Starting phenix.real_space_refine on Fri Aug 22 21:12:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wd6_37455/08_2025/8wd6_37455.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wd6_37455/08_2025/8wd6_37455.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wd6_37455/08_2025/8wd6_37455.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wd6_37455/08_2025/8wd6_37455.map" model { file = "/net/cci-nas-00/data/ceres_data/8wd6_37455/08_2025/8wd6_37455.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wd6_37455/08_2025/8wd6_37455.cif" } resolution = 2.87 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= -0.004 sd= 0.075 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: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 5206 2.51 5 N 1325 2.21 5 O 1390 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7973 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3983 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 17, 'TRANS': 494} Chain breaks: 4 Chain: "B" Number of atoms: 3990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3990 Classifications: {'peptide': 513} Link IDs: {'PTRANS': 17, 'TRANS': 495} Chain breaks: 4 Time building chain proxies: 1.90, per 1000 atoms: 0.24 Number of scatterers: 7973 At special positions: 0 Unit cell: (82.125, 101.835, 127.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 1390 8.00 N 1325 7.00 C 5206 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 606 " - pdb=" SG CYS A 622 " distance=2.03 Simple disulfide: pdb=" SG CYS B 606 " - pdb=" SG CYS B 622 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.50 Conformation dependent library (CDL) restraints added in 306.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1878 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 5 sheets defined 68.0% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 106 through 116 removed outlier: 3.690A pdb=" N LEU A 110 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 140 removed outlier: 3.610A pdb=" N LYS A 140 " --> pdb=" O LYS A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 169 Processing helix chain 'A' and resid 174 through 189 Processing helix chain 'A' and resid 208 through 222 removed outlier: 3.918A pdb=" N GLU A 220 " --> pdb=" O SER A 216 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 222 " --> pdb=" O ALA A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 255 removed outlier: 3.538A pdb=" N ALA A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 274 Processing helix chain 'A' and resid 292 through 303 removed outlier: 4.502A pdb=" N MET A 296 " --> pdb=" O GLY A 292 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ALA A 297 " --> pdb=" O ARG A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 320 Processing helix chain 'A' and resid 379 through 406 removed outlier: 5.016A pdb=" N LYS A 399 " --> pdb=" O HIS A 395 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N GLU A 400 " --> pdb=" O ARG A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 425 removed outlier: 3.532A pdb=" N PHE A 412 " --> pdb=" O LEU A 408 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLN A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 455 Proline residue: A 451 - end of helix Processing helix chain 'A' and resid 457 through 462 Processing helix chain 'A' and resid 462 through 472 removed outlier: 3.534A pdb=" N SER A 472 " --> pdb=" O ARG A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 492 Processing helix chain 'A' and resid 493 through 508 removed outlier: 4.305A pdb=" N TRP A 505 " --> pdb=" O THR A 501 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N MET A 506 " --> pdb=" O PHE A 502 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR A 508 " --> pdb=" O TYR A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 541 removed outlier: 3.824A pdb=" N ILE A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 560 Processing helix chain 'A' and resid 570 through 574 removed outlier: 3.779A pdb=" N VAL A 574 " --> pdb=" O SER A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 579 removed outlier: 3.562A pdb=" N TYR A 578 " --> pdb=" O TRP A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 594 removed outlier: 3.586A pdb=" N TYR A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 605 removed outlier: 3.514A pdb=" N GLY A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 629 Processing helix chain 'A' and resid 634 through 660 removed outlier: 3.568A pdb=" N SER A 638 " --> pdb=" O GLY A 634 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL A 639 " --> pdb=" O MET A 635 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG A 650 " --> pdb=" O PHE A 646 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE A 660 " --> pdb=" O ALA