --> pdb=" O ASN B 466 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TYR B 468 " --> pdb=" O LEU B 495 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N LEU B 497 " --> pdb=" O TYR B 468 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE B 470 " --> pdb=" O LEU B 497 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ILE B 467 " --> pdb=" O VAL B 518 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 561 through 563 removed outlier: 3.526A pdb=" N ILE B 611 " --> pdb=" O VAL B 562 " (cutoff:3.500A) 417 hydrogen bonds defined for protein. 1170 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: 1.24 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3212 1.34 - 1.46: 1542 1.46 - 1.57: 5220 1.57 - 1.69: 10 1.69 - 1.80: 38 Bond restraints: 10022 Sorted by residual: bond pdb=" O3A ANP A 801 " pdb=" PB ANP A 801 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.17e+01 bond pdb=" O3A ANP B 801 " pdb=" PB ANP B 801 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.12e+01 bond pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 1.795 1.692 0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" N3B ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sigma weight residual 1.795 1.692 0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" O5' ANP B 801 " pdb=" PA ANP B 801 " ideal model delta sigma weight residual 1.655 1.582 0.073 2.00e-02 2.50e+03 1.35e+01 ... (remaining 10017 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.46: 13486 3.46 - 6.93: 30 6.93 - 10.39: 7 10.39 - 13.86: 1 13.86 - 17.32: 2 Bond angle restraints: 13526 Sorted by residual: angle pdb=" PB ANP B 801 " pdb=" N3B ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sigma weight residual 126.95 109.63 17.32 3.00e+00 1.11e-01 3.33e+01 angle pdb=" PB ANP A 801 " pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 126.95 109.73 17.22 3.00e+00 1.11e-01 3.30e+01 angle pdb=" O1B ANP B 801 " pdb=" PB ANP B 801 " pdb=" O2B ANP B 801 " ideal model delta sigma weight residual 120.08 109.60 10.48 3.00e+00 1.11e-01 1.22e+01 angle pdb=" O1B ANP A 801 " pdb=" PB ANP A 801 " pdb=" O2B ANP A 801 " ideal model delta sigma weight residual 120.08 109.69 10.39 3.00e+00 1.11e-01 1.20e+01 angle pdb=" N ILE A 20 " pdb=" CA ILE A 20 " pdb=" C ILE A 20 " ideal model delta sigma weight residual 113.71 110.65 3.06 9.50e-01 1.11e+00 1.04e+01 ... (remaining 13521 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 5759 17.80 - 35.60: 330 35.60 - 53.39: 67 53.39 - 71.19: 21 71.19 - 88.99: 15 Dihedral angle restraints: 6192 sinusoidal: 2628 harmonic: 3564 Sorted by residual: dihedral pdb=" CB GLU B 76 " pdb=" CG GLU B 76 " pdb=" CD GLU B 76 " pdb=" OE1 GLU B 76 " ideal model delta sinusoidal sigma weight residual 0.00 -88.99 88.99 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU B 513 " pdb=" CG GLU B 513 " pdb=" CD GLU B 513 " pdb=" OE1 GLU B 513 " ideal model delta sinusoidal sigma weight residual 0.00 88.90 -88.90 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" O1B ANP A 801 " pdb=" N3B ANP A 801 " pdb=" PB ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sinusoidal sigma weight residual 35.15 -53.13 88.28 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 6189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1325 0.055 - 0.109: 188 0.109 - 0.164: 19 0.164 - 0.218: 0 0.218 - 0.273: 2 Chirality restraints: 1534 Sorted by residual: chirality pdb=" C3' ANP B 801 " pdb=" C2' ANP B 801 " pdb=" C4' ANP B 801 " pdb=" O3' ANP B 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" C3' ANP A 801 " pdb=" C2' ANP A 801 " pdb=" C4' ANP A 801 " pdb=" O3' ANP A 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA ILE B 77 " pdb=" N ILE B 77 " pdb=" C ILE B 77 " pdb=" CB ILE B 77 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 1531 not shown) Planarity restraints: 1724 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 354 " 0.019 5.00e-02 4.00e+02 2.88e-02 1.32e+00 pdb=" N PRO A 355 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 355 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 