Starting phenix.real_space_refine on Thu Aug 6 20:26:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dow_47094/08_2026/9dow_47094.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dow_47094/08_2026/9dow_47094.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dow_47094/08_2026/9dow_47094.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dow_47094/08_2026/9dow_47094.map" model { file = "/net/cci-nas-00/data/ceres_data/9dow_47094/08_2026/9dow_47094.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dow_47094/08_2026/9dow_47094.cif" } resolution = 3.1 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= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9143 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 75 5.49 5 S 56 5.16 5 Na 1 4.78 5 C 5968 2.51 5 N 1680 2.21 5 O 2036 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9816 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 4100 Classifications: {'peptide': 506} Link IDs: {'PTRANS': 29, 'TRANS': 476} Chain: "B" Number of atoms: 4092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 4092 Classifications: {'peptide': 505} Link IDs: {'PTRANS': 29, 'TRANS': 475} Chain: "C" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1557 Classifications: {'RNA': 73} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 30, 'rna3p_pyr': 30} Link IDs: {'rna2p': 13, 'rna3p': 59} Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.51, per 1000 atoms: 0.26 Number of scatterers: 9816 At special positions: 0 Unit cell: (81.32, 104.86, 136.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 56 16.00 P 75 15.00 Na 1 11.00 O 2036 8.00 N 1680 7.00 C 5968 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 299.8 milliseconds 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1898 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 9 sheets defined 40.0% alpha, 20.4% beta 27 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 74 through 90 Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 165 through 176 removed outlier: 3.702A pdb=" N LYS A 175 " --> pdb=" O HIS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 229 Processing helix chain 'A' and resid 229 through 237 Processing helix chain 'A' and resid 238 through 261 removed outlier: 3.826A pdb=" N GLN A 242 " --> pdb=" O ASP A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 311 Processing helix chain 'A' and resid 346 through 366 removed outlier: 4.219A pdb=" N GLU A 352 " --> pdb=" O HIS A 348 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE A 353 " --> pdb=" O ASP A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 405 Processing helix chain 'A' and resid 410 through 414 Processing helix chain 'A' and resid 416 through 430 Processing helix chain 'A' and resid 439 through 452 Processing helix chain 'A' and resid 453 through 456 Processing helix chain 'A' and resid 504 through 519 removed outlier: 3.630A pdb=" N LYS A 519 " --> pdb=" O GLN A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 539 Processing helix chain 'A' and resid 551 through 559 Processing helix chain 'A' and resid 563 through 567 Processing helix chain 'B' and resid 73 through 90 Processing helix chain 'B' and resid 104 through 113 Processing helix chain 'B' and resid 165 through 176 Processing helix chain 'B' and resid 222 through 229 Processing helix chain 'B' and resid 229 through 237 Processing helix chain 'B' and resid 238 through 261 removed outlier: 3.905A pdb=" N GLN B 242 " --> pdb=" O ASP B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 311 Processing helix chain 'B' and resid 346 through 366 removed outlier: 4.077A pdb=" N GLU B 352 " --> pdb=" O HIS B 348 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE B 353 " --> pdb=" O ASP B 349 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU B 355 " --> pdb=" O MET B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 405 Processing helix chain 'B' and resid 418 through 430 Processing helix chain 'B' and resid 439 through 452 removed outlier: 3.805A pdb=" N LEU B 443 " --> pdb=" O THR B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 456 Processing helix chain 'B' and resid 468 through 470 No H-bonds generated for 'chain 'B' and resid 468 through 470' Processing helix chain 'B' and resid 504 through 521 Processing helix chain 'B' and resid 530 through 539 Processing helix chain 'B' and resid 551 through 559 Processing helix chain 'B' and resid 563 through 568 removed outlier: 4.152A pdb=" N VAL B 567 " --> pdb=" O ASN B 563 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 204 through 207 removed outlier: 6.834A pdb=" N ILE A 181 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 8.828A pdb=" N LYS A 153 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 