Starting phenix.real_space_refine on Fri Jul 3 14:00:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mz5_24083/07_2026/7mz5_24083.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mz5_24083/07_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_24083/07_2026/7mz5_24083.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mz5_24083/07_2026/7mz5_24083.map" model { file = "/net/cci-nas-00/data/ceres_data/7mz5_24083/07_2026/7mz5_24083.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mz5_24083/07_2026/7mz5_24083.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7mz5_24083/07_2026/7mz5_24083.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mz5_24083/07_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-6108/lib/python3.11/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: 3.25, per 1000 atoms: 0.23 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: 1.08 Conformation dependent library (CDL) restraints added in 619.1 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: 0.32 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: 2.13 Time building geometry restraints manager: 1.46 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: 8082 17.77 - 35.55: 351 35.55 - 53.32: 76 53.32 - 71.09: 18 71.09 - 88.87: 5 Dihedral angle restraints: 8532 sinusoidal: 3432 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 8529 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.190 Find NCS groups from input model: 0.310 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:7.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 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 : 10.939 88.866 5252 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/Z covalent geometry : bond 0.00484 / 0.24 (14644) covalent geometry : angle 0.72092 / 0.38 (19848) hydrogen bonds : bond 0.13344 / 9.35 ( 910) hydrogen bonds : angle 5.13460 / 3.69 ( 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 : 0.516 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: 0.5700 time to fit residues: 281.7967 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 : 0.543 ------------------------------------------------------------------------------- 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... 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 = 0.4228 r_free = 0.4228 target = 0.195928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.120343 restraints weight = 16914.404| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.09 r_work: 0.3175 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2285 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 : 0.567 7.929 19848 Z= 0.304 Chirality : 0.040 0.173 2240 Planarity : 0.003 0.036 2412 Dihedral : 6.362 58.526 1960 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.48 % Allowed : 11.47 % Favored : 85.05 % 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: 2.20 (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 0.007 0.001 ARG B 474 TYR 0.022 0.001 TYR A 351 PHE 0.027 0.002 PHE A 304 TRP 0.016 0.002 TRP C 697 HIS 0.005 0.001 HIS B 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.19 (14644) covalent geometry : angle 0.56734 / 0.30 (19848) hydrogen bonds : bond 0.04779 / 3.17 ( 910) hydrogen bonds : angle 4.22031 / 3.01 ( 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 395 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 341 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 GLN cc_start: 0.8561 (tp40) cc_final: 0.8039 (mm-40) REVERT: A 427 ASP cc_start: 0.8886 (m-30) cc_final: 0.8637 (m-30) REVERT: A 465 LEU cc_start: 0.8569 (tp) cc_final: 0.8304 (tp) REVERT: A 499 ARG cc_start: 0.8348 (mmm160) cc_final: 0.8015 (mmm160) REVERT: A 559 PHE cc_start: 0.7254 (m-80) cc_final: 0.6895 (m-10) REVERT: A 562 MET cc_start: 0.8824 (mtm) cc_final: 0.8540 (ttm) REVERT: A 656 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8663 (tmtp) REVERT: A 682 MET cc_start: 0.8878 (mmt) cc_final: 0.8482 (mmm) REVERT: A 694 LYS cc_start: 0.8258 (mtmt) cc_final: 0.7900 (pttt) REVERT: C 293 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7632 (mt-10) REVERT: C 308 MET cc_start: 0.8238 (mmm) cc_final: 0.8014 (mpp) REVERT: C 423 GLN cc_start: 0.8537 (tp40) cc_final: 0.7989 (mm-40) REVERT: C 427 ASP cc_start: 0.8855 (m-30) cc_final: 0.8333 (m-30) REVERT: C 478 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8549 (mt-10) REVERT: C 499 ARG cc_start: 0.8570 (mmm160) cc_final: 0.8116 (mmm160) REVERT: C 509 ASP cc_start: 0.7862 (t0) cc_final: 0.7492 (p0) REVERT: C 639 LYS cc_start: 0.9190 (mttt) cc_final: 0.8629 (mtmt) REVERT: C 656 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8679 (tmtp) REVERT: D 423 GLN cc_start: 0.8525 (tp40) cc_final: 0.8137 (mm-40) REVERT: D 464 LYS cc_start: 0.7983 (mmtp) cc_final: 0.7684 (mmmm) REVERT: D 478 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8352 (mt-10) REVERT: D 499 ARG cc_start: 0.8563 (mmm160) cc_final: 0.8158 (mmm160) REVERT: D 535 LYS cc_start: 0.8767 (mtmm) cc_final: 0.8523 (mtpt) REVERT: D 627 TYR cc_start: 0.7495 (m-80) cc_final: 0.7095 (m-80) REVERT: D 636 GLU cc_start: 0.8998 (mm-30) cc_final: 0.8689 (mm-30) REVERT: D 639 LYS cc_start: 0.9198 (mttt) cc_final: 0.8922 (mmtp) REVERT: D 709 GLU cc_start: 0.8807 (tt0) cc_final: 0.8564 (tt0) REVERT: B 293 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7240 (mp0) REVERT: B 308 MET cc_start: 0.8300 (mmt) cc_final: 0.7823 (mpp) REVERT: B 423 GLN cc_start: 0.8509 (tp40) cc_final: 0.8120 (mm-40) REVERT: B 427 ASP cc_start: 0.8816 (m-30) cc_final: 0.8575 (m-30) REVERT: B 506 LEU cc_start: 0.8854 (tp) cc_final: 0.8499 (tp) REVERT: B 534 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.7094 (mmm160) REVERT: B 535 LYS cc_start: 0.8734 (mtmm) cc_final: 0.8459 (mtpt) REVERT: B 536 GLU cc_start: 0.8887 (mp0) cc_final: 0.8577 (mp0) REVERT: B 560 GLN cc_start: 0.8441 (tp40) cc_final: 0.8052 (tp40) REVERT: B 564 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8667 (tp) REVERT: B 627 TYR cc_start: 0.7563 (m-80) cc_final: 0.6966 (m-80) REVERT: B 682 MET cc_start: 0.8877 (mmt) cc_final: 0.8463 (mmt) REVERT: B 697 TRP cc_start: 0.8342 (t60) cc_final: 0.8015 (t60) REVERT: B 705 ILE cc_start: 0.9418 (mt) cc_final: 0.9104 (mp) REVERT: B 709 GLU cc_start: 0.8846 (tt0) cc_final: 0.8462 (tt0) outliers start: 54 outliers final: 22 residues processed: 367 average time/residue: 0.5090 time to fit residues: 205.7039 Evaluate side-chains 330 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 304 time to evaluate : 0.422 ------------------------------------------------------------------------------- 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: 5.9990 chunk 104 optimal weight: 3.9990 chunk 138 optimal weight: 9.9990 chunk 123 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 129 optimal weight: 10.0000 chunk 64 optimal weight: 0.7980 chunk 112 optimal weight: 0.5980 chunk 132 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4212 r_free = 0.4212 target = 0.194465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.119933 restraints weight = 17099.492| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.07 r_work: 0.3170 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 14644 Z= 0.188 Angle : 0.556 7.669 19848 Z= 0.297 Chirality : 0.040 0.153 2240 Planarity : 0.003 0.035 2412 Dihedral : 6.265 59.936 1960 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 4.06 % Allowed : 13.66 % Favored : 82.28 % 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: 1.49 (0.21), residues: 1700 helix: 2.04 (0.15), residues: 1132 sheet: -1.80 (0.79), residues: 64 loop : -1.10 (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 0.012 0.001 TRP C 697 HIS 0.003 0.001 HIS B 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.19 (14644) covalent geometry : angle 0.55616 / 0.30 (19848) hydrogen bonds : bond 0.04580 / 3.03 ( 910) hydrogen bonds : angle 4.18591 / 2.98 ( 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 390 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 327 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8147 (mt-10) REVERT: A 423 GLN cc_start: 0.8587 (tp40) cc_final: 0.8054 (mm-40) REVERT: A 427 ASP cc_start: 0.8810 (m-30) cc_final: 0.8551 (m-30) REVERT: A 499 ARG cc_start: 0.8326 (mmm160) cc_final: 0.7979 (mmm160) REVERT: A 513 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8583 (tp30) REVERT: A 559 PHE cc_start: 0.7153 (m-80) cc_final: 0.6715 (m-10) REVERT: A 562 MET cc_start: 0.8912 (mtm) cc_final: 0.8499 (ttm) REVERT: A 694 LYS cc_start: 0.8210 (mtmt) cc_final: 0.7841 (pttt) REVERT: C 308 MET cc_start: 0.8242 (mmm) cc_final: 0.7862 (mpp) REVERT: C 423 GLN cc_start: 0.8669 (tp40) cc_final: 0.8098 (mm-40) REVERT: C 427 ASP cc_start: 0.8818 (m-30) cc_final: 0.8397 (m-30) REVERT: C 499 ARG cc_start: 0.8527 (mmm160) cc_final: 0.8098 (mmm160) REVERT: C 635 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8862 (mm) REVERT: C 639 LYS cc_start: 0.9205 (mttt) cc_final: 0.8829 (mmtp) REVERT: C 682 MET cc_start: 0.8905 (mmt) cc_final: 0.8245 (mmt) REVERT: D 293 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8066 (mt-10) REVERT: D 423 GLN cc_start: 0.8598 (tp40) cc_final: 0.8043 (mm-40) REVERT: D 427 ASP cc_start: 0.8879 (m-30) cc_final: 0.8415 (m-30) REVERT: D 464 LYS cc_start: 0.8094 (mmtp) cc_final: 0.7801 (mmmm) REVERT: D 478 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8338 (mt-10) REVERT: D 499 ARG cc_start: 0.8561 (mmm160) cc_final: 0.8149 (mmm160) REVERT: D 534 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.7189 (mmm160) REVERT: D 535 LYS cc_start: 0.8722 (mtmm) cc_final: 0.8446 (mtpt) REVERT: D 536 GLU cc_start: 0.8914 (mp0) cc_final: 0.8648 (mp0) REVERT: D 562 MET cc_start: 0.8211 (mmt) cc_final: 0.7998 (mmt) REVERT: D 639 LYS cc_start: 0.9209 (mttt) cc_final: 0.8899 (mtmm) REVERT: D 682 MET cc_start: 0.8952 (mmt) cc_final: 0.8601 (mmt) REVERT: D 705 ILE cc_start: 0.9352 (mt) cc_final: 0.9090 (mp) REVERT: B 293 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7769 (mt-10) REVERT: B 308 MET cc_start: 0.8146 (mmt) cc_final: 0.7625 (mpp) REVERT: B 423 GLN cc_start: 0.8565 (tp40) cc_final: 0.8168 (mm-40) REVERT: B 425 LYS cc_start: 0.8894 (mttm) cc_final: 0.8560 (mttm) REVERT: B 427 ASP cc_start: 0.8833 (m-30) cc_final: 0.8554 (m-30) REVERT: B 464 LYS cc_start: 0.8073 (mmtp) cc_final: 0.7766 (mmmm) REVERT: B 467 ASN cc_start: 0.8064 (t0) cc_final: 0.7704 (t0) REVERT: B 534 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.7111 (mmm160) REVERT: B 535 LYS cc_start: 0.8703 (mtmm) cc_final: 0.8476 (mtpt) REVERT: B 536 GLU cc_start: 0.8898 (mp0) cc_final: 0.8665 (mp0) REVERT: B 627 TYR cc_start: 0.7593 (m-80) cc_final: 0.6973 (m-80) REVERT: B 682 MET cc_start: 0.8868 (mmt) cc_final: 0.8251 (mmt) REVERT: B 709 GLU cc_start: 0.8887 (tt0) cc_final: 0.8446 (tt0) outliers start: 63 outliers final: 26 residues processed: 356 average time/residue: 0.5491 time to fit residues: 213.9469 Evaluate side-chains 335 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 306 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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 556 THR 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 413 LEU 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 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 534 ARG Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 714 LYS 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 556 THR Chi-restraints excluded: chain B residue 562 MET 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: 1.9990 chunk 23 optimal weight: 0.9990 chunk 42 optimal weight: 9.9990 chunk 158 optimal weight: 0.9990 chunk 126 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 96 optimal weight: 9.9990 chunk 151 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 117 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 301 ASN A 419 ASN C 301 ASN D 301 ASN D 408 ASN B 419 ASN B 691 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.196132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.122539 