Starting phenix.real_space_refine on Fri Jul 3 17:36:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9p96_71400/07_2026/9p96_71400.cif Found real_map, /net/cci-nas-00/data/ceres_data/9p96_71400/07_2026/9p96_71400.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9p96_71400/07_2026/9p96_71400.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9p96_71400/07_2026/9p96_71400.map" model { file = "/net/cci-nas-00/data/ceres_data/9p96_71400/07_2026/9p96_71400.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9p96_71400/07_2026/9p96_71400.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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: 6 Type Number sf(0) Gaussians Ca 6 9.91 5 S 33 5.16 5 C 4678 2.51 5 N 1301 2.21 5 O 1428 1.98 5 H 7257 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14703 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 8964 Classifications: {'peptide': 587} Link IDs: {'PTRANS': 26, 'TRANS': 560} Chain: "B" Number of atoms: 5733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 5733 Classifications: {'peptide': 373} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 351} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Time building chain proxies: 2.52, per 1000 atoms: 0.17 Number of scatterers: 14703 At special positions: 0 Unit cell: (68.442, 115.566, 120.054, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 6 19.99 S 33 16.00 O 1428 8.00 N 1301 7.00 C 4678 6.00 H 7257 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 58 " - pdb=" SG CYS A 68 " distance=2.03 Simple disulfide: pdb=" SG CYS A 81 " - pdb=" SG CYS A 85 " distance=2.03 Simple disulfide: pdb=" SG CYS A 111 " - pdb=" SG CYS A 132 " distance=2.03 Simple disulfide: pdb=" SG CYS A 150 " - pdb=" SG CYS A 165 " distance=2.02 Simple disulfide: pdb=" SG CYS A 453 " - pdb=" SG CYS A 462 " distance=2.03 Simple disulfide: pdb=" SG CYS A 468 " - pdb=" SG CYS A 524 " distance=2.03 Simple disulfide: pdb=" SG CYS B 197 " - pdb=" SG CYS B 204 " distance=2.03 Simple disulfide: pdb=" SG CYS B 252 " - pdb=" SG CYS B 292 " distance=2.03 Simple disulfide: pdb=" SG CYS B 393 " - pdb=" SG CYS B 409 " distance=2.04 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: 1.10 Conformation dependent library (CDL) restraints added in 435.1 milliseconds 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1752 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 19 sheets defined 13.8% alpha, 29.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 140 through 144 Processing helix chain 'A' and resid 184 through 189 removed outlier: 3.893A pdb=" N TRP A 188 " --> pdb=" O GLY A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 245 Processing helix chain 'A' and resid 359 through 364 Processing helix chain 'A' and resid 388 through 390 No H-bonds generated for 'chain 'A' and resid 388 through 390' Processing helix chain 'B' and resid 142 through 144 No H-bonds generated for 'chain 'B' and resid 142 through 144' Processing helix chain 'B' and resid 145 through 153 Processing helix chain 'B' and resid 154 through 165 removed outlier: 4.590A pdb=" N ALA B 158 " --> pdb=" O GLN B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 194 removed outlier: 4.141A pdb=" N ARG B 194 " --> pdb=" O PRO B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 228 removed outlier: 3.504A pdb=" N PHE B 223 " --> pdb=" O ASP B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 252 Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.707A pdb=" N ILE B 256 " --> pdb=" O CYS B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 283 Processing helix chain 'B' and resid 300 through 304 removed outlier: 4.620A pdb=" N THR B 304 " --> pdb=" O SER B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 321 Processing helix chain 'B' and resid 333 through 342 removed outlier: 3.619A pdb=" N LYS B 342 " --> pdb=" O GLN B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 373 Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 removed outlier: 4.858A pdb=" N ILE A 405 " --> pdb=" O ASP A 414 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ALA A 416 " --> pdb=" O GLY A 403 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N GLY A 403 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N GLY A 418 " --> pdb=" O ILE A 401 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE A 401 " --> pdb=" O GLY A 418 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 22 through 28 removed outlier: 4.441A pdb=" N ILE A 55 " --> pdb=" O LEU A 71 