Starting phenix.real_space_refine on Fri Sep 11 14:54:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6xlc_22239/09_2026/6xlc_22239.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xlc_22239/09_2026/6xlc_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_22239/09_2026/6xlc_22239.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xlc_22239/09_2026/6xlc_22239.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6xlc_22239/09_2026/6xlc_22239.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6xlc_22239/09_2026/6xlc_22239.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6xlc_22239/09_2026/6xlc_22239.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xlc_22239/09_2026/6xlc_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-2.2.1-6174/lib/python3.11/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: 2.22, per 1000 atoms: 0.23 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: 0.86 Conformation dependent library (CDL) restraints added in 348.4 milliseconds 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: 0.18 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: 1.23 Time building geometry restraints manager: 1.13 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: 5716 17.80 - 35.60: 322 35.60 - 53.39: 64 53.39 - 71.19: 21 71.19 - 88.99: 13 Dihedral angle restraints: 6136 sinusoidal: 2572 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 6133 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.470 Find NCS groups from input model: 0.120 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6385 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 : 12.739 88.987 3812 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 are 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/Z covalent geometry : bond 0.00349 / 0.18 (10022) covalent geometry : angle 0.52260 / 0.25 (13526) hydrogen bonds : bond 0.22192 / 14.13 ( 417) hydrogen bonds : angle 7.79497 / 5.41 ( 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 : 0.353 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: 0.6025 (mmtm) cc_final: 0.5820 (tptp) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.1117 time to fit residues: 39.7408 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 : 0.292 ------------------------------------------------------------------------------- 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... 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 = 0.3935 r_free = 0.3935 target = 0.130568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.115008 restraints weight = 20838.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.118107 restraints weight = 12394.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.120253 restraints weight = 8588.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.121754 restraints weight = 6496.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.122698 restraints weight = 5213.992| |-----------------------------------------------------------------------------| r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.5438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 10022 Z= 0.250 Angle : 0.737 8.696 13526 Z= 0.382 Chirality : 0.048 0.183 1534 Planarity : 0.005 0.044 1724 Dihedral : 5.760 81.082 1302 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.77 % Allowed : 13.10 % 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 are not related in a simple way. whole: -1.74 (0.22), residues: 1196 helix: -0.73 (0.22), residues: 490 sheet: -0.87 (0.34), residues: 214 loop : -1.58 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 174 TYR 0.027 0.002 TYR B 125 PHE 0.021 0.003 PHE B 104 TRP 0.014 0.002 TRP A 357 HIS 0.005 0.002 HIS A 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.25 (10022) covalent geometry : angle 0.73654 / 0.38 (13526) hydrogen bonds : bond 0.04386 / 2.84 ( 417) hydrogen bonds : angle 5.42112 / 3.63 ( 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 169 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 0.385 Fit side-chains REVERT: A 205 ILE cc_start: 0.7672 (mm) cc_final: 0.7364 (mt) REVERT: A 314 ARG cc_start: 0.7703 (mpt-90) cc_final: 0.7427 (mmt-90) REVERT: B 205 ILE cc_start: 0.7577 (mm) cc_final: 0.7202 (mt) REVERT: B 386 LYS cc_start: 0.7320 (mmtm) cc_final: 0.6952 (tptp) REVERT: B 589 MET cc_start: 0.7310 (mmt) cc_final: 0.7027 (mmt) outliers start: 30 outliers final: 16 residues processed: 158 average time/residue: 0.0933 time to fit residues: 20.7641 Evaluate side-chains 112 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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: 0.9990 chunk 64 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 89 optimal weight: 0.4980 chunk 4 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 21 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 ASN ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.130501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.115454 restraints weight = 20572.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.118577 restraints weight = 12061.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.120661 restraints weight = 8190.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.122098 restraints weight = 6118.