restraints weight = 16985.020| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.06 r_work: 0.3207 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14644 Z= 0.142 Angle : 0.529 7.357 19848 Z= 0.281 Chirality : 0.039 0.158 2240 Planarity : 0.003 0.040 2412 Dihedral : 5.681 54.283 1952 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.48 % Allowed : 15.98 % Favored : 80.54 % 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: 1.55 (0.21), residues: 1700 helix: 2.10 (0.15), residues: 1132 sheet: -1.62 (0.79), residues: 64 loop : -1.14 (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 0.009 0.001 TRP C 697 HIS 0.002 0.001 HIS B 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (14644) covalent geometry : angle 0.52853 / 0.28 (19848) hydrogen bonds : bond 0.04120 / 2.73 ( 910) hydrogen bonds : angle 4.08839 / 2.92 ( 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 372 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 318 time to evaluate : 0.386 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: 0.8511 (mt-10) cc_final: 0.8150 (mt-10) REVERT: A 308 MET cc_start: 0.7134 (OUTLIER) cc_final: 0.6387 (mpt) REVERT: A 423 GLN cc_start: 0.8528 (tp40) cc_final: 0.7945 (mm-40) REVERT: A 427 ASP cc_start: 0.8819 (m-30) cc_final: 0.8497 (m-30) REVERT: A 478 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8417 (mt-10) REVERT: A 559 PHE cc_start: 0.7137 (m-80) cc_final: 0.6618 (m-10) REVERT: A 562 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.8515 (ttm) REVERT: A 572 MET cc_start: 0.8761 (mtp) cc_final: 0.8533 (ttm) REVERT: C 293 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7473 (pm20) REVERT: C 308 MET cc_start: 0.8268 (mmm) cc_final: 0.7977 (mpp) REVERT: C 423 GLN cc_start: 0.8651 (tp40) cc_final: 0.8030 (mm-40) REVERT: C 427 ASP cc_start: 0.8824 (m-30) cc_final: 0.8333 (m-30) REVERT: C 499 ARG cc_start: 0.8484 (mmm160) cc_final: 0.8064 (mmm160) REVERT: C 627 TYR cc_start: 0.7465 (m-80) cc_final: 0.6910 (m-80) REVERT: C 635 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8653 (tp) REVERT: C 639 LYS cc_start: 0.9165 (mttt) cc_final: 0.8624 (mmtm) REVERT: D 293 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8093 (mt-10) REVERT: D 308 MET cc_start: 0.7437 (OUTLIER) cc_final: 0.6920 (mpp) REVERT: D 401 TYR cc_start: 0.7910 (m-80) cc_final: 0.7620 (m-80) REVERT: D 423 GLN cc_start: 0.8561 (tp40) cc_final: 0.7956 (mm-40) REVERT: D 427 ASP cc_start: 0.8874 (m-30) cc_final: 0.8383 (m-30) REVERT: D 432 ARG cc_start: 0.8633 (mpt180) cc_final: 0.8432 (mmt90) REVERT: D 464 LYS cc_start: 0.8098 (mmtp) cc_final: 0.7829 (mmmm) REVERT: D 478 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8310 (mt-10) REVERT: D 499 ARG cc_start: 0.8519 (mmm160) cc_final: 0.8241 (mmt180) REVERT: D 535 LYS cc_start: 0.8712 (mtmm) cc_final: 0.8479 (mtpt) REVERT: D 627 TYR cc_start: 0.7509 (m-80) cc_final: 0.7096 (m-80) REVERT: D 639 LYS cc_start: 0.9157 (mttt) cc_final: 0.8859 (mtmm) REVERT: D 682 MET cc_start: 0.8958 (mmt) cc_final: 0.8625 (mmm) REVERT: B 293 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7790 (mt-10) REVERT: B 308 MET cc_start: 0.8115 (mmt) cc_final: 0.7727 (mpp) REVERT: B 423 GLN cc_start: 0.8504 (tp40) cc_final: 0.8076 (mm-40) REVERT: B 427 ASP cc_start: 0.8823 (m-30) cc_final: 0.8548 (m-30) REVERT: B 432 ARG cc_start: 0.8629 (mpt-90) cc_final: 0.8380 (mmt90) REVERT: B 464 LYS cc_start: 0.8072 (mmtp) cc_final: 0.7769 (mmmm) REVERT: B 467 ASN cc_start: 0.8016 (t0) cc_final: 0.7643 (t0) REVERT: B 534 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.7074 (mmm160) REVERT: B 535 LYS cc_start: 0.8698 (mtmm) cc_final: 0.8454 (mtpt) REVERT: B 536 GLU cc_start: 0.8846 (mp0) cc_final: 0.8636 (mp0) REVERT: B 627 TYR cc_start: 0.7522 (m-80) cc_final: 0.6951 (m-80) outliers start: 54 outliers final: 16 residues processed: 337 average time/residue: 0.5258 time to fit residues: 195.3917 Evaluate side-chains 318 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 297 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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 C residue 413 LEU Chi-restraints excluded: chain C residue 483 SER 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 308 MET Chi-restraints excluded: chain D residue 413 LEU 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 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: 1.9990 chunk 72 optimal weight: 0.9980 chunk 93 optimal weight: 7.9990 chunk 89 optimal weight: 5.9990 chunk 163 optimal weight: 1.9990 chunk 58 optimal weight: 0.0770 chunk 37 optimal weight: 0.6980 chunk 128 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 139 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 301 ASN A 419 ASN C 301 ASN D 301 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.194729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.120254 restraints weight = 17072.935| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.10 r_work: 0.3176 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14644 Z= 0.175 Angle : 0.552 7.194 19848 Z= 0.291 Chirality : 0.040 0.164 2240 Planarity : 0.003 0.042 2412 Dihedral : 5.519 52.651 1948 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.29 % Allowed : 17.40 % Favored : 79.32 % 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: 1.72 (0.21), residues: 1700 helix: 2.18 (0.15), residues: 1108 sheet: -1.64 (0.79), residues: 64 loop : -0.78 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 575 TYR 0.010 0.001 TYR C 666 PHE 0.017 0.002 PHE C 489 TRP 0.021 0.001 TRP B 697 HIS 0.002 0.001 HIS B 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (14644) covalent geometry : angle 0.55206 / 0.29 (19848) hydrogen bonds : bond 0.04312 / 2.85 ( 910) hydrogen bonds : angle 4.17967 / 2.98 ( 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 360 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 309 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8226 (mt-10) REVERT: A 423 GLN cc_start: 0.8539 (tp40) cc_final: 0.7923 (mm-40) REVERT: A 427 