Starting phenix.real_space_refine on Wed Mar 4 07:05:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qe5_13930/03_2026/7qe5_13930_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qe5_13930/03_2026/7qe5_13930.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7qe5_13930/03_2026/7qe5_13930_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qe5_13930/03_2026/7qe5_13930_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7qe5_13930/03_2026/7qe5_13930.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qe5_13930/03_2026/7qe5_13930.map" } resolution = 4.7 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= 0.001 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 37 5.16 5 C 3793 2.51 5 N 905 2.21 5 O 985 1.98 5 H 5932 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11652 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 9794 Classifications: {'peptide': 616} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 588} Chain: "B" Number of atoms: 1858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1858 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain breaks: 1 Time building chain proxies: 1.81, per 1000 atoms: 0.16 Number of scatterers: 11652 At special positions: 0 Unit cell: (108.36, 94.6, 86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 37 16.00 O 985 8.00 N 905 7.00 C 3793 6.00 H 5932 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 460 " - pdb=" SG CYS B 534 " distance=2.06 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: 0.99 Conformation dependent library (CDL) restraints added in 276.8 milliseconds 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1360 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 2 sheets defined 74.9% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 1 through 5 Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.527A pdb=" N LEU A 28 " --> pdb=" O ILE A 24 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN A 31 " --> pdb=" O ILE A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 62 removed outlier: 3.661A pdb=" N GLU A 42 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LYS A 45 " --> pdb=" O GLU A 41 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 46 " --> pdb=" O GLU A 42 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL A 49 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 75 removed outlier: 3.873A pdb=" N ASN A 73 " --> pdb=" O ASP A 69 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 74 " --> pdb=" O PHE A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 107 removed outlier: 3.884A pdb=" N PHE A 96 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN A 107 " --> pdb=" O ILE A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 117 Processing helix chain 'A' and resid 121 through 149 removed outlier: 4.355A pdb=" N PHE A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU A 128 " --> pdb=" O ILE A 124 " (cutoff:3.500A) Proline residue: A 129 - end of helix Processing helix chain 'A' and resid 155 through 173 removed outlier: 4.073A pdb=" N PHE A 159 " --> pdb=" O PRO A 155 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 179 Processing helix chain 'A' and resid 180 through 186 removed outlier: 6.301A pdb=" N SER A 183 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASN A 184 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ILE A 186 " --> pdb=" O SER A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 190 No H-bonds generated for 'chain 'A' and resid 188 through 190' Processing helix chain 'A' and resid 191 through 206 Processing helix chain 'A' and resid 209 through 225 removed outlier: 3.720A pdb=" N PHE A 222 " --> pdb=" O THR A 218 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N MET A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 241 removed outlier: 3.879A pdb=" N THR A 234 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N VAL A 238 " --> pdb=" O THR A 234 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR A 239 " --> pdb=" O GLU A 235 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 262 removed outlier: 4.109A pdb=" N ALA A 248 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL A 249 " --> pdb=" O PRO A 245 " (cutoff:3.500A) Proline residue: A 250 - end of helix Processing helix chain 'A' and resid 263 through 276 removed outlier: 4.280A pdb=" N ARG A 267 " --> pdb=" O GLY A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 299 removed outlier: 4.137A pdb=" N LEU A 292 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU A 293 " --> pdb=" O GLY A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 320 removed outlier: 5.585A pdb=" N GLN A 310 " --> pdb=" O GLY A 306 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N LEU A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 340 removed outlier: 3.504A pdb=" N GLY A 337 " --> pdb=" O SER A 333 " (cutoff:3.500A) Proline residue: A 338 - end of helix Processing helix chain 'A' and resid 343 through 354 Processing helix chain 'A' and resid 356 through 387 removed outlier: 3.501A pdb=" N LEU A 360 " --> pdb=" O SER A 356 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA A 363 " --> pdb=" O LYS A 359 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ILE A 366 " --> pdb=" O