Starting phenix.real_space_refine on Thu Feb 5 05:06:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9p96_71400/02_2026/9p96_71400.cif Found real_map, /net/cci-nas-00/data/ceres_data/9p96_71400/02_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 { model { file = "/net/cci-nas-00/data/ceres_data/9p96_71400/02_2026/9p96_71400.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9p96_71400/02_2026/9p96_71400.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9p96_71400/02_2026/9p96_71400.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9p96_71400/02_2026/9p96_71400.map" } 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-2.0-5952/lib/python3.9/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, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.19, per 1000 atoms: 0.15 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: 1.19 Conformation dependent library (CDL) restraints added in 414.0 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: 3.05 Time building geometry restraints manager: 1.67 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 2.040 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: 2.100 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: 0.050 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.630 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 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 covalent geometry : bond 0.00316 ( 7603) covalent geometry : angle 0.56989 (10307) SS BOND : bond 0.00263 ( 9) SS BOND : angle 2.02567 ( 18) hydrogen bonds : bond 0.21764 ( 223) hydrogen bonds : angle 11.11831 ( 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 : 0.358 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: 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: 0.2102 time to fit residues: 41.6283 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 : 0.314 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4161 r_free = 0.4161 target = 0.163397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.143841 restraints weight = 30993.532| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 2.29 r_work: 0.3791 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3645 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.0925 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= 0.276 Angle : 0.615 5.162 10325 Z= 0.337 Chirality : 0.048 0.183 1128 Planarity : 0.005 0.046 1362 Dihedral : 6.778 57.262 1059 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 3.07 % Allowed : 14.97 % Favored : 81.96 % 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: -1.78 (0.27), residues: 956 helix: -0.54 (0.55), residues: 83 sheet: -1.35 (0.29), residues: 316 loop : -1.13 (0.27), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 263 TYR 0.018 0.002 TYR B 389 PHE 0.019 0.002 PHE A 273 TRP 0.016 0.002 TRP A 33 HIS 0.005 0.001 HIS A 26 Details of bonding type rmsd covalent geometry : bond 0.00600 ( 7603) covalent geometry : angle 0.61412 (10307) SS BOND : bond 0.00202 ( 9) SS BOND : angle 1.14986 ( 18) hydrogen bonds : bond 0.05099 ( 223) hydrogen bonds : angle 8.06970 ( 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 166 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 0.246 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 230 GLN cc_start: 0.7883 (mp10) cc_final: 0.7645 (mp10) REVERT: A 272 TYR cc_start: 0.7893 (OUTLIER) cc_final: 0.7354 (t80) REVERT: A 302 GLU cc_start: 0.6641 (mt-10) cc_final: 0.6227 (mt-10) REVERT: A 317 VAL cc_start: 0.8552 (p) cc_final: 0.8230 (m) REVERT: B 322 ASN cc_start: 0.7855 (t0) cc_final: 0.7643 (t0) outliers start: 25 outliers final: 17 residues processed: 157 average time/residue: 0.1985 time to fit residues: 40.7951 Evaluate side-chains 152 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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 213 VAL Chi-restraints excluded: chain B residue 236 LEU 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: 0.6980 chunk 49 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 92 optimal weight: 0.0010 chunk 2 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4179 r_free = 0.4179 target = 0.164790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.145988 restraints weight = 30986.827| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 2.17 r_work: 0.3820 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3680 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.0979 