Starting phenix.real_space_refine on Tue Dec 31 01:49:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mz5_24083/12_2024/7mz5_24083.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mz5_24083/12_2024/7mz5_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_24083/12_2024/7mz5_24083.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mz5_24083/12_2024/7mz5_24083.map" model { file = "/net/cci-nas-00/data/ceres_data/7mz5_24083/12_2024/7mz5_24083.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mz5_24083/12_2024/7mz5_24083.cif" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 9.01, per 1000 atoms: 0.63 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: 5.29 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.26 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: 3.86 Time building geometry restraints manager: 4.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3081 1.33 - 1.45: 3430 1.45 - 1.57: 7981 1.57 - 1.69: 0 1.69 - 1.81: 152 Bond restraints: 14644 Sorted by residual: bond pdb=" CBK 6EU B 901 " pdb=" OAF 6EU B 901 " ideal model delta sigma weight residual 1.329 1.456 -0.127 2.00e-02 2.50e+03 4.02e+01 bond pdb=" CBK 6EU D 901 " pdb=" OAF 6EU D 901 " ideal model delta sigma weight residual 1.329 1.455 -0.126 2.00e-02 2.50e+03 3.98e+01 bond pdb=" CBK 6EU A 901 " pdb=" OAF 6EU A 901 " ideal model delta sigma weight residual 1.329 1.454 -0.125 2.00e-02 2.50e+03 3.92e+01 bond pdb=" CBK 6EU C 901 " pdb=" OAF 6EU C 901 " ideal model delta sigma weight residual 1.329 1.454 -0.125 2.00e-02 2.50e+03 3.92e+01 bond pdb=" N PHE A 712 " pdb=" CA PHE A 712 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.29e-02 6.01e+03 6.75e+00 ... (remaining 14639 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 19356 1.96 - 3.93: 385 3.93 - 5.89: 88 5.89 - 7.86: 13 7.86 - 9.82: 6 Bond angle restraints: 19848 Sorted by residual: angle pdb=" N ASP A 654 " pdb=" CA ASP A 654 " pdb=" C ASP A 654 " ideal model delta sigma weight residual 110.14 100.32 9.82 1.47e+00 4.63e-01 4.46e+01 angle pdb=" N ASP C 654 " pdb=" CA ASP C 654 " pdb=" C ASP C 654 " ideal model delta sigma weight residual 110.14 100.51 9.63 1.47e+00 4.63e-01 4.29e+01 angle pdb=" O TYR A 653 " pdb=" C TYR A 653 " pdb=" N ASP A 654 " ideal model delta sigma weight residual 123.26 126.73 -3.47 1.05e+00 9.07e-01 1.10e+01 angle pdb=" N LEU C 713 " pdb=" CA LEU C 713 " pdb=" C LEU C 713 " ideal model delta sigma weight residual 110.80 117.80 -7.00 2.13e+00 2.20e-01 1.08e+01 angle pdb=" N PHE A 712 " pdb=" CA PHE A 712 " pdb=" C PHE A 712 " ideal model delta sigma weight residual 110.80 117.69 -6.89 2.13e+00 2.20e-01 1.05e+01 ... (remaining 19843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 8395 17.77 - 35.55: 366 35.55 - 53.32: 80 53.32 - 71.09: 30 71.09 - 88.87: 5 Dihedral angle restraints: 8876 sinusoidal: 3776 harmonic: 5100 Sorted by residual: dihedral pdb=" N PHE A 712 " pdb=" C PHE A 712 " pdb=" CA PHE A 712 " pdb=" CB PHE A 712 " ideal model delta harmonic sigma weight residual 122.80 139.54 -16.74 0 2.50e+00 1.60e-01 4.48e+01 dihedral pdb=" C PHE A 712 " pdb=" N PHE A 712 " pdb=" CA PHE A 712 " pdb=" CB PHE A 712 " ideal model delta harmonic sigma weight residual -122.60 -139.00 16.40 0 2.50e+00 1.60e-01 4.30e+01 dihedral pdb=" N PHE D 712 " pdb=" C PHE D 712 " pdb=" CA PHE D 712 " pdb=" CB PHE D 712 " ideal model delta harmonic sigma weight residual 122.80 139.08 -16.28 0 2.50e+00 1.60e-01 4.24e+01 ... (remaining 8873 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 2216 0.128 - 0.255: 14 0.255 - 0.383: 6 0.383 - 0.510: 0 0.510 - 0.638: 4 Chirality restraints: 2240 Sorted by residual: chirality pdb=" CA PHE A 712 " pdb=" N PHE A 712 " pdb=" C PHE A 712 " pdb=" CB PHE A 712 " both_signs ideal model delta sigma weight residual False 2.51 1.87 0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" CA PHE B 712 " pdb=" N PHE B 712 " pdb=" C PHE B 712 " pdb=" CB PHE B 712 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.62 2.00e-01 2.50e+01 9.52e+00 chirality pdb=" CA PHE D 712 " pdb=" N PHE D 712 " pdb=" C PHE D 712 " pdb=" CB PHE D 712 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.43e+00 ... (remaining 2237 not shown) Planarity restraints: 2412 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 546 " -0.012 2.00e-02 2.50e+03 2.43e-02 5.89e+00 pdb=" C ALA A 546 " 0.042 2.00e-02 2.50e+03 pdb=" O ALA A 546 " -0.016 2.00e-02 2.50e+03 pdb=" N MET A 547 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 546 " 0.012 2.00e-02 2.50e+03 2.41e-02 5.79e+00 pdb=" C ALA B 546 " -0.042 2.00e-02 2.50e+03 pdb=" O ALA B 546 " 0.016 2.00e-02 2.50e+03 pdb=" N MET B 547 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 546 " -0.012 2.00e-02 2.50e+03 2.40e-02 5.77e+00 pdb=" C ALA D 546 " 0.042 2.00e-02 