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 88 removed outlier: 3.614A pdb=" N LYS A 116 " --> pdb=" O GLU A 88 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 97 through 100 removed outlier: 3.916A pdb=" N THR A 97 " --> pdb=" O CYS A 111 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 171 through 173 Processing sheet with id=AA6, first strand: chain 'A' and resid 234 through 239 removed outlier: 3.636A pdb=" N VAL A 235 " --> pdb=" O PHE A 251 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 234 through 239 removed outlier: 3.636A pdb=" N VAL A 235 " --> pdb=" O PHE A 251 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 277 through 280 removed outlier: 4.561A pdb=" N VAL A 308 " --> pdb=" O THR A 323 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N THR A 323 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N ILE A 310 " --> pdb=" O MET A 321 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N MET A 321 " --> pdb=" O ILE A 310 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 339 through 341 Processing sheet with id=AB1, first strand: chain 'A' and resid 339 through 341 removed outlier: 3.646A pdb=" N GLN A 383 " --> pdb=" O ILE A 369 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 471 through 472 removed outlier: 3.568A pdb=" N LYS A 472 " --> pdb=" O ILE A 435 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 440 through 441 removed outlier: 3.668A pdb=" N SER A 441 " --> pdb=" O THR A 466 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N THR A 466 " --> pdb=" O SER A 441 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG A 525 " --> pdb=" O LEU A 467 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 453 through 455 Processing sheet with id=AB5, first strand: chain 'A' and resid 479 through 484 removed outlier: 3.733A pdb=" N GLY A 513 " --> pdb=" O TYR A 484 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 542 through 547 removed outlier: 3.548A pdb=" N ILE A 542 " --> pdb=" O ILE A 583 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 83 through 88 removed outlier: 6.095A pdb=" N ARG B 108 " --> pdb=" O LEU B 87 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 104 through 105 Processing sheet with id=AB9, first strand: chain 'B' and resid 104 through 105 Processing sheet with id=AC1, first strand: chain 'B' and resid 211 through 217 removed outlier: 7.764A pdb=" N VAL B 213 " --> pdb=" O SER B 176 " (cutoff:3.500A) removed outlier: 9.328A pdb=" N SER B 176 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N SER B 215 " --> pdb=" O PHE B 174 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N PHE B 174 " --> pdb=" O SER B 215 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N VAL B 133 " --> pdb=" O ARG B 171 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N GLY B 173 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU B 135 " --> pdb=" O GLY B 173 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N GLY B 175 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TYR B 137 " --> pdb=" O GLY B 175 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N PHE B 177 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N MET B 139 " --> pdb=" O PHE B 177 " (cutoff:3.500A) 244 hydrogen bonds defined for protein. 624 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: 3.09 Time building geometry restraints manager: 1.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7255 1.03 - 1.23: 67 1.23 - 1.43: 3176 1.43 - 1.62: 4316 1.62 - 1.82: 46 Bond restraints: 14860 Sorted by residual: bond pdb=" N GLY B 82 " pdb=" H1 GLY B 82 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" N TYR A 1 " pdb=" CA TYR A 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.62e+00 bond pdb=" N TYR A 1 " pdb=" H TYR A 1 " ideal model delta sigma weight residual 0.860 0.891 -0.031 2.00e-02 2.50e+03 2.36e+00 bond pdb=" CB ASN B 322 " pdb=" CG ASN B 322 " ideal model delta sigma weight residual 1.516 1.490 0.026 2.50e-02 1.60e+03 1.05e+00 bond pdb=" CA ASP A 437 " pdb=" C ASP A 437 " ideal model delta sigma weight residual 1.531 1.521 0.010 1.12e-02 7.97e+03 8.45e-01 ... (remaining 14855 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 25941 1.34 - 2.68: 795 2.68 - 4.03: 52 4.03 - 5.37: 6 5.37 - 6.71: 3 Bond angle restraints: 26797 Sorted by residual: angle pdb=" CA GLU A 475 " pdb=" CB GLU A 475 " pdb=" CG GLU A 475 " ideal model delta sigma weight residual 114.10 119.11 -5.01 2.00e+00 2.50e-01 6.27e+00 angle pdb=" CA CYS B 393 " pdb=" CB CYS B 393 " pdb=" SG CYS B 393 " ideal model delta sigma weight residual 114.40 119.75 -5.35 2.30e+00 1.89e-01 5.41e+00 angle pdb=" CB MET B 364 " pdb=" CG MET B 364 " pdb=" SD MET B 364 " ideal model delta sigma weight residual 112.70 119.41 -6.71 3.00e+00 1.11e-01 5.00e+00 angle pdb=" CB MET A 318 " pdb=" CG MET A 318 " pdb=" SD MET A 318 " ideal model delta sigma weight residual 112.70 119.01 -6.31 3.00e+00 1.11e-01 4.42e+00 angle pdb=" CA GLY B 82 " pdb=" N GLY B 82 " pdb=" H1 GLY B 82 " ideal model delta sigma weight residual 120.00 114.01 5.99 3.00e+00 1.11e-01 3.98e+00 ... (remaining 26792 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 6255 17.94 - 35.88: 572 35.88 - 53.82: 172 53.82 - 71.76: 48 71.76 - 89.70: 18 Dihedral angle restraints: 7065 sinusoidal: 3848 harmonic: 3217 Sorted by residual: dihedral pdb=" CB CYS B 393 " pdb=" SG CYS B 393 " pdb=" SG CYS B 409 " pdb=" CB CYS B 409 " ideal model delta sinusoidal sigma weight residual -86.00 -158.21 72.21 1 1.00e+01 1.00e-02 6.67e+01 dihedral pdb=" CA GLN B 408 " pdb=" C GLN B 408 " pdb=" N CYS B 409 " pdb=" CA CYS B 409 " ideal model delta harmonic sigma weight residual 180.00 158.50 21.50 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CB CYS A 453 " pdb=" SG CYS A 453 " pdb=" SG CYS A 462 " pdb=" CB CYS A 462 " ideal model delta sinusoidal sigma weight residual 93.00 57.00 36.00 1 1.00e+01 1.00e-02 1.83e+01 ... (remaining 7062 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 641 0.029 - 0.058: 319 0.058 - 0.088: 73 0.088 - 0.117: 64 0.117 - 0.146: 31 Chirality restraints: 1128 Sorted by residual: chirality pdb=" CA ILE B 326 " pdb=" N ILE B 326 " pdb=" C ILE B 326 " pdb=" CB ILE B 326 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.33e-01 chirality pdb=" CA ILE A 250 " pdb=" N ILE A 250 " pdb=" C ILE A 250 " pdb=" CB ILE A 250 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CA ILE A 178 " pdb=" N ILE A 178 " pdb=" C ILE A 178 " pdb=" CB ILE A 178 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.85e-01 ... (remaining 1125 not shown) Planarity restraints: 2273 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 475 " 0.009 2.00e-02 2.50e+03 1.73e-02 3.00e+00 pdb=" C GLU A 475 " -0.030 2.00e-02 2.50e+03 pdb=" O GLU A 475 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL A 476 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 567 " -0.023 5.00e-02 4.00e+02 3.49e-02 1.94e+00 pdb=" N PRO A 568 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 568 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 568 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 38 " 0.023 5.00e-02 4.00e+02 3.47e-02 1.92e+00 pdb=" N PRO A 39 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 39 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 39 " 0.019 5.00e-02 4.00e+02 ... (remaining 2270 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.41: 7054 2.41 - 2.95: 34781 2.95 - 3.50: 38300 3.50 - 4.05: 53757 4.05 - 4.60: 77724 Nonbonded interactions: 211616 Sorted by model distance: nonbonded pdb=" HG SER B 288 " pdb="HE22 GLN B 313 " model vdw 1.857 2.100 nonbonded pdb=" HE2 PHE A 158 " pdb=" HZ2 TRP A 188 " model vdw 1.861 2.100 nonbonded pdb=" H THR B 199 " pdb=" HG1 THR B 199 " model vdw 1.861 2.100 nonbonded pdb="HD21 ASN B 235 " pdb="CA CA B 501 " model vdw 1.878 2.780 nonbonded pdb=" HG SER A 503 " pdb=" HE1 PHE A 530 " model vdw 1.890 2.100 ... (remaining 211611 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.080 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.870 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7612 Z= 0.153 Angle : 0.576 6.708 10325 Z= 0.316 Chirality : 0.045 0.146 1128 Planarity : 0.004 0.035 1362 Dihedral : 15.506 89.703 2792 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 1.60 % Allowed : 15.58 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -1.57 (0.27), residues: 956 helix: -0.38 (0.54), residues: 81 sheet: -1.20 (0.31), residues: 297 loop : -1.02 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 110 TYR 0.009 0.001 TYR A 195 PHE 0.011 0.001 PHE A 397 TRP 0.011 0.001 TRP A 115 HIS 0.005 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 ( 7603) covalent geometry : angle 0.56989 / 0.31 (10307) SS BOND : bond 0.00263 / 0.12 ( 9) SS BOND : angle 2.02567 / 1.12 ( 18) hydrogen bonds : bond 0.21764 / 14.12 ( 223) hydrogen bonds : angle 11.11831 / 7.75 ( 624) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 0.416 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: A 2 ASN cc_start: 0.8392 (p0) cc_final: 0.7950 (p0) REVERT: A 198 THR cc_start: 0.6841 (p) cc_final: 0.6461 (m) REVERT: A 302 GLU cc_start: 0.6731 (mt-10) cc_final: 0.6289 (mt-10) REVERT: A 317 VAL cc_start: 0.8478 (p) cc_final: 0.8147 (m) outliers start: 13 outliers final: 10 residues processed: 151 average time/residue: 0.2144 time to fit residues: 42.8626 Evaluate side-chains 153 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 143 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 531 MET Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 443 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 90 GLN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.163626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.144806 restraints weight = 31081.680| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 2.15 r_work: 0.3810 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3667 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 7612 Z= 0.277 Angle : 0.617 5.118 10325 Z= 0.338 Chirality : 0.047 0.183 1128 Planarity : 0.005 0.045 1362 Dihedral : 6.759 53.973 1059 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 3.07 % Allowed : 15.21 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -1.81 (0.27), residues: 956 helix: -0.59 (0.54), residues: 83 sheet: -1.33 (0.29), residues: 312 loop : -1.18 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 263 TYR 0.017 0.002 TYR B 389 PHE 0.020 0.002 PHE A 273 TRP 0.016 0.002 TRP A 33 HIS 0.005 0.001 HIS B 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00602 / 0.28 ( 7603) covalent geometry : angle 0.61529 / 0.34 (10307) SS BOND : bond 0.00201 / 0.10 ( 9) SS BOND : angle 1.13973 / 0.65 ( 18) hydrogen bonds : bond 0.05211 / 3.44 ( 223) hydrogen bonds : angle 8.12553 / 5.64 ( 624) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.396 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: A 2 ASN cc_start: 0.8351 (p0) cc_final: 0.7828 (p0) REVERT: A 230 GLN cc_start: 0.7873 (mp10) cc_final: 0.7647 (mp10) REVERT: A 272 TYR cc_start: 0.7879 (OUTLIER) cc_final: 0.7348 (t80) REVERT: A 302 GLU cc_start: 0.6611 (mt-10) cc_final: 0.6188 (mt-10) REVERT: A 317 VAL cc_start: 0.8560 (p) cc_final: 0.8249 (m) outliers start: 25 outliers final: 18 residues processed: 160 average time/residue: 0.2091 time to fit residues: 44.5863 Evaluate side-chains 157 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 531 MET Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 443 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 52 optimal weight: 2.9990 chunk 56 optimal weight: 0.0980 chunk 7 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 90 GLN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.164645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.145777 restraints weight = 31130.682| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 2.18 r_work: 0.3820 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3680 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7612 Z= 0.203 Angle : 0.564 5.487 10325 Z= 0.305 Chirality : 0.046 0.169 1128 Planarity : 0.005 0.045 1362 Dihedral : 6.154 51.588 1053 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 3.80 % Allowed : 15.21 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -1.82 (0.27), residues: 956 helix: -0.64 (0.53), residues: 83 sheet: -1.30 (0.29), residues: 319 loop : -1.20 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 203 TYR 0.013 0.002 TYR A 195 PHE 0.018 0.002 PHE A 273 TRP 0.012 0.002 TRP A 188 HIS 0.004 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.20 ( 7603) covalent geometry : angle 0.56232 / 0.30 (10307) SS BOND : bond 0.00207 / 0.10 ( 9) SS BOND : angle 1.22834 / 0.69 ( 18) hydrogen bonds : bond 0.04309 / 2.81 ( 223) hydrogen bonds : angle 7.32861 / 5.06 ( 624) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 0.383 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: A 2 ASN cc_start: 0.8348 (p0) cc_final: 0.7857 (p0) REVERT: A 230 GLN cc_start: 0.7939 (mp10) cc_final: 0.7603 (mp10) REVERT: A 272 TYR cc_start: 0.7836 (OUTLIER) cc_final: 0.7299 (t80) REVERT: A 302 GLU cc_start: 0.6753 (mt-10) cc_final: 0.6170 (mt-10) REVERT: A 317 VAL cc_start: 0.8564 (p) cc_final: 0.8208 (m) REVERT: A 318 MET cc_start: 0.7056 (mmt) cc_final: 0.6744 (mmm) REVERT: B 176 SER cc_start: 0.7995 (OUTLIER) cc_final: 0.7300 (p) REVERT: B 322 ASN cc_start: 0.7837 (t0) cc_final: 0.7612 (t0) REVERT: B 354 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.6537 (tm-30) outliers start: 31 outliers final: 20 residues processed: 160 average time/residue: 