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= 0.171 Angle : 0.546 5.173 10325 Z= 0.294 Chirality : 0.046 0.168 1128 Planarity : 0.004 0.045 1362 Dihedral : 6.054 51.456 1053 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 3.07 % Allowed : 15.46 % Favored : 81.47 % 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: -1.69 (0.27), residues: 956 helix: -0.51 (0.54), residues: 83 sheet: -1.28 (0.29), residues: 325 loop : -1.05 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 203 TYR 0.012 0.002 TYR A 195 PHE 0.017 0.001 PHE A 273 TRP 0.011 0.002 TRP A 188 HIS 0.003 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 7603) covalent geometry : angle 0.54360 (10307) SS BOND : bond 0.00209 ( 9) SS BOND : angle 1.22437 ( 18) hydrogen bonds : bond 0.04123 ( 223) hydrogen bonds : angle 7.24871 ( 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 162 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 0.377 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: 0.8360 (p0) cc_final: 0.7953 (p0) REVERT: A 230 GLN cc_start: 0.7907 (mp10) cc_final: 0.7585 (mp10) REVERT: A 272 TYR cc_start: 0.7817 (OUTLIER) cc_final: 0.7270 (t80) REVERT: A 289 ASP cc_start: 0.8495 (OUTLIER) cc_final: 0.7575 (m-30) REVERT: A 302 GLU cc_start: 0.6737 (mt-10) cc_final: 0.6152 (mt-10) REVERT: A 317 VAL cc_start: 0.8549 (p) cc_final: 0.8207 (m) REVERT: A 318 MET cc_start: 0.7050 (mmt) cc_final: 0.6746 (mmm) REVERT: B 165 GLU cc_start: 0.7439 (mm-30) cc_final: 0.7235 (mm-30) REVERT: B 176 SER cc_start: 0.7975 (OUTLIER) cc_final: 0.7279 (p) REVERT: B 322 ASN cc_start: 0.7812 (t0) cc_final: 0.7583 (t0) outliers start: 25 outliers final: 17 residues processed: 154 average time/residue: 0.2158 time to fit residues: 43.7560 Evaluate side-chains 156 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 0.263 ------------------------------------------------------------------------------- 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 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 213 VAL Chi-restraints excluded: chain B residue 349 VAL 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: 0.8980 chunk 47 optimal weight: 0.9980 chunk 68 optimal weight: 0.1980 chunk 88 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 78 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4172 r_free = 0.4172 target = 0.164372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.145011 restraints weight = 30964.578| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 2.31 r_work: 0.3799 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3653 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7612 Z= 0.189 Angle : 0.547 4.751 10325 Z= 0.297 Chirality : 0.045 0.155 1128 Planarity : 0.004 0.043 1362 Dihedral : 6.049 50.765 1053 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 3.68 % Allowed : 15.71 % Favored : 80.61 % 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: -1.68 (0.27), residues: 956 helix: -0.49 (0.54), residues: 83 sheet: -1.24 (0.29), residues: 325 loop : -1.08 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 203 TYR 0.014 0.002 TYR A 195 PHE 0.017 0.002 PHE A 273 TRP 0.013 0.002 TRP A 188 HIS 0.004 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 7603) covalent geometry : angle 0.54504 (10307) SS BOND : bond 0.00190 ( 9) SS BOND : angle 1.31295 ( 18) hydrogen bonds : bond 0.03891 ( 223) hydrogen bonds : angle 6.91784 ( 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 168 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 0.355 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: 0.8400 (p0) cc_final: 0.7941 (p0) REVERT: A 230 GLN cc_start: 0.7962 (mp10) cc_final: 0.7585 (mp10) REVERT: A 272 TYR cc_start: 0.7832 (OUTLIER) cc_final: 0.7283 (t80) REVERT: A 302 GLU cc_start: 0.6752 (mt-10) cc_final: 0.6128 (mt-10) REVERT: A 317 VAL cc_start: 0.8519 (p) cc_final: 0.8215 (m) REVERT: B 85 GLU cc_start: 0.7347 (tt0) cc_final: 0.6994 (tm-30) REVERT: B 110 ARG cc_start: 0.7787 (ttt-90) cc_final: 0.7355 (ttp-170) REVERT: B 165 GLU cc_start: 0.7441 (mm-30) cc_final: 0.7225 (mm-30) REVERT: B 176 SER cc_start: 0.7994 (OUTLIER) cc_final: 0.7332 (p) REVERT: B 267 PHE cc_start: 0.6555 (t80) cc_final: 0.6324 (t80) outliers start: 30 outliers final: 22 residues processed: 159 average time/residue: 0.2203 time to fit residues: 46.1478 Evaluate side-chains 159 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 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 