Starting phenix.real_space_refine on Sun May 3 11:48:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11mv_75847/05_2026/11mv_75847.cif Found real_map, /net/cci-nas-00/data/ceres_data/11mv_75847/05_2026/11mv_75847.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/11mv_75847/05_2026/11mv_75847.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11mv_75847/05_2026/11mv_75847.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/11mv_75847/05_2026/11mv_75847.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11mv_75847/05_2026/11mv_75847.map" } resolution = 2.47 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= 0.007 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: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 7182 2.51 5 N 2067 2.21 5 O 3351 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12654 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3851 Classifications: {'peptide': 489} Link IDs: {'PTRANS': 19, 'TRANS': 469} Chain breaks: 1 Chain: "B" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3851 Classifications: {'peptide': 489} Link IDs: {'PTRANS': 19, 'TRANS': 469} Chain breaks: 1 Chain: "C" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3851 Classifications: {'peptide': 489} Link IDs: {'PTRANS': 19, 'TRANS': 469} Chain breaks: 1 Chain: "A" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 370 Classifications: {'water': 370} Link IDs: {None: 369} Chain: "B" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 354 Classifications: {'water': 354} Link IDs: {None: 353} Chain: "C" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 377 Classifications: {'water': 377} Link IDs: {None: 376} Time building chain proxies: 3.32, per 1000 atoms: 0.26 Number of scatterers: 12654 At special positions: 0 Unit cell: (91.875, 87.465, 147, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 3351 8.00 N 2067 7.00 C 7182 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 482 " distance=2.03 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 293 " distance=2.04 Simple disulfide: pdb=" SG CYS A 80 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 297 " - pdb=" SG CYS A 321 " distance=2.03 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 482 " distance=2.03 Simple disulfide: pdb=" SG CYS B 68 " - pdb=" SG CYS B 293 " distance=2.05 Simple disulfide: pdb=" SG CYS B 80 " - pdb=" SG CYS B 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 297 " - pdb=" SG CYS B 321 " distance=2.03 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 482 " distance=2.03 Simple disulfide: pdb=" SG CYS C 68 " - pdb=" SG CYS C 293 " distance=2.05 Simple disulfide: pdb=" SG CYS C 80 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 155 " distance=2.03 Simple disulfide: pdb=" SG CYS C 297 " - pdb=" SG CYS C 321 " distance=2.03 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: 0.87 Conformation dependent library (CDL) restraints added in 512.4 milliseconds 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2718 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 36 sheets defined 27.3% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 81 through 88 Processing helix chain 'A' and resid 89 through 96 removed outlier: 3.696A pdb=" N ASP A 93 " --> pdb=" O PRO A 90 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLY A 94 " --> pdb=" O GLN A 91 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN A 96 " --> pdb=" O ASP A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'A' and resid 203 through 212 Processing helix chain 'A' and resid 383 through 399 Processing helix chain 'A' and resid 420 through 472 Processing helix chain 'A' and resid 490 through 499 Processing helix chain 'A' and resid 503 through 516 removed outlier: 4.410A pdb=" N TYR A 507 " --> pdb=" O ASP A 503 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N ASP A 509 " --> pdb=" O ASN A 505 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N GLU A 510 " --> pdb=" O VAL A 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 88 Processing helix chain 'B' and resid 89 through 96 removed outlier: 3.766A pdb=" N ASP B 93 " --> pdb=" O PRO B 90 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N GLY B 94 " --> pdb=" O GLN B 91 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN B 96 " --> pdb=" O ASP B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 132 Processing helix chain 'B' and resid 203 through 212 Processing helix chain 'B' and resid 382 through 399 removed outlier: 3.617A pdb=" N THR B 386 " --> pdb=" O ASP B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 472 Processing helix chain 'B' and resid 490 through 499 Processing helix chain 'B' and resid 503 through 516 removed outlier: 4.300A pdb=" N TYR B 507 " --> pdb=" O ASP B 503 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ASP B 509 " --> pdb=" O ASN B 505 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N GLU B 510 " --> pdb=" O VAL B 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 88 Processing helix chain 'C' and resid 89 through 96 removed outlier: 3.658A pdb=" N ASP C 93 " --> pdb=" O PRO C 90 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N GLY C 94 " --> pdb=" O GLN C 91 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN C 96 " --> pdb=" O ASP C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 132 Processing helix chain 'C' and resid 203 through 212 Processing helix chain 'C' and resid 382 through 399 removed outlier: 3.636A pdb=" N THR C 386 " --> pdb=" O ASP C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 472 Processing helix chain 'C' and resid 490 through 499 Processing helix chain 'C' and resid 503 through 516 removed outlier: 4.426A pdb=" N TYR C 507 " --> pdb=" O ASP C 503 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ASP C 509 " --> pdb=" O ASN C 505 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N GLU C 510 " --> pdb=" O VAL C 506 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 377 through 382 removed outlier: 4.741A pdb=" N TYR A 367 " --> pdb=" O ASP A 382 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 40 through 42 Processing sheet with id=AA3, first strand: chain 'A' and resid 55 through 57 Processing sheet with id=AA4, first strand: chain 'A' and resid 59 through 60 Processing sheet with id=AA5, first strand: chain 'A' and resid 67 through 68 removed outlier: 5.994A pdb=" N ILE A 67 " --> pdb=" O GLY A 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 74 through 76 removed outlier: 6.723A pdb=" N LEU A 75 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N PHE A 103 " --> pdb=" O MET A 284 