ASP cc_start: 0.8806 (m-30) cc_final: 0.8521 (m-30) REVERT: A 499 ARG cc_start: 0.8303 (mmm160) cc_final: 0.7838 (mmm160) REVERT: A 559 PHE cc_start: 0.7155 (m-80) cc_final: 0.6624 (m-10) REVERT: A 561 GLN cc_start: 0.8609 (mm-40) cc_final: 0.7627 (mp10) REVERT: A 562 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8498 (ttm) REVERT: A 572 MET cc_start: 0.8826 (mtp) cc_final: 0.8557 (ttm) REVERT: A 644 MET cc_start: 0.9345 (mmm) cc_final: 0.8232 (mmm) REVERT: A 692 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7724 (mp0) REVERT: C 293 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7469 (pm20) REVERT: C 308 MET cc_start: 0.8290 (mmm) cc_final: 0.7976 (mpp) REVERT: C 423 GLN cc_start: 0.8670 (tp40) cc_final: 0.8184 (mm-40) REVERT: C 499 ARG cc_start: 0.8491 (mmm160) cc_final: 0.8132 (mmm160) REVERT: C 627 TYR cc_start: 0.7630 (m-80) cc_final: 0.7001 (m-80) REVERT: C 635 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8696 (tp) REVERT: C 639 LYS cc_start: 0.9196 (mttt) cc_final: 0.8824 (mmtp) REVERT: C 682 MET cc_start: 0.8903 (mmt) cc_final: 0.8311 (mmt) REVERT: D 293 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8016 (mt-10) REVERT: D 308 MET cc_start: 0.7490 (OUTLIER) cc_final: 0.6975 (mpp) REVERT: D 401 TYR cc_start: 0.7921 (m-80) cc_final: 0.7645 (m-80) REVERT: D 423 GLN cc_start: 0.8624 (tp40) cc_final: 0.8014 (mm-40) REVERT: D 427 ASP cc_start: 0.8824 (m-30) cc_final: 0.8337 (m-30) REVERT: D 432 ARG cc_start: 0.8647 (mpt180) cc_final: 0.8398 (mmt90) REVERT: D 464 LYS cc_start: 0.8112 (mmtp) cc_final: 0.7848 (mmmm) REVERT: D 478 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8348 (mt-10) REVERT: D 499 ARG cc_start: 0.8546 (mmm160) cc_final: 0.8282 (mmt180) REVERT: D 535 LYS cc_start: 0.8716 (mtmm) cc_final: 0.8499 (mtpt) REVERT: D 627 TYR cc_start: 0.7471 (m-80) cc_final: 0.7046 (m-80) REVERT: D 639 LYS cc_start: 0.9188 (mttt) cc_final: 0.8638 (mtmt) REVERT: D 682 MET cc_start: 0.8903 (mmt) cc_final: 0.8240 (mmt) REVERT: B 293 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7803 (mt-10) REVERT: B 308 MET cc_start: 0.8089 (mmt) cc_final: 0.7632 (mpp) REVERT: B 423 GLN cc_start: 0.8535 (tp40) cc_final: 0.8059 (mm-40) REVERT: B 427 ASP cc_start: 0.8852 (m-30) cc_final: 0.8551 (m-30) REVERT: B 432 ARG cc_start: 0.8663 (mpt-90) cc_final: 0.8426 (mmt90) REVERT: B 534 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.7149 (mmm160) REVERT: B 535 LYS cc_start: 0.8681 (mtmm) cc_final: 0.8415 (mtpt) REVERT: B 536 GLU cc_start: 0.8876 (mp0) cc_final: 0.8617 (mp0) REVERT: B 562 MET cc_start: 0.8954 (mmm) cc_final: 0.8349 (mmt) REVERT: B 627 TYR cc_start: 0.7568 (m-80) cc_final: 0.6938 (m-80) REVERT: B 635 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8780 (tp) REVERT: B 644 MET cc_start: 0.9366 (mmm) cc_final: 0.8321 (mmm) outliers start: 51 outliers final: 19 residues processed: 329 average time/residue: 0.5464 time to fit residues: 197.6721 Evaluate side-chains 323 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 299 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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 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 443 LEU Chi-restraints excluded: chain C residue 483 SER 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 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 601 ASP Chi-restraints excluded: chain D residue 678 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 678 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 150 optimal weight: 0.9980 chunk 162 optimal weight: 0.7980 chunk 113 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 126 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 137 optimal weight: 9.9990 chunk 79 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 157 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4225 r_free = 0.4225 target = 0.195734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.121950 restraints weight = 17013.131| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.06 r_work: 0.3216 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14644 Z= 0.141 Angle : 0.539 7.372 19848 Z= 0.284 Chirality : 0.039 0.160 2240 Planarity : 0.003 0.044 2412 Dihedral : 5.175 49.893 1942 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.84 % Allowed : 18.04 % Favored : 79.12 % 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: 2.23 (0.15), residues: 1108 sheet: -1.52 (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 D 666 PHE 0.017 0.001 PHE C 489 TRP 0.028 0.001 TRP B 697 HIS 0.001 0.000 HIS B 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (14644) covalent geometry : angle 0.53859 / 0.28 (19848) hydrogen bonds : bond 0.04042 / 2.68 ( 910) hydrogen bonds : angle 4.11857 / 2.94 ( 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 361 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 317 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8234 (mt-10) REVERT: A 308 MET cc_start: 0.7237 (OUTLIER) cc_final: 0.6680 (mpp) REVERT: A 423 GLN cc_start: 0.8576 (tp40) cc_final: 0.7989 (mm-40) REVERT: A 427 ASP cc_start: 0.8820 (m-30) cc_final: 0.8500 (m-30) REVERT: A 499 ARG cc_start: 0.8285 (mmm160) cc_final: 0.7855 (mmm160) REVERT: A 559 PHE cc_start: 0.7174 (m-80) cc_final: 0.6683 (m-10) REVERT: A 561 GLN cc_start: 0.8571 (mm-40) cc_final: 0.7718 (mp10) REVERT: A 562 MET cc_start: 0.8929 (OUTLIER) cc_final: 0.8167 (mtt) REVERT: A 572 MET cc_start: 0.8810 (mtp) cc_final: 0.8518 (ttm) REVERT: A 644 MET cc_start: 0.9349 (mmm) cc_final: 0.8245 (mmm) REVERT: C 308 MET cc_start: 0.8308 (mmm) cc_final: 0.7995 (mpp) REVERT: C 423 GLN cc_start: 0.8641 (tp40) cc_final: 0.8063 (mm-40) REVERT: C 427 ASP cc_start: 0.8776 (m-30) cc_final: 0.8368 (m-30) REVERT: C 471 ASP cc_start: 0.8590 (t70) cc_final: 0.8249 (t70) REVERT: C 499 ARG cc_start: 0.8471 (mmm160) cc_final: 0.8161 (mmm160) REVERT: C 561 GLN cc_start: 0.8638 (mm110) cc_final: 0.7502 (mp10) REVERT: C 635 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8676 (tp) REVERT: C 639 LYS cc_start: 0.9174 (mttt) cc_final: 0.8803 (mmtp) REVERT: C 682 MET cc_start: 0.8868 (mmt) cc_final: 0.8252 (mmt) REVERT: D 293 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8142 (mt-10) REVERT: D 308 MET cc_start: 0.7642 (OUTLIER) cc_final: 0.7092 (mpp) REVERT: D 423 GLN cc_start: 0.8657 (tp40) cc_final: 0.7978 (mm-40) REVERT: D 427 ASP cc_start: 0.8843 (m-30) cc_final: 0.8389 (m-30) REVERT: D 432 ARG cc_start: 0.8648 (mpt180) cc_final: 0.8431 (mmt90) REVERT: D 474 ARG cc_start: 0.8574 (ttp80) cc_final: 0.8162 (ttp80) REVERT: D 478 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8169 (mt-10) REVERT: D 499 ARG cc_start: 0.8531 (mmm160) cc_final: 0.8137 (mmm160) REVERT: D 534 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.7099 (mmm160) REVERT: D 535 LYS cc_start: 0.8701 (mtmm) cc_final: 0.8470 (mtpt) REVERT: D 536 GLU cc_start: 0.8947 (mp0) cc_final: 0.8715 (mp0) REVERT: D 639 LYS cc_start: 0.9166 (mttt) cc_final: 0.8626 (mtmt) REVERT: D 682 MET cc_start: 0.8936 (mmt) cc_final: 0.8408 (mmt) REVERT: D 705 ILE cc_start: 0.9387 (mt) cc_final: 0.9120 (mp) REVERT: B 293 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7803 (mt-10) REVERT: B 308 MET cc_start: 0.8112 (mmt) cc_final: 0.7661 (mpp) REVERT: B 423 GLN cc_start: 0.8554 (tp40) cc_final: 0.8118 (mm-40) REVERT: B 427 ASP cc_start: 0.8853 (m-30) cc_final: 0.8593 (m-30) REVERT: B 432 ARG cc_start: 0.8679 (mpt-90) cc_final: 0.8439 (mmt90) REVERT: B 464 LYS cc_start: 0.8013 (mmtp) cc_final: 0.7684 (mmmm) REVERT: B 478 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8471 (mt-10) REVERT: B 534 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.7129 (mmm160) REVERT: B 535 LYS cc_start: 0.8664 (mtmm) cc_final: 0.8416 (mtpt) REVERT: B 536 GLU cc_start: 0.8847 (mp0) cc_final: 0.8543 (mp0) REVERT: B 562 MET cc_start: 0.8987 (mmm) cc_final: 0.8478 (mmt) REVERT: B 627 TYR cc_start: 0.7551 (m-80) cc_final: 0.6914 (m-80) REVERT: B 635 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8786 (tp) outliers start: 44 outliers final: 15 residues processed: 333 average time/residue: 0.5398 time to fit residues: 197.4743 Evaluate side-chains 314 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 292 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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 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 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 483 SER Chi-restraints excluded: chain D residue 534 ARG Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 678 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 572 MET Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 678 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 79 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 153 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 169 optimal weight: 0.2980 chunk 87 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 35 optimal weight: 0.3980 chunk 76 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4237 r_free = 0.4237 target = 0.196984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.124123 restraints weight = 16901.117| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.06 r_work: 0.3242 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14644 Z= 0.128 Angle : 0.533 8.046 19848 Z= 0.280 Chirality : 0.038 0.160 2240 Planarity : 0.004 0.052 2412 Dihedral : 5.070 46.506 1942 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.71 % Allowed : 18.56 % Favored : 78.74 % 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: 1.76 (0.21), residues: 1700 helix: 2.20 (0.15), residues: 1112 sheet: -1.39 (0.80), residues: 64 loop : -0.79 (0.29), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 575 TYR 0.008 0.001 TYR C 631 PHE 0.018 0.001 PHE C 489 TRP 0.030 0.001 TRP B 697 HIS 0.002 0.000 HIS B 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (14644) covalent geometry : angle 0.53276 / 0.28 (19848) hydrogen bonds : bond 0.03879 / 2.58 ( 910) hydrogen bonds : angle 4.08306 / 2.92 ( 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 363 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 321 time to evaluate : 0.604 Fit side-chains revert: symmetry clash REVERT: A 293 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8254 (mt-10) REVERT: A 308 MET cc_start: 0.7524 (OUTLIER) cc_final: 0.6974 (mpp) REVERT: A 423 GLN cc_start: 0.8475 (tp40) cc_final: 0.8091 (mm-40) REVERT: A 499 ARG cc_start: 0.8275 (mmm160) cc_final: 0.7887 (mmm160) REVERT: A 559 PHE cc_start: 0.7114 (m-80) cc_final: 0.6604 (m-10) REVERT: A 561 GLN cc_start: 0.8561 (mm-40) cc_final: 0.7636 (mp10) REVERT: A 562 MET cc_start: 0.8910 (OUTLIER) cc_final: 0.8453 (ttm) REVERT: A 572 MET cc_start: 0.8792 (mtp) cc_final: 0.8484 (ttm) REVERT: A 644 MET cc_start: 0.9355 (mmm) cc_final: 0.8192 (mmm) REVERT: C 293 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7568 (pm20) REVERT: C 308 MET cc_start: 0.8306 (mmm) cc_final: 0.7993 (mpp) REVERT: C 423 GLN cc_start: 0.8626 (tp40) cc_final: 0.8066 (mm-40) REVERT: C 427 ASP cc_start: 0.8798 (m-30) cc_final: 0.8375 (m-30) REVERT: C 499 ARG cc_start: 0.8488 (mmm160) cc_final: 0.8175 (mmm160) REVERT: C 559 PHE cc_start: 0.6558 (m-80) cc_final: 0.4778 (t80) REVERT: C 635 LEU cc_start: 0.9022 (mt) cc_final: 0.8664 (tp) REVERT: C 639 LYS cc_start: 0.9166 (mttt) cc_final: 0.8866 (mmtp) REVERT: C 682 MET cc_start: 0.8914 (mmt) cc_final: 0.8291 (mmt) REVERT: D 293 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8212 (mt-10) REVERT: D 308 MET cc_start: 0.7598 (OUTLIER) cc_final: 0.7063 (mpp) REVERT: D 408 ASN cc_start: 0.7558 (OUTLIER) cc_final: 0.7111 (t0) REVERT: D 411 ASP cc_start: 0.7578 (m-30) cc_final: 0.7214 (m-30) REVERT: D 423 GLN cc_start: 0.8623 (tp40) cc_final: 0.7954 (mm-40) REVERT: D 427 ASP cc_start: 0.8794 (m-30) cc_final: 0.8385 (m-30) REVERT: D 432 ARG cc_start: 0.8647 (mpt180) cc_final: 0.8414 (mmt90) REVERT: D 478 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8320 (mt-10) REVERT: D 499 ARG cc_start: 