Starting phenix.real_space_refine on Thu Sep 18 13:42:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dow_47094/09_2025/9dow_47094.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dow_47094/09_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_47094/09_2025/9dow_47094.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dow_47094/09_2025/9dow_47094.map" model { file = "/net/cci-nas-00/data/ceres_data/9dow_47094/09_2025/9dow_47094.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dow_47094/09_2025/9dow_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-2.0-5805/lib/python3.9/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: 2.48, per 1000 atoms: 0.25 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: 0.78 Conformation dependent library (CDL) restraints added in 416.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.00 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: 1.65 Time building geometry restraints manager: 1.06 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 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.570 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.090 ------------------------------------------------------------------------------- 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 : 10.10 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 aren 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 covalent geometry : bond 0.00436 (10193) covalent geometry : angle 0.72660 (14132) hydrogen bonds : bond 0.13089 ( 445) hydrogen bonds : angle 5.90210 ( 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 : 0.366 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: 0.1014 time to fit residues: 14.0928 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 : 0.288 ------------------------------------------------------------------------------- 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: 30.0000 chunk 106 optimal weight: 20.0000 chunk 38 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN B 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.130832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.080650 restraints weight = 16545.556| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.95 r_work: 0.2928 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.0991 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= 0.160 Angle : 0.583 6.446 14132 Z= 0.290 Chirality : 0.038 0.158 1598 Planarity : 0.005 0.055 1549 Dihedral : 18.682 103.225 2301 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.12 % Allowed : 22.63 % 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 aren not related in a simple way. whole: -0.09 (0.27), residues: 1007 helix: 1.43 (0.27), residues: 368 sheet: -0.29 (0.36), residues: 227 loop : -1.27 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 393 TYR 0.008 0.001 TYR A 316 PHE 0.030 0.002 PHE A 340 TRP 0.013 0.002 TRP A 547 HIS 0.003 0.001 HIS A 287 Details of bonding type rmsd covalent geometry : bond 0.00371 (10193) covalent geometry : angle 0.58297 (14132) hydrogen bonds : bond 0.04249 ( 445) hydrogen bonds : angle 4.81721 ( 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 109 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 81 time to evaluate : 0.308 Fit side-chains REVERT: A 494 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7446 (tp30) REVERT: B 107 ASP cc_start: 0.8712 (t70) cc_final: 0.8387 (t0) REVERT: B 119 ASP cc_start: 0.7993 (OUTLIER) cc_final: 0.6883 (m-30) REVERT: B 123 ASP cc_start: 0.8593 (p0) cc_final: 0.8372 (p0) REVERT: B 407 LYS cc_start: 0.9116 (mptt) cc_final: 0.8668 (tptt) REVERT: B 421 LYS cc_start: 0.8649 (mmtm) cc_final: 0.8403 (mmtm) outliers start: 28 outliers final: 16 residues processed: 103 average time/residue: 0.0825 time to fit residues: 12.6690 Evaluate side-chains 91 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.221 ------------------------------------------------------------------------------- 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 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 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 44 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 45 optimal weight: 7.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.131886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.081852 restraints weight = 16593.257| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.99 r_work: 0.2928 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1270 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= 0.132 Angle : 0.551 7.348 14132 Z= 0.271 Chirality : 0.037 0.150 1598 Planarity : 0.005 0.055 1549 Dihedral : 18.498 101.294 2290 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.79 % Allowed : 22.85 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.27), residues: 1007 helix: 1.45 (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 ARG 0.002 0.000 ARG A 228 TYR 0.008 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 covalent geometry : bond 0.00304 (10193) covalent geometry : angle 0.55072 (14132) hydrogen bonds : bond 0.03913 ( 445) hydrogen bonds : angle 4.59366 ( 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 103 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 78 time to evaluate : 0.339 Fit side-chains REVERT: A 494 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7500 (tp30) REVERT: B 107 ASP cc_start: 0.8556 (t70) cc_final: 0.8291 (t0) REVERT: B 123 ASP cc_start: 0.8648 (p0) cc_final: 0.8271 (p0) REVERT: B 124 