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.122984 restraints weight = 4880.469| |-----------------------------------------------------------------------------| r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.5896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10022 Z= 0.121 Angle : 0.528 7.920 13526 Z= 0.270 Chirality : 0.042 0.170 1534 Planarity : 0.003 0.039 1724 Dihedral : 5.046 81.562 1302 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.11 % Allowed : 17.44 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.24), residues: 1196 helix: 0.13 (0.24), residues: 490 sheet: -0.90 (0.34), residues: 216 loop : -1.18 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 174 TYR 0.008 0.001 TYR A 125 PHE 0.020 0.001 PHE A 579 TRP 0.008 0.001 TRP A 148 HIS 0.003 0.000 HIS B 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (10022) covalent geometry : angle 0.52797 / 0.27 (13526) hydrogen bonds : bond 0.03336 / 2.23 ( 417) hydrogen bonds : angle 4.83609 / 3.25 ( 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 128 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.270 Fit side-chains REVERT: A 205 ILE cc_start: 0.7702 (mm) cc_final: 0.7304 (mt) REVERT: A 589 MET cc_start: 0.7640 (mmt) cc_final: 0.7343 (mmt) REVERT: B 105 MET cc_start: 0.8108 (mmm) cc_final: 0.7856 (mmm) REVERT: B 116 MET cc_start: 0.7322 (mpp) cc_final: 0.6973 (mtt) REVERT: B 205 ILE cc_start: 0.7563 (mm) cc_final: 0.7061 (mt) REVERT: B 289 TYR cc_start: 0.5315 (t80) cc_final: 0.5069 (t80) REVERT: B 343 ARG cc_start: 0.7244 (mmm-85) cc_final: 0.6682 (ptp-110) REVERT: B 386 LYS cc_start: 0.7387 (mmtm) cc_final: 0.7020 (tptp) REVERT: B 396 LEU cc_start: 0.9072 (tp) cc_final: 0.8830 (tp) REVERT: B 589 MET cc_start: 0.7213 (mmt) cc_final: 0.6922 (mmt) outliers start: 12 outliers final: 9 residues processed: 125 average time/residue: 0.0825 time to fit residues: 14.8732 Evaluate side-chains 100 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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 474 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 36 optimal weight: 0.7980 chunk 85 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 59 optimal weight: 0.0970 chunk 74 optimal weight: 10.0000 chunk 40 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 91 ASN B 426 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.130999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.115893 restraints weight = 20750.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.119573 restraints weight = 11738.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.121349 restraints weight = 7995.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.122416 restraints weight = 5807.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.122887 restraints weight = 5290.275| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.6213 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= 0.100 Angle : 0.505 7.601 13526 Z= 0.254 Chirality : 0.041 0.172 1534 Planarity : 0.003 0.038 1724 Dihedral : 4.888 82.668 1302 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.01 % Allowed : 17.99 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.25), residues: 1196 helix: 0.48 (0.24), residues: 490 sheet: -0.78 (0.35), residues: 216 loop : -0.97 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 174 TYR 0.009 0.001 TYR B 289 PHE 0.019 0.001 PHE A 579 TRP 0.010 0.001 TRP A 148 HIS 0.003 0.000 HIS B 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (10022) covalent geometry : angle 0.50458 / 0.25 (13526) hydrogen bonds : bond 0.02838 / 1.89 ( 417) hydrogen bonds : angle 4.58710 / 3.10 ( 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 116 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.386 Fit side-chains REVERT: A 205 ILE cc_start: 0.7630 (mm) cc_final: 0.7303 (mt) REVERT: B 105 MET cc_start: 0.8095 (mmm) cc_final: 0.7845 (mmm) REVERT: B 116 MET cc_start: 0.7266 (mpp) cc_final: 0.6901 (mtt) REVERT: B 205 ILE cc_start: 0.7587 (mm) cc_final: 0.7320 (mt) REVERT: B 386 LYS cc_start: 0.7396 (mmtm) cc_final: 0.7001 (tptp) REVERT: B 396 LEU cc_start: 0.9051 (tp) cc_final: 0.8802 (tp) REVERT: B 614 LYS cc_start: 0.7814 (mmtm) cc_final: 0.7100 (tmtt) outliers start: 11 outliers final: 7 residues processed: 114 average time/residue: 0.0783 time to fit residues: 13.5106 Evaluate side-chains 93 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 339 LEU 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 127 LEU Chi-restraints excluded: chain B residue 147 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 31 optimal weight: 0.0870 chunk 4 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 110 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 overall best weight: 0.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 381 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.129019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.114050 restraints weight = 20579.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.117070 restraints weight = 12007.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.119172 restraints weight = 8184.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.120612 restraints weight = 6110.