Starting phenix.real_space_refine on Sun May 3 10:46:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11mu_75846/05_2026/11mu_75846.cif Found real_map, /net/cci-nas-00/data/ceres_data/11mu_75846/05_2026/11mu_75846.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/11mu_75846/05_2026/11mu_75846.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11mu_75846/05_2026/11mu_75846.map" model { file = "/net/cci-nas-00/data/ceres_data/11mu_75846/05_2026/11mu_75846.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11mu_75846/05_2026/11mu_75846.cif" } resolution = 2.67 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= 0.006 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 3004 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 12307 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: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 262 Classifications: {'water': 262} Link IDs: {None: 261} Chain: "B" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 225 Classifications: {'water': 225} Link IDs: {None: 224} Chain: "C" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 267 Classifications: {'water': 267} Link IDs: {None: 266} Time building chain proxies: 2.97, per 1000 atoms: 0.24 Number of scatterers: 12307 At special positions: 0 Unit cell: (89.67, 85.26, 148.47, 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 3004 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=2.05 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: 0.95 Conformation dependent library (CDL) restraints added in 402.8 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 27.1% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 81 through 88 Processing helix chain 'A' and resid 89 through 96 removed outlier: 3.601A pdb=" N ASP A 93 " --> pdb=" O PRO A 90 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N GLY A 94 " --> pdb=" O GLN A 91 " (cutoff:3.500A) removed outlier: 3.770A 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 401 Processing helix chain 'A' and resid 420 through 472 removed outlier: 3.566A pdb=" N ASP A 424 " --> pdb=" O GLY A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 499 Processing helix chain 'A' and resid 507 through 516 Processing helix chain 'B' and resid 81 through 88 Processing helix chain 'B' and resid 89 through 96 removed outlier: 3.830A pdb=" N ASP B 93 " --> pdb=" O PRO B 90 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N GLY B 94 " --> pdb=" O GLN B 91 " (cutoff:3.500A) removed outlier: 3.843A 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 383 through 401 Processing helix chain 'B' and resid 422 through 472 Processing helix chain 'B' and resid 490 through 499 Processing helix chain 'B' and resid 503 through 516 removed outlier: 4.378A pdb=" N TYR B 507 " --> pdb=" O ASP B 503 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ASP B 509 " --> pdb=" O ASN B 505 " (cutoff:3.500A) removed outlier: 5.727A 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: 3.812A pdb=" N ASP C 93 " --> pdb=" O PRO C 90 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N GLY C 94 " --> pdb=" O GLN C 91 " (cutoff:3.500A) removed outlier: 3.904A 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 383 through 401 Processing helix chain 'C' and resid 421 through 472 Processing helix chain 'C' and resid 490 through 499 Processing helix chain 'C' and resid 503 through 516 removed outlier: 4.315A pdb=" N TYR C 507 " --> pdb=" O ASP C 503 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ASP C 509 " --> pdb=" O ASN C 505 " (cutoff:3.500A) removed outlier: 5.626A 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: 4.772A 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: 6.121A 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: 6.473A pdb=" N LEU A 75 " --> pdb=" O VAL A 104 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 136 through 138 removed outlier: 6.500A pdb=" N GLY A 272 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ILE A 195 " --> pdb=" O GLY A 272 " (cutoff:3.500A) removed outlier: 7.781A 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: 6.500A pdb=" N GLY A 272 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 5.021A 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: 4.617A 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 297 through 299 removed outlier: 4.291A pdb=" N CYS A 297 " --> pdb=" O ILE A 304 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 319 through 320 removed outlier: 3.593A pdb=" N LYS A 407 " --> pdb=" O GLY A 319 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 377 through 382 removed outlier: 4.663A pdb=" N TYR B 367 " --> pdb=" O ASP B 382 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 40 through 42 Processing sheet with id=AB7, first strand: chain 'B' and resid 55 through 57 Processing sheet with id=AB8, first strand: chain 'B' and resid 59 through 60 Processing sheet with id=AB9, first strand: chain 'B' and resid 67 through 68 removed outlier: 6.259A pdb=" N ILE B 67 " --> pdb=" O GLY B 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 74 through 76 removed outlier: 6.768A pdb=" N LEU B 75 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N PHE B 103 " --> pdb=" O MET B 284 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 116 through 117 removed outlier: 4.970A pdb=" N ILE B 195 " --> pdb=" O GLY B 272 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLY B 272 " --> pdb=" O ILE B 195 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 116 through 117 removed outlier: 7.738A pdb=" N ILE B 195 " --> pdb=" O PRO B 270 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AC5, first strand: chain 'B' and resid 152 through 156 Processing sheet with id=AC6, first strand: chain 'B' and resid 180 through 185 Processing sheet with id=AC7, first strand: chain 'B' and resid 302 through 304 removed outlier: 4.391A pdb=" N CYS B 297 " --> pdb=" O ILE B 304 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 377 