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 236 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 46 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 83 optimal weight: 0.3980 chunk 25 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.4144 r_free = 0.4144 target = 0.160386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.140868 restraints weight = 30573.219| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 2.24 r_work: 0.3791 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3654 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 7612 Z= 0.261 Angle : 0.594 6.255 10325 Z= 0.323 Chirality : 0.047 0.164 1128 Planarity : 0.005 0.043 1362 Dihedral : 6.113 50.545 1050 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 3.68 % Allowed : 16.56 % Favored : 79.75 % 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: -1.80 (0.27), residues: 956 helix: -0.53 (0.55), residues: 83 sheet: -1.28 (0.29), residues: 317 loop : -1.21 (0.27), residues: 556 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 A 273 TRP 0.017 0.003 TRP A 33 HIS 0.004 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00572 ( 7603) covalent geometry : angle 0.59157 (10307) SS BOND : bond 0.00190 ( 9) SS BOND : angle 1.46500 ( 18) hydrogen bonds : bond 0.04290 ( 223) hydrogen bonds : angle 7.05412 ( 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 169 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 0.365 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: 0.8347 (p0) cc_final: 0.7844 (p0) REVERT: A 230 GLN cc_start: 0.7935 (mp10) cc_final: 0.7538 (mp10) REVERT: A 272 TYR cc_start: 0.7858 (OUTLIER) cc_final: 0.7322 (t80) REVERT: A 302 GLU cc_start: 0.6684 (mt-10) cc_final: 0.6086 (mt-10) REVERT: A 317 VAL cc_start: 0.8643 (p) cc_final: 0.8347 (m) REVERT: B 165 GLU cc_start: 0.7403 (mm-30) cc_final: 0.7203 (mm-30) outliers start: 30 outliers final: 25 residues processed: 159 average time/residue: 0.2022 time to fit residues: 42.4828 Evaluate side-chains 163 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 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 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 272 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 0.8980 chunk 78 optimal weight: 0.4980 chunk 87 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 83 optimal weight: 0.1980 chunk 11 optimal weight: 0.9990 chunk 40 optimal weight: 0.0870 chunk 64 optimal weight: 0.9980 chunk 9 optimal weight: 0.0980 chunk 93 optimal weight: 0.8980 overall best weight: 0.3558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4182 r_free = 0.4182 target = 0.165411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.146343 restraints weight = 30447.146| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 2.22 r_work: 0.3822 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3680 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7612 Z= 0.142 Angle : 0.526 4.944 10325 Z= 0.282 Chirality : 0.045 0.158 1128 Planarity : 0.004 0.042 1362 Dihedral : 5.790 52.695 1050 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 3.68 % Allowed : 16.32 % Favored : 80.00 % 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: -1.64 (0.27), residues: 956 helix: -0.38 (0.55), residues: 83 sheet: -1.22 (0.29), residues: 323 loop : -1.07 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 203 TYR 0.013 0.001 TYR A 21 PHE 0.013 0.001 PHE A 273 TRP 0.010 0.001 TRP A 188 HIS 0.003 0.001 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 7603) covalent geometry : angle 0.52278 (10307) SS BOND : bond 0.00255 ( 9) SS BOND : angle 1.51090 ( 18) hydrogen bonds : bond 0.03395 ( 223) hydrogen bonds : angle 6.55648 ( 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 170 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 140 time to evaluate : 0.417 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: A 2 ASN cc_start: 0.8352 (p0) cc_final: 0.7920 (p0) REVERT: A 198 THR cc_start: 0.6812 (p) cc_final: 0.6389 (m) REVERT: A 230 GLN cc_start: 0.7968 (mp10) cc_final: 0.7554 (mp10) REVERT: A 255 GLU cc_start: 0.7580 (tm-30) cc_final: 0.7353 (tm-30) REVERT: A 272 TYR cc_start: 0.7775 (OUTLIER) cc_final: 0.7168 (t80) REVERT: A 302 GLU cc_start: 0.6656 (mt-10) cc_final: 0.6010 (mt-10) REVERT: A 317 VAL cc_start: 0.8560 (p) cc_final: 0.8253 (m) REVERT: B 165 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7237 (mm-30) REVERT: B 