ILE cc_start: 0.7417 (OUTLIER) cc_final: 0.7186 (pp) outliers start: 25 outliers final: 14 residues processed: 98 average time/residue: 0.0809 time to fit residues: 12.0277 Evaluate side-chains 88 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 39 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 82 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 chunk 105 optimal weight: 30.0000 chunk 44 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.131200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.080890 restraints weight = 16674.773| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 3.00 r_work: 0.2928 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1384 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= 0.122 Angle : 0.540 5.987 14132 Z= 0.265 Chirality : 0.036 0.143 1598 Planarity : 0.004 0.056 1549 Dihedral : 18.404 100.165 2287 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.46 % Allowed : 22.52 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.27), residues: 1007 helix: 1.49 (0.27), residues: 372 sheet: -0.30 (0.36), residues: 227 loop : -1.19 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 247 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 A 476 Details of bonding type rmsd covalent geometry : bond 0.00281 (10193) covalent geometry : angle 0.53953 (14132) hydrogen bonds : bond 0.03772 ( 445) hydrogen bonds : angle 4.47783 ( 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 107 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 76 time to evaluate : 0.373 Fit side-chains REVERT: A 285 THR cc_start: 0.8722 (m) cc_final: 0.8399 (p) REVERT: A 494 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7535 (tp30) REVERT: A 527 MET cc_start: 0.7813 (ppp) cc_final: 0.7500 (ppp) REVERT: B 107 ASP cc_start: 0.8557 (t70) cc_final: 0.8268 (t0) REVERT: B 123 ASP cc_start: 0.8634 (p0) cc_final: 0.8259 (p0) outliers start: 31 outliers final: 20 residues processed: 101 average time/residue: 0.0796 time to fit residues: 12.3385 Evaluate side-chains 94 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 42 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 106 optimal weight: 30.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.132732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.081969 restraints weight = 17701.690| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.92 r_work: 0.3029 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10193 Z= 0.182 Angle : 0.569 5.880 14132 Z= 0.281 Chirality : 0.037 0.150 1598 Planarity : 0.005 0.056 1549 Dihedral : 18.401 98.721 2287 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.68 % Allowed : 21.85 % 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 aren not related in a simple way. whole: -0.07 (0.27), residues: 1007 helix: 1.47 (0.27), residues: 370 sheet: -0.38 (0.35), residues: 232 loop : -1.25 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 247 TYR 0.011 0.001 TYR A 499 PHE 0.032 0.002 PHE A 340 TRP 0.013 0.002 TRP B 547 HIS 0.002 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00427 (10193) covalent geometry : angle 0.56870 (14132) hydrogen bonds : bond 0.04121 ( 445) hydrogen bonds : angle 4.58768 ( 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: 33 poor density : 78 time to evaluate : 0.292 Fit side-chains REVERT: A 285 THR cc_start: 0.8934 (m) cc_final: 0.8583 (p) REVERT: A 445 ASP cc_start: 0.8957 (OUTLIER) cc_final: 0.8754 (p0) REVERT: A 494 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7505 (tp30) REVERT: B 107 ASP cc_start: 0.8631 (t70) cc_final: 0.8321 (t0) REVERT: B 123 ASP cc_start: 0.8487 (p0) cc_final: 0.8041 (p0) REVERT: B 407 LYS cc_start: 0.9071 (mptt) cc_final: 0.8626 (tptt) outliers start: 33 outliers final: 23 residues processed: 105 average time/residue: 0.0756 time to fit residues: 12.1820 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 : 0.229 ------------------------------------------------------------------------------- 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 445 ASP 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 329 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 84 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 97 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 12 optimal weight: 0.7980 chunk 64 optimal weight: 7.9990 chunk 29 optimal weight: 0.7980 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.134243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.083641 restraints weight = 17679.779| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.93 r_work: 0.3049 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1612 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= 0.119 Angle : 0.541 6.440 14132 Z= 0.265 Chirality : 0.036 0.144 1598 Planarity : 0.004 0.055 1549 Dihedral : 18.290 96.558 2287 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.71 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.27), residues: 1007 helix: 1.47 (0.27), residues: 373 sheet: -0.29 (0.36), residues: 227 loop : -1.14 (0.30), residues: 407 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 0.027 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 covalent geometry : bond 0.00273 (10193) covalent geometry : angle 0.54127 (14132) hydrogen bonds : bond 0.03762 ( 445) hydrogen bonds : angle 4.44932 ( 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 108 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 76 time to evaluate : 0.381 Fit side-chains REVERT: A 