through 382 removed outlier: 4.727A pdb=" N TYR C 367 " --> pdb=" O ASP C 382 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 40 through 42 Processing sheet with id=AD1, first strand: chain 'C' and resid 55 through 57 Processing sheet with id=AD2, first strand: chain 'C' and resid 59 through 60 Processing sheet with id=AD3, first strand: chain 'C' and resid 67 through 68 removed outlier: 6.297A pdb=" N ILE C 67 " --> pdb=" O GLY C 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'C' and resid 74 through 76 removed outlier: 6.682A pdb=" N LEU C 75 " --> pdb=" O VAL C 104 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 116 through 117 removed outlier: 4.960A pdb=" N ILE C 195 " --> pdb=" O GLY C 272 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLY C 272 " --> pdb=" O ILE C 195 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 116 through 117 removed outlier: 7.718A pdb=" N ILE C 195 " --> pdb=" O PRO C 270 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 146 through 147 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: 4.244A pdb=" N CYS C 297 " --> pdb=" O ILE C 304 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASN C 405 " --> pdb=" O CYS C 321 " (cutoff:3.500A) 526 hydrogen bonds defined for protein. 1452 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: 2.36 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1995 1.32 - 1.44: 3109 1.44 - 1.57: 6602 1.57 - 1.69: 0 1.69 - 1.82: 72 Bond restraints: 11778 Sorted by residual: bond pdb=" N VAL C 118 " pdb=" CA VAL C 118 " ideal model delta sigma weight residual 1.458 1.492 -0.034 7.70e-03 1.69e+04 1.98e+01 bond pdb=" N GLY C 291 " pdb=" CA GLY C 291 " ideal model delta sigma weight residual 1.444 1.480 -0.036 1.02e-02 9.61e+03 1.21e+01 bond pdb=" N VAL B 118 " pdb=" CA VAL B 118 " ideal model delta sigma weight residual 1.460 1.491 -0.032 9.30e-03 1.16e+04 1.15e+01 bond pdb=" C ASP C 117 " pdb=" O ASP C 117 " ideal model delta sigma weight residual 1.235 1.194 0.041 1.22e-02 6.72e+03 1.13e+01 bond pdb=" N ILE C 290 " pdb=" CA ILE C 290 " ideal model delta sigma weight residual 1.458 1.497 -0.038 1.21e-02 6.83e+03 1.01e+01 ... (remaining 11773 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 15545 1.64 - 3.28: 308 3.28 - 4.92: 64 4.92 - 6.56: 8 6.56 - 8.20: 5 Bond angle restraints: 15930 Sorted by residual: angle pdb=" CA ASP C 117 " pdb=" CB ASP C 117 " pdb=" CG ASP C 117 " ideal model delta sigma weight residual 112.60 117.23 -4.63 1.00e+00 1.00e+00 2.15e+01 angle pdb=" CA ASP B 120 " pdb=" C ASP B 120 " pdb=" O ASP B 120 " ideal model delta sigma weight residual 122.63 117.30 5.33 1.29e+00 6.01e-01 1.70e+01 angle pdb=" N PRO A 119 " pdb=" CA PRO A 119 " pdb=" C PRO A 119 " ideal model delta sigma weight residual 113.81 119.16 -5.35 1.45e+00 4.76e-01 1.36e+01 angle pdb=" CA GLY B 291 " pdb=" C GLY B 291 " pdb=" O GLY B 291 " ideal model delta sigma weight residual 121.47 118.17 3.30 9.00e-01 1.23e+00 1.34e+01 angle pdb=" N GLY B 291 " pdb=" CA GLY B 291 " pdb=" C GLY B 291 " ideal model delta sigma weight residual 110.90 116.16 -5.26 1.53e+00 4.27e-01 1.18e+01 ... (remaining 15925 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 6510 17.83 - 35.66: 521 35.66 - 53.49: 86 53.49 - 71.32: 27 71.32 - 89.15: 14 Dihedral angle restraints: 7158 sinusoidal: 2934 harmonic: 4224 Sorted by residual: 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 180.00 161.75 18.25 0 5.00e+00 4.00e-02 1.33e+01 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 180.00 162.16 17.84 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA TRP A 100 " pdb=" C TRP A 100 " pdb=" N ASP A 101 " pdb=" CA ASP A 101 " ideal model delta harmonic sigma weight residual 180.00 162.18 17.82 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 7155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1486 0.061 - 0.123: 221 0.123 - 0.184: 16 0.184 - 0.246: 3 0.246 - 0.307: 2 Chirality restraints: 1728 Sorted by residual: chirality pdb=" CA PRO A 119 " pdb=" N PRO A 119 " pdb=" C PRO A 119 " pdb=" CB PRO A 119 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CA VAL B 118 " pdb=" N VAL B 118 " pdb=" C VAL B 118 " pdb=" CB VAL B 118 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA CYS B 293 " pdb=" N CYS B 293 " pdb=" C CYS B 293 " pdb=" CB CYS B 293 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 1725 not shown) Planarity restraints: 2106 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS B 293 " -0.020 2.00e-02 2.50e+03 4.14e-02 1.71e+01 pdb=" C CYS B 293 " 0.072 2.00e-02 2.50e+03 pdb=" O CYS B 293 " -0.027 2.00e-02 2.50e+03 pdb=" N LYS B 294 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS C 293 " 0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C CYS C 293 " -0.060 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 SER B 295 " 0.009 2.00e-02 2.50e+03 1.92e-02 3.68e+00 pdb=" C SER B 295 " -0.033 2.00e-02 2.50e+03 pdb=" O SER B 295 " 0.012 2.00e-02 2.50e+03 pdb=" N GLU B 296 " 0.011 2.00e-02 2.50e+03 ... (remaining 2103 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 813 2.73 - 3.27: 11613 3.27 - 3.81: 21386 3.81 - 4.36: 27715 4.36 - 4.90: 45450 Nonbonded interactions: 106977 Sorted by model distance: nonbonded pdb=" OE1 GLU C 57 " pdb=" OG1 THR C 329 " model vdw 2.185 3.040 nonbonded pdb=" O LYS C 280 " pdb=" OH TYR C 318 " model vdw 2.263 3.040 nonbonded pdb=" O CYS B 68 " pdb=" O HOH B 601 " model vdw 2.274 3.040 nonbonded pdb=" OD1 ASP B 424 " pdb=" O HOH B 602 " model vdw 2.303 3.040 nonbonded pdb=" O THR C 46 " pdb=" O HOH C 601 " model vdw 2.308 3.040 ... (remaining 106972 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: 6.