Starting phenix.real_space_refine on Wed Mar 4 15:14:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mz5_24083/03_2026/7mz5_24083.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mz5_24083/03_2026/7mz5_24083.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mz5_24083/03_2026/7mz5_24083.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mz5_24083/03_2026/7mz5_24083.map" model { file = "/net/cci-nas-00/data/ceres_data/7mz5_24083/03_2026/7mz5_24083.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mz5_24083/03_2026/7mz5_24083.cif" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 92 5.16 5 Na 3 4.78 5 C 9428 2.51 5 N 2252 2.21 5 O 2516 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14291 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3526 Classifications: {'peptide': 431} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 420} Chain breaks: 2 Chain: "C" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3526 Classifications: {'peptide': 431} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 420} Chain breaks: 2 Chain: "D" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3526 Classifications: {'peptide': 431} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 420} Chain breaks: 2 Chain: "B" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3526 Classifications: {'peptide': 431} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 420} Chain breaks: 2 Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {' NA': 3, '6EU': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.06, per 1000 atoms: 0.21 Number of scatterers: 14291 At special positions: 0 Unit cell: (122.808, 122.808, 102.168, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 92 16.00 Na 3 11.00 O 2516 8.00 N 2252 7.00 C 9428 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 468.0 milliseconds 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3280 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 4 sheets defined 70.0% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 286 through 295 removed outlier: 3.542A pdb=" N ALA A 290 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 320 Processing helix chain 'A' and resid 324 through 328 removed outlier: 4.028A pdb=" N ILE A 328 " --> pdb=" O LEU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 343 Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 362 through 366 Processing helix chain 'A' and resid 394 through 401 Processing helix chain 'A' and resid 411 through 414 Processing helix chain 'A' and resid 415 through 429 Processing helix chain 'A' and resid 429 through 454 Processing helix chain 'A' and resid 468 through 500 Processing helix chain 'A' and resid 510 through 532 Processing helix chain 'A' and resid 536 through 557 removed outlier: 3.811A pdb=" N PHE A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU A 553 " --> pdb=" O TRP A 549 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N TYR A 554 " --> pdb=" O THR A 550 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N TYR A 555 " --> pdb=" O ASN A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 576 removed outlier: 3.965A pdb=" N ALA A 566 " --> pdb=" O MET A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 599 removed outlier: 3.552A pdb=" N PHE A 580 " --> pdb=" O ASP A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 642 removed outlier: 3.908A pdb=" N PHE A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N THR A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE A 642 " --> pdb=" O PHE A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 683 Processing helix chain 'A' and resid 688 through 712 Processing helix chain 'C' and resid 286 through 295 removed outlier: 3.602A pdb=" N ALA C 290 " --> pdb=" O THR C 286 " (cutoff:3.500A) removed outlier: 4.021A 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 324 through 328 removed outlier: 4.078A pdb=" N ILE C 328 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 343 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 362 through 366 Processing helix chain 'C' and resid 394 through 401 Processing helix chain 'C' and resid 409 through 414 removed outlier: 4.210A pdb=" N LEU C 413 " --> pdb=" O HIS C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 429 Processing helix chain 'C' and resid 429 through 454 Processing helix chain 'C' and resid 468 through 500 Processing helix chain 'C' and resid 510 through 532 Processing helix chain 'C' and resid 536 through 557 removed outlier: 3.875A pdb=" N PHE C 543 " --> pdb=" O ALA C 539 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU C 553 " --> pdb=" O TRP C 549 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N TYR C 554 " --> pdb=" O THR C 550 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N TYR C 555 " --> pdb=" O ASN C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 576 removed outlier: 3.859A pdb=" N ALA C 566 " --> pdb=" O MET C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 599 Processing helix chain 'C' and resid 629 through 642 removed outlier: 3.929A pdb=" N PHE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N THR C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE C 642 " --> pdb=" O PHE C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 683 Processing helix chain 'C' and resid 688 through 712 Processing helix chain 'D' and resid 286 through 295 removed outlier: 3.564A pdb=" N ALA D 290 " --> pdb=" O THR D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 320 Processing helix chain 'D' and resid 324 through 328 removed outlier: 4.194A pdb=" N ILE D 328 " --> pdb=" O LEU D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 344 Processing helix chain 'D' and resid 345 through 354 Processing helix chain 'D' and resid 362 through 366 Processing helix chain 'D' and resid 394 through 401 Processing helix chain 'D' and resid 408 through 414 removed outlier: 4.279A pdb=" N LEU D 413 " --> pdb=" O HIS D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 429 Processing helix chain 'D' and resid 429 through 454 Processing helix chain 'D' and resid 468 through 500 Processing helix chain 'D' and resid 510 through 532 Processing helix chain 'D' and resid 536 through 552 removed outlier: 3.792A pdb=" N PHE D 543 " --> pdb=" O ALA D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 557 Processing helix chain 'D' and resid 562 through 576 removed outlier: 3.885A pdb=" N ALA D 566 " --> pdb=" O MET D 562 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 599 removed outlier: 3.960A pdb=" N PHE D 580 " --> pdb=" O ASP D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 642 removed outlier: 3.916A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N THR D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE D 642 " --> pdb=" O PHE D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 683 Processing helix chain 'D' and resid 687 through 712 removed outlier: 3.675A pdb=" N GLN D 691 " --> pdb=" O ASN D 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 295 removed outlier: 3.547A 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 324 through 328 removed outlier: 4.063A pdb=" N ILE B 328 " --> pdb=" O LEU B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 343 Processing helix chain 'B' and resid 345 through 354 Processing helix chain 'B' and resid 362 through 366 Processing helix chain 'B' and resid 394 through 401 Processing helix chain 'B' and resid 411 through 414 Processing helix chain 'B' and resid 415 through 429 Processing helix chain 'B' and resid 429 through 454 Processing helix chain 'B' and resid 468 through 500 Processing helix chain 'B' and resid 510 through 532 Processing helix chain 'B' and resid 536 through 557 removed outlier: 3.784A pdb=" N PHE B 543 " --> pdb=" O ALA B 539 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU B 553 " --> pdb=" O TRP B 549 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N