ILE A 362 " (cutoff:3.500A) Proline residue: A 367 - end of helix removed outlier: 4.247A pdb=" N LYS A 385 " --> pdb=" O ARG A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 422 removed outlier: 4.229A pdb=" N TRP A 408 " --> pdb=" O LYS A 404 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ALA A 409 " --> pdb=" O GLN A 405 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU A 411 " --> pdb=" O PHE A 407 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N THR A 412 " --> pdb=" O TRP A 408 " (cutoff:3.500A) Proline residue: A 413 - end of helix removed outlier: 3.574A pdb=" N ILE A 416 " --> pdb=" O THR A 412 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE A 420 " --> pdb=" O ILE A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 445 Processing helix chain 'A' and resid 452 through 486 removed outlier: 3.537A pdb=" N GLU A 460 " --> pdb=" O ASN A 456 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A 467 " --> pdb=" O ALA A 463 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASP A 480 " --> pdb=" O THR A 476 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N MET A 481 " --> pdb=" O PHE A 477 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ALA A 483 " --> pdb=" O GLY A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 497 removed outlier: 3.738A pdb=" N ARG A 490 " --> pdb=" O GLN A 486 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL A 494 " --> pdb=" O ARG A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 518 removed outlier: 3.504A pdb=" N VAL A 505 " --> pdb=" O SER A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 540 removed outlier: 5.206A pdb=" N PHE A 527 " --> pdb=" O LEU A 523 " (cutoff:3.500A) Proline residue: A 531 - end of helix Proline residue: A 535 - end of helix Processing helix chain 'A' and resid 543 through 560 removed outlier: 3.504A pdb=" N VAL A 549 " --> pdb=" O ILE A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 576 removed outlier: 3.783A pdb=" N PHE A 569 " --> pdb=" O GLY A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 587 removed outlier: 3.652A pdb=" N LYS A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 603 removed outlier: 3.578A pdb=" N VAL A 593 " --> pdb=" O PHE A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 615 removed outlier: 4.141A pdb=" N VAL A 610 " --> pdb=" O ILE A 606 " (cutoff:3.500A) Proline residue: A 611 - end of helix Processing helix chain 'B' and resid 525 through 529 Processing sheet with id=AA1, first strand: chain 'B' and resid 38 through 40 removed outlier: 3.708A pdb=" N LEU B 456 " --> pdb=" O MET B 521 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 473 through 477 removed outlier: 4.384A pdb=" N ALA B 530 " --> pdb=" O VAL B 559 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL B 559 " --> pdb=" O ALA B 530 " (cutoff:3.500A) 366 hydrogen bonds defined for protein. 1068 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.14 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.13: 5927 1.13 - 1.30: 903 1.30 - 1.48: 2290 1.48 - 1.65: 2601 1.65 - 1.83: 67 Bond restraints: 11788 Sorted by residual: bond pdb=" N ARG B 483 " pdb=" H ARG B 483 " ideal model delta sigma weight residual 0.860 1.036 -0.176 2.00e-02 2.50e+03 7.78e+01 bond pdb=" N SER B 543 " pdb=" H SER B 543 " ideal model delta sigma weight residual 0.860 1.036 -0.176 2.00e-02 2.50e+03 7.76e+01 bond pdb=" N ARG A 80 " pdb=" H ARG A 80 " ideal model delta sigma weight residual 0.860 1.036 -0.176 2.00e-02 2.50e+03 7.76e+01 bond pdb=" N TYR B 552 " pdb=" H TYR B 552 " ideal model delta sigma weight residual 0.860 1.036 -0.176 2.00e-02 2.50e+03 7.75e+01 bond pdb=" N TRP B 553 " pdb=" H TRP B 553 " ideal model delta sigma weight residual 0.860 1.036 -0.176 2.00e-02 2.50e+03 7.75e+01 ... (remaining 11783 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.65: 20286 4.65 - 9.31: 1049 9.31 - 13.96: 36 13.96 - 18.62: 4 18.62 - 23.27: 1 Bond angle restraints: 21376 Sorted by residual: angle pdb=" C TYR B 550 " pdb=" CA TYR B 550 " pdb=" CB TYR B 550 " ideal model delta sigma weight residual 110.68 87.41 23.27 1.70e+00 3.46e-01 1.87e+02 angle pdb=" CA ASP B 471 " pdb=" CB ASP B 471 " pdb=" CG ASP B 471 " ideal model delta sigma weight residual 112.60 122.37 -9.77 1.00e+00 1.00e+00 9.55e+01 angle pdb=" C PRO A 76 " pdb=" CA PRO A 76 " pdb=" CB PRO A 76 " ideal model delta sigma weight residual 111.22 97.57 13.65 1.51e+00 4.39e-01 8.17e+01 angle pdb=" CA PHE A 222 " pdb=" CB PHE A 222 " pdb=" CG PHE A 222 " ideal model delta sigma weight residual 113.80 122.71 -8.91 1.00e+00 1.00e+00 7.94e+01 angle pdb=" N TYR B 552 " pdb=" CA TYR B 552 " pdb=" C TYR B 552 " ideal model delta sigma weight residual 108.14 121.26 -13.12 1.52e+00 4.33e-01 7.45e+01 ... (remaining 21371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 4908 17.40 - 34.79: 394 34.79 - 52.19: 113 52.19 - 69.58: 116 69.58 - 86.98: 11 Dihedral angle restraints: 5542 sinusoidal: 2956 harmonic: 2586 Sorted by residual: dihedral pdb=" C TYR B 550 " pdb=" N TYR B 550 " pdb=" CA TYR B 550 " pdb=" CB TYR B 550 " ideal model delta harmonic sigma weight residual -122.60 -103.61 -18.99 0 2.50e+00 1.60e-01 5.77e+01 dihedral pdb=" C ILE A 615 " pdb=" N ILE A 615 " pdb=" CA ILE A 615 " pdb=" CB ILE A 615 " ideal model delta harmonic sigma weight residual -122.00 -139.87 17.87 0 2.50e+00 1.60e-01 5.11e+01 dihedral pdb=" CD ARG B 536 " pdb=" NE ARG B 536 " pdb=" CZ ARG B 536 " pdb=" NH1 ARG B 536 " ideal model delta sinusoidal sigma weight residual 0.00 57.93 -57.93 1 1.00e+01 1.00e-02 4.50e+01 ... (remaining 5539 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 706 0.112 - 0.224: 195 0.224 - 0.336: 33 0.336 - 0.448: 7 0.448 - 0.560: 2 Chirality restraints: 943 Sorted by residual: chirality pdb=" CA ILE A 615 " pdb=" N ILE A 615 " pdb=" C ILE A 615 " pdb=" CB ILE A 615 " both_signs ideal model delta sigma weight residual False 2.43 1.87 0.56 2.00e-01 2.50e+01 7.85e+00 chirality pdb=" CA GLN A 143 " pdb=" N GLN A 143 " pdb=" C GLN A 143 " pdb=" CB GLN A 143 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.77e+00 chirality pdb=" CA HIS B 470 " pdb=" N HIS B 470 " pdb=" C HIS B 470 " pdb=" CB HIS B 470 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.66e+00 ... (remaining 940 not shown) Planarity restraints: 1680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 536 " 1.338 9.50e-02 1.11e+02 4.59e-01 4.67e+02 pdb=" NE ARG B 536 " 0.132 2.00e-02 2.50e+03 pdb=" CZ ARG B 536 " -0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG B 536 " -0.038 2.00e-02 2.50e+03 pdb=" NH2 ARG B 536 " -0.068 2.00e-02 2.50e+03 pdb="HH11 ARG B 536 " -0.187 2.00e-02 2.50e+03 pdb="HH12 ARG B 536 " 0.149 2.00e-02 2.50e+03 pdb="HH21 ARG B 536 " -0.128 2.00e-02 2.50e+03 pdb="HH22 ARG B 536 " 0.100 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 546 " -0.124 2.00e-02 2.50e+03 1.36e-01 2.78e+02 pdb=" CG ASN B 546 " 0.003 2.00e-02 2.50e+03 pdb=" OD1 ASN B 546 " 0.143 2.00e-02 2.50e+03 pdb=" ND2 ASN B 546 " -0.076 2.00e-02 2.50e+03 pdb="HD21 ASN B 546 " 0.211 2.00e-02 2.50e+03 pdb="HD22 ASN B 546 " -0.157 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 477 " -0.128 2.00e-02 2.50e+03 1.23e-01 2.27e+02 pdb=" CD GLN B 477 " 0.020 2.00e-02 2.50e+03 pdb=" OE1 GLN B 477 " 0.103 2.00e-02 2.50e+03 pdb=" NE2 GLN B 477 " 0.083 2.00e-02 2.50e+03 pdb="HE21 GLN B 477 " 0.125 2.00e-02 2.50e+03 pdb="HE22 GLN B 477 " -0.203 2.00e-02 2.50e+03 ... (remaining 1677 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 725 2.19 - 2.79: 21236 2.79 - 3.39: 33116 3.39 - 4.00: 41706 4.00 - 4.60: 60408 Nonbonded interactions: 157191 Sorted by model distance: nonbonded pdb=" O THR A 330 " pdb=" HG SER A 333 " model vdw 1.586 2.450 nonbonded pdb=" HG SER A 426 " pdb=" OE2 GLU A 429 " model vdw 1.609 2.450 nonbonded pdb=" HH TYR A 221 " pdb=" OE2 GLU A 485 " model vdw 1.616 2.450 nonbonded pdb=" O LEU A 54 " pdb=" HG SER A 57 " model vdw 1.622 2.450 nonbonded pdb=" OD1 ASP B 468 " pdb=" HG SER B 491 " model vdw 1.632 2.450 ... (remaining 157186 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.580 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 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 : 0.013 0.092 5857 Z= 0.801 Angle : 2.056 23.272 7957 Z= 1.372 Chirality : 0.108 0.560 943 Planarity : 0.023 0.473 973 Dihedral : 14.367 86.978 2058 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.77 % Favored : 94.96 % Rotamer: Outliers : 1.14 % Allowed : 8.28 % Favored : 90.58 % Cbeta Deviations : 2.50 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.59 (0.26), residues: 734 helix: -1.69 (0.18), residues: 471 sheet: -1.82 (1.41), residues: 15 loop : -1.37 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.002 ARG B 536 TYR 0.152 0.026 TYR A 252 PHE 0.107 0.015 PHE A 48 TRP 0.099 0.023 TRP A 227 HIS 0.010 0.004 HIS A 65 Details of bonding type rmsd covalent geometry : bond 0.01316 ( 5856) covalent geometry : angle 2.05573 ( 7955) SS BOND : bond 0.02687 ( 1) SS BOND : angle 1.06634 ( 2) hydrogen bonds : bond 0.18515 ( 366) hydrogen bonds : angle 8.15751 ( 1068) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 214 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ILE cc_start: 0.9196 (tp) cc_final: 0.8803 (tp) REVERT: A 63 GLN cc_start: 0.8598 (tp40) cc_final: 0.7812 (mt0) REVERT: A 78 LYS cc_start: 0.2644 (OUTLIER) cc_final: 0.2334 (tmtt) REVERT: A 97 LEU cc_start: 0.8563 (mm) cc_final: 0.8353 (mm) REVERT: A 158 PHE cc_start: 0.7614 (t80) cc_final: 0.7232 (t80) REVERT: A 283 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7476 (mmt) REVERT: A 311 LEU cc_start: 0.9073 (mm) cc_final: 0.8404 (mm) REVERT: A 317 ARG cc_start: 0.9302 (ttt180) cc_final: 0.8823 (ttp80) REVERT: A 339 LEU cc_start: 0.8426 (mt) cc_final: 0.8178 (mt) REVERT: A 518 MET cc_start: 0.8796 (mtm) cc_final: 0.8453 (mtm) REVERT: A 556 MET cc_start: 0.8388 (mtp) cc_final: 0.8035 (mtp) REVERT: A 589 PHE cc_start: 0.8610 (m-80) cc_final: 0.8246 (m-80) outliers start: 7 outliers final: 3 residues processed: 218 average time/residue: 0.1410 time to fit residues: 41.5481 Evaluate side-chains 189 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 184 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS B 35 GLN ** B 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.106108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.090353 restraints weight = 63639.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.094559 restraints weight = 33455.