9.248A pdb=" N ILE A 198 " --> pdb=" O LYS A 153 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N GLN A 155 " --> pdb=" O ILE A 198 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N MET A 157 " --> pdb=" O PRO A 200 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ALA A 134 " --> pdb=" O ASP A 146 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ARG A 148 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ILE A 132 " --> pdb=" O ARG A 148 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 264 through 265 removed outlier: 5.776A pdb=" N LEU A 264 " --> pdb=" O TYR A 316 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ILE A 318 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE A 495 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N GLU A 494 " --> pdb=" O VAL A 490 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL A 490 " --> pdb=" O GLU A 494 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N CYS A 496 " --> pdb=" O LEU A 488 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 271 through 272 Processing sheet with id=AA4, first strand: chain 'A' and resid 370 through 373 Processing sheet with id=AA5, first strand: chain 'A' and resid 465 through 466 Processing sheet with id=AA6, first strand: chain 'B' and resid 153 through 158 removed outlier: 4.285A pdb=" N LEU B 142 " --> pdb=" O SER B 138 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ALA B 134 " --> pdb=" O ASP B 146 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ARG B 148 " --> pdb=" O ILE B 132 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ILE B 132 " --> pdb=" O ARG B 148 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ILE B 181 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N LEU B 205 " --> pdb=" O ILE B 181 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLY B 183 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ILE B 203 " --> pdb=" O GLY B 183 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N GLN B 185 " --> pdb=" O TYR B 201 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 271 through 272 removed outlier: 4.007A pdb=" N MET B 292 " --> pdb=" O HIS B 287 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 314 through 322 removed outlier: 6.626A pdb=" N ILE B 495 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLU B 494 " --> pdb=" O VAL B 490 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL B 490 " --> pdb=" O GLU B 494 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N CYS B 496 " --> pdb=" O LEU B 488 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLU B 484 " --> pdb=" O THR B 500 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N HIS B 465 " --> pdb=" O THR B 483 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ARG B 485 " --> pdb=" O CYS B 463 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N CYS B 463 " --> pdb=" O ARG B 485 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLU B 487 " --> pdb=" O PHE B 461 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE B 461 " --> pdb=" O GLU B 487 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 370 through 373 376 hydrogen bonds defined for protein. 1080 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 69 hydrogen bonds 114 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 1.66 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2870 1.34 - 1.46: 2102 1.46 - 1.58: 4978 1.58 - 1.70: 147 1.70 - 1.82: 96 Bond restraints: 10193 Sorted by residual: bond pdb=" C4 AMP B 602 " pdb=" C5 AMP B 602 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" C4 AMP A 602 " pdb=" C5 AMP A 602 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" C5 AMP B 602 " pdb=" C6 AMP B 602 " ideal model delta sigma weight residual 1.490 1.405 0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" C5 AMP A 602 " pdb=" C6 AMP A 602 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" C ARG A 392 " pdb=" N ARG A 393 " ideal model delta sigma weight residual 1.330 1.373 -0.043 1.40e-02 5.10e+03 9.58e+00 ... (remaining 10188 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 13595 1.99 - 3.98: 484 3.98 - 5.98: 34 5.98 - 7.97: 14 7.97 - 9.96: 5 Bond angle restraints: 14132 Sorted by residual: angle pdb=" O5' U C 39 " pdb=" C5' U C 39 " pdb=" C4' U C 39 " ideal model delta sigma weight residual 109.40 113.11 -3.71 8.00e-01 1.56e+00 2.16e+01 angle pdb=" CA ASP A 445 " pdb=" CB ASP A 445 " pdb=" CG ASP A 445 " ideal model delta sigma weight residual 112.60 116.99 -4.39 1.00e+00 1.00e+00 1.93e+01 angle pdb=" O4' A C 38 " pdb=" C1' A C 38 " pdb=" N9 A C 38 " ideal model delta sigma weight residual 108.20 111.46 -3.26 8.00e-01 1.56e+00 1.66e+01 angle pdb=" C1' C C 40 " pdb=" N1 C C 40 " pdb=" C2 C C 40 " ideal model