TYR B 554 " --> pdb=" O THR B 550 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N TYR B 555 " --> pdb=" O ASN B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 575 removed outlier: 4.263A pdb=" N ALA B 566 " --> pdb=" O MET B 562 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU B 570 " --> pdb=" O ALA B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 599 removed outlier: 3.896A pdb=" N PHE B 580 " --> pdb=" O ASP B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 642 removed outlier: 3.928A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N THR B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE B 642 " --> pdb=" O PHE B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 683 Processing helix chain 'B' and resid 688 through 712 Processing sheet with id=AA1, first strand: chain 'A' and resid 369 through 373 removed outlier: 6.655A pdb=" N SER A 379 " --> pdb=" O GLU A 371 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 369 through 373 removed outlier: 6.604A pdb=" N SER C 379 " --> pdb=" O GLU C 371 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 369 through 373 removed outlier: 6.554A pdb=" N SER D 379 " --> pdb=" O GLU D 371 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 369 through 373 removed outlier: 6.706A pdb=" N SER B 379 " --> pdb=" O GLU B 371 " (cutoff:3.500A) 910 hydrogen bonds defined for protein. 2661 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.29 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3081 1.33 - 1.45: 3430 1.45 - 1.57: 7981 1.57 - 1.69: 0 1.69 - 1.81: 152 Bond restraints: 14644 Sorted by residual: bond pdb=" CBK 6EU B 901 " pdb=" OAF 6EU B 901 " ideal model delta sigma weight residual 1.329 1.456 -0.127 2.00e-02 2.50e+03 4.02e+01 bond pdb=" CBK 6EU D 901 " pdb=" OAF 6EU D 901 " ideal model delta sigma weight residual 1.329 1.455 -0.126 2.00e-02 2.50e+03 3.98e+01 bond pdb=" CBK 6EU A 901 " pdb=" OAF 6EU A 901 " ideal model delta sigma weight residual 1.329 1.454 -0.125 2.00e-02 2.50e+03 3.92e+01 bond pdb=" CBK 6EU C 901 " pdb=" OAF 6EU C 901 " ideal model delta sigma weight residual 1.329 1.454 -0.125 2.00e-02 2.50e+03 3.92e+01 bond pdb=" N PHE A 712 " pdb=" CA PHE A 712 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.29e-02 6.01e+03 6.75e+00 ... (remaining 14639 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 19356 1.96 - 3.93: 385 3.93 - 5.89: 88 5.89 - 7.86: 13 7.86 - 9.82: 6 Bond angle restraints: 19848 Sorted by residual: angle pdb=" N ASP A 654 " pdb=" CA ASP A 654 " pdb=" C ASP A 654 " ideal model delta sigma weight residual 110.14 100.32 9.82 1.47e+00 4.63e-01 4.46e+01 angle pdb=" N ASP C 654 " pdb=" CA ASP C 654 " pdb=" C ASP C 654 " ideal model delta sigma weight residual 110.14 100.51 9.63 1.47e+00 4.63e-01 4.29e+01 angle pdb=" O TYR A 653 " pdb=" C TYR A 653 " pdb=" N ASP A 654 " ideal model delta sigma weight residual 123.26 126.73 -3.47 1.05e+00 9.07e-01 1.10e+01 angle pdb=" N LEU C 713 " pdb=" CA LEU C 713 " pdb=" C LEU C 713 " ideal model delta sigma weight residual 110.80 117.80 -7.00 2.13e+00 2.20e-01 1.08e+01 angle pdb=" N PHE A 712 " pdb=" CA PHE A 712 " pdb=" C PHE A 712 " ideal model delta sigma weight residual 110.80 117.69 -6.89 2.13e+00 2.20e-01 1.05e+01 ... (remaining 19843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 8395 17.77 - 35.55: 366 35.55 - 53.32: 80 53.32 - 71.09: 30 71.09 - 88.87: 5 Dihedral angle restraints: 8876 sinusoidal: 3776 harmonic: 5100 Sorted by residual: dihedral pdb=" N PHE A 712 " pdb=" C PHE A 712 " pdb=" CA PHE A 712 " pdb=" CB PHE A 712 " ideal model delta harmonic sigma weight residual 122.80 139.54 -16.74 0 2.50e+00 1.60e-01 4.48e+01 dihedral pdb=" C PHE A 712 " pdb=" N PHE A 712 " pdb=" CA PHE A 712 " pdb=" CB PHE A 712 " ideal model delta harmonic sigma weight residual -122.60 -139.00 16.40 0 2.50e+00 1.60e-01 4.30e+01 dihedral pdb=" N PHE D 712 " pdb=" C PHE D 712 " pdb=" CA PHE D 712 " pdb=" CB PHE D 712 " ideal model delta harmonic sigma weight residual 122.80 139.08 -16.28 0 2.50e+00 1.60e-01 4.24e+01 ... (remaining 8873 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 2216 0.128 - 0.255: 14 0.255 - 0.383: 6 0.383 - 0.510: 0 0.510 - 0.638: 4 Chirality restraints: 2240 Sorted by residual: chirality pdb=" CA PHE A 712 " pdb=" N PHE A 712 " pdb=" C PHE A 712 " pdb=" CB PHE A 712 " both_signs ideal model delta sigma weight residual False 2.51 1.87 0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" CA PHE B 712 " pdb=" N PHE B 712 " pdb=" C PHE B 712 " pdb=" CB PHE B 712 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.62 2.00e-01 2.50e+01 9.52e+00 chirality pdb=" CA PHE D 712 " pdb=" N PHE D 712 " pdb=" C PHE D 712 " pdb=" CB PHE D 712 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.43e+00 ... (remaining 2237 not shown) Planarity restraints: 2412 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 546 " -0.012 2.00e-02 2.50e+03 2.43e-02 5.89e+00 pdb=" C ALA A 546 " 0.042 2.00e-02 2.50e+03 pdb=" O ALA A 546 " -0.016 2.00e-02 2.50e+03 pdb=" N MET A 547 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 546 " 0.012 2.00e-02 2.50e+03 2.41e-02 5.79e+00 pdb=" C ALA B 546 " -0.042 2.00e-02 2.50e+03 pdb=" O ALA B 546 " 0.016 2.00e-02 2.50e+03 pdb=" N MET B 547 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 546 " -0.012 2.00e-02 2.50e+03 2.40e-02 5.77e+00 pdb=" C ALA D 546 " 0.042 2.00e-02 2.50e+03 pdb=" O ALA D 546 " -0.016 2.00e-02 2.50e+03 pdb=" N MET D 547 " -0.014 2.00e-02 2.50e+03 ... (remaining 2409 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 202 2.69 - 3.24: 14535 3.24 - 3.80: 23211 3.80 - 4.35: 30295 4.35 - 4.90: 50628 Nonbonded interactions: 118871 Sorted by model distance: nonbonded pdb=" O LEU C 673 " pdb=" OH TYR D 565 " model vdw 2.138 3.040 nonbonded pdb=" OH TYR A 565 " pdb=" O LEU D 673 " model vdw 2.178 3.040 nonbonded pdb=" OH TYR C 565 " pdb=" O LEU B 673 " model vdw 2.185 3.040 nonbonded pdb=" OG SER C 379 " pdb=" OD1 ASP C 745 " model vdw 2.221 3.040 nonbonded pdb=" NH1 ARG C 557 " pdb=" OE1 GLU C 570 " model vdw 2.248 3.120 ... (remaining 118866 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 282 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.160 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: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 12.910 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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:6.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 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 : 0.005 0.127 14644 Z= 0.239 Angle : 0.721 9.820 19848 Z= 0.380 Chirality : 0.049 0.638 2240 Planarity : 0.004 0.030 2412 Dihedral : 11.209 88.866 5596 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 1.25 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.12 % Favored : 95.47 % Rotamer: Outliers : 1.03 % Allowed : 0.84 % Favored : 98.13 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.21), residues: 1700 helix: 1.82 (0.15), residues: 1100 sheet: -1.87 (0.74), residues: 64 loop : -0.87 (0.29), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 355 TYR 0.011 0.001 TYR D 309 PHE 0.016 0.002 PHE C 489 TRP 0.008 0.001 TRP B 549 HIS 0.003 0.001 HIS B 410 Details of bonding type rmsd covalent geometry : bond 0.00484 (14644) covalent geometry : angle 0.72092 (19848) hydrogen bonds : bond 0.13344 ( 910) hydrogen bonds : angle 5.13460 ( 2661) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 441 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 LYS cc_start: 0.8258 (mmtt) cc_final: 0.7408 (mmmt) REVERT: A 423 GLN cc_start: 0.8518 (tp40) cc_final: 0.8168 (mm-40) REVERT: A 424 ASP cc_start: 0.8351 (t70) cc_final: 0.8001 (t0) REVERT: A 427 ASP cc_start: 0.8410 (m-30) cc_final: 0.8157 (m-30) REVERT: A 536 GLU cc_start: 0.8158 (mp0) cc_final: 0.7568 (mp0) REVERT: A 559 PHE cc_start: 0.6945 (m-80) cc_final: 0.5459 (t80) REVERT: A 