Starting phenix.real_space_refine on Wed May 6 02:21:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t0c_40940/05_2026/8t0c_40940_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t0c_40940/05_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 { model { file = "/net/cci-nas-00/data/ceres_data/8t0c_40940/05_2026/8t0c_40940_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t0c_40940/05_2026/8t0c_40940_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t0c_40940/05_2026/8t0c_40940.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t0c_40940/05_2026/8t0c_40940.map" } 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-2.1rc2-6044/lib/python3.9/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, 27 Unusual residues: {' NA': 2, 'NKN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 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: 6.04, per 1000 atoms: 0.17 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: 4.07 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.77 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: 8.08 Time building geometry restraints manager: 5.52 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: 5.360 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: 0.200 Extract box with map and model: 0.460 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 33.950 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 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 covalent geometry : bond 0.00588 (17812) covalent geometry : angle 1.00455 (24100) hydrogen bonds : bond 0.12007 ( 1016) hydrogen bonds : angle 4.40407 ( 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 : 0.937 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: 0.3146 time to fit residues: 241.7919 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 : 0.713 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3941 r_free = 0.3941 target = 0.167861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.113114 restraints weight = 70983.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.118595 restraints weight = 25185.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.121798 restraints weight = 14512.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.123316 restraints weight = 10987.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.124298 restraints weight = 9678.640| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.0861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17812 Z= 0.113 Angle : 0.471 5.564 24100 Z= 0.255 Chirality : 0.034 0.134 2700 Planarity : 0.003 0.030 2976 Dihedral : 7.122 76.163 2452 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 1.28 % Allowed : 6.76 % Favored : 91.97 % 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: -1.03 (0.56), residues: 92 loop : -1.13 (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 C 351 PHE 0.009 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 covalent geometry : bond 0.00243 (17812) covalent geometry : angle 0.47115 (24100) hydrogen bonds : bond 0.04480 ( 1016) hydrogen bonds : angle 3.70436 ( 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 563 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 539 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 700 GLN cc_start: 0.9142 (mt0) cc_final: 0.8910 (mt0) REVERT: D 700 GLN cc_start: 0.9149 (mt0) cc_final: 0.8915 (mt0) REVERT: B 700 GLN cc_start: 0.9149 (mt0) cc_final: 0.8917 (mt0) REVERT: C 700 GLN cc_start: 0.9148 (mt0) cc_final: 0.8914 (mt0) outliers start: 24 outliers final: 24 residues processed: 542 average time/residue: 0.3171 time to fit residues: 261.0679 Evaluate side-chains 557 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 533 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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 592 SER 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 592 SER 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 592 SER 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 592 SER 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: 10.0000 chunk 98 optimal weight: 0.8980 chunk 157 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 162 optimal weight: 9.9990 chunk 191 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.164969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.109903 restraints weight = 71288.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.115179 restraints weight = 25509.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.118196 restraints weight = 14814.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.119860 restraints weight = 11329.