2.50e+03 pdb=" O ALA D 546 " -0.016 2.00e-02 2.50e+03 pdb=" N MET D 547 " -0.014 2.00e-02 2.50e+03 ... (remaining 2409 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 202 2.69 - 3.24: 14535 3.24 - 3.80: 23211 3.80 - 4.35: 30295 4.35 - 4.90: 50628 Nonbonded interactions: 118871 Sorted by model distance: nonbonded pdb=" O LEU C 673 " pdb=" OH TYR D 565 " model vdw 2.138 3.040 nonbonded pdb=" OH TYR A 565 " pdb=" O LEU D 673 " model vdw 2.178 3.040 nonbonded pdb=" OH TYR C 565 " pdb=" O LEU B 673 " model vdw 2.185 3.040 nonbonded pdb=" OG SER C 379 " pdb=" OD1 ASP C 745 " model vdw 2.221 3.040 nonbonded pdb=" NH1 ARG C 557 " pdb=" OE1 GLU C 570 " model vdw 2.248 3.120 ... (remaining 118866 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 282 through 745 or resid 901)) selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 32.560 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.070 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:12.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.127 14644 Z= 0.310 Angle : 0.721 9.820 19848 Z= 0.380 Chirality : 0.049 0.638 2240 Planarity : 0.004 0.030 2412 Dihedral : 11.209 88.866 5596 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 1.25 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.12 % Favored : 95.47 % Rotamer: Outliers : 1.03 % Allowed : 0.84 % Favored : 98.13 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.008 0.001 TRP B 549 HIS 0.003 0.001 HIS B 410 PHE 0.016 0.002 PHE C 489 TYR 0.011 0.001 TYR D 309 ARG 0.003 0.000 ARG D 355 *********************** 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 : 1.718 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: 0.8425 (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: 1.4271 time to fit residues: 704.6025 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 : 1.599 ------------------------------------------------------------------------------- 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 145 optimal weight: 0.9980 chunk 130 optimal weight: 20.0000 chunk 72 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 chunk 69 optimal weight: 0.0980 chunk 134 optimal weight: 6.9990 chunk 52 optimal weight: 20.0000 chunk 81 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 156 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN A 310 ASN A 419 ASN A 467 ASN C 301 ASN C 419 ASN D 301 ASN D 419 ASN B 301 ASN B 419 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14644 Z= 0.192 Angle : 0.542 7.935 19848 Z= 0.291 Chirality : 0.039 0.164 2240 Planarity : 0.003 0.038 2412 Dihedral : 7.534 57.690 2304 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.51 % Allowed : 12.24 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.21), residues: 1700 helix: 2.35 (0.15), residues: 1108 sheet: -1.74 (0.77), residues: 64 loop : -0.69 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 697 HIS 0.004 0.001 HIS B 410 PHE 0.027 0.002 PHE A 304 TYR 0.023 0.001 TYR A 351 ARG 0.007 0.000 ARG B 474 *********************** 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 377 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 338 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 GLN cc_start: 0.8617 (tp40) cc_final: 0.8097 (mm-40) REVERT: A 427 ASP cc_start: 0.8510 (m-30) cc_final: 0.8253 (m-30) REVERT: A 559 PHE cc_start: 0.7044 (m-80) cc_final: 0.5447 (t80) REVERT: C 423 GLN cc_start: 0.8582 (tp40) cc_final: 0.8060 (mm-40) REVERT: C 427 ASP cc_start: 0.8486 (m-30) cc_final: 0.7966 (m-30) REVERT: C 478 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7491 (mt-10) REVERT: C 559 PHE cc_start: 0.6993 (m-80) cc_final: 0.5698 (t80) REVERT: C 639 LYS cc_start: 0.8644 (mttt) cc_final: 0.8146 (mtmt) REVERT: D 293 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8280 (mt-10) REVERT: D 423 GLN cc_start: 0.8560 (tp40) cc_final: 0.8120 (mm-40) REVERT: D 425 LYS cc_start: 0.8826 (mttm) cc_final: 0.8542 (mttm) REVERT: D 427 ASP cc_start: 0.8482 (m-30) cc_final: 0.8157 (m-30) REVERT: D 535 LYS cc_start: 0.8435 (mtmm) cc_final: 0.8232 (mtpt) REVERT: B 293 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7433 (mp0) REVERT: B 308 MET cc_start: 0.8266 (mmt) cc_final: 0.7977 (mpp) REVERT: B 423 GLN cc_start: 0.8540 (tp40) cc_final: 0.8084 (mm-40) REVERT: B 425 LYS cc_start: 0.8964 (mttm) cc_final: 0.8520 (mttm) REVERT: B 427 ASP cc_start: 0.8422 (m-30) cc_final: 0.8079 (m-30) REVERT: B 534 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.6808 (mmm160) REVERT: B 535 LYS cc_start: 0.8409 (mtmm) cc_final: 0.8190 (mtpt) REVERT: B 564 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8399 (tp) REVERT: B 709 GLU cc_start: 0.8452 (tt0) cc_final: 0.8158 (tt0) outliers start: 39 outliers final: 14 residues processed: 360 average time/residue: 1.2695 time to