Starting phenix.real_space_refine on Thu Mar 5 02:00:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l2x_23144/03_2026/7l2x_23144.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l2x_23144/03_2026/7l2x_23144.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7l2x_23144/03_2026/7l2x_23144.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l2x_23144/03_2026/7l2x_23144.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7l2x_23144/03_2026/7l2x_23144.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l2x_23144/03_2026/7l2x_23144.map" } resolution = 3.26 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 100 5.16 5 C 11655 2.51 5 N 2817 2.21 5 O 3169 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17745 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4349 Classifications: {'peptide': 536} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 521} Chain: "D" Number of atoms: 4349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4349 Classifications: {'peptide': 536} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 521} Chain: "B" Number of atoms: 4349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4349 Classifications: {'peptide': 536} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 521} Chain: "C" Number of atoms: 4349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4349 Classifications: {'peptide': 536} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 521} Chain: "A" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 122 Unusual residues: {'6EU': 1, '6IY': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 97 Unusual residues: {'6EU': 1, '6IY': 1, 'XPJ': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 84 Unusual residues: {'6EU': 1, '6IY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.20, per 1000 atoms: 0.24 Number of scatterers: 17745 At special positions: 0 Unit cell: (126.92, 127.755, 110.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 100 16.00 P 4 15.00 O 3169 8.00 N 2817 7.00 C 11655 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 608.7 milliseconds 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4056 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 4 sheets defined 63.5% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 203 through 212 Processing helix chain 'A' and resid 213 through 223 Processing helix chain 'A' and resid 250 through 258 Processing helix chain 'A' and resid 260 through 270 Processing helix chain 'A' and resid 286 through 294 Processing helix chain 'A' and resid 298 through 320 Processing helix chain 'A' and resid 324 through 328 Processing helix chain 'A' and resid 335 through 344 Processing helix chain 'A' and resid 345 through 354 removed outlier: 3.535A pdb=" N GLN A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 366 Processing helix chain 'A' and resid 394 through 401 Processing helix chain 'A' and resid 411 through 414 Processing helix chain 'A' and resid 415 through 429 removed outlier: 3.521A pdb=" N PHE A 429 " --> pdb=" O LYS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 454 removed outlier: 3.634A pdb=" N ILE A 433 " --> pdb=" O PHE A 429 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 500 Processing helix chain 'A' and resid 510 through 532 Processing helix chain 'A' and resid 536 through 551 removed outlier: 3.692A pdb=" N SER A 540 " --> pdb=" O GLU A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 557 Processing helix chain 'A' and resid 562 through 575 removed outlier: 4.259A pdb=" N ALA A 566 " --> pdb=" O MET A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 599 removed outlier: 4.307A pdb=" N PHE A 582 " --> pdb=" O CYS A 578 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 642 Processing helix chain 'A' and resid 655 through 671 Processing helix chain 'A' and resid 673 through 689 removed outlier: 3.650A pdb=" N ILE A 689 " --> pdb=" O THR A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 712 removed outlier: 3.590A pdb=" N LYS A 698 " --> pdb=" O LYS A 694 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU A 699 " --> pdb=" O ASN A 695 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 211 Processing helix chain 'D' and resid 213 through 223 Processing helix chain 'D' and resid 250 through 258 Processing helix chain 'D' and resid 260 through 270 Processing helix chain 'D' and resid 286 through 294 Processing helix chain 'D' and resid 298 through 320 Processing helix chain 'D' and resid 324 through 328 removed outlier: 3.560A pdb=" N GLU D 327 " --> pdb=" O LYS D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 344 Processing helix chain 'D' and resid 345 through 354 Processing helix chain 'D' and resid 362 through 366 Processing helix chain 'D' and resid 394 through 401 Processing helix chain 'D' and resid 410 through 414 Processing helix chain 'D' and resid 415 through 429 Processing helix chain 'D' and resid 429 through 454 removed outlier: 3.599A pdb=" N ILE D 433 " --> pdb=" O PHE D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 500 Processing helix chain 'D' and resid 510 through 532 Processing helix chain 'D' and resid 536 through 551 Processing helix chain 'D' and resid 552 through 557 Processing helix chain 'D' and resid 562 through 575 removed outlier: 4.243A pdb=" N ALA D 566 " --> pdb=" O MET D 562 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 599 removed outlier: 4.544A pdb=" N PHE D 582 " --> pdb=" O CYS D 578 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL D 583 " --> pdb=" O ARG D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 642 Processing helix chain 'D' and resid 655 through 671 Processing helix chain 'D' and resid 672 through 690 removed outlier: 3.832A pdb=" N ASN D 676 " --> pdb=" O ILE D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 692 through 711 removed outlier: 3.531A pdb=" N LYS D 698 " --> pdb=" O LYS D 694 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER D 711 " --> pdb=" O ASP D 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 211 Processing helix chain 'B' and resid 213 through 223 Processing helix chain 'B' and resid 233 through 237 removed outlier: 3.598A pdb=" N LYS B 237 " --> pdb=" O ASP B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 258 Processing helix chain 'B' and resid 260 through 270 removed outlier: 3.522A pdb=" N VAL B 264 " --> pdb=" O GLN B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 294 Processing helix chain 'B' and resid 298 through 320 Processing helix chain 'B' and resid 324 through 328 removed outlier: 3.599A pdb=" N GLU B 327 " --> pdb=" O LYS B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 344 Processing helix chain 'B' and resid 345 through 354 Processing helix chain 'B' and resid 394 through 401 Processing helix chain 'B' and resid 410 through 414 Processing helix chain 'B' and resid 415 through 429 removed outlier: 3.598A pdb=" N PHE B 429 " --> pdb=" O LYS B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 454 Processing helix chain 'B' and resid 468 through 500 Processing helix chain 'B' and resid 510 through 532 