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.121648 restraints weight = 4851.232| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.6551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10022 Z= 0.103 Angle : 0.499 7.025 13526 Z= 0.253 Chirality : 0.041 0.161 1534 Planarity : 0.003 0.037 1724 Dihedral : 4.863 81.669 1302 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.57 % Allowed : 18.82 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.25), residues: 1196 helix: 0.72 (0.25), residues: 488 sheet: -0.58 (0.36), residues: 216 loop : -0.92 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 343 TYR 0.011 0.001 TYR B 289 PHE 0.018 0.001 PHE B 6 TRP 0.009 0.001 TRP A 148 HIS 0.001 0.000 HIS A 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.10 (10022) covalent geometry : angle 0.49945 / 0.25 (13526) hydrogen bonds : bond 0.02791 / 1.87 ( 417) hydrogen bonds : angle 4.49444 / 3.02 ( 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 115 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.397 Fit side-chains REVERT: A 205 ILE cc_start: 0.7584 (mm) cc_final: 0.7223 (mt) REVERT: A 314 ARG cc_start: 0.7485 (OUTLIER) cc_final: 0.7072 (mtt-85) REVERT: A 589 MET cc_start: 0.7678 (mmt) cc_final: 0.7387 (mmt) REVERT: B 116 MET cc_start: 0.7215 (mpp) cc_final: 0.6930 (mtt) REVERT: B 205 ILE cc_start: 0.7562 (mm) cc_final: 0.7158 (mt) REVERT: B 386 LYS cc_start: 0.7282 (mmtm) cc_final: 0.6992 (tptp) REVERT: B 396 LEU cc_start: 0.9031 (tp) cc_final: 0.8820 (tp) REVERT: B 614 LYS cc_start: 0.7720 (mmtm) cc_final: 0.7041 (tmtt) outliers start: 17 outliers final: 11 residues processed: 109 average time/residue: 0.0855 time to fit residues: 13.6382 Evaluate side-chains 100 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 584 ASN 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 81 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 117 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 76 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 442 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.120136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.105901 restraints weight = 20905.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.108421 restraints weight = 11621.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.109961 restraints weight = 8675.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.111286 restraints weight = 6339.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.111681 restraints weight = 5787.503| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.7843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 10022 Z= 0.218 Angle : 0.646 9.515 13526 Z= 0.334 Chirality : 0.045 0.163 1534 Planarity : 0.004 0.041 1724 Dihedral : 5.595 76.368 1302 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.40 % Allowed : 18.54 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.25), residues: 1196 helix: 0.39 (0.24), residues: 490 sheet: -0.72 (0.36), residues: 216 loop : -1.06 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 343 TYR 0.015 0.002 TYR B 125 PHE 0.030 0.002 PHE A 6 TRP 0.011 0.002 TRP B 581 HIS 0.003 0.001 HIS A 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.22 (10022) covalent geometry : angle 0.64650 / 0.33 (13526) hydrogen bonds : bond 0.03700 / 2.41 ( 417) hydrogen bonds : angle 5.03923 / 3.41 ( 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 124 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 0.236 Fit side-chains REVERT: A 116 MET cc_start: 0.7295 (mtt) cc_final: 0.7065 (mtt) REVERT: A 192 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8110 (tt0) REVERT: A 205 ILE cc_start: 0.7738 (mm) cc_final: 0.7390 (mt) REVERT: B 16 MET cc_start: 0.8212 (tpp) cc_final: 0.7904 (tpt) REVERT: B 195 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7772 (tttm) REVERT: B 205 ILE cc_start: 0.7758 (mm) cc_final: 0.7370 (mt) REVERT: B 322 ARG cc_start: 0.5696 (ppt170) cc_final: 0.5039 (ttt180) REVERT: B 386 LYS cc_start: 0.8072 (mmtm) cc_final: 0.7690 (tptp) REVERT: B 553 ILE cc_start: 0.7973 (mm) cc_final: 0.7663 (mm) outliers start: 26 outliers final: 14 residues processed: 121 average time/residue: 0.0858 time to fit residues: 15.1554 Evaluate side-chains 90 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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 192 GLU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 82 ILE 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 393 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: 0.9980 chunk 67 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 81 optimal weight: 6.9990 chunk 114 optimal weight: 0.3980 chunk 9 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 14 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.122898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.108562 restraints weight = 20706.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.111110 restraints weight = 11741.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.113028 restraints weight = 8213.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.115832 restraints weight = 5957.