355 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 20 " -0.005 2.00e-02 2.50e+03 9.43e-03 8.90e-01 pdb=" C ILE A 20 " 0.016 2.00e-02 2.50e+03 pdb=" O ILE A 20 " -0.006 2.00e-02 2.50e+03 pdb=" N ASN A 21 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 543 " 0.005 2.00e-02 2.50e+03 6.32e-03 8.00e-01 pdb=" CG TYR B 543 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR B 543 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR B 543 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 543 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 543 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 543 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 543 " -0.000 2.00e-02 2.50e+03 ... (remaining 1721 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 128 2.64 - 3.21: 8674 3.21 - 3.77: 15184 3.77 - 4.34: 21623 4.34 - 4.90: 34910 Nonbonded interactions: 80519 Sorted by model distance: nonbonded pdb=" O1B ANP B 801 " pdb="MG MG B 802 " model vdw 2.079 2.170 nonbonded pdb=" O1B ANP A 801 " pdb="MG MG A 802 " model vdw 2.089 2.170 nonbonded pdb=" O1A ANP B 801 " pdb="MG MG B 802 " model vdw 2.249 2.170 nonbonded pdb=" OD1 ASN B 37 " pdb="MG MG B 802 " model vdw 2.250 2.170 nonbonded pdb=" OH TYR B 456 " pdb=" O GLU B 493 " model vdw 2.255 3.040 ... (remaining 80514 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' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.950 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.150 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 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:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6316 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 0.144 10022 Z= 0.176 Angle : 0.523 17.324 13526 Z= 0.249 Chirality : 0.039 0.273 1534 Planarity : 0.002 0.029 1724 Dihedral : 12.917 88.987 3868 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % 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: -2.69 (0.20), residues: 1196 helix: -1.88 (0.19), residues: 492 sheet: -0.99 (0.34), residues: 218 loop : -1.87 (0.23), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 440 TYR 0.016 0.001 TYR B 543 PHE 0.006 0.001 PHE A 652 TRP 0.003 0.000 TRP B 273 HIS 0.001 0.000 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00349 (10022) covalent geometry : angle 0.52260 (13526) hydrogen bonds : bond 0.22192 ( 417) hydrogen bonds : angle 7.79497 ( 1170) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: A 144 GLU cc_start: 0.6751 (mm-30) cc_final: 0.6541 (mm-30) REVERT: A 610 GLU cc_start: 0.7411 (mp0) cc_final: 0.7104 (mp0) REVERT: A 614 LYS cc_start: 0.6948 (pttm) cc_final: 0.6537 (ptmm) REVERT: B 379 LEU cc_start: 0.5857 (pt) cc_final: 0.5551 (pp) REVERT: B 386 LYS cc_start: 0.6026 (mmtm) cc_final: 0.5820 (tptp) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.1120 time to fit residues: 39.4864 Evaluate side-chains 146 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 0.0570 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 117 optimal weight: 4.9990 overall best weight: 2.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 ASN A 466 ASN A 673 ASN B 304 HIS B 380 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.130677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.115108 restraints weight = 20805.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.118264 restraints weight = 12375.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.120416 restraints weight = 8511.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.121895 restraints weight = 6441.