delta sigma weight residual 118.80 123.19 -4.39 1.10e+00 8.26e-01 1.59e+01 angle pdb=" O5' C C 61 " pdb=" C5' C C 61 " pdb=" C4' C C 61 " ideal model delta sigma weight residual 109.40 112.37 -2.97 8.00e-01 1.56e+00 1.38e+01 ... (remaining 14127 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.95: 5607 25.95 - 51.91: 488 51.91 - 77.86: 180 77.86 - 103.81: 12 103.81 - 129.77: 3 Dihedral angle restraints: 6290 sinusoidal: 3339 harmonic: 2951 Sorted by residual: dihedral pdb=" CA PRO B 409 " pdb=" C PRO B 409 " pdb=" N GLU B 410 " pdb=" CA GLU B 410 " ideal model delta harmonic sigma weight residual -180.00 -162.53 -17.47 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" C2' AMP B 602 " pdb=" C1' AMP B 602 " pdb=" N9 AMP B 602 " pdb=" C4 AMP B 602 " ideal model delta sinusoidal sigma weight residual 91.55 151.75 -60.19 1 2.00e+01 2.50e-03 1.21e+01 dihedral pdb=" CA THR B 388 " pdb=" C THR B 388 " pdb=" N PRO B 389 " pdb=" CA PRO B 389 " ideal model delta harmonic sigma weight residual -180.00 -163.32 -16.68 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 6287 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1177 0.043 - 0.085: 260 0.085 - 0.128: 84 0.128 - 0.170: 72 0.170 - 0.213: 5 Chirality restraints: 1598 Sorted by residual: chirality pdb=" CA HIS B 465 " pdb=" N HIS B 465 " pdb=" C HIS B 465 " pdb=" CB HIS B 465 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA HIS A 465 " pdb=" N HIS A 465 " pdb=" C HIS A 465 " pdb=" CB HIS A 465 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.72e-01 chirality pdb=" CA MET B 271 " pdb=" N MET B 271 " pdb=" C MET B 271 " pdb=" CB MET B 271 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.67e-01 ... (remaining 1595 not shown) Planarity restraints: 1549 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 393 " -0.237 9.50e-02 1.11e+02 1.06e-01 6.91e+00 pdb=" NE ARG A 393 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A 393 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 393 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 393 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 241 " 0.219 9.50e-02 1.11e+02 9.80e-02 5.89e+00 pdb=" NE ARG B 241 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG B 241 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG B 241 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 241 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 507 " -0.208 9.50e-02 1.11e+02 9.31e-02 5.33e+00 pdb=" NE ARG B 507 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG B 507 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG B 507 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 507 " -0.007 2.00e-02 2.50e+03 ... (remaining 1546 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1697 2.77 - 3.30: 9443 3.30 - 3.83: 17905 3.83 - 4.37: 20643 4.37 - 4.90: 33515 Nonbonded interactions: 83203 Sorted by model distance: nonbonded pdb=" O GLN A 86 " pdb=" ND2 ASN A 90 " model vdw 2.236 3.120 nonbonded pdb=" O ALA A 137 " pdb=" N6 A C 38 " model vdw 2.242 3.120 nonbonded pdb=" OD1 ASP A 386 " pdb=" OG1 THR A 388 " model vdw 2.270 3.040 nonbonded pdb=" N GLU B 168 " pdb=" OE1 GLU B 168 " model vdw 2.285 3.120 nonbonded pdb=" O2' A C 38 " pdb=" O5' U C 39 " model vdw 2.294 3.040 ... (remaining 83198 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 72 through 576 or resid 601 through 602)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.100 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 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 : 0.004 0.110 10193 Z= 0.268 Angle : 0.753 9.960 14132 Z= 0.488 Chirality : 0.049 0.213 1598 Planarity : 0.007 0.106 1549 Dihedral : 20.023 129.766 4392 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.56 % Allowed : 25.86 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.26), residues: 1007 helix: 1.24 (0.27), residues: 356 sheet: -0.37 (0.36), residues: 228 loop : -1.35 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 420 TYR 0.007 0.001 TYR A 316 PHE 0.038 0.001 PHE B 414 TRP 0.010 0.002 TRP B 547 HIS 0.003 0.000 HIS A 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.27 (10193) covalent geometry : angle 0.75265 / 0.49 (14132) hydrogen bonds : bond 0.13089 / 8.84 ( 445) hydrogen bonds : angle 5.90210 / 4.15 ( 1194) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: B 107 ASP cc_start: 0.8559 (t70) cc_final: 0.8353 (t0) REVERT: B 157 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.6994 (ptp) outliers start: 14 outliers final: 10 residues processed: 97 average time/residue: 0.0915 time to fit residues: 12.7309 Evaluate side-chains 86 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 601 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 50.0000 chunk 106 