Starting phenix.real_space_refine on Sun Jun 15 09:55:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dow_47094/06_2025/9dow_47094.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dow_47094/06_2025/9dow_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_47094/06_2025/9dow_47094.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dow_47094/06_2025/9dow_47094.map" model { file = "/net/cci-nas-00/data/ceres_data/9dow_47094/06_2025/9dow_47094.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dow_47094/06_2025/9dow_47094.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.020 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 6.64, per 1000 atoms: 0.68 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: 2.67 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 3.73 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: 3.61 Time building geometry restraints manager: 3.12 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 - 2.14: 13807 2.14 - 4.27: 268 4.27 - 6.41: 37 6.41 - 8.54: 12 8.54 - 10.68: 8 Bond angle restraints: 14132 Sorted by residual: 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=" CA LYS B 407 " pdb=" CB LYS B 407 " pdb=" CG LYS B 407 " ideal model delta sigma weight residual 114.10 121.42 -7.32 2.00e+00 2.50e-01 1.34e+01 angle pdb=" C1' AMP B 602 " pdb=" C2' AMP B 602 " pdb=" C3' AMP B 602 " ideal model delta sigma weight residual 111.00 100.32 10.68 3.00e+00 1.11e-01 1.27e+01 angle pdb=" C2' AMP B 602 " pdb=" C3' AMP B 602 " pdb=" C4' AMP B 602 " ideal model delta sigma weight residual 111.00 100.42 10.58 3.00e+00 1.11e-01 1.24e+01 angle pdb=" C1' AMP A 602 " pdb=" C2' AMP A 602 " pdb=" C3' AMP A 602 " ideal model delta sigma weight residual 111.00 100.91 10.09 3.00e+00 1.11e-01 1.13e+01 ... (remaining 14127 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.95: 5539 23.95 - 47.91: 525 47.91 - 71.86: 192 71.86 - 95.81: 31 95.81 - 119.77: 3 Dihedral angle restraints: 6290 sinusoidal: 3339 harmonic: 2951 Sorted by residual: dihedral pdb=" C4' AMP B 602 " pdb=" C5' AMP B 602 " pdb=" O5' AMP B 602 " pdb=" P AMP B 602 " ideal model delta sinusoidal sigma weight residual -180.00 -60.23 -119.77 1 2.00e+01 2.50e-03 3.59e+01 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 ... (remaining 6287 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1252 0.043 - 0.085: 246 0.085 - 0.128: 76 0.128 - 0.170: 19 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 or resid 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 29.550 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 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= 0.260 Angle : 0.727 10.676 14132 Z= 0.397 Chirality : 0.041 0.213 1598 Planarity : 0.007 0.106 1549 Dihedral : 20.015 119.766 4392 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 10.16 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.010 0.002 TRP B 547 HIS 0.003 0.000 HIS A 465 PHE 0.038 0.001 PHE B 414 TYR 0.007 0.001 TYR A 316 ARG 0.003 0.000 ARG B 420 Details of bonding type rmsd hydrogen bonds : bond 0.13089 ( 445) hydrogen bonds : angle 5.90210 ( 1194) covalent geometry : bond 0.00436 (10193) covalent geometry : angle 0.72660 (14132) *********************** 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 : 1.078 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: 0.2314 time to fit residues: 32.1081 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 : 0.933 ------------------------------------------------------------------------------- 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 90 optimal weight: 5.9990 chunk 81 optimal weight: 0.6980 chunk 45 optimal weight: 0.0770 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 32 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3940 r_free = 0.3940 target = 0.131737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.081607 restraints weight = 16374.126| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.96 r_work: 0.2941 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.0902 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= 0.138 Angle : 0.576 6.801 14132 Z= 0.285 Chirality : 0.037 0.158 1598 Planarity : 0.005 0.055 1549 Dihedral : 18.676 103.388 2301 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.01 % Allowed : 22.63 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.27), residues: 1007 helix: 1.45 (0.27), residues: 369 sheet: -0.25 (0.36), residues: 227 loop : -1.24 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 547 HIS 0.002 0.001 HIS A 287 PHE 0.028 0.001 PHE A 340 TYR 0.007 0.001 TYR A 316 ARG 0.004 0.000 ARG B 241 Details of bonding type rmsd hydrogen bonds : bond 0.04124 ( 445) hydrogen bonds : angle 4.79094 ( 1194) covalent geometry : bond 0.00316 (10193) covalent geometry : angle 0.57569 (14132) *********************** 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 109 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 82 time to evaluate : 0.933 Fit side-chains REVERT: A 494 