285 THR cc_start: 0.8840 (m) cc_final: 0.8575 (p) REVERT: A 445 ASP cc_start: 0.8952 (OUTLIER) cc_final: 0.8746 (p0) REVERT: A 494 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7583 (tp30) REVERT: B 123 ASP cc_start: 0.8355 (p0) cc_final: 0.7858 (p0) outliers start: 32 outliers final: 22 residues processed: 102 average time/residue: 0.0728 time to fit residues: 11.5253 Evaluate side-chains 97 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 73 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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 445 ASP 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 93 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 = 0.4010 r_free = 0.4010 target = 0.133957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.083414 restraints weight = 17493.705| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.91 r_work: 0.3054 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10193 Z= 0.134 Angle : 0.544 6.567 14132 Z= 0.267 Chirality : 0.036 0.143 1598 Planarity : 0.004 0.056 1549 Dihedral : 18.233 94.964 2287 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.68 % Allowed : 22.52 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.27), residues: 1007 helix: 1.46 (0.27), residues: 372 sheet: -0.28 (0.36), residues: 227 loop : -1.16 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 247 TYR 0.009 0.001 TYR A 499 PHE 0.028 0.001 PHE A 340 TRP 0.012 0.002 TRP B 547 HIS 0.002 0.000 HIS A 476 Details of bonding type rmsd covalent geometry : bond 0.00313 (10193) covalent geometry : angle 0.54425 (14132) hydrogen bonds : bond 0.03821 ( 445) hydrogen bonds : angle 4.43526 ( 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 109 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 76 time to evaluate : 0.371 Fit side-chains REVERT: A 285 THR cc_start: 0.8886 (m) cc_final: 0.8615 (p) REVERT: A 445 ASP cc_start: 0.8943 (OUTLIER) cc_final: 0.8733 (p0) REVERT: A 477 ARG cc_start: 0.8112 (ttm-80) cc_final: 0.7896 (mtm-85) REVERT: A 494 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7555 (tp30) REVERT: A 573 MET cc_start: 0.8959 (mmm) cc_final: 0.8695 (mmm) REVERT: B 123 ASP cc_start: 0.8271 (p0) cc_final: 0.7655 (p0) REVERT: B 407 LYS cc_start: 0.9056 (mptt) cc_final: 0.8732 (tptt) outliers start: 33 outliers final: 22 residues processed: 103 average time/residue: 0.0839 time to fit residues: 13.1921 Evaluate side-chains 98 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 74 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 445 ASP 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 66 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 64 optimal weight: 8.9990 chunk 28 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 105 optimal weight: 30.0000 chunk 106 optimal weight: 20.0000 chunk 82 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.4008 r_free = 0.4008 target = 0.133845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.083120 restraints weight = 17656.770| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.87 r_work: 0.3053 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1745 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= 0.142 Angle : 0.553 6.726 14132 Z= 0.272 Chirality : 0.037 0.151 1598 Planarity : 0.004 0.055 1549 Dihedral : 18.206 93.987 2287 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.12 % Allowed : 22.85 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.27), residues: 1007 helix: 1.50 (0.27), residues: 371 sheet: -0.30 (0.36), residues: 227 loop : -1.15 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 247 TYR 0.008 0.001 TYR A 316 PHE 0.029 0.001 PHE A 340 TRP 0.012 0.002 TRP B 547 HIS 0.002 0.001 HIS A 476 Details of bonding type rmsd covalent geometry : bond 0.00333 (10193) covalent geometry : angle 0.55269 (14132) hydrogen bonds : bond 0.03850 ( 445) hydrogen bonds : angle 4.42731 ( 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 106 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 78 time to evaluate : 0.376 Fit side-chains REVERT: A 285 THR cc_start: 0.8889 (m) cc_final: 0.8614 (p) REVERT: A 445 ASP cc_start: 0.8955 (OUTLIER) cc_final: 0.8751 (p0) REVERT: A 477 ARG cc_start: 0.8115 (ttm-80) cc_final: 0.7899 (mtm-85) REVERT: A 494 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7516 (tp30) REVERT: A 573 MET cc_start: 0.8951 (mmm) cc_final: 0.8686 (mmm) REVERT: B 123 ASP cc_start: 0.8244 (p0) cc_final: 0.7704 (p0) REVERT: B 407 LYS cc_start: 0.9053 (mptt) cc_final: 0.8666 (tptt) outliers start: 28 outliers final: 20 residues processed: 101 average time/residue: 0.0865 time to fit residues: 13.3550 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 : 0.442 ------------------------------------------------------------------------------- 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 445 ASP 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 44 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 18 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 chunk 95 optimal weight: 9.9990 chunk 2 optimal weight: 0.2980 chunk 76 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 7 optimal weight: 0.0570 chunk 37 optimal weight: 0.