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.120584 restraints weight = 9904.339| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 17812 Z= 0.168 Angle : 0.480 4.816 24100 Z= 0.266 Chirality : 0.035 0.127 2700 Planarity : 0.003 0.026 2976 Dihedral : 7.326 76.952 2452 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 1.60 % Allowed : 8.62 % Favored : 89.79 % 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: 1.88 (0.19), residues: 2120 helix: 2.82 (0.15), residues: 1264 sheet: -1.38 (0.52), residues: 92 loop : -1.25 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 743 TYR 0.009 0.001 TYR B 351 PHE 0.010 0.001 PHE A 649 TRP 0.004 0.001 TRP D 697 HIS 0.002 0.001 HIS B 410 Details of bonding type rmsd covalent geometry : bond 0.00370 (17812) covalent geometry : angle 0.47995 (24100) hydrogen bonds : bond 0.04629 ( 1016) hydrogen bonds : angle 3.76195 ( 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 582 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 552 time to evaluate : 0.938 Fit side-chains REVERT: A 700 GLN cc_start: 0.9206 (mt0) cc_final: 0.8967 (mt0) REVERT: D 700 GLN cc_start: 0.9212 (mt0) cc_final: 0.8970 (mt0) REVERT: B 700 GLN cc_start: 0.9211 (mt0) cc_final: 0.8971 (mt0) REVERT: C 700 GLN cc_start: 0.9211 (mt0) cc_final: 0.8969 (mt0) outliers start: 30 outliers final: 30 residues processed: 556 average time/residue: 0.3055 time to fit residues: 257.7884 Evaluate side-chains 582 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 552 time to evaluate : 0.921 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 92 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 186 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 197 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.166906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.110890 restraints weight = 70802.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.116091 restraints weight = 25792.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.119131 restraints weight = 15228.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.120618 restraints weight = 11708.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.121571 restraints weight = 10359.449| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1266 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= 0.150 Angle : 0.467 4.751 24100 Z= 0.257 Chirality : 0.035 0.125 2700 Planarity : 0.003 0.033 2976 Dihedral : 7.384 80.041 2452 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.33 % Allowed : 10.48 % Favored : 88.19 % 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: 1.91 (0.19), residues: 2120 helix: 2.88 (0.15), residues: 1260 sheet: -1.43 (0.50), residues: 92 loop : -1.26 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 743 TYR 0.008 0.001 TYR D 351 PHE 0.009 0.001 PHE B 649 TRP 0.005 0.001 TRP A 697 HIS 0.002 0.001 HIS B 410 Details of bonding type rmsd covalent geometry : bond 0.00327 (17812) covalent geometry : angle 0.46737 (24100) hydrogen bonds : bond 0.04404 ( 1016) hydrogen bonds : angle 3.67045 ( 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 579 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 554 time to evaluate : 0.946 Fit side-chains REVERT: A 700 GLN cc_start: 0.9217 (mt0) cc_final: 0.8967 (mt0) REVERT: D 700 GLN cc_start: 0.9222 (mt0) cc_final: 0.8983 (mt0) REVERT: B 293 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8642 (mt-10) REVERT: B 700 GLN cc_start: 0.9220 (mt0) cc_final: 0.8968 (mt0) REVERT: C 293 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8646 (mt-10) REVERT: C 700 GLN cc_start: 0.9219 (mt0) cc_final: 0.8980 (mt0) outliers start: 25 outliers final: 23 residues processed: 558 average time/residue: 0.3116 time to fit residues: 264.8490 Evaluate side-chains 577 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 554 time to evaluate : 0.901 ------------------------------------------------------------------------------- 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: 4.9990 chunk 147 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 39 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 148 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 156 optimal weight: 7.9990 chunk 173 optimal weight: 5.9990 chunk 174 optimal weight: 0.9990 chunk 208 optimal weight: 3.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.165006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.115744 restraints weight = 71375.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.118329 restraints weight = 34137.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.118740 restraints weight = 20877.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.119515 restraints weight = 15175.