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.140 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 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 : 0.003 0.043 11793 Z= 0.209 Angle : 0.602 8.197 15960 Z= 0.353 Chirality : 0.046 0.307 1728 Planarity : 0.003 0.041 2106 Dihedral : 13.831 89.150 4395 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.16 % Allowed : 0.47 % Favored : 99.38 % 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 (0.21), residues: 1455 helix: 2.79 (0.27), residues: 351 sheet: 0.10 (0.28), residues: 315 loop : -0.73 (0.20), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 515 TYR 0.018 0.001 TYR C 116 PHE 0.010 0.001 PHE C 369 TRP 0.012 0.001 TRP C 250 HIS 0.004 0.001 HIS A 371 Details of bonding type rmsd covalent geometry : bond 0.00340 (11778) covalent geometry : angle 0.59927 (15930) SS BOND : bond 0.00807 ( 15) SS BOND : angle 1.45779 ( 30) hydrogen bonds : bond 0.14776 ( 498) hydrogen bonds : angle 6.97637 ( 1452) *********************** 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 213 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 211 time to evaluate : 0.469 Fit side-chains REVERT: A 91 GLN cc_start: 0.7546 (mm110) cc_final: 0.6980 (pt0) REVERT: A 187 LYS cc_start: 0.8436 (mmpt) cc_final: 0.8160 (mttt) REVERT: A 224 ARG cc_start: 0.7765 (ttm-80) cc_final: 0.7518 (mtm180) REVERT: A 280 LYS cc_start: 0.7566 (ptpt) cc_final: 0.7207 (pptt) REVERT: A 294 LYS cc_start: 0.7498 (tmtt) cc_final: 0.7231 (tttm) REVERT: A 364 ASP cc_start: 0.7789 (m-30) cc_final: 0.7518 (t70) REVERT: A 370 ARG cc_start: 0.7873 (ttm170) cc_final: 0.7557 (ttm170) REVERT: A 414 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7762 (mm-30) REVERT: A 465 GLU cc_start: 0.8141 (tp30) cc_final: 0.7713 (tt0) REVERT: B 91 GLN cc_start: 0.7476 (mm110) cc_final: 0.7073 (pt0) REVERT: B 205 LYS cc_start: 0.8070 (ttmm) cc_final: 0.7634 (mptt) REVERT: B 224 ARG cc_start: 0.7942 (ttp80) cc_final: 0.7422 (ttp80) REVERT: B 277 ARG cc_start: 0.7378 (mtt-85) cc_final: 0.6742 (mtm180) REVERT: B 280 LYS cc_start: 0.7808 (mtmm) cc_final: 0.7238 (pttt) REVERT: B 312 ASN cc_start: 0.8397 (t0) cc_final: 0.8122 (t0) REVERT: C 147 LYS cc_start: 0.8382 (ttmt) cc_final: 0.8035 (ttpp) REVERT: C 254 LYS cc_start: 0.8385 (mmtt) cc_final: 0.7166 (mppt) REVERT: C 277 ARG cc_start: 0.7790 (ptp-110) cc_final: 0.7448 (ptp90) outliers start: 2 outliers final: 0 residues processed: 212 average time/residue: 0.7284 time to fit residues: 164.8050 Evaluate side-chains 121 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.0770 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.0770 overall best weight: 1.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 47 ASN A 410 GLN A 451 HIS B 262 ASN C 410 GLN C 491 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.122139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.097804 restraints weight = 13635.772| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.78 r_work: 0.2996 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 11793 Z= 0.188 Angle : 0.579 8.708 15960 Z= 0.300 Chirality : 0.047 0.144 1728 Planarity : 0.004 0.036 2106 Dihedral : 4.391 20.781 1584 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.95 % Allowed : 7.34 % Favored : 90.71 % 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: 0.46 (0.21), residues: 1455 helix: 2.70 (0.26), residues: 354 sheet: 0.16 (0.29), residues: 294 loop : -0.76 (0.19), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 224 TYR 0.013 0.002 TYR B 502 PHE 0.016 0.001 PHE C 369 TRP 0.011 0.001 TRP A 437 HIS 0.005 0.001 HIS B 409 Details of bonding type rmsd covalent geometry : bond 0.00463 (11778) covalent geometry : angle 0.57860 (15930) SS BOND : bond 0.00337 ( 15) SS BOND : angle 0.81165 ( 30) hydrogen bonds : bond 0.05078 ( 498) hydrogen bonds : angle 5.18540 ( 1452) *********************** 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 151 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.463 Fit side-chains REVERT: A 91 GLN cc_start: 0.7648 (mm110) cc_final: 0.6799 (pt0) REVERT: A 187 LYS cc_start: 0.8386 (mmpt) cc_final: 0.8181 (mmmt) REVERT: A 224 ARG cc_start: 0.7686 (ttm-80) cc_final: 0.7342 (mtm180) REVERT: A 280 LYS cc_start: 0.7543 (ptpt) cc_final: 0.7087 (pptt) REVERT: A 294 LYS cc_start: 0.7695 (tmtt) cc_final: 0.7466 (tttm) REVERT: A 364 ASP cc_start: 0.7871 (m-30) cc_final: 0.7408 (t70) REVERT: A 414 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7519 (mm-30) REVERT: A 465 GLU cc_start: 0.8090 (tp30) cc_final: 0.7546 (tt0) REVERT: A 514 ASN cc_start: 0.8202 (m-40) cc_final: 0.7646 (m-40) REVERT: B 91 GLN cc_start: 0.7395 (mm110) cc_final: 0.6933 (pt0) REVERT: B 205 LYS cc_start: 0.8053 (ttmm) cc_final: 0.7550 (mptt) REVERT: B 277 ARG cc_start: 0.7646 (mtt-85) cc_final: 0.6883 (mtm180) REVERT: B 280 LYS cc_start: 0.7827 (mtmm) cc_final: 0.7188 (pttt) REVERT: B 360 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6839 (mm-30) REVERT: B 377 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7577 (mtt90) REVERT: B 450 GLN cc_start: 0.8696 (tp40) cc_final: 0.8386 (tp40) REVERT: C 147 LYS cc_start: 0.8285 (ttmt) cc_final: 0.7635 (ttpp) REVERT: C 226 GLN cc_start: 0.9050 (OUTLIER) cc_final: 0.8486 (pt0) REVERT: C 254 LYS cc_start: 0.8333 (mmtt) cc_final: 0.6898 (mppt) REVERT: C 277 ARG cc_start: 0.8072 (ptp-110) cc_final: 0.7565 (ptp90) REVERT: C 442 GLU cc_start: 0.8079 (tp30) cc_final: 0.7853 (mm-30) REVERT: C 448 GLU cc_start: 0.8522 (tp30) cc_final: 0.8315 (mm-30) outliers start: 25 outliers final: 5 residues processed: 139 average time/residue: 0.7090 time to fit residues: 105.8038 Evaluate side-chains 118 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 377 ARG Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 226 GLN Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 392 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 49 optimal weight: 8.9990 chunk 4 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 121 optimal weight: 0.9990 chunk 2 optimal weight: 0.0980 chunk 25 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 47 ASN A 451 HIS C 91 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.123159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.098816 restraints weight = 