Processing helix chain 'B' and resid 536 through 551 removed outlier: 4.069A pdb=" N PHE B 543 " --> pdb=" O ALA B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 557 Processing helix chain 'B' and resid 563 through 575 removed outlier: 3.676A pdb=" N VAL B 567 " --> pdb=" O GLY B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 599 removed outlier: 4.488A pdb=" N PHE B 582 " --> pdb=" O CYS B 578 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 642 Processing helix chain 'B' and resid 655 through 671 Processing helix chain 'B' and resid 672 through 688 removed outlier: 3.931A pdb=" N ASN B 676 " --> pdb=" O ILE B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 712 Processing helix chain 'C' and resid 203 through 211 Processing helix chain 'C' and resid 213 through 223 Processing helix chain 'C' and resid 250 through 258 Processing helix chain 'C' and resid 260 through 270 Processing helix chain 'C' and resid 286 through 294 Processing helix chain 'C' and resid 298 through 320 Processing helix chain 'C' and resid 335 through 344 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 362 through 366 Processing helix chain 'C' and resid 394 through 401 Processing helix chain 'C' and resid 410 through 414 Processing helix chain 'C' and resid 415 through 429 removed outlier: 3.519A pdb=" N PHE C 429 " --> pdb=" O LYS C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 454 removed outlier: 3.631A pdb=" N ILE C 433 " --> pdb=" O PHE C 429 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR C 454 " --> pdb=" O ALA C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 500 Processing helix chain 'C' and resid 510 through 532 Processing helix chain 'C' and resid 536 through 551 removed outlier: 3.628A pdb=" N SER C 540 " --> pdb=" O GLU C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 557 Processing helix chain 'C' and resid 563 through 599 removed outlier: 3.731A pdb=" N VAL C 567 " --> pdb=" O GLY C 563 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N CYS C 578 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG C 579 " --> pdb=" O ARG C 575 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N PHE C 582 " --> pdb=" O CYS C 578 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL C 583 " --> pdb=" O ARG C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 642 Processing helix chain 'C' and resid 655 through 672 Processing helix chain 'C' and resid 673 through 689 Processing helix chain 'C' and resid 692 through 712 removed outlier: 4.336A pdb=" N LYS C 698 " --> pdb=" O LYS C 694 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 368 through 373 removed outlier: 6.860A pdb=" N SER A 379 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ALA A 373 " --> pdb=" O VAL A 377 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 368 through 373 removed outlier: 6.702A pdb=" N SER D 379 " --> pdb=" O GLU D 371 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ALA D 373 " --> pdb=" O VAL D 377 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 368 through 373 removed outlier: 5.226A pdb=" N THR B 370 " --> pdb=" O LEU B 381 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU B 381 " --> pdb=" O THR B 370 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 369 through 373 removed outlier: 6.826A pdb=" N SER C 379 " --> pdb=" O GLU C 371 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N ALA C 373 " --> pdb=" O VAL C 377 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N VAL C 377 " --> pdb=" O ALA C 373 " (cutoff:3.500A) 996 hydrogen bonds defined for protein. 2883 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.49 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2722 1.30 - 1.43: 5097 1.43 - 1.55: 10189 1.55 - 1.68: 8 1.68 - 1.81: 164 Bond restraints: 18180 Sorted by residual: bond pdb=" CBK 6EU B 901 " pdb=" OAF 6EU B 901 " ideal model delta sigma weight residual 1.329 1.453 -0.124 2.00e-02 2.50e+03 3.87e+01 bond pdb=" CBK 6EU D 901 " pdb=" OAF 6EU D 901 " ideal model delta sigma weight residual 1.329 1.453 -0.124 2.00e-02 2.50e+03 3.85e+01 bond pdb=" CBK 6EU A 901 " pdb=" OAF 6EU A 901 " ideal model delta sigma weight residual 1.329 1.453 -0.124 2.00e-02 2.50e+03 3.85e+01 bond pdb=" CBK 6EU C 901 " pdb=" OAF 6EU C 901 " ideal model delta sigma weight residual 1.329 1.453 -0.124 2.00e-02 2.50e+03 3.84e+01 bond pdb=" C13 6IY B 902 " pdb=" O6 6IY B 902 " ideal model delta sigma weight residual 1.333 1.418 -0.085 2.00e-02 2.50e+03 1.81e+01 ... (remaining 18175 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.75: 24470 4.75 - 9.51: 143 9.51 - 14.26: 14 14.26 - 19.01: 0 19.01 - 23.77: 4 Bond angle restraints: 24631 Sorted by residual: angle pdb=" O3 6IY B 902 " pdb=" P 6IY B 902 " pdb=" O4 6IY B 902 " ideal model delta sigma weight residual 123.06 99.29 23.77 3.00e+00 1.11e-01 6.28e+01 angle pdb=" O3 6IY A 903 " pdb=" P 6IY A 903 " pdb=" O4 6IY A 903 " ideal model delta sigma weight residual 123.06 100.73 22.33 3.00e+00 1.11e-01 5.54e+01 angle pdb=" O3 6IY D 902 " pdb=" P 6IY D 902 " pdb=" O4 6IY D 902 " ideal model delta sigma weight residual 123.06 100.88 22.18 3.00e+00 1.11e-01 5.46e+01 angle pdb=" O3 6IY A 902 " pdb=" P 6IY A 902 " pdb=" O4 6IY A 902 " ideal model delta sigma weight residual 123.06 102.23 20.83 3.00e+00 1.11e-01 4.82e+01 angle pdb=" C SER A 711 " pdb=" N PHE A 712 " pdb=" CA PHE A 712 " ideal model delta sigma weight residual 121.54 130.89 -9.35 1.91e+00 2.74e-01 2.40e+01 ... (remaining 24626 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.45: 10498 21.45 - 42.90: 411 42.90 - 64.35: 80 64.35 - 85.80: 47 85.80 - 107.26: 13 Dihedral angle restraints: 11049 sinusoidal: 4729 harmonic: 6320 Sorted by residual: dihedral pdb=" CA VAL B 415 " pdb=" C VAL B 415 " pdb=" N GLU B 416 " pdb=" CA GLU B 416 " ideal model delta harmonic sigma weight residual -180.00 -153.73 -26.27 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA VAL D 415 " pdb=" C VAL D 415 " pdb=" N GLU D 416 " pdb=" CA GLU D 416 " ideal model delta harmonic sigma weight residual -180.00 -155.61 -24.39 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA GLN D 561 " pdb=" C GLN D 561 " pdb=" N MET D 562 " pdb=" CA MET D 562 " ideal model delta harmonic sigma weight residual -180.00 -156.85 -23.15 0 5.00e+00 4.00e-02 2.14e+01 ... (remaining 11046 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 2541 0.087 - 0.173: 207 0.173 - 0.260: 2 0.260 - 0.346: 1 0.346 - 0.433: 5 Chirality restraints: 2756 Sorted by residual: chirality pdb=" CAO 6EU B 901 " pdb=" CAJ 6EU B 901 " pdb=" CAR 6EU B 901 " pdb=" CAW 6EU B 901 " both_signs ideal model delta sigma weight residual False -2.24 -2.67 0.43 2.00e-01 2.50e+01 4.69e+00 chirality pdb=" CAO 6EU A 901 " pdb=" CAJ 6EU A 901 " pdb=" CAR 6EU A 901 " pdb=" CAW 6EU A 901 " both_signs ideal model delta sigma weight residual False -2.24 -2.67 0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" CAO 6EU C 901 " pdb=" CAJ 6EU C 901 " pdb=" CAR 6EU C 901 " pdb=" CAW 6EU C 901 " both_signs ideal model delta sigma weight residual False -2.24 -2.67 0.43 2.00e-01 2.50e+01 4.64e+00 ... (remaining 2753 not shown) Planarity restraints: 3020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA D 539 " 0.015 2.00e-02 2.50e+03 3.00e-02 9.02e+00 pdb=" C ALA D 539 " -0.052 2.00e-02 2.50e+03 pdb=" O ALA D 539 " 0.019 2.00e-02 2.50e+03 pdb=" N SER D 540 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 569 " 0.015 2.00e-02 2.50e+03 3.00e-02 9.01e+00 pdb=" C ILE B 569 " -0.052 2.00e-02 2.50e+03 pdb=" O ILE B 569 " 0.020 2.00e-02 2.50e+03 pdb=" N GLU B 570 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 541 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.07e+00 pdb=" C MET A 541 " -0.049 2.00e-02 2.50e+03 pdb=" O MET A 541 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL A 542 " 0.017 2.00e-02 2.50e+03 ... (remaining 3017 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1345 2.72 - 3.27: 18126 3.27 - 3.81: 28164 3.81 - 4.36: 34050 4.36 - 4.90: 59353 Nonbonded interactions: 141038 Sorted by model distance: nonbonded pdb=" OG1 THR B 731 " pdb=" OD1 ASP B 733 " model vdw 2.179 3.040 nonbonded pdb=" OG1 THR C 731 " pdb=" OD1 ASP C 733 " model vdw 2.229 3.040 nonbonded pdb=" OG1 THR D 731 " pdb=" OD1 ASP D 733 " model vdw 2.233 3.040 nonbonded pdb=" O ALA C 719 " pdb=" NH1 ARG C 721 " model vdw 2.247 3.120 nonbonded pdb=" NH2 ARG C 557 " pdb=" OE1 GLU C 570 " model vdw 2.257 3.120 ... (remaining 141033 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 193 through 901) selection = (chain 'B' and resid 193 through 901) selection = chain 'C' selection = (chain 'D' and resid 193 through 901) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.900 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.340 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 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 : 0.010 0.124 18180 Z= 0.473 Angle : 1.058 23.766 24631 Z= 0.524 Chirality : 0.053 0.433 2756 Planarity : 0.006 0.042 3020 Dihedral : 13.940 107.256 6993 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.01 % Favored : 94.94 % Rotamer: Outliers : 0.79 % Allowed : 1.58 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.61 (0.18), residues: 2136 helix: 1.51 (0.13), residues: 1248 sheet: -0.77 (0.55), residues: 76 loop : -1.25 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 455 TYR 0.030 0.003 TYR D 627 PHE 0.039 0.003 PHE B 304 TRP 0.016 0.002 TRP D 372 HIS 0.008 0.002 HIS D 410 Details of bonding type rmsd covalent geometry : bond 0.01047 (18180) covalent geometry : angle 1.05816 (24631) hydrogen bonds : bond 0.14725 ( 996) hydrogen bonds : angle 5.22942 ( 2883) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 619 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 GLN cc_start: 0.8809 (tp40) cc_final: 0.8466 (tp-100) REVERT: A 504 LYS cc_start: 0.8839 (mttt) cc_final: 0.8632 (mttm) REVERT: A 557 ARG cc_start: 0.8923 (mtt180) cc_final: 0.8618 (mtt-85) REVERT: A 636 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7309 (tp30) REVERT: D 368 LYS cc_start: 0.8286 (tttt) cc_final: 0.7759 (tttp) REVERT: D 374 TYR cc_start: 0.6458 (m-80) cc_final: 0.5886 (m-10) REVERT: D 378 HIS cc_start: 0.7501 (p-80) cc_final: 0.6941 (p90) REVERT: D 410 HIS cc_start: 0.8477 (p-80) cc_final: 0.8209 (p90) REVERT: D 423 GLN cc_start: 0.8717 (tp40) cc_final: 0.8480 (tp-100) REVERT: D 571 LYS cc_start: 0.8454 (mmtt) cc_final: 0.8192 (tptp) REVERT: D 581 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7319 (mmt) REVERT: B 211 ARG cc_start: 0.8199 (mtt180) cc_final: 0.7965 (mmm160) REVERT: B 324 LYS cc_start: 0.8923 (mttt) cc_final: 0.8639 (mptt) REVERT: B 410 HIS cc_start: 0.7874 (m90) cc_final: 0.7639 (m-70) REVERT: B 416 GLU cc_start: 0.7553 (tp30) cc_final: 0.6926 (tp30) REVERT: B 420 ARG cc_start: 0.8478 (mmt180) cc_final: 0.8118 (mmm-85) REVERT: B 423 GLN cc_start: 0.8895 (tp40) cc_final: 0.8496 (tp-100) REVERT: B 703 ILE cc_start: 0.9621 (mt) cc_final: 0.9378 (mp) REVERT: C 343 SER cc_start: 0.9075 (m) cc_final: 0.8785 (p) REVERT: C 483 SER cc_start: 0.9483 (t) cc_final: 0.9278 (p) REVERT: C 636 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7962 (mm-30) outliers start: 15 outliers final: 4 residues processed: 629 average time/residue: 0.1545 time to fit residues: 140.0397 Evaluate side-chains 412 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 407 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 632 SER Chi-restraints excluded: chain C residue 653 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 0.6980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 200 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 378 HIS D 410 HIS ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 GLN B 289 HIS B 378 HIS C 285 ASN C 378 HIS C 393 ASN C 410 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.153721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.103716 restraints weight = 28863.432| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.66 r_work: 0.3027 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 18180 Z= 0.134 Angle : 0.587 7.151 24631 Z= 0.310 Chirality : 0.039 0.171 2756 Planarity : 0.004 0.046 3020 Dihedral : 11.582 105.382 2930 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.73 % Favored : 95.18 % Rotamer: Outliers : 1.85 % Allowed : 8.33 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.62 (0.18), residues: 2136 helix: 2.49 (0.14), residues: 1252 sheet: -0.53 (0.54), residues: 76 loop : -1.12 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 575 TYR 0.029 0.001 TYR A 309 PHE 0.048 0.001 PHE D 304 TRP 0.011 0.001 TRP D 426 HIS 0.009 0.001 HIS B 378 Details of bonding type rmsd covalent geometry : bond 0.00276 (18180) covalent geometry : angle 0.58699 (24631) hydrogen bonds : bond 0.04975 ( 996) hydrogen bonds : angle 3.85642 ( 2883) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 460 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 TYR cc_start: 0.8982 (t80) cc_final: 0.8720 (t80) REVERT: A 378 HIS cc_start: 0.7883 (p-80) cc_final: 0.7657 (p90) REVERT: A 423 GLN cc_start: 0.9029 (tp40) cc_final: 0.8770 (tp-100) REVERT: A 504 LYS cc_start: 0.9090 (mttt) cc_final: 0.8831 (mtpp) REVERT: A 636 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8268 (tp30) REVERT: A 707 ASP cc_start: 0.9062 (m-30) cc_final: 0.8797 (m-30) REVERT: D 410 HIS cc_start: 0.8259 (p90) cc_final: 0.7803 (p90) REVERT: D 433 ILE cc_start: 0.9363 (mm) cc_final: 0.9150 (mt) REVERT: D 571 LYS cc_start: 0.8696 (mmtt) cc_final: 0.8387 (tptp) REVERT: B 250 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7727 (mt) REVERT: B 324 LYS cc_start: 0.8965 (mttt) cc_final: 0.8515 (mptt) REVERT: B 410 HIS cc_start: 0.7980 (m90) cc_final: 0.7723 (m-70) REVERT: B 416 GLU cc_start: 0.7803 (tp30) cc_final: 0.7270 (tp30) REVERT: B 420 ARG cc_start: 0.8779 (mmt180) cc_final: 0.8427 (mmm-85) REVERT: B 423 GLN cc_start: 0.9131 (tp40) cc_final: 0.8738 (tp-100) REVERT: B 653 TYR cc_start: 0.6506 (OUTLIER) cc_final: 0.5523 (p90) REVERT: B 700 GLN cc_start: 0.8720 (tp40) cc_final: 0.8178 (tp40) REVERT: B 724 LYS cc_start: 0.8811 (tmtt) cc_final: 0.8554 (tmtt) REVERT: C 309 TYR cc_start: 0.8947 (t80) cc_final: 0.8535 (t80) REVERT: C 342 SER cc_start: 0.9163 (t) cc_final: 0.8848 (p) REVERT: C 343 SER cc_start: 0.9003 (m) cc_final: 0.8584 (p) REVERT: C 420 ARG cc_start: 0.8772 (mmm-85) cc_final: 0.8436 (mmm-85) REVERT: C 471 ASP cc_start: 0.8633 (m-30) cc_final: 0.7744 (t0) REVERT: C 648 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7762 (mm-30) REVERT: C 700 GLN cc_start: 0.8932 (tp40) cc_final: 0.8695 (tp40) REVERT: C 716 MET cc_start: 0.4863 (ptm) cc_final: 0.4220 (ptp) REVERT: C 740 TRP cc_start: 0.8618 (m100) cc_final: 0.8230 (m100) REVERT: C 743 ARG cc_start: 0.8528 (ttm-80) cc_final: 0.7715 (tpp80) outliers start: 35 outliers final: 19 residues processed: 477 average time/residue: 0.1273 time to fit residues: 92.7061 Evaluate side-chains 423 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 402 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 466 LYS Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 694 LYS Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 404 SER Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 653 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 23 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 201 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 184 optimal weight: 0.6980 chunk 181 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 273 GLN B 378 HIS C 206 HIS C 393 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.151859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.101571 restraints weight = 29254.609| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.64 r_work: 0.2995 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18180 Z= 0.160 Angle : 0.568 7.270 24631 Z= 0.297 Chirality : 0.039 0.148 2756 Planarity : 0.004 0.045 3020 Dihedral : 10.394 93.027 2923 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.87 % Favored : 95.08 % Rotamer: Outliers : 1.79 % Allowed : 11.39 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.86 (0.19), residues: 2136 helix: 2.69 (0.14), residues: 1272 sheet: -0.40 (0.56), residues: 76 loop : -1.15 (0.23), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 701 TYR 0.015 0.001 TYR A 309 PHE 0.045 0.001 PHE D 304 TRP 0.010 0.001 TRP D 549 HIS 0.014 0.001 HIS B 378 Details of bonding type rmsd covalent geometry : bond 0.00371 (18180) covalent geometry : angle 0.56765 (24631) hydrogen bonds : bond 0.04832 ( 996) hydrogen bonds : angle 3.85890 ( 2883) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 429 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 LEU cc_start: 0.8413 (mt) cc_final: 0.8191 (mt) REVERT: A 378 HIS cc_start: 0.7871 (p-80) cc_final: 0.7653 (p90) REVERT: A 423 GLN cc_start: 0.9075 (tp40) cc_final: 0.8803 (tp-100) REVERT: A 504 LYS cc_start: 0.9058 (mttt) cc_final: 0.8800 (mtpp) REVERT: A 584 TYR cc_start: 0.8853 (t80) cc_final: 0.8610 (t80) REVERT: A 636 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8249 (tp30) REVERT: D 410 HIS cc_start: 0.8325 (p90) cc_final: 0.7732 (p90) REVERT: D 424 ASP cc_start: 0.9029 (t70) cc_final: 0.8751 (t70) REVERT: D 571 LYS cc_start: 0.8754 (mmtt) cc_final: 0.8484 (tptp) REVERT: D 653 TYR cc_start: 0.7130 (OUTLIER) cc_final: 0.5607 (p90) REVERT: B 324 LYS cc_start: 0.8963 (mttt) cc_final: 0.8540 (mptt) REVERT: B 354 GLN cc_start: 0.8680 (mt0) cc_final: 0.8424 (mt0) REVERT: B 410 HIS cc_start: 0.7971 (m90) cc_final: 0.7737 (m-70) REVERT: B 416 GLU cc_start: 0.7839 (tp30) cc_final: 0.7214 (tp30) REVERT: B 420 ARG cc_start: 0.8825 (mmt180) cc_final: 0.8403 (mmm-85) REVERT: B 423 GLN cc_start: 0.9164 (tp40) cc_final: 0.8757 (tp-100) REVERT: B 653 TYR cc_start: 0.6482 (OUTLIER) cc_final: 0.5532 (p90) REVERT: B 724 LYS cc_start: 0.8752 (tmtt) cc_final: 0.8459 (tmtt) REVERT: C 331 ARG cc_start: 0.8294 (ttm-80) cc_final: 0.7771 (tpp80) REVERT: C 342 SER cc_start: 0.9171 (t) cc_final: 0.8899 (p) REVERT: C 343 SER cc_start: 0.9017 (m) cc_final: 0.8606 (p) REVERT: C 420 ARG cc_start: 0.8788 (mmm-85) cc_final: 0.8430 (mmm-85) REVERT: C 471 ASP cc_start: 0.8618 (m-30) cc_final: 0.7730 (t0) REVERT: C 503 LEU cc_start: 0.8829 (mp) cc_final: 0.8608 (mt) REVERT: C 648 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7764 (mm-30) REVERT: C 700 GLN cc_start: 0.8932 (tp40) cc_final: 0.8418 (tp-100) REVERT: C 716 MET cc_start: 0.5012 (ptm) cc_final: 0.4227 (ptp) REVERT: C 740 TRP cc_start: 0.8639 (m100) cc_final: 0.8245 (m100) REVERT: C 743 ARG cc_start: 0.8526 (ttm-80) cc_final: 0.7735 (tpp80) outliers start: 34 outliers final: 22 residues processed: 447 average time/residue: 0.1178 time to fit residues: 82.4901 Evaluate side-chains 417 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 393 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 694 LYS Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain D residue 653 TYR Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 653 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 24 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 189 optimal weight: 5.9990 chunk 180 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 151 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 206 HIS C 393 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.153902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.102985 restraints weight = 29063.455| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.67 r_work: 0.3023 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 18180 Z= 0.120 Angle : 0.537 7.696 24631 Z= 0.278 Chirality : 0.038 0.148 2756 Planarity : 0.003 0.063 3020 Dihedral : 9.429 89.674 2923 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.82 % Favored : 95.13 % Rotamer: Outliers : 2.00 % Allowed : 12.29 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.00 (0.19), residues: 2136 helix: 2.83 (0.14), residues: 1280 sheet: -0.13 (0.58), residues: 76 loop : -1.22 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 331 TYR 0.023 0.001 TYR C 309 PHE 0.041 0.001 PHE D 304 TRP 0.010 0.001 TRP A 372 HIS 0.004 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00271 (18180) covalent geometry : angle 0.53687 (24631) hydrogen bonds : bond 0.04143 ( 996) hydrogen bonds : angle 3.71766 ( 2883) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 416 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 HIS cc_start: 0.7840 (p-80) cc_final: 0.7619 (p90) REVERT: A 423 GLN cc_start: 0.9080 (tp40) cc_final: 0.8813 (tp-100) REVERT: A 584 TYR cc_start: 0.8738 (t80) cc_final: 0.8431 (t80) REVERT: A 636 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8260 (tp30) REVERT: D 354 GLN cc_start: 0.8764 (mt0) cc_final: 0.8422 (mt0) REVERT: D 424 ASP cc_start: 0.9040 (t70) cc_final: 0.8697 (t70) REVERT: D 571 LYS cc_start: 0.8753 (mmtt) cc_final: 0.8477 (tptp) REVERT: D 653 TYR cc_start: 0.7115 (OUTLIER) cc_final: 0.5563 (p90) REVERT: D 746 GLU cc_start: 0.7944 (tt0) cc_final: 0.7463 (tm-30) REVERT: B 324 LYS cc_start: 0.8953 (mttt) cc_final: 0.8503 (mptt) REVERT: B 354 GLN cc_start: 0.8667 (mt0) cc_final: 0.8377 (mt0) REVERT: B 410 HIS