Starting phenix.real_space_refine on Mon Jul 6 11:26:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t0c_40940/07_2026/8t0c_40940_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t0c_40940/07_2026/8t0c_40940.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t0c_40940/07_2026/8t0c_40940.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t0c_40940/07_2026/8t0c_40940.map" model { file = "/net/cci-nas-00/data/ceres_data/8t0c_40940/07_2026/8t0c_40940_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t0c_40940/07_2026/8t0c_40940_trim.cif" } resolution = 3.5 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= 1.000 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: 7 Type Number sf(0) Gaussians P 4 5.49 5 S 100 5.16 5 Na 2 4.78 5 C 11408 2.51 5 N 2800 2.21 5 O 3084 1.98 5 H 17464 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34862 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 8690 Classifications: {'peptide': 532} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 517} Chain: "D" Number of atoms: 8690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 8690 Classifications: {'peptide': 532} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 517} Chain: "B" Number of atoms: 8690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 8690 Classifications: {'peptide': 532} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 517} Chain: "C" Number of atoms: 8690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 8690 Classifications: {'peptide': 532} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 517} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 25 Ad-hoc single atom residues: {' NA': 2} Unusual residues: {'NKN': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "D" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'NKN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'NKN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'NKN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.18, per 1000 atoms: 0.18 Number of scatterers: 34862 At special positions: 0 Unit cell: (121.075, 121.075, 112.725, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 100 16.00 P 4 15.00 Na 2 11.00 O 3084 8.00 N 2800 7.00 C 11408 6.00 H 17464 1.00 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: 3.43 Conformation dependent library (CDL) restraints added in 901.2 milliseconds 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4024 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 4 sheets defined 65.0% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 203 through 211 Processing helix chain 'A' and resid 213 through 223 removed outlier: 3.857A pdb=" N ASN A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 250 through 258 Processing helix chain 'A' and resid 260 through 269 Processing helix chain 'A' and resid 286 through 295 removed outlier: 3.550A pdb=" N ALA A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 320 Processing helix chain 'A' and resid 335 through 344 Processing helix chain 'A' and resid 345 through 353 Processing helix chain 'A' and resid 362 through 366 Processing helix chain 'A' and resid 394 through 402 Processing helix chain 'A' and resid 410 through 414 removed outlier: 3.836A pdb=" N LEU A 413 " --> pdb=" O HIS A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 454 removed outlier: 5.660A pdb=" N LYS A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ARG A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 500 Processing helix chain 'A' and resid 510 through 532 removed outlier: 3.719A pdb=" N LEU A 515 " --> pdb=" O TYR A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 551 Processing helix chain 'A' and resid 552 through 557 removed outlier: 3.841A pdb=" N ARG A 557 " --> pdb=" O TYR A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 576 Processing helix chain 'A' and resid 576 through 599 removed outlier: 4.119A pdb=" N VAL A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N TYR A 584 " --> pdb=" O PHE A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 628 Processing helix chain 'A' and resid 629 through 639 Processing helix chain 'A' and resid 655 through 684 Processing helix chain 'A' and resid 687 through 690 Processing helix chain 'A' and resid 691 through 712 Processing helix chain 'D' and resid 203 through 211 Processing helix chain 'D' and resid 213 through 223 removed outlier: 3.857A pdb=" N ASN D 223 " --> pdb=" O LEU D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 237 Processing helix chain 'D' and resid 250 through 258 Processing helix chain 'D' and resid 260 through 269 Processing helix chain 'D' and resid 286 through 295 removed outlier: 3.550A pdb=" N ALA D 295 " --> pdb=" O LEU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 320 Processing helix chain 'D' and resid 335 through 344 Processing helix chain 'D' and resid 345 through 353 Processing helix chain 'D' and resid 362 through 366 Processing helix chain 'D' and resid 394 through 402 Processing helix chain 'D' and resid 410 through 414 removed outlier: 3.836A pdb=" N LEU D 413 " --> pdb=" O HIS D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 454 removed outlier: 5.660A pdb=" N LYS D 431 " --> pdb=" O ASP D 427 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ARG D 432 " --> pdb=" O ARG D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 500 Processing helix chain 'D' and resid 510 through 532 removed outlier: 3.719A pdb=" N LEU D 515 " --> pdb=" O TYR D 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 551 Processing helix chain 'D' and resid 552 through 557 removed outlier: 3.841A pdb=" N ARG D 557 " --> pdb=" O TYR D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 576 Processing helix chain 'D' and resid 576 through 599 removed outlier: 4.119A pdb=" N VAL