optimal weight: 50.0000 chunk 38 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 ASN ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN B 229 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.131368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.081750 restraints weight = 16547.314| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.97 r_work: 0.2941 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.0738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10193 Z= 0.160 Angle : 0.575 8.282 14132 Z= 0.295 Chirality : 0.038 0.278 1598 Planarity : 0.005 0.056 1549 Dihedral : 18.796 117.897 2301 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.01 % Allowed : 22.52 % Favored : 74.47 % 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: -0.08 (0.27), residues: 1007 helix: 1.39 (0.27), residues: 369 sheet: -0.19 (0.36), residues: 227 loop : -1.29 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 178 TYR 0.008 0.001 TYR A 539 PHE 0.029 0.001 PHE A 340 TRP 0.012 0.002 TRP A 547 HIS 0.002 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (10193) covalent geometry : angle 0.57512 / 0.30 (14132) hydrogen bonds : bond 0.04868 / 3.42 ( 445) hydrogen bonds : angle 4.99128 / 3.54 ( 1194) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 80 time to evaluate : 0.248 Fit side-chains REVERT: A 494 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7275 (tp30) REVERT: B 107 ASP cc_start: 0.8728 (t70) cc_final: 0.8375 (t0) REVERT: B 119 ASP cc_start: 0.8092 (OUTLIER) cc_final: 0.6888 (m-30) REVERT: B 407 LYS cc_start: 0.9174 (mptt) cc_final: 0.8720 (tptt) REVERT: B 421 LYS cc_start: 0.8618 (mmtm) cc_final: 0.8404 (mmtm) outliers start: 27 outliers final: 15 residues processed: 102 average time/residue: 0.0724 time to fit residues: 11.2376 Evaluate side-chains 91 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 351 MET Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 490 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 44 optimal weight: 0.0050 chunk 51 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 45 optimal weight: 7.9990 overall best weight: 1.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.130466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.080271 restraints weight = 16462.554| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.96 r_work: 0.2940 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10193 Z= 0.171 Angle : 0.553 8.226 14132 Z= 0.285 Chirality : 0.038 0.278 1598 Planarity : 0.005 0.056 1549 Dihedral : 18.717 120.751 2291 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.46 % Allowed : 21.74 % Favored : 74.80 % 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: -0.08 (0.27), residues: 1007 helix: 1.39 (0.27), residues: 370 sheet: -0.22 (0.36), residues: 228 loop : -1.29 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 148 TYR 0.009 0.001 TYR A 316 PHE 0.030 0.002 PHE A 340 TRP 0.012 0.002 TRP B 547 HIS 0.003 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (10193) covalent geometry : angle 0.55260 / 0.28 (14132) hydrogen bonds : bond 0.04661 / 3.31 ( 445) hydrogen bonds : angle 4.76671 / 3.39 ( 1194) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 80 time to evaluate : 0.208 Fit side-chains REVERT: A 494 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7373 (tp30) REVERT: B 107 ASP cc_start: 0.8624 (t70) cc_final: 0.8390 (t0) REVERT: B 123 ASP cc_start: 0.8489 (p0) cc_final: 0.8281 (p0) REVERT: B 407 LYS cc_start: 0.9146 (mptt) cc_final: 0.8713 (tptt) REVERT: B 421 LYS cc_start: 0.8659 (mmtm) cc_final: 0.8406 (mmtm) REVERT: B 566 GLU cc_start: 0.8997 (mm-30) cc_final: 0.8759 (mm-30) outliers start: 31 outliers final: 20 residues processed: 105 average time/residue: 0.0633 time to fit residues: 10.4502 Evaluate side-chains 96 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 490 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 39 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 95 optimal weight: 8.9990 chunk 105 optimal weight: 50.0000 chunk 44 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.131163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.080974 restraints weight = 16555.945| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.98 r_work: 0.2936 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10193 Z= 0.126 Angle : 0.525 6.766 14132 Z= 0.270 Chirality : 0.037 0.273 1598 Planarity : 0.005 0.055 1549 Dihedral : 18.647 119.390 2288 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.90 % Allowed : 22.85 % Favored : 74.25 % 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: -0.07 (0.27), residues: 1007 helix: 1.42 (0.27), residues: 370 sheet: -0.25 (0.36), residues: 228 loop : -1.28 