cc_start: 0.7915 (m90) cc_final: 0.7660 (m-70) REVERT: B 483 SER cc_start: 0.9294 (t) cc_final: 0.9054 (p) REVERT: B 653 TYR cc_start: 0.6578 (OUTLIER) cc_final: 0.5590 (p90) REVERT: B 724 LYS cc_start: 0.8700 (tmtt) cc_final: 0.8395 (tmtt) REVERT: C 342 SER cc_start: 0.9175 (t) cc_final: 0.8931 (p) REVERT: C 343 SER cc_start: 0.9003 (m) cc_final: 0.8569 (p) REVERT: C 420 ARG cc_start: 0.8787 (mmm-85) cc_final: 0.8406 (mmm-85) REVERT: C 471 ASP cc_start: 0.8568 (m-30) cc_final: 0.8254 (m-30) REVERT: C 648 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7773 (mm-30) REVERT: C 700 GLN cc_start: 0.8965 (tp40) cc_final: 0.8527 (tp-100) REVERT: C 716 MET cc_start: 0.5139 (ptm) cc_final: 0.4335 (ptp) REVERT: C 740 TRP cc_start: 0.8604 (m100) cc_final: 0.8302 (m100) REVERT: C 743 ARG cc_start: 0.8495 (ttm-80) cc_final: 0.7764 (tpp80) outliers start: 38 outliers final: 23 residues processed: 434 average time/residue: 0.1219 time to fit residues: 82.0256 Evaluate side-chains 422 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 397 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 694 LYS Chi-restraints excluded: chain A residue 741 CYS Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain D residue 653 TYR Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 741 CYS Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 653 TYR Chi-restraints excluded: chain C residue 741 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 113 optimal weight: 0.7980 chunk 17 optimal weight: 7.9990 chunk 110 optimal weight: 4.9990 chunk 165 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN A 498 GLN A 727 GLN B 273 GLN B 378 HIS C 206 HIS C 393 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.150105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.099296 restraints weight = 29164.679| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.62 r_work: 0.2961 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 18180 Z= 0.241 Angle : 0.609 7.908 24631 Z= 0.314 Chirality : 0.041 0.160 2756 Planarity : 0.004 0.074 3020 Dihedral : 9.309 88.860 2923 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.29 % Favored : 94.66 % Rotamer: Outliers : 2.37 % Allowed : 13.08 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.75 (0.19), residues: 2136 helix: 2.66 (0.14), residues: 1280 sheet: -0.20 (0.60), residues: 76 loop : -1.39 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 331 TYR 0.017 0.002 TYR B 584 PHE 0.044 0.002 PHE D 304 TRP 0.012 0.001 TRP A 372 HIS 0.011 0.001 HIS B 378 Details of bonding type rmsd covalent geometry : bond 0.00573 (18180) covalent geometry : angle 0.60877 (24631) hydrogen bonds : bond 0.05207 ( 996) hydrogen bonds : angle 3.99498 ( 2883) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 394 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 ASN cc_start: 0.8791 (t0) cc_final: 0.8575 (m-40) REVERT: A 378 HIS cc_start: 0.7917 (p-80) cc_final: 0.7641 (p90) REVERT: A 423 GLN cc_start: 0.9122 (tp40) cc_final: 0.8854 (tp-100) REVERT: A 584 TYR cc_start: 0.8892 (t80) cc_final: 0.8657 (t80) REVERT: D 331 ARG cc_start: 0.8276 (ttm-80) cc_final: 0.7766 (mtt90) REVERT: D 354 GLN cc_start: 0.8756 (mt0) cc_final: 0.8357 (mp10) REVERT: D 410 HIS cc_start: 0.8567 (p90) cc_final: 0.8244 (p90) REVERT: D 424 ASP cc_start: 0.9042 (t70) cc_final: 0.8702 (t70) REVERT: D 571 LYS cc_start: 0.8755 (mmtt) cc_final: 0.8396 (tptp) REVERT: D 653 TYR cc_start: 0.7321 (OUTLIER) cc_final: 0.5819 (p90) REVERT: D 716 MET cc_start: 0.5076 (ppp) cc_final: 0.4760 (ppp) REVERT: B 324 LYS cc_start: 0.8946 (mttt) cc_final: 0.8463 (mptt) REVERT: B 410 HIS cc_start: 0.7948 (m90) cc_final: 0.7706 (m-70) REVERT: B 416 GLU cc_start: 0.7872 (tp30) cc_final: 0.7456 (tp30) REVERT: B 420 ARG cc_start: 0.9006 (mmm-85) cc_final: 0.8488 (mmm-85) REVERT: B 423 GLN cc_start: 0.9195 (tp-100) cc_final: 0.8834 (tp-100) REVERT: B 653 TYR cc_start: 0.6624 (OUTLIER) cc_final: 0.5790 (p90) REVERT: C 342 SER cc_start: 0.9194 (t) cc_final: 0.8927 (p) REVERT: C 343 SER cc_start: 0.9026 (m) cc_final: 0.8571 (p) REVERT: C 420 ARG cc_start: 0.8766 (mmm-85) cc_final: 0.8394 (mmm-85) REVERT: C 471 ASP cc_start: 0.8729 (m-30) cc_final: 0.8408 (m-30) REVERT: C 504 LYS cc_start: 0.9038 (ttmt) cc_final: 0.8711 (ttmm) REVERT: C 648 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7706 (mm-30) REVERT: C 700 GLN cc_start: 0.8963 (tp40) cc_final: 0.8575 (tp-100) REVERT: C 716 MET cc_start: 0.5139 (ptm) cc_final: 0.4273 (ptp) REVERT: C 743 ARG cc_start: 0.8508 (ttm-80) cc_final: 0.7815 (tpp80) outliers start: 45 outliers final: 32 residues processed: 419 average time/residue: 0.1216 time to fit residues: 79.1718 Evaluate side-chains 413 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 379 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain A residue 694 LYS Chi-restraints excluded: chain A residue 741 CYS Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain D residue 653 TYR Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 741 CYS Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 653 TYR Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain C residue 741 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 84 optimal weight: 0.3980 chunk 191 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 205 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 270 ASN B 378 HIS C 206 HIS C 393 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.153903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.103794 restraints weight = 28857.858| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.64 r_work: 0.3027 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 18180 Z= 0.113 Angle : 0.541 10.416 24631 Z= 0.279 Chirality : 0.038 0.310 2756 Planarity : 0.003 0.038 3020 Dihedral : 8.694 87.765 2923 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.74 % Allowed : 14.35 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.98 (0.19), residues: 2136 helix: 2.91 (0.14), residues: 1256 sheet: -0.13 (0.60), residues: 76 loop : -1.27 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 331 TYR 0.029 0.001 TYR A 309 PHE 0.048 0.001 PHE D 304 TRP 0.011 0.001 TRP A 272 HIS 0.011 0.001 HIS B 378 Details of bonding type rmsd covalent geometry : bond 0.00251 (18180) covalent geometry : angle 0.54077 (24631) hydrogen bonds : bond 0.04019 ( 996) hydrogen bonds : angle 3.79064 ( 2883) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 403 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8508 (mt-10) REVERT: A 378 HIS cc_start: 0.7868 (p-80) cc_final: 0.7591 (p90) REVERT: A 423 GLN cc_start: 0.9074 (tp40) cc_final: 0.8813 (tp-100) REVERT: A 584 TYR cc_start: 0.8746 (t80) cc_final: 0.8470 (t80) REVERT: D 354 GLN cc_start: 0.8745 (mt0) cc_final: 0.8326 (mt0) REVERT: D 410 HIS cc_start: 0.8490 (p90) cc_final: 0.8163 (p90) REVERT: D 424 ASP cc_start: 0.9003 (t70) cc_final: 0.8670 (t70) REVERT: D 571 LYS cc_start: 0.8731 (mmtt) cc_final: 0.8456 (tptp) REVERT: D 653 TYR cc_start: 0.7236 (OUTLIER) cc_final: 0.5689 (p90) REVERT: B 324 LYS cc_start: 0.8882 (mttt) cc_final: 0.8353 (mmtt) REVERT: B 354 GLN cc_start: 0.8570 (mt0) cc_final: 0.8273 (mt0) REVERT: B 410 HIS cc_start: 0.7861 (m90) cc_final: 0.7615 (m-70) REVERT: B 420 ARG cc_start: 0.9028 (mmm-85) cc_final: 0.8816 (mmm-85) REVERT: B 653 TYR cc_start: 0.6609 (OUTLIER) cc_final: 0.5715 (p90) REVERT: B 724 LYS cc_start: 0.8691 (tmtt) cc_final: 0.8378 (tmtt) REVERT: C 309 TYR cc_start: 0.8662 (t80) cc_final: 0.8422 (t80) REVERT: C 342 SER cc_start: 0.9200 (t) cc_final: 0.8967 (p) REVERT: C 343 SER cc_start: 0.9025 (m) cc_final: 0.8577 (p) REVERT: C 351 TYR cc_start: 0.8670 (t80) cc_final: 0.8467 (t80) REVERT: C 391 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8283 (mm-30) REVERT: C 420 ARG cc_start: 0.8773 (mmm-85) cc_final: 0.8392 (mmm-85) REVERT: C 471 ASP cc_start: 0.8583 (m-30) cc_final: 0.8258 (m-30) REVERT: C 504 LYS cc_start: 0.9003 (ttmt) cc_final: 0.8654 (ttmm) REVERT: C 648 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7659 (mm-30) REVERT: C 653 TYR cc_start: 0.6654 (OUTLIER) cc_final: 0.5246 (p90) REVERT: C 700 GLN cc_start: 0.8947 (tp40) cc_final: 0.8524 (tp-100) REVERT: C 716 MET cc_start: 0.5095 (ptm) cc_final: 0.4318 (ptp) REVERT: C 740 TRP cc_start: 0.8574 (m100) cc_final: 0.8362 (m100) REVERT: C 743 ARG cc_start: 0.8482 (ttm-80) cc_final: 0.7806 (tpp80) outliers start: 33 outliers final: 19 residues processed: 422 average time/residue: 0.1221 time to fit residues: 80.2371 Evaluate side-chains 416 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 394 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 504 LYS Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 694 LYS Chi-restraints excluded: chain A residue 741 CYS Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain D residue 653 TYR Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 741 CYS Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 653 TYR Chi-restraints excluded: chain C residue 741 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 136 optimal weight: 0.0570 chunk 6 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 59 optimal weight: 10.0000 chunk 119 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 202 optimal weight: 0.0010 chunk 106 optimal weight: 20.0000 overall best weight: 1.7908 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 378 HIS C 206 HIS C 393 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.152509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.101611 restraints weight = 28898.203| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.64 r_work: 0.2999 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 18180 Z= 0.161 Angle : 0.564 10.405 24631 Z= 0.290 Chirality : 0.039 0.302 2756 Planarity : 0.003 0.039 3020 Dihedral : 8.592 87.608 2923 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.06 % Allowed : 14.40 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.94 (0.19), residues: 2136 helix: 2.86 (0.14), residues: 1252 sheet: -0.14 (0.60), residues: 76 loop : -1.24 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 717 TYR 0.026 0.001 TYR A 309 PHE 0.046 0.001 PHE D 304 TRP 0.014 0.001 TRP A 372 HIS 0.014 0.001 HIS B 378 Details of bonding type rmsd covalent geometry : bond 0.00379 (18180) covalent geometry : angle 0.56433 (24631) hydrogen bonds : bond 0.04408 ( 996) hydrogen bonds : angle 3.86447 ( 2883) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 397 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8499 (mt-10) REVERT: A 378 HIS cc_start: 0.7942 (p-80) cc_final: 0.7661 (p90) REVERT: A 423 GLN cc_start: 0.9081 (tp40) cc_final: 0.8817 (tp-100) REVERT: A 584 TYR cc_start: 0.8833 (t80) cc_final: 0.8555 (t80) REVERT: A 707 ASP cc_start: 0.8938 (m-30) cc_final: 0.8732 (m-30) REVERT: D 354 GLN cc_start: 0.8748 (mt0) cc_final: 0.8342 (mp10) REVERT: D 410 HIS cc_start: 0.8505 (p90) cc_final: 0.8170 (p90) REVERT: D 424 ASP cc_start: 0.8996 (t70) cc_final: 0.8663 (t70) REVERT: D 571 LYS cc_start: 0.8766 (mmtt) cc_final: 0.8478 (tptp) REVERT: D 653 TYR cc_start: 0.7296 (OUTLIER) cc_final: 0.5851 (p90) REVERT: B 324 LYS cc_start: 0.8881 (mttt) cc_final: 0.8355 (mmtt) REVERT: B 354 GLN cc_start: 0.8624 (mt0) cc_final: 0.8383 (mt0) REVERT: B 410 HIS cc_start: 0.7864 (m90) cc_final: 0.7618 (m-70) REVERT: B 420 ARG cc_start: 0.9020 (mmm-85) cc_final: 0.8787 (mmm-85) REVERT: B 653 TYR cc_start: 0.6643 (OUTLIER) cc_final: 0.5727 (p90) REVERT: B 724 LYS cc_start: 0.8702 (tmtt) cc_final: 0.8390 (tmtt) REVERT: C 309 TYR cc_start: 0.8699 (t80) cc_final: 0.8429 (t80) REVERT: C 342 SER cc_start: 0.9196 (t) cc_final: 0.8945 (p) REVERT: C 343 SER cc_start: 0.9032 (m) cc_final: 0.8580 (p) REVERT: C 351 TYR cc_start: 0.8740 (t80) cc_final: 0.8482 (t80) REVERT: C 420 ARG cc_start: 0.8781 (mmm-85) cc_final: 0.8403 (mmm-85) REVERT: C 424 ASP cc_start: 0.9011 (t70) cc_final: 0.8784 (t70) REVERT: C 471 ASP cc_start: 0.8690 (m-30) cc_final: 0.8372 (m-30) REVERT: C 504 LYS cc_start: 0.9025 (ttmt) cc_final: 0.8679 (ttmm) REVERT: C 648 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7628 (mm-30) REVERT: C 653 TYR cc_start: 0.6751 (OUTLIER) cc_final: 0.5275 (p90) REVERT: C 700 GLN cc_start: 0.8947 (tp40) cc_final: 0.8520 (tp-100) REVERT: C 716 MET cc_start: 0.5070 (ptm) cc_final: 0.4326 (ptp) REVERT: C 740 TRP cc_start: 0.8576 (m100) cc_final: 0.8364 (m100) REVERT: C 743 ARG cc_start: 0.8501 (ttm-80) cc_final: 0.7850 (tpp80) outliers start: 39 outliers final: 30 residues processed: 417 average time/residue: 0.1227 time to fit residues: 79.7260 Evaluate side-chains 417 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 384 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 504 LYS Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 694 LYS Chi-restraints excluded: chain A residue 741 CYS Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain D residue 653 TYR Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 741 CYS Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 494 GLN Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 393 ASN Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 653 TYR Chi-restraints excluded: chain C residue 741 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 126 optimal weight: 0.1980 chunk 90 optimal weight: 3.9990 chunk 199 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 163 optimal weight: 4.9990 chunk 201 optimal weight: 0.6980 chunk 68 optimal weight: 6.9990 chunk 195 optimal weight: 0.8980 chunk 211 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 378 HIS C 206 HIS C 393 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.154785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.104534 restraints weight = 28952.654| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.65 r_work: 0.3040 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18180 Z= 0.111 Angle : 0.546 11.614 24631 Z= 0.280 Chirality : 0.037 0.263 2756 Planarity : 0.003 0.039 3020 Dihedral : 8.207 87.352 2923 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.90 % Allowed : 15.03 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.03 (0.19), residues: 