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 136 through 138 removed outlier: 6.517A pdb=" N GLY A 272 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ILE A 195 " --> pdb=" O GLY A 272 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N ILE A 195 " --> pdb=" O PRO A 270 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 136 through 138 removed outlier: 6.517A pdb=" N GLY A 272 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ILE A 195 " --> pdb=" O GLY A 272 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 146 through 147 Processing sheet with id=AB1, first strand: chain 'A' and resid 152 through 156 removed outlier: 4.663A pdb=" N CYS A 155 " --> pdb=" O SER A 162 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 180 through 185 Processing sheet with id=AB3, first strand: chain 'A' and resid 302 through 304 removed outlier: 4.388A pdb=" N CYS A 297 " --> pdb=" O ILE A 304 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 377 through 381 Processing sheet with id=AB5, first strand: chain 'B' and resid 40 through 42 Processing sheet with id=AB6, first strand: chain 'B' and resid 55 through 57 Processing sheet with id=AB7, first strand: chain 'B' and resid 59 through 60 Processing sheet with id=AB8, first strand: chain 'B' and resid 67 through 68 removed outlier: 6.190A pdb=" N ILE B 67 " --> pdb=" O GLY B 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 74 through 76 removed outlier: 6.699A pdb=" N LEU B 75 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N PHE B 103 " --> pdb=" O MET B 284 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 136 through 138 removed outlier: 6.550A pdb=" N GLY B 272 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ILE B 195 " --> pdb=" O GLY B 272 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ILE B 195 " --> pdb=" O PRO B 270 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 136 through 138 removed outlier: 6.550A pdb=" N GLY B 272 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ILE B 195 " --> pdb=" O GLY B 272 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AC4, first strand: chain 'B' and resid 152 through 156 Processing sheet with id=AC5, first strand: chain 'B' and resid 180 through 185 Processing sheet with id=AC6, first strand: chain 'B' and resid 302 through 304 removed outlier: 4.389A pdb=" N CYS B 297 " --> pdb=" O ILE B 304 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 377 through 381 Processing sheet with id=AC8, first strand: chain 'C' and resid 40 through 42 Processing sheet with id=AC9, first strand: chain 'C' and resid 55 through 57 Processing sheet with id=AD1, first strand: chain 'C' and resid 59 through 60 Processing sheet with id=AD2, first strand: chain 'C' and resid 67 through 68 removed outlier: 6.166A pdb=" N ILE C 67 " --> pdb=" O GLY C 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'C' and resid 74 through 76 removed outlier: 6.693A pdb=" N LEU C 75 " --> pdb=" O VAL C 104 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 136 through 138 removed outlier: 6.554A pdb=" N GLY C 272 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ILE C 195 " --> pdb=" O GLY C 272 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ILE C 195 " --> pdb=" O PRO C 270 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 136 through 138 removed outlier: 6.554A pdb=" N GLY C 272 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ILE C 195 " --> pdb=" O GLY C 272 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 146 through 147 Processing sheet with id=AD7, first strand: chain 'C' and resid 152 through 156 Processing sheet with id=AD8, first strand: chain 'C' and resid 180 through 185 Processing sheet with id=AD9, first strand: chain 'C' and resid 302 through 304 removed outlier: 4.356A pdb=" N CYS C 297 " --> pdb=" O ILE C 304 " (cutoff:3.500A) 504 hydrogen bonds defined for protein. 1398 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: 2.71 Time building geometry restraints manager: 1.19 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: 2576 1.33 - 1.45: 2605 1.45 - 1.57: 6525 1.57 - 1.69: 0 1.69 - 1.82: 72 Bond restraints: 11778 Sorted by residual: bond pdb=" N GLY B 291 " pdb=" CA GLY B 291 " ideal model delta sigma weight residual 1.444 1.478 -0.035 1.02e-02 9.61e+03 1.15e+01 bond pdb=" N ILE B 290 " pdb=" CA ILE B 290 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.20e-02 6.94e+03 1.10e+01 bond pdb=" N ILE C 290 " pdb=" CA ILE C 290 " ideal model delta sigma weight residual 1.457 1.501 -0.044 1.32e-02 5.74e+03 1.09e+01 bond pdb=" C ALA C 288 " pdb=" N PRO C 289 " ideal model delta sigma weight residual 1.329 1.368 -0.040 1.20e-02 6.94e+03 1.09e+01 bond pdb=" N GLN B 189 " pdb=" CA GLN B 189 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.10e-02 8.26e+03 1.04e+01 ... (remaining 11773 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 15059 1.61 - 3.21: 723 3.21 - 4.82: 119 4.82 - 6.42: 22 6.42 - 8.03: 7 Bond angle restraints: 15930 Sorted by residual: angle pdb=" CA ALA C 288 " pdb=" C ALA C 288 " pdb=" N PRO C 289 " ideal model delta sigma weight residual 118.23 122.68 -4.45 9.20e-01 1.18e+00 2.34e+01 angle pdb=" CA ASN A 47 " pdb=" CB ASN A 47 " pdb=" CG ASN A 47 " ideal model delta sigma weight residual 112.60 117.25 -4.65 1.00e+00 1.00e+00 2.16e+01 angle pdb=" CA ALA B 288 " pdb=" C ALA B 288 " pdb=" N PRO B 289 " ideal model delta sigma weight residual 118.23 122.43 -4.20 9.20e-01 1.18e+00 2.08e+01 angle pdb=" CA ASN C 47 " pdb=" CB ASN C 47 " pdb=" CG ASN C 47 " ideal model delta sigma weight residual 112.60 117.05 -4.45 1.00e+00 1.00e+00 1.98e+01 angle pdb=" N LYS A 292 " pdb=" CA LYS A 292 " pdb=" C LYS A 292 " ideal model delta sigma weight residual 113.16 107.88 5.28 1.24e+00 6.50e-01 1.81e+01 ... (remaining 15925 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 6504 17.76 - 35.51: 516 35.51 - 53.27: 90 53.27 - 71.03: 28 71.03 - 88.79: 20 Dihedral angle restraints: 7158 sinusoidal: 2934 harmonic: 4224 Sorted by residual: dihedral pdb=" CA CYS B 80 " pdb=" C CYS B 80 " pdb=" N THR B 81 " pdb=" CA THR B 81 " ideal model delta harmonic sigma weight residual 180.00 159.22 20.78 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA CYS C 80 " pdb=" C CYS C 80 " pdb=" N THR C 81 " pdb=" CA THR C 81 " ideal model delta harmonic sigma weight residual 180.00 159.25 20.75 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" N TYR A 121 " pdb=" C TYR A 121 " pdb=" CA TYR A 121 " pdb=" CB TYR A 121 " ideal model delta harmonic sigma weight residual 122.80 112.43 10.37 0 2.50e+00 1.60e-01 1.72e+01 ... (remaining 7155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1467 