A 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 116 removed outlier: 3.548A pdb=" N LEU B 110 " --> pdb=" O GLY B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 141 removed outlier: 4.144A pdb=" N ARG B 141 " --> pdb=" O GLN B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 169 Processing helix chain 'B' and resid 174 through 189 Processing helix chain 'B' and resid 208 through 220 removed outlier: 4.172A pdb=" N GLU B 220 " --> pdb=" O SER B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 255 removed outlier: 3.506A pdb=" N ALA B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 274 removed outlier: 3.591A pdb=" N GLN B 273 " --> pdb=" O SER B 269 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N MET B 274 " --> pdb=" O ARG B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 303 removed outlier: 4.535A pdb=" N ALA B 297 " --> pdb=" O ARG B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 320 Processing helix chain 'B' and resid 379 through 406 removed outlier: 5.045A pdb=" N LYS B 399 " --> pdb=" O HIS B 395 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N GLU B 400 " --> pdb=" O ARG B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 425 Processing helix chain 'B' and resid 432 through 455 Proline residue: B 451 - end of helix Processing helix chain 'B' and resid 457 through 462 removed outlier: 3.546A pdb=" N GLU B 462 " --> pdb=" O THR B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 472 Processing helix chain 'B' and resid 476 through 492 Processing helix chain 'B' and resid 493 through 508 removed outlier: 3.503A pdb=" N ALA B 497 " --> pdb=" O LEU B 493 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N TRP B 505 " --> pdb=" O THR B 501 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N MET B 506 " --> pdb=" O PHE B 502 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR B 508 " --> pdb=" O TYR B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 541 removed outlier: 3.780A pdb=" N ILE B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 561 Processing helix chain 'B' and resid 570 through 579 removed outlier: 3.755A pdb=" N VAL B 574 " --> pdb=" O SER B 571 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N TRP B 575 " --> pdb=" O GLY B 572 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET B 576 " --> pdb=" O MET B 573 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS B 577 " --> pdb=" O VAL B 574 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL B 579 " --> pdb=" O MET B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 594 removed outlier: 3.568A pdb=" N TYR B 584 " --> pdb=" O SER B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 604 Processing helix chain 'B' and resid 619 through 630 removed outlier: 3.805A pdb=" N GLU B 628 " --> pdb=" O PHE B 624 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL B 629 " --> pdb=" O VAL B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 660 removed outlier: 3.657A pdb=" N SER B 638 " --> pdb=" O GLY B 634 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL B 639 " --> pdb=" O MET B 635 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG B 650 " --> pdb=" O PHE B 646 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE B 660 " --> pdb=" O ALA B 656 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 89 through 91 removed outlier: 3.645A pdb=" N GLY A 89 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE A 42 " --> pdb=" O GLY A 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 261 through 263 removed outlier: 7.171A pdb=" N VAL A 278 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N VAL A 289 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU A 280 " --> pdb=" O LEU A 287 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 142 through 143 Processing sheet with id=AA4, first strand: chain 'B' and resid 89 through 91 removed outlier: 3.694A pdb=" N LYS B 126 " --> pdb=" O VAL B 43 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 142 through 145 removed outlier: 6.041A pdb=" N GLY B 143 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU B 228 " --> pdb=" O VAL B 261 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N SER B 263 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N LEU B 230 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL B 278 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N VAL B 289 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU B 280 " --> pdb=" O LEU B 287 " (cutoff:3.500A) 485 hydrogen bonds defined for protein. 