0.2111 time to fit residues: 44.8132 Evaluate side-chains 159 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 531 MET Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 443 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 23 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 68 optimal weight: 0.0870 chunk 88 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 90 GLN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.160953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.141704 restraints weight = 30865.262| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 2.24 r_work: 0.3799 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3656 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 7612 Z= 0.228 Angle : 0.576 5.747 10325 Z= 0.314 Chirality : 0.046 0.161 1128 Planarity : 0.005 0.043 1362 Dihedral : 6.209 50.177 1053 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 3.68 % Allowed : 16.20 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -1.87 (0.27), residues: 956 helix: -0.63 (0.54), residues: 83 sheet: -1.27 (0.29), residues: 317 loop : -1.28 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 263 TYR 0.016 0.002 TYR A 195 PHE 0.018 0.002 PHE A 273 TRP 0.015 0.002 TRP A 188 HIS 0.004 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.23 ( 7603) covalent geometry : angle 0.57372 / 0.31 (10307) SS BOND : bond 0.00203 / 0.10 ( 9) SS BOND : angle 1.38531 / 0.79 ( 18) hydrogen bonds : bond 0.04182 / 2.72 ( 223) hydrogen bonds : angle 7.09516 / 4.87 ( 624) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 140 time to evaluate : 0.358 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: A 2 ASN cc_start: 0.8350 (p0) cc_final: 0.7819 (p0) REVERT: A 230 GLN cc_start: 0.7977 (mp10) cc_final: 0.7610 (mp10) REVERT: A 272 TYR cc_start: 0.7865 (OUTLIER) cc_final: 0.7316 (t80) REVERT: A 289 ASP cc_start: 0.7433 (OUTLIER) cc_final: 0.7051 (m-30) REVERT: A 302 GLU cc_start: 0.6571 (mt-10) cc_final: 0.5946 (mt-10) REVERT: B 176 SER cc_start: 0.7961 (OUTLIER) cc_final: 0.7290 (p) REVERT: B 267 PHE cc_start: 0.6578 (t80) cc_final: 0.6317 (t80) REVERT: B 354 GLU cc_start: 0.6783 (OUTLIER) cc_final: 0.6474 (tm-30) outliers start: 30 outliers final: 20 residues processed: 162 average time/residue: 0.2076 time to fit residues: 44.9117 Evaluate side-chains 161 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 443 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 46 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 83 optimal weight: 0.0970 chunk 25 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 90 GLN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.161728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.142051 restraints weight = 30611.705| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 2.25 r_work: 0.3802 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3663 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7612 Z= 0.221 Angle : 0.571 5.637 10325 Z= 0.310 Chirality : 0.046 0.164 1128 Planarity : 0.005 0.042 1362 Dihedral : 6.065 51.522 1050 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 3.93 % Allowed : 16.81 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -1.88 (0.27), residues: 956 helix: -0.61 (0.54), residues: 83 sheet: -1.29 (0.29), residues: 317 loop : -1.28 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 263 TYR 0.015 0.002 TYR A 195 PHE 0.018 0.002 PHE A 273 TRP 0.014 0.002 TRP A 188 HIS 0.004 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.22 ( 7603) covalent geometry : angle 0.56845 / 0.31 (10307) SS BOND : bond 0.00233 / 0.11 ( 9) SS BOND : angle 1.47532 / 0.83 ( 18) hydrogen bonds : bond 0.04029 / 2.63 ( 223) hydrogen bonds : angle 6.91252 / 4.74 ( 624) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 0.376 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: A 2 ASN cc_start: 0.8323 (p0) cc_final: 0.7818 (p0) REVERT: A 230 GLN cc_start: 0.7950 (mp10) cc_final: 0.7542 (mp10) REVERT: A 272 TYR cc_start: 0.7861 (OUTLIER) cc_final: 0.7241 (t80) REVERT: A 289 ASP cc_start: 0.7414 (OUTLIER) cc_final: 0.7011 (m-30) REVERT: A 302 GLU cc_start: 0.6696 (mt-10) cc_final: 0.6095 (mt-10) REVERT: A 318 MET cc_start: 0.7102 (mmt) cc_final: 0.6730 (mmm) REVERT: B 176 SER cc_start: 0.7958 (OUTLIER) cc_final: 0.7324 (p) REVERT: B 267 PHE cc_start: 0.6519 (t80) cc_final: 0.6250 (t80) REVERT: B 354 GLU cc_start: 0.6735 (OUTLIER) cc_final: 0.6393 (tm-30) outliers start: 32 outliers final: 23 residues processed: 162 average time/residue: 0.2081 time