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.122848 restraints weight = 5172.809| |-----------------------------------------------------------------------------| r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.5369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 10022 Z= 0.248 Angle : 0.736 8.672 13526 Z= 0.380 Chirality : 0.048 0.222 1534 Planarity : 0.005 0.043 1724 Dihedral : 6.777 80.846 1358 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.86 % Allowed : 13.01 % Favored : 84.13 % 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: -1.75 (0.22), residues: 1196 helix: -0.75 (0.22), residues: 490 sheet: -0.86 (0.34), residues: 214 loop : -1.57 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 432 TYR 0.024 0.002 TYR B 125 PHE 0.020 0.003 PHE B 652 TRP 0.014 0.002 TRP A 357 HIS 0.004 0.002 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00583 (10022) covalent geometry : angle 0.73600 (13526) hydrogen bonds : bond 0.04500 ( 417) hydrogen bonds : angle 5.42852 ( 1170) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 0.292 Fit side-chains REVERT: A 144 GLU cc_start: 0.7408 (mm-30) cc_final: 0.7186 (mm-30) REVERT: A 205 ILE cc_start: 0.7670 (mm) cc_final: 0.7360 (mt) REVERT: A 314 ARG cc_start: 0.7687 (mpt-90) cc_final: 0.7405 (mmt-90) REVERT: A 589 MET cc_start: 0.7567 (mmt) cc_final: 0.7361 (mmt) REVERT: B 205 ILE cc_start: 0.7578 (mm) cc_final: 0.7202 (mt) REVERT: B 386 LYS cc_start: 0.7315 (mmtm) cc_final: 0.6927 (tptp) REVERT: B 589 MET cc_start: 0.7359 (mmt) cc_final: 0.7055 (mmt) outliers start: 31 outliers final: 16 residues processed: 159 average time/residue: 0.1009 time to fit residues: 22.1728 Evaluate side-chains 110 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 441 TYR Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 611 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 86 optimal weight: 6.9990 chunk 64 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 chunk 89 optimal weight: 0.2980 chunk 4 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN B 14 GLN B 431 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.131815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.116733 restraints weight = 20596.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.119840 restraints weight = 12146.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.121984 restraints weight = 8269.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.123445 restraints weight = 6147.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.124335 restraints weight = 4893.145| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.5687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10022 Z= 0.110 Angle : 0.521 8.029 13526 Z= 0.267 Chirality : 0.042 0.167 1534 Planarity : 0.003 0.040 1724 Dihedral : 6.221 79.897 1358 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.01 % Allowed : 17.62 % Favored : 81.37 % 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: -0.98 (0.24), residues: 1196 helix: 0.11 (0.24), residues: 490 sheet: -0.89 (0.34), residues: 216 loop : -1.19 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 174 TYR 0.009 0.001 TYR B 289 PHE 0.023 0.001 PHE A 579 TRP 0.008 0.001 TRP A 148 HIS 0.003 0.001 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00257 (10022) covalent geometry : angle 0.52136 (13526) hydrogen bonds : bond 0.03243 ( 417) hydrogen bonds : angle 4.82558 ( 1170) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: A 144 GLU cc_start: 0.7343 (mm-30) cc_final: 0.7121 (mm-30) REVERT: A 205 ILE cc_start: 0.7666 (mm) cc_final: 0.7268 (mt) REVERT: B 105 MET cc_start: 0.8050 (mmm) cc_final: 0.7806 (mmm) REVERT: B 116 MET cc_start: 0.7294 (mpp) cc_final: 0.6838 (mtt) REVERT: B 205 ILE cc_start: 0.7517 (mm) cc_final: 0.7004 (mt) REVERT: B 386 LYS cc_start: 0.7396 (mmtm) cc_final: 0.6941 (tptp) REVERT: B 396 LEU cc_start: 0.9067 (tp) cc_final: 0.8837 (tp) REVERT: B 589 MET cc_start: 0.7252 (mmt) cc_final: 0.6971 (mmt) outliers start: 11 outliers final: 9 residues processed: 122 average time/residue: 0.0767 time to fit residues: 13.5254 Evaluate side-chains 102 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 163 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 36 optimal weight: 0.6980 chunk 85 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 chunk 93 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 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 381 GLN B 442 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.125782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.110584 restraints weight = 20941.