1425 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.03 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2474 1.34 - 1.46: 1890 1.46 - 1.58: 3693 1.58 - 1.70: 0 1.70 - 1.81: 86 Bond restraints: 8143 Sorted by residual: bond pdb=" N VAL A 43 " pdb=" CA VAL A 43 " ideal model delta sigma weight residual 1.457 1.493 -0.037 1.15e-02 7.56e+03 1.01e+01 bond pdb=" N VAL B 43 " pdb=" CA VAL B 43 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.15e-02 7.56e+03 1.00e+01 bond pdb=" N PHE A 459 " pdb=" CA PHE A 459 " ideal model delta sigma weight residual 1.461 1.489 -0.028 9.20e-03 1.18e+04 9.00e+00 bond pdb=" N GLU A 232 " pdb=" CA GLU A 232 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.41e-02 5.03e+03 7.12e+00 bond pdb=" C PHE A 459 " pdb=" N PRO A 460 " ideal model delta sigma weight residual 1.335 1.368 -0.033 1.28e-02 6.10e+03 6.67e+00 ... (remaining 8138 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 10808 1.74 - 3.47: 174 3.47 - 5.21: 40 5.21 - 6.95: 6 6.95 - 8.68: 2 Bond angle restraints: 11030 Sorted by residual: angle pdb=" C PHE A 299 " pdb=" CA PHE A 299 " pdb=" CB PHE A 299 " ideal model delta sigma weight residual 110.85 117.56 -6.71 1.70e+00 3.46e-01 1.56e+01 angle pdb=" CA LYS B 140 " pdb=" CB LYS B 140 " pdb=" CG LYS B 140 " ideal model delta sigma weight residual 114.10 120.85 -6.75 2.00e+00 2.50e-01 1.14e+01 angle pdb=" CA PHE A 459 " pdb=" C PHE A 459 " pdb=" O PHE A 459 " ideal model delta sigma weight residual 118.73 115.50 3.23 9.80e-01 1.04e+00 1.08e+01 angle pdb=" CA PHE A 459 " pdb=" C PHE A 459 " pdb=" N PRO A 460 " ideal model delta sigma weight residual 120.77 123.90 -3.13 9.70e-01 1.06e+00 1.04e+01 angle pdb=" CA CYS B 622 " pdb=" C CYS B 622 " pdb=" O CYS B 622 " ideal model delta sigma weight residual 120.42 117.22 3.20 1.06e+00 8.90e-01 9.11e+00 ... (remaining 11025 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.25: 4001 16.25 - 32.49: 565 32.49 - 48.74: 179 48.74 - 64.99: 26 64.99 - 81.23: 9 Dihedral angle restraints: 4780 sinusoidal: 1855 harmonic: 2925 Sorted by residual: dihedral pdb=" CB CYS B 606 " pdb=" SG CYS B 606 " pdb=" SG CYS B 622 " pdb=" CB CYS B 622 " ideal model delta sinusoidal sigma weight residual 93.00 135.71 -42.71 1 1.00e+01 1.00e-02 2.55e+01 dihedral pdb=" C PHE A 299 " pdb=" N PHE A 299 " pdb=" CA PHE A 299 " pdb=" CB PHE A 299 " ideal model delta harmonic sigma weight residual -122.60 -132.61 10.01 0 2.50e+00 1.60e-01 1.60e+01 dihedral pdb=" CG ARG B 214 " pdb=" CD ARG B 214 " pdb=" NE ARG B 214 " pdb=" CZ ARG B 214 " ideal model delta sinusoidal sigma weight residual 90.00 134.54 -44.54 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 4777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1122 0.055 - 0.109: 159 0.109 - 0.164: 21 0.164 - 0.219: 2 0.219 - 0.273: 2 Chirality restraints: 1306 Sorted by residual: chirality pdb=" CA PHE A 299 " pdb=" N PHE A 299 " pdb=" C PHE A 299 " pdb=" CB PHE A 299 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CB VAL B 43 " pdb=" CA VAL B 43 " pdb=" CG1 VAL B 43 " pdb=" CG2 VAL B 43 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CB VAL A 43 " pdb=" CA VAL A 43 " pdb=" CG1 VAL A 43 " pdb=" CG2 VAL A 43 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 1303 not shown) Planarity restraints: 1351 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU B 598 " -0.013 2.00e-02 2.50e+03 2.69e-02 7.26e+00 pdb=" CD GLU B 598 " 0.047 2.00e-02 2.50e+03 pdb=" OE1 GLU B 598 " -0.016 2.00e-02 2.50e+03 pdb=" OE2 GLU B 598 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 463 " 0.226 9.50e-02 1.11e+02 1.01e-01 6.45e+00 pdb=" NE ARG B 463 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG B 463 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG B 463 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG B 463 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 314 " -0.010 2.00e-02 2.50e+03 2.14e-02 4.58e+00 pdb=" CG ASP A 314 " 0.037 2.00e-02 2.50e+03 pdb=" OD1 ASP A 314 " -0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP A 314 " -0.013 2.00e-02 2.50e+03 ... (remaining 1348 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.93: 3277 2.93 - 3.42: 7771 3.42 - 3.91: 12625 3.91 - 4.41: 13867 4.41 - 4.90: 24153 Nonbonded interactions: 61693 Sorted by model distance: nonbonded pdb=" O LEU A 409 " pdb=" NE2 GLN A 413 " model vdw 2.431 3.120 nonbonded pdb=" O GLU A 183 " pdb=" OE1 GLU A 183 " model vdw 2.436 3.040 nonbonded pdb=" OG SER B 405 " pdb=" OE2 GLU B 492 " model vdw 2.439 3.040 nonbonded pdb=" O ARG A 141 " pdb=" N SER A 226 " model vdw 2.452 3.120 nonbonded pdb=" O GLN A 137 " pdb=" NZ LYS A 140 " model vdw 2.453 3.120 ... (remaining 61688 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' selection = (chain 'B' and (resid 35 through 119 or resid 125 through 660)) } 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: 0.990 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: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 