0.8491 (mmm160) cc_final: 0.8152 (mmm160) REVERT: D 534 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8416 (mmt180) REVERT: D 535 LYS cc_start: 0.8694 (mtmm) cc_final: 0.8465 (mtpt) REVERT: D 639 LYS cc_start: 0.9148 (mttt) cc_final: 0.8663 (mttt) REVERT: D 682 MET cc_start: 0.8888 (mmt) cc_final: 0.8311 (mmt) REVERT: D 705 ILE cc_start: 0.9385 (mt) cc_final: 0.9132 (mp) REVERT: B 293 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7864 (mt-10) REVERT: B 308 MET cc_start: 0.8137 (mmt) cc_final: 0.7671 (mpp) REVERT: B 423 GLN cc_start: 0.8516 (tp40) cc_final: 0.8216 (mm-40) REVERT: B 432 ARG cc_start: 0.8694 (mpt-90) cc_final: 0.8435 (mmt90) REVERT: B 464 LYS cc_start: 0.8085 (mmtp) cc_final: 0.7868 (mmmm) REVERT: B 534 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.7037 (mmm160) REVERT: B 535 LYS cc_start: 0.8646 (mtmm) cc_final: 0.8379 (mtpt) REVERT: B 536 GLU cc_start: 0.8844 (mp0) cc_final: 0.8538 (mp0) REVERT: B 562 MET cc_start: 0.8941 (mmm) cc_final: 0.8469 (mmt) REVERT: B 627 TYR cc_start: 0.7411 (m-80) cc_final: 0.6838 (m-80) REVERT: B 644 MET cc_start: 0.9401 (mmm) cc_final: 0.8282 (mmm) REVERT: B 705 ILE cc_start: 0.9353 (mt) cc_final: 0.9125 (mp) outliers start: 42 outliers final: 9 residues processed: 332 average time/residue: 0.5471 time to fit residues: 201.3299 Evaluate side-chains 314 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 299 time to evaluate : 0.525 ------------------------------------------------------------------------------- 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 C residue 413 LEU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain D residue 308 MET Chi-restraints excluded: chain D residue 408 ASN Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 534 ARG Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 534 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 36 optimal weight: 0.9990 chunk 84 optimal weight: 7.9990 chunk 86 optimal weight: 20.0000 chunk 3 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 chunk 158 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4218 r_free = 0.4218 target = 0.195017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.121206 restraints weight = 16886.796| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.05 r_work: 0.3199 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14644 Z= 0.177 Angle : 0.582 11.301 19848 Z= 0.304 Chirality : 0.041 0.298 2240 Planarity : 0.004 0.056 2412 Dihedral : 4.859 36.302 1936 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.38 % Allowed : 19.33 % Favored : 78.29 % 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: 1.62 (0.21), residues: 1700 helix: 2.09 (0.15), residues: 1108 sheet: -1.37 (0.80), residues: 64 loop : -0.81 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 575 TYR 0.013 0.001 TYR A 584 PHE 0.018 0.002 PHE C 489 TRP 0.036 0.001 TRP B 697 HIS 0.002 0.001 HIS D 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 (14644) covalent geometry : angle 0.58244 / 0.30 (19848) hydrogen bonds : bond 0.04268 / 2.83 ( 910) hydrogen bonds : angle 4.21169 / 3.02 ( 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 341 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 304 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8199 (mt-10) REVERT: A 308 MET cc_start: 0.7407 (OUTLIER) cc_final: 0.6862 (mpp) REVERT: A 423 GLN cc_start: 0.8569 (tp40) cc_final: 0.7923 (mm-40) REVERT: A 427 ASP cc_start: 0.8788 (m-30) cc_final: 0.8323 (m-30) REVERT: A 499 ARG cc_start: 0.8272 (mmm160) cc_final: 0.7843 (mmm160) REVERT: A 559 PHE cc_start: 0.7120 (m-80) cc_final: 0.6657 (m-10) REVERT: A 561 GLN cc_start: 0.8639 (mm-40) cc_final: 0.7650 (mp10) REVERT: A 562 MET cc_start: 0.8941 (OUTLIER) cc_final: 0.8514 (ttm) REVERT: A 572 MET cc_start: 0.8800 (mtp) cc_final: 0.8467 (ttm) REVERT: A 644 MET cc_start: 0.9364 (mmm) cc_final: 0.8188 (mmm) REVERT: C 293 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7668 (pm20) REVERT: C 308 MET cc_start: 0.8313 (mmm) cc_final: 0.8028 (mpp) REVERT: C 423 GLN cc_start: 0.8627 (tp40) cc_final: 0.8146 (mm-40) REVERT: C 499 ARG cc_start: 0.8488 (mmm160) cc_final: 0.8178 (mmm160) REVERT: C 559 PHE cc_start: 0.6597 (m-80) cc_final: 0.6229 (m-10) REVERT: C 560 GLN cc_start: 0.8558 (tp40) cc_final: 0.8231 (tp40) REVERT: C 635 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8719 (tp) REVERT: C 639 LYS cc_start: 0.9193 (mttt) cc_final: 0.8824 (mmtp) REVERT: D 293 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8147 (mt-10) REVERT: D 308 MET cc_start: 0.7623 (OUTLIER) cc_final: 0.7083 (mpp) REVERT: D 423 GLN cc_start: 0.8650 (tp40) cc_final: 0.7954 (mm-40) REVERT: D 427 ASP cc_start: 0.8754 (m-30) cc_final: 0.8285 (m-30) REVERT: D 432 ARG cc_start: 0.8700 (mpt180) cc_final: 0.8488 (mmt90) REVERT: D 478 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8290 (mt-10) REVERT: D 499 ARG cc_start: 0.8517 (mmm160) cc_final: 0.8160 (mmm160) REVERT: D 639 LYS cc_start: 0.9167 (mttt) cc_final: 0.8873 (mmtp) REVERT: D 692 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7478 (mp0) REVERT: B 293 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7886 (mt-10) REVERT: B 308 MET cc_start: 0.8141 (mmt) cc_final: 0.7678 (mpp) REVERT: B 423 GLN cc_start: 0.8584 (tp40) cc_final: 0.8099 (mm-40) REVERT: B 427 ASP cc_start: 0.8862 (m-30) cc_final: 0.8471 (m-30) REVERT: B 432 ARG cc_start: 0.8714 (mpt-90) cc_final: 0.8467 (mmt90) REVERT: B 464 LYS cc_start: 0.8082 (mmtp) cc_final: 0.7865 (mmmm) REVERT: B 534 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.7141 (mmm160) REVERT: B 535 LYS cc_start: 0.8692 (mtmm) cc_final: 0.8409 (mtpt) REVERT: B 536 GLU cc_start: 0.8859 (mp0) cc_final: 0.8547 (mp0) REVERT: B 562 MET cc_start: 0.8994 (mmm) cc_final: 0.8414 (mmt) REVERT: B 627 TYR cc_start: 0.7540 (m-80) cc_final: 0.6950 (m-80) REVERT: B 644 MET cc_start: 0.9392 (mmm) cc_final: 0.8310 (mmm) outliers start: 37 outliers final: 17 residues processed: 317 average time/residue: 0.5809 time to fit residues: 202.5262 