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.114325 restraints weight = 11868.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.115935 restraints weight = 7824.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.116809 restraints weight = 5854.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.117223 restraints weight = 5641.064| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.6727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10022 Z= 0.162 Angle : 0.572 8.300 13526 Z= 0.293 Chirality : 0.043 0.171 1534 Planarity : 0.004 0.041 1724 Dihedral : 6.325 80.860 1358 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.49 % Allowed : 17.07 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.24), residues: 1196 helix: 0.31 (0.24), residues: 488 sheet: -0.87 (0.35), residues: 216 loop : -1.21 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 575 TYR 0.011 0.001 TYR B 184 PHE 0.018 0.002 PHE B 6 TRP 0.008 0.001 TRP B 581 HIS 0.002 0.001 HIS A 426 Details of bonding type rmsd covalent geometry : bond 0.00388 (10022) covalent geometry : angle 0.57213 (13526) hydrogen bonds : bond 0.03349 ( 417) hydrogen bonds : angle 4.86515 ( 1170) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 106 time to evaluate : 0.391 Fit side-chains REVERT: A 116 MET cc_start: 0.7366 (mpp) cc_final: 0.7086 (mtt) REVERT: A 133 ARG cc_start: 0.7768 (ttp-170) cc_final: 0.7486 (ttp-170) REVERT: A 205 ILE cc_start: 0.7619 (mm) cc_final: 0.7308 (mt) REVERT: A 614 LYS cc_start: 0.8277 (mmtt) cc_final: 0.7765 (ptmt) REVERT: B 16 MET cc_start: 0.8261 (tpp) cc_final: 0.7731 (tpt) REVERT: B 105 MET cc_start: 0.8164 (mmm) cc_final: 0.7913 (mmm) REVERT: B 205 ILE cc_start: 0.7697 (mm) cc_final: 0.7420 (mt) REVERT: B 362 LYS cc_start: 0.7165 (tppt) cc_final: 0.6805 (mmtt) REVERT: B 386 LYS cc_start: 0.7618 (mmtm) cc_final: 0.7213 (tptp) REVERT: B 396 LEU cc_start: 0.9090 (tp) cc_final: 0.8837 (tp) REVERT: B 553 ILE cc_start: 0.8037 (mm) cc_final: 0.7707 (mm) outliers start: 27 outliers final: 17 residues processed: 128 average time/residue: 0.0749 time to fit residues: 14.1383 Evaluate side-chains 104 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 441 TYR Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 474 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 31 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 13 optimal weight: 0.0870 chunk 53 optimal weight: 10.0000 chunk 110 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.126692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.111331 restraints weight = 20549.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.114413 restraints weight = 12071.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.116506 restraints weight = 8227.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.117964 restraints weight = 6174.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.118862 restraints weight = 4935.407| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.6895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10022 Z= 0.105 Angle : 0.513 7.110 13526 Z= 0.262 Chirality : 0.041 0.166 1534 Planarity : 0.003 0.044 1724 Dihedral : 6.104 77.002 1358 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.38 % Allowed : 19.10 % Favored : 79.52 % 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: -0.54 (0.25), residues: 1196 helix: 0.56 (0.24), residues: 494 sheet: -0.81 (0.35), residues: 216 loop : -0.99 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 343 TYR 0.010 0.001 TYR B 289 PHE 0.016 0.001 PHE B 6 TRP 0.009 0.001 TRP A 148 HIS 0.002 0.000 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00249 (10022) covalent geometry : angle 0.51253 (13526) hydrogen bonds : bond 0.02876 ( 417) hydrogen bonds : angle 4.63604 ( 1170) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: A 116 MET cc_start: 0.7101 (mpp) cc_final: 0.6871 (mtt) REVERT: A 205 ILE cc_start: 0.7698 (mm) cc_final: 0.7339 (mt) REVERT: A 589 