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.119658 restraints weight = 13949.295| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 17812 Z= 0.190 Angle : 0.493 4.736 24100 Z= 0.274 Chirality : 0.035 0.123 2700 Planarity : 0.003 0.040 2976 Dihedral : 7.570 82.975 2452 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 1.76 % Allowed : 11.44 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.19), residues: 2120 helix: 2.74 (0.15), residues: 1260 sheet: -1.54 (0.49), residues: 92 loop : -1.28 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 743 TYR 0.010 0.001 TYR D 351 PHE 0.011 0.001 PHE D 649 TRP 0.004 0.001 TRP C 697 HIS 0.002 0.001 HIS B 410 Details of bonding type rmsd covalent geometry : bond 0.00422 (17812) covalent geometry : angle 0.49293 (24100) hydrogen bonds : bond 0.04675 ( 1016) hydrogen bonds : angle 3.77758 ( 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 578 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 545 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8342 (mt-10) REVERT: A 411 ASP cc_start: 0.8359 (p0) cc_final: 0.7867 (t0) REVERT: A 427 ASP cc_start: 0.8706 (t0) cc_final: 0.8438 (t0) REVERT: A 646 ASP cc_start: 0.9023 (t0) cc_final: 0.8553 (t0) REVERT: A 700 GLN cc_start: 0.9285 (mt0) cc_final: 0.9032 (mt0) REVERT: D 326 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8341 (mt-10) REVERT: D 411 ASP cc_start: 0.8356 (p0) cc_final: 0.7861 (t0) REVERT: D 427 ASP cc_start: 0.8703 (t0) cc_final: 0.8436 (t0) REVERT: D 646 ASP cc_start: 0.9040 (t0) cc_final: 0.8566 (t0) REVERT: D 700 GLN cc_start: 0.9286 (mt0) cc_final: 0.9033 (mt0) REVERT: B 326 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8348 (mt-10) REVERT: B 411 ASP cc_start: 0.8358 (p0) cc_final: 0.7872 (t0) REVERT: B 427 ASP cc_start: 0.8769 (t0) cc_final: 0.8569 (t0) REVERT: B 646 ASP cc_start: 0.9036 (t0) cc_final: 0.8559 (t0) REVERT: B 700 GLN cc_start: 0.9286 (mt0) cc_final: 0.9033 (mt0) REVERT: C 326 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8345 (mt-10) REVERT: C 411 ASP cc_start: 0.8357 (p0) cc_final: 0.7870 (t0) REVERT: C 427 ASP cc_start: 0.8768 (t0) cc_final: 0.8566 (t0) REVERT: C 646 ASP cc_start: 0.9044 (t0) cc_final: 0.8567 (t0) REVERT: C 700 GLN cc_start: 0.9289 (mt0) cc_final: 0.9034 (mt0) outliers start: 33 outliers final: 31 residues processed: 549 average time/residue: 0.3115 time to fit residues: 257.7855 Evaluate side-chains 579 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 548 time to evaluate : 0.804 ------------------------------------------------------------------------------- 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 681 LEU Chi-restraints excluded: chain A residue 684 GLU 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 681 LEU Chi-restraints excluded: chain D residue 684 GLU 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 681 LEU Chi-restraints excluded: chain B residue 684 GLU 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: 0.9980 chunk 33 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 201 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 51 optimal weight: 0.2980 chunk 157 optimal weight: 7.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.165738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.110436 restraints weight = 71223.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.115680 restraints weight = 25500.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.118714 restraints weight = 14833.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.120271 restraints weight = 11304.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.121148 restraints weight = 9936.887| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1474 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= 0.126 Angle : 0.459 5.120 24100 Z= 0.250 Chirality : 0.035 0.149 2700 Planarity : 0.003 0.044 2976 Dihedral : 7.449 89.348 2452 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 1.22 % Allowed : 12.77 % Favored : 86.01 % 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: 2.95 (0.15), residues: 1260 sheet: -1.40 (0.49), residues: 92 loop : -1.23 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 743 TYR 0.007 0.001 TYR D 351 PHE 0.007 0.001 PHE A 649 TRP 0.006 0.001 TRP D 697 HIS 0.001 0.000 HIS D 378 Details of bonding type rmsd covalent geometry : bond 0.00276 (17812) covalent geometry : angle 0.45852 (24100) hydrogen bonds : bond 0.04203 ( 1016) hydrogen bonds : angle 3.58643 ( 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 572 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 549 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 326 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8356 (mt-10) REVERT: A 491 ARG cc_start: 0.5964 (ttp-170) cc_final: 0.5694 (ttp80) REVERT: A 700 GLN cc_start: 