644 MET cc_start: 0.9102 (mmm) cc_final: 0.8877 (mmm) REVERT: C 308 MET cc_start: 0.8189 (mmm) cc_final: 0.7987 (mpp) REVERT: C 423 GLN cc_start: 0.8575 (tp40) cc_final: 0.8256 (mm-40) REVERT: C 424 ASP cc_start: 0.8426 (t70) cc_final: 0.8090 (t0) REVERT: C 536 GLU cc_start: 0.8188 (mp0) cc_final: 0.7651 (mp0) REVERT: C 559 PHE cc_start: 0.6856 (m-80) cc_final: 0.5709 (t80) REVERT: C 639 LYS cc_start: 0.8638 (mttt) cc_final: 0.8080 (mtmt) REVERT: C 644 MET cc_start: 0.9101 (mmm) cc_final: 0.8881 (mmm) REVERT: C 705 ILE cc_start: 0.9536 (mt) cc_final: 0.9326 (mp) REVERT: D 383 ASP cc_start: 0.7871 (t0) cc_final: 0.7579 (t0) REVERT: D 423 GLN cc_start: 0.8535 (tp40) cc_final: 0.8235 (mm-40) REVERT: D 424 ASP cc_start: 0.8386 (t70) cc_final: 0.8043 (t0) REVERT: D 427 ASP cc_start: 0.8422 (m-30) cc_final: 0.8220 (m-30) REVERT: D 536 GLU cc_start: 0.8157 (mp0) cc_final: 0.7540 (mp0) REVERT: D 639 LYS cc_start: 0.8634 (mttt) cc_final: 0.8363 (mmtp) REVERT: D 644 MET cc_start: 0.9109 (mmm) cc_final: 0.8880 (mmm) REVERT: B 285 ASN cc_start: 0.5795 (p0) cc_final: 0.5445 (p0) REVERT: B 308 MET cc_start: 0.8257 (mmt) cc_final: 0.7776 (mpp) REVERT: B 423 GLN cc_start: 0.8544 (tp40) cc_final: 0.8176 (mm-40) REVERT: B 424 ASP cc_start: 0.8399 (t70) cc_final: 0.7957 (t0) REVERT: B 427 ASP cc_start: 0.8449 (m-30) cc_final: 0.8248 (m-30) REVERT: B 478 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7558 (mt-10) REVERT: B 536 GLU cc_start: 0.8154 (mp0) cc_final: 0.7537 (mp0) REVERT: B 644 MET cc_start: 0.9106 (mmm) cc_final: 0.8878 (mmm) outliers start: 16 outliers final: 8 residues processed: 453 average time/residue: 0.6657 time to fit residues: 327.5803 Evaluate side-chains 316 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 308 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 714 LYS Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain D residue 714 LYS Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 714 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN A 310 ASN A 419 ASN A 467 ASN C 301 ASN C 419 ASN D 301 ASN D 419 ASN B 301 ASN B 419 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.195821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.120235 restraints weight = 16919.842| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.08 r_work: 0.3175 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14644 Z= 0.188 Angle : 0.566 7.820 19848 Z= 0.304 Chirality : 0.040 0.159 2240 Planarity : 0.003 0.037 2412 Dihedral : 7.707 59.862 2304 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.41 % Allowed : 11.47 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.21), residues: 1700 helix: 2.21 (0.15), residues: 1112 sheet: -1.82 (0.77), residues: 64 loop : -0.70 (0.29), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 474 TYR 0.023 0.001 TYR A 351 PHE 0.028 0.002 PHE A 304 TRP 0.016 0.002 TRP C 697 HIS 0.004 0.001 HIS B 289 Details of bonding type rmsd covalent geometry : bond 0.00415 (14644) covalent geometry : angle 0.56559 (19848) hydrogen bonds : bond 0.04778 ( 910) hydrogen bonds : angle 4.21916 ( 2661) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 339 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 GLN cc_start: 0.8573 (tp40) cc_final: 0.8055 (mm-40) REVERT: A 427 ASP cc_start: 0.8885 (m-30) cc_final: 0.8575 (m-30) REVERT: A 465 LEU cc_start: 0.8567 (tp) cc_final: 0.8306 (tp) REVERT: A 499 ARG cc_start: 0.8346 (mmm160) cc_final: 0.8012 (mmm160) REVERT: A 559 PHE cc_start: 0.7256 (m-80) cc_final: 0.6895 (m-10) REVERT: A 562 MET cc_start: 0.8829 (mtm) cc_final: 0.8550 (ttm) REVERT: A 656 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8652 (tmtp) REVERT: A 682 MET cc_start: 0.8871 (mmt) cc_final: 0.8475 (mmm) REVERT: A 694 LYS cc_start: 0.8259 (mtmt) cc_final: 0.7899 (pttt) REVERT: C 293 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7653 (mt-10) REVERT: C 308 MET cc_start: 0.8242 (mmm) cc_final: 0.8018 (mpp) REVERT: C 423 GLN cc_start: 0.8546 (tp40) cc_final: 0.8000 (mm-40) REVERT: C 427 ASP cc_start: 0.8856 (m-30) cc_final: 0.8336 (m-30) REVERT: C 478 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8556 (mt-10) REVERT: C 499 ARG cc_start: 0.8562 (mmm160) cc_final: 0.8110 (mmm160) REVERT: C 509 ASP cc_start: 0.7865 (t0) cc_final: 0.7482 (p0) REVERT: C 639 LYS cc_start: 0.9188 (mttt) cc_final: 0.8626 (mtmt) REVERT: C 656 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8683 (tmtp) REVERT: D 293 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8070 (mt-10) REVERT: D 423 GLN cc_start: 0.8537 (tp40) cc_final: 0.8145 (mm-40) REVERT: D 478 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8352 (mt-10) REVERT: D 499 ARG cc_start: 0.8557 (mmm160) cc_final: 0.8149 (mmm160) REVERT: D 535 LYS cc_start: 0.8766 (mtmm) cc_final: 0.8527 (mtpt) REVERT: D 627 TYR cc_start: 0.7491 (m-80) cc_final: 0.7092 (m-80) REVERT: D 636 GLU cc_start: 0.8996 (mm-30) cc_final: 0.8686 (mm-30) REVERT: D 639 LYS cc_start: 0.9197 (mttt) cc_final: 0.8922 (mmtp) REVERT: D 709 GLU cc_start: 0.8805 (tt0) cc_final: 0.8546 (tt0) REVERT: B 293 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7248 (mp0) REVERT: B 308 MET cc_start: 0.8306 (mmt) cc_final: 0.7826 (mpp) REVERT: B 423 GLN cc_start: 0.8518 (tp40) cc_final: 0.8127 (mm-40) REVERT: B 427 ASP cc_start: 0.8815 (m-30) cc_final: 0.8571 (m-30) REVERT: B 506 LEU cc_start: 0.8853 (tp) cc_final: 0.8491 (tp) REVERT: B 534 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.7098 (mmm160) REVERT: B 535 LYS cc_start: 0.8738 (mtmm) cc_final: 0.8462 (mtpt) REVERT: B 536 GLU cc_start: 0.8889 (mp0) cc_final: 0.8580 (mp0) REVERT: B 564 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8668 (tp) REVERT: B 627 TYR cc_start: 0.7555 (m-80) cc_final: 0.6953 (m-80) REVERT: B 682 MET cc_start: 0.8872 (mmt) cc_final: 0.8454 (mmt) REVERT: B 705 ILE cc_start: 0.9431 (mt) cc_final: 0.9113 (mp) REVERT: B 709 GLU cc_start: 0.8814 (tt0) cc_final: 0.8431 (tt0) outliers start: 53 outliers final: 22 residues processed: 364 average time/residue: 0.5874 time to fit residues: 234.5748 Evaluate side-chains 329 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 303 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 656 LYS Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 556 THR Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 656 LYS Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 714 LYS Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 571 LYS Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain D residue 714 LYS Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 534 ARG Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 562 MET Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 714 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 40 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 138 optimal weight: 8.9990 chunk 123 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 chunk 136 optimal weight: 0.6980 chunk 129 optimal weight: 10.0000 chunk 64 optimal weight: 0.8980 chunk 112 optimal weight: 0.5980 chunk 132 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN A 310 ASN A 419 ASN A 467 ASN C 419 ASN C 467 ASN D 301 ASN D 408 ASN D 419 ASN B 301 ASN B 419 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.195606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.121214 restraints weight = 17143.447| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.08 r_work: 0.3191 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 14644 Z= 0.164 Angle : 0.544 7.716 19848 Z= 0.290 Chirality : 0.039 0.152 2240 Planarity : 0.003 0.033 2412 Dihedral : 7.557 59.785 2304 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.54 % Allowed : 14.05 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.21), residues: 1700 helix: 2.10 (0.15), residues: 1132 sheet: -1.76 (0.78), residues: 64 loop : -1.11 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 575 