fit residues: 504.3323 Evaluate side-chains 318 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 302 time to evaluate : 1.875 ------------------------------------------------------------------------------- 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 678 LEU Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain C residue 483 SER 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 678 LEU Chi-restraints excluded: chain D residue 714 LYS Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 534 ARG Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 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 86 optimal weight: 20.0000 chunk 48 optimal weight: 5.9990 chunk 129 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 156 optimal weight: 2.9990 chunk 169 optimal weight: 6.9990 chunk 139 optimal weight: 10.0000 chunk 155 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 125 optimal weight: 0.6980 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 419 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.053 14644 Z= 0.583 Angle : 0.711 7.690 19848 Z= 0.374 Chirality : 0.049 0.157 2240 Planarity : 0.005 0.038 2412 Dihedral : 8.016 59.830 2304 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 5.28 % Allowed : 13.66 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.21), residues: 1700 helix: 1.66 (0.15), residues: 1112 sheet: -2.16 (0.74), residues: 64 loop : -0.75 (0.30), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 697 HIS 0.007 0.001 HIS B 289 PHE 0.026 0.003 PHE A 649 TYR 0.025 0.002 TYR A 351 ARG 0.007 0.001 ARG B 474 *********************** 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 415 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 333 time to evaluate : 1.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8296 (mt-10) REVERT: A 423 GLN cc_start: 0.8626 (tp40) cc_final: 0.8090 (mm-40) REVERT: A 424 ASP cc_start: 0.8506 (t70) cc_final: 0.8141 (t0) REVERT: A 499 ARG cc_start: 0.7678 (mmm160) cc_final: 0.7389 (mmm160) REVERT: A 559 PHE cc_start: 0.7093 (m-80) cc_final: 0.6869 (m-10) REVERT: A 562 MET cc_start: 0.7717 (OUTLIER) cc_final: 0.7126 (ttm) REVERT: A 627 TYR cc_start: 0.7311 (m-80) cc_final: 0.6945 (m-80) REVERT: A 656 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8476 (tmtp) REVERT: A 676 ASN cc_start: 0.8808 (m-40) cc_final: 0.8561 (m110) REVERT: C 423 GLN cc_start: 0.8605 (tp40) cc_final: 0.8301 (tp-100) REVERT: C 424 ASP cc_start: 0.8511 (t70) cc_final: 0.8145 (t0) REVERT: C 627 TYR cc_start: 0.7257 (m-80) cc_final: 0.6903 (m-80) REVERT: D 293 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8298 (mt-10) REVERT: D 310 ASN cc_start: 0.6486 (t0) cc_final: 0.6259 (t0) REVERT: D 423 GLN cc_start: 0.8639 (tp40) cc_final: 0.8119 (mm-40) REVERT: D 424 ASP cc_start: 0.8566 (t70) cc_final: 0.8216 (t0) REVERT: D 499 ARG cc_start: 0.7771 (mmm160) cc_final: 0.7473 (mmm160) REVERT: D 535 LYS cc_start: 0.8460 (mtmm) cc_final: 0.8212 (mtpt) REVERT: D 627 TYR cc_start: 0.7348 (m-80) cc_final: 0.7041 (m-80) REVERT: D 636 GLU cc_start: 0.8245 (mm-30) cc_final: 0.8045 (tp30) REVERT: B 293 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8107 (mt-10) REVERT: B 308 MET cc_start: 0.8129 (mmt) cc_final: 0.7833 (mpp) REVERT: B 423 GLN cc_start: 0.8641 (tp40) cc_final: 0.8083 (mm-40) REVERT: B 424 ASP cc_start: 0.8613 (t70) cc_final: 0.8259 (t0) REVERT: B 535 LYS cc_start: 0.8436 (mtmm) cc_final: 0.8180 (mtpt) REVERT: B 572 MET cc_start: 0.8209 (ttm) cc_final: 0.7984 (ttm) REVERT: B 635 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8778 (tp) REVERT: B 656 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8487 (tmtp) outliers start: 82 outliers final: 35 residues processed: 372 average time/residue: 1.2158 time to fit residues: 497.9962 Evaluate side-chains 354 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 315 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 656 LYS Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 556 THR Chi-restraints excluded: chain C residue 599 ILE Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 703 ILE Chi-restraints excluded: chain C residue 714 LYS Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain D residue 571 LYS Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 483 SER 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 632 SER Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 656 LYS 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 154 optimal weight: 0.6980 chunk 117 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 74 optimal weight: 0.5980 chunk 105 optimal weight: 0.9990 chunk 157 optimal weight: 2.9990 chunk 166 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN ** A 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 ASN A 691 GLN C 