7.180 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8145 Z= 0.174 Angle : 0.563 8.682 11034 Z= 0.309 Chirality : 0.040 0.273 1306 Planarity : 0.005 0.101 1351 Dihedral : 16.494 81.232 2896 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.12 % Allowed : 31.10 % Favored : 68.79 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.27), residues: 1005 helix: 1.98 (0.21), residues: 649 sheet: 0.04 (0.72), residues: 70 loop : -0.83 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 463 TYR 0.007 0.001 TYR B 480 PHE 0.026 0.001 PHE B 36 TRP 0.007 0.001 TRP B 447 HIS 0.004 0.001 HIS B 395 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 8143) covalent geometry : angle 0.56318 (11030) SS BOND : bond 0.00170 ( 2) SS BOND : angle 0.55800 ( 4) hydrogen bonds : bond 0.13691 ( 485) hydrogen bonds : angle 4.44847 ( 1425) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 145 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7660 (mttt) cc_final: 0.7426 (tptt) REVERT: A 568 LYS cc_start: 0.7780 (mmtt) cc_final: 0.7227 (tmmt) REVERT: B 41 LYS cc_start: 0.8245 (tttt) cc_final: 0.7792 (ttmt) REVERT: B 291 LYS cc_start: 0.6949 (tttt) cc_final: 0.6312 (ttmm) REVERT: B 568 LYS cc_start: 0.7686 (mmtt) cc_final: 0.7207 (tmmt) REVERT: B 576 MET cc_start: 0.8152 (ttm) cc_final: 0.7904 (mtm) outliers start: 1 outliers final: 1 residues processed: 145 average time/residue: 0.5356 time to fit residues: 81.8784 Evaluate side-chains 126 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 660 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.0060 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 100 optimal weight: 0.1980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 HIS B 454 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.169107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.126464 restraints weight = 9621.887| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.08 r_work: 0.3369 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 8145 Z= 0.100 Angle : 0.467 6.718 11034 Z= 0.237 Chirality : 0.038 0.132 1306 Planarity : 0.003 0.030 1351 Dihedral : 3.618 26.122 1107 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.74 % Allowed : 28.67 % Favored : 66.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.98 (0.28), residues: 1005 helix: 2.24 (0.21), residues: 655 sheet: 0.10 (0.65), residues: 76 loop : -0.63 (0.39), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 141 TYR 0.011 0.001 TYR B 430 PHE 0.015 0.001 PHE A 624 TRP 0.006 0.001 TRP B 447 HIS 0.002 0.001 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 8143) covalent geometry : angle 0.46709 (11030) SS BOND : bond 0.00118 ( 2) SS BOND : angle 0.28886 ( 4) hydrogen bonds : bond 0.04056 ( 485) hydrogen bonds : angle 3.36890 ( 1425) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 140 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7979 (mttt) cc_final: 0.7519 (tppt) REVERT: A 568 LYS cc_start: 0.8094 (mmtt) cc_final: 0.7293 (tmmt) REVERT: A 602 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.7339 (ppt-90) REVERT: A 658 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7481 (ttp-110) REVERT: B 41 LYS cc_start: 0.8103 (tttt) cc_final: 0.7516 (ttmt) REVERT: B 168 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.6608 (ptm160) REVERT: B 291 LYS cc_start: 0.7005 (tttt) cc_final: 0.6259 (ttmm) REVERT: B 568 LYS cc_start: 0.7970 (mmtt) cc_final: 0.7314 (tmmt) REVERT: B 576 MET cc_start: 0.8354 (ttm) cc_final: 0.8043 (mtm) REVERT: B 658 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7428 (ttp-110) outliers start: 41 outliers final: 13 residues processed: 168 average time/residue: 0.4887 time to fit residues: 86.9159 Evaluate side-chains 144 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain A residue 658 ARG Chi-restraints excluded: chain B residue 168 ARG Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 658 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 3 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 45 optimal weight: 0.3980 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN B 265 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.161977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.118775 restraints weight = 9569.884| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.07 r_work: 0.3251 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8145 Z= 0.216 Angle : 0.612 7.396 11034 Z= 0.310 Chirality : 0.042 0.149 1306 Planarity : 0.004 0.033 1351 Dihedral : 3.912 16.215 1105 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 5.20 % Allowed : 29.71 % Favored : 65.