2136 helix: 2.92 (0.14), residues: 1252 sheet: -0.01 (0.61), residues: 76 loop : -1.19 (0.23), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 211 TYR 0.014 0.001 TYR B 584 PHE 0.047 0.001 PHE D 304 TRP 0.012 0.001 TRP A 372 HIS 0.012 0.001 HIS B 378 Details of bonding type rmsd covalent geometry : bond 0.00243 (18180) covalent geometry : angle 0.54621 (24631) hydrogen bonds : bond 0.03813 ( 996) hydrogen bonds : angle 3.77920 ( 2883) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 416 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8488 (mt-10) REVERT: A 378 HIS cc_start: 0.7935 (p-80) cc_final: 0.7662 (p90) REVERT: A 423 GLN cc_start: 0.9044 (tp40) cc_final: 0.8784 (tp-100) REVERT: A 584 TYR cc_start: 0.8680 (t80) cc_final: 0.8315 (t80) REVERT: D 354 GLN cc_start: 0.8751 (mt0) cc_final: 0.8312 (mp10) REVERT: D 410 HIS cc_start: 0.8467 (p90) cc_final: 0.8135 (p90) REVERT: D 416 GLU cc_start: 0.7469 (tp30) cc_final: 0.7239 (tp30) REVERT: D 424 ASP cc_start: 0.8997 (t70) cc_final: 0.8651 (t70) REVERT: D 571 LYS cc_start: 0.8727 (mmtt) cc_final: 0.8405 (tptp) REVERT: D 653 TYR cc_start: 0.7221 (OUTLIER) cc_final: 0.5672 (p90) REVERT: D 746 GLU cc_start: 0.7910 (tt0) cc_final: 0.7632 (tt0) REVERT: B 324 LYS cc_start: 0.8862 (mttt) cc_final: 0.8344 (mmtt) REVERT: B 354 GLN cc_start: 0.8579 (mt0) cc_final: 0.8277 (mt0) REVERT: B 410 HIS cc_start: 0.7811 (m90) cc_final: 0.7562 (m-70) REVERT: B 483 SER cc_start: 0.9284 (t) cc_final: 0.9043 (p) REVERT: B 653 TYR cc_start: 0.6651 (OUTLIER) cc_final: 0.5717 (p90) REVERT: B 724 LYS cc_start: 0.8641 (tmtt) cc_final: 0.8333 (tmtt) REVERT: C 309 TYR cc_start: 0.8718 (t80) cc_final: 0.8381 (t80) REVERT: C 342 SER cc_start: 0.9188 (t) cc_final: 0.8980 (p) REVERT: C 343 SER cc_start: 0.8987 (m) cc_final: 0.8550 (p) REVERT: C 351 TYR cc_start: 0.8676 (t80) cc_final: 0.8458 (t80) REVERT: C 410 HIS cc_start: 0.8321 (m90) cc_final: 0.8120 (m-70) REVERT: C 420 ARG cc_start: 0.8793 (mmm-85) cc_final: 0.8420 (mmm-85) REVERT: C 424 ASP cc_start: 0.8915 (t70) cc_final: 0.8708 (t70) REVERT: C 471 ASP cc_start: 0.8596 (m-30) cc_final: 0.8274 (m-30) REVERT: C 504 LYS cc_start: 0.9004 (ttmt) cc_final: 0.8650 (ttmm) REVERT: C 584 TYR cc_start: 0.8887 (t80) cc_final: 0.8263 (t80) REVERT: C 648 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7626 (mm-30) REVERT: C 653 TYR cc_start: 0.6652 (OUTLIER) cc_final: 0.5358 (p90) REVERT: C 700 GLN cc_start: 0.8930 (tp40) cc_final: 0.8499 (tp-100) REVERT: C 716 MET cc_start: 0.5093 (ptm) cc_final: 0.4330 (ptp) REVERT: C 743 ARG cc_start: 0.8468 (ttm-80) cc_final: 0.7820 (tpp80) outliers start: 36 outliers final: 26 residues processed: 433 average time/residue: 0.1194 time to fit residues: 80.7682 Evaluate side-chains 426 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 397 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 504 LYS Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 694 LYS Chi-restraints excluded: chain A residue 741 CYS Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain D residue 653 TYR Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 741 CYS Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 653 TYR Chi-restraints excluded: chain C residue 741 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 94 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 206 optimal weight: 4.9990 chunk 205 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 378 HIS C 206 HIS C 259 ASN C 393 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.153708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.103251 restraints weight = 28796.894| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.63 r_work: 0.3020 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18180 Z= 0.139 Angle : 0.568 11.184 24631 Z= 0.291 Chirality : 0.039 0.224 2756 Planarity : 0.003 0.039 3020 Dihedral : 8.142 88.060 2923 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.95 % Allowed : 15.82 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.94 (0.19), residues: 2136 helix: 2.84 (0.14), residues: 1256 sheet: -0.03 (0.61), residues: 76 loop : -1.23 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 420 TYR 0.015 0.001 TYR B 584 PHE 0.049 0.001 PHE D 304 TRP 0.013 0.001 TRP A 372 HIS 0.013 0.001 HIS B 378 Details of bonding type rmsd covalent geometry : bond 0.00325 (18180) covalent geometry : angle 0.56844 (24631) hydrogen bonds : bond 0.04099 ( 996) hydrogen bonds : angle 3.83247 ( 2883) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 408 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8497 (mt-10) REVERT: A 354 GLN cc_start: 0.8718 (mt0) cc_final: 0.8281 (mp10) REVERT: A 378 HIS cc_start: 0.7930 (p-80) cc_final: 0.7649 (p90) REVERT: A 423 GLN cc_start: 0.9063 (tp40) cc_final: 0.8799 (tp-100) REVERT: A 584 TYR cc_start: 0.8754 (t80) cc_final: 0.8398 (t80) REVERT: D 354 GLN cc_start: 0.8759 (mt0) cc_final: 0.8316 (mp10) REVERT: D 410 HIS cc_start: 0.8487 (p90) cc_final: 0.8158 (p90) REVERT: D 424 ASP cc_start: 0.8985 (t70) cc_final: 0.8649 (t70) REVERT: D 536 GLU cc_start: 0.8779 (mp0) cc_final: 0.8574 (mp0) REVERT: D 571 LYS cc_start: 0.8751 (mmtt) cc_final: 0.8423 (tptp) REVERT: D 653 TYR cc_start: 0.7256 (OUTLIER) cc_final: 0.5719 (p90) REVERT: D 746 GLU cc_start: 0.7919 (tt0) cc_final: 0.7640 (tt0) REVERT: B 311 GLU cc_start: 0.9152 (mm-30) cc_final: 0.8905 (mm-30) REVERT: B 319 LEU cc_start: 0.8823 (mp) cc_final: 0.8417 (tp) REVERT: B 324 LYS cc_start: 0.8879 (mttt) cc_final: 0.8336 (mmtt) REVERT: B 354 GLN cc_start: 0.8597 (mt0) cc_final: 0.8311 (mt0) REVERT: B 410 HIS cc_start: 0.7814 (m90) cc_final: 0.7570 (m-70) REVERT: B 423 GLN cc_start: 0.9188 (tp-100) cc_final: 0.8849 (tp-100) REVERT: B 483 SER cc_start: 0.9294 (t) cc_final: 0.9033 (p) REVERT: B 653 TYR cc_start: 0.6642 (OUTLIER) cc_final: 0.5724 (p90) REVERT: B 663 LEU cc_start: 0.9494 (OUTLIER) cc_final: 0.9245 (mt) REVERT: B 724 LYS cc_start: 0.8659 (tmtt) cc_final: 0.8356 (tmtt) REVERT: C 309 TYR cc_start: 0.8756 (t80) cc_final: 0.8357 (t80) REVERT: C 342 SER cc_start: 0.9176 (t) cc_final: 0.8923 (p) REVERT: C 343 SER cc_start: 0.8972 (m) cc_final: 0.8528 (p) REVERT: C 351 TYR cc_start: 0.8718 (t80) cc_final: 0.8450 (t80) REVERT: C 383 ASP cc_start: 0.8271 (t0) cc_final: 0.7942 (t0) REVERT: C 385 SER cc_start: 0.9061 (t) cc_final: 0.8618 (m) REVERT: C 420 ARG cc_start: 0.8808 (mmm-85) cc_final: 0.8436 (mmm-85) REVERT: C 424 ASP cc_start: 0.8910 (t70) cc_final: 0.8684 (t70) REVERT: C 471 ASP cc_start: 0.8650 (m-30) cc_final: 0.8331 (m-30) REVERT: C 504 LYS cc_start: 0.9019 (ttmt) cc_final: 0.8667 (ttmm) REVERT: C 648 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7568 (mm-30) REVERT: C 649 PHE cc_start: 0.8219 (m-10) cc_final: 0.8001 (m-80) REVERT: C 653 TYR cc_start: 0.6749 (OUTLIER) cc_final: 0.5412 (p90) REVERT: C 700 GLN cc_start: 0.8926 (tp40) cc_final: 0.8503 (tp-100) REVERT: C 716 MET cc_start: 0.4952 (ptm) cc_final: 0.4255 (ptp) REVERT: C 743 ARG cc_start: 0.8436 (ttm-80) cc_final: 0.7759 (tpp80) outliers start: 37 outliers final: 29 residues processed: 