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7448 (tp30) REVERT: B 107 ASP cc_start: 0.8699 (t70) cc_final: 0.8389 (t0) REVERT: B 119 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7095 (m-30) REVERT: B 123 ASP cc_start: 0.8565 (p0) cc_final: 0.8331 (p0) REVERT: B 407 LYS cc_start: 0.9114 (mptt) cc_final: 0.8661 (tptt) REVERT: B 421 LYS cc_start: 0.8648 (mmtm) cc_final: 0.8407 (mmtm) outliers start: 27 outliers final: 16 residues processed: 103 average time/residue: 0.1857 time to fit residues: 28.8565 Evaluate side-chains 92 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 213 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 157 MET 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 411 THR Chi-restraints excluded: chain B residue 419 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 19 optimal weight: 0.1980 chunk 50 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 86 optimal weight: 0.0050 chunk 40 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 104 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 101 optimal weight: 20.0000 overall best weight: 0.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.130918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.080795 restraints weight = 16550.558| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.97 r_work: 0.2931 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1238 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= 0.142 Angle : 0.555 6.762 14132 Z= 0.274 Chirality : 0.037 0.150 1598 Planarity : 0.005 0.055 1549 Dihedral : 18.509 101.444 2290 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.12 % Allowed : 22.19 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.27), residues: 1007 helix: 1.46 (0.27), residues: 371 sheet: -0.28 (0.36), residues: 228 loop : -1.21 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 547 HIS 0.002 0.001 HIS A 287 PHE 0.029 0.002 PHE A 340 TYR 0.008 0.001 TYR A 316 ARG 0.003 0.000 ARG B 241 Details of bonding type rmsd hydrogen bonds : bond 0.03963 ( 445) hydrogen bonds : angle 4.60056 ( 1194) covalent geometry : bond 0.00330 (10193) covalent geometry : angle 0.55543 (14132) *********************** 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 105 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 77 time to evaluate : 0.952 Fit side-chains REVERT: A 494 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7460 (tp30) REVERT: B 107 ASP cc_start: 0.8583 (t70) cc_final: 0.8314 (t0) REVERT: B 123 ASP cc_start: 0.8621 (p0) cc_final: 0.8265 (p0) REVERT: B 124 ILE cc_start: 0.7405 (OUTLIER) cc_final: 0.7187 (pp) outliers start: 28 outliers final: 15 residues processed: 100 average time/residue: 0.1860 time to fit residues: 28.5574 Evaluate side-chains 89 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.954 ------------------------------------------------------------------------------- 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 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 124 ILE Chi-restraints excluded: chain B residue 195 GLU 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 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 72 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 100 optimal weight: 30.0000 chunk 87 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 83 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.127798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.077546 restraints weight = 16679.522| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.97 r_work: 0.2844 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 10193 Z= 0.269 Angle : 0.627 5.787 14132 Z= 0.314 Chirality : 0.040 0.158 1598 Planarity : 0.005 0.055 1549 Dihedral : 18.614 100.557 2287 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.34 % Allowed : 21.74 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.27), residues: 1007 helix: 1.27 (0.27), residues: 370 sheet: -0.47 (0.35), residues: 232 loop : -1.32 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B 547 HIS 0.004 0.001 HIS A 215 PHE 0.037 0.002 PHE A 340 TYR 0.012 0.001 TYR B 539 ARG 0.003 0.000 ARG B 485 Details of bonding type rmsd hydrogen bonds : bond 0.04647 ( 445) hydrogen bonds : angle 4.84949 ( 1194) covalent geometry : bond 0.00637 (10193) covalent geometry : angle 0.62682 (14132) *********************** 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 107 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 77 time to evaluate : 0.938 Fit side-chains REVERT: A 451 PHE cc_start: 0.8857 (m-80) cc_final: 0.8537 (m-80) REVERT: A 494 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7344 (tp30) REVERT: B 107 ASP cc_start: 0.8622 (t70) cc_final: 0.8313 (t0) REVERT: B 123 ASP cc_start: 0.8767 (p0) cc_final: 0.8436 (p0) REVERT: B 407 LYS cc_start: 0.9132 (mptt) cc_final: 0.8712 (tptt) REVERT: B 566 GLU cc_start: 0.9070 (mm-30) cc_final: 0.8802 (mm-30) outliers start: 30 outliers final: 21 residues processed: 101 average time/residue: 0.1798 