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 247 TYR 0.009 0.001 TYR A 316 PHE 0.028 0.001 PHE A 340 TRP 0.011 0.002 TRP B 547 HIS 0.002 0.000 HIS A 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (10193) covalent geometry : angle 0.52501 / 0.27 (14132) hydrogen bonds : bond 0.04304 / 3.06 ( 445) hydrogen bonds : angle 4.62102 / 3.29 ( 1194) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 80 time to evaluate : 0.269 Fit side-chains REVERT: A 494 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7407 (tp30) REVERT: B 107 ASP cc_start: 0.8608 (t70) cc_final: 0.8332 (t0) REVERT: B 116 GLN cc_start: 0.8359 (pm20) cc_final: 0.7947 (pm20) REVERT: B 119 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7385 (m-30) REVERT: B 123 ASP cc_start: 0.8561 (p0) cc_final: 0.8266 (p0) REVERT: B 407 LYS cc_start: 0.9120 (mptt) cc_final: 0.8675 (tptt) REVERT: B 566 GLU cc_start: 0.8985 (mm-30) cc_final: 0.8770 (mm-30) outliers start: 26 outliers final: 15 residues processed: 100 average time/residue: 0.0693 time to fit residues: 10.4956 Evaluate side-chains 92 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 490 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 42 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 106 optimal weight: 50.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.131198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.081106 restraints weight = 16621.527| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.97 r_work: 0.2913 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10193 Z= 0.153 Angle : 0.529 6.518 14132 Z= 0.271 Chirality : 0.037 0.271 1598 Planarity : 0.005 0.056 1549 Dihedral : 18.617 121.998 2287 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.46 % Allowed : 22.85 % Favored : 73.69 % 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: -0.07 (0.27), residues: 1007 helix: 1.42 (0.27), residues: 370 sheet: -0.26 (0.36), residues: 227 loop : -1.28 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 247 TYR 0.012 0.001 TYR A 499 PHE 0.029 0.002 PHE A 340 TRP 0.012 0.002 TRP B 547 HIS 0.003 0.001 HIS A 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (10193) covalent geometry : angle 0.52899 / 0.27 (14132) hydrogen bonds : bond 0.04343 / 3.09 ( 445) hydrogen bonds : angle 4.60521 / 3.27 ( 1194) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 80 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: A 285 THR cc_start: 0.8791 (m) cc_final: 0.8414 (p) REVERT: A 494 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7402 (tp30) REVERT: B 107 ASP cc_start: 0.8614 (t70) cc_final: 0.8325 (t0) REVERT: B 123 ASP cc_start: 0.8621 (p0) cc_final: 0.8301 (p0) REVERT: B 407 LYS cc_start: 0.9120 (mptt) cc_final: 0.8728 (tptt) REVERT: B 566 GLU cc_start: 0.9006 (mm-30) cc_final: 0.8634 (mm-30) outliers start: 31 outliers final: 20 residues processed: 104 average time/residue: 0.0713 time to fit residues: 11.3369 Evaluate side-chains 96 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 512 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 84 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 104 optimal weight: 20.0000 chunk 12 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.131107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.081107 restraints weight = 16665.539| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.96 r_work: 0.2913 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10193 Z= 0.145 Angle : 0.529 7.065 14132 Z= 0.269 Chirality : 0.037 0.271 1598 Planarity : 0.005 0.055 1549 Dihedral : 18.595 122.690 2287 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.57 % Allowed : 22.85 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.27), residues: 1007 helix: 1.44 (0.27), residues: 371 sheet: -0.27 (0.36), residues: 227 loop : -1.27 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 247 TYR 0.009 0.001 TYR A 316 PHE 0.029 0.002 PHE A 340 TRP 0.012 0.002 TRP B 547 HIS 0.002 0.001 HIS B 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (10193) covalent geometry : angle 0.52880 / 0.27 (14132) hydrogen bonds : bond 0.04264 / 3.03 ( 445) hydrogen bonds : angle 4.56017 / 3.24 ( 1194) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 80 time to evaluate : 0.353 Fit side-chains REVERT: A 285 THR cc_start: 0.8797 (m) cc_final: 0.8416 (p) REVERT: A 494 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7417 (tp30) REVERT: B 107 ASP cc_start: 0.8604 (t70) cc_final: 0.8298 (t0) REVERT: B 119 ASP cc_start: 0.8108 (m-30) cc_final: 0.7798 (m-30) REVERT: B 123 ASP cc_start: 0.8650 (p0) cc_final: 0.8294 (p0) REVERT: B 407 LYS cc_start: 0.9106 (mptt) cc_final: 0.8719 (tptt) outliers start: 32 outliers final: 20 residues processed: 105 average time/residue: 0.0633 time to fit