D 583 " --> pdb=" O ARG D 579 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N TYR D 584 " --> pdb=" O PHE D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 602 through 628 Processing helix chain 'D' and resid 629 through 639 Processing helix chain 'D' and resid 655 through 684 Processing helix chain 'D' and resid 687 through 690 Processing helix chain 'D' and resid 691 through 712 Processing helix chain 'B' and resid 203 through 211 Processing helix chain 'B' and resid 213 through 223 removed outlier: 3.857A pdb=" N ASN B 223 " --> pdb=" O LEU B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 237 Processing helix chain 'B' and resid 250 through 258 Processing helix chain 'B' and resid 260 through 269 Processing helix chain 'B' and resid 286 through 295 removed outlier: 3.550A pdb=" N ALA B 295 " --> pdb=" O LEU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 320 Processing helix chain 'B' and resid 335 through 344 Processing helix chain 'B' and resid 345 through 353 Processing helix chain 'B' and resid 362 through 366 Processing helix chain 'B' and resid 394 through 402 Processing helix chain 'B' and resid 410 through 414 removed outlier: 3.836A pdb=" N LEU B 413 " --> pdb=" O HIS B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 454 removed outlier: 5.660A pdb=" N LYS B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ARG B 432 " --> pdb=" O ARG B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 500 Processing helix chain 'B' and resid 510 through 532 removed outlier: 3.719A pdb=" N LEU B 515 " --> pdb=" O TYR B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 551 Processing helix chain 'B' and resid 552 through 557 removed outlier: 3.841A pdb=" N ARG B 557 " --> pdb=" O TYR B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 576 Processing helix chain 'B' and resid 576 through 599 removed outlier: 4.119A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N TYR B 584 " --> pdb=" O PHE B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 628 Processing helix chain 'B' and resid 629 through 639 Processing helix chain 'B' and resid 655 through 684 Processing helix chain 'B' and resid 687 through 690 Processing helix chain 'B' and resid 691 through 712 Processing helix chain 'C' and resid 203 through 211 Processing helix chain 'C' and resid 213 through 223 removed outlier: 3.857A pdb=" N ASN C 223 " --> pdb=" O LEU C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 237 Processing helix chain 'C' and resid 250 through 258 Processing helix chain 'C' and resid 260 through 269 Processing helix chain 'C' and resid 286 through 295 removed outlier: 3.550A pdb=" N ALA C 295 " --> pdb=" O LEU C 291 " (cutoff:3.500A) 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 353 Processing helix chain 'C' and resid 362 through 366 Processing helix chain 'C' and resid 394 through 402 Processing helix chain 'C' and resid 410 through 414 removed outlier: 3.836A pdb=" N LEU C 413 " --> pdb=" O HIS C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 454 removed outlier: 5.660A pdb=" N LYS C 431 " --> pdb=" O ASP C 427 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ARG C 432 " --> pdb=" O ARG C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 500 Processing helix chain 'C' and resid 510 through 532 removed outlier: 3.719A pdb=" N LEU C 515 " --> pdb=" O TYR C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 551 Processing helix chain 'C' and resid 552 through 557 removed outlier: 3.841A pdb=" N ARG C 557 " --> pdb=" O TYR C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 576 Processing helix chain 'C' and resid 576 through 599 removed outlier: 4.119A pdb=" N VAL C 583 " --> pdb=" O ARG C 579 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N TYR C 584 " --> pdb=" O PHE C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 602 through 628 Processing helix chain 'C' and resid 629 through 639 Processing helix chain 'C' and resid 655 through 684 Processing helix chain 'C' and resid 687 through 690 Processing helix chain 'C' and resid 691 through 712 Processing sheet with id=AA1, first strand: chain 'A' and resid 368 through 374 removed outlier: 7.072A pdb=" N SER A 379 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ALA A 373 " --> pdb=" O VAL A 377 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU A 746 " --> pdb=" O HIS A 378 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR A 382 " --> pdb=" O PHE A 742 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 368 through 374 removed outlier: 7.072A pdb=" N SER D 379 " --> pdb=" O GLU D 371 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ALA D 373 " --> pdb=" O VAL D 377 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU D 746 " --> pdb=" O HIS D 378 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR D 382 " --> pdb=" O PHE D 742 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 368 through 374 removed outlier: 7.072A pdb=" N SER B 379 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ALA B 373 " --> pdb=" O VAL B 377 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU B 746 " --> pdb=" O HIS B 378 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR B 382 " --> pdb=" O PHE B 742 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 368 through 374 removed outlier: 7.072A pdb=" N SER C 379 " --> pdb=" O GLU C 371 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ALA C 373 " --> pdb=" O VAL C 377 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL C 377 " --> pdb=" O ALA C 373 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU C 746 " --> pdb=" O HIS C 378 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR C 382 " --> pdb=" O PHE C 742 " (cutoff:3.500A) 1016 hydrogen bonds defined for protein. 