0.074 - 0.147: 224 0.147 - 0.221: 31 0.221 - 0.294: 2 0.294 - 0.368: 4 Chirality restraints: 1728 Sorted by residual: chirality pdb=" CA TYR A 121 " pdb=" N TYR A 121 " pdb=" C TYR A 121 " pdb=" CB TYR A 121 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.38e+00 chirality pdb=" CA TYR C 121 " pdb=" N TYR C 121 " pdb=" C TYR C 121 " pdb=" CB TYR C 121 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" CA TYR B 121 " pdb=" N TYR B 121 " pdb=" C TYR B 121 " pdb=" CB TYR B 121 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 1725 not shown) Planarity restraints: 2106 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS C 293 " 0.016 2.00e-02 2.50e+03 3.37e-02 1.14e+01 pdb=" C CYS C 293 " -0.058 2.00e-02 2.50e+03 pdb=" O CYS C 293 " 0.022 2.00e-02 2.50e+03 pdb=" N LYS C 294 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 293 " -0.015 2.00e-02 2.50e+03 3.17e-02 1.01e+01 pdb=" C CYS B 293 " 0.055 2.00e-02 2.50e+03 pdb=" O CYS B 293 " -0.021 2.00e-02 2.50e+03 pdb=" N LYS B 294 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 293 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.70e+00 pdb=" C CYS A 293 " 0.041 2.00e-02 2.50e+03 pdb=" O CYS A 293 " -0.015 2.00e-02 2.50e+03 pdb=" N LYS A 294 " -0.014 2.00e-02 2.50e+03 ... (remaining 2103 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3738 2.82 - 3.34: 11537 3.34 - 3.86: 23377 3.86 - 4.38: 28901 4.38 - 4.90: 45475 Nonbonded interactions: 113028 Sorted by model distance: nonbonded pdb=" O SER C 235 " pdb=" O HOH C 601 " model vdw 2.300 3.040 nonbonded pdb=" OD2 ASP B 391 " pdb=" O HOH B 601 " model vdw 2.301 3.040 nonbonded pdb=" O ASN A 357 " pdb=" O HOH A 601 " model vdw 2.301 3.040 nonbonded pdb=" OE1 GLU C 135 " pdb=" O HOH C 602 " model vdw 2.301 3.040 nonbonded pdb=" OD1 ASN B 54 " pdb=" O HOH B 602 " model vdw 2.301 3.040 ... (remaining 113023 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 6.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.420 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 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:9.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 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 0.044 11793 Z= 0.325 Angle : 0.777 8.027 15960 Z= 0.500 Chirality : 0.056 0.368 1728 Planarity : 0.005 0.050 2106 Dihedral : 14.150 88.786 4395 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.70 % Allowed : 1.72 % Favored : 97.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.42 (0.20), residues: 1455 helix: 2.31 (0.27), residues: 354 sheet: 0.29 (0.28), residues: 327 loop : -0.70 (0.19), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 472 TYR 0.015 0.002 TYR A 121 PHE 0.024 0.002 PHE B 190 TRP 0.013 0.001 TRP B 250 HIS 0.007 0.001 HIS C 409 Details of bonding type rmsd covalent geometry : bond 0.00492 (11778) covalent geometry : angle 0.77435 (15930) SS BOND : bond 0.00780 ( 15) SS BOND : angle 1.66015 ( 30) hydrogen bonds : bond 0.10305 ( 492) hydrogen bonds : angle 6.24522 ( 1398) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 203 time to evaluate : 0.442 Fit side-chains REVERT: A 91 GLN cc_start: 0.7909 (mm110) cc_final: 0.7052 (pt0) REVERT: A 187 LYS cc_start: 0.8339 (mmmt) cc_final: 0.8103 (mttt) REVERT: A 224 ARG cc_start: 0.7891 (ttm-80) cc_final: 0.7329 (ttp80) REVERT: A 277 ARG cc_start: 0.7742 (mtt-85) cc_final: 0.7215 (mtp180) REVERT: A 280 LYS cc_start: 0.8167 (ptpt) cc_final: 0.7522 (pttt) REVERT: A 406 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8202 (mt-10) REVERT: A 488 LYS cc_start: 0.7696 (tttm) cc_final: 0.7464 (mttt) REVERT: B 91 GLN cc_start: 0.7492 (mm-40) cc_final: 0.6867 (pt0) REVERT: B 205 LYS cc_start: 0.8151 (ttpp) cc_final: 0.7897 (tttm) REVERT: B 224 ARG cc_start: 0.7869 (ttm-80) cc_final: 0.7455 (ttp80) REVERT: B 277 ARG cc_start: 0.7401 (mtt-85) cc_final: 0.6940 (mtm180) REVERT: B 280 LYS cc_start: 0.8105 (ptpt) cc_final: 0.7680 (pttt) REVERT: B 488 LYS cc_start: 0.7610 (tttm) cc_final: 0.7377 (mttt) REVERT: C 49 ARG cc_start: 0.7817 (mtp85) cc_final: 0.7274 (mtp85) REVERT: C 91 GLN cc_start: 0.7365 (mm110) cc_final: 0.6729 (pt0) REVERT: C 144 THR cc_start: 0.8685 (p) cc_final: 0.8422 (m) REVERT: C 205 LYS cc_start: 0.7919 (tttm) cc_final: 0.7054 (tptt) REVERT: C 224 ARG cc_start: 0.7684 (ttm-80) cc_final: 0.7261 (ttp80) REVERT: C 277 ARG cc_start: 0.7786 (mtt-85) cc_final: 0.7206 (mtm180) REVERT: C 356 GLU cc_start: 0.6494 (OUTLIER) cc_final: 0.6226 (mm-30) REVERT: C 417 GLU cc_start: 0.7285 (mm-30) cc_final: 0.6522 (mm-30) REVERT: C 457 ASP cc_start: 0.8163 (m-30) cc_final: 0.7934 (m-30) REVERT: C 488 LYS cc_start: 0.7580 (tttm) cc_final: 0.7337 (mttt) outliers start: 9 outliers final: 1 residues processed: 207 average time/residue: 0.8171 time to fit residues: 180.3019 Evaluate side-chains 126 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 124 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain C residue 356 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 189 GLN B 262 ASN B 450 GLN C 392 GLN ** C 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.126839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.099160 restraints weight = 12581.307| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.55 r_work: 0.2989 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11793 Z= 0.167 Angle : 0.570 7.834 15960 Z= 0.302 Chirality : 0.046 0.150 1728 Planarity : 0.004 0.053 2106 Dihedral : 4.926 58.019 1589 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.72 % Allowed : 7.49 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.51 (0.21), residues: 1455 helix: 2.59 (0.26), residues: 354 sheet: 0.30 (0.27), residues: 348 loop : -0.76 (0.19), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 472 TYR 0.012 0.002 TYR B 502 PHE 0.013 0.001 PHE A 369 TRP 0.009 0.001 TRP B 250 HIS 0.007 0.001 HIS C 409 Details of bonding type rmsd covalent geometry : bond 0.00401 (11778) covalent geometry : angle 0.56994 (15930) SS BOND : bond 0.00257 ( 15) SS BOND : angle 0.78363 ( 30) hydrogen bonds : bond 0.05255 ( 492) hydrogen bonds : angle 5.13255 ( 1398) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.415 Fit side-chains REVERT: A 91 GLN cc_start: 0.7831 (mm110) cc_final: 0.6955 (pt0) REVERT: A 224 ARG cc_start: 0.7755 (ttm-80) cc_final: 0.7219 (ttp80) REVERT: A 277 ARG cc_start: 0.7698 (mtt-85) cc_final: 0.7233 (mtm180) REVERT: A 280 LYS cc_start: 0.8358 (ptpt) cc_final: 0.7706 (pttt) REVERT: A 417 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7260 (mp0) REVERT: A 453 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.8141 (mp) REVERT: B 91 GLN cc_start: 0.7476 (mm-40) cc_final: 0.6804 (pt0) REVERT: B 205 LYS cc_start: 0.8236 (ttpp) cc_final: 0.7981 (tttm) REVERT: B 224 ARG cc_start: 0.7895 (ttm-80) cc_final: 0.7500 (ttp80) REVERT: B 277 ARG cc_start: 0.7629 (mtt-85) cc_final: 0.7190 (mtm180) REVERT: B 280 LYS cc_start: 0.8322 (ptpt) cc_final: 0.7736 (pttt) REVERT: B 360 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.6839 (mt-10) REVERT: B 417 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7026 (mp0) REVERT: B 431 ASP cc_start: 0.8611 (OUTLIER) cc_final: 0.8374 (t70) REVERT: B 453 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.7767 (mp) REVERT: B 488 LYS cc_start: 0.7755 (tttm) cc_final: 0.7518 (mttt) REVERT: C 49 ARG cc_start: 0.8055 (mtp85) cc_final: 0.7701 (mtp-110) REVERT: C 91 GLN cc_start: 0.7510 (mm110) cc_final: 0.6801 (pt0) REVERT: C 224 ARG cc_start: 0.7720 (ttm-80) cc_final: 0.7408 (ttp80) REVERT: C 277 ARG cc_start: 0.7890 (mtt-85) cc_final: 0.7303 (mtm180) REVERT: C 360 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.6704 (mt-10) REVERT: C 417 GLU cc_start: 0.7362 (mm-30) cc_final: 0.6647 (mm-30) REVERT: C 453 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.7778 (mp) REVERT: C 457 ASP cc_start: 0.8162 (m-30) cc_final: 0.7873 (m-30) outliers start: 22 outliers final: 8 residues processed: 133 average time/residue: 0.6969 time to fit residues: 99.8139 Evaluate side-chains 124 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 360 GLU Chi-restraints excluded: chain C residue 453 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 90 optimal weight: 4.9990 chunk 134 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 131 optimal weight: 9.9990 chunk 119 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN A 423 GLN B 54 ASN B 206 ASN C 206 ASN C 262 ASN C 392 GLN C 423 GLN ** C 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.125122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.097673 restraints weight = 12682.044| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.51 r_work: 0.2967 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 11793 Z= 0.201 Angle : 0.582 8.182 15960 Z= 0.308 Chirality : 0.047 0.151 1728 Planarity : 0.005 0.054 2106 Dihedral : 4.574 22.278 1584 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.19 % Allowed : 8.90 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.49 (0.20), residues: 1455 helix: 2.49 (0.26), residues: 354 sheet: 0.45 (0.28), residues: 312 loop : -0.77 (0.19), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 49 TYR 0.012 0.002 TYR B 502 PHE 0.014 0.002 PHE C 369 TRP 0.009 0.001 TRP A 437 HIS 0.006 0.001 HIS C 409 Details of bonding type rmsd covalent geometry : bond 0.00485 (11778) covalent geometry : angle 0.58215 (15930) SS BOND : bond 0.00272 ( 15) SS BOND : angle 0.69044 ( 30) hydrogen bonds : bond 0.05520 ( 492) hydrogen bonds : angle 5.15057 ( 1398) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.444 Fit side-chains REVERT: A 91 GLN cc_start: 0.7873 (mm110) cc_final: 0.6925 (pt0) REVERT: A 224 ARG cc_start: 0.7784 (ttm-80) cc_final: 0.7221 (ttp80) REVERT: A 277 ARG cc_start: 0.7724 (mtt-85) cc_final: 0.7320 (mtp180) REVERT: A 280 LYS cc_start: 0.8413 (ptpt) cc_final: 0.7809 (pttt) REVERT: A 356 GLU cc_start: 0.7087 (mt-10) cc_final: 0.6780 (mm-30) REVERT: A 417 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.6686 (mm-30) REVERT: A 453 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.8172 (mp) REVERT: B 51 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8159 (tt0) REVERT: B 91 GLN cc_start: 0.7560 (mm-40) cc_final: 0.6824 (pt0) REVERT: B 205 LYS cc_start: 0.8219 (ttpp) cc_final: 0.7162 (tptt) REVERT: B 224 ARG cc_start: 0.7826 (ttm-80) cc_final: 0.7412 (ttp80) REVERT: B 277 ARG cc_start: 0.7699 (mtt-85) cc_final: 0.7243 (mtm180) REVERT: B 280 LYS cc_start: 0.8360 (ptpt) cc_final: 0.7712 (pttt) REVERT: B 356 GLU cc_start: 0.7051 (mt-10) cc_final: 0.6714 (mm-30) REVERT: B 360 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.6858 (mt-10) REVERT: B 417 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7126 (mp0) REVERT: B 426 GLU cc_start: 0.8960 (OUTLIER) cc_final: 0.8546 (mt-10) REVERT: B 431 ASP cc_start: 0.8565 (OUTLIER) cc_final: 0.8323 (t70) REVERT: B 453 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.7795 (mp) REVERT: B 488 LYS cc_start: 0.7841 (tttm) cc_final: 0.7555 (mttt) REVERT: C 49 ARG cc_start: 0.8074 (mtp85) cc_final: 0.7744 (mtp-110) REVERT: C 91 GLN cc_start: 0.7669 (mm110) cc_final: 0.6848 (pt0) REVERT: C 224 ARG cc_start: 0.7795 (ttm-80) cc_final: 0.7421 (ttp80) REVERT: C 277 ARG cc_start: 0.7933 (mtt-85) cc_final: 0.7367 (mtm180) REVERT: C 360 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.6742 (mt-10) REVERT: C 414 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8212 (mt-10) REVERT: C 417 GLU cc_start: 0.7405 (mm-30) cc_final: 0.6696 (mm-30) REVERT: C 453 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.7813 (mp) REVERT: C 457 ASP cc_start: 0.8212 (m-30) cc_final: 0.7926 (m-30) REVERT: C 462 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8097 (mtmt) outliers start: 28 outliers final: 10 residues processed: 128 average time/residue: 0.6899 time to fit residues: 95.2631 Evaluate side-chains 131 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 360 GLU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 462 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 61 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 55 optimal weight: 0.0370 chunk 143 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 overall best weight: 1.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 ASN B 410 GLN C 392 GLN ** C 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.126158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.098604 restraints weight = 12629.415| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.54 r_work: 0.2982 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11793 Z= 0.143 Angle : 0.520 7.151 15960 Z= 0.276 Chirality : 0.045 0.149 1728 Planarity : 0.004 0.050 2106 Dihedral : 4.346 20.929 1584 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.95 % Allowed : 9.52 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.63 (0.21), residues: 1455 helix: 2.80 (0.26), residues: 351 sheet: 0.36 (0.27), residues: 348 loop : -0.73 (0.20), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 49 TYR 0.010 0.001 TYR B 502 PHE 0.012 0.001 PHE C 369 TRP 0.009 0.001 TRP A 437 HIS 0.004 0.001 HIS C 409 Details of bonding type rmsd covalent geometry : bond 0.00338 (11778) covalent geometry : angle 0.52012 (15930) SS BOND : bond 0.00230 ( 15) SS BOND : angle 0.60782 ( 30) hydrogen bonds : bond 0.04943 ( 492) hydrogen bonds : angle 4.95601 ( 1398) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 0.501 Fit side-chains REVERT: A 64 ILE cc_start: 0.8103 (OUTLIER) cc_final: 0.7885 (pt) REVERT: A 91 GLN cc_start: 0.7825 (mm110) cc_final: 0.6874 (pt0) REVERT: A 224 ARG cc_start: 0.7818 (ttm-80) cc_final: 0.7224 (ttp80) REVERT: A 277 ARG cc_start: 0.7747 (mtt-85) cc_final: 0.7340 (mtp180) REVERT: A 280 LYS cc_start: 0.8396 (ptpt) cc_final: 0.7751 (pttp) REVERT: A 356 GLU cc_start: 0.7012 (mt-10) cc_final: 0.6704 (mm-30) REVERT: A 417 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.6684 (mm-30) REVERT: A 453 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.8151 (mp) REVERT: B 51 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.8109 (tt0) REVERT: B 91 GLN cc_start: 0.7549 (mm-40) cc_final: 0.6771 (pt0) REVERT: B 205 LYS cc_start: 0.8191 (ttpp) cc_final: 0.7897 (tttm) REVERT: B 224 ARG cc_start: 0.7827 (ttm-80) cc_final: 0.7359 (ttp80) REVERT: B 277 ARG cc_start: 0.7717 (mtt-85) cc_final: 0.7256 (mtm180) REVERT: B 280 LYS cc_start: 0.8350 (ptpt) cc_final: 0.7691 (pttt) REVERT: B 356 GLU cc_start: 0.7039 (mt-10) cc_final: 0.6714 (mm-30) REVERT: B 417 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.6559 (mm-30) REVERT: B 426 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8514 (mt-10) REVERT: B 431 ASP cc_start: 0.8573 (OUTLIER) cc_final: 0.8340 (t70) REVERT: B 453 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.7762 (mp) REVERT: B 488 LYS cc_start: 0.7857 (tttm) cc_final: 0.7618 (mttt) REVERT: C 49 ARG cc_start: 0.8099 (mtp85) cc_final: 0.7804 (mtp-110) REVERT: C 91 GLN cc_start: 0.7697 (mm110) cc_final: 0.6841 (pt0) REVERT: C 224 ARG cc_start: 0.7793 (ttm-80) cc_final: 0.7412 (ttp80) REVERT: C 277 ARG cc_start: 0.7908 (mtt-85) cc_final: 0.7303 (mtm180) REVERT: C 360 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.6755 (mt-10) REVERT: C 414 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8217 (mt-10) REVERT: C 417 GLU cc_start: 0.7428 (mm-30) cc_final: 0.6629 (mm-30) REVERT: C 453 ILE cc_start: 0.8347 (OUTLIER) cc_final: 0.7642 (mp) REVERT: C 457 ASP cc_start: 0.8185 (m-30) cc_final: 0.7892 (m-30) outliers start: 25 outliers final: 11 residues processed: 129 average time/residue: 0.6924 time to fit residues: 96.3991 Evaluate side-chains 132 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 360 GLU Chi-restraints excluded: chain C residue 453 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 112 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 119 optimal weight: 0.5980 chunk 141 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 48 optimal weight: 10.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 392 GLN ** C 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.129585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.104663 restraints weight = 13206.366| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.43 r_work: 0.3122 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11793 Z= 0.132 Angle : 0.502 6.985 15960 Z= 0.266 Chirality : 0.044 0.150 1728 Planarity : 0.004 0.049 2106 Dihedral : 4.220 20.153 1584 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.95 % Allowed : 10.15 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.71 (0.21), residues: 1455 helix: 2.90 (0.26), residues: 351 sheet: 0.40 (0.27), residues: 348 loop : -0.69 (0.20), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 49 TYR 0.010 0.001 TYR C 502 PHE 0.012 0.001 PHE C 369 TRP 0.009 0.001 TRP A 437 HIS 0.003 0.001 HIS C 409 Details of bonding type rmsd covalent geometry : bond 0.00310 (11778) covalent geometry : angle 0.50145 (15930) SS BOND : bond 0.00222 ( 15) SS BOND : angle 0.57838 ( 30) hydrogen bonds : bond 0.04742 ( 492) hydrogen bonds : angle 4.86047 ( 1398) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 0.464 Fit side-chains REVERT: A 64 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7902 (pt) REVERT: A 91 GLN cc_start: 0.7844 (mm110) cc_final: 0.7016 (pt0) REVERT: A 224 ARG cc_start: 0.7773 (ttm-80) cc_final: 0.7350 (ttp80) REVERT: A 277 ARG cc_start: 0.7762 (mtt-85) cc_final: 0.7440 (mtp180) REVERT: A 280 LYS cc_start: 0.8471 (ptpt) cc_final: 0.7833 (pttp) REVERT: A 372 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7658 (tt0) REVERT: A 417 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.6883 (mm-30) REVERT: A 453 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.8240 (mp) REVERT: B 49 ARG cc_start: 0.8356 (mtp85) cc_final: 0.7964 (mtp-110) REVERT: B 91 GLN cc_start: 0.7662 (mm-40) cc_final: 0.6993 (pt0) REVERT: B 205 LYS cc_start: 0.8288 (ttpp) cc_final: 0.8040 (tttm) REVERT: B 224 ARG cc_start: 0.7809 (ttm-80) cc_final: 0.7476 (ttp80) REVERT: B 277 ARG cc_start: 0.7776 (mtt-85) cc_final: 0.7414 (mtm180) REVERT: B 280 LYS cc_start: 0.8458 (ptpt) cc_final: 0.7881 (pttt) REVERT: B 356 GLU cc_start: 0.7013 (mt-10) cc_final: 0.6777 (mm-30) REVERT: B 417 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.6726 (mm-30) REVERT: B 426 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8543 (mt-10) REVERT: B 431 ASP cc_start: 0.8578 (OUTLIER) cc_final: 0.8364 (t70) REVERT: B 453 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.7899 (mp) REVERT: C 49 ARG cc_start: 0.8081 (mtp85) cc_final: 0.7781 (mtp-110) REVERT: C 91 GLN cc_start: 0.7793 (mm110) cc_final: 0.7060 (pt0) REVERT: C 205 LYS cc_start: 0.8215 (tttp) cc_final: 0.7261 (tptt) REVERT: C 224 ARG cc_start: 0.7844 (ttm-80) cc_final: 0.7553 (ttp80) REVERT: C 277 ARG cc_start: 0.7808 (mtt-85) cc_final: 0.7416 (mtm180) REVERT: C 360 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6730 (mt-10) REVERT: C 414 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8220 (mt-10) REVERT: C 417 GLU cc_start: 0.7408 (mm-30) cc_final: 0.6710 (mm-30) REVERT: C 453 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.7744 (mp) REVERT: C 457 ASP cc_start: 0.8162 (m-30) cc_final: 0.7902 (m-30) outliers start: 25 outliers final: 11 residues processed: 129 average time/residue: 0.7184 time to fit residues: 100.0493 Evaluate side-chains 134 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 360 GLU Chi-restraints excluded: chain C residue 453 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 78 optimal weight: 0.0870 chunk 36 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 137 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 GLN C 392 GLN ** C 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.125361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.097398 