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.097330 restraints weight = 20538.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.099253 restraints weight = 13815.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.100691 restraints weight = 9978.141| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5857 Z= 0.223 Angle : 0.823 8.329 7957 Z= 0.467 Chirality : 0.045 0.177 943 Planarity : 0.009 0.162 973 Dihedral : 7.840 30.935 787 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.22 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.28), residues: 734 helix: -0.77 (0.21), residues: 471 sheet: -1.88 (0.84), residues: 35 loop : -1.37 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 267 TYR 0.037 0.003 TYR B 550 PHE 0.027 0.002 PHE A 361 TRP 0.019 0.002 TRP B 553 HIS 0.010 0.003 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00446 ( 5856) covalent geometry : angle 0.82287 ( 7955) SS BOND : bond 0.00895 ( 1) SS BOND : angle 0.42290 ( 2) hydrogen bonds : bond 0.07367 ( 366) hydrogen bonds : angle 5.79832 ( 1068) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ILE cc_start: 0.9553 (tp) cc_final: 0.9215 (tp) REVERT: A 158 PHE cc_start: 0.7562 (t80) cc_final: 0.7156 (t80) REVERT: A 235 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7495 (tm-30) REVERT: A 236 LYS cc_start: 0.8714 (ttmt) cc_final: 0.7802 (mmmt) REVERT: A 258 LEU cc_start: 0.9163 (mt) cc_final: 0.8888 (mt) REVERT: A 259 MET cc_start: 0.9303 (tpp) cc_final: 0.9084 (tpp) REVERT: A 285 HIS cc_start: 0.8706 (m-70) cc_final: 0.8408 (m170) REVERT: A 304 ASP cc_start: 0.9265 (m-30) cc_final: 0.8862 (m-30) REVERT: A 311 LEU cc_start: 0.9315 (mm) cc_final: 0.9076 (mm) REVERT: A 518 MET cc_start: 0.9208 (mtm) cc_final: 0.8776 (mtm) REVERT: A 527 PHE cc_start: 0.8732 (m-80) cc_final: 0.7914 (m-80) REVERT: A 532 MET cc_start: 0.9229 (pmm) cc_final: 0.8423 (pmm) REVERT: A 533 LEU cc_start: 0.8902 (mt) cc_final: 0.8415 (mt) REVERT: A 555 MET cc_start: 0.9294 (mmt) cc_final: 0.9020 (tpp) REVERT: B 505 ARG cc_start: 0.8740 (mmm160) cc_final: 0.8478 (mmp80) REVERT: B 534 CYS cc_start: -0.0374 (p) cc_final: -0.0877 (p) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.1337 time to fit residues: 35.8477 Evaluate side-chains 174 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 0.2980 chunk 2 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 558 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.104643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.089121 restraints weight = 66449.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.093254 restraints weight = 34801.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.096066 restraints weight = 21334.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.097940 restraints weight = 14382.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.099344 restraints weight = 10373.141| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.4661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 5857 Z= 0.210 Angle : 0.720 7.170 7957 Z= 0.411 Chirality : 0.042 0.167 943 Planarity : 0.007 0.104 973 Dihedral : 7.150 29.803 787 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.77 % Favored : 95.10 % Rotamer: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.29), residues: 734 helix: -0.37 (0.22), residues: 466 sheet: -1.09 (0.82), residues: 47 loop : -1.68 (0.41), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 80 TYR 0.024 0.003 TYR A 349 PHE 0.023 0.002 PHE A 98 TRP 0.019 0.002 TRP B 544 HIS 0.009 0.003 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 5856) covalent geometry : angle 0.71998 ( 7955) SS BOND : bond 0.01245 ( 1) SS BOND : angle 1.13238 ( 2) hydrogen bonds : bond 0.05922 ( 366) hydrogen bonds : angle 5.37202 ( 1068) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.9518 (mttm) cc_final: 0.9079 (mmmt) REVERT: A 158 PHE cc_start: 0.7832 (t80) cc_final: 0.7356 (t80) REVERT: A 204 MET cc_start: 0.8819 (mmm) cc_final: 0.8563 (mmm) REVERT: A 214 LEU cc_start: 0.9200 (mp) cc_final: 0.8775 (mm) REVERT: A 235 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7970 (tm-30) REVERT: A 304 ASP cc_start: 0.9250 (m-30) cc_final: 0.8806 (m-30) REVERT: A 311 LEU cc_start: 0.9360 (mm) cc_final: 0.9101 (mm) REVERT: A 330 THR cc_start: 0.9106 (t) cc_final: 0.8899 (t) REVERT: A 405 GLN cc_start: 0.8929 (pt0) cc_final: 0.8451 (tm-30) REVERT: A 518 MET cc_start: 0.9203 (mtm) cc_final: 0.8856 (mtm) REVERT: A 532 MET cc_start: 0.9150 (pmm) cc_final: 0.8315 (pmm) REVERT: A 533 LEU cc_start: 0.8919 (mt) cc_final: 0.8407 (mt) REVERT: A 555 MET cc_start: 0.9332 (mmt) cc_final: 0.8963 (tpp) REVERT: A 589 PHE cc_start: 0.9177 (m-10) cc_final: 0.8886 (m-10) REVERT: B 534 CYS cc_start: 0.0020 (p) cc_final: -0.0557 (p) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.1375 time to fit residues: 36.7507 Evaluate side-chains 176 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 59 optimal weight: 0.2980 chunk 9 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 44 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.106465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.089918 restraints weight = 61591.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.094464 restraints weight = 30934.