2940 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: 7.34 Time building geometry restraints manager: 4.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 17230 1.03 - 1.23: 266 1.23 - 1.42: 7588 1.42 - 1.62: 10024 1.62 - 1.81: 168 Bond restraints: 35276 Sorted by residual: bond pdb=" OAB NKN D 901 " pdb=" PAC NKN D 901 " ideal model delta sigma weight residual 1.668 1.458 0.210 2.00e-02 2.50e+03 1.11e+02 bond pdb=" OAB NKN C 901 " pdb=" PAC NKN C 901 " ideal model delta sigma weight residual 1.668 1.458 0.210 2.00e-02 2.50e+03 1.11e+02 bond pdb=" OAB NKN B 901 " pdb=" PAC NKN B 901 " ideal model delta sigma weight residual 1.668 1.458 0.210 2.00e-02 2.50e+03 1.11e+02 bond pdb=" OAB NKN A 901 " pdb=" PAC NKN A 901 " ideal model delta sigma weight residual 1.668 1.458 0.210 2.00e-02 2.50e+03 1.11e+02 bond pdb=" OAA NKN A 901 " pdb=" PAC NKN A 901 " ideal model delta sigma weight residual 1.667 1.458 0.209 2.00e-02 2.50e+03 1.09e+02 ... (remaining 35271 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.00: 63560 10.00 - 19.99: 4 19.99 - 29.99: 8 29.99 - 39.99: 0 39.99 - 49.99: 4 Bond angle restraints: 63576 Sorted by residual: angle pdb=" OAA NKN B 901 " pdb=" PAC NKN B 901 " pdb=" OAB NKN B 901 " ideal model delta sigma weight residual 54.49 104.48 -49.99 3.00e+00 1.11e-01 2.78e+02 angle pdb=" OAA NKN A 901 " pdb=" PAC NKN A 901 " pdb=" OAB NKN A 901 " ideal model delta sigma weight residual 54.49 104.48 -49.99 3.00e+00 1.11e-01 2.78e+02 angle pdb=" OAA NKN D 901 " pdb=" PAC NKN D 901 " pdb=" OAB NKN D 901 " ideal model delta sigma weight residual 54.49 104.48 -49.99 3.00e+00 1.11e-01 2.78e+02 angle pdb=" OAA NKN C 901 " pdb=" PAC NKN C 901 " pdb=" OAB NKN C 901 " ideal model delta sigma weight residual 54.49 104.48 -49.99 3.00e+00 1.11e-01 2.78e+02 angle pdb=" OAB NKN C 901 " pdb=" PAC NKN C 901 " pdb=" OAD NKN C 901 " ideal model delta sigma weight residual 128.49 104.17 24.32 3.00e+00 1.11e-01 6.57e+01 ... (remaining 63571 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 14873 17.87 - 35.74: 1259 35.74 - 53.62: 400 53.62 - 71.49: 60 71.49 - 89.36: 44 Dihedral angle restraints: 16636 sinusoidal: 8832 harmonic: 7804 Sorted by residual: dihedral pdb=" CA LEU C 574 " pdb=" C LEU C 574 " pdb=" N ARG C 575 " pdb=" CA ARG C 575 " ideal model delta harmonic sigma weight residual 180.00 -161.09 -18.91 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA LEU A 574 " pdb=" C LEU A 574 " pdb=" N ARG A 575 " pdb=" CA ARG A 575 " ideal model delta harmonic sigma weight residual -180.00 -161.09 -18.91 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA LEU B 574 " pdb=" C LEU B 574 " pdb=" N ARG B 575 " pdb=" CA ARG B 575 " ideal model delta harmonic sigma weight residual -180.00 -161.09 -18.91 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 16633 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1862 0.032 - 0.063: 626 0.063 - 0.094: 172 0.094 - 0.126: 32 0.126 - 0.157: 8 Chirality restraints: 2700 Sorted by residual: chirality pdb=" CA MET A 716 " pdb=" N MET A 716 " pdb=" C MET A 716 " pdb=" CB MET A 716 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.20e-01 chirality pdb=" CA MET B 716 " pdb=" N MET B 716 " pdb=" C MET B 716 " pdb=" CB MET B 716 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.92e-01 chirality pdb=" CA MET D 716 " pdb=" N MET D 716 " pdb=" C MET D 716 " pdb=" CB MET D 716 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.79e-01 ... (remaining 2697 not shown) Planarity restraints: 5044 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 354 " -0.018 2.00e-02 2.50e+03 5.08e-01 3.87e+03 pdb=" CD GLN B 354 " -0.004 2.00e-02 2.50e+03 pdb=" OE1 GLN B 354 " 0.019 2.00e-02 2.50e+03 pdb=" NE2 GLN B 354 " 0.000 2.00e-02 2.50e+03 pdb="HE21 GLN B 354 " 0.881 2.00e-02 2.50e+03 pdb="HE22 GLN B 354 " -0.878 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 354 " -0.019 2.00e-02 2.50e+03 5.08e-01 3.87e+03 pdb=" CD GLN C 354 " -0.004 2.00e-02 2.50e+03 pdb=" OE1 GLN C 354 " 0.020 2.00e-02 2.50e+03 pdb=" NE2 GLN C 354 " 0.000 2.00e-02 2.50e+03 pdb="HE21 GLN C 354 " 0.881 2.00e-02 2.50e+03 pdb="HE22 GLN C 354 " -0.878 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 354 " 0.019 2.00e-02 2.50e+03 5.08e-01 3.87e+03 pdb=" CD GLN A 354 " 0.003 2.00e-02 2.50e+03 pdb=" OE1 GLN A 354 " -0.019 2.00e-02 2.50e+03 pdb=" NE2 GLN A 354 " -0.000 2.00e-02 2.50e+03 pdb="HE21 GLN A 354 " -0.881 2.00e-02 2.50e+03 pdb="HE22 GLN A 354 " 0.878 2.00e-02 2.50e+03 ... (remaining 5041 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.20: 2259 2.20 - 2.80: 71452 2.80 - 3.40: 95023 3.40 - 4.00: 118158 4.00 - 4.60: 184772 Nonbonded interactions: 471664 Sorted by model distance: nonbonded pdb=" H LYS C 466 " pdb=" OD2 ASP C 471 " model vdw 1.606 2.450 nonbonded pdb=" H LYS B 466 " pdb=" OD2 ASP B 471 " model vdw 1.607 2.450 nonbonded pdb=" H LYS D 466 " pdb=" OD2 ASP D 471 " model vdw 1.607 2.450 nonbonded pdb=" H LYS A 466 " pdb=" OD2 ASP A 471 " model vdw 1.607 2.450 nonbonded pdb=" O LEU B 553 " pdb=" HG1 THR B 556 " model vdw 1.616 2.450 ... (remaining 471659 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 198 through 901) selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.830 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: 0.270 Extract box with map and model: 0.720 Check model and map are aligned: 0.130 Set scattering table: 0.130 Process input model: 31.520 Find NCS groups from input model: 0.590 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: 0.010 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 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 : 0.006 0.210 17812 Z= 0.312 Angle : 1.005 49.985 24100 Z= 0.441 Chirality : 0.035 0.157 2700 Planarity : 0.003 0.039 2976 Dihedral : 15.035 88.319 6496 