MET cc_start: 0.7632 (mmt) cc_final: 0.7342 (mmt) REVERT: A 667 LEU cc_start: 0.7062 (OUTLIER) cc_final: 0.6761 (mt) REVERT: B 116 MET cc_start: 0.7117 (mtt) cc_final: 0.6793 (mtt) REVERT: B 205 ILE cc_start: 0.7752 (mm) cc_final: 0.7422 (mt) REVERT: B 322 ARG cc_start: 0.5672 (ppt170) cc_final: 0.5069 (ttt180) REVERT: B 386 LYS cc_start: 0.7736 (mmtm) cc_final: 0.7369 (tptp) REVERT: B 553 ILE cc_start: 0.7731 (mm) cc_final: 0.7385 (mm) REVERT: B 674 ILE cc_start: 0.4107 (OUTLIER) cc_final: 0.3899 (pt) outliers start: 15 outliers final: 12 residues processed: 111 average time/residue: 0.0725 time to fit residues: 11.9247 Evaluate side-chains 98 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 674 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 81 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 117 optimal weight: 2.9990 chunk 42 optimal weight: 0.2980 chunk 8 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 chunk 71 optimal weight: 0.0010 chunk 91 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 76 optimal weight: 8.9990 chunk 100 optimal weight: 6.9990 overall best weight: 1.0190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.125589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.110157 restraints weight = 20754.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.113269 restraints weight = 12193.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.115206 restraints weight = 8291.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.116707 restraints weight = 6326.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.117746 restraints weight = 5067.789| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.7205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10022 Z= 0.113 Angle : 0.509 7.342 13526 Z= 0.262 Chirality : 0.041 0.161 1534 Planarity : 0.004 0.051 1724 Dihedral : 6.118 77.982 1358 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.85 % Allowed : 18.91 % Favored : 79.24 % 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: -0.39 (0.25), residues: 1196 helix: 0.69 (0.25), residues: 490 sheet: -0.64 (0.36), residues: 216 loop : -0.96 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 376 TYR 0.012 0.001 TYR A 203 PHE 0.016 0.001 PHE B 6 TRP 0.008 0.001 TRP A 148 HIS 0.002 0.000 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00269 (10022) covalent geometry : angle 0.50885 (13526) hydrogen bonds : bond 0.02803 ( 417) hydrogen bonds : angle 4.57749 ( 1170) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: A 116 MET cc_start: 0.7257 (mpp) cc_final: 0.6892 (mtt) REVERT: A 205 ILE cc_start: 0.7752 (mm) cc_final: 0.7433 (mt) REVERT: B 116 MET cc_start: 0.7035 (mtt) cc_final: 0.6782 (mtt) REVERT: B 205 ILE cc_start: 0.7776 (mm) cc_final: 0.7370 (mt) REVERT: B 322 ARG cc_start: 0.5660 (ppt170) cc_final: 0.5092 (ttt180) REVERT: B 378 MET cc_start: 0.6858 (ppp) cc_final: 0.6607 (ppp) REVERT: B 386 LYS cc_start: 0.7767 (mmtm) cc_final: 0.7421 (tptp) REVERT: B 553 ILE cc_start: 0.7700 (mm) cc_final: 0.7364 (mm) outliers start: 20 outliers final: 13 residues processed: 111 average time/residue: 0.0772 time to fit residues: 12.9335 Evaluate side-chains 94 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 474 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 88 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 90 optimal weight: 0.0010 chunk 2 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 81 optimal weight: 20.0000 chunk 114 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 overall best weight: 1.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.122794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.107398 restraints weight = 20839.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.110488 restraints weight = 12333.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.112572 restraints weight = 8463.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.114020 restraints weight = 6409.