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.097598 restraints weight = 18334.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.099627 restraints weight = 11990.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.101122 restraints weight = 8462.736| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.5196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5857 Z= 0.139 Angle : 0.616 6.174 7957 Z= 0.343 Chirality : 0.040 0.157 943 Planarity : 0.007 0.108 973 Dihedral : 6.519 27.988 787 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.63 % Favored : 95.23 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.30), residues: 734 helix: 0.14 (0.23), residues: 463 sheet: -1.38 (0.86), residues: 44 loop : -1.21 (0.42), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 536 TYR 0.015 0.002 TYR B 550 PHE 0.021 0.002 PHE A 98 TRP 0.010 0.001 TRP B 553 HIS 0.006 0.002 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 5856) covalent geometry : angle 0.61615 ( 7955) SS BOND : bond 0.00932 ( 1) SS BOND : angle 1.23922 ( 2) hydrogen bonds : bond 0.05138 ( 366) hydrogen bonds : angle 4.91259 ( 1068) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LEU cc_start: 0.9335 (tp) cc_final: 0.9106 (tp) REVERT: A 45 LYS cc_start: 0.9487 (mttm) cc_final: 0.9063 (mmmt) REVERT: A 158 PHE cc_start: 0.7733 (t80) cc_final: 0.7377 (t80) REVERT: A 214 LEU cc_start: 0.9257 (mp) cc_final: 0.8835 (mm) REVERT: A 235 GLU cc_start: 0.8314 (tm-30) cc_final: 0.7714 (tm-30) REVERT: A 236 LYS cc_start: 0.8861 (ttmt) cc_final: 0.7814 (mmtt) REVERT: A 259 MET cc_start: 0.9037 (tpp) cc_final: 0.8367 (tpp) REVERT: A 285 HIS cc_start: 0.8706 (m-70) cc_final: 0.8420 (m170) REVERT: A 304 ASP cc_start: 0.9159 (m-30) cc_final: 0.8772 (m-30) REVERT: A 311 LEU cc_start: 0.9332 (mm) cc_final: 0.9121 (mm) REVERT: A 316 MET cc_start: 0.8601 (mmm) cc_final: 0.8312 (mmm) REVERT: A 330 THR cc_start: 0.9110 (t) cc_final: 0.8878 (t) REVERT: A 405 GLN cc_start: 0.8984 (pt0) cc_final: 0.8231 (tm-30) REVERT: A 489 MET cc_start: 0.8781 (mmm) cc_final: 0.8525 (mmm) REVERT: A 518 MET cc_start: 0.9251 (mtm) cc_final: 0.8848 (mtm) REVERT: A 532 MET cc_start: 0.9059 (pmm) cc_final: 0.8238 (pmm) REVERT: A 533 LEU cc_start: 0.8866 (mt) cc_final: 0.8354 (mt) REVERT: A 539 GLN cc_start: 0.8570 (tp-100) cc_final: 0.7971 (tp40) REVERT: A 550 MET cc_start: 0.8684 (tmm) cc_final: 0.8193 (tmm) REVERT: A 589 PHE cc_start: 0.9224 (m-10) cc_final: 0.8939 (m-10) outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.1288 time to fit residues: 35.7498 Evaluate side-chains 183 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 16 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 68 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 14 optimal weight: 0.4980 chunk 9 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 520 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.105474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.090110 restraints weight = 64229.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.094253 restraints weight = 34197.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.097086 restraints weight = 20973.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.099001 restraints weight = 14045.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.100522 restraints weight = 10084.548| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.5560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 5857 Z= 0.143 Angle : 0.604 7.424 7957 Z= 0.335 Chirality : 0.040 0.175 943 Planarity : 0.006 0.082 973 Dihedral : 6.233 28.071 787 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.77 % Favored : 95.10 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.30), residues: 734 helix: 0.27 (0.23), residues: 463 sheet: -1.43 (0.85), residues: 44 loop : -1.19 (0.42), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 536 TYR 0.027 0.002 TYR B 540 PHE 0.014 0.001 PHE A 98 TRP 0.008 0.001 TRP B 553 HIS 0.004 0.001 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 5856) covalent geometry : angle 0.60394 ( 7955) SS BOND : bond 0.00600 ( 1) SS BOND : angle 1.74497 ( 2) hydrogen bonds : bond 0.04772 ( 366) hydrogen bonds : angle 4.78662 ( 1068) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LEU cc_start: 0.9333 (tp) cc_final: 0.9099 (tp) REVERT: A 45 LYS cc_start: 0.9518 (mttm) cc_final: 0.9175 (mtpt) REVERT: A 158 PHE cc_start: 0.7741 (t80) cc_final: 0.7395 (t80) REVERT: A 304 ASP cc_start: 0.9146 (m-30) cc_final: 0.8787 (m-30) REVERT: A 311 LEU cc_start: 0.9327 (mm) cc_final: 0.9085 (mm) REVERT: A 330 THR cc_start: 0.9124 (t) cc_final: 0.8902 (t) REVERT: A 405 GLN cc_start: 0.8993 (pt0) cc_final: 0.8211 (tm-30) REVERT: A 467 VAL cc_start: 0.9237 (p) cc_final: 0.8988 (m) REVERT: A 518 MET cc_start: 0.9176 (mtm) cc_final: 0.8739 (mtm) REVERT: A 532 MET cc_start: 0.8971 (pmm) cc_final: 0.8217 (pmm) REVERT: A 550 MET cc_start: 0.8829 (tmm) cc_final: 0.8294 (tmm) REVERT: A 566 MET cc_start: 0.8924 (ttt) cc_final: 0.8371 (mtp) REVERT: A 589 PHE cc_start: 0.9184 (m-10) cc_final: 0.8885 (m-10) REVERT: B 534 CYS cc_start: -0.0158 (p) cc_final: -0.1214 (p) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.1223 time to fit residues: 33.3718 Evaluate side-chains 182 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 49 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 71 optimal weight: 0.4980 chunk 53 optimal weight: 0.3980 chunk 46 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.105543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.090085 restraints weight = 64493.