Evaluate side-chains 316 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 294 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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 601 ASP 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 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 601 ASP 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 564 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 139 optimal weight: 10.0000 chunk 131 optimal weight: 0.9990 chunk 170 optimal weight: 10.0000 chunk 70 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 115 optimal weight: 0.5980 chunk 152 optimal weight: 0.3980 chunk 77 optimal weight: 4.9990 chunk 92 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 301 ASN A 419 ASN D 301 ASN ** D 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 410 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.196552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.123297 restraints weight = 16987.119| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.06 r_work: 0.3230 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3696 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= 0.144 Angle : 0.568 10.350 19848 Z= 0.298 Chirality : 0.040 0.263 2240 Planarity : 0.004 0.060 2412 Dihedral : 4.800 35.742 1936 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.06 % Allowed : 20.04 % Favored : 77.90 % 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: 1.70 (0.21), residues: 1700 helix: 2.16 (0.15), residues: 1108 sheet: -1.33 (0.80), residues: 64 loop : -0.81 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 575 TYR 0.010 0.001 TYR A 584 PHE 0.018 0.001 PHE D 489 TRP 0.041 0.001 TRP B 697 HIS 0.001 0.000 HIS D 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (14644) covalent geometry : angle 0.56841 / 0.30 (19848) hydrogen bonds : bond 0.04000 / 2.66 ( 910) hydrogen bonds : angle 4.16957 / 2.99 ( 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 336 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 304 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 293 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8231 (mt-10) REVERT: A 308 MET cc_start: 0.7429 (OUTLIER) cc_final: 0.6913 (mpp) REVERT: A 423 GLN cc_start: 0.8525 (tp40) cc_final: 0.7861 (mm-40) REVERT: A 427 ASP cc_start: 0.8833 (m-30) cc_final: 0.8370 (m-30) REVERT: A 499 ARG cc_start: 0.8284 (mmm160) cc_final: 0.7859 (mmm160) REVERT: A 547 MET cc_start: 0.9107 (mtp) cc_final: 0.8904 (mtp) REVERT: A 559 PHE cc_start: 0.7017 (m-80) cc_final: 0.6560 (m-10) REVERT: A 561 GLN cc_start: 0.8619 (mm-40) cc_final: 0.7616 (mp10) REVERT: A 562 MET cc_start: 0.8924 (OUTLIER) cc_final: 0.8503 (ttm) REVERT: A 572 MET cc_start: 0.8786 (mtp) cc_final: 0.8446 (ttm) REVERT: A 644 MET cc_start: 0.9348 (mmm) cc_final: 0.8186 (mmm) REVERT: C 308 MET cc_start: 0.8338 (mmm) cc_final: 0.7944 (mpp) REVERT: C 423 GLN cc_start: 0.8595 (tp40) cc_final: 0.8240 (mm-40) REVERT: C 427 ASP cc_start: 0.8789 (m-30) cc_final: 0.8527 (m-30) REVERT: C 471 ASP cc_start: 0.8589 (t70) cc_final: 0.8266 (t70) REVERT: C 499 ARG cc_start: 0.8405 (mmm160) cc_final: 0.8081 (mmm160) REVERT: C 547 MET cc_start: 0.9066 (mtp) cc_final: 0.8839 (mtp) REVERT: C 559 PHE cc_start: 0.6565 (m-80) cc_final: 0.6183 (m-10) REVERT: C 560 GLN cc_start: 0.8497 (tp40) cc_final: 0.8203 (tp40) REVERT: C 635 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8695 (tp) REVERT: C 639 LYS cc_start: 0.9153 (mttt) cc_final: 0.8920 (mmtp) REVERT: D 293 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8190 (mt-10) REVERT: D 308 MET cc_start: 0.7605 (OUTLIER) cc_final: 0.7069 (mpp) REVERT: D 423 GLN cc_start: 0.8558 (tp40) cc_final: 0.7825 (mm-40) REVERT: D 427 ASP cc_start: 0.8773 (m-30) cc_final: 0.8293 (m-30) REVERT: D 432 ARG cc_start: 0.8647 (mpt180) cc_final: 0.8421 (mmt90) REVERT: D 474 ARG cc_start: 0.8488 (ttp80) cc_final: 0.8009 (ttp80) REVERT: D 478 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8107 (mt-10) REVERT: D 499 ARG cc_start: 0.8509 (mmm160) cc_final: 0.8183 (mmm160) REVERT: D 547 MET cc_start: 0.9124 (mtp) cc_final: 0.8921 (mtp) REVERT: D 639 LYS cc_start: 0.9125 (mttt) cc_final: 0.8917 (mmtp) REVERT: D 682 MET cc_start: 0.8769 (mmt) cc_final: 0.8491 (mmm) REVERT: D 705 ILE cc_start: 0.9327 (mt) cc_final: 0.9061 (mp) REVERT: B 293 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7871 (mt-10) REVERT: B 308 MET cc_start: 0.8112 (mmt) cc_final: 0.7663 (mpp) REVERT: B 423 GLN cc_start: 0.8555 (tp40) cc_final: 0.8075 (mm-40) REVERT: B 427 ASP cc_start: 0.8842 (m-30) cc_final: 0.8455 (m-30) REVERT: B 432 ARG cc_start: 0.8676 (mpt-90) cc_final: 0.8421 (mmt90) REVERT: B 464 LYS cc_start: 0.8160 (mmtp) cc_final: 0.7940 (mmmm) REVERT: B 534 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.6999 (mmm160) REVERT: B 535 LYS cc_start: 0.8647 (mtmm) cc_final: 0.8379 (mtpt) REVERT: B 536 GLU cc_start: 0.8831 (mp0) cc_final: 0.8474 (mp0) REVERT: B 547 MET cc_start: 0.9075 (mtp) cc_final: 0.8852 (mtp) REVERT: B 562 MET cc_start: 0.8886 (mmm) cc_final: 0.8434 (mmt) REVERT: B 627 TYR cc_start: 0.7392 (m-80) cc_final: 0.6743 (m-80) REVERT: B 644 MET cc_start: 0.9371 (mmm) cc_final: 0.8279 (mmm) outliers start: 32 outliers final: 12 residues processed: 311 average time/residue: 0.5772 time to fit residues: 197.8172 Evaluate side-chains 313 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 296 time to evaluate : 0.527 ------------------------------------------------------------------------------- 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 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 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 685 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 50 optimal weight: 0.3980 chunk 120 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 166 optimal weight: 0.7980 chunk 6 optimal weight: 7.9990 chunk 33 optimal weight: 0.3980 chunk 144 optimal weight: 0.9980 chunk 154 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 301 ASN A 419 