time to fit residues: 27.6125 Evaluate side-chains 97 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 0.999 ------------------------------------------------------------------------------- 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 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 510 GLN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 0.5980 chunk 105 optimal weight: 30.0000 chunk 95 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.131998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.082318 restraints weight = 17139.033| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.80 r_work: 0.3027 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10193 Z= 0.176 Angle : 0.570 5.885 14132 Z= 0.282 Chirality : 0.037 0.149 1598 Planarity : 0.005 0.054 1549 Dihedral : 18.511 100.097 2287 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.79 % Allowed : 21.63 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.27), residues: 1007 helix: 1.32 (0.27), residues: 371 sheet: -0.45 (0.35), residues: 232 loop : -1.30 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 547 HIS 0.002 0.001 HIS A 215 PHE 0.030 0.002 PHE A 340 TYR 0.010 0.001 TYR A 316 ARG 0.003 0.000 ARG A 255 Details of bonding type rmsd hydrogen bonds : bond 0.04088 ( 445) hydrogen bonds : angle 4.68709 ( 1194) covalent geometry : bond 0.00412 (10193) covalent geometry : angle 0.56998 (14132) *********************** 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 112 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 78 time to evaluate : 0.933 Fit side-chains REVERT: A 285 THR cc_start: 0.8895 (m) cc_final: 0.8600 (p) REVERT: A 451 PHE cc_start: 0.8972 (m-80) cc_final: 0.8651 (m-80) REVERT: A 494 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7473 (tp30) REVERT: B 123 ASP cc_start: 0.8482 (p0) cc_final: 0.7958 (p0) REVERT: B 392 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7687 (mtp85) REVERT: B 407 LYS cc_start: 0.9111 (mptt) cc_final: 0.8683 (tptt) outliers start: 34 outliers final: 23 residues processed: 106 average time/residue: 0.1882 time to fit residues: 29.6241 Evaluate side-chains 99 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 74 time to evaluate : 0.926 ------------------------------------------------------------------------------- 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 195 GLU Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 210 LEU 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 392 ARG 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 63 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 71 optimal weight: 0.0980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.133069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.082405 restraints weight = 17510.613| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.91 r_work: 0.3035 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1721 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= 0.141 Angle : 0.558 5.948 14132 Z= 0.276 Chirality : 0.037 0.151 1598 Planarity : 0.005 0.055 1549 Dihedral : 18.391 99.242 2287 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.90 % Allowed : 21.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.27), residues: 1007 helix: 1.38 (0.27), residues: 370 sheet: -0.48 (0.35), residues: 233 loop : -1.25 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 547 HIS 0.002 0.000 HIS A 476 PHE 0.028 0.001 PHE A 340 TYR 0.010 0.001 TYR A 499 ARG 0.002 0.000 ARG A 485 Details of bonding type rmsd hydrogen bonds : bond 0.03885 ( 445) hydrogen bonds : angle 4.57530 ( 1194) covalent geometry : bond 0.00328 (10193) covalent geometry : angle 0.55846 (14132) *********************** 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 111 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 76 time to evaluate : 0.972 Fit side-chains REVERT: A 285 THR cc_start: 0.8880 (m) cc_final: 0.8614 (p) REVERT: A 451 PHE cc_start: 0.8948 (m-80) cc_final: 0.8617 (m-80) REVERT: A 477 ARG cc_start: 0.8106 (ttm-80) cc_final: 0.7903 (mtm-85) REVERT: A 494 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7559 (tp30) REVERT: B 123 ASP cc_start: 0.8349 (p0) cc_final: 0.7760 (p0) REVERT: B 392 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7683 (mtp85) REVERT: B 407 LYS cc_start: 0.9089 (mptt) cc_final: 0.8782 (tptt) outliers start: 35 outliers final: 20 residues processed: 104 average time/residue: 0.1998 time to fit residues: 31.0292 Evaluate side-chains 96 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.975 ------------------------------------------------------------------------------- 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 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 195 GLU Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 218 PHE Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 392 ARG 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 20 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 101 optimal