13742.828| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.80 r_work: 0.3010 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1544 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= 0.129 Angle : 0.502 7.106 15960 Z= 0.262 Chirality : 0.044 0.142 1728 Planarity : 0.004 0.038 2106 Dihedral : 4.138 19.147 1584 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.72 % Allowed : 8.82 % Favored : 89.46 % 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: 0.60 (0.21), residues: 1455 helix: 2.97 (0.26), residues: 354 sheet: 0.18 (0.29), residues: 294 loop : -0.72 (0.19), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 224 TYR 0.011 0.001 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 A 34 Details of bonding type rmsd covalent geometry : bond 0.00310 (11778) covalent geometry : angle 0.50125 (15930) SS BOND : bond 0.00247 ( 15) SS BOND : angle 0.66463 ( 30) hydrogen bonds : bond 0.04513 ( 498) hydrogen bonds : angle 4.89175 ( 1452) *********************** 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 132 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.426 Fit side-chains REVERT: A 91 GLN cc_start: 0.7626 (mm110) cc_final: 0.6784 (pt0) REVERT: A 187 LYS cc_start: 0.8341 (mmpt) cc_final: 0.8095 (mmmt) REVERT: A 224 ARG cc_start: 0.7662 (ttm-80) cc_final: 0.7331 (mtm180) REVERT: A 280 LYS cc_start: 0.7531 (ptpt) cc_final: 0.7074 (pptt) REVERT: A 294 LYS cc_start: 0.7748 (tmtt) cc_final: 0.7112 (tttp) REVERT: A 364 ASP cc_start: 0.7904 (m-30) cc_final: 0.7411 (t70) REVERT: A 414 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7532 (mm-30) REVERT: A 465 GLU cc_start: 0.8094 (tp30) cc_final: 0.7540 (tt0) REVERT: A 478 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.7709 (mtp) REVERT: A 514 ASN cc_start: 0.8160 (m-40) cc_final: 0.7585 (m-40) REVERT: B 91 GLN cc_start: 0.7395 (mm110) cc_final: 0.6928 (pt0) REVERT: B 205 LYS cc_start: 0.8031 (ttmm) cc_final: 0.7536 (mptt) REVERT: B 277 ARG cc_start: 0.7622 (mtt-85) cc_final: 0.6897 (mtm180) REVERT: B 280 LYS cc_start: 0.7829 (mtmm) cc_final: 0.7170 (pttt) REVERT: B 360 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6658 (mm-30) REVERT: B 377 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7838 (mtt90) REVERT: B 450 GLN cc_start: 0.8674 (tp40) cc_final: 0.8367 (tp40) REVERT: C 126 SER cc_start: 0.8803 (OUTLIER) cc_final: 0.8557 (p) REVERT: C 147 LYS cc_start: 0.8261 (ttmt) cc_final: 0.7608 (ttpp) REVERT: C 226 GLN cc_start: 0.9045 (OUTLIER) cc_final: 0.8492 (pt0) REVERT: C 254 LYS cc_start: 0.8317 (mmtt) cc_final: 0.6877 (mppt) REVERT: C 277 ARG cc_start: 0.8151 (ptp-110) cc_final: 0.7609 (ptp90) REVERT: C 417 GLU cc_start: 0.7854 (pt0) cc_final: 0.7610 (pt0) REVERT: C 448 GLU cc_start: 0.8672 (tp30) cc_final: 0.8461 (mm-30) REVERT: C 493 CYS cc_start: 0.8095 (t) cc_final: 0.7570 (t) outliers start: 22 outliers final: 6 residues processed: 125 average time/residue: 0.6502 time to fit residues: 87.6947 Evaluate side-chains 119 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 377 ARG Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 226 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 1 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS B 213 GLN ** B 423 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 = 0.3376 r_free = 0.3376 target = 0.119292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.094962 restraints weight = 13766.396| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 1.79 r_work: 0.2954 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 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 : 0.007 0.044 11793 Z= 0.263 Angle : 0.619 9.406 15960 Z= 0.319 Chirality : 0.049 0.151 1728 Planarity : 0.005 0.046 2106 Dihedral : 4.561 21.711 1584 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.11 % Allowed : 9.76 % Favored : 88.13 % 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: 0.30 (0.20), residues: 1455 helix: 2.53 (0.26), residues: 357 sheet: -0.01 (0.29), residues: 294 loop : -0.83 (0.19), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 277 TYR 0.014 0.002 TYR B 502 PHE 0.015 0.002 PHE B 369 TRP 0.010 0.002 TRP A 437 HIS 0.007 0.002 HIS B 34 Details of bonding type rmsd covalent geometry : bond 0.00655 (11778) covalent geometry : angle 0.61897 (15930) SS BOND : bond 0.00372 ( 15) SS BOND : angle 0.65049 ( 30) hydrogen bonds : bond 0.05589 ( 498) hydrogen bonds : angle 5.15539 ( 1452) *********************** 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 132 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.410 Fit side-chains REVERT: A 91 GLN cc_start: 0.7611 (mm110) cc_final: 0.6729 (pt0) REVERT: A 187 LYS cc_start: 0.8405 (mmpt) cc_final: 0.8160 (mmmt) REVERT: A 224 ARG cc_start: 0.7735 (ttm-80) cc_final: 0.7302 (mtm180) REVERT: A 280 LYS cc_start: 0.7609 (ptpt) cc_final: 0.7144 (ptmt) REVERT: A 294 LYS cc_start: 0.7907 (tmtt) cc_final: 0.7245 (tttp) REVERT: A 364 ASP cc_start: 0.7992 (m-30) cc_final: 0.7411 (t70) REVERT: A 414 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7503 (mm-30) REVERT: A 451 HIS cc_start: 0.7264 (m90) cc_final: 0.6958 (m90) REVERT: A 465 GLU cc_start: 0.8180 (tp30) cc_final: 0.7647 (tt0) REVERT: A 478 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7994 (mtp) REVERT: A 514 ASN cc_start: 0.8218 (m-40) cc_final: 0.7611 (m-40) REVERT: B 91 GLN cc_start: 0.7535 (mm110) cc_final: 0.6970 (pt0) REVERT: B 135 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8445 (tt0) REVERT: B 205 LYS cc_start: 0.8161 (ttmm) cc_final: 0.7594 (mptt) REVERT: B 277 ARG cc_start: 0.7752 (mtt-85) cc_final: 0.7026 (mtp180) REVERT: B 280 LYS cc_start: 0.7912 (mtmm) cc_final: 0.7255 (pttp) REVERT: B 360 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6980 (mt-10) REVERT: B 377 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7883 (mtt90) REVERT: B 417 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7454 (mt-10) REVERT: B 450 GLN cc_start: 0.8689 (tp40) cc_final: 0.8397 (tp40) REVERT: C 126 SER cc_start: 0.8846 (OUTLIER) cc_final: 0.8585 (p) REVERT: C 127 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8012 (tt) REVERT: C 226 GLN cc_start: 0.9015 (OUTLIER) cc_final: 0.8447 (pt0) REVERT: C 254 LYS cc_start: 0.8303 (mmtt) cc_final: 0.7481 (mmtm) REVERT: C 417 GLU cc_start: 0.7917 (pt0) cc_final: 0.7667 (pt0) REVERT: C 493 CYS cc_start: 0.8239 (t) cc_final: 0.7735 (t) outliers start: 27 outliers final: 8 residues processed: 123 average time/residue: 0.6894 time to fit residues: 90.9207 Evaluate side-chains 116 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain B residue 48 ASP Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 377 ARG Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 226 GLN Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 392 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 87 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 48 optimal weight: 10.0000 chunk 60 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 137 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 47 ASN B 213 GLN B 312 ASN B 423 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.122344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.098085 restraints weight = 13745.634| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.80 r_work: 0.2998 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1823 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= 0.118 Angle : 0.483 6.714 15960 Z= 0.253 Chirality : 0.043 0.142 1728 Planarity : 0.004 0.040 2106 Dihedral : 4.121 18.806 1584 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.03 % Allowed : 10.15 % Favored : 87.82 % 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: 0.60 (0.21), residues: 1455 helix: 3.02 (0.25), residues: 354 sheet: 0.07 (0.29), residues: 294 loop : -0.70 (0.19), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 224 TYR 0.011 0.001 TYR B 502 PHE 0.013 0.001 PHE C 369 TRP 0.010 0.001 TRP A 437 HIS 0.004 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00279 (11778) covalent geometry : angle 0.48288 (15930) SS BOND : bond 0.00236 ( 15) SS BOND : angle 0.59565 ( 30) hydrogen bonds : bond 0.04394 ( 498) hydrogen bonds : angle 4.77637 ( 1452) *********************** 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 134 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 0.359 Fit side-chains REVERT: A 91 GLN cc_start: 0.7582 (mm110) cc_final: 0.6732 (pt0) REVERT: A 144 THR cc_start: 0.8677 (t) cc_final: 0.8405 (p) REVERT: A 187 LYS cc_start: 0.8352 (mmpt) cc_final: 0.8085 (mmmt) REVERT: A 224 ARG cc_start: 0.7685 (ttm-80) cc_final: 0.7348 (mtm180) REVERT: A 280 LYS cc_start: 0.7544 (ptpt) cc_final: 0.7117 (pptt) REVERT: A 294 LYS cc_start: 0.7873 (tmtt) cc_final: 0.7226 (tttp) REVERT: A 364 ASP cc_start: 0.7978 (m-30) cc_final: 0.7389 (t70) REVERT: A 414 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7553 (mm-30) REVERT: A 451 HIS cc_start: 0.7275 (m90) cc_final: 0.6587 (t70) REVERT: A 465 GLU cc_start: 0.8152 (tp30) cc_final: 0.7702 (tt0) REVERT: A 514 ASN cc_start: 0.8223 (m-40) cc_final: 0.7655 (m-40) REVERT: B 91 GLN cc_start: 0.7486 (mm110) cc_final: 0.6997 (pt0) REVERT: B 205 LYS cc_start: 0.8080 (ttmm) cc_final: 0.7559 (mptt) REVERT: B 214 SER cc_start: 0.8636 (OUTLIER) cc_final: 0.8415 (m) REVERT: B 277 ARG cc_start: 0.7747 (mtt-85) cc_final: 0.7012 (mtp180) REVERT: B 280 LYS cc_start: 0.7940 (mtmm) cc_final: 0.7237 (pttp) REVERT: B 377 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7804 (mtt90) REVERT: B 393 ILE cc_start: 0.7656 (OUTLIER) cc_final: 0.7371 (mt) REVERT: B 450 GLN cc_start: 0.8673 (tp40) cc_final: 0.8402 (tp40) REVERT: B 478 MET cc_start: 0.8631 (mtp) cc_final: 0.8408 (mtm) REVERT: C 127 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8003 (tt) REVERT: C 254 LYS cc_start: 0.8267 (mmtt) cc_final: 0.6868 (mppt) REVERT: C 258 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8412 (tt) REVERT: C 417 GLU cc_start: 0.7884 (pt0) cc_final: 0.7638 (pt0) REVERT: C 493 CYS cc_start: 0.8214 (t) cc_final: 0.7702 (t) REVERT: C 499 ASN cc_start: 0.7538 (m-40) cc_final: 0.6154 (t0) outliers start: 26 outliers final: 7 residues processed: 124 average time/residue: 0.5960 time to fit residues: 79.9381 Evaluate side-chains 114 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 377 ARG Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain B residue 507 TYR Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 392 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 18 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 95 optimal weight: 0.0050 chunk 86 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS C 491 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.119888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.095483 restraints weight = 13664.230| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.80 r_work: 0.2959 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 11793 Z= 0.217 Angle : 0.565 8.717 15960 Z= 0.292 Chirality : 0.047 0.145 1728 Planarity : 0.004 0.044 2106 Dihedral : 4.391 21.012 1584 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.26 % Allowed : 10.62 % Favored : 87.12 % 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: 2.78 (0.25), residues: 354 sheet: 0.01 (0.29), residues: 294 loop : -0.79 (0.19), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 224 TYR 0.013 0.002 TYR B 502 PHE 0.014 0.002 PHE C 369 TRP 0.010 0.001 TRP A 437 HIS 0.005 0.001 HIS B 34 Details of bonding type rmsd covalent geometry : bond 0.00537 (11778) covalent geometry : angle 0.56519 (15930) SS BOND : bond 0.00326 ( 15) SS BOND : angle 0.58888 ( 30) hydrogen bonds : bond 0.05168 ( 498) hydrogen bonds : angle 4.99145 ( 1452) *********************** 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 128 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 99 time to evaluate : 0.506 Fit side-chains REVERT: A 91 GLN cc_start: 0.7710 (mm110) cc_final: 0.6791 (pt0) REVERT: A 144 THR cc_start: 0.8780 (t) cc_final: 0.8452 (p) REVERT: A 187 LYS cc_start: 0.8401 (mmpt) cc_final: 0.8161 (mmmt) REVERT: A 224 ARG cc_start: 0.7778 (ttm-80) cc_final: 0.7380 (mtm180) REVERT: A 280 LYS cc_start: 0.7573 (ptpt) cc_final: 0.7152 (pptt) REVERT: A 294 LYS cc_start: 0.7939 (tmtt) cc_final: 0.7262 (tttp) REVERT: A 364 ASP cc_start: 0.8015 (m-30) cc_final: 0.7393 (t70) REVERT: A 414 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7574 (mm-30) REVERT: A 451 HIS cc_start: 0.7298 (m90) cc_final: 0.6594 (t70) REVERT: A 465 GLU cc_start: 0.8214 (tp30) cc_final: 0.7684 (tt0) REVERT: A 478 MET cc_start: 0.8321 (OUTLIER) cc_final: 0.7681 (mtp) REVERT: A 514 ASN cc_start: 0.8265 (m-40) cc_final: 0.7660 (m-40) REVERT: B 51 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8381 (tt0) REVERT: B 91 GLN cc_start: 0.7560 (mm110) cc_final: 0.7043 (pt0) REVERT: B 205 LYS cc_start: 0.8183 (ttmm) cc_final: 0.7639 (mptt) REVERT: B 277 ARG cc_start: 0.7771 (mtt-85) cc_final: 0.7023 (mtp180) REVERT: B 280 LYS cc_start: 0.7951 (mtmm) cc_final: 0.7308 (pttp) REVERT: B 377 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7863 (mtt90) REVERT: B 450 GLN cc_start: 0.8705 (tp40) cc_final: 0.8418 (tp40) REVERT: C 127 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8027 (tt) REVERT: C 226 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8462 (pt0) REVERT: C 254 LYS cc_start: 0.8272 (mmtt) cc_final: 0.6968 (mppt) REVERT: C 417 GLU cc_start: 0.8000 (pt0) cc_final: 0.7759 (pt0) REVERT: C 493 CYS cc_start: 0.8231 (t) cc_final: 0.7731 (t) outliers start: 29 outliers final: 10 residues processed: 119 average time/residue: 0.6586 time to fit residues: 84.6839 Evaluate side-chains 110 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 377 ARG Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 507 TYR Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 226 GLN Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 392 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 74 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 chunk 38 optimal weight: 0.9990 chunk 96 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 47 ASN A 372 GLN C 491 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.119271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.095189 restraints weight = 13731.474| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.78 r_work: 0.2958 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 11793 Z= 0.217 Angle : 0.567 8.626 15960 Z= 0.294 Chirality : 0.047 0.145 1728 Planarity : 0.004 0.046 2106 Dihedral : 4.449 21.101 1584 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.19 % Allowed : 11.09 % Favored : 86.73 % 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: 0.37 (0.20), residues: 1455 helix: 2.72 (0.25), residues: 354 sheet: -0.01 (0.29), residues: 294 loop : -0.81 (0.19), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 224 TYR 0.013 0.002 TYR B 502 PHE 0.013 0.002 PHE B 369 TRP 0.010 0.001 TRP A 437 HIS 0.005 0.001 HIS B 34 Details of bonding type rmsd covalent geometry : bond 0.00538 (11778) covalent geometry : angle 0.56669 (15930) SS BOND : bond 0.00334 ( 15) SS BOND : angle 0.55173 ( 30) hydrogen bonds : bond 0.05183 ( 498) hydrogen bonds : angle 5.01788 ( 1452) *********************** 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 124 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 0.496 Fit side-chains REVERT: A 91 GLN cc_start: 0.7717 (mm110) cc_final: 0.6791 (pt0) REVERT: A 187 LYS cc_start: 0.8383 (mmpt) cc_final: 0.8143 (mmmt) REVERT: A 224 ARG cc_start: 0.7742 (ttm-80) cc_final: 0.7351 (mtm180) REVERT: A 280 LYS cc_start: 0.7552 (ptpt) cc_final: 0.7122 (pptt) REVERT: A 294 LYS cc_start: 0.7956 (tmtt) cc_final: 0.7319 (tttp) REVERT: A 364 ASP cc_start: 0.8000 (m-30) cc_final: 0.7347 (t70) REVERT: A 414 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7503 (mm-30) REVERT: A 451 HIS cc_start: 0.7249 (m90) cc_final: 0.6528 (t70) REVERT: A 465 GLU cc_start: 0.8200 (tp30) cc_final: 0.7707 (tt0) REVERT: A 478 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.7672 (mtp) REVERT: A 514 ASN cc_start: 0.8243 (m-40) cc_final: 0.7629 (m-40) REVERT: B 91 GLN cc_start: 0.7571 (mm110) cc_final: 0.7018 (pt0) REVERT: B 135 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8425 (tt0) REVERT: B 205 LYS cc_start: 0.8166 (ttmm) cc_final: 0.7588 (mptt) REVERT: B 277 ARG cc_start: 0.7790 (mtt-85) cc_final: 0.7044 (mtp180) REVERT: B 280 LYS cc_start: 0.7930 (mtmm) cc_final: 0.7268 (pttp) REVERT: B 377 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7529 (mtt-85) REVERT: B 450 GLN cc_start: 0.8690 (tp40) cc_final: 0.8398 (tp40) REVERT: C 127 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.7997 (tt) REVERT: C 226 GLN cc_start: 0.8988 (OUTLIER) cc_final: 0.8437 (pt0) REVERT: C 254 LYS cc_start: 0.8253 (mmtt) cc_final: 0.6939 (mppt) REVERT: C 417 GLU cc_start: 0.7936 (pt0) cc_final: 0.7695 (pt0) REVERT: C 493 CYS cc_start: 0.8266 (t) cc_final: 0.7768 (t) REVERT: C 499 ASN cc_start: 0.7540 (m110) cc_final: 0.6162 (t0) outliers start: 28 outliers final: 12 residues processed: 116 average time/residue: 0.6665 time to fit residues: 83.3063 Evaluate side-chains 111 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 377 ARG Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 507 TYR Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 226 GLN Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 392 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 23 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 109 optimal weight: 0.0670 chunk 133 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 121 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 47 ASN B 34 HIS C 491 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.120917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.096778 restraints weight = 13646.934| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.78 r_work: 