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.21 % Allowed : 0.64 % Favored : 99.15 % 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: 2.15 (0.20), residues: 2120 helix: 2.87 (0.15), residues: 1264 sheet: 0.62 (0.84), residues: 40 loop : -0.95 (0.24), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 557 TYR 0.014 0.001 TYR D 653 PHE 0.007 0.001 PHE C 649 TRP 0.005 0.001 TRP C 697 HIS 0.001 0.000 HIS C 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00588 / 0.31 (17812) covalent geometry : angle 1.00455 / 0.44 (24100) hydrogen bonds : bond 0.12007 / 8.23 ( 1016) hydrogen bonds : angle 4.40407 / 3.20 ( 2940) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 508 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 676 ASN cc_start: 0.8935 (m110) cc_final: 0.8379 (m110) REVERT: C 676 ASN cc_start: 0.8936 (m110) cc_final: 0.8382 (m110) outliers start: 4 outliers final: 4 residues processed: 508 average time/residue: 0.3041 time to fit residues: 235.9761 Evaluate side-chains 496 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 492 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain C residue 681 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.0870 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.167837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.118326 restraints weight = 71004.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.124056 restraints weight = 28117.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.123605 restraints weight = 17597.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.124047 restraints weight = 14146.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.124353 restraints weight = 13207.697| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.0871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17812 Z= 0.113 Angle : 0.471 5.547 24100 Z= 0.255 Chirality : 0.034 0.135 2700 Planarity : 0.003 0.029 2976 Dihedral : 7.120 76.182 2452 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 1.06 % Allowed : 7.02 % Favored : 91.91 % 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: 2.10 (0.20), residues: 2120 helix: 2.92 (0.15), residues: 1280 sheet: -1.04 (0.56), residues: 92 loop : -1.15 (0.24), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 743 TYR 0.007 0.001 TYR A 351 PHE 0.008 0.001 PHE C 591 TRP 0.004 0.001 TRP B 740 HIS 0.002 0.000 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (17812) covalent geometry : angle 0.47109 / 0.26 (24100) hydrogen bonds : bond 0.04451 / 2.96 ( 1016) hydrogen bonds : angle 3.70036 / 2.67 ( 2940) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 539 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 700 GLN cc_start: 0.9189 (mt0) cc_final: 0.8955 (mt0) REVERT: D 700 GLN cc_start: 0.9194 (mt0) cc_final: 0.8959 (mt0) REVERT: B 700 GLN cc_start: 0.9196 (mt0) cc_final: 0.8962 (mt0) REVERT: C 700 GLN cc_start: 0.9196 (mt0) cc_final: 0.8961 (mt0) outliers start: 20 outliers final: 20 residues processed: 542 average time/residue: 0.3041 time to fit residues: 253.2146 Evaluate side-chains 551 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 531 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain D residue 703 ILE Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 703 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 56 optimal weight: 9.9990 chunk 98 optimal weight: 0.5980 chunk 157 optimal weight: 0.0470 chunk 61 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 162 optimal weight: 9.9990 chunk 191 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.166611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.111432 restraints weight = 71187.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.116762 restraints weight = 25529.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.119891 restraints weight = 14842.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.121591 restraints weight = 11273.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.122312 restraints weight = 9834.303| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17812 Z= 0.135 Angle : 0.459 4.785 24100 Z= 0.252 Chirality : 0.034 0.128 2700 Planarity : 0.003 0.027 2976 Dihedral : 7.163 76.407 2452 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 1.49 % Allowed : 8.40 % Favored : 90.11 % 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 (0.20), residues: 2120 helix: 2.93 (0.15), residues: 1264 sheet: -1.27 (0.52), residues: 92 loop : -1.23 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 743 TYR 0.008 0.001 TYR A 351 PHE 0.009 0.001 PHE A 649 TRP 0.004 0.000 TRP D 697 HIS 0.001 0.001 HIS B 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (17812) covalent geometry : angle 0.45871 / 0.25 (24100) hydrogen bonds : bond 0.04349 / 2.88 ( 1016) hydrogen bonds : angle 3.67182 / 2.65 ( 2940) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 544 time to evaluate : 0.900 Fit side-chains REVERT: A 700 GLN cc_start: 0.9168 (mt0) cc_final: 0.8942 (mt0) REVERT: D 700 GLN cc_start: 0.9172 (mt0) cc_final: 0.8945 (mt0) REVERT: B 700 GLN cc_start: 0.9174 (mt0) cc_final: 0.8945 (mt0) REVERT: C 700 GLN cc_start: 0.9173 (mt0) cc_final: 0.8944 (mt0) outliers start: 28 outliers final: 28 residues processed: 548 average time/residue: 0.2918 time to fit residues: 245.9870 Evaluate side-chains 572 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 544 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain D residue 703 ILE Chi-restraints excluded: chain D residue 708 THR Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain B residue 708 THR Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 703 ILE Chi-restraints excluded: chain C residue 708 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 92 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 186 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 166 optimal weight: 7.9990 chunk 197 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.167586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.111518 restraints weight = 70755.