TYR 0.022 0.001 TYR A 351 PHE 0.022 0.002 PHE A 304 TRP 0.011 0.001 TRP C 697 HIS 0.002 0.001 HIS B 289 Details of bonding type rmsd covalent geometry : bond 0.00358 (14644) covalent geometry : angle 0.54374 (19848) hydrogen bonds : bond 0.04414 ( 910) hydrogen bonds : angle 4.12602 ( 2661) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 321 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 423 GLN cc_start: 0.8591 (tp40) cc_final: 0.8043 (mm-40) REVERT: A 427 ASP cc_start: 0.8819 (m-30) cc_final: 0.8562 (m-30) REVERT: A 478 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8308 (mt-10) REVERT: A 499 ARG cc_start: 0.8319 (mmm160) cc_final: 0.8003 (mmm160) REVERT: A 513 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8556 (tp30) REVERT: A 559 PHE cc_start: 0.6979 (m-80) cc_final: 0.6590 (m-10) REVERT: A 562 MET cc_start: 0.8903 (mtm) cc_final: 0.8524 (ttm) REVERT: A 682 MET cc_start: 0.8900 (mmt) cc_final: 0.8502 (mmt) REVERT: A 694 LYS cc_start: 0.8125 (mtmt) cc_final: 0.7761 (pttt) REVERT: C 293 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7729 (mt-10) REVERT: C 308 MET cc_start: 0.8240 (mmm) cc_final: 0.7928 (mpp) REVERT: C 423 GLN cc_start: 0.8655 (tp40) cc_final: 0.8097 (mm-40) REVERT: C 427 ASP cc_start: 0.8828 (m-30) cc_final: 0.8405 (m-30) REVERT: C 499 ARG cc_start: 0.8517 (mmm160) cc_final: 0.8155 (mmm160) REVERT: C 635 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8842 (mm) REVERT: C 639 LYS cc_start: 0.9184 (mttt) cc_final: 0.8861 (mmmm) REVERT: C 682 MET cc_start: 0.8941 (mmt) cc_final: 0.8343 (mmt) REVERT: D 293 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8080 (mt-10) REVERT: D 423 GLN cc_start: 0.8569 (tp40) cc_final: 0.7977 (mm-40) REVERT: D 427 ASP cc_start: 0.8900 (m-30) cc_final: 0.8372 (m-30) REVERT: D 464 LYS cc_start: 0.7996 (mmtp) cc_final: 0.7714 (mmmm) REVERT: D 478 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8345 (mt-10) REVERT: D 499 ARG cc_start: 0.8557 (mmm160) cc_final: 0.8133 (mmm160) REVERT: D 534 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.7095 (mmm160) REVERT: D 535 LYS cc_start: 0.8717 (mtmm) cc_final: 0.8440 (mtpt) REVERT: D 536 GLU cc_start: 0.8909 (mp0) cc_final: 0.8566 (mp0) REVERT: D 562 MET cc_start: 0.8227 (mmt) cc_final: 0.7973 (mmt) REVERT: D 639 LYS cc_start: 0.9186 (mttt) cc_final: 0.8886 (mtmm) REVERT: D 682 MET cc_start: 0.8931 (mmt) cc_final: 0.8588 (mmt) REVERT: B 293 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7776 (mt-10) REVERT: B 308 MET cc_start: 0.8140 (mmt) cc_final: 0.7725 (mpp) REVERT: B 423 GLN cc_start: 0.8527 (tp40) cc_final: 0.8130 (mm-40) REVERT: B 425 LYS cc_start: 0.8860 (mttm) cc_final: 0.8514 (mttm) REVERT: B 427 ASP cc_start: 0.8788 (m-30) cc_final: 0.8494 (m-30) REVERT: B 464 LYS cc_start: 0.8065 (mmtp) cc_final: 0.7769 (mmmm) REVERT: B 467 ASN cc_start: 0.8028 (t0) cc_final: 0.7664 (t0) REVERT: B 534 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.7106 (mmm160) REVERT: B 535 LYS cc_start: 0.8705 (mtmm) cc_final: 0.8464 (mtpt) REVERT: B 536 GLU cc_start: 0.8898 (mp0) cc_final: 0.8673 (mp0) REVERT: B 564 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8648 (tp) REVERT: B 627 TYR cc_start: 0.7623 (m-80) cc_final: 0.7026 (m-80) REVERT: B 635 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8834 (tp) REVERT: B 682 MET cc_start: 0.8866 (mmt) cc_final: 0.8220 (mmt) REVERT: B 709 GLU cc_start: 0.8916 (tt0) cc_final: 0.8498 (tt0) outliers start: 55 outliers final: 15 residues processed: 352 average time/residue: 0.6398 time to fit residues: 245.8036 Evaluate side-chains 317 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 297 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 556 THR Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 714 LYS Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 534 ARG Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain D residue 714 LYS Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 534 ARG Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 685 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 120 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 42 optimal weight: 10.0000 chunk 158 optimal weight: 0.9980 chunk 126 optimal weight: 0.0270 chunk 35 optimal weight: 0.8980 chunk 96 optimal weight: 8.9990 chunk 151 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 chunk 117 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN A 419 ASN C 301 ASN D 301 ASN D 408 ASN B 301 ASN B 419 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.196926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.123113 restraints weight = 16998.723| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.09 r_work: 0.3219 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14644 Z= 0.130 Angle : 0.526 7.439 19848 Z= 0.277 Chirality : 0.038 0.155 2240 Planarity : 0.003 0.039 2412 Dihedral : 7.004 55.200 2296 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.03 % Allowed : 16.24 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.21), residues: 1700 helix: 2.20 (0.15), residues: 1132 sheet: -1.57 (0.79), residues: 64 loop : -1.17 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 575 TYR 0.018 0.001 TYR A 351 PHE 0.016 0.001 PHE C 489 TRP 0.016 0.001 TRP B 697 HIS 0.001 0.000 HIS C 289 Details of bonding type rmsd covalent geometry : bond 0.00277 (14644) covalent geometry : angle 0.52649 (19848) hydrogen bonds : bond 0.03976 ( 910) hydrogen bonds : angle 4.01760 ( 2661) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 323 time to evaluate : 0.549 Fit side-chains revert: symmetry clash REVERT: A 293 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8054 (mt-10) REVERT: A 308 MET cc_start: 0.7218 (OUTLIER) cc_final: 0.6819 (mpp) REVERT: A 423 GLN cc_start: 0.8482 (tp40) cc_final: 0.7911 (mm-40) REVERT: A 427 ASP cc_start: 0.8833 (m-30) cc_final: 0.8524 (m-30) REVERT: A 559 PHE cc_start: 0.6989 (m-80) cc_final: 0.6511 (m-10) REVERT: A 561 GLN cc_start: 0.8537 (mm110) cc_final: 0.7661 (mp10) REVERT: A 562 MET cc_start: 0.8919 (mtm) cc_final: 0.8541 (ttm) REVERT: A 572 MET cc_start: 0.8791 (mtp) cc_final: 0.8579 (ttm) REVERT: A 694 LYS cc_start: 0.8076 (mtmt) cc_final: 0.7683 (pttt) REVERT: C 308 MET cc_start: 0.8262 (mmm) cc_final: 0.7918 (mpp) REVERT: C 423 GLN cc_start: 0.8595 (tp40) cc_final: 0.7989 (mm-40) REVERT: C 427 ASP cc_start: 0.8875 (m-30) cc_final: 0.8422 (m-30) REVERT: C 499 ARG cc_start: 0.8469 (mmm160) cc_final: 0.8011 (mmm160) REVERT: C 635 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8645 (tp) REVERT: C 639 LYS cc_start: 0.9147 (mttt) cc_final: 0.8762 (mmtp) REVERT: D 293 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8083 (mt-10) REVERT: D 308 MET cc_start: 0.7530 (OUTLIER) cc_final: 0.7010 (mpp) REVERT: D 401 TYR cc_start: 0.7894 (m-80) cc_final: 0.7625 (m-80) REVERT: D 423 GLN cc_start: 0.8587 (tp40) cc_final: 0.8009 (mm-40) REVERT: D 427 ASP cc_start: 0.8877 (m-30) cc_final: 0.8361 (m-30) REVERT: D 432 ARG cc_start: 0.8669 (mpt-90) cc_final: 0.8452 (mmt90) REVERT: D 464 LYS cc_start: 0.8065 (mmtp) cc_final: 0.7862 (mmmm) REVERT: D 474 ARG cc_start: 0.8515 (ttp80) cc_final: 0.8153 (ttp80) REVERT: D 478 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8151 (mt-10) REVERT: D 499 ARG cc_start: 0.8499 (mmm160) cc_final: 0.8213 (mmt180) REVERT: D 534 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.7056 (mmm160) REVERT: D 535 LYS cc_start: 0.8657 (mtmm) cc_final: 0.8426 (mtpt) REVERT: D 536 GLU cc_start: 0.8951 (mp0) cc_final: 0.8662 (mp0) REVERT: D 562 MET cc_start: 0.8068 (mmt) cc_final: 0.7831 (mmt) REVERT: D 682 MET cc_start: 0.8897 (mmt) cc_final: 0.8446 (mmt) REVERT: B 293 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7811 (mt-10) REVERT: B 308 MET cc_start: 0.8112 (mmt) cc_final: 0.7728 (mpp) REVERT: B 423 GLN cc_start: 0.8502 (tp40) cc_final: 0.8048 (mm-40) REVERT: B 427 ASP cc_start: 0.8812 (m-30) cc_final: 0.8472 (m-30) REVERT: B 432 ARG cc_start: 0.8631 (mpt-90) cc_final: 0.8382 (mmt90) REVERT: B 464 LYS cc_start: 0.8160 (mmtp) cc_final: 0.7837 (mmmm) REVERT: B 467 ASN cc_start: 0.7977 (t0) cc_final: 0.7579 (t0) REVERT: B 534 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.7028 (mmm160) REVERT: B 535 LYS cc_start: 0.8690 (mtmm) cc_final: 0.8447 (mtpt) REVERT: B 536 GLU cc_start: 0.8861 (mp0) cc_final: 0.8629 (mp0) REVERT: B 564 ILE cc_start: 0.8861 (OUTLIER) cc_final: 0.8644 (tp) REVERT: B 627 TYR cc_start: 0.7510 (m-80) cc_final: 0.6913 (m-80) REVERT: B 635 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8784 (tp) REVERT: B 682 MET cc_start: 0.8866 (mmt) cc_final: 0.8433 (mmt) outliers start: 47 outliers final: 13 residues processed: 343 average time/residue: 0.5991 time to fit residues: 225.2960 Evaluate side-chains 316 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 296 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 714 LYS Chi-restraints excluded: chain D residue 308 MET Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 534 ARG Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 534 ARG Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 571 LYS Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 678 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 71 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 163 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 128 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 chunk 139 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN A 419 ASN A 676 ASN C 301 ASN D 301 ASN D 408 ASN B 419 ASN B 691 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.194283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.119550 restraints weight = 17045.570| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.07 r_work: 0.3178 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14644 Z= 0.197 Angle : 0.565 7.302 19848 Z= 0.298 Chirality : 0.040 0.155 2240 Planarity : 0.004 0.041 2412 Dihedral : 7.039 58.587 2290 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.61 % Allowed : 16.62 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.21), residues: 1700 helix: 2.15 (0.15), residues: 1108 sheet: -1.65 (0.79), residues: 64 loop : -0.79 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 575 TYR 0.011 0.001 TYR A 584 PHE 0.016 0.002 PHE A 649 TRP 0.020 0.001 TRP B 697 HIS 0.002 0.001 HIS B 289 Details of bonding type rmsd covalent geometry : bond 0.00441 (14644) covalent geometry : angle 0.56545 (19848) hydrogen bonds : bond 0.04449 ( 910) hydrogen bonds : angle 4.19259 ( 2661) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 299 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 293 GLU cc_start: 0.8407 (mt-10) cc_final: 0.7959 (mt-10) REVERT: A 423 GLN cc_start: 0.8543 (tp40) cc_final: 0.7960 (mm-40) REVERT: A 427 ASP cc_start: 0.8819 (m-30) cc_final: 0.8534 (m-30) REVERT: A 499 ARG cc_start: 0.8308 (mmm160) cc_final: 0.7817 (mmm160) REVERT: A 559 PHE cc_start: 0.7104 (m-80) cc_final: 0.6581 (m-10) REVERT: A 562 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.8540 (ttm) REVERT: A 572 MET cc_start: 0.8834 (mtp) cc_final: 0.8566 (ttm) REVERT: A 644 MET cc_start: 0.9317 (mmm) cc_final: 0.8273 (mmm) REVERT: C 293 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7486 (pm20) REVERT: C 308 MET cc_start: 0.8300 (mmm) cc_final: 0.7989 (mpp) REVERT: C 423 GLN cc_start: 0.8674 (tp40) cc_final: 0.8186 (mm-40) REVERT: C 499 ARG cc_start: 0.8482 (mmm160) cc_final: 0.8136 (mmm-85) REVERT: C 627 TYR cc_start: 0.7552 (m-80) cc_final: 0.6863 (m-80) REVERT: C 635 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8683 (tp) REVERT: C 639 LYS cc_start: 0.9191 (mttt) cc_final: 0.8667 (mmtm) REVERT: D 293 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8143 (mt-10) REVERT: D 308 MET cc_start: 0.7541 (OUTLIER) cc_final: 0.7013 (mpp) REVERT: D 423 GLN cc_start: 0.8608 (tp40) cc_final: 0.8006 (mm-40) REVERT: D 427 ASP cc_start: 0.8832 (m-30) cc_final: 0.8352 (m-30) REVERT: D 432 ARG cc_start: 0.8640 (mpt-90) cc_final: 0.8390 (mmt90) REVERT: D 464 LYS cc_start: 0.8140 (mmtp) cc_final: 0.7938 (mmmm) REVERT: D 478 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8266 (mt-10) REVERT: D 499 ARG cc_start: 0.8525 (mmm160) cc_final: 0.8264 (mmt180) REVERT: D 535 LYS cc_start: 0.8694 (mtmm) cc_final: 0.8465 (mtpt) REVERT: B 293 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7855 (mt-10) REVERT: B 308 MET cc_start: 0.8096 (mmt) cc_final: 0.7649 (mpp) REVERT: B 423 GLN cc_start: 0.8524 (tp40) cc_final: 0.8064 (mm-40) REVERT: B 427 ASP cc_start: 0.8828 (m-30) cc_final: 0.8540 (m-30) REVERT: B 432 ARG cc_start: 0.8655 (mpt-90) cc_final: 0.8418 (mmt90) REVERT: B 467 ASN cc_start: 0.7988 (t0) cc_final: 0.7579 (t0) REVERT: B 499 ARG cc_start: 0.8007 (mmm160) cc_final: 0.7724 (mmm160) REVERT: B 534 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.7112 (mmm160) REVERT: B 535 LYS cc_start: 0.8693 (mtmm) cc_final: 0.8437 (mtpt) REVERT: B 536 GLU cc_start: 0.8844 (mp0) cc_final: 0.8620 (mp0) REVERT: B 562 MET cc_start: 0.8987 (mmm) cc_final: 0.8435 (mmt) REVERT: B 627 TYR cc_start: 0.7594 (m-80) cc_final: 0.6949 (m-80) REVERT: B 635 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8774 (tp) outliers start: 56 outliers final: 22 residues processed: 316 average time/residue: 0.6126 time to fit residues: 211.5896 Evaluate side-chains 312 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 285 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 556 THR Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 703 ILE Chi-restraints excluded: chain D residue 308 MET Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 534 ARG Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 534 ARG Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 678 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 150 optimal weight: 0.5980 chunk 162 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 126 optimal weight: 3.9990 chunk 8 optimal weight: 0.0670 chunk 137 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 chunk 83 optimal weight: 0.4980 chunk 2 optimal weight: 7.9990 chunk 157 optimal weight: 0.9980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN A 419 ASN C 301 ASN D 301 ASN D 408 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.197300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.123814 restraints weight = 17034.483| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.07 r_work: 0.3238 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14644 Z= 0.126 Angle : 0.542 7.678 19848 Z= 0.283 Chirality : 0.038 0.157 2240 Planarity : 0.003 0.046 2412 Dihedral : 6.663 54.728 2286 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.77 % Allowed : 17.46 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.21), residues: 1700 helix: 2.29 (0.15), residues: 1108 sheet: -1.48 (0.80), residues: 64 loop : -0.79 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 575 TYR 0.008 0.001 TYR A 584 PHE 0.018 0.001 PHE C 489 TRP 0.024 0.001 TRP B 697 HIS 0.001 0.000 HIS B 410 Details of bonding type rmsd covalent geometry : bond 0.00271 (14644) covalent geometry : angle 0.54152 (19848) hydrogen bonds : bond 0.03925 ( 910) hydrogen bonds : angle 4.07879 ( 2661) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 316 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 GLU cc_start: 0.8435 (mt-10) cc_final: 0.7994 (mt-10) REVERT: A 308 MET cc_start: 0.7476 (OUTLIER) cc_final: 0.6918 (mpp) REVERT: A 423 GLN cc_start: 0.8544 (tp40) cc_final: 0.8054 (mm-40) REVERT: A 499 ARG cc_start: 0.8253 (mmm160) cc_final: 0.7819 (mmm160) REVERT: A 559 PHE cc_start: 0.7105 (m-80) cc_final: 0.6621 (m-10) REVERT: A 561 GLN cc_start: 0.8534 (mm-40) cc_final: 0.7589 (mp10) REVERT: A 562 MET cc_start: 0.8934 (OUTLIER) cc_final: 0.8202 (mtt) REVERT: A 572 MET cc_start: 0.8758 (mtp) cc_final: 0.8481 (ttm) REVERT: A 644 MET cc_start: 0.9317 (mmm) cc_final: 0.8174 (mmm) REVERT: C 293 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7624 (pm20) REVERT: C 308 MET cc_start: 0.8301 (mmm) cc_final: 0.7989 (mpp) REVERT: C 423 GLN cc_start: 0.8605 (tp40) cc_final: 0.7988 (mm-40) REVERT: C 427 ASP cc_start: 0.8795 (m-30) cc_final: 0.8370 (m-30) REVERT: C 471 ASP cc_start: 0.8548 (t70) cc_final: 0.8213 (t70) REVERT: C 499 ARG cc_start: 0.8412 (mmm160) cc_final: 0.8095 (mmm-85) REVERT: C 561 GLN cc_start: 0.8623 (mm110) cc_final: 0.7451 (mp10) REVERT: C 635 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8666 (tp) REVERT: C 639 LYS cc_start: 0.9141 (mttt) cc_final: 0.8756 (mmtp) REVERT: D 293 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8183 (mt-10) REVERT: D 308 MET cc_start: 0.7583 (OUTLIER) cc_final: 0.7048 (mpp) REVERT: D 423 GLN cc_start: 0.8603 (tp40) cc_final: 0.7909 (mm-40) REVERT: D 427 ASP cc_start: 0.8839 (m-30) cc_final: 0.8349 (m-30) REVERT: D 432 ARG cc_start: 0.8646 (mpt-90) cc_final: 0.8415 (mmt90) REVERT: D 474 ARG cc_start: 0.8547 (ttp80) cc_final: 0.8190 (ttp80) REVERT: D 478 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8124 (mt-10) REVERT: D 499 ARG cc_start: 0.8490 (mmm160) cc_final: 0.8083 (mmm160) REVERT: D 534 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.6994 (mmm160) REVERT: D 535 LYS cc_start: 0.8654 (mtmm) cc_final: 0.8427 (mtpt) REVERT: D 536 GLU cc_start: 0.8880 (mp0) cc_final: 0.8585 (mp0) REVERT: D 692 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7259 (mp0) REVERT: D 705 ILE cc_start: 0.9374 (mt) cc_final: 0.9109 (mp) REVERT: B 293 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7817 (mt-10) REVERT: B 308 MET cc_start: 0.8111 (mmt) cc_final: 0.7673 (mpp) REVERT: B 423 GLN cc_start: 0.8511 (tp40) cc_final: 0.8076 (mm-40) REVERT: B 427 ASP cc_start: 0.8863 (m-30) cc_final: 0.8612 (m-30) REVERT: B 432 ARG cc_start: 0.8683 (mpt-90) cc_final: 0.8430 (mmt90) REVERT: B 464 LYS cc_start: 0.7952 (mmtp) cc_final: 0.7636 (mmmm) REVERT: B 499 ARG cc_start: 0.7959 (mmm160) cc_final: 0.7670 (mmm160) REVERT: B 534 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.6929 (mmm160) REVERT: B 535 LYS cc_start: 0.8634 (mtmm) cc_final: 0.8413 (mtpt) REVERT: B 536 GLU cc_start: 0.8826 (mp0) cc_final: 0.8449 (mp0) REVERT: B 562 MET cc_start: 0.9005 (mmm) cc_final: 0.8455 (mmt) REVERT: B 627 TYR cc_start: 0.7518 (m-80) cc_final: 0.6843 (m-80) REVERT: B 635 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8751 (tp) REVERT: B 644 MET cc_start: 0.9360 (mmm) cc_final: 0.8279 (mmm) REVERT: B 705 ILE cc_start: 0.9336 (mt) cc_final: 0.9106 (mp) outliers start: 43 outliers final: 13 residues processed: 334 average time/residue: 0.5789 time to fit residues: 211.7312 Evaluate side-chains 314 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 294 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain D residue 308 MET Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 534 ARG Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 534 ARG Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 635 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 79 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 87 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 35 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN A 419 ASN D 301 ASN D 408 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.195258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.121264 restraints weight = 16903.174| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.07 r_work: 0.3194 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14644 Z= 0.162 Angle : 0.550 7.997 19848 Z= 0.290 Chirality : 0.039 0.159 2240 Planarity : 0.004 0.049 2412 Dihedral : 6.676 57.346 2282 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.84 % Allowed : 18.49 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.21), residues: 1700 helix: 2.17 (0.15), residues: 1108 sheet: -1.44 (0.80), residues: 64 loop : -0.80 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 575 TYR 0.010 0.001 TYR A 584 PHE 0.017 0.002 PHE C 489 TRP 0.029 0.001 TRP B 697 HIS 0.002 0.001 HIS D 289 Details of bonding type rmsd covalent geometry : bond 0.00362 (14644) covalent geometry : angle 0.55000 (19848) hydrogen bonds : bond 0.04197 ( 910) hydrogen bonds : angle 4.15503 ( 2661) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 302 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 GLU cc_start: 0.8391 (mt-10) cc_final: 0.7961 (mt-10) REVERT: A 308 MET cc_start: 0.7371 (OUTLIER) cc_final: 0.6864 (mpp) REVERT: A 423 GLN cc_start: 0.8523 (tp40) cc_final: 0.7868 (mm-40) REVERT: A 427 ASP cc_start: 0.8762 (m-30) cc_final: 0.8268 (m-30) REVERT: A 499 ARG cc_start: 0.8306 (mmm160) cc_final: 0.7866 (mmm160) REVERT: A 559 PHE cc_start: 0.7042 (m-80) cc_final: 0.6559 (m-10) REVERT: A 561 GLN cc_start: 0.8595 (mm-40) cc_final: 0.7620 (mp10) REVERT: A 562 MET cc_start: 0.8938 (OUTLIER) cc_final: 0.8481 (ttm) REVERT: A 572 MET cc_start: 0.8764 (mtp) cc_final: 0.8453 (ttm) REVERT: A 644 MET cc_start: 0.9336 (mmm) cc_final: 0.8240 (mmm) REVERT: C 308 MET cc_start: 0.8279 (mmm) cc_final: 0.7968 (mpp) REVERT: C 423 GLN cc_start: 0.8581 (tp40) cc_final: 0.8050 (mm-40) REVERT: C 499 ARG cc_start: 0.8507 (mmm160) cc_final: 0.8102 (mmm160) REVERT: C 559 PHE cc_start: 0.6527 (m-80) cc_final: 0.6000 (m-10) REVERT: C 635 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8711 (tp) REVERT: C 639 LYS cc_start: 0.9165 (mttt) cc_final: 0.8786 (mmtp) REVERT: D 293 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8211 (mt-10) REVERT: D 308 MET cc_start: 0.7573 (OUTLIER) cc_final: 0.7061 (mpp) REVERT: D 423 GLN cc_start: 0.8612 (tp40) cc_final: 0.7931 (mm-40) REVERT: D 427 ASP cc_start: 0.8795 (m-30) cc_final: 0.8327 (m-30) REVERT: D 432 ARG cc_start: 0.8650 (mpt-90) cc_final: 0.8433 (mmt90) REVERT: D 478 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8279 (mt-10) REVERT: D 499 ARG cc_start: 0.8531 (mmm160) cc_final: 0.8135 (mmm160) REVERT: D 535 LYS cc_start: 0.8635 (mtmm) cc_final: 0.8407 (mtpt) REVERT: D 692 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7331 (mp0) REVERT: D 705 ILE cc_start: 0.9339 (mt) cc_final: 0.9075 (mp) REVERT: B 293 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7792 (mt-10) REVERT: B 308 MET cc_start: 0.8107 (mmt) cc_final: 0.7639 (mpp) REVERT: B 423 GLN cc_start: 0.8500 (tp40) cc_final: 0.8073 (mm-40) REVERT: B 427 ASP cc_start: 0.8839 (m-30) cc_final: 0.8596 (m-30) REVERT: B 432 ARG cc_start: 0.8691 (mpt-90) cc_final: 0.8443 (mmt90) REVERT: B 464 LYS cc_start: 0.8027 (mmtp) cc_final: 0.7803 (mmmm) REVERT: B 467 ASN cc_start: 0.7987 (t0) cc_final: 0.7593 (t0) REVERT: B 499 ARG cc_start: 0.7998 (mmm160) cc_final: 0.7703 (mmm160) REVERT: B 534 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.7086 (mmm160) REVERT: B 535 LYS cc_start: 0.8668 (mtmm) cc_final: 0.8372 (mtpt) REVERT: B 536 GLU cc_start: 0.8855 (mp0) cc_final: 0.8497 (mp0) REVERT: B 562 MET cc_start: 0.9038 (mmm) cc_final: 0.8496 (mmt) REVERT: B 627 TYR cc_start: 0.7488 (m-80) cc_final: 0.6886 (m-80) REVERT: B 635 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8800 (tp) REVERT: B 705 ILE cc_start: 0.9301 (mt) cc_final: 0.9067 (mp) outliers start: 44 outliers final: 15 residues processed: 318 average time/residue: 0.5942 time to fit residues: 207.4575 Evaluate side-chains 312 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 291 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain D residue 308 MET Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 534 ARG Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain B residue 285 ASN Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 534 ARG Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 635 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 36 optimal weight: 0.5980 chunk 84 