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.27), residues: 1005 helix: 1.63 (0.20), residues: 666 sheet: 0.10 (0.60), residues: 82 loop : -0.99 (0.39), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 436 TYR 0.011 0.002 TYR B 526 PHE 0.014 0.002 PHE B 275 TRP 0.011 0.002 TRP A 426 HIS 0.006 0.001 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00532 ( 8143) covalent geometry : angle 0.61157 (11030) SS BOND : bond 0.00383 ( 2) SS BOND : angle 0.50375 ( 4) hydrogen bonds : bond 0.06113 ( 485) hydrogen bonds : angle 3.64081 ( 1425) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 138 time to evaluate : 0.186 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7941 (mttt) cc_final: 0.7457 (tppt) REVERT: A 87 VAL cc_start: 0.6108 (OUTLIER) cc_final: 0.5874 (t) REVERT: A 568 LYS cc_start: 0.8225 (mmtt) cc_final: 0.7421 (tmmt) REVERT: A 602 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.7277 (ppt-90) REVERT: B 41 LYS cc_start: 0.7905 (tttt) cc_final: 0.7214 (ttmt) REVERT: B 168 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.6622 (ptm160) REVERT: B 291 LYS cc_start: 0.7179 (tttt) cc_final: 0.6261 (ttmm) REVERT: B 568 LYS cc_start: 0.8132 (mmtt) cc_final: 0.7447 (tmmt) REVERT: B 576 MET cc_start: 0.8530 (ttm) cc_final: 0.7679 (tpp) outliers start: 45 outliers final: 25 residues processed: 172 average time/residue: 0.5011 time to fit residues: 91.2658 Evaluate side-chains 152 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 124 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 168 ARG Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 454 ASN Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain B residue 632 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 74 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 56 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.164173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.122015 restraints weight = 9743.561| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.03 r_work: 0.3324 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8145 Z= 0.122 Angle : 0.511 7.591 11034 Z= 0.257 Chirality : 0.038 0.127 1306 Planarity : 0.003 0.031 1351 Dihedral : 3.689 14.639 1105 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.97 % Allowed : 30.98 % Favored : 64.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.28), residues: 1005 helix: 1.86 (0.21), residues: 664 sheet: -0.31 (0.58), residues: 88 loop : -0.90 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 141 TYR 0.007 0.001 TYR A 430 PHE 0.017 0.001 PHE A 624 TRP 0.008 0.001 TRP A 386 HIS 0.002 0.001 HIS B 484 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 8143) covalent geometry : angle 0.51068 (11030) SS BOND : bond 0.00437 ( 2) SS BOND : angle 0.32238 ( 4) hydrogen bonds : bond 0.04469 ( 485) hydrogen bonds : angle 3.37217 ( 1425) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 133 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 409 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7957 (mp) REVERT: A 474 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.7566 (ttt) REVERT: A 568 LYS cc_start: 0.8214 (mmtt) cc_final: 0.7414 (tmmt) REVERT: A 602 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.7310 (ppt-90) REVERT: A 658 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7765 (ttp-110) REVERT: B 41 LYS cc_start: 0.7826 (tttt) cc_final: 0.7092 (ttmt) REVERT: B 291 LYS cc_start: 0.7088 (tttt) cc_final: 0.6196 (ttmm) REVERT: B 310 MET cc_start: 0.5624 (OUTLIER) cc_final: 0.4466 (ptp) REVERT: B 568 LYS cc_start: 0.8193 (mmtt) cc_final: 0.7447 (tmmt) REVERT: B 655 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8200 (mt) REVERT: B 658 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7759 (ttp-110) outliers start: 43 outliers final: 19 residues processed: 162 average time/residue: 0.5790 time to fit residues: 99.4072 Evaluate side-chains 154 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain A residue 658 ARG Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 454 ASN Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 658 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 81 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.162839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.119927 restraints weight = 9708.086| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.09 r_work: 0.3296 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8145 Z= 0.150 Angle : 0.553 8.143 11034 Z= 0.277 Chirality : 0.040 0.134 1306 Planarity : 0.003 0.031 1351 Dihedral : 3.741 15.104 1105 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 5.09 % Allowed : 30.52 % Favored : 64.