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.114949 restraints weight = 5160.866| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.7805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10022 Z= 0.149 Angle : 0.565 8.913 13526 Z= 0.290 Chirality : 0.043 0.161 1534 Planarity : 0.004 0.058 1724 Dihedral : 6.228 74.598 1358 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.03 % Allowed : 20.30 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.25), residues: 1196 helix: 0.68 (0.25), residues: 490 sheet: -0.65 (0.35), residues: 216 loop : -0.94 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 343 TYR 0.009 0.001 TYR A 203 PHE 0.031 0.002 PHE A 6 TRP 0.008 0.001 TRP B 581 HIS 0.002 0.001 HIS B 197 Details of bonding type rmsd covalent geometry : bond 0.00360 (10022) covalent geometry : angle 0.56471 (13526) hydrogen bonds : bond 0.03092 ( 417) hydrogen bonds : angle 4.78247 ( 1170) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: A 86 LYS cc_start: 0.7576 (tptm) cc_final: 0.7373 (tptm) REVERT: A 116 MET cc_start: 0.7315 (mpp) cc_final: 0.6838 (mtt) REVERT: A 205 ILE cc_start: 0.7630 (mm) cc_final: 0.7314 (mt) REVERT: A 595 ARG cc_start: 0.4128 (mmt180) cc_final: 0.3894 (ttm170) REVERT: B 195 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7722 (tttm) REVERT: B 205 ILE cc_start: 0.7825 (mm) cc_final: 0.7424 (mt) REVERT: B 322 ARG cc_start: 0.5713 (ppt170) cc_final: 0.5266 (ttt180) REVERT: B 386 LYS cc_start: 0.8014 (mmtm) cc_final: 0.7700 (tptp) REVERT: B 553 ILE cc_start: 0.7839 (mm) cc_final: 0.7497 (mm) outliers start: 22 outliers final: 16 residues processed: 111 average time/residue: 0.0797 time to fit residues: 12.6393 Evaluate side-chains 92 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 474 SER 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: 57.4784 > 50: distance: 93 - 98: 19.897 distance: 98 - 99: 17.901 distance: 99 - 100: 25.711 distance: 99 - 102: 22.151 distance: 100 - 101: 22.084 distance: 100 - 103: 25.072 distance: 103 - 104: 16.729 distance: 104 - 105: 20.986 distance: 104 - 107: 28.427 distance: 105 - 106: 19.388 distance: 105 - 115: 12.441 distance: 107 - 108: 8.779 distance: 108 - 109: 10.260 distance: 108 - 110: 9.601 distance: 109 - 111: 4.495 distance: 110 - 112: 5.429 distance: 111 - 113: 9.570 distance: 112 - 113: 11.982 distance: 113 - 114: 5.711 distance: 115 - 116: 13.818 distance: 115 - 121: 24.682 distance: 116 - 117: 22.106 distance: 116 - 119: 22.141 distance: 117 - 118: 23.456 distance: 117 - 122: 22.069 distance: 119 - 120: 19.249 distance: 120 - 121: 19.446 distance: 122 - 123: 7.804 distance: 123 - 124: 11.956 distance: 123 - 126: 23.713 distance: 124 - 125: 22.756 distance: 124 - 130: 14.400 distance: 126 - 127: 17.400 distance: 126 - 128: 14.233 distance: 127 - 129: 21.019 distance: 130 - 131: 6.752 distance: 131 - 132: 13.734 distance: 131 - 134: 10.404 distance: 132 - 133: 16.847 distance: 132 - 139: 9.346 distance: 134 - 135: 26.386 distance: 135 - 136: 25.815 distance: 136 - 137: 14.352 distance: 136 - 138: 46.898 distance: 139 - 140: 5.366 distance: 139 - 205: 12.197 distance: 140 - 141: 23.804 distance: 140 - 143: 29.142 distance: 141 - 142: 24.699 distance: 141 - 147: 21.509 distance: 142 - 202: 25.287 distance: 143 - 144: 14.035 distance: 144 - 145: 15.632 distance: 144 - 146: 12.885 distance: 147 - 148: 13.522 distance: 148 - 149: 18.293 distance: 148 - 151: 9.885 distance: 149 - 150: 14.681 distance: 149 - 155: 35.688 distance: 151 - 152: 20.345 distance: 152 - 153: 32.999 distance: 152 - 154: 25.601 distance: 155 - 188: 22.992 distance: 156 - 157: 3.936 distance: 156 - 159: 16.936 distance: 157 - 158: 11.302 distance: 157 - 162: 32.720 distance: 158 - 185: 27.255 distance: 159 - 160: 8.088 distance: 159 - 161: 23.148 distance: 162 - 163: 21.365 distance: 163 - 164: 14.186 distance: 163 - 166: 25.244 distance: 164 - 165: 7.651 distance: 166 - 167: 6.931 distance: 166 - 168: 16.055 distance: 169 - 170: 10.824 distance: 170 - 171: 10.030 distance: 170 - 173: 10.104 distance: 171 - 172: 11.576 distance: 171 - 176: 25.035 distance: 173 - 174: 9.818 distance: 173 - 175: 18.402