weight: 20.0000 chunk 55 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.131595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.080623 restraints weight = 17888.421| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.86 r_work: 0.3009 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10193 Z= 0.214 Angle : 0.595 5.875 14132 Z= 0.295 Chirality : 0.038 0.152 1598 Planarity : 0.005 0.055 1549 Dihedral : 18.396 98.468 2287 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.12 % Allowed : 22.97 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.27), residues: 1007 helix: 1.29 (0.27), residues: 371 sheet: -0.54 (0.35), residues: 232 loop : -1.26 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 547 HIS 0.003 0.001 HIS A 215 PHE 0.032 0.002 PHE A 340 TYR 0.014 0.001 TYR A 499 ARG 0.003 0.000 ARG B 485 Details of bonding type rmsd hydrogen bonds : bond 0.04283 ( 445) hydrogen bonds : angle 4.70388 ( 1194) covalent geometry : bond 0.00506 (10193) covalent geometry : angle 0.59477 (14132) *********************** 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 105 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 77 time to evaluate : 0.985 Fit side-chains REVERT: A 285 THR cc_start: 0.8925 (m) cc_final: 0.8589 (p) REVERT: A 477 ARG cc_start: 0.8151 (ttm-80) cc_final: 0.7948 (mtm-85) REVERT: A 494 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7418 (tp30) REVERT: B 107 ASP cc_start: 0.8795 (t70) cc_final: 0.8397 (t0) REVERT: B 123 ASP cc_start: 0.8366 (p0) cc_final: 0.7866 (p0) REVERT: B 392 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7726 (mtp85) REVERT: B 407 LYS cc_start: 0.9074 (mptt) cc_final: 0.8754 (tptt) outliers start: 28 outliers final: 23 residues processed: 99 average time/residue: 0.1924 time to fit residues: 28.4868 Evaluate side-chains 100 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 1.037 ------------------------------------------------------------------------------- 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 274 ILE 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 195 GLU Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 210 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 392 ARG 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 24 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 70 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.133838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.083354 restraints weight = 17701.779| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.86 r_work: 0.3059 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1822 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= 0.115 Angle : 0.555 7.713 14132 Z= 0.271 Chirality : 0.036 0.144 1598 Planarity : 0.005 0.055 1549 Dihedral : 18.281 98.052 2287 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.57 % Allowed : 22.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.27), residues: 1007 helix: 1.42 (0.27), residues: 371 sheet: -0.46 (0.36), residues: 228 loop : -1.17 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 547 HIS 0.002 0.000 HIS A 476 PHE 0.026 0.001 PHE A 340 TYR 0.009 0.001 TYR A 316 ARG 0.002 0.000 ARG B 442 Details of bonding type rmsd hydrogen bonds : bond 0.03750 ( 445) hydrogen bonds : angle 4.50528 ( 1194) covalent geometry : bond 0.00261 (10193) covalent geometry : angle 0.55465 (14132) *********************** 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 107 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 75 time to evaluate : 0.961 Fit side-chains REVERT: A 285 THR cc_start: 0.8852 (m) cc_final: 0.8605 (p) REVERT: A 451 PHE cc_start: 0.9005 (m-80) cc_final: 0.8734 (m-80) REVERT: A 477 ARG cc_start: 0.8121 (ttm-80) cc_final: 0.7903 (mtm-85) REVERT: A 494 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7571 (tp30) REVERT: B 107 ASP cc_start: 0.8742 (t70) cc_final: 0.8364 (t0) REVERT: B 123 ASP cc_start: 0.8278 (p0) cc_final: 0.7709 (p0) REVERT: B 168 GLU cc_start: 0.8475 (pm20) cc_final: 0.8223 (pm20) REVERT: B 407 LYS cc_start: 0.9065 (mptt) cc_final: 0.8701 (tptt) outliers start: 32 outliers final: 20 residues processed: 103 average time/residue: 0.1847 time to fit residues: 28.4568 Evaluate side-chains 97 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 191 THR 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 195 GLU Chi-restraints excluded: chain B residue 198 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 22 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 106 optimal weight: 20.0000 chunk 93 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 4 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.130707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.081109 restraints weight = 16695.913| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.94 r_work: 0.2917 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1843 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= 0.125 Angle : 0.555 8.644 14132 Z= 0.272 Chirality : 0.037 0.143 1598 Planarity : 0.005 0.055 1549 Dihedral : 18.211 95.841 2287 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.90 % Allowed : 23.30 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.27), residues: 1007 helix: 1.44 (0.27), residues: 373 sheet: -0.40 (0.36), residues: 227 loop : -1.13 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 547 HIS 0.002 0.000 HIS B 304 PHE 0.027 0.001 PHE A 340 TYR 0.010 0.001 TYR A 499 ARG 0.002 0.000 ARG B 247 Details of bonding type rmsd hydrogen bonds : bond 0.03749 ( 445) hydrogen bonds : angle 4.43701 ( 1194) covalent geometry : bond 0.00290 (10193) covalent geometry : angle 0.55516 (14132) *********************** 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 102 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 76 time to evaluate : 0.983 Fit side-chains REVERT: A 285 THR cc_start: 0.8751 (m) cc_final: 0.8446 (p) REVERT: A 451 PHE cc_start: 0.8911 (m-80) cc_final: 0.8621 (m-80) REVERT: A 477 ARG cc_start: 0.7883 (ttm-80) cc_final: 0.7667 (mtm-85) REVERT: A 494 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7568 (tp30) REVERT: B 107 ASP cc_start: 0.8709 (t70) cc_final: 0.8342 (t0) REVERT: B 123 ASP cc_start: 0.8394 (p0) cc_final: 0.7970 (p0) REVERT: B 168 GLU cc_start: 0.8504 (pm20) cc_final: 0.8191 (pm20) REVERT: B 407 LYS cc_start: 0.9024 (mptt) cc_final: 0.8664 (tptt) outliers start: 26 outliers final: 21 residues processed: 99 average time/residue: 0.2213 time to fit residues: 32.5188 Evaluate side-chains 97 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 191 THR 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 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 34 optimal weight: 0.8980 chunk 79 optimal weight: 0.1980 chunk 7 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.131048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.081423 restraints weight = 16599.603| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.93 r_work: 0.2952 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10193 Z= 0.122 Angle : 0.552 8.753 14132 Z= 0.269 Chirality : 0.037 0.151 1598 Planarity : 0.005 0.055 1549 Dihedral : 18.149 94.124 2287 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.45 % Allowed : 23.52 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.27), residues: 1007 helix: 1.44 (0.27), residues: 373 sheet: -0.41 (0.36), residues: 227 loop : -1.11 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 547 HIS 0.002 0.000 HIS A 85 PHE 0.027 0.001 PHE A 340 TYR 0.011 0.001 TYR A 499 ARG 0.003 0.000 ARG A 323 Details of bonding type rmsd hydrogen bonds : bond 0.03715 ( 445) hydrogen bonds : angle 4.40101 ( 1194) covalent geometry : bond 0.00284 (10193) covalent geometry : angle 0.55239 (14132) ********************** 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 99 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 1.934 Fit side-chains REVERT: A 285 THR cc_start: 0.8786 (m) cc_final: 0.8480 (p) REVERT: A 451 PHE cc_start: 0.8937 (m-80) cc_final: 0.8650 (m-80) REVERT: A 477 ARG cc_start: 0.7909 (ttm-80) cc_final: 0.7706 (mtm-85) REVERT: A 494 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7533 (tp30) REVERT: B 107 ASP cc_start: 0.8712 (t70) cc_final: 0.8339 (t0) REVERT: B 123 ASP cc_start: 0.8371 (p0) cc_final: 0.7938 (p0) REVERT: B 168 GLU cc_start: 0.8506 (pm20) cc_final: 0.8200 (pm20) REVERT: B 407 LYS cc_start: 0.9037 (mptt) cc_final: 0.8641 (tptt) outliers start: 22 outliers final: 21 residues processed: 96 average time/residue: 0.2323 time to fit residues: 34.2044 Evaluate side-chains 98 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 191 THR 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 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 18 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 45 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.131302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.081634 restraints weight = 16682.199| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.95 r_work: 0.2956 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1925 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= 0.119 Angle : 0.550 8.608 14132 Z= 0.268 Chirality : 0.037 0.149 1598 Planarity : 0.005 0.055 1549 Dihedral : 18.076 93.730 2287 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.68 % Allowed : 23.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.27), residues: 1007 helix: 1.47 (0.27), residues: 373 sheet: -0.43 (0.36), residues: 227 loop : -1.08 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 547 HIS 0.001 0.000 HIS A 476 PHE 0.026 0.001 PHE A 340 TYR 0.010 0.001 TYR A 499 ARG 0.003 0.000 ARG A 323 Details of bonding type rmsd hydrogen bonds : bond 0.03694 ( 445) hydrogen bonds : angle 4.36380 ( 1194) covalent geometry : bond 0.00276 (10193) covalent geometry : angle 0.55041 (14132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5235.75 seconds wall clock time: 91 minutes 39.64 seconds (5499.64 seconds total)