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.094203 restraints weight = 34251.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.097051 restraints weight = 21029.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.098985 restraints weight = 14156.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.100387 restraints weight = 10077.571| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.5862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5857 Z= 0.146 Angle : 0.619 7.475 7957 Z= 0.340 Chirality : 0.040 0.162 943 Planarity : 0.006 0.080 973 Dihedral : 6.090 30.896 787 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.77 % Favored : 95.10 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.30), residues: 734 helix: 0.36 (0.23), residues: 464 sheet: -1.39 (0.85), residues: 44 loop : -1.18 (0.41), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 536 TYR 0.025 0.002 TYR A 349 PHE 0.039 0.002 PHE A 361 TRP 0.009 0.001 TRP B 553 HIS 0.003 0.001 HIS A 100 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 5856) covalent geometry : angle 0.61914 ( 7955) SS BOND : bond 0.00970 ( 1) SS BOND : angle 1.23353 ( 2) hydrogen bonds : bond 0.04603 ( 366) hydrogen bonds : angle 4.72298 ( 1068) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LEU cc_start: 0.9339 (tp) cc_final: 0.9111 (tp) REVERT: A 45 LYS cc_start: 0.9519 (mttm) cc_final: 0.9152 (mmmt) REVERT: A 158 PHE cc_start: 0.7732 (t80) cc_final: 0.7373 (t80) REVERT: A 259 MET cc_start: 0.9012 (tpp) cc_final: 0.8372 (tpp) REVERT: A 304 ASP cc_start: 0.9158 (m-30) cc_final: 0.8850 (m-30) REVERT: A 311 LEU cc_start: 0.9329 (mm) cc_final: 0.9080 (mm) REVERT: A 330 THR cc_start: 0.9151 (t) cc_final: 0.8918 (t) REVERT: A 405 GLN cc_start: 0.9112 (pt0) cc_final: 0.8224 (tm-30) REVERT: A 471 MET cc_start: 0.8598 (tpp) cc_final: 0.8278 (tpp) REVERT: A 518 MET cc_start: 0.9170 (mtm) cc_final: 0.8770 (mtm) REVERT: A 532 MET cc_start: 0.8907 (pmm) cc_final: 0.8134 (pmm) REVERT: A 550 MET cc_start: 0.8941 (tmm) cc_final: 0.8402 (tmm) REVERT: A 566 MET cc_start: 0.8925 (ttt) cc_final: 0.8372 (mtp) REVERT: B 534 CYS cc_start: 0.0228 (p) cc_final: -0.0273 (p) REVERT: B 546 ASN cc_start: 0.8462 (t0) cc_final: 0.8072 (t0) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.1226 time to fit residues: 33.1205 Evaluate side-chains 179 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 8 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 26 optimal weight: 0.1980 chunk 13 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** 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 = 0.3639 r_free = 0.3639 target = 0.105668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.090370 restraints weight = 63908.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.094566 restraints weight = 33854.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.097416 restraints weight = 20680.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.099338 restraints weight = 13797.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.100715 restraints weight = 9822.311| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.6083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5857 Z= 0.142 Angle : 0.589 6.902 7957 Z= 0.327 Chirality : 0.040 0.198 943 Planarity : 0.006 0.083 973 Dihedral : 5.880 29.494 787 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.36 % Favored : 95.50 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.31), residues: 734 helix: 0.55 (0.23), residues: 462 sheet: -1.53 (0.84), residues: 44 loop : -1.26 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 536 TYR 0.030 0.002 TYR B 540 PHE 0.012 0.001 PHE A 48 TRP 0.007 0.001 TRP B 544 HIS 0.003 0.001 HIS A 100 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 5856) covalent geometry : angle 0.58937 ( 7955) SS BOND : bond 0.00878 ( 1) SS BOND : angle 0.83095 ( 2) hydrogen bonds : bond 0.04386 ( 366) hydrogen bonds : angle 4.66024 ( 1068) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LEU cc_start: 0.9314 (tp) cc_final: 0.9087 (tp) REVERT: A 45 LYS cc_start: 0.9528 (mttm) cc_final: 0.9159 (mmmt) REVERT: A 158 PHE cc_start: 0.7909 (t80) cc_final: 0.7552 (t80) REVERT: A 259 MET cc_start: 0.8972 (tpp) cc_final: 0.8171 (tpp) REVERT: A 304 ASP cc_start: 0.9162 (m-30) cc_final: 0.8874 (m-30) REVERT: A 311 LEU cc_start: 0.9369 (mm) cc_final: 0.9102 (mm) REVERT: A 316 MET cc_start: 0.8922 (mmm) cc_final: 0.8659 (mmm) REVERT: A 330 THR cc_start: 0.9172 (t) cc_final: 0.8939 (t) REVERT: A 346 MET cc_start: 0.9490 (tpp) cc_final: 0.8754 (tmm) REVERT: A 405 GLN cc_start: 0.9090 (pt0) cc_final: 0.8191 (tm-30) REVERT: A 518 MET cc_start: 0.9131 (mtm) cc_final: 0.8733 (mtm) REVERT: A 532 MET cc_start: 0.8923 (pmm) cc_final: 0.8172 (pmm) REVERT: A 550 MET cc_start: 0.8961 (tmm) cc_final: 0.8427 (tmm) REVERT: A 566 MET cc_start: 0.8906 (ttt) cc_final: 0.8357 (mtp) REVERT: B 534 CYS cc_start: 0.0150 (p) cc_final: -0.1145 (p) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.1307 time to fit residues: 37.2055 Evaluate side-chains 184 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 9 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 59 optimal weight: 0.4980 chunk 6 optimal weight: 0.0970 chunk 12 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.105731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.090419 restraints weight = 63283.