restraints weight = 12774.999| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.60 r_work: 0.2961 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 11793 Z= 0.162 Angle : 0.529 7.549 15960 Z= 0.280 Chirality : 0.045 0.149 1728 Planarity : 0.004 0.050 2106 Dihedral : 4.346 21.005 1584 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.19 % Allowed : 9.91 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.67 (0.21), residues: 1455 helix: 2.85 (0.26), residues: 351 sheet: 0.39 (0.27), residues: 348 loop : -0.71 (0.20), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 49 TYR 0.010 0.002 TYR B 502 PHE 0.013 0.001 PHE C 369 TRP 0.009 0.001 TRP A 437 HIS 0.004 0.001 HIS C 409 Details of bonding type rmsd covalent geometry : bond 0.00388 (11778) covalent geometry : angle 0.52931 (15930) SS BOND : bond 0.00247 ( 15) SS BOND : angle 0.58379 ( 30) hydrogen bonds : bond 0.05073 ( 492) hydrogen bonds : angle 4.94931 ( 1398) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 0.486 Fit side-chains REVERT: A 64 ILE cc_start: 0.8077 (OUTLIER) cc_final: 0.7860 (pt) REVERT: A 91 GLN cc_start: 0.7794 (mm110) cc_final: 0.6820 (pt0) REVERT: A 224 ARG cc_start: 0.7795 (ttm-80) cc_final: 0.7194 (ttp80) REVERT: A 277 ARG cc_start: 0.7823 (mtt-85) cc_final: 0.7381 (mtp180) REVERT: A 280 LYS cc_start: 0.8409 (ptpt) cc_final: 0.7678 (pttp) REVERT: A 372 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7647 (tt0) REVERT: A 417 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.6703 (mm-30) REVERT: B 49 ARG cc_start: 0.8392 (mtp85) cc_final: 0.7908 (mtp-110) REVERT: B 91 GLN cc_start: 0.7601 (mm-40) cc_final: 0.6796 (pt0) REVERT: B 205 LYS cc_start: 0.8231 (ttpp) cc_final: 0.7923 (tttm) REVERT: B 224 ARG cc_start: 0.7847 (ttm-80) cc_final: 0.7371 (ttp80) REVERT: B 277 ARG cc_start: 0.7801 (mtt-85) cc_final: 0.7298 (mtm180) REVERT: B 280 LYS cc_start: 0.8421 (ptpt) cc_final: 0.7740 (pttt) REVERT: B 356 GLU cc_start: 0.7004 (mt-10) cc_final: 0.6647 (mm-30) REVERT: B 417 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.6546 (mm-30) REVERT: B 426 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8509 (mt-10) REVERT: B 431 ASP cc_start: 0.8585 (OUTLIER) cc_final: 0.8342 (t70) REVERT: B 453 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.7778 (mp) REVERT: C 49 ARG cc_start: 0.8068 (mtp85) cc_final: 0.7772 (mtp-110) REVERT: C 91 GLN cc_start: 0.7715 (mm110) cc_final: 0.6807 (pt0) REVERT: C 205 LYS cc_start: 0.8139 (tttp) cc_final: 0.7061 (tptt) REVERT: C 224 ARG cc_start: 0.7829 (ttm-80) cc_final: 0.7362 (ttp80) REVERT: C 277 ARG cc_start: 0.7932 (mtt-85) cc_final: 0.7406 (mtm180) REVERT: C 360 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.6767 (mt-10) REVERT: C 399 ARG cc_start: 0.7097 (ttp80) cc_final: 0.6620 (ttt180) REVERT: C 414 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8251 (mt-10) REVERT: C 417 GLU cc_start: 0.7501 (mm-30) cc_final: 0.6605 (mm-30) REVERT: C 453 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.7773 (mp) REVERT: C 457 ASP cc_start: 0.8247 (m-30) cc_final: 0.7960 (m-30) outliers start: 28 outliers final: 13 residues processed: 131 average time/residue: 0.7436 time to fit residues: 104.6403 Evaluate side-chains 134 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 360 GLU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 455 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 135 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 117 optimal weight: 0.4980 chunk 66 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 47 ASN C 392 GLN C 470 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.129351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.104448 restraints weight = 13183.891| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.42 r_work: 0.3117 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11793 Z= 0.135 Angle : 0.501 7.007 15960 Z= 0.265 Chirality : 0.044 0.148 1728 Planarity : 0.004 0.048 2106 Dihedral : 4.219 20.029 1584 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.34 % Allowed : 10.30 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.76 (0.21), residues: 1455 helix: 2.99 (0.26), residues: 351 sheet: 0.43 (0.27), residues: 348 loop : -0.67 (0.20), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 49 TYR 0.009 0.001 TYR C 502 PHE 0.012 0.001 PHE C 369 TRP 0.009 0.001 TRP A 437 HIS 0.003 0.001 HIS C 371 Details of bonding type rmsd covalent geometry : bond 0.00317 (11778) covalent geometry : angle 0.50048 (15930) SS BOND : bond 0.00232 ( 15) SS BOND : angle 0.56289 ( 30) hydrogen bonds : bond 0.04744 ( 492) hydrogen bonds : angle 4.85369 ( 1398) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 0.380 Fit side-chains REVERT: A 64 ILE cc_start: 0.8138 (OUTLIER) cc_final: 0.7913 (pt) REVERT: A 91 GLN cc_start: 0.7843 (mm110) cc_final: 0.6996 (pt0) REVERT: A 224 ARG cc_start: 0.7773 (ttm-80) cc_final: 0.7348 (ttp80) REVERT: A 277 ARG cc_start: 0.7832 (mtt-85) cc_final: 0.7488 (mtp180) REVERT: A 280 LYS cc_start: 0.8474 (ptpt) cc_final: 0.7817 (pttp) REVERT: A 372 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7656 (tt0) REVERT: A 417 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.6890 (mm-30) REVERT: A 488 LYS cc_start: 0.8225 (mttm) cc_final: 0.8022 (mttt) REVERT: B 49 ARG cc_start: 0.8352 (mtp85) cc_final: 0.8000 (mtp-110) REVERT: B 91 GLN cc_start: 0.7701 (mm-40) cc_final: 0.7009 (pt0) REVERT: B 205 LYS cc_start: 0.8288 (ttpp) cc_final: 0.8038 (tttm) REVERT: B 224 ARG cc_start: 0.7860 (ttm-80) cc_final: 0.7513 (ttp80) REVERT: B 277 ARG cc_start: 0.7838 (mtt-85) cc_final: 0.7446 (mtm180) REVERT: B 280 LYS cc_start: 0.8470 (ptpt) cc_final: 0.7887 (pttt) REVERT: B 356 GLU cc_start: 0.7047 (mt-10) cc_final: 0.6776 (mm-30) REVERT: B 372 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7805 (tt0) REVERT: B 417 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.6741 (mm-30) REVERT: B 426 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8542 (mt-10) REVERT: B 431 ASP cc_start: 0.8569 (OUTLIER) cc_final: 0.8353 (t70) REVERT: B 453 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.7912 (mp) REVERT: C 49 ARG cc_start: 0.8023 (mtp85) cc_final: 0.7823 (mtp-110) REVERT: C 91 GLN cc_start: 0.7811 (mm110) cc_final: 0.7053 (pt0) REVERT: C 205 LYS cc_start: 0.8198 (tttp) cc_final: 0.7248 (tptt) REVERT: C 224 ARG cc_start: 0.7859 (ttm-80) cc_final: 0.7536 (ttp80) REVERT: C 277 ARG cc_start: 0.7833 (mtt-85) cc_final: 0.7435 (mtm180) REVERT: C 414 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8219 (mt-10) REVERT: C 417 GLU cc_start: 0.7519 (mm-30) cc_final: 0.6752 (mm-30) REVERT: C 453 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.7787 (mp) REVERT: C 457 ASP cc_start: 0.8173 (m-30) cc_final: 0.7916 (m-30) outliers start: 30 outliers final: 13 residues processed: 135 average time/residue: 0.6505 time to fit residues: 94.5315 Evaluate side-chains 137 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 372 GLN Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 453 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 26 optimal weight: 1.9990 chunk 123 optimal weight: 0.4980 chunk 142 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 21 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 GLN C 47 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.125584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.097766 restraints weight = 12686.253| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.59 r_work: 0.2966 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11793 Z= 0.147 Angle : 0.511 7.266 15960 Z= 0.270 Chirality : 0.045 0.147 1728 Planarity : 0.004 0.048 2106 Dihedral : 4.269 20.427 1584 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.03 % Allowed : 10.38 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.75 (0.21), residues: 1455 helix: 2.98 (0.25), residues: 351 sheet: 0.42 (0.27), residues: 348 loop : -0.68 (0.20), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 49 TYR 0.010 0.001 TYR B 502 PHE 0.012 0.001 PHE C 369 TRP 0.009 0.001 TRP A 437 HIS 0.003 0.001 HIS C 409 Details of bonding type rmsd covalent geometry : bond 0.00348 (11778) covalent geometry : angle 0.51122 (15930) SS BOND : bond 0.00237 ( 15) SS BOND : angle 0.56008 ( 30) hydrogen bonds : bond 0.04867 ( 492) hydrogen bonds : angle 4.87979 ( 1398) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 0.493 Fit side-chains REVERT: A 64 ILE cc_start: 0.8065 (OUTLIER) cc_final: 0.7848 (pt) REVERT: A 91 GLN cc_start: 0.7778 (mm110) cc_final: 0.6818 (pt0) REVERT: A 224 ARG cc_start: 0.7795 (ttm-80) cc_final: 0.7193 (ttp80) REVERT: A 277 ARG cc_start: 0.7836 (mtt-85) cc_final: 0.7374 (mtp180) REVERT: A 280 LYS cc_start: 0.8409 (ptpt) cc_final: 0.7668 (pttp) REVERT: A 372 GLN cc_start: 0.7993 (OUTLIER) cc_final: 0.7629 (tt0) REVERT: A 417 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.6711 (mm-30) REVERT: A 488 LYS cc_start: 0.8132 (mttm) cc_final: 0.7912 (mttt) REVERT: B 49 ARG cc_start: 0.8393 (mtp85) cc_final: 0.7934 (mtp-110) REVERT: B 91 GLN cc_start: 0.7603 (mm-40) cc_final: 0.6758 (pt0) REVERT: B 205 LYS cc_start: 0.8216 (ttpp) cc_final: 0.7906 (tttm) REVERT: B 224 ARG cc_start: 0.7794 (ttm-80) cc_final: 0.7356 (ttp80) REVERT: B 277 ARG cc_start: 0.7797 (mtt-85) cc_final: 0.7317 (mtm180) REVERT: B 280 LYS cc_start: 0.8406 (ptpt) cc_final: 0.7720 (pttt) REVERT: B 356 GLU cc_start: 0.7000 (mt-10) cc_final: 0.6641 (mm-30) REVERT: B 372 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7759 (tt0) REVERT: B 417 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.6558 (mm-30) REVERT: B 426 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8493 (mt-10) REVERT: B 431 ASP cc_start: 0.8632 (OUTLIER) cc_final: 0.8390 (t70) REVERT: B 453 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.7757 (mp) REVERT: C 49 ARG cc_start: 0.8047 (mtp85) cc_final: 0.7802 (mtp-110) REVERT: C 91 GLN cc_start: 0.7763 (mm110) cc_final: 0.6841 (pt0) REVERT: C 205 LYS cc_start: 0.8131 (tttp) cc_final: 0.7047 (tptt) REVERT: C 224 ARG cc_start: 0.7814 (ttm-80) cc_final: 0.7341 (ttp80) REVERT: C 277 ARG cc_start: 0.7938 (mtt-85) cc_final: 0.7380 (mtm180) REVERT: C 399 ARG cc_start: 0.7077 (ttp80) cc_final: 0.6624 (ttt180) REVERT: C 414 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8228 (mt-10) REVERT: C 417 GLU cc_start: 0.7491 (mm-30) cc_final: 0.6598 (mm-30) REVERT: C 453 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.7715 (mp) REVERT: C 457 ASP cc_start: 0.8240 (m-30) cc_final: 0.7952 (m-30) outliers start: 26 outliers final: 14 residues processed: 130 average time/residue: 0.6567 time to fit residues: 92.1956 Evaluate side-chains 138 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 372 GLN Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 455 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 13 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 63 optimal weight: 0.0070 chunk 59 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 overall best weight: 1.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 47 ASN C 513 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.125755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.097896 restraints weight = 12838.280| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.61 r_work: 0.2969 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11793 Z= 0.142 Angle : 0.506 7.578 15960 Z= 0.268 Chirality : 0.044 0.147 1728 Planarity : 0.004 0.048 2106 Dihedral : 4.250 20.215 1584 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.03 % Allowed : 10.38 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.76 (0.21), residues: 1455 helix: 2.89 (0.26), residues: 357 sheet: 0.43 (0.27), residues: 348 loop : -0.66 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 49 TYR 0.010 0.001 TYR B 502 PHE 0.012 0.001 PHE B 369 TRP 0.009 0.001 TRP A 437 HIS 0.003 0.001 HIS C 371 Details of bonding type rmsd covalent geometry : bond 0.00334 (11778) covalent geometry : angle 0.50615 (15930) SS BOND : bond 0.00240 ( 15) SS BOND : angle 0.56193 ( 30) hydrogen bonds : bond 0.04795 ( 492) hydrogen bonds : angle 4.86841 ( 1398) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 0.541 Fit side-chains REVERT: A 64 ILE cc_start: 0.8063 (OUTLIER) cc_final: 0.7846 (pt) REVERT: A 91 GLN cc_start: 0.7768 (mm110) cc_final: 0.6807 (pt0) REVERT: A 224 ARG cc_start: 0.7801 (ttm-80) cc_final: 0.7186 (ttp80) REVERT: A 277 ARG cc_start: 0.7825 (mtt-85) cc_final: 0.7370 (mtp180) REVERT: A 280 LYS cc_start: 0.8408 (ptpt) cc_final: 0.7665 (pttp) REVERT: A 372 GLN cc_start: 0.7993 (OUTLIER) cc_final: 0.7612 (tt0) REVERT: A 417 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.6730 (mm-30) REVERT: A 488 LYS cc_start: 0.8140 (mttm) cc_final: 0.7921 (mttt) REVERT: B 49 ARG cc_start: 0.8385 (mtp85) cc_final: 0.7936 (mtp-110) REVERT: B 91 GLN cc_start: 0.7623 (mm-40) cc_final: 0.6755 (pt0) REVERT: B 205 LYS cc_start: 0.8217 (ttpp) cc_final: 0.7907 (tttm) REVERT: B 224 ARG cc_start: 0.7816 (ttm-80) cc_final: 0.7333 (ttp80) REVERT: B 277 ARG cc_start: 0.7805 (mtt-85) cc_final: 0.7312 (mtm180) REVERT: B 280 LYS cc_start: 0.8399 (ptpt) cc_final: 0.7714 (pttt) REVERT: B 356 GLU cc_start: 0.6976 (mt-10) cc_final: 0.6623 (mm-30) REVERT: B 372 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7738 (tt0) REVERT: B 417 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.6563 (mm-30) REVERT: B 426 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8500 (mt-10) REVERT: B 431 ASP cc_start: 0.8627 (OUTLIER) cc_final: 0.8389 (t70) REVERT: B 453 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.7751 (mp) REVERT: C 49 ARG cc_start: 0.8051 (mtp85) cc_final: 0.7793 (mtp-110) REVERT: C 91 GLN cc_start: 0.7764 (mm110) cc_final: 0.6839 (pt0) REVERT: C 205 LYS cc_start: 0.8125 (tttp) cc_final: 0.7038 (tptt) REVERT: C 224 ARG cc_start: 0.7830 (ttm-80) cc_final: 0.7350 (ttp80) REVERT: C 277 ARG cc_start: 0.7934 (mtt-85) cc_final: 0.7382 (mtm180) REVERT: C 399 ARG cc_start: 0.7056 (ttp80) cc_final: 0.6609 (ttt180) REVERT: C 414 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8227 (mt-10) REVERT: C 417 GLU cc_start: 0.7480 (mm-30) cc_final: 0.6587 (mm-30) REVERT: C 453 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.7668 (mp) REVERT: C 457 ASP cc_start: 0.8234 (m-30) cc_final: 0.7943 (m-30) REVERT: C 514 ASN cc_start: 0.8427 (m110) cc_final: 0.8127 (m-40) outliers start: 26 outliers final: 14 residues processed: 132 average time/residue: 0.6936 time to fit residues: 98.9858 Evaluate side-chains 138 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 372 GLN Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 455 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 68 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 122 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 47 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.125336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.097474 restraints weight = 12821.182| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.60 r_work: 0.2962 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11793 Z= 0.154 Angle : 0.520 8.234 15960 Z= 0.275 Chirality : 0.045 0.148 1728 Planarity : 0.004 0.048 2106 Dihedral : 4.313 20.613 1584 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.03 % Allowed : 10.54 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.73 (0.21), residues: 1455 helix: 2.85 (0.26), residues: 357 sheet: 0.42 (0.27), residues: 348 loop : -0.67 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 49 TYR 0.010 0.002 TYR B 502 PHE 0.013 0.001 PHE C 369 TRP 0.009 0.001 TRP A 437 HIS 0.004 0.001 HIS C 409 Details of bonding type rmsd covalent geometry : bond 0.00365 (11778) covalent geometry : angle 0.52025 (15930) SS BOND : bond 0.00246 ( 15) SS BOND : angle 0.56878 ( 30) hydrogen bonds : bond 0.04923 ( 492) hydrogen bonds : angle 4.92833 ( 1398) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.490 Fit side-chains REVERT: A 64 ILE cc_start: 0.8075 (OUTLIER) cc_final: 0.7856 (pt) REVERT: A 91 GLN cc_start: 0.7789 (mm110) cc_final: 0.6818 (pt0) REVERT: A 224 ARG cc_start: 0.7796 (ttm-80) cc_final: 0.7191 (ttp80) REVERT: A 277 ARG cc_start: 0.7851 (mtt-85) cc_final: 0.7386 (mtp180) REVERT: A 280 LYS cc_start: 0.8406 (ptpt) cc_final: 0.7686 (pttp) REVERT: A 372 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7627 (tt0) REVERT: A 417 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.6749 (mm-30) REVERT: A 488 LYS cc_start: 0.8147 (mttm) cc_final: 0.7930 (mttt) REVERT: B 49 ARG cc_start: 0.8391 (mtp85) cc_final: 0.7945 (mtp-110) REVERT: B 91 GLN cc_start: 0.7712 (mm-40) cc_final: 0.6811 (pt0) REVERT: B 205 LYS cc_start: 0.8224 (ttpp) cc_final: 0.7904 (tttm) REVERT: B 224 ARG cc_start: 0.7885 (ttm-80) cc_final: 0.7386 (ttp80) REVERT: B 277 ARG cc_start: 0.7801 (mtt-85) cc_final: 0.7306 (mtm180) REVERT: B 280 LYS cc_start: 0.8405 (ptpt) cc_final: 0.7719 (pttt) REVERT: B 356 GLU cc_start: 0.6963 (mt-10) cc_final: 0.6640 (mm-30) REVERT: B 372 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7741 (tt0) REVERT: B 417 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.6581 (mm-30) REVERT: B 426 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8501 (mt-10) REVERT: B 431 ASP cc_start: 0.8595 (OUTLIER) cc_final: 0.8347 (t70) REVERT: B 453 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.7770 (mp) REVERT: C 49 ARG cc_start: 0.8077 (mtp85) cc_final: 0.7801 (mtp-110) REVERT: C 91 GLN cc_start: 0.7775 (mm110) cc_final: 0.6851 (pt0) REVERT: C 205 LYS cc_start: 0.8134 (tttp) cc_final: 0.7050 (tptt) REVERT: C 224 ARG cc_start: 0.7823 (ttm-80) cc_final: 0.7365 (ttp80) REVERT: C 277 ARG cc_start: 0.7944 (mtt-85) cc_final: 0.7390 (mtm180) REVERT: C 399 ARG cc_start: 0.7091 (ttp80) cc_final: 0.6631 (ttt180) REVERT: C 414 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8241 (mt-10) REVERT: C 417 GLU cc_start: 0.7507 (mm-30) cc_final: 0.6613 (mm-30) REVERT: C 453 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.7728 (mp) REVERT: C 457 ASP cc_start: 0.8243 (m-30) cc_final: 0.7958 (m-30) REVERT: C 514 ASN cc_start: 0.8481 (m110) cc_final: 0.8175 (m-40) outliers start: 26 outliers final: 16 residues processed: 129 average time/residue: 0.7161 time to fit residues: 99.5412 Evaluate side-chains 138 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 372 GLN Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 455 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 14 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 7 optimal weight: 0.2980 chunk 65 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN B 213 GLN C 47 ASN C 213 GLN C 513 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.123338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.095616 restraints weight = 12844.132| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.59 r_work: 0.2934 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 11793 Z= 0.256 Angle : 0.613 9.417 15960 Z= 0.323 Chirality : 0.049 0.158 1728 Planarity : 0.005 0.052 2106 Dihedral : 4.647 22.335 1584 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.03 % Allowed : 10.62 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.36 (0.20), residues: 1455 helix: 2.61 (0.26), residues: 357 sheet: 0.24 (0.27), residues: 324 loop : -0.95 (0.19), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 323 TYR 0.014 0.002 TYR B 177 PHE 0.016 0.002 PHE C 369 TRP 0.008 0.002 TRP A 437 HIS 0.006 0.001 HIS C 371 Details of bonding type rmsd covalent geometry : bond 0.00625 (11778) covalent geometry : angle 0.61318 (15930) SS BOND : bond 0.00354 ( 15) SS BOND : angle 0.68930 ( 30) hydrogen bonds : bond 0.05783 ( 492) hydrogen bonds : angle 5.19539 ( 1398) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4562.87 seconds wall clock time: 78 minutes 44.69 seconds (4724.69 seconds total)