ASN D 301 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.196870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.124015 restraints weight = 17006.680| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.08 r_work: 0.3238 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14644 Z= 0.138 Angle : 0.585 12.564 19848 Z= 0.302 Chirality : 0.040 0.330 2240 Planarity : 0.004 0.060 2412 Dihedral : 4.763 35.716 1936 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.29 % Allowed : 21.07 % Favored : 77.64 % 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: 1.79 (0.21), residues: 1700 helix: 2.20 (0.15), residues: 1108 sheet: -1.33 (0.79), residues: 64 loop : -0.69 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 575 TYR 0.010 0.001 TYR C 631 PHE 0.018 0.001 PHE D 489 TRP 0.044 0.001 TRP B 697 HIS 0.002 0.000 HIS B 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (14644) covalent geometry : angle 0.58541 / 0.30 (19848) hydrogen bonds : bond 0.03923 / 2.61 ( 910) hydrogen bonds : angle 4.13377 / 2.96 ( 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: 20 poor density : 302 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 293 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8311 (mt-10) REVERT: A 308 MET cc_start: 0.7440 (OUTLIER) cc_final: 0.6921 (mpp) REVERT: A 423 GLN cc_start: 0.8532 (tp40) cc_final: 0.8058 (mm-40) REVERT: A 427 ASP cc_start: 0.8831 (m-30) cc_final: 0.8565 (m-30) REVERT: A 499 ARG cc_start: 0.8268 (mmm160) cc_final: 0.7860 (mmm160) REVERT: A 559 PHE cc_start: 0.7049 (m-80) cc_final: 0.6568 (m-10) REVERT: A 562 MET cc_start: 0.8908 (OUTLIER) cc_final: 0.8446 (ttm) REVERT: A 572 MET cc_start: 0.8783 (mtp) cc_final: 0.8457 (ttm) REVERT: A 644 MET cc_start: 0.9382 (mmm) cc_final: 0.8238 (mmm) REVERT: C 308 MET cc_start: 0.8360 (mmm) cc_final: 0.7962 (mpp) REVERT: C 423 GLN cc_start: 0.8644 (tp40) cc_final: 0.8310 (mm-40) REVERT: C 427 ASP cc_start: 0.8791 (m-30) cc_final: 0.8537 (m-30) REVERT: C 471 ASP cc_start: 0.8565 (t70) cc_final: 0.8224 (t70) REVERT: C 499 ARG cc_start: 0.8355 (mmm160) cc_final: 0.8143 (mmm160) REVERT: C 547 MET cc_start: 0.9060 (mtp) cc_final: 0.8849 (mtp) REVERT: C 559 PHE cc_start: 0.6501 (m-80) cc_final: 0.6146 (m-10) REVERT: C 560 GLN cc_start: 0.8527 (tp40) cc_final: 0.8217 (tp40) REVERT: C 635 LEU cc_start: 0.9021 (mt) cc_final: 0.8687 (tp) REVERT: C 639 LYS cc_start: 0.9158 (mttt) cc_final: 0.8874 (mmtp) REVERT: D 293 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8179 (mt-10) REVERT: D 308 MET cc_start: 0.7620 (OUTLIER) cc_final: 0.7077 (mpp) REVERT: D 411 ASP cc_start: 0.7581 (m-30) cc_final: 0.7223 (m-30) REVERT: D 423 GLN cc_start: 0.8590 (tp40) cc_final: 0.7867 (mm-40) REVERT: D 427 ASP cc_start: 0.8720 (m-30) cc_final: 0.8240 (m-30) REVERT: D 432 ARG cc_start: 0.8697 (mpt180) cc_final: 0.8473 (mmt90) REVERT: D 474 ARG cc_start: 0.8555 (ttp80) cc_final: 0.8167 (ttp80) REVERT: D 478 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8133 (mt-10) REVERT: D 499 ARG cc_start: 0.8499 (mmm160) cc_final: 0.8204 (mmm160) REVERT: D 635 LEU cc_start: 0.9061 (mt) cc_final: 0.8668 (tp) REVERT: D 639 LYS cc_start: 0.9112 (mttt) cc_final: 0.8893 (mmtp) REVERT: D 682 MET cc_start: 0.8818 (mmt) cc_final: 0.8540 (mmm) REVERT: B 293 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7911 (mt-10) REVERT: B 423 GLN cc_start: 0.8564 (tp40) cc_final: 0.7982 (mm-40) REVERT: B 427 ASP cc_start: 0.8790 (m-30) cc_final: 0.8372 (m-30) REVERT: B 432 ARG cc_start: 0.8718 (mpt-90) cc_final: 0.8464 (mmt90) REVERT: B 464 LYS cc_start: 0.8148 (mmtp) cc_final: 0.7933 (mmmm) REVERT: B 534 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.7078 (mmm160) REVERT: B 535 LYS cc_start: 0.8653 (mtmm) cc_final: 0.8406 (mtpt) REVERT: B 536 GLU cc_start: 0.8860 (mp0) cc_final: 0.8555 (mp0) REVERT: B 562 MET cc_start: 0.8856 (mmm) cc_final: 0.8512 (mmt) REVERT: B 575 ARG cc_start: 0.8564 (mtm110) cc_final: 0.8353 (mmp80) REVERT: B 691 GLN cc_start: 0.7618 (pt0) cc_final: 0.7376 (mm-40) outliers start: 20 outliers final: 11 residues processed: 310 average time/residue: 0.5436 time to fit residues: 185.8857 Evaluate side-chains 311 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 296 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 C residue 413 LEU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain D residue 308 MET Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain B residue 389 THR 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 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: 0.0010 chunk 112 optimal weight: 0.6980 chunk 120 optimal weight: 0.8980 chunk 134 optimal weight: 8.9990 chunk 96 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 138 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 301 ASN A 419 ASN D 301 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.197022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.124366 restraints weight = 16920.440| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.06 r_work: 0.3241 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.3822 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= 0.138 Angle : 0.581 12.157 19848 Z= 0.301 Chirality : 0.040 0.324 2240 Planarity : 0.004 0.063 2412 Dihedral : 4.764 36.750 1936 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.55 % Allowed : 21.13 % Favored : 77.32 % 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: 1.79 (0.21), residues: 1700 helix: 2.19 (0.15), residues: 1108 sheet: -1.30 (0.80), residues: 64 loop : -0.68 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 575 TYR 0.010 0.001 TYR A 584 PHE 0.018 0.001 PHE D 489 TRP 0.045 0.001 TRP B 697 HIS 0.003 0.000 HIS B 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (14644) covalent geometry : angle 0.58092 / 0.30 (19848) hydrogen bonds : bond 0.03936 / 2.63 ( 910) hydrogen bonds : angle 4.14599 / 2.97 ( 2661) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6727.21 seconds wall clock time: 115 minutes 3.38 seconds (6903.38 seconds total)