residues: 10.1686 Evaluate side-chains 98 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 512 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 93 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 45 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 33 optimal weight: 7.9990 chunk 16 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 120 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.130774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.080677 restraints weight = 16384.739| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.96 r_work: 0.2930 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10193 Z= 0.126 Angle : 0.531 8.780 14132 Z= 0.269 Chirality : 0.037 0.270 1598 Planarity : 0.005 0.055 1549 Dihedral : 18.562 122.545 2287 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.01 % Allowed : 23.30 % Favored : 73.69 % 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: -0.02 (0.27), residues: 1007 helix: 1.45 (0.27), residues: 371 sheet: -0.24 (0.36), residues: 227 loop : -1.23 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 247 TYR 0.009 0.001 TYR A 316 PHE 0.028 0.001 PHE A 340 TRP 0.011 0.002 TRP B 547 HIS 0.002 0.000 HIS A 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (10193) covalent geometry : angle 0.53107 / 0.27 (14132) hydrogen bonds : bond 0.04187 / 2.99 ( 445) hydrogen bonds : angle 4.51435 / 3.20 ( 1194) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 79 time to evaluate : 0.335 Fit side-chains REVERT: A 285 THR cc_start: 0.8785 (m) cc_final: 0.8431 (p) REVERT: A 494 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7410 (tp30) REVERT: B 107 ASP cc_start: 0.8587 (t70) cc_final: 0.8222 (t0) REVERT: B 123 ASP cc_start: 0.8601 (p0) cc_final: 0.8243 (p0) REVERT: B 195 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7346 (mp0) outliers start: 27 outliers final: 19 residues processed: 101 average time/residue: 0.0664 time to fit residues: 10.4251 Evaluate side-chains 98 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 512 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 66 optimal weight: 0.9990 chunk 4 optimal weight: 0.1980 chunk 75 optimal weight: 0.0370 chunk 42 optimal weight: 1.9990 chunk 64 optimal weight: 9.9990 chunk 28 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 105 optimal weight: 50.0000 chunk 106 optimal weight: 50.0000 chunk 82 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 120 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.135384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.084838 restraints weight = 17524.782| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.88 r_work: 0.3089 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10193 Z= 0.104 Angle : 0.518 7.928 14132 Z= 0.263 Chirality : 0.037 0.264 1598 Planarity : 0.004 0.055 1549 Dihedral : 18.495 121.456 2287 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.01 % Allowed : 23.63 % Favored : 73.36 % 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: 0.03 (0.27), residues: 1007 helix: 1.52 (0.27), residues: 371 sheet: -0.25 (0.36), residues: 227 loop : -1.21 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 323 TYR 0.008 0.001 TYR A 316 PHE 0.025 0.001 PHE A 340 TRP 0.010 0.002 TRP B 547 HIS 0.002 0.000 HIS A 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 (10193) covalent geometry : angle 0.51834 / 0.26 (14132) hydrogen bonds : bond 0.04026 / 2.87 ( 445) hydrogen bonds : angle 4.43661 / 3.15 ( 1194) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 78 time to evaluate : 0.338 Fit side-chains REVERT: A 285 THR cc_start: 0.8882 (m) cc_final: 0.8611 (p) REVERT: A 406 MET cc_start: 0.8071 (pmm) cc_final: 0.7334 (pmm) REVERT: B 107 ASP cc_start: 0.8601 (t70) cc_final: 0.8283 (t0) REVERT: B 123 ASP cc_start: 0.8328 (p0) cc_final: 0.7873 (p0) outliers start: 27 outliers final: 19 residues processed: 102 average time/residue: 0.0702 time to fit residues: 11.2290 Evaluate side-chains 93 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 218 PHE Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 512 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 44 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 18 optimal weight: 0.5980 chunk 57 optimal weight: 4.9990 chunk 95 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 120 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.134958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.084187 restraints weight = 17599.955| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.94 r_work: 0.3075 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10193 Z= 0.122 Angle : 0.527 10.736 14132 Z= 0.265 Chirality : 0.037 0.294 1598 Planarity : 0.005 0.055 1549 Dihedral : 18.458 123.140 2287 