426 average time/residue: 0.1219 time to fit residues: 81.0004 Evaluate side-chains 432 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 399 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 504 LYS Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 694 LYS Chi-restraints excluded: chain A residue 741 CYS Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 568 MET Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain D residue 653 TYR Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 741 CYS Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 393 ASN Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 653 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 152 optimal weight: 0.6980 chunk 111 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 187 optimal weight: 0.9990 chunk 184 optimal weight: 0.9980 chunk 208 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 156 optimal weight: 0.4980 chunk 35 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 132 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 378 HIS C 206 HIS C 259 ASN C 393 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.153415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.103104 restraints weight = 28700.775| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.63 r_work: 0.3025 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.170 18180 Z= 0.212 Angle : 0.824 59.198 24631 Z= 0.490 Chirality : 0.039 0.284 2756 Planarity : 0.004 0.138 3020 Dihedral : 8.153 88.040 2923 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.92 % Favored : 95.04 % Rotamer: Outliers : 1.79 % Allowed : 15.88 % Favored : 82.33 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 7.14 % 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: 1.96 (0.19), residues: 2136 helix: 2.85 (0.14), residues: 1256 sheet: -0.02 (0.61), residues: 76 loop : -1.22 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 420 TYR 0.015 0.001 TYR B 584 PHE 0.048 0.001 PHE D 304 TRP 0.013 0.001 TRP A 372 HIS 0.012 0.001 HIS B 378 Details of bonding type rmsd covalent geometry : bond 0.00402 (18180) covalent geometry : angle 0.82369 (24631) hydrogen bonds : bond 0.04065 ( 996) hydrogen bonds : angle 3.83704 ( 2883) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 400 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8495 (mt-10) REVERT: A 354 GLN cc_start: 0.8717 (mt0) cc_final: 0.8279 (mp10) REVERT: A 378 HIS cc_start: 0.7927 (p-80) cc_final: 0.7644 (p90) REVERT: A 423 GLN cc_start: 0.9059 (tp40) cc_final: 0.8794 (tp-100) REVERT: A 584 TYR cc_start: 0.8748 (t80) cc_final: 0.8422 (t80) REVERT: D 354 GLN cc_start: 0.8759 (mt0) cc_final: 0.8316 (mp10) REVERT: D 410 HIS cc_start: 0.8491 (p90) cc_final: 0.8159 (p90) REVERT: D 424 ASP cc_start: 0.8988 (t70) cc_final: 0.8652 (t70) REVERT: D 571 LYS cc_start: 0.8750 (mmtt) cc_final: 0.8423 (tptp) REVERT: D 653 TYR cc_start: 0.7250 (OUTLIER) cc_final: 0.5712 (p90) REVERT: D 746 GLU cc_start: 0.7937 (tt0) cc_final: 0.7639 (tt0) REVERT: B 311 GLU cc_start: 0.9152 (mm-30) cc_final: 0.8903 (mm-30) REVERT: B 319 LEU cc_start: 0.8822 (mp) cc_final: 0.8416 (tp) REVERT: B 324 LYS cc_start: 0.8878 (mttt) cc_final: 0.8333 (mmtt) REVERT: B 354 GLN cc_start: 0.8597 (mt0) cc_final: 0.8313 (mt0) REVERT: B 410 HIS cc_start: 0.7808 (m90) cc_final: 0.7562 (m-70) REVERT: B 423 GLN cc_start: 0.9191 (tp-100) cc_final: 0.8852 (tp-100) REVERT: B 483 SER cc_start: 0.9291 (t) cc_final: 0.9034 (p) REVERT: B 653 TYR cc_start: 0.6660 (OUTLIER) cc_final: 0.5726 (p90) REVERT: B 663 LEU cc_start: 0.9492 (OUTLIER) cc_final: 0.9241 (mt) REVERT: B 724 LYS cc_start: 0.8660 (tmtt) cc_final: 0.8356 (tmtt) REVERT: C 309 TYR cc_start: 0.8759 (t80) cc_final: 0.8354 (t80) REVERT: C 342 SER cc_start: 0.9179 (t) cc_final: 0.8931 (p) REVERT: C 343 SER cc_start: 0.8980 (m) cc_final: 0.8537 (p) REVERT: C 351 TYR cc_start: 0.8724 (t80) cc_final: 0.8458 (t80) REVERT: C 383 ASP cc_start: 0.8267 (t0) cc_final: 0.7929 (t0) REVERT: C 385 SER cc_start: 0.9063 (t) cc_final: 0.8614 (m) REVERT: C 420 ARG cc_start: 0.8811 (mmm-85) cc_final: 0.8438 (mmm-85) REVERT: C 424 ASP cc_start: 0.8910 (t70) cc_final: 0.8685 (t70) REVERT: C 471 ASP cc_start: 0.8647 (m-30) cc_final: 0.8327 (m-30) REVERT: C 504 LYS cc_start: 0.9023 (ttmt) cc_final: 0.8675 (ttmm) REVERT: C 648 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7559 (mm-30) REVERT: C 649 PHE cc_start: 0.8284 (m-10) cc_final: 0.8055 (m-80) REVERT: C 653 TYR cc_start: 0.6741 (OUTLIER) cc_final: 0.5416 (p90) REVERT: C 700 GLN cc_start: 0.8925 (tp40) cc_final: 0.8499 (tp-100) REVERT: C 716 MET cc_start: 0.4951 (ptm) cc_final: 0.4252 (ptp) REVERT: C 743 ARG cc_start: 0.8448 (ttm-80) cc_final: 0.7773 (tpp80) outliers start: 34 outliers final: 29 residues processed: 417 average time/residue: 0.1188 time to fit residues: 76.6841 Evaluate side-chains 431 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 398 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 504 LYS Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 694 LYS Chi-restraints excluded: chain A residue 741 CYS Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 568 MET Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain D residue 653 TYR Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 741 CYS Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 653 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 1 optimal weight: 9.9990 chunk 194 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 112 optimal weight: 9.9990 chunk 182 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 209 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 chunk 144 optimal weight: 3.9990 chunk 200 optimal weight: 0.8980 chunk 175 optimal weight: 5.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 378 HIS C 206 HIS C 259 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.153386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.103026 restraints weight = 28964.810| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.64 r_work: 0.3023 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.170 18180 Z= 0.212 Angle : 0.824 59.198 24631 Z= 0.490 Chirality : 0.039 0.284 2756 Planarity : 0.004 0.138 3020 Dihedral : 8.153 88.040 2923 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.92 % Favored : 95.04 % Rotamer: Outliers : 1.79 % Allowed : 15.98 % Favored : 82.23 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 7.14 % 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: 1.96 (0.19), residues: 2136 helix: 2.85 (0.14), residues: 1256 sheet: -0.02 (0.61), residues: 76 loop : -1.22 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 420 TYR 0.015 0.001 TYR B 584 PHE 0.048 0.001 PHE D 304 TRP 0.013 0.001 TRP A 372 HIS 0.012 0.001 HIS B 378 Details of bonding type rmsd covalent geometry : bond 0.00402 (18180) covalent geometry : angle 0.82369 (24631) hydrogen bonds : bond 0.04065 ( 996) hydrogen bonds : angle 3.83704 ( 2883) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4520.38 seconds wall clock time: 78 minutes 28.88 seconds (4708.88 seconds total)