to fit residues: 44.9593 Evaluate side-chains 168 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 531 MET Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 443 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 11 optimal weight: 0.3980 chunk 40 optimal weight: 0.0770 chunk 64 optimal weight: 0.9990 chunk 9 optimal weight: 0.0970 chunk 93 optimal weight: 0.0970 overall best weight: 0.2534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 90 GLN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.167066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.147726 restraints weight = 30665.019| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 2.31 r_work: 0.3842 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3697 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7612 Z= 0.120 Angle : 0.514 4.545 10325 Z= 0.276 Chirality : 0.045 0.150 1128 Planarity : 0.004 0.041 1362 Dihedral : 5.710 54.286 1050 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.19 % Allowed : 17.42 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -1.62 (0.27), residues: 956 helix: -0.35 (0.55), residues: 83 sheet: -1.09 (0.30), residues: 311 loop : -1.14 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 203 TYR 0.010 0.001 TYR A 484 PHE 0.012 0.001 PHE A 273 TRP 0.011 0.001 TRP A 115 HIS 0.004 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 7603) covalent geometry : angle 0.51091 / 0.27 (10307) SS BOND : bond 0.00193 / 0.09 ( 9) SS BOND : angle 1.42966 / 0.81 ( 18) hydrogen bonds : bond 0.03196 / 2.07 ( 223) hydrogen bonds : angle 6.42556 / 4.38 ( 624) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 0.394 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: A 2 ASN cc_start: 0.8356 (p0) cc_final: 0.7924 (p0) REVERT: A 198 THR cc_start: 0.6796 (p) cc_final: 0.6394 (m) REVERT: A 230 GLN cc_start: 0.7986 (mp10) cc_final: 0.7553 (mp10) REVERT: A 255 GLU cc_start: 0.7617 (tm-30) cc_final: 0.7262 (tm-30) REVERT: A 272 TYR cc_start: 0.7791 (OUTLIER) cc_final: 0.7176 (t80) REVERT: A 302 GLU cc_start: 0.6670 (mt-10) cc_final: 0.5998 (mt-10) REVERT: A 318 MET cc_start: 0.7168 (mmt) cc_final: 0.6771 (mmm) REVERT: B 176 SER cc_start: 0.7915 (OUTLIER) cc_final: 0.7465 (p) REVERT: B 354 GLU cc_start: 0.6628 (OUTLIER) cc_final: 0.6231 (tm-30) REVERT: B 365 ASP cc_start: 0.6733 (m-30) cc_final: 0.6525 (m-30) outliers start: 26 outliers final: 18 residues processed: 161 average time/residue: 0.2096 time to fit residues: 45.0917 Evaluate side-chains 161 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 443 PHE Chi-restraints excluded: chain B residue 449 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 74 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 55 optimal weight: 0.0470 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 90 GLN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 GLN B 361 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.161528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.142027 restraints weight = 30398.008| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 2.23 r_work: 0.3810 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3669 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 7612 Z= 0.243 Angle : 0.580 5.640 10325 Z= 0.316 Chirality : 0.046 0.158 1128 Planarity : 0.005 0.042 1362 Dihedral : 5.998 52.174 1050 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 3.07 % Allowed : 17.91 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -1.82 (0.27), residues: 956 helix: -0.55 (0.55), residues: 85 sheet: -1.23 (0.29), residues: 311 loop : -1.26 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 263 TYR 0.018 0.002 TYR A 195 PHE 0.019 0.002 PHE B 267 TRP 0.013 0.002 TRP A 33 HIS 0.004 0.001 HIS B 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.24 ( 7603) covalent geometry : angle 0.57626 / 0.31 (10307) SS BOND : bond 0.00213 / 0.10 ( 9) SS BOND : angle 1.68445 / 0.97 ( 18) hydrogen bonds : bond 0.04042 / 2.65 ( 223) hydrogen bonds : angle 6.72299 / 4.59 ( 624) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 0.374 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: A 2 ASN cc_start: 0.8348 (p0) cc_final: 0.7825 (p0) REVERT: A 230 GLN cc_start: 0.8001 (mp10) cc_final: 0.7556 (mp10) REVERT: A 272 TYR cc_start: 0.7878 (OUTLIER) cc_final: 0.7349 (t80) REVERT: A 318 MET cc_start: 0.7046 (mmt) cc_final: 0.6656 (mmm) REVERT: B 354 GLU cc_start: 0.6718 (OUTLIER) cc_final: 0.6319 (tm-30) outliers start: 25 outliers final: 18 residues processed: 158 average