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.27), residues: 1005 helix: 1.77 (0.21), residues: 665 sheet: -0.11 (0.63), residues: 78 loop : -0.99 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 141 TYR 0.008 0.001 TYR A 475 PHE 0.017 0.002 PHE A 275 TRP 0.008 0.001 TRP A 426 HIS 0.003 0.001 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 8143) covalent geometry : angle 0.55283 (11030) SS BOND : bond 0.00281 ( 2) SS BOND : angle 0.36111 ( 4) hydrogen bonds : bond 0.04913 ( 485) hydrogen bonds : angle 3.42826 ( 1425) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 132 time to evaluate : 0.358 Fit side-chains REVERT: A 41 LYS cc_start: 0.7791 (mttt) cc_final: 0.7531 (ttmt) REVERT: A 90 MET cc_start: 0.7611 (OUTLIER) cc_final: 0.7213 (tpp) REVERT: A 409 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7926 (mp) REVERT: A 474 MET cc_start: 0.8067 (OUTLIER) cc_final: 0.7702 (ttt) REVERT: A 568 LYS cc_start: 0.8250 (mmtt) cc_final: 0.7451 (tmmt) REVERT: A 658 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7735 (ttp-110) REVERT: B 41 LYS cc_start: 0.7780 (tttt) cc_final: 0.7066 (ttmt) REVERT: B 291 LYS cc_start: 0.7138 (tttt) cc_final: 0.6222 (ttmm) REVERT: B 568 LYS cc_start: 0.8216 (mmtt) cc_final: 0.7448 (tmmt) REVERT: B 576 MET cc_start: 0.8548 (mtp) cc_final: 0.7835 (tpp) REVERT: B 655 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8211 (mt) REVERT: B 658 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7422 (ttp-110) outliers start: 44 outliers final: 25 residues processed: 164 average time/residue: 0.5237 time to fit residues: 91.5721 Evaluate side-chains 159 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 658 ARG Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 658 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.162971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.120034 restraints weight = 9647.049| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.09 r_work: 0.3298 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8145 Z= 0.146 Angle : 0.550 8.372 11034 Z= 0.276 Chirality : 0.039 0.131 1306 Planarity : 0.003 0.030 1351 Dihedral : 3.731 14.817 1105 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 5.78 % Allowed : 29.48 % Favored : 64.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.28), residues: 1005 helix: 1.79 (0.21), residues: 664 sheet: -0.83 (0.62), residues: 77 loop : -0.80 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 141 TYR 0.007 0.001 TYR B 526 PHE 0.016 0.002 PHE A 624 TRP 0.007 0.001 TRP B 425 HIS 0.003 0.001 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 8143) covalent geometry : angle 0.54984 (11030) SS BOND : bond 0.00265 ( 2) SS BOND : angle 0.37098 ( 4) hydrogen bonds : bond 0.04733 ( 485) hydrogen bonds : angle 3.38984 ( 1425) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 128 time to evaluate : 0.320 Fit side-chains REVERT: A 87 VAL cc_start: 0.6186 (OUTLIER) cc_final: 0.5969 (t) REVERT: A 409 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7894 (mp) REVERT: A 568 LYS cc_start: 0.8276 (mmtt) cc_final: 0.7448 (tmmt) REVERT: A 602 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.7260 (ppt-90) REVERT: A 658 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7204 (ttp-110) REVERT: B 41 LYS cc_start: 0.7743 (tttt) cc_final: 0.7000 (ttmt) REVERT: B 168 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.6515 (ptm160) REVERT: B 291 LYS cc_start: 0.7150 (tttt) cc_final: 0.6227 (ttmm) REVERT: B 568 LYS cc_start: 0.8235 (mmtt) cc_final: 0.7455 (tmmt) REVERT: B 576 MET cc_start: 0.8568 (mtp) cc_final: 0.7779 (tpp) REVERT: B 655 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8204 (mt) REVERT: B 658 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7415 (ttp-110) outliers start: 50 outliers final: 29 residues processed: 167 average time/residue: 0.5011 time to fit residues: 88.8790 Evaluate side-chains 157 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 121 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 658 ARG Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 168 ARG Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 658 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 90 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 45 optimal weight: 0.0470 chunk 15 optimal weight: 0.0060 chunk 52 optimal weight: 9.9990 chunk 37 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 31 optimal weight: 0.3980 overall best weight: 0.3894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.166975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.124965 restraints weight = 9646.290| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.05 r_work: 0.3358 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8145 Z= 0.098 Angle : 0.495 8.279 11034 Z= 0.246 Chirality : 0.037 0.123 1306 Planarity : 0.003 0.030 1351 Dihedral : 3.458 14.208 1105 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 4.05 % Allowed : 31.56 % Favored : 64.