0.2980 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11793 Z= 0.144 Angle : 0.504 7.729 15960 Z= 0.263 Chirality : 0.044 0.142 1728 Planarity : 0.004 0.048 2106 Dihedral : 4.214 19.714 1584 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.87 % Allowed : 11.40 % Favored : 86.73 % 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: 0.54 (0.21), residues: 1455 helix: 2.99 (0.25), residues: 354 sheet: 0.04 (0.29), residues: 294 loop : -0.74 (0.19), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 224 TYR 0.011 0.001 TYR B 502 PHE 0.013 0.001 PHE C 369 TRP 0.010 0.001 TRP A 437 HIS 0.007 0.001 HIS B 34 Details of bonding type rmsd covalent geometry : bond 0.00349 (11778) covalent geometry : angle 0.50361 (15930) SS BOND : bond 0.00268 ( 15) SS BOND : angle 0.55068 ( 30) hydrogen bonds : bond 0.04615 ( 498) hydrogen bonds : angle 4.81436 ( 1452) *********************** 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 124 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.542 Fit side-chains REVERT: A 91 GLN cc_start: 0.7688 (mm110) cc_final: 0.6785 (pt0) REVERT: A 144 THR cc_start: 0.8745 (t) cc_final: 0.8441 (p) REVERT: A 187 LYS cc_start: 0.8388 (mmpt) cc_final: 0.8137 (mmmt) REVERT: A 224 ARG cc_start: 0.7735 (ttm-80) cc_final: 0.7470 (mtm180) REVERT: A 280 LYS cc_start: 0.7536 (ptpt) cc_final: 0.7121 (pptt) REVERT: A 294 LYS cc_start: 0.7942 (tmtt) cc_final: 0.7326 (tttp) REVERT: A 364 ASP cc_start: 0.8012 (m-30) cc_final: 0.7362 (t70) REVERT: A 414 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7563 (mm-30) REVERT: A 451 HIS cc_start: 0.7270 (m90) cc_final: 0.6566 (t70) REVERT: A 465 GLU cc_start: 0.8189 (tp30) cc_final: 0.7689 (tt0) REVERT: A 478 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.7584 (mtp) REVERT: A 514 ASN cc_start: 0.8255 (m-40) cc_final: 0.7659 (m-40) REVERT: B 91 GLN cc_start: 0.7564 (mm110) cc_final: 0.7045 (pt0) REVERT: B 205 LYS cc_start: 0.8187 (ttmm) cc_final: 0.7649 (mptt) REVERT: B 277 ARG cc_start: 0.7817 (mtt-85) cc_final: 0.7009 (mtp180) REVERT: B 280 LYS cc_start: 0.7961 (mtmm) cc_final: 0.7275 (pttp) REVERT: B 377 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7780 (mtt90) REVERT: B 393 ILE cc_start: 0.7713 (OUTLIER) cc_final: 0.7474 (mt) REVERT: B 450 GLN cc_start: 0.8687 (tp40) cc_final: 0.8406 (tp40) REVERT: C 127 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8013 (tt) REVERT: C 226 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8423 (pt0) REVERT: C 254 LYS cc_start: 0.8239 (mmtt) cc_final: 0.6856 (mppt) REVERT: C 258 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8371 (tt) REVERT: C 417 GLU cc_start: 0.7967 (pt0) cc_final: 0.7303 (mm-30) REVERT: C 493 CYS cc_start: 0.8211 (t) cc_final: 0.7702 (t) REVERT: C 499 ASN cc_start: 0.7524 (m110) cc_final: 0.6178 (t0) outliers start: 24 outliers final: 10 residues processed: 118 average time/residue: 0.6601 time to fit residues: 83.9614 Evaluate side-chains 113 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 377 ARG Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 507 TYR Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 226 GLN Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 392 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 71 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 chunk 123 optimal weight: 0.8980 chunk 75 optimal weight: 0.5980 chunk 143 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS B 34 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.119035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.095015 restraints weight = 13647.868| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.77 r_work: 0.2956 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 11793 Z= 0.227 Angle : 0.573 8.787 15960 Z= 0.297 Chirality : 0.047 0.145 1728 Planarity : 0.005 0.052 2106 Dihedral : 4.457 21.138 1584 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.95 % Allowed : 11.87 % Favored : 86.18 % 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: 0.35 (0.20), residues: 1455 helix: 2.71 (0.25), residues: 354 sheet: -0.04 (0.29), residues: 294 loop : -0.82 (0.19), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 224 TYR 0.013 0.002 TYR B 502 PHE 0.014 0.002 PHE C 369 TRP 0.010 0.001 TRP A 437 HIS 0.008 0.002 HIS B 34 Details of bonding type rmsd covalent geometry : bond 0.00564 (11778) covalent geometry : angle 0.57262 (15930) SS BOND : bond 0.00341 ( 15) SS BOND : angle 0.54989 ( 30) hydrogen bonds : bond 0.05232 ( 498) hydrogen bonds : angle 5.02126 ( 1452) *********************** 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 123 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 0.341 Fit side-chains REVERT: A 91 GLN cc_start: 0.7707 (mm110) cc_final: 0.6781 (pt0) REVERT: A 144 THR cc_start: 0.8775 (t) cc_final: 0.8435 (p) REVERT: A 187 LYS cc_start: 0.8396 (mmpt) cc_final: 0.8157 (mmmt) REVERT: A 224 ARG cc_start: 0.7707 (ttm-80) cc_final: 0.7383 (mtm180) REVERT: A 280 LYS cc_start: 0.7550 (ptpt) cc_final: 0.7110 (pptt) REVERT: A 294 LYS cc_start: 0.7954 (tmtt) cc_final: 0.7322 (tttp) REVERT: A 364 ASP cc_start: 0.8004 (m-30) cc_final: 0.7320 (t70) REVERT: A 451 HIS cc_start: 0.7217 (m90) cc_final: 0.6495 (t70) REVERT: A 465 GLU cc_start: 0.8195 (tp30) cc_final: 0.7699 (tt0) REVERT: A 478 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.7674 (mtp) REVERT: A 514 ASN cc_start: 0.8227 (m-40) cc_final: 0.7639 (m-40) REVERT: B 91 GLN cc_start: 0.7576 (mm110) cc_final: 0.7024 (pt0) REVERT: B 135 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8417 (tt0) REVERT: B 205 LYS cc_start: 0.8171 (ttmm) cc_final: 0.7577 (mptt) REVERT: B 277 ARG cc_start: 0.7850 (mtt-85) cc_final: 0.7087 (mtp180) REVERT: B 280 LYS cc_start: 0.7915 (mtmm) cc_final: 0.7261 (pttp) REVERT: B 377 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7520 (mtt-85) REVERT: B 393 ILE cc_start: 0.7685 (OUTLIER) cc_final: 0.7455 (mt) REVERT: B 450 GLN cc_start: 0.8681 (tp40) cc_final: 0.8379 (tp40) REVERT: C 127 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.7993 (tt) REVERT: C 226 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.8420 (pt0) REVERT: C 254 LYS cc_start: 0.8248 (mmtt) cc_final: 0.6940 (mppt) REVERT: C 336 MET cc_start: 0.8940 (ptm) cc_final: 0.8648 (ptp) REVERT: C 417 GLU cc_start: 0.7908 (pt0) cc_final: 0.7260 (mm-30) REVERT: C 493 CYS cc_start: 0.8272 (t) cc_final: 0.7773 (t) REVERT: C 499 ASN cc_start: 0.7559 (m110) cc_final: 0.6231 (t0) outliers start: 25 outliers final: 13 residues processed: 117 average time/residue: 0.6807 time to fit residues: 85.8766 Evaluate side-chains 115 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 377 ARG Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 507 TYR Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 226 GLN Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 392 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 96 optimal weight: 10.0000 chunk 140 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 48 optimal weight: 10.0000 chunk 7 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 133 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 136 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS B 34 HIS C 491 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.122107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.097897 restraints weight = 13719.426| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.79 r_work: 0.2995 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11793 Z= 0.114 Angle : 0.481 7.174 15960 Z= 0.253 Chirality : 0.043 0.140 1728 Planarity : 0.004 0.058 2106 Dihedral : 4.098 18.753 1584 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.48 % Allowed : 12.41 % Favored : 86.10 % 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: 0.59 (0.21), residues: 1455 helix: 3.10 (0.25), residues: 354 sheet: -0.04 (0.28), residues: 330 loop : -0.73 (0.20), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 224 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 0.009 0.001 HIS B 34 Details of bonding type rmsd covalent geometry : bond 0.00269 (11778) covalent geometry : angle 0.48125 (15930) SS BOND : bond 0.00229 ( 15) SS BOND : angle 0.57125 ( 30) hydrogen bonds : bond 0.04339 ( 498) hydrogen bonds : angle 4.71101 ( 1452) ********************** 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 121 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.456 Fit side-chains REVERT: A 91 GLN cc_start: 0.7636 (mm110) cc_final: 0.6741 (pt0) REVERT: A 144 THR cc_start: 0.8713 (t) cc_final: 0.8435 (p) REVERT: A 187 LYS cc_start: 0.8376 (mmpt) cc_final: 0.8117 (mmmt) REVERT: A 224 ARG cc_start: 0.7725 (ttm-80) cc_final: 0.7469 (mtm180) REVERT: A 280 LYS cc_start: 0.7501 (ptpt) cc_final: 0.7085 (pptt) REVERT: A 294 LYS cc_start: 0.7938 (tmtt) cc_final: 0.7295 (tttp) REVERT: A 364 ASP cc_start: 0.7997 (m-30) cc_final: 0.7338 (t70) REVERT: A 414 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7559 (mm-30) REVERT: A 451 HIS cc_start: 0.7261 (m90) cc_final: 0.6552 (t70) REVERT: A 465 GLU cc_start: 0.8167 (tp30) cc_final: 0.7670 (tt0) REVERT: A 478 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.7525 (mtp) REVERT: A 514 ASN cc_start: 0.8227 (m-40) cc_final: 0.7658 (m-40) REVERT: B 91 GLN cc_start: 0.7508 (mm110) cc_final: 0.7002 (pt0) REVERT: B 205 LYS cc_start: 0.8168 (ttmm) cc_final: 0.7626 (mptt) REVERT: B 277 ARG cc_start: 0.7807 (mtt-85) cc_final: 0.7018 (mtp180) REVERT: B 280 LYS cc_start: 0.7954 (mtmm) cc_final: 0.7262 (pttp) REVERT: B 360 GLU cc_start: 0.7004 (mp0) cc_final: 0.6567 (mp0) REVERT: B 377 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7758 (mtt90) REVERT: B 393 ILE cc_start: 0.7707 (OUTLIER) cc_final: 0.7469 (mt) REVERT: B 450 GLN cc_start: 0.8671 (tp40) cc_final: 0.8393 (tp40) REVERT: C 127 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.7986 (tt) REVERT: C 254 LYS cc_start: 0.8207 (mmtt) cc_final: 0.6823 (mppt) REVERT: C 417 GLU cc_start: 0.7910 (pt0) cc_final: 0.7268 (mm-30) REVERT: C 493 CYS cc_start: 0.8167 (t) cc_final: 0.7647 (t) REVERT: C 499 ASN cc_start: 0.7505 (m110) cc_final: 0.6217 (t0) outliers start: 19 outliers final: 9 residues processed: 117 average time/residue: 0.6618 time to fit residues: 83.8157 Evaluate side-chains 110 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 377 ARG Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 507 TYR Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 392 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 107 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 125 optimal weight: 5.9990 chunk 115 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 109 optimal weight: 0.1980 chunk 102 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS B 34 HIS B 312 ASN C 262 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.122399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.098194 restraints weight = 13613.278| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.78 r_work: 0.2998 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11793 Z= 0.114 Angle : 0.480 7.419 15960 Z= 0.251 Chirality : 0.043 0.139 1728 Planarity : 0.004 0.058 2106 Dihedral : 4.018 18.570 1584 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.41 % Allowed : 12.57 % Favored : 86.03 % 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: 3.20 (0.25), residues: 354 sheet: 0.06 (0.28), residues: 333 loop : -0.63 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 224 TYR 0.010 0.001 TYR B 502 PHE 0.012 0.001 PHE C 369 TRP 0.010 0.001 TRP A 437 HIS 0.009 0.001 HIS B 34 Details of bonding type rmsd covalent geometry : bond 0.00267 (11778) covalent geometry : angle 0.47971 (15930) SS BOND : bond 0.00228 ( 15) SS BOND : angle 0.56337 ( 30) hydrogen bonds : bond 0.04261 ( 498) hydrogen bonds : angle 4.63793 ( 1452) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3966.51 seconds wall clock time: 68 minutes 31.03 seconds (4111.03 seconds total)