time/residue: 0.2099 time to fit residues: 44.1427 Evaluate side-chains 160 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 531 MET Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 443 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 89 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 69 optimal weight: 0.0980 chunk 68 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 70 optimal weight: 0.0670 chunk 58 optimal weight: 0.9990 chunk 71 optimal weight: 0.2980 overall best weight: 0.3318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 90 GLN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.166225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.147126 restraints weight = 30790.876| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 2.23 r_work: 0.3826 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3686 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7612 Z= 0.138 Angle : 0.524 4.595 10325 Z= 0.282 Chirality : 0.045 0.151 1128 Planarity : 0.004 0.040 1362 Dihedral : 5.769 53.170 1050 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 3.19 % Allowed : 18.16 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -1.63 (0.27), residues: 956 helix: -0.37 (0.54), residues: 85 sheet: -1.07 (0.30), residues: 305 loop : -1.17 (0.27), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 114 TYR 0.011 0.001 TYR A 195 PHE 0.013 0.001 PHE A 273 TRP 0.010 0.001 TRP A 115 HIS 0.004 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 ( 7603) covalent geometry : angle 0.52100 / 0.28 (10307) SS BOND : bond 0.00215 / 0.10 ( 9) SS BOND : angle 1.41106 / 0.80 ( 18) hydrogen bonds : bond 0.03292 / 2.14 ( 223) hydrogen bonds : angle 6.35336 / 4.32 ( 624) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.392 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: A 2 ASN cc_start: 0.8317 (p0) cc_final: 0.7884 (p0) REVERT: A 198 THR cc_start: 0.6786 (p) cc_final: 0.6375 (m) REVERT: A 230 GLN cc_start: 0.7999 (mp10) cc_final: 0.7577 (mp10) REVERT: A 272 TYR cc_start: 0.7814 (OUTLIER) cc_final: 0.7198 (t80) REVERT: A 302 GLU cc_start: 0.6683 (mt-10) cc_final: 0.6036 (mt-10) REVERT: A 318 MET cc_start: 0.7093 (mmt) cc_final: 0.6673 (mmm) REVERT: B 176 SER cc_start: 0.7916 (OUTLIER) cc_final: 0.7227 (p) REVERT: B 212 HIS cc_start: 0.6320 (t-170) cc_final: 0.6112 (t-170) REVERT: B 354 GLU cc_start: 0.6666 (OUTLIER) cc_final: 0.6252 (tm-30) outliers start: 26 outliers final: 21 residues processed: 157 average time/residue: 0.2169 time to fit residues: 45.4712 Evaluate side-chains 162 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 531 MET Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 443 PHE Chi-restraints excluded: chain B residue 449 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 1 optimal weight: 0.4980 chunk 79 optimal weight: 0.9990 chunk 7 optimal weight: 0.3980 chunk 83 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 94 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 = 0.4157 r_free = 0.4157 target = 0.161315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.141806 restraints weight = 30479.714| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 2.25 r_work: 0.3807 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3669 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 7612 Z= 0.249 Angle : 0.590 6.657 10325 Z= 0.321 Chirality : 0.046 0.161 1128 Planarity : 0.005 0.042 1362 Dihedral : 6.043 51.365 1050 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 3.19 % Allowed : 18.40 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -1.83 (0.27), residues: 956 helix: -0.54 (0.55), residues: 86 sheet: -1.24 (0.29), residues: 311 loop : -1.28 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 263 TYR 0.018 0.002 TYR A 195 PHE 0.016 0.002 PHE A 273 TRP 0.015 0.002 TRP A 33 HIS 0.004 0.001 HIS B 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.25 ( 7603) covalent geometry : angle 0.58480 / 0.32 (10307) SS BOND : bond 0.00256 / 0.11 ( 9) SS BOND : angle 1.92841 / 1.12 ( 18) hydrogen bonds : bond 0.04016 / 2.64 ( 223) hydrogen bonds : angle 6.69778 / 4.57 ( 624) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 0.374 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: A 230 GLN cc_start: 0.8033 (mp10) cc_final: 0.7608 (mp10) REVERT: A 272 TYR cc_start: 0.7881 (OUTLIER) cc_final: 0.7348 (t80) REVERT: A 302 GLU cc_start: 0.6509 (mt-10) cc_final: 0.5848 (mt-10) REVERT: A 318 MET cc_start: 0.7071 (mmt) cc_final: 0.6648 (mmm) REVERT: A 467 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7557 (mp) REVERT: B 176 SER cc_start: 0.7967 (OUTLIER) cc_final: 0.7183 (m) REVERT: B 354 GLU cc_start: 0.6715 (OUTLIER) cc_final: 0.6296 (tm-30) outliers start: 26 outliers final: 21 residues processed: 154 average time/residue: 0.2189 time to fit residues: 44.8632 Evaluate side-chains 163 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 531 MET Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 443 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 24 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 70 optimal weight: 0.0370 chunk 64 optimal weight: 0.8980 chunk 83 optimal weight: 0.0980 chunk 37 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 94 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 = 0.4182 r_free = 0.4182 target = 0.163491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.143933 restraints weight = 30605.507| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 2.29 r_work: 0.3818 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3679 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7612 Z= 0.161 Angle : 0.547 5.954 10325 Z= 0.294 Chirality : 0.045 0.152 1128 Planarity : 0.004 0.047 1362 Dihedral : 5.873 52.289 1050 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 2.70 % Allowed : 18.77 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -1.74 (0.27), residues: 956 helix: -0.52 (0.53), residues: 86 sheet: -1.18 (0.29), residues: 315 loop : -1.20 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 57 TYR 0.012 0.001 TYR A 195 PHE 0.013 0.001 PHE A 273 TRP 0.010 0.002 TRP A 115 HIS 0.003 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 ( 7603) covalent geometry : angle 0.54231 / 0.29 (10307) SS BOND : bond 0.00239 / 0.11 ( 9) SS BOND : angle 1.75130 / 1.01 ( 18) hydrogen bonds : bond 0.03456 / 2.24 ( 223) hydrogen bonds : angle 6.40047 / 4.35 ( 624) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 0.482 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: A 2 ASN cc_start: 0.8308 (p0) cc_final: 0.7940 (p0) REVERT: A 198 THR cc_start: 0.6772 (p) cc_final: 0.6357 (m) REVERT: A 230 GLN cc_start: 0.8050 (mp10) cc_final: 0.7629 (mp10) REVERT: A 255 GLU cc_start: 0.7619 (tm-30) cc_final: 0.7324 (tm-30) REVERT: A 272 TYR cc_start: 0.7826 (OUTLIER) cc_final: 0.7306 (t80) REVERT: A 302 GLU cc_start: 0.6662 (mt-10) cc_final: 0.6000 (mt-10) REVERT: A 440 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8309 (mt) REVERT: A 467 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.7280 (mp) REVERT: B 176 SER cc_start: 0.7987 (OUTLIER) cc_final: 0.7314 (p) REVERT: B 354 GLU cc_start: 0.6657 (OUTLIER) cc_final: 0.6226 (tm-30) outliers start: 22 outliers final: 17 residues processed: 152 average time/residue: 0.2094 time to fit residues: 42.5376 Evaluate side-chains 162 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 531 MET Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 443 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 0 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 34 optimal weight: 0.0970 chunk 89 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 82 optimal weight: 0.0980 chunk 25 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 94 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 = 0.4174 r_free = 0.4174 target = 0.162831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.143204 restraints weight = 30734.480| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 2.28 r_work: 0.3812 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3672 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7612 Z= 0.190 Angle : 0.556 5.927 10325 Z= 0.301 Chirality : 0.046 0.156 1128 Planarity : 0.004 0.049 1362 Dihedral : 5.892 51.961 1050 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 2.70 % Allowed : 19.14 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -1.76 (0.27), residues: 956 helix: -0.51 (0.54), residues: 86 sheet: -1.21 (0.29), residues: 315 loop : -1.21 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 259 TYR 0.015 0.002 TYR A 195 PHE 0.013 0.002 PHE A 273 TRP 0.012 0.002 TRP A 33 HIS 0.007 0.001 HIS B 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.19 ( 7603) covalent geometry : angle 0.55284 / 0.30 (10307) SS BOND : bond 0.00208 / 0.10 ( 9) SS BOND : angle 1.60572 / 0.92 ( 18) hydrogen bonds : bond 0.03612 / 2.35 ( 223) hydrogen bonds : angle 6.48434 / 4.41 ( 624) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4586.40 seconds wall clock time: 78 minutes 33.21 seconds (4713.21 seconds total)