301 ASN C 691 GLN D 301 ASN D 419 ASN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 GLN B 301 ASN B 691 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14644 Z= 0.210 Angle : 0.551 7.258 19848 Z= 0.297 Chirality : 0.039 0.162 2240 Planarity : 0.004 0.038 2412 Dihedral : 7.232 57.248 2292 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.22 % Allowed : 18.43 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.21), residues: 1700 helix: 1.83 (0.15), residues: 1132 sheet: -1.96 (0.78), residues: 64 loop : -1.15 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 697 HIS 0.002 0.001 HIS D 289 PHE 0.017 0.002 PHE C 489 TYR 0.020 0.001 TYR A 351 ARG 0.008 0.001 ARG D 575 *********************** 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 379 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 329 time to evaluate : 1.558 Fit side-chains revert: symmetry clash REVERT: A 293 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8380 (mt-10) REVERT: A 308 MET cc_start: 0.7359 (OUTLIER) cc_final: 0.6460 (mpt) REVERT: A 423 GLN cc_start: 0.8630 (tp40) cc_final: 0.7997 (mm-40) REVERT: A 427 ASP cc_start: 0.8488 (m-30) cc_final: 0.8157 (m-30) REVERT: A 559 PHE cc_start: 0.7002 (m-80) cc_final: 0.6734 (m-10) REVERT: A 562 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.7522 (mtt) REVERT: A 627 TYR cc_start: 0.7172 (m-80) cc_final: 0.6856 (m-80) REVERT: A 656 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8452 (tmtp) REVERT: A 676 ASN cc_start: 0.8694 (m-40) cc_final: 0.8479 (m110) REVERT: C 293 GLU cc_start: 0.8289 (mt-10) cc_final: 0.7822 (pm20) REVERT: C 423 GLN cc_start: 0.8577 (tp40) cc_final: 0.7964 (mm-40) REVERT: C 627 TYR cc_start: 0.7064 (m-80) cc_final: 0.6769 (m-80) REVERT: D 293 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8321 (mt-10) REVERT: D 383 ASP cc_start: 0.7873 (t0) cc_final: 0.7647 (t70) REVERT: D 423 GLN cc_start: 0.8627 (tp40) cc_final: 0.8107 (mm-40) REVERT: D 427 ASP cc_start: 0.8496 (m-30) cc_final: 0.8219 (m-30) REVERT: D 432 ARG cc_start: 0.8046 (mpt-90) cc_final: 0.7786 (mmt90) REVERT: D 478 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7372 (mt-10) REVERT: D 499 ARG cc_start: 0.7669 (mmm160) cc_final: 0.7454 (mmm160) REVERT: D 627 TYR cc_start: 0.7066 (m-80) cc_final: 0.6845 (m-80) REVERT: D 636 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7767 (tp30) REVERT: B 293 GLU cc_start: 0.8327 (mt-10) cc_final: 0.8105 (mt-10) REVERT: B 308 MET cc_start: 0.8170 (mmt) cc_final: 0.7852 (mpp) REVERT: B 423 GLN cc_start: 0.8642 (tp40) cc_final: 0.8140 (mm-40) REVERT: B 427 ASP cc_start: 0.8502 (m-30) cc_final: 0.8205 (m-30) REVERT: B 432 ARG cc_start: 0.8031 (mpt180) cc_final: 0.7779 (mmt90) REVERT: B 499 ARG cc_start: 0.7522 (mmm160) cc_final: 0.7266 (mmm160) REVERT: B 572 MET cc_start: 0.8202 (ttm) cc_final: 0.7942 (ttm) outliers start: 50 outliers final: 19 residues processed: 348 average time/residue: 1.2027 time to fit residues: 461.6722 Evaluate side-chains 324 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 302 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 460 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 656 LYS Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 571 LYS Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 564 ILE 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 138 optimal weight: 9.9990 chunk 94 optimal weight: 9.9990 chunk 2 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 141 optimal weight: 3.9990 chunk 114 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 0.0030 chunk 149 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN A 419 ASN C 301 ASN C 419 ASN C 467 ASN D 301 ASN D 676 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14644 Z= 0.218 Angle : 0.547 7.205 19848 Z= 0.292 Chirality : 0.039 0.160 2240 Planarity : 0.003 0.041 2412 Dihedral : 7.107 57.670 2288 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.90 % Allowed : 19.01 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.21), residues: 1700 helix: 2.06 (0.15), residues: 1108 sheet: -1.83 (0.79), residues: 64 loop : -0.82 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 697 HIS 0.003 0.001 HIS C 410 PHE 0.018 0.001 PHE C 489 TYR 0.011 0.001 TYR B 627 ARG 0.008 0.001 ARG C 575 *********************** 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 359 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 314 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8438 (mt-10) REVERT: A 423 GLN cc_start: 0.8554 (tp40) cc_final: 0.7936 (mm-40) REVERT: A 427 ASP cc_start: 0.8482 (m-30) cc_final: 0.8134 (m-30) REVERT: A 559 PHE cc_start: 0.6976 (m-80) cc_final: 0.6750 (m-10) REVERT: A 627 TYR cc_start: 0.7072 (m-80) cc_final: 0.6786 (m-80) REVERT: A 676 ASN cc_start: 0.8691 (m-40) cc_final: 0.8394 (m110) REVERT: C 308 MET cc_start: 0.8293 (tpp) cc_final: 0.7792 (mpp) REVERT: C 423 GLN cc_start: 0.8559 (tp40) cc_final: 0.8030 (mm-40) REVERT: C 627 TYR cc_start: 0.7033 (m-80) cc_final: 0.6774 (m-80) REVERT: D 293 GLU cc_start: 0.8727 (mt-10) cc_final: 0.8363 (mt-10) REVERT: D 308 MET cc_start: 0.7339 (OUTLIER) cc_final: 0.6494 (mpt) REVERT: D 423 GLN cc_start: 0.8603 (tp40) cc_final: 0.8021 (mm-40) REVERT: D 427 ASP cc_start: 0.8508 (m-30) cc_final: 0.8202 (m-30) REVERT: D 432 ARG cc_start: 0.8034 (mpt-90) cc_final: 0.7809 (mmt90) REVERT: D 499 ARG cc_start: 0.7663 (mmm160) cc_final: 0.7452 (mmm160) REVERT: D 636 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7789 (tp30) REVERT: B 293 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8135 (mt-10) REVERT: B 308 MET cc_start: 0.8151 (mmt) cc_final: 0.7841 (mpp) REVERT: B 423 GLN cc_start: 0.8603 (tp40) cc_final: 0.8094 (mm-40) REVERT: B 427 ASP cc_start: 0.8520 (m-30) cc_final: 0.8183 (m-30) REVERT: B 432 ARG cc_start: 0.8026 (mpt180) cc_final: 0.7765 (mmt90) REVERT: B 499 ARG cc_start: 0.7515 (mmm160) cc_final: 0.7270 (mmm160) REVERT: B 562 MET cc_start: 0.8737 (mmm) cc_final: 0.8271 (mmt) REVERT: B 568 MET cc_start: 0.8964 (mtp) cc_final: 0.8697 (mtt) REVERT: B 572 MET cc_start: 0.8246 (ttm) cc_final: 0.7943 (ttm) REVERT: B 644 MET cc_start: 0.9096 (mmm) cc_final: 0.7799 (mmm) outliers start: 45 outliers final: 19 residues processed: 331 average time/residue: 1.2074 time to fit residues: 441.2105 Evaluate side-chains 319 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 299 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 703 ILE Chi-restraints excluded: chain D residue 308 MET Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 571 LYS 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 55 optimal weight: 10.0000 chunk 149 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 chunk 166 optimal weight: 0.0980 chunk 138 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 87 optimal weight: 20.0000 chunk 160 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN A 419 ASN C 408 ASN C 467 ASN D 301 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3541 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= 0.204 Angle : 0.558 7.933 19848 Z= 0.295 Chirality : 0.039 0.161 2240 Planarity : 0.004 0.045 2412 Dihedral : 6.962 56.544 2288 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.26 % Allowed : 19.59 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.21), residues: 1700 helix: 2.10 (0.15), residues: 1108 sheet: -1.67 (0.81), residues: 64 loop : -0.81 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 697 HIS 0.002 0.000 HIS C 410 PHE 0.018 0.001 PHE C 489 TYR 0.011 0.001 TYR D 627 ARG 0.011 0.001 ARG D 575 *********************** 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 357 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 322 time to evaluate : 1.585 Fit side-chains revert: symmetry clash REVERT: A 293 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8451 (mt-10) REVERT: A 308 MET cc_start: 0.7395 (OUTLIER) cc_final: 0.6843 (mpp) REVERT: A 423 GLN cc_start: 0.8528 (tp40) cc_final: 0.7938 (mm-40) REVERT: A 427 ASP cc_start: 0.8458 (m-30) cc_final: 0.8082 (m-30) REVERT: A 627 TYR cc_start: 0.7030 (m-80) cc_final: 0.6792 (m-80) REVERT: A 644 MET cc_start: 0.9100 (mmm) cc_final: 0.7609 (mmm) REVERT: A 676 ASN cc_start: 0.8660 (m-40) cc_final: 0.8341 (m110) REVERT: C 293 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7803 (pm20) REVERT: C 308 MET cc_start: 0.8323 (tpp) cc_final: 0.7873 (mpp) REVERT: C 423 GLN cc_start: 0.8578 (tp40) cc_final: 0.8099 (mm-40) REVERT: C 559 PHE cc_start: 0.6584 (m-80) cc_final: 0.5031 (t80) REVERT: C 627 TYR cc_start: 0.7038 (m-80) cc_final: 0.6774 (m-80) REVERT: D 293 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8395 (mt-10) REVERT: D 308 MET cc_start: 0.7508 (OUTLIER) cc_final: 0.6991 (mpp) REVERT: D 423 GLN cc_start: 0.8597 (tp40) cc_final: 0.8028 (mm-40) REVERT: D 427 ASP cc_start: 0.8464 (m-30) cc_final: 0.8151 (m-30) REVERT: D 432 ARG cc_start: 0.8077 (mpt-90) cc_final: 0.7841 (mmt90) REVERT: D 499 ARG cc_start: 0.7648 (mmm160) cc_final: 0.7441 (mmm160) REVERT: B 293 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8138 (mt-10) REVERT: B 308 MET cc_start: 0.8090 (mmt) cc_final: 0.7821 (mpp) REVERT: B 423 GLN cc_start: 0.8590 (tp40) cc_final: 0.8082 (mm-40) REVERT: B 427 ASP cc_start: 0.8498 (m-30) cc_final: 0.8153 (m-30) REVERT: B 432 ARG cc_start: 0.8024 (mpt180) cc_final: 0.7758 (mmt90) REVERT: B 499 ARG cc_start: 0.7507 (mmm160) cc_final: 0.7294 (mmm160) REVERT: B 562 MET cc_start: 0.8703 (mmm) cc_final: 0.8287 (mmt) REVERT: B 572 MET cc_start: 0.8229 (ttm) cc_final: 0.7892 (ttm) REVERT: B 644 MET cc_start: 0.9119 (mmm) cc_final: 0.7762 (mmm) outliers start: 35 outliers final: 14 residues processed: 336 average time/residue: 1.1720 time to fit residues: 436.3519 Evaluate side-chains 314 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 298 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 703 ILE Chi-restraints excluded: chain D residue 308 MET Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 685 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 chunk 121 optimal weight: 0.8980 chunk 140 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 165 optimal weight: 0.9990 chunk 103 optimal weight: 0.4980 chunk 101 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 chunk 102 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN A 419 ASN C 419 ASN C 467 ASN D 301 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14644 Z= 0.190 Angle : 0.554 7.437 19848 Z= 0.294 Chirality : 0.039 0.162 2240 Planarity : 0.004 0.051 2412 Dihedral : 6.803 55.731 2286 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.26 % Allowed : 19.91 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.21), residues: 1700 helix: 2.12 (0.15), residues: 1108 sheet: -1.59 (0.81), residues: 64 loop : -0.79 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 697 HIS 0.001 0.000 HIS B 410 PHE 0.019 0.001 PHE D 489 TYR 0.010 0.001 TYR B 631 ARG 0.011 0.001 ARG D 575 *********************** 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 356 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 321 time to evaluate : 1.675 Fit side-chains REVERT: A 293 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8463 (mt-10) REVERT: A 308 MET cc_start: 0.7668 (OUTLIER) cc_final: 0.7113 (mpp) REVERT: A 423 GLN cc_start: 0.8545 (tp40) cc_final: 0.8047 (mm-40) REVERT: A 427 ASP cc_start: 0.8441 (m-30) cc_final: 0.8229 (m-30) REVERT: A 627 TYR cc_start: 0.7021 (m-80) cc_final: 0.6744 (m-80) REVERT: A 676 ASN cc_start: 0.8607 (m-40) cc_final: 0.8286 (m110) REVERT: C 293 GLU cc_start: 0.8361 (mt-10) cc_final: 0.7930 (pm20) REVERT: C 308 MET cc_start: 0.8288 (tpp) cc_final: 0.7765 (mpp) REVERT: C 423 GLN cc_start: 0.8584 (tp40) cc_final: 0.8011 (mm-40) REVERT: C 559 PHE cc_start: 0.6534 (m-80) cc_final: 0.4962 (t80) REVERT: C 627 TYR cc_start: 0.7028 (m-80) cc_final: 0.6740 (m-80) REVERT: D 293 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8449 (mt-10) REVERT: D 308 MET cc_start: 0.7531 (OUTLIER) cc_final: 0.7029 (mpp) REVERT: D 423 GLN cc_start: 0.8572 (tp40) cc_final: 0.7975 (mm-40) REVERT: D 427 ASP cc_start: 0.8458 (m-30) cc_final: 0.8120 (m-30) REVERT: D 432 ARG cc_start: 0.8080 (mpt-90) cc_final: 0.7838 (mmt90) REVERT: B 293 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8148 (mt-10) REVERT: B 308 MET cc_start: 0.8080 (mmt) cc_final: 0.7815 (mpp) REVERT: B 423 GLN cc_start: 0.8581 (tp40) cc_final: 0.8117 (mm-40) REVERT: B 427 ASP cc_start: 0.8506 (m-30) cc_final: 0.8244 (m-30) REVERT: B 432 ARG cc_start: 0.8048 (mpt180) cc_final: 0.7762 (mmt90) REVERT: B 499 ARG cc_start: 0.7460 (mmm160) cc_final: 0.7220 (mmm160) REVERT: B 562 MET cc_start: 0.8690 (mmm) cc_final: 0.8347 (mmt) REVERT: B 572 MET cc_start: 0.8245 (ttm) cc_final: 0.7904 (ttm) outliers start: 35 outliers final: 17 residues processed: 337 average time/residue: 1.1990 time to fit residues: 447.2230 Evaluate side-chains 318 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 299 time to evaluate : 1.453 ------------------------------------------------------------------------------- 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 460 LEU Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain D residue 308 MET Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 685 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 112 optimal weight: 0.6980 chunk 81 optimal weight: 0.0170 chunk 15 optimal weight: 0.9990 chunk 130 optimal weight: 9.9990 chunk 150 optimal weight: 2.9990 chunk 158 optimal weight: 0.9980 chunk 144 optimal weight: 0.9990 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN A 419 ASN D 301 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3772 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= 0.195 Angle : 0.578 9.349 19848 Z= 0.304 Chirality : 0.039 0.162 2240 Planarity : 0.004 0.055 2412 Dihedral : 6.726 56.006 2284 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.19 % Allowed : 20.