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.115975 restraints weight = 4406.383| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.7954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10022 Z= 0.117 Angle : 0.531 7.730 13526 Z= 0.273 Chirality : 0.042 0.166 1534 Planarity : 0.004 0.043 1724 Dihedral : 5.218 77.113 1302 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.57 % Allowed : 22.23 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.25), residues: 1196 helix: 0.62 (0.25), residues: 490 sheet: -0.66 (0.36), residues: 216 loop : -0.95 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 343 TYR 0.010 0.001 TYR B 289 PHE 0.017 0.001 PHE A 6 TRP 0.009 0.001 TRP A 148 HIS 0.001 0.000 HIS A 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (10022) covalent geometry : angle 0.53115 / 0.27 (13526) hydrogen bonds : bond 0.02924 / 1.96 ( 417) hydrogen bonds : angle 4.70146 / 3.20 ( 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 109 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: A 205 ILE cc_start: 0.7785 (mm) cc_final: 0.7397 (mt) REVERT: B 16 MET cc_start: 0.8169 (tpp) cc_final: 0.7915 (tpt) REVERT: B 205 ILE cc_start: 0.7733 (mm) cc_final: 0.7336 (mt) REVERT: B 386 LYS cc_start: 0.8031 (mmtm) cc_final: 0.7700 (tptp) REVERT: B 553 ILE cc_start: 0.7621 (mm) cc_final: 0.7266 (mm) outliers start: 17 outliers final: 9 residues processed: 106 average time/residue: 0.0794 time to fit residues: 12.8058 Evaluate side-chains 86 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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 584 ASN Chi-restraints excluded: chain A residue 625 VAL 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 102 optimal weight: 0.8980 chunk 2 optimal weight: 7.9990 chunk 89 optimal weight: 0.3980 chunk 3 optimal weight: 0.6980 chunk 80 optimal weight: 7.9990 chunk 37 optimal weight: 0.1980 chunk 50 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 66 optimal weight: 0.0370 chunk 40 optimal weight: 0.0470 overall best weight: 0.2756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 380 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 = 0.3884 r_free = 0.3884 target = 0.126712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.111619 restraints weight = 20614.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.114841 restraints weight = 12139.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.116975 restraints weight = 8173.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.118366 restraints weight = 6104.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.119415 restraints weight = 4897.782| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.7949 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= 0.093 Angle : 0.513 7.547 13526 Z= 0.262 Chirality : 0.041 0.163 1534 Planarity : 0.003 0.041 1724 Dihedral : 4.931 79.768 1302 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.74 % Allowed : 23.25 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.25), residues: 1196 helix: 0.82 (0.25), residues: 490 sheet: -0.56 (0.37), residues: 218 loop : -0.80 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 343 TYR 0.013 0.001 TYR A 289 PHE 0.012 0.001 PHE A 6 TRP 0.014 0.001 TRP A 148 HIS 0.001 0.000 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.09 (10022) covalent geometry : angle 0.51280 / 0.26 (13526) hydrogen bonds : bond 0.02619 / 1.75 ( 417) hydrogen bonds : angle 4.48998 / 3.05 ( 1170) *********************** REFINEMENT MACRO_CYCLE 8 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 103 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: A 205 ILE cc_start: 0.7721 (mm) cc_final: 0.7357 (mt) REVERT: A 346 ILE cc_start: 0.8534 (pt) cc_final: 0.8218 (mm) REVERT: A 614 LYS cc_start: 0.7877 (mmpt) cc_final: 0.7648 (tttp) REVERT: B 86 LYS cc_start: 0.8115 (tptp) cc_final: 0.7834 (tptm) REVERT: B 378 MET cc_start: 0.6690 (ppp) cc_final: 0.6481 (ppp) REVERT: B 386 LYS cc_start: 0.7931 (mmtm) cc_final: 0.7629 (tptp) REVERT: B 553 ILE cc_start: 0.7547 (mm) cc_final: 0.7074 (mm) outliers start: 8 outliers final: 8 residues processed: 101 average time/residue: 0.0776 time to fit residues: 11.5456 Evaluate side-chains 89 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 584 ASN Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 260 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 63 optimal weight: 0.8980 chunk 73 optimal weight: 8.9990 chunk 11 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 38 optimal weight: 0.0170 chunk 78 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.126581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.111636 restraints weight = 20332.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.114800 restraints weight = 11771.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.116910 restraints weight = 7953.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.118348 restraints weight = 5947.