0.9222 (mt0) cc_final: 0.8965 (mt0) REVERT: D 326 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8357 (mt-10) REVERT: D 491 ARG cc_start: 0.5963 (ttp-170) cc_final: 0.5690 (ttp80) REVERT: D 700 GLN cc_start: 0.9225 (mt0) cc_final: 0.8968 (mt0) REVERT: B 491 ARG cc_start: 0.5965 (ttp-170) cc_final: 0.5693 (ttp80) REVERT: B 700 GLN cc_start: 0.9224 (mt0) cc_final: 0.8967 (mt0) REVERT: C 326 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8347 (mt-10) REVERT: C 491 ARG cc_start: 0.5965 (ttp-170) cc_final: 0.5690 (ttp80) REVERT: C 700 GLN cc_start: 0.9223 (mt0) cc_final: 0.8965 (mt0) outliers start: 23 outliers final: 23 residues processed: 553 average time/residue: 0.3053 time to fit residues: 256.5073 Evaluate side-chains 568 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 545 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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=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: 0.5980 chunk 8 optimal weight: 3.9990 chunk 201 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 172 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 chunk 200 optimal weight: 0.4980 chunk 52 optimal weight: 7.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.166966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.111535 restraints weight = 71345.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.116807 restraints weight = 25458.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.119930 restraints weight = 14836.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.121594 restraints weight = 11274.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.122315 restraints weight = 9880.736| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17812 Z= 0.108 Angle : 0.447 5.241 24100 Z= 0.242 Chirality : 0.034 0.139 2700 Planarity : 0.003 0.047 2976 Dihedral : 7.101 84.859 2452 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 1.01 % Allowed : 14.04 % Favored : 84.95 % 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: 2.11 (0.20), residues: 2120 helix: 3.04 (0.15), residues: 1260 sheet: -1.35 (0.48), residues: 92 loop : -1.20 (0.24), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 743 TYR 0.008 0.001 TYR C 653 PHE 0.007 0.001 PHE A 649 TRP 0.005 0.001 TRP D 697 HIS 0.001 0.000 HIS C 378 Details of bonding type rmsd covalent geometry : bond 0.00234 (17812) covalent geometry : angle 0.44655 (24100) hydrogen bonds : bond 0.03920 ( 1016) hydrogen bonds : angle 3.50056 ( 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 559 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 540 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 491 ARG cc_start: 0.5943 (ttp-170) cc_final: 0.5676 (ttp80) REVERT: A 601 ASP cc_start: 0.8358 (p0) cc_final: 0.7994 (p0) REVERT: A 700 GLN cc_start: 0.9215 (mt0) cc_final: 0.8960 (mt0) REVERT: D 491 ARG cc_start: 0.5940 (ttp-170) cc_final: 0.5674 (ttp80) REVERT: D 601 ASP cc_start: 0.8355 (p0) cc_final: 0.7996 (p0) REVERT: D 700 GLN cc_start: 0.9208 (mt0) cc_final: 0.8953 (mt0) REVERT: B 491 ARG cc_start: 0.5945 (ttp-170) cc_final: 0.5674 (ttp80) REVERT: B 601 ASP cc_start: 0.8353 (p0) cc_final: 0.8075 (p0) REVERT: B 700 GLN cc_start: 0.9218 (mt0) cc_final: 0.8960 (mt0) REVERT: C 491 ARG cc_start: 0.5942 (ttp-170) cc_final: 0.5675 (ttp80) REVERT: C 601 ASP cc_start: 0.8354 (p0) cc_final: 0.8074 (p0) REVERT: C 700 GLN cc_start: 0.9207 (mt0) cc_final: 0.8950 (mt0) outliers start: 19 outliers final: 15 residues processed: 548 average time/residue: 0.3070 time to fit residues: 254.8106 Evaluate side-chains 551 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 536 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain D residue 527 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 527 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 527 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: 1.9990 chunk 64 optimal weight: 2.9990 chunk 139 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 160 optimal weight: 6.9990 chunk 21 optimal weight: 0.0070 chunk 141 optimal weight: 1.9990 chunk 180 optimal weight: 0.0870 chunk 181 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 overall best weight: 0.5576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 676 ASN C 676 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.168247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.112808 restraints weight = 71351.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.118187 restraints weight = 25529.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.121260 restraints weight = 14830.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.122965 restraints weight = 11316.