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.132235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.082740 restraints weight = 16698.054| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.95 r_work: 0.2974 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1759 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 : 0.547 7.908 14132 Z= 0.265 Chirality : 0.036 0.161 1598 Planarity : 0.004 0.055 1549 Dihedral : 18.120 94.447 2287 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.56 % Allowed : 23.52 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.27), residues: 1007 helix: 1.55 (0.27), residues: 372 sheet: -0.33 (0.36), residues: 228 loop : -1.06 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 442 TYR 0.008 0.001 TYR A 316 PHE 0.024 0.001 PHE A 340 TRP 0.010 0.002 TRP B 547 HIS 0.002 0.000 HIS B 114 Details of bonding type rmsd covalent geometry : bond 0.00235 (10193) covalent geometry : angle 0.54663 (14132) hydrogen bonds : bond 0.03611 ( 445) hydrogen bonds : angle 4.33090 ( 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 : 0.369 Fit side-chains REVERT: A 285 THR cc_start: 0.8775 (m) cc_final: 0.8503 (p) REVERT: A 445 ASP cc_start: 0.8955 (OUTLIER) cc_final: 0.8734 (p0) REVERT: A 477 ARG cc_start: 0.7873 (ttm-80) cc_final: 0.7650 (mtm-85) REVERT: A 494 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7529 (tp30) REVERT: A 527 MET cc_start: 0.7706 (ppp) cc_final: 0.7200 (ppp) REVERT: A 573 MET cc_start: 0.8851 (mmm) cc_final: 0.8581 (mmm) REVERT: B 123 ASP cc_start: 0.8401 (p0) cc_final: 0.7935 (p0) REVERT: B 407 LYS cc_start: 0.9012 (mptt) cc_final: 0.8608 (tptt) outliers start: 23 outliers final: 18 residues processed: 95 average time/residue: 0.0873 time to fit residues: 12.6631 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 : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 445 ASP 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 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: 7.9990 chunk 20 optimal weight: 0.0870 chunk 105 optimal weight: 30.0000 chunk 92 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 47 optimal weight: 0.0870 chunk 24 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.5336 ------------------------------------------------------------------------------- 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 = 0.3960 r_free = 0.3960 target = 0.132565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.083105 restraints weight = 16533.481| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.94 r_work: 0.2954 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10193 Z= 0.106 Angle : 0.543 8.297 14132 Z= 0.264 Chirality : 0.036 0.154 1598 Planarity : 0.004 0.056 1549 Dihedral : 18.061 94.621 2287 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.45 % Allowed : 23.63 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.27), residues: 1007 helix: 1.61 (0.27), residues: 372 sheet: -0.31 (0.36), residues: 228 loop : -1.01 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 247 TYR 0.007 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 covalent geometry : bond 0.00241 (10193) covalent geometry : angle 0.54303 (14132) hydrogen bonds : bond 0.03596 ( 445) hydrogen bonds : angle 4.29182 ( 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 101 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 79 time to evaluate : 0.370 Fit side-chains REVERT: A 285 THR cc_start: 0.8761 (m) cc_final: 0.8457 (p) REVERT: A 445 ASP cc_start: 0.8948 (OUTLIER) cc_final: 0.8724 (p0) REVERT: A 451 PHE cc_start: 0.8897 (m-80) cc_final: 0.8625 (m-80) REVERT: A 477 ARG cc_start: 0.7825 (ttm-80) cc_final: 0.7607 (mtm-85) REVERT: A 527 MET cc_start: 0.7663 (ppp) cc_final: 0.7261 (ppp) REVERT: A 573 MET cc_start: 0.8825 (mmm) cc_final: 0.8567 (mmm) REVERT: B 123 ASP cc_start: 0.8352 (p0) cc_final: 0.7906 (p0) REVERT: B 407 LYS cc_start: 0.8980 (mptt) cc_final: 0.8562 (tptt) REVERT: B 434 CYS cc_start: 0.7408 (p) cc_final: 0.7133 (p) outliers start: 22 outliers final: 19 residues processed: 98 average time/residue: 0.0878 time to fit residues: 13.0566 Evaluate side-chains 98 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 452 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 97 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 104 optimal weight: 10.0000 chunk 4 optimal weight: 0.2980 chunk 17 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 102 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 25 optimal weight: 0.1980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3960 r_free = 0.3960 target = 0.133229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.083155 restraints weight = 16790.374| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 3.06 r_work: 0.2964 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1886 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= 0.102 Angle : 0.539 8.918 14132 Z= 0.260 Chirality : 0.036 0.150 1598 Planarity : 0.004 0.055 1549 Dihedral : 18.011 94.736 2286 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.56 % Allowed : 23.30 % Favored : 74.14 % 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 aren not related in a simple way. whole: 0.19 (0.27), residues: 1007 helix: 1.64 (0.27), residues: 372 sheet: -0.30 (0.36), residues: 228 loop : -1.01 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 247 TYR 0.007 0.001 TYR B 231 PHE 0.024 0.001 PHE A 340 TRP 0.010 0.001 TRP B 547 HIS 0.001 0.000 HIS A 476 Details of bonding type rmsd covalent geometry : bond 0.00232 (10193) covalent geometry : angle 0.53910 (14132) hydrogen bonds : bond 0.03555 ( 445) hydrogen bonds : angle 4.22288 ( 1194) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2534.68 seconds wall clock time: 44 minutes 2.77 seconds (2642.77 seconds total)