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.28), residues: 1005 helix: 2.16 (0.21), residues: 657 sheet: -0.69 (0.62), residues: 77 loop : -0.66 (0.39), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 141 TYR 0.006 0.001 TYR B 480 PHE 0.016 0.001 PHE A 624 TRP 0.008 0.001 TRP A 386 HIS 0.003 0.001 HIS B 484 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 8143) covalent geometry : angle 0.49509 (11030) SS BOND : bond 0.00118 ( 2) SS BOND : angle 0.23038 ( 4) hydrogen bonds : bond 0.03376 ( 485) hydrogen bonds : angle 3.17624 ( 1425) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 131 time to evaluate : 0.248 Fit side-chains REVERT: A 40 LEU cc_start: 0.8294 (tt) cc_final: 0.8011 (tp) REVERT: A 41 LYS cc_start: 0.8002 (tttt) cc_final: 0.7616 (ttmt) REVERT: A 409 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7973 (mp) REVERT: A 568 LYS cc_start: 0.8238 (mmtt) cc_final: 0.7468 (tmmt) REVERT: A 602 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.7190 (ppt-90) REVERT: B 41 LYS cc_start: 0.7788 (tttt) cc_final: 0.7286 (ttmt) REVERT: B 90 MET cc_start: 0.7802 (ttt) cc_final: 0.7411 (ttp) REVERT: B 114 VAL cc_start: 0.7298 (OUTLIER) cc_final: 0.7018 (p) REVERT: B 168 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.6409 (ptm160) REVERT: B 291 LYS cc_start: 0.7199 (tttt) cc_final: 0.6256 (ttmm) REVERT: B 482 MET cc_start: 0.8447 (mmm) cc_final: 0.8077 (mmm) REVERT: B 568 LYS cc_start: 0.8174 (mmtt) cc_final: 0.7413 (tmmt) REVERT: B 576 MET cc_start: 0.8427 (mtp) cc_final: 0.7877 (tpp) outliers start: 35 outliers final: 10 residues processed: 159 average time/residue: 0.5098 time to fit residues: 85.9461 Evaluate side-chains 137 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 168 ARG Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 282 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.160384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.117518 restraints weight = 9787.765| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.09 r_work: 0.3252 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 8145 Z= 0.251 Angle : 0.668 8.767 11034 Z= 0.336 Chirality : 0.044 0.155 1306 Planarity : 0.004 0.048 1351 Dihedral : 3.988 16.152 1105 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.16 % Allowed : 32.14 % Favored : 63.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.27), residues: 1005 helix: 1.46 (0.20), residues: 664 sheet: -0.73 (0.62), residues: 71 loop : -0.90 (0.39), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 158 TYR 0.012 0.002 TYR B 526 PHE 0.015 0.002 PHE A 304 TRP 0.012 0.002 TRP A 426 HIS 0.007 0.001 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00622 ( 8143) covalent geometry : angle 0.66838 (11030) SS BOND : bond 0.00439 ( 2) SS BOND : angle 0.78503 ( 4) hydrogen bonds : bond 0.06261 ( 485) hydrogen bonds : angle 3.64739 ( 1425) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 125 time to evaluate : 0.384 Fit side-chains REVERT: A 41 LYS cc_start: 0.7957 (tttt) cc_final: 0.7705 (ttmt) REVERT: A 87 VAL cc_start: 0.6314 (OUTLIER) cc_final: 0.5988 (t) REVERT: A 285 LYS cc_start: 0.6019 (mmmt) cc_final: 0.5557 (mmpt) REVERT: A 394 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7824 (mp) REVERT: A 568 LYS cc_start: 0.8394 (mmtt) cc_final: 0.7507 (tmmt) REVERT: B 41 LYS cc_start: 0.7733 (tttt) cc_final: 0.6935 (ttmt) REVERT: B 291 LYS cc_start: 0.7276 (tttt) cc_final: 0.7043 (tttm) REVERT: B 394 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7830 (mp) REVERT: B 568 LYS cc_start: 0.8285 (mmtt) cc_final: 0.7426 (tmmt) outliers start: 36 outliers final: 18 residues processed: 154 average time/residue: 0.4753 time to fit residues: 78.0917 Evaluate side-chains 139 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 394 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 46 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 68 optimal weight: 0.0010 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 0.2980 chunk 31 optimal weight: 1.9990 overall best weight: 0.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.163949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.121181 restraints weight = 9672.640| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.09 r_work: 0.3312 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8145 Z= 0.123 Angle : 0.550 8.707 11034 Z= 0.276 Chirality : 0.039 0.137 1306 Planarity : 0.004 0.034 1351 Dihedral : 3.694 14.506 1105 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.77 % Allowed : 33.53 % Favored : 63.