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.094463 restraints weight = 34064.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.097377 restraints weight = 21250.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.099309 restraints weight = 14212.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.100707 restraints weight = 10074.003| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.6362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5857 Z= 0.133 Angle : 0.593 6.819 7957 Z= 0.324 Chirality : 0.039 0.171 943 Planarity : 0.006 0.083 973 Dihedral : 5.777 29.638 787 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.22 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.31), residues: 734 helix: 0.62 (0.23), residues: 464 sheet: -1.49 (0.83), residues: 44 loop : -1.22 (0.42), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 549 TYR 0.036 0.002 TYR B 540 PHE 0.011 0.001 PHE A 20 TRP 0.007 0.001 TRP B 553 HIS 0.004 0.001 HIS A 100 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 5856) covalent geometry : angle 0.59264 ( 7955) SS BOND : bond 0.00203 ( 1) SS BOND : angle 1.04154 ( 2) hydrogen bonds : bond 0.04233 ( 366) hydrogen bonds : angle 4.53147 ( 1068) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LEU cc_start: 0.9295 (tp) cc_final: 0.9068 (tp) REVERT: A 45 LYS cc_start: 0.9524 (mttm) cc_final: 0.8976 (mmmt) REVERT: A 158 PHE cc_start: 0.7904 (t80) cc_final: 0.7550 (t80) REVERT: A 236 LYS cc_start: 0.8965 (ttmt) cc_final: 0.8379 (tppt) REVERT: A 259 MET cc_start: 0.8817 (tpp) cc_final: 0.8067 (tpp) REVERT: A 304 ASP cc_start: 0.9161 (m-30) cc_final: 0.8878 (m-30) REVERT: A 311 LEU cc_start: 0.9354 (mm) cc_final: 0.9111 (mm) REVERT: A 316 MET cc_start: 0.8906 (mmm) cc_final: 0.8640 (mmm) REVERT: A 330 THR cc_start: 0.9183 (t) cc_final: 0.8945 (t) REVERT: A 346 MET cc_start: 0.9473 (tpp) cc_final: 0.8735 (tmm) REVERT: A 347 ILE cc_start: 0.9601 (pt) cc_final: 0.9373 (pt) REVERT: A 405 GLN cc_start: 0.9133 (pt0) cc_final: 0.8198 (tm-30) REVERT: A 518 MET cc_start: 0.9134 (mtm) cc_final: 0.8775 (mtm) REVERT: A 532 MET cc_start: 0.8943 (pmm) cc_final: 0.8225 (pmm) REVERT: A 550 MET cc_start: 0.8899 (tmm) cc_final: 0.8390 (tmm) REVERT: A 566 MET cc_start: 0.8902 (ttt) cc_final: 0.8384 (mtp) REVERT: B 534 CYS cc_start: 0.0464 (p) cc_final: -0.0062 (p) REVERT: B 546 ASN cc_start: 0.7936 (t0) cc_final: 0.7695 (t0) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.1204 time to fit residues: 33.3300 Evaluate side-chains 189 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 27 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 57 optimal weight: 0.3980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** 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 = 0.3623 r_free = 0.3623 target = 0.104284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.089148 restraints weight = 63047.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.093278 restraints weight = 32968.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.096148 restraints weight = 19927.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.098089 restraints weight = 13263.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.099416 restraints weight = 9359.695| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.6560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5857 Z= 0.145 Angle : 0.586 6.374 7957 Z= 0.325 Chirality : 0.040 0.183 943 Planarity : 0.005 0.082 973 Dihedral : 5.742 28.986 787 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.90 % Favored : 94.96 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.31), residues: 734 helix: 0.70 (0.24), residues: 458 sheet: -1.21 (0.83), residues: 44 loop : -1.29 (0.41), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 536 TYR 0.019 0.002 TYR B 550 PHE 0.017 0.001 PHE A 603 TRP 0.033 0.002 TRP A 227 HIS 0.004 0.001 HIS A 100 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 5856) covalent geometry : angle 0.58575 ( 7955) SS BOND : bond 0.01210 ( 1) SS BOND : angle 0.81369 ( 2) hydrogen bonds : bond 0.04121 ( 366) hydrogen bonds : angle 4.58729 ( 1068) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LEU cc_start: 0.9314 (tp) cc_final: 0.9080 (tp) REVERT: A 45 LYS cc_start: 0.9530 (mttm) cc_final: 0.9137 (mtpt) REVERT: A 158 PHE cc_start: 0.8029 (t80) cc_final: 0.7664 (t80) REVERT: A 200 TRP cc_start: 0.9411 (t60) cc_final: 0.8913 (t60) REVERT: A 236 LYS cc_start: 0.8954 (ttmt) cc_final: 0.8371 (tppt) REVERT: A 259 MET cc_start: 0.8861 (tpp) cc_final: 0.7935 (tpp) REVERT: A 304 ASP cc_start: 0.9106 (m-30) cc_final: 0.8880 (m-30) REVERT: A 311 LEU cc_start: 0.9369 (mm) cc_final: 0.9118 (mm) REVERT: A 316 MET cc_start: 0.8949 (mmm) cc_final: 