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.116726 restraints weight = 25938.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.119764 restraints weight = 15314.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.121422 restraints weight = 11754.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.122151 restraints weight = 10317.484| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 17812 Z= 0.148 Angle : 0.468 4.811 24100 Z= 0.257 Chirality : 0.034 0.124 2700 Planarity : 0.003 0.027 2976 Dihedral : 7.328 79.697 2452 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 1.44 % Allowed : 9.84 % Favored : 88.72 % 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: 1.95 (0.19), residues: 2120 helix: 2.90 (0.15), residues: 1260 sheet: -1.33 (0.50), residues: 92 loop : -1.23 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 743 TYR 0.008 0.001 TYR B 351 PHE 0.009 0.001 PHE A 649 TRP 0.005 0.001 TRP A 697 HIS 0.002 0.001 HIS B 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (17812) covalent geometry : angle 0.46783 / 0.26 (24100) hydrogen bonds : bond 0.04344 / 2.87 ( 1016) hydrogen bonds : angle 3.65663 / 2.64 ( 2940) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 549 time to evaluate : 0.790 Fit side-chains REVERT: A 700 GLN cc_start: 0.9208 (mt0) cc_final: 0.8947 (mt0) REVERT: A 743 ARG cc_start: 0.7809 (ttm-80) cc_final: 0.7541 (ttm-80) REVERT: D 700 GLN cc_start: 0.9212 (mt0) cc_final: 0.8948 (mt0) REVERT: D 743 ARG cc_start: 0.7813 (ttm-80) cc_final: 0.7544 (ttm-80) REVERT: B 700 GLN cc_start: 0.9213 (mt0) cc_final: 0.8949 (mt0) REVERT: B 743 ARG cc_start: 0.7816 (ttm-80) cc_final: 0.7549 (ttm-80) REVERT: C 700 GLN cc_start: 0.9210 (mt0) cc_final: 0.8945 (mt0) REVERT: C 743 ARG cc_start: 0.7818 (ttm-80) cc_final: 0.7549 (ttm-80) outliers start: 27 outliers final: 23 residues processed: 553 average time/residue: 0.2976 time to fit residues: 253.1898 Evaluate side-chains 569 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 546 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain D residue 684 GLU Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 681 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 8 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 chunk 39 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 148 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 156 optimal weight: 4.9990 chunk 173 optimal weight: 5.9990 chunk 174 optimal weight: 2.9990 chunk 208 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.164052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.108307 restraints weight = 71348.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.113377 restraints weight = 26339.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.116267 restraints weight = 15573.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.117858 restraints weight = 11999.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.118557 restraints weight = 10542.556| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 17812 Z= 0.222 Angle : 0.517 5.159 24100 Z= 0.289 Chirality : 0.036 0.126 2700 Planarity : 0.003 0.026 2976 Dihedral : 7.701 82.394 2452 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 1.65 % Allowed : 11.33 % Favored : 87.02 % 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: 1.61 (0.19), residues: 2120 helix: 2.58 (0.15), residues: 1260 sheet: -1.62 (0.49), residues: 92 loop : -1.26 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 743 TYR 0.011 0.001 TYR A 351 PHE 0.012 0.001 PHE A 649 TRP 0.004 0.001 TRP C 697 HIS 0.002 0.001 HIS A 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.22 (17812) covalent geometry : angle 0.51693 / 0.29 (24100) hydrogen bonds : bond 0.04966 / 3.29 ( 1016) hydrogen bonds : angle 3.87898 / 2.79 ( 2940) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 540 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 326 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8429 (mt-10) REVERT: A 646 ASP cc_start: 0.9049 (t0) cc_final: 0.8779 (t0) REVERT: A 700 GLN cc_start: 0.9244 (mt0) cc_final: 0.8993 (mt0) REVERT: A 743 ARG cc_start: 0.7874 (ttm-80) cc_final: 0.7590 (ttm-80) REVERT: D 326 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8439 (mt-10) REVERT: D 646 ASP cc_start: 0.9045 (t0) cc_final: 0.8776 (t0) REVERT: D 700 GLN cc_start: 0.9248 (mt0) cc_final: 0.8996 (mt0) REVERT: D 743 ARG cc_start: 0.7879 (ttm-80) cc_final: 0.7594 (ttm-80) REVERT: B 326 GLU cc_start: 0.8661 (mt-10) cc_final: 0.8449 (mt-10) REVERT: B 646 ASP cc_start: 0.9048 (t0) cc_final: 0.8784 (t0) REVERT: B 700 GLN cc_start: 0.9244 (mt0) cc_final: 0.8991 (mt0) REVERT: B 743 ARG cc_start: 0.7878 (ttm-80) cc_final: 0.7594 (ttm-80) REVERT: C 326 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8445 (mt-10) REVERT: C 646 ASP cc_start: 0.9044 (t0) cc_final: 0.8780 (t0) REVERT: C 700 GLN cc_start: 0.9248 (mt0) cc_final: 0.8995 (mt0) REVERT: C 743 ARG cc_start: 0.7883 (ttm-80) cc_final: 0.7597 (ttm-80) outliers start: 31 outliers final: 31 residues processed: 544 average time/residue: 0.2849 time to fit residues: 237.1491 Evaluate side-chains 565 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 534 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 679 ILE Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain D residue 708 THR Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 679 ILE Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 708 THR Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 708 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 198 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 201 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 157 optimal weight: 0.7980 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.164085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.108994 restraints weight = 71489.