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.119383 restraints weight = 4741.198| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.8053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10022 Z= 0.104 Angle : 0.529 8.075 13526 Z= 0.271 Chirality : 0.042 0.163 1534 Planarity : 0.004 0.053 1724 Dihedral : 4.936 79.780 1302 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.92 % Allowed : 23.06 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.25), residues: 1196 helix: 0.88 (0.25), residues: 490 sheet: -0.61 (0.38), residues: 196 loop : -0.71 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 343 TYR 0.011 0.001 TYR A 289 PHE 0.031 0.001 PHE B 124 TRP 0.008 0.001 TRP B 581 HIS 0.001 0.000 HIS B 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.10 (10022) covalent geometry : angle 0.52885 / 0.27 (13526) hydrogen bonds : bond 0.02607 / 1.74 ( 417) hydrogen bonds : angle 4.51195 / 3.05 ( 1170) *********************** REFINEMENT MACRO_CYCLE 9 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 95 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.278 Fit side-chains revert: symmetry clash REVERT: A 205 ILE cc_start: 0.7687 (mm) cc_final: 0.7367 (mt) REVERT: A 614 LYS cc_start: 0.7862 (mmpt) cc_final: 0.7659 (tttp) REVERT: B 86 LYS cc_start: 0.8160 (tptp) cc_final: 0.7866 (tptm) REVERT: B 386 LYS cc_start: 0.7968 (mmtm) cc_final: 0.7632 (tptp) REVERT: B 553 ILE cc_start: 0.7405 (mm) cc_final: 0.7044 (mm) outliers start: 10 outliers final: 8 residues processed: 92 average time/residue: 0.0946 time to fit residues: 12.9294 Evaluate side-chains 83 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 584 ASN 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 70 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 101 optimal weight: 0.0000 chunk 52 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 380 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 = 0.3884 r_free = 0.3884 target = 0.126398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.111508 restraints weight = 20167.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.114666 restraints weight = 11825.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.116767 restraints weight = 8018.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.118212 restraints weight = 6004.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.119231 restraints weight = 4794.372| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.8181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10022 Z= 0.105 Angle : 0.531 7.987 13526 Z= 0.271 Chirality : 0.042 0.249 1534 Planarity : 0.004 0.057 1724 Dihedral : 4.932 79.088 1302 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.83 % Allowed : 23.43 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.25), residues: 1196 helix: 0.87 (0.25), residues: 490 sheet: -0.55 (0.38), residues: 202 loop : -0.72 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 343 TYR 0.011 0.001 TYR A 289 PHE 0.026 0.001 PHE A 124 TRP 0.009 0.001 TRP B 148 HIS 0.001 0.000 HIS B 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (10022) covalent geometry : angle 0.53121 / 0.27 (13526) hydrogen bonds : bond 0.02607 / 1.74 ( 417) hydrogen bonds : angle 4.55260 / 3.07 ( 1170) ********************** REFINEMENT MACRO_CYCLE 10 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 91 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: A 205 ILE cc_start: 0.7645 (mm) cc_final: 0.7329 (mt) REVERT: A 614 LYS cc_start: 0.7841 (mmpt) cc_final: 0.7630 (tttp) REVERT: A 644 GLU cc_start: 0.6591 (mm-30) cc_final: 0.6359 (mm-30) REVERT: B 86 LYS cc_start: 0.8201 (tptp) cc_final: 0.7942 (tptm) REVERT: B 386 LYS cc_start: 0.7982 (mmtm) cc_final: 0.7665 (tptp) REVERT: B 553 ILE cc_start: 0.7403 (mm) cc_final: 0.7034 (mm) outliers start: 9 outliers final: 9 residues processed: 88 average time/residue: 0.0867 time to fit residues: 11.3527 Evaluate side-chains 84 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 584 ASN Chi-restraints excluded: chain B residue 34 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 65 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 98 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.124091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.109162 restraints weight = 20377.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.112196 restraints weight = 12213.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.114270 restraints weight = 8398.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.115578 restraints weight = 6330.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.116705 restraints weight = 5147.593| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.8371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10022 Z= 0.122 Angle : 0.547 8.242 13526 Z= 0.279 Chirality : 0.042 0.178 1534 Planarity : 0.004 0.061 1724 Dihedral : 5.021 78.891 1302 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.01 % Allowed : 23.52 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.25), residues: 1196 helix: 0.84 (0.25), residues: 490 sheet: -0.55 (0.38), residues: 202 loop : -0.75 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 343 TYR 0.010 0.001 TYR A 289 PHE 0.026 0.001 PHE A 124 TRP 0.008 0.001 TRP B 581 HIS 0.001 0.000 HIS A 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.12 (10022) covalent geometry : angle 0.54680 / 0.28 (13526) hydrogen bonds : bond 0.02742 / 1.82 ( 417) hydrogen bonds : angle 4.58317 / 3.08 ( 1170) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1389.91 seconds wall clock time: 24 minutes 54.37 seconds (1494.37 seconds total)