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.28), residues: 1005 helix: 1.83 (0.21), residues: 663 sheet: -0.85 (0.61), residues: 77 loop : -0.80 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 158 TYR 0.012 0.001 TYR B 430 PHE 0.015 0.001 PHE B 304 TRP 0.008 0.001 TRP B 425 HIS 0.003 0.001 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 8143) covalent geometry : angle 0.54983 (11030) SS BOND : bond 0.00214 ( 2) SS BOND : angle 0.39713 ( 4) hydrogen bonds : bond 0.04225 ( 485) hydrogen bonds : angle 3.34505 ( 1425) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.315 Fit side-chains REVERT: A 40 LEU cc_start: 0.8275 (tt) cc_final: 0.8024 (tp) REVERT: A 41 LYS cc_start: 0.7996 (tttt) cc_final: 0.7399 (ttmt) REVERT: A 285 LYS cc_start: 0.6010 (mmmt) cc_final: 0.5589 (mmpt) REVERT: A 568 LYS cc_start: 0.8367 (mmtt) cc_final: 0.7457 (tmmt) REVERT: B 41 LYS cc_start: 0.7748 (tttt) cc_final: 0.7207 (ttmt) REVERT: B 90 MET cc_start: 0.7805 (ttt) cc_final: 0.7427 (ttp) REVERT: B 291 LYS cc_start: 0.7169 (tttt) cc_final: 0.6225 (ttmm) REVERT: B 568 LYS cc_start: 0.8350 (mmtt) cc_final: 0.7459 (tmmt) REVERT: B 576 MET cc_start: 0.8560 (mtp) cc_final: 0.7779 (tpp) REVERT: B 598 GLU cc_start: 0.7937 (pp20) cc_final: 0.7253 (mm-30) outliers start: 24 outliers final: 17 residues processed: 140 average time/residue: 0.4883 time to fit residues: 72.4594 Evaluate side-chains 138 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 479 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 64 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 72 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 57 optimal weight: 0.4980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.161987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.119311 restraints weight = 9695.959| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.06 r_work: 0.3283 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8145 Z= 0.178 Angle : 0.615 8.782 11034 Z= 0.307 Chirality : 0.041 0.139 1306 Planarity : 0.004 0.034 1351 Dihedral : 3.844 14.885 1105 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.43 % Allowed : 33.41 % Favored : 64.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.27), residues: 1005 helix: 1.67 (0.20), residues: 663 sheet: -1.02 (0.60), residues: 77 loop : -0.83 (0.40), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 158 TYR 0.009 0.002 TYR B 526 PHE 0.016 0.002 PHE A 304 TRP 0.009 0.002 TRP A 426 HIS 0.004 0.001 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 8143) covalent geometry : angle 0.61511 (11030) SS BOND : bond 0.00311 ( 2) SS BOND : angle 0.60950 ( 4) hydrogen bonds : bond 0.05240 ( 485) hydrogen bonds : angle 3.49313 ( 1425) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.315 Fit side-chains REVERT: A 41 LYS cc_start: 0.7985 (tttt) cc_final: 0.7277 (ttmt) REVERT: A 87 VAL cc_start: 0.6257 (OUTLIER) cc_final: 0.5947 (t) REVERT: A 285 LYS cc_start: 0.6042 (mmmt) cc_final: 0.5610 (mmpt) REVERT: A 568 LYS cc_start: 0.8406 (mmtt) cc_final: 0.7465 (tmmt) REVERT: B 41 LYS cc_start: 0.7751 (tttt) cc_final: 0.7182 (ttmt) REVERT: B 90 MET cc_start: 0.7710 (ttt) cc_final: 0.7323 (ttp) REVERT: B 291 LYS cc_start: 0.7280 (tttt) cc_final: 0.7045 (tttm) REVERT: B 568 LYS cc_start: 0.8362 (mmtt) cc_final: 0.7440 (tmmt) REVERT: B 576 MET cc_start: 0.8616 (mtp) cc_final: 0.7914 (tpp) outliers start: 21 outliers final: 18 residues processed: 132 average time/residue: 0.4615 time to fit residues: 65.0295 Evaluate side-chains 135 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 479 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 55 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 99 optimal weight: 0.5980 chunk 67 optimal weight: 0.7980 chunk 47 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.164302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.121794 restraints weight = 9637.246| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.07 r_work: 0.3312 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8145 Z= 0.119 Angle : 0.554 8.807 11034 Z= 0.277 Chirality : 0.039 0.129 1306 Planarity : 0.003 0.031 1351 Dihedral : 3.647 14.444 1105 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.97 % Allowed : 33.87 % Favored : 64.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.28), residues: 1005 helix: 1.99 (0.21), residues: 653 sheet: -0.81 (0.61), residues: 77 loop : -0.73 (0.39), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 141 TYR 0.012 0.001 TYR B 430 PHE 0.016 0.001 PHE B 304 TRP 0.008 0.001 TRP B 425 HIS 0.002 0.001 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 8143) covalent geometry : angle 0.55399 (11030) SS BOND : bond 0.00177 ( 2) SS BOND : angle 0.38075 ( 4) hydrogen bonds : bond 0.04065 ( 485) hydrogen bonds : angle 3.29515 ( 1425) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3014.92 seconds wall clock time: 51 minutes 57.52 seconds (3117.52 seconds total)