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.114145 restraints weight = 25709.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.117098 restraints weight = 14954.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.118731 restraints weight = 11433.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.119435 restraints weight = 10002.461| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 17812 Z= 0.167 Angle : 0.482 5.057 24100 Z= 0.265 Chirality : 0.035 0.148 2700 Planarity : 0.003 0.026 2976 Dihedral : 7.585 87.366 2452 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 1.38 % Allowed : 12.71 % Favored : 85.90 % 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: 2120 helix: 2.69 (0.15), residues: 1264 sheet: -1.59 (0.49), residues: 92 loop : -1.22 (0.24), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 701 TYR 0.009 0.001 TYR A 351 PHE 0.009 0.001 PHE A 649 TRP 0.004 0.001 TRP A 697 HIS 0.001 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 (17812) covalent geometry : angle 0.48162 / 0.26 (24100) hydrogen bonds : bond 0.04570 / 3.02 ( 1016) hydrogen bonds : angle 3.74914 / 2.70 ( 2940) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 545 time to evaluate : 0.854 Fit side-chains revert: symmetry clash REVERT: A 326 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8377 (mt-10) REVERT: A 646 ASP cc_start: 0.9037 (t0) cc_final: 0.8753 (t0) REVERT: A 700 GLN cc_start: 0.9246 (mt0) cc_final: 0.8985 (mt0) REVERT: A 743 ARG cc_start: 0.7880 (ttm-80) cc_final: 0.7584 (ttm-80) REVERT: D 326 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8394 (mt-10) REVERT: D 646 ASP cc_start: 0.9032 (t0) cc_final: 0.8750 (t0) REVERT: D 700 GLN cc_start: 0.9264 (mt0) cc_final: 0.9002 (mt0) REVERT: D 743 ARG cc_start: 0.7887 (ttm-80) cc_final: 0.7590 (ttm-80) REVERT: B 326 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8411 (mt-10) REVERT: B 646 ASP cc_start: 0.9026 (t0) cc_final: 0.8745 (t0) REVERT: B 700 GLN cc_start: 0.9248 (mt0) cc_final: 0.8986 (mt0) REVERT: B 743 ARG cc_start: 0.7883 (ttm-80) cc_final: 0.7588 (ttm-80) REVERT: C 326 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8399 (mt-10) REVERT: C 646 ASP cc_start: 0.9026 (t0) cc_final: 0.8746 (t0) REVERT: C 700 GLN cc_start: 0.9262 (mt0) cc_final: 0.8998 (mt0) REVERT: C 743 ARG cc_start: 0.7890 (ttm-80) cc_final: 0.7592 (ttm-80) outliers start: 26 outliers final: 26 residues processed: 550 average time/residue: 0.2811 time to fit residues: 237.0904 Evaluate side-chains 563 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 537 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain D residue 684 GLU Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 684 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 128 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 138 optimal weight: 0.6980 chunk 8 optimal weight: 4.9990 chunk 201 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 172 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.165519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.109975 restraints weight = 71473.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.115210 restraints weight = 25720.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.118253 restraints weight = 14997.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.119846 restraints weight = 11462.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.120574 restraints weight = 10069.592| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17812 Z= 0.129 Angle : 0.462 5.268 24100 Z= 0.251 Chirality : 0.035 0.142 2700 Planarity : 0.003 0.027 2976 Dihedral : 7.378 81.639 2452 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 1.49 % Allowed : 14.04 % Favored : 84.47 % 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: 1.95 (0.20), residues: 2120 helix: 2.87 (0.15), residues: 1264 sheet: -1.55 (0.48), residues: 92 loop : -1.16 (0.24), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 701 TYR 0.007 0.001 TYR C 351 PHE 0.008 0.001 PHE A 649 TRP 0.006 0.001 TRP D 697 HIS 0.001 0.000 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (17812) covalent geometry : angle 0.46171 / 0.25 (24100) hydrogen bonds : bond 0.04234 / 2.79 ( 1016) hydrogen bonds : angle 3.62863 / 2.61 ( 2940) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 544 time to evaluate : 0.884 Fit side-chains revert: symmetry clash REVERT: A 325 LEU cc_start: 0.9029 (tp) cc_final: 0.8814 (tp) REVERT: A 326 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8367 (mt-10) REVERT: A 700 GLN cc_start: 0.9202 (mt0) cc_final: 0.8963 (mt0) REVERT: A 743 ARG cc_start: 0.7816 (ttm-80) cc_final: 0.7508 (ttm-80) REVERT: D 325 LEU cc_start: 0.9030 (tp) cc_final: 0.8816 (tp) REVERT: D 326 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8344 (mt-10) REVERT: D 700 GLN cc_start: 0.9218 (mt0) cc_final: 0.8964 (mt0) REVERT: D 743 ARG cc_start: 0.7818 (ttm-80) cc_final: 0.7508 (ttm-80) REVERT: B 325 LEU cc_start: 0.9031 (tp) cc_final: 0.8819 (tp) REVERT: B 646 ASP cc_start: 0.9040 (t0) cc_final: 0.8741 (t0) REVERT: B 700 GLN cc_start: 0.9217 (mt0) cc_final: 0.8975 (mt0) REVERT: B 743 ARG cc_start: 0.7820 (ttm-80) cc_final: 0.7509 (ttm-80) REVERT: C 325 LEU cc_start: 0.9032 (tp) cc_final: 0.8817 (tp) REVERT: C 326 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8352 (mt-10) REVERT: C 646 ASP cc_start: 0.9040 (t0) cc_final: 0.8749 (t0) REVERT: C 700 GLN cc_start: 0.9220 (mt0) cc_final: 0.8964 (mt0) REVERT: C 743 ARG cc_start: 0.7822 (ttm-80) cc_final: 0.7508 (ttm-80) outliers start: 28 outliers final: 28 residues processed: 552 average time/residue: 0.2909 time to fit residues: 247.8651 Evaluate side-chains 570 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 542 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain D residue 684 GLU Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 684 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 128 optimal weight: 0.9990 chunk 64 optimal weight: 7.9990 chunk 139 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 160 optimal weight: 8.9990 chunk 21 optimal weight: 0.5980 chunk 141 optimal weight: 1.9990 chunk 180 optimal weight: 4.9990 chunk 181 optimal weight: 0.9990 chunk 104 optimal weight: 6.