0.8684 (mmm) REVERT: A 330 THR cc_start: 0.9200 (t) cc_final: 0.8961 (t) REVERT: A 346 MET cc_start: 0.9468 (tpp) cc_final: 0.8719 (tmm) REVERT: A 347 ILE cc_start: 0.9610 (pt) cc_final: 0.9369 (pt) REVERT: A 405 GLN cc_start: 0.9177 (pt0) cc_final: 0.8218 (tm-30) REVERT: A 471 MET cc_start: 0.8694 (tpp) cc_final: 0.8420 (tpp) REVERT: A 518 MET cc_start: 0.9140 (mtm) cc_final: 0.8796 (mtm) REVERT: A 532 MET cc_start: 0.8948 (pmm) cc_final: 0.8128 (pmm) REVERT: A 566 MET cc_start: 0.8847 (ttt) cc_final: 0.8319 (mtp) REVERT: B 534 CYS cc_start: 0.0185 (p) cc_final: -0.0367 (p) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.1257 time to fit residues: 34.6762 Evaluate side-chains 175 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 15 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 23 optimal weight: 0.0980 chunk 63 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.104017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.089039 restraints weight = 65668.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.093115 restraints weight = 34856.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.095919 restraints weight = 21415.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.097826 restraints weight = 14396.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.099185 restraints weight = 10194.969| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.6824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5857 Z= 0.142 Angle : 0.579 6.414 7957 Z= 0.320 Chirality : 0.039 0.170 943 Planarity : 0.005 0.080 973 Dihedral : 5.645 28.603 787 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.63 % Favored : 95.23 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.31), residues: 734 helix: 0.77 (0.24), residues: 465 sheet: -1.08 (0.85), residues: 44 loop : -1.38 (0.41), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 226 TYR 0.017 0.002 TYR B 550 PHE 0.013 0.001 PHE A 20 TRP 0.027 0.002 TRP A 227 HIS 0.004 0.001 HIS A 100 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 5856) covalent geometry : angle 0.57910 ( 7955) SS BOND : bond 0.00938 ( 1) SS BOND : angle 0.66786 ( 2) hydrogen bonds : bond 0.03999 ( 366) hydrogen bonds : angle 4.54884 ( 1068) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LEU cc_start: 0.9300 (tp) cc_final: 0.9088 (tp) REVERT: A 158 PHE cc_start: 0.8049 (t80) cc_final: 0.7688 (t80) REVERT: A 200 TRP cc_start: 0.9440 (t60) cc_final: 0.8906 (t60) REVERT: A 236 LYS cc_start: 0.8966 (ttmt) cc_final: 0.8374 (tppt) REVERT: A 259 MET cc_start: 0.8843 (tpp) cc_final: 0.7945 (tpp) REVERT: A 304 ASP cc_start: 0.9085 (m-30) cc_final: 0.8865 (m-30) REVERT: A 311 LEU cc_start: 0.9373 (mm) cc_final: 0.9115 (mm) REVERT: A 316 MET cc_start: 0.8991 (mmm) cc_final: 0.8705 (mmm) REVERT: A 329 ILE cc_start: 0.9353 (mm) cc_final: 0.8830 (tp) REVERT: A 346 MET cc_start: 0.9487 (tpp) cc_final: 0.8650 (tmm) REVERT: A 347 ILE cc_start: 0.9647 (pt) cc_final: 0.9344 (pt) REVERT: A 471 MET cc_start: 0.8730 (tpp) cc_final: 0.8410 (tpp) REVERT: A 518 MET cc_start: 0.9127 (mtm) cc_final: 0.8782 (mtm) REVERT: A 532 MET cc_start: 0.8936 (pmm) cc_final: 0.8110 (pmm) REVERT: A 566 MET cc_start: 0.8846 (ttt) cc_final: 0.8315 (mtp) REVERT: A 589 PHE cc_start: 0.9134 (m-10) cc_final: 0.8823 (m-80) REVERT: B 534 CYS cc_start: 0.0098 (p) cc_final: -0.0197 (p) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.1294 time to fit residues: 34.6422 Evaluate side-chains 176 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 58 optimal weight: 0.2980 chunk 31 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 46 optimal weight: 0.2980 chunk 63 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** 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 = 0.3626 r_free = 0.3626 target = 0.104649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.089446 restraints weight = 63519.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.093542 restraints weight = 34052.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.096389 restraints weight = 20945.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.098323 restraints weight = 14000.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.099686 restraints weight = 9984.513| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.6966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5857 Z= 0.124 Angle : 0.560 6.299 7957 Z= 0.306 Chirality : 0.039 0.169 943 Planarity : 0.005 0.080 973 Dihedral : 5.465 27.861 787 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.63 % Favored : 95.23 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.31), residues: 734 helix: 1.03 (0.24), residues: 455 sheet: -1.12 (0.83), residues: 44 loop : -1.27 (0.40), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 226 TYR 0.016 0.002 TYR B 550 PHE 0.013 0.001 PHE A 20 TRP 0.010 0.001 TRP A 39 HIS 0.004 0.001 HIS A 100 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 5856) covalent geometry : angle 0.55994 ( 7955) SS BOND : bond 0.01011 ( 1) SS BOND : angle 0.64119 ( 2) hydrogen bonds : bond 0.03848 ( 366) hydrogen bonds : angle 4.45420 ( 1068) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2235.08 seconds wall clock time: 38 minutes 41.68 seconds (2321.68 seconds total)