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.123729 restraints weight = 9898.166| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17812 Z= 0.098 Angle : 0.450 5.175 24100 Z= 0.240 Chirality : 0.034 0.134 2700 Planarity : 0.003 0.050 2976 Dihedral : 6.438 80.410 2452 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.22 % Allowed : 14.63 % Favored : 84.15 % 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: 2.19 (0.20), residues: 2120 helix: 3.09 (0.15), residues: 1264 sheet: -1.36 (0.48), residues: 92 loop : -1.16 (0.24), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 743 TYR 0.006 0.001 TYR C 653 PHE 0.007 0.001 PHE D 659 TRP 0.004 0.000 TRP D 740 HIS 0.002 0.000 HIS B 410 Details of bonding type rmsd covalent geometry : bond 0.00212 (17812) covalent geometry : angle 0.45014 (24100) hydrogen bonds : bond 0.03682 ( 1016) hydrogen bonds : angle 3.42469 ( 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 554 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 531 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 601 ASP cc_start: 0.8326 (p0) cc_final: 0.7967 (p0) REVERT: A 700 GLN cc_start: 0.9204 (mt0) cc_final: 0.8971 (mt0) REVERT: D 601 ASP cc_start: 0.8323 (p0) cc_final: 0.7964 (p0) REVERT: D 700 GLN cc_start: 0.9205 (mt0) cc_final: 0.8971 (mt0) REVERT: B 491 ARG cc_start: 0.5972 (ttp-170) cc_final: 0.5706 (ttp80) REVERT: B 700 GLN cc_start: 0.9208 (mt0) cc_final: 0.8968 (mt0) REVERT: C 700 GLN cc_start: 0.9206 (mt0) cc_final: 0.8966 (mt0) outliers start: 23 outliers final: 18 residues processed: 540 average time/residue: 0.3039 time to fit residues: 248.9094 Evaluate side-chains 543 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 525 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 527 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 673 LEU Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain B residue 527 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 B residue 684 GLU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 527 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 167 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 177 optimal weight: 6.9990 chunk 157 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 173 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.162075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.106707 restraints weight = 71747.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.111683 restraints weight = 26159.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.114617 restraints weight = 15396.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.116019 restraints weight = 11790.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.116896 restraints weight = 10435.110| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 17812 Z= 0.265 Angle : 0.560 5.542 24100 Z= 0.314 Chirality : 0.038 0.149 2700 Planarity : 0.004 0.050 2976 Dihedral : 7.209 80.848 2452 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 1.65 % Allowed : 14.84 % Favored : 83.51 % 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: 1.57 (0.19), residues: 2120 helix: 2.53 (0.15), residues: 1264 sheet: -1.66 (0.48), residues: 92 loop : -1.26 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 743 TYR 0.014 0.001 TYR B 530 PHE 0.015 0.001 PHE C 649 TRP 0.007 0.001 TRP C 549 HIS 0.002 0.001 HIS C 364 Details of bonding type rmsd covalent geometry : bond 0.00590 (17812) covalent geometry : angle 0.55961 (24100) hydrogen bonds : bond 0.05040 ( 1016) hydrogen bonds : angle 3.91019 ( 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: 31 poor density : 548 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 ASP cc_start: 0.8575 (p0) cc_final: 0.7701 (t0) REVERT: A 646 ASP cc_start: 0.9044 (t0) cc_final: 0.8626 (t0) REVERT: A 700 GLN cc_start: 0.9268 (mt0) cc_final: 0.9029 (mt0) REVERT: D 411 ASP cc_start: 0.8584 (p0) cc_final: 0.7703 (t0) REVERT: D 646 ASP cc_start: 0.9037 (t0) cc_final: 0.8627 (t0) REVERT: D 700 GLN cc_start: 0.9268 (mt0) cc_final: 0.9013 (mt0) REVERT: B 411 ASP cc_start: 0.8577 (p0) cc_final: 0.7701 (t0) REVERT: B 646 ASP cc_start: 0.9033 (t0) cc_final: 0.8794 (t0) REVERT: B 700 GLN cc_start: 0.9264 (mt0) cc_final: 0.9027 (mt0) REVERT: C 411 ASP cc_start: 0.8572 (p0) cc_final: 0.7701 (t0) REVERT: C 511 TYR cc_start: 0.8960 (t80) cc_final: 0.8748 (t80) REVERT: C 646 ASP cc_start: 0.9055 (t0) cc_final: 0.8823 (t0) REVERT: C 700 GLN cc_start: 0.9263 (mt0) cc_final: 0.9008 (mt0) outliers start: 31 outliers final: 29 residues processed: 554 average time/residue: 0.3064 time to fit residues: 256.1117 Evaluate side-chains 577 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 548 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 LEU 