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.165621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.109876 restraints weight = 71483.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.115126 restraints weight = 25868.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.118126 restraints weight = 15100.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.119612 restraints weight = 11560.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.120569 restraints weight = 10184.482| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17812 Z= 0.132 Angle : 0.466 5.323 24100 Z= 0.253 Chirality : 0.035 0.144 2700 Planarity : 0.003 0.026 2976 Dihedral : 7.062 85.720 2452 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 1.49 % Allowed : 14.04 % Favored : 84.47 % 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: 1.96 (0.20), residues: 2120 helix: 2.88 (0.15), residues: 1264 sheet: -1.54 (0.48), residues: 92 loop : -1.17 (0.24), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 743 TYR 0.008 0.001 TYR D 653 PHE 0.008 0.001 PHE A 649 TRP 0.005 0.001 TRP A 697 HIS 0.001 0.000 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (17812) covalent geometry : angle 0.46643 / 0.25 (24100) hydrogen bonds : bond 0.04180 / 2.76 ( 1016) hydrogen bonds : angle 3.60440 / 2.60 ( 2940) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 546 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 325 LEU cc_start: 0.9024 (tp) cc_final: 0.8808 (tp) REVERT: A 326 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8376 (mt-10) REVERT: A 601 ASP cc_start: 0.8419 (p0) cc_final: 0.8079 (p0) REVERT: A 700 GLN cc_start: 0.9216 (mt0) cc_final: 0.8982 (mt0) REVERT: A 743 ARG cc_start: 0.7855 (ttm-80) cc_final: 0.7541 (ttm-80) REVERT: D 325 LEU cc_start: 0.9024 (tp) cc_final: 0.8807 (tp) REVERT: D 326 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8352 (mt-10) REVERT: D 601 ASP cc_start: 0.8417 (p0) cc_final: 0.8078 (p0) REVERT: D 700 GLN cc_start: 0.9221 (mt0) cc_final: 0.8973 (mt0) REVERT: D 743 ARG cc_start: 0.7859 (ttm-80) cc_final: 0.7543 (ttm-80) REVERT: B 325 LEU cc_start: 0.9027 (tp) cc_final: 0.8816 (tp) REVERT: B 700 GLN cc_start: 0.9222 (mt0) cc_final: 0.8971 (mt0) REVERT: B 743 ARG cc_start: 0.7856 (ttm-80) cc_final: 0.7547 (ttm-80) REVERT: C 325 LEU cc_start: 0.9024 (tp) cc_final: 0.8807 (tp) REVERT: C 326 GLU cc_start: 0.8661 (mt-10) cc_final: 0.8360 (mt-10) REVERT: C 646 ASP cc_start: 0.9034 (t0) cc_final: 0.8739 (t0) REVERT: C 700 GLN cc_start: 0.9224 (mt0) cc_final: 0.8972 (mt0) REVERT: C 743 ARG cc_start: 0.7858 (ttm-80) cc_final: 0.7544 (ttm-80) outliers start: 28 outliers final: 26 residues processed: 556 average time/residue: 0.2902 time to fit residues: 249.9919 Evaluate side-chains 568 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 542 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain D residue 684 GLU Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 684 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 167 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 16 optimal weight: 0.0270 chunk 1 optimal weight: 0.8980 chunk 177 optimal weight: 6.9990 chunk 157 optimal weight: 3.9990 chunk 145 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.165534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.110143 restraints weight = 71111.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.115312 restraints weight = 25626.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.118361 restraints weight = 14974.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.119841 restraints weight = 11399.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.120838 restraints weight = 10029.237| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17812 Z= 0.138 Angle : 0.477 5.324 24100 Z= 0.259 Chirality : 0.035 0.146 2700 Planarity : 0.003 0.027 2976 Dihedral : 6.721 76.777 2452 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 1.76 % Allowed : 14.26 % Favored : 83.99 % 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: 1.97 (0.20), residues: 2120 helix: 2.88 (0.15), residues: 1264 sheet: -1.57 (0.48), residues: 92 loop : -1.16 (0.24), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 280 TYR 0.008 0.001 TYR B 653 PHE 0.009 0.001 PHE D 649 TRP 0.005 0.000 TRP A 697 HIS 0.001 0.000 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (17812) covalent geometry : angle 0.47695 / 0.26 (24100) hydrogen bonds : bond 0.04188 / 2.76 ( 1016) hydrogen bonds : angle 3.60450 / 2.59 ( 2940) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 546 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 LEU cc_start: 0.9015 (tp) cc_final: 0.8813 (tp) REVERT: A 326 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8396 (mt-10) REVERT: A 411 ASP cc_start: 0.8590 (p0) cc_final: 0.7698 (t0) REVERT: A 700 GLN cc_start: 0.9237 (mt0) cc_final: 0.9006 (mt0) REVERT: A 743 ARG cc_start: 0.7847 (ttm-80) cc_final: 0.7533 (ttm-80) REVERT: D 325 LEU cc_start: 0.9018 (tp) cc_final: 0.8801 (tp) REVERT: D 326 