optimal weight: 0.0570 chunk 86 optimal weight: 20.0000 chunk 3 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 158 optimal weight: 0.6980 chunk 144 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 85 optimal weight: 8.9990 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN A 419 ASN D 301 ASN D 408 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.196158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.122889 restraints weight = 16825.478| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.05 r_work: 0.3225 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14644 Z= 0.145 Angle : 0.559 8.378 19848 Z= 0.292 Chirality : 0.039 0.160 2240 Planarity : 0.004 0.055 2412 Dihedral : 6.602 55.917 2282 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.77 % Allowed : 18.69 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.21), residues: 1700 helix: 2.21 (0.15), residues: 1108 sheet: -1.36 (0.80), residues: 64 loop : -0.85 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 575 TYR 0.009 0.001 TYR C 631 PHE 0.018 0.001 PHE D 489 TRP 0.034 0.001 TRP B 697 HIS 0.002 0.000 HIS D 289 Details of bonding type rmsd covalent geometry : bond 0.00322 (14644) covalent geometry : angle 0.55944 (19848) hydrogen bonds : bond 0.04015 ( 910) hydrogen bonds : angle 4.12542 ( 2661) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 311 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 293 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8009 (mt-10) REVERT: A 308 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.6885 (mpp) REVERT: A 423 GLN cc_start: 0.8553 (tp40) cc_final: 0.7876 (mm-40) REVERT: A 427 ASP cc_start: 0.8798 (m-30) cc_final: 0.8322 (m-30) REVERT: A 499 ARG cc_start: 0.8291 (mmm160) cc_final: 0.7858 (mmm160) REVERT: A 559 PHE cc_start: 0.7061 (m-80) cc_final: 0.6565 (m-10) REVERT: A 561 GLN cc_start: 0.8587 (mm-40) cc_final: 0.7681 (mp10) REVERT: A 562 MET cc_start: 0.8940 (OUTLIER) cc_final: 0.8523 (ttm) REVERT: A 572 MET cc_start: 0.8773 (mtp) cc_final: 0.8453 (ttm) REVERT: A 644 MET cc_start: 0.9346 (mmm) cc_final: 0.8197 (mmm) REVERT: C 293 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7761 (pm20) REVERT: C 308 MET cc_start: 0.8303 (mmm) cc_final: 0.8014 (mpp) REVERT: C 423 GLN cc_start: 0.8598 (tp40) cc_final: 0.7974 (mm-40) REVERT: C 427 ASP cc_start: 0.8793 (m-30) cc_final: 0.8348 (m-30) REVERT: C 499 ARG cc_start: 0.8444 (mmm160) cc_final: 0.8034 (mmm160) REVERT: C 559 PHE cc_start: 0.6619 (m-80) cc_final: 0.6188 (m-10) REVERT: C 635 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8680 (tp) REVERT: C 639 LYS cc_start: 0.9151 (mttt) cc_final: 0.8773 (mmtp) REVERT: D 293 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8264 (mt-10) REVERT: D 308 MET cc_start: 0.7593 (OUTLIER) cc_final: 0.7088 (mpp) REVERT: D 423 GLN cc_start: 0.8596 (tp40) cc_final: 0.7899 (mm-40) REVERT: D 427 ASP cc_start: 0.8769 (m-30) cc_final: 0.8286 (m-30) REVERT: D 432 ARG cc_start: 0.8630 (mpt-90) cc_final: 0.8404 (mmt90) REVERT: D 474 ARG cc_start: 0.8537 (ttp80) cc_final: 0.8150 (ttp80) REVERT: D 478 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8135 (mt-10) REVERT: D 499 ARG cc_start: 0.8487 (mmm160) cc_final: 0.8128 (mmm160) REVERT: D 534 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.6967 (mmm160) REVERT: D 535 LYS cc_start: 0.8623 (mtmm) cc_final: 0.8395 (mtpt) REVERT: D 692 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7754 (mm-30) REVERT: D 705 ILE cc_start: 0.9357 (mt) cc_final: 0.9085 (mp) REVERT: B 293 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7858 (mt-10) REVERT: B 308 MET cc_start: 0.8132 (mmt) cc_final: 0.7678 (mpp) REVERT: B 423 GLN cc_start: 0.8536 (tp40) cc_final: 0.8099 (mm-40) REVERT: B 427 ASP cc_start: 0.8841 (m-30) cc_final: 0.8601 (m-30) REVERT: B 432 ARG cc_start: 0.8654 (mpt-90) cc_final: 0.8391 (mmt90) REVERT: B 464 LYS cc_start: 0.8082 (mmtp) cc_final: 0.7861 (mmmm) REVERT: B 499 ARG cc_start: 0.7964 (mmm160) cc_final: 0.7658 (mmm160) REVERT: B 534 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.6985 (mmm160) REVERT: B 535 LYS cc_start: 0.8675 (mtmm) cc_final: 0.8414 (mtpt) REVERT: B 536 GLU cc_start: 0.8838 (mp0) cc_final: 0.8467 (mp0) REVERT: B 562 MET cc_start: 0.8987 (mmm) cc_final: 0.8446 (mmt) REVERT: B 627 TYR cc_start: 0.7446 (m-80) cc_final: 0.6824 (m-80) REVERT: B 635 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8760 (tp) REVERT: B 644 MET cc_start: 0.9350 (mmm) cc_final: 0.8287 (mmm) REVERT: B 705 ILE cc_start: 0.9330 (mt) cc_final: 0.9101 (mp) outliers start: 43 outliers final: 16 residues processed: 327 average time/residue: 0.5475 time to fit residues: 196.5486 Evaluate side-chains 322 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 299 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain D residue 308 MET Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 534 ARG Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain B residue 285 ASN Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 534 ARG Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 685 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 139 optimal weight: 0.0020 chunk 131 optimal weight: 1.9990 chunk 170 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 113 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 115 optimal weight: 0.5980 chunk 152 optimal weight: 0.7980 chunk 77 optimal weight: 0.1980 chunk 92 optimal weight: 8.9990 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN A 419 ASN D 301 ASN ** D 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 410 HIS ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.198168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.125906 restraints weight = 16980.492| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.08 r_work: 0.3265 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14644 Z= 0.122 Angle : 0.557 8.217 19848 Z= 0.290 Chirality : 0.038 0.161 2240 Planarity : 0.004 0.061 2412 Dihedral : 6.472 55.280 2282 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.80 % Allowed : 19.78 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.21), residues: 1700 helix: 2.30 (0.15), residues: 1108 sheet: -1.28 (0.80), residues: 64 loop : -0.85 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 575 TYR 0.009 0.001 TYR C 631 PHE 0.019 0.001 PHE C 489 TRP 0.037 0.001 TRP B 697 HIS 0.001 0.000 HIS B 410 Details of bonding type rmsd covalent geometry : bond 0.00262 (14644) covalent geometry : angle 0.55699 (19848) hydrogen bonds : bond 0.03771 ( 910) hydrogen bonds : angle 4.08129 ( 2661) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 326 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 293 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8040 (mt-10) REVERT: A 308 MET cc_start: 0.7510 (OUTLIER) cc_final: 0.7008 (mpp) REVERT: A 423 GLN cc_start: 0.8535 (tp40) cc_final: 0.8033 (mm-40) REVERT: A 427 ASP cc_start: 0.8815 (m-30) cc_final: 0.8514 (m-30) REVERT: A 499 ARG cc_start: 0.8257 (mmm160) cc_final: 0.7874 (mmm160) REVERT: A 559 PHE cc_start: 0.7109 (m-80) cc_final: 0.6640 (m-10) REVERT: A 561 GLN cc_start: 0.8547 (mm-40) cc_final: 0.7636 (mp10) REVERT: A 562 MET cc_start: 0.8907 (OUTLIER) cc_final: 0.8473 (ttm) REVERT: A 572 MET cc_start: 0.8757 (mtp) cc_final: 0.8449 (ttm) REVERT: C 293 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7782 (pm20) REVERT: C 308 MET cc_start: 0.8352 (mmm) cc_final: 0.8028 (mpp) REVERT: C 423 GLN cc_start: 0.8609 (tp40) cc_final: 0.8261 (mm-40) REVERT: C 427 ASP cc_start: 0.8780 (m-30) cc_final: 0.8509 (m-30) REVERT: C 471 ASP cc_start: 0.8603 (t70) cc_final: 0.8296 (t70) REVERT: C 499 ARG cc_start: 0.8419 (mmm160) cc_final: 0.8034 (mmm160) REVERT: C 559 PHE cc_start: 0.6631 (m-80) cc_final: 0.4884 (t80) REVERT: C 635 LEU cc_start: 0.9003 (mt) cc_final: 0.8649 (tp) REVERT: C 639 LYS cc_start: 0.9164 (mttt) cc_final: 0.8866 (mmtp) REVERT: D 293 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8282 (mt-10) REVERT: D 308 MET cc_start: 0.7666 (OUTLIER) cc_final: 0.7186 (mpp) REVERT: D 423 GLN cc_start: 0.8609 (tp40) cc_final: 0.8101 (mm-40) REVERT: D 427 ASP cc_start: 0.8764 (m-30) cc_final: 0.8458 (m-30) REVERT: D 432 ARG cc_start: 0.8675 (mpt-90) cc_final: 0.8441 (mmt90) REVERT: D 467 ASN cc_start: 0.7910 (t0) cc_final: 0.7488 (t0) REVERT: D 474 ARG cc_start: 0.8560 (ttp80) cc_final: 0.8133 (ttp80) REVERT: D 478 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8161 (mt-10) REVERT: D 499 ARG cc_start: 0.8453 (mmm160) cc_final: 0.8163 (mmm160) REVERT: D 535 LYS cc_start: 0.8627 (mtmm) cc_final: 0.8323 (mtpp) REVERT: D 654 ASP cc_start: 0.8364 (m-30) cc_final: 0.8042 (m-30) REVERT: D 705 ILE cc_start: 0.9384 (mt) cc_final: 0.9124 (mp) REVERT: B 293 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7894 (mt-10) REVERT: B 308 MET cc_start: 0.8137 (mmt) cc_final: 0.7683 (mpp) REVERT: B 423 GLN cc_start: 0.8528 (tp40) cc_final: 0.8264 (mm-40) REVERT: B 432 ARG cc_start: 0.8685 (mpt-90) cc_final: 0.8424 (mmt90) REVERT: B 464 LYS cc_start: 0.8059 (mmtp) cc_final: 0.7851 (mmmm) REVERT: B 499 ARG cc_start: 0.7948 (mmm160) cc_final: 0.7692 (mmm160) REVERT: B 534 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.7063 (mmm160) REVERT: B 535 LYS cc_start: 0.8637 (mtmm) cc_final: 0.8394 (mtpt) REVERT: B 536 GLU cc_start: 0.8894 (mp0) cc_final: 0.8594 (mp0) REVERT: B 562 MET cc_start: 0.8894 (mmm) cc_final: 0.8626 (mmp) REVERT: B 644 MET cc_start: 0.9402 (mmm) cc_final: 0.8318 (mmm) REVERT: B 705 ILE cc_start: 0.9374 (mt) cc_final: 0.9137 (mp) outliers start: 28 outliers final: 14 residues processed: 339 average time/residue: 0.5454 time to fit residues: 204.1079 Evaluate side-chains 320 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 302 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain D residue 308 MET Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 534 ARG Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 534 ARG Chi-restraints excluded: chain B residue 564 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 50 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 166 optimal weight: 0.9980 chunk 6 optimal weight: 10.0000 chunk 33 optimal weight: 0.6980 chunk 144 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN A 419 ASN D 301 ASN ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.195358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.121530 restraints weight = 17004.236| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.07 r_work: 0.3205 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14644 Z= 0.177 Angle : 0.607 12.101 19848 Z= 0.313 Chirality : 0.041 0.360 2240 Planarity : 0.004 0.059 2412 Dihedral : 6.621 57.218 2280 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 1.55 % Allowed : 20.43 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.21), residues: 1700 helix: 2.08 (0.15), residues: 1112 sheet: -1.32 (0.80), residues: 64 loop : -0.75 (0.30), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 575 TYR 0.013 0.001 TYR A 584 PHE 0.018 0.002 PHE C 489 TRP 0.041 0.001 TRP B 697 HIS 0.002 0.001 HIS B 410 Details of bonding type rmsd covalent geometry : bond 0.00399 (14644) covalent geometry : angle 0.60690 (19848) hydrogen bonds : bond 0.04266 ( 910) hydrogen bonds : angle 4.21836 ( 2661) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 298 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8044 (mt-10) REVERT: A 308 MET cc_start: 0.7540 (OUTLIER) cc_final: 0.7040 (mpp) REVERT: A 423 GLN cc_start: 0.8608 (tp40) cc_final: 0.7917 (mm-40) REVERT: A 427 ASP cc_start: 0.8827 (m-30) cc_final: 0.8377 (m-30) REVERT: A 499 ARG cc_start: 0.8298 (mmm160) cc_final: 0.7876 (mmm160) REVERT: A 559 PHE cc_start: 0.7040 (m-80) cc_final: 0.6590 (m-10) REVERT: A 562 MET cc_start: 0.8934 (OUTLIER) cc_final: 0.8477 (ttm) REVERT: A 572 MET cc_start: 0.8811 (mtp) cc_final: 0.8475 (ttm) REVERT: C 308 MET cc_start: 0.8355 (mmm) cc_final: 0.7957 (mpp) REVERT: C 423 GLN cc_start: 0.8629 (tp40) cc_final: 0.8180 (mm-40) REVERT: C 499 ARG cc_start: 0.8415 (mmm160) cc_final: 0.8099 (mmm-85) REVERT: C 559 PHE cc_start: 0.6614 (m-80) cc_final: 0.6124 (m-10) REVERT: C 560 GLN cc_start: 0.8577 (tp40) cc_final: 0.8267 (tp40) REVERT: C 635 LEU cc_start: 0.9070 (mt) cc_final: 0.8716 (tp) REVERT: C 639 LYS cc_start: 0.9187 (mttt) cc_final: 0.8814 (mmtp) REVERT: D 293 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8212 (mt-10) REVERT: D 308 MET cc_start: 0.7653 (OUTLIER) cc_final: 0.7151 (mpp) REVERT: D 423 GLN cc_start: 0.8634 (tp40) cc_final: 0.8145 (mm-40) REVERT: D 432 ARG cc_start: 0.8669 (mpt-90) cc_final: 0.8445 (mmt90) REVERT: D 478 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8299 (mt-10) REVERT: D 499 ARG cc_start: 0.8478 (mmm160) cc_final: 0.8153 (mmm160) REVERT: D 535 LYS cc_start: 0.8626 (mtmm) cc_final: 0.8312 (mtpp) REVERT: B 293 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7906 (mt-10) REVERT: B 308 MET cc_start: 0.8130 (mmt) cc_final: 0.7677 (mpp) REVERT: B 423 GLN cc_start: 0.8600 (tp40) cc_final: 0.8081 (mm-40) REVERT: B 427 ASP cc_start: 0.8837 (m-30) cc_final: 0.8405 (m-30) REVERT: B 432 ARG cc_start: 0.8700 (mpt-90) cc_final: 0.8449 (mmt90) REVERT: B 464 LYS cc_start: 0.8163 (mmtp) cc_final: 0.7949 (mmmm) REVERT: B 499 ARG cc_start: 0.7996 (mmm160) cc_final: 0.7698 (mmm160) REVERT: B 534 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.7155 (mmm160) REVERT: B 535 LYS cc_start: 0.8678 (mtmm) cc_final: 0.8394 (mtpt) REVERT: B 536 GLU cc_start: 0.8857 (mp0) cc_final: 0.8515 (mp0) REVERT: B 562 MET cc_start: 0.8945 (mmm) cc_final: 0.8486 (mmt) REVERT: B 575 ARG cc_start: 0.8303 (mmp80) cc_final: 0.7861 (mtm110) REVERT: B 627 TYR cc_start: 0.7429 (m-80) cc_final: 0.6833 (m-80) REVERT: B 705 ILE cc_start: 0.9377 (mt) cc_final: 0.9149 (mp) outliers start: 24 outliers final: 15 residues processed: 308 average time/residue: 0.6137 time to fit residues: 206.9805 Evaluate side-chains 308 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 289 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain D residue 308 MET Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 534 ARG Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 534 ARG Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 685 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 146 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 112 optimal weight: 0.6980 chunk 120 optimal weight: 2.9990 chunk 134 optimal weight: 0.0060 chunk 96 optimal weight: 3.9990 chunk 60 optimal weight: 0.2980 chunk 13 optimal weight: 0.9990 chunk 138 optimal weight: 10.0000 chunk 145 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN A 419 ASN D 301 ASN ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.197151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.124403 restraints weight = 16940.196| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.08 r_work: 0.3250 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14644 Z= 0.132 Angle : 0.584 12.199 19848 Z= 0.300 Chirality : 0.040 0.330 2240 Planarity : 0.004 0.060 2412 Dihedral : 6.403 55.158 2280 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.55 % Allowed : 20.94 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.21), residues: 1700 helix: 2.21 (0.15), residues: 1108 sheet: -1.24 (0.80), residues: 64 loop : -0.75 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 575 TYR 0.010 0.001 TYR A 584 PHE 0.019 0.001 PHE D 489 TRP 0.041 0.001 TRP B 697 HIS 0.002 0.000 HIS B 410 Details of bonding type rmsd covalent geometry : bond 0.00290 (14644) covalent geometry : angle 0.58361 (19848) hydrogen bonds : bond 0.03907 ( 910) hydrogen bonds : angle 4.13952 ( 2661) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7254.04 seconds wall clock time: 123 minutes 42.24 seconds (7422.24 seconds total)