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.21), residues: 1700 helix: 2.05 (0.15), residues: 1112 sheet: -1.46 (0.81), residues: 64 loop : -0.80 (0.29), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP B 697 HIS 0.001 0.000 HIS C 410 PHE 0.020 0.001 PHE D 489 TYR 0.009 0.001 TYR B 631 ARG 0.013 0.001 ARG D 575 *********************** 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 347 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 313 time to evaluate : 1.555 Fit side-chains REVERT: A 293 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8470 (mt-10) REVERT: A 308 MET cc_start: 0.7598 (OUTLIER) cc_final: 0.7072 (mpp) REVERT: A 423 GLN cc_start: 0.8550 (tp40) cc_final: 0.8077 (mm-40) REVERT: A 427 ASP cc_start: 0.8439 (m-30) cc_final: 0.8222 (m-30) REVERT: A 676 ASN cc_start: 0.8544 (m-40) cc_final: 0.8194 (m110) REVERT: C 293 GLU cc_start: 0.8391 (mt-10) cc_final: 0.7892 (pm20) REVERT: C 308 MET cc_start: 0.8366 (tpp) cc_final: 0.7885 (mpp) REVERT: C 423 GLN cc_start: 0.8561 (tp40) cc_final: 0.8275 (mm-40) REVERT: C 547 MET cc_start: 0.8530 (mtp) cc_final: 0.8303 (mtp) REVERT: C 559 PHE cc_start: 0.6464 (m-80) cc_final: 0.4962 (t80) REVERT: C 627 TYR cc_start: 0.7066 (m-80) cc_final: 0.6760 (m-80) REVERT: D 293 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8448 (mt-10) REVERT: D 308 MET cc_start: 0.7647 (OUTLIER) cc_final: 0.7140 (mpp) REVERT: D 423 GLN cc_start: 0.8559 (tp40) cc_final: 0.8038 (mm-40) REVERT: D 427 ASP cc_start: 0.8448 (m-30) cc_final: 0.8137 (m-30) REVERT: D 432 ARG cc_start: 0.8098 (mpt-90) cc_final: 0.7841 (mmt90) REVERT: D 499 ARG cc_start: 0.7684 (mmm160) cc_final: 0.7440 (mmm160) REVERT: B 293 GLU cc_start: 0.8378 (mt-10) cc_final: 0.8133 (mt-10) REVERT: B 423 GLN cc_start: 0.8556 (tp40) cc_final: 0.8094 (mm-40) REVERT: B 427 ASP cc_start: 0.8492 (m-30) cc_final: 0.8251 (m-30) REVERT: B 432 ARG cc_start: 0.8045 (mpt180) cc_final: 0.7755 (mmt90) REVERT: B 499 ARG cc_start: 0.7471 (mmm160) cc_final: 0.7233 (mmm160) REVERT: B 547 MET cc_start: 0.8531 (mtp) cc_final: 0.8318 (mtp) REVERT: B 562 MET cc_start: 0.8634 (mmm) cc_final: 0.8287 (mmt) REVERT: B 572 MET cc_start: 0.8251 (ttm) cc_final: 0.7878 (ttm) REVERT: B 644 MET cc_start: 0.9142 (mmm) cc_final: 0.7807 (mmm) outliers start: 34 outliers final: 18 residues processed: 328 average time/residue: 1.2249 time to fit residues: 444.4097 Evaluate side-chains 321 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 301 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain D residue 308 MET Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 685 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 67 optimal weight: 0.9990 chunk 121 optimal weight: 0.8980 chunk 47 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 chunk 146 optimal weight: 0.7980 chunk 153 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 chunk 163 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN A 419 ASN C 408 ASN D 301 ASN D 410 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14644 Z= 0.211 Angle : 0.590 11.241 19848 Z= 0.310 Chirality : 0.040 0.162 2240 Planarity : 0.004 0.060 2412 Dihedral : 6.644 56.297 2280 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 1.80 % Allowed : 21.26 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.21), residues: 1700 helix: 2.02 (0.15), residues: 1108 sheet: -1.46 (0.80), residues: 64 loop : -0.75 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP B 697 HIS 0.001 0.000 HIS D 289 PHE 0.020 0.001 PHE C 489 TYR 0.011 0.001 TYR B 631 ARG 0.013 0.001 ARG A 575 *********************** 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 332 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 304 time to evaluate : 1.668 Fit side-chains REVERT: A 293 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8456 (mt-10) REVERT: A 308 MET cc_start: 0.7590 (OUTLIER) cc_final: 0.7075 (mpp) REVERT: A 423 GLN cc_start: 0.8549 (tp40) cc_final: 0.8072 (mm-40) REVERT: A 427 ASP cc_start: 0.8431 (m-30) cc_final: 0.8221 (m-30) REVERT: A 627 TYR cc_start: 0.6977 (m-80) cc_final: 0.6695 (m-80) REVERT: C 308 MET cc_start: 0.8331 (tpp) cc_final: 0.7920 (mpp) REVERT: C 423 GLN cc_start: 0.8548 (tp40) cc_final: 0.8002 (mm-40) REVERT: C 559 PHE cc_start: 0.6728 (m-80) cc_final: 0.6494 (m-10) REVERT: C 627 TYR cc_start: 0.7063 (m-80) cc_final: 0.6761 (m-80) REVERT: C 682 MET cc_start: 0.7623 (mtp) cc_final: 0.7362 (mtp) REVERT: D 293 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8439 (mt-10) REVERT: D 308 MET cc_start: 0.7648 (OUTLIER) cc_final: 0.7186 (mpp) REVERT: D 423 GLN cc_start: 0.8552 (tp40) cc_final: 0.7947 (mm-40) REVERT: D 427 ASP cc_start: 0.8450 (m-30) cc_final: 0.8008 (m-30) REVERT: D 432 ARG cc_start: 0.8104 (mpt-90) cc_final: 0.7801 (mmt90) REVERT: D 547 MET cc_start: 0.8543 (mtp) cc_final: 0.8280 (mtp) REVERT: B 293 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8145 (mt-10) REVERT: B 423 GLN cc_start: 0.8577 (tp40) cc_final: 0.8102 (mm-40) REVERT: B 427 ASP cc_start: 0.8485 (m-30) cc_final: 0.8222 (m-30) REVERT: B 432 ARG cc_start: 0.8050 (mpt180) cc_final: 0.7761 (mmt90) REVERT: B 499 ARG cc_start: 0.7494 (mmm160) cc_final: 0.7254 (mmm160) REVERT: B 562 MET cc_start: 0.8580 (mmm) cc_final: 0.8221 (mmt) REVERT: B 572 MET cc_start: 0.8239 (ttm) cc_final: 0.7937 (ttm) REVERT: B 644 MET cc_start: 0.9143 (mmm) cc_final: 0.7818 (mmm) REVERT: B 682 MET cc_start: 0.7488 (mtp) cc_final: 0.7260 (mtp) outliers start: 28 outliers final: 19 residues processed: 319 average time/residue: 1.2122 time to fit residues: 427.1411 Evaluate side-chains 317 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 296 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain D residue 308 MET Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 685 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 171 optimal weight: 6.9990 chunk 157 optimal weight: 0.6980 chunk 136 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 83 optimal weight: 0.0970 chunk 108 optimal weight: 4.9990 chunk 145 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN C 408 ASN D 301 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3925 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= 0.191 Angle : 0.593 9.014 19848 Z= 0.309 Chirality : 0.040 0.163 2240 Planarity : 0.004 0.060 2412 Dihedral : 6.571 54.981 2280 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 1.87 % Allowed : 21.65 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.21), residues: 1700 helix: 2.05 (0.15), residues: 1108 sheet: -1.45 (0.79), residues: 64 loop : -0.76 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP B 697 HIS 0.001 0.000 HIS B 410 PHE 0.019 0.001 PHE C 489 TYR 0.011 0.001 TYR B 631 ARG 0.014 0.001 ARG A 575 ********************** 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 335 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 306 time to evaluate : 1.545 Fit side-chains revert: symmetry clash REVERT: A 293 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8529 (mt-10) REVERT: A 308 MET cc_start: 0.7577 (OUTLIER) cc_final: 0.7113 (mpp) REVERT: A 423 GLN cc_start: 0.8542 (tp40) cc_final: 0.8223 (mm-40) REVERT: A 471 ASP cc_start: 0.8086 (t70) cc_final: 0.7865 (t70) REVERT: C 293 GLU cc_start: 0.8531 (mt-10) cc_final: 0.7932 (pm20) REVERT: C 308 MET cc_start: 0.8303 (tpp) cc_final: 0.7944 (mpp) REVERT: C 423 GLN cc_start: 0.8550 (tp40) cc_final: 0.8017 (mm-40) REVERT: C 432 ARG cc_start: 0.8076 (mpt180) cc_final: 0.7851 (tpp-160) REVERT: C 627 TYR cc_start: 0.7007 (m-80) cc_final: 0.6725 (m-80) REVERT: D 293 GLU cc_start: 0.8815 (mt-10) cc_final: 0.8450 (mt-10) REVERT: D 308 MET cc_start: 0.7670 (OUTLIER) cc_final: 0.7138 (mpp) REVERT: D 423 GLN cc_start: 0.8543 (tp40) cc_final: 0.8005 (mm-40) REVERT: D 427 ASP cc_start: 0.8430 (m-30) cc_final: 0.8116 (m-30) REVERT: D 432 ARG cc_start: 0.8099 (mpt-90) cc_final: 0.7840 (mmt90) REVERT: D 547 MET cc_start: 0.8510 (mtp) cc_final: 0.8269 (mtp) REVERT: B 293 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8151 (mt-10) REVERT: B 423 GLN cc_start: 0.8523 (tp40) cc_final: 0.8021 (mm-40) REVERT: B 427 ASP cc_start: 0.8465 (m-30) cc_final: 0.8225 (m-30) REVERT: B 432 ARG cc_start: 0.8066 (mpt180) cc_final: 0.7783 (mmt90) REVERT: B 499 ARG cc_start: 0.7484 (mmm160) cc_final: 0.7271 (mmm160) REVERT: B 572 MET cc_start: 0.8226 (ttm) cc_final: 0.7926 (ttm) outliers start: 29 outliers final: 19 residues processed: 318 average time/residue: 1.2366 time to fit residues: 439.4104 Evaluate side-chains 317 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 296 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain D residue 308 MET Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 685 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 41 optimal weight: 8.9990 chunk 125 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 136 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 140 optimal weight: 0.0980 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 119 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN D 301 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.197262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.124964 restraints weight = 16893.531| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.06 r_work: 0.3250 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14644 Z= 0.193 Angle : 0.583 8.418 19848 Z= 0.307 Chirality : 0.040 0.163 2240 Planarity : 0.004 0.065 2412 Dihedral : 6.568 55.446 2280 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.74 % Allowed : 22.10 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.21), residues: 1700 helix: 2.07 (0.15), residues: 1108 sheet: -1.40 (0.79), residues: 64 loop : -0.73 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP B 697 HIS 0.001 0.000 HIS D 289 PHE 0.019 0.001 PHE C 489 TYR 0.010 0.001 TYR A 631 ARG 0.015 0.001 ARG B 575 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6802.50 seconds wall clock time: 122 minutes 21.05 seconds (7341.05 seconds total)