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.56 % Allowed : 23.97 % Favored : 73.47 % 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: 0.05 (0.27), residues: 1007 helix: 1.51 (0.27), residues: 371 sheet: -0.22 (0.36), residues: 227 loop : -1.18 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 323 TYR 0.008 0.001 TYR A 316 PHE 0.027 0.001 PHE A 340 TRP 0.011 0.002 TRP B 547 HIS 0.002 0.000 HIS B 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (10193) covalent geometry : angle 0.52658 / 0.26 (14132) hydrogen bonds : bond 0.04107 / 2.93 ( 445) hydrogen bonds : angle 4.44423 / 3.15 ( 1194) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 77 time to evaluate : 0.220 Fit side-chains REVERT: A 285 THR cc_start: 0.8910 (m) cc_final: 0.8619 (p) REVERT: A 406 MET cc_start: 0.8123 (pmm) cc_final: 0.7386 (pmm) REVERT: B 107 ASP cc_start: 0.8617 (t70) cc_final: 0.8232 (t0) REVERT: B 123 ASP cc_start: 0.8261 (p0) cc_final: 0.7798 (p0) REVERT: B 195 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7383 (mp0) outliers start: 23 outliers final: 18 residues processed: 95 average time/residue: 0.0667 time to fit residues: 9.9541 Evaluate side-chains 94 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 512 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 95 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 105 optimal weight: 50.0000 chunk 92 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 66 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 120 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.135040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.084007 restraints weight = 17446.642| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.95 r_work: 0.3074 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10193 Z= 0.124 Angle : 0.531 11.224 14132 Z= 0.267 Chirality : 0.037 0.273 1598 Planarity : 0.005 0.055 1549 Dihedral : 18.412 124.025 2287 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.23 % Allowed : 24.30 % Favored : 73.47 % 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: 0.05 (0.27), residues: 1007 helix: 1.50 (0.27), residues: 371 sheet: -0.25 (0.36), residues: 227 loop : -1.16 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 323 TYR 0.008 0.001 TYR A 316 PHE 0.027 0.001 PHE A 340 TRP 0.010 0.002 TRP B 547 HIS 0.002 0.000 HIS A 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (10193) covalent geometry : angle 0.53123 / 0.27 (14132) hydrogen bonds : bond 0.04098 / 2.92 ( 445) hydrogen bonds : angle 4.43970 / 3.15 ( 1194) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 0.238 Fit side-chains REVERT: A 285 THR cc_start: 0.8911 (m) cc_final: 0.8622 (p) REVERT: A 406 MET cc_start: 0.8189 (pmm) cc_final: 0.7466 (pmm) REVERT: A 477 ARG cc_start: 0.8120 (ttm-80) cc_final: 0.7889 (mtm-85) REVERT: B 107 ASP cc_start: 0.8628 (t70) cc_final: 0.8236 (t0) REVERT: B 123 ASP cc_start: 0.8259 (p0) cc_final: 0.7785 (p0) REVERT: B 195 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7318 (mp0) outliers start: 20 outliers final: 18 residues processed: 92 average time/residue: 0.0661 time to fit residues: 9.5071 Evaluate side-chains 92 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 218 PHE Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 512 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 97 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 104 optimal weight: 20.0000 chunk 4 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 102 optimal weight: 20.0000 chunk 24 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 120 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.135241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.084309 restraints weight = 17643.885| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.90 r_work: 0.3082 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10193 Z= 0.115 Angle : 0.523 10.653 14132 Z= 0.263 Chirality : 0.037 0.285 1598 Planarity : 0.004 0.055 1549 Dihedral : 18.373 123.510 2287 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.45 % Allowed : 24.19 % Favored : 73.36 % 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: 0.07 (0.27), residues: 1007 helix: 1.51 (0.27), residues: 371 sheet: -0.17 (0.36), residues: 222 loop : -1.16 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 323 TYR 0.008 0.001 TYR A 316 PHE 0.026 0.001 PHE A 340 TRP 0.010 0.002 TRP B 547 HIS 0.001 0.000 HIS A 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (10193) covalent geometry : angle 0.52335 / 0.26 (14132) hydrogen bonds : bond 0.04066 / 2.90 ( 445) hydrogen bonds : angle 4.41900 / 3.13 ( 1194) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2037.27 seconds wall clock time: 35 minutes 39.87 seconds (2139.87 seconds total)