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 678 LEU Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain D residue 524 LEU 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 678 LEU Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain B residue 524 LEU 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 678 LEU Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 527 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: 0.7980 chunk 76 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 142 optimal weight: 0.7980 chunk 113 optimal weight: 0.6980 chunk 155 optimal weight: 0.0170 chunk 41 optimal weight: 0.9990 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.166805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.111230 restraints weight = 71414.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.116504 restraints weight = 25490.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.119585 restraints weight = 14836.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.121178 restraints weight = 11313.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.121897 restraints weight = 9967.418| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17812 Z= 0.108 Angle : 0.474 5.726 24100 Z= 0.254 Chirality : 0.034 0.127 2700 Planarity : 0.003 0.048 2976 Dihedral : 6.285 63.550 2452 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 1.01 % Allowed : 15.43 % 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: 2.02 (0.20), residues: 2120 helix: 2.96 (0.15), residues: 1264 sheet: -1.54 (0.48), residues: 92 loop : -1.22 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 743 TYR 0.018 0.001 TYR B 511 PHE 0.007 0.001 PHE C 429 TRP 0.007 0.001 TRP C 697 HIS 0.001 0.000 HIS C 378 Details of bonding type rmsd covalent geometry : bond 0.00237 (17812) covalent geometry : angle 0.47415 (24100) hydrogen bonds : bond 0.04050 ( 1016) hydrogen bonds : angle 3.52799 ( 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 557 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 538 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 ASP cc_start: 0.8394 (p0) cc_final: 0.8014 (p0) REVERT: A 700 GLN cc_start: 0.9216 (mt0) cc_final: 0.8973 (mt0) REVERT: D 601 ASP cc_start: 0.8394 (p0) cc_final: 0.8010 (p0) REVERT: D 700 GLN cc_start: 0.9216 (mt0) cc_final: 0.8969 (mt0) REVERT: B 491 ARG cc_start: 0.6067 (ttp-170) cc_final: 0.5807 (ttp80) REVERT: B 700 GLN cc_start: 0.9214 (mt0) cc_final: 0.8966 (mt0) REVERT: C 700 GLN cc_start: 0.9212 (mt0) cc_final: 0.8970 (mt0) outliers start: 19 outliers final: 16 residues processed: 546 average time/residue: 0.3122 time to fit residues: 257.0152 Evaluate side-chains 553 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 537 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 527 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 D residue 527 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 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 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: 0.8980 chunk 185 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 195 optimal weight: 2.9990 chunk 139 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 188 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 676 ASN B 676 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.165950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.110260 restraints weight = 71714.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.115509 restraints weight = 25712.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.118487 restraints weight = 14955.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.120012 restraints weight = 11472.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.120906 restraints weight = 10113.686| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1782 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= 0.137 Angle : 0.485 5.590 24100 Z= 0.263 Chirality : 0.035 0.122 2700 Planarity : 0.003 0.050 2976 Dihedral : 6.163 56.151 2452 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 0.96 % Allowed : 15.27 % Favored : 83.78 % 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: 2.91 (0.15), residues: 1264 sheet: -1.65 (0.47), residues: 92 loop : -1.21 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 743 TYR 0.021 0.001 TYR B 511 PHE 0.008 0.001 PHE A 649 TRP 0.004 0.000 TRP D 740 HIS 0.001 0.000 HIS C 378 Details of bonding type rmsd covalent geometry : bond 0.00303 (17812) covalent geometry : angle 0.48456 (24100) hydrogen bonds : bond 0.04174 ( 1016) hydrogen bonds : angle 3.57994 ( 2940) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6953.90 seconds wall clock time: 118 minutes 59.95 seconds (7139.95 seconds total)