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8349 (mt-10) REVERT: D 411 ASP cc_start: 0.8586 (p0) cc_final: 0.7697 (t0) REVERT: D 700 GLN cc_start: 0.9244 (mt0) cc_final: 0.9013 (mt0) REVERT: D 743 ARG cc_start: 0.7852 (ttm-80) cc_final: 0.7537 (ttm-80) REVERT: B 326 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8362 (mt-10) REVERT: B 411 ASP cc_start: 0.8591 (p0) cc_final: 0.7707 (t0) REVERT: B 646 ASP cc_start: 0.9021 (t0) cc_final: 0.8753 (t0) REVERT: B 700 GLN cc_start: 0.9239 (mt0) cc_final: 0.9006 (mt0) REVERT: B 743 ARG cc_start: 0.7851 (ttm-80) cc_final: 0.7536 (ttm-80) REVERT: C 325 LEU cc_start: 0.9026 (tp) cc_final: 0.8808 (tp) REVERT: C 326 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8351 (mt-10) REVERT: C 646 ASP cc_start: 0.9020 (t0) cc_final: 0.8758 (t0) REVERT: C 700 GLN cc_start: 0.9242 (mt0) cc_final: 0.9006 (mt0) REVERT: C 743 ARG cc_start: 0.7851 (ttm-80) cc_final: 0.7535 (ttm-80) outliers start: 33 outliers final: 32 residues processed: 557 average time/residue: 0.2980 time to fit residues: 252.6327 Evaluate side-chains 580 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 548 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 681 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 26 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 104 optimal weight: 0.0570 chunk 181 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 83 optimal weight: 0.0870 chunk 142 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 chunk 155 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.9880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.166472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.111354 restraints weight = 71376.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.116525 restraints weight = 26231.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.119527 restraints weight = 15414.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.121128 restraints weight = 11781.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.121826 restraints weight = 10357.615| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17812 Z= 0.124 Angle : 0.470 5.512 24100 Z= 0.254 Chirality : 0.034 0.136 2700 Planarity : 0.003 0.027 2976 Dihedral : 6.231 62.365 2452 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 1.33 % Allowed : 15.11 % Favored : 83.56 % 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 (0.20), residues: 2120 helix: 2.95 (0.15), residues: 1264 sheet: -1.53 (0.48), residues: 92 loop : -1.17 (0.24), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 409 TYR 0.008 0.001 TYR D 653 PHE 0.007 0.001 PHE C 659 TRP 0.006 0.001 TRP C 697 HIS 0.001 0.000 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (17812) covalent geometry : angle 0.47002 / 0.25 (24100) hydrogen bonds : bond 0.04043 / 2.67 ( 1016) hydrogen bonds : angle 3.55086 / 2.55 ( 2940) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 549 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8372 (mt-10) REVERT: A 646 ASP cc_start: 0.8922 (t0) cc_final: 0.8689 (t0) REVERT: A 700 GLN cc_start: 0.9199 (mt0) cc_final: 0.8966 (mt0) REVERT: A 743 ARG cc_start: 0.7791 (ttm-80) cc_final: 0.7478 (ttm-80) REVERT: D 411 ASP cc_start: 0.8587 (p0) cc_final: 0.7628 (t0) REVERT: D 646 ASP cc_start: 0.8916 (t0) cc_final: 0.8688 (t0) REVERT: D 700 GLN cc_start: 0.9206 (mt0) cc_final: 0.8976 (mt0) REVERT: D 743 ARG cc_start: 0.7794 (ttm-80) cc_final: 0.7477 (ttm-80) REVERT: B 326 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8364 (mt-10) REVERT: B 646 ASP cc_start: 0.9043 (t0) cc_final: 0.8729 (t0) REVERT: B 700 GLN cc_start: 0.9208 (mt0) cc_final: 0.8973 (mt0) REVERT: B 743 ARG cc_start: 0.7792 (ttm-80) cc_final: 0.7477 (ttm-80) REVERT: C 646 ASP cc_start: 0.9034 (t0) cc_final: 0.8730 (t0) REVERT: C 700 GLN cc_start: 0.9202 (mt0) cc_final: 0.8969 (mt0) REVERT: C 743 ARG cc_start: 0.7795 (ttm-80) cc_final: 0.7478 (ttm-80) outliers start: 25 outliers final: 25 residues processed: 561 average time/residue: 0.2990 time to fit residues: 256.2424 Evaluate side-chains 575 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 550 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 681 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 72 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 195 optimal weight: 1.9990 chunk 139 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.165430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.109734 restraints weight = 71729.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.114959 restraints weight = 25950.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.117983 restraints weight = 15110.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.119572 restraints weight = 11533.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.120274 restraints weight = 10138.113| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17812 Z= 0.152 Angle : 0.487 5.527 24100 Z= 0.265 Chirality : 0.035 0.121 2700 Planarity : 0.003 0.026 2976 Dihedral : 6.284 57.670 2452 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 1.70 % Allowed : 15.11 % Favored : 83.19 % 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: 1.96 (0.20), residues: 2120 helix: 2.88 (0.15), residues: 1264 sheet: -1.60 (0.47), residues: 92 loop : -1.17 (0.24), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 409 TYR 0.009 0.001 TYR B 653 PHE 0.009 0.001 PHE B 649 TRP 0.005 0.000 TRP B 697 HIS 0.001 0.000 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (17812) covalent geometry : angle 0.48657 / 0.26 (24100) hydrogen bonds : bond 0.04229 / 2.79 ( 1016) hydrogen bonds : angle 3.61667 / 2.60 ( 2940) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6625.07 seconds wall clock time: 113 minutes 23.42 seconds (6803.42 seconds total)