176 SER cc_start: 0.7957 (OUTLIER) cc_final: 0.7283 (p) outliers start: 30 outliers final: 23 residues processed: 159 average time/residue: 0.2118 time to fit residues: 44.5777 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 : 0.332 ------------------------------------------------------------------------------- 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 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 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 569 ILE 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 236 LEU Chi-restraints excluded: chain B residue 349 VAL 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: 0.9990 chunk 94 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 10 optimal weight: 0.0980 chunk 52 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 55 optimal weight: 0.1980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 GLN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.161206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.142140 restraints weight = 30263.554| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 2.21 r_work: 0.3803 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3660 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.1623 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= 0.222 Angle : 0.568 5.760 10325 Z= 0.308 Chirality : 0.046 0.157 1128 Planarity : 0.005 0.043 1362 Dihedral : 5.966 51.663 1050 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 3.19 % Allowed : 17.30 % Favored : 79.51 % 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: -1.73 (0.27), residues: 956 helix: -0.49 (0.55), residues: 85 sheet: -1.19 (0.29), residues: 311 loop : -1.19 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 263 TYR 0.016 0.002 TYR A 195 PHE 0.016 0.002 PHE B 267 TRP 0.014 0.002 TRP A 33 HIS 0.003 0.001 HIS B 293 Details of bonding type rmsd covalent geometry : bond 0.00487 ( 7603) covalent geometry : angle 0.56358 (10307) SS BOND : bond 0.00223 ( 9) SS BOND : angle 1.69404 ( 18) hydrogen bonds : bond 0.03912 ( 223) hydrogen bonds : angle 6.71287 ( 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 168 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.271 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: 0.8360 (p0) cc_final: 0.7871 (p0) REVERT: A 230 GLN cc_start: 0.8004 (mp10) cc_final: 0.7567 (mp10) REVERT: A 255 GLU cc_start: 0.7649 (tm-30) cc_final: 0.7449 (tm-30) REVERT: A 272 TYR cc_start: 0.7823 (OUTLIER) cc_final: 0.7280 (t80) REVERT: A 302 GLU cc_start: 0.6524 (mt-10) cc_final: 0.5875 (mt-10) REVERT: A 317 VAL cc_start: 0.8582 (p) cc_final: 0.8282 (m) REVERT: B 165 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7266 (mm-30) outliers start: 26 outliers final: 24 residues processed: 157 average time/residue: 0.2044 time to fit residues: 42.3047 Evaluate side-chains 167 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 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 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 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 358 ASN 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: 2.9990 chunk 57 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 69 optimal weight: 0.0770 chunk 68 optimal weight: 0.2980 chunk 15 optimal weight: 1.9990 chunk 70 optimal weight: 0.0980 chunk 58 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4172 r_free = 0.4172 target = 0.162701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.143652 restraints weight = 30836.910| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 2.24 r_work: 0.3816 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3675 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7612 Z= 0.151 Angle : 0.527 4.791 10325 Z= 0.283 Chirality : 0.045 0.152 1128 Planarity : 0.004 0.039 1362 Dihedral : 5.792 52.130 1050 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 3.56 % Allowed : 16.69 % Favored : 79.75 % 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: -1.61 (0.27), residues: 956 helix: -0.38 (0.54), residues: 85 sheet: -1.14 (0.29), residues: 317 loop : -1.09 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 114 TYR 0.015 0.002 TYR A 21 PHE 0.013 0.001 PHE A 273 TRP 0.009 0.002 TRP A 188 HIS 0.003 0.001 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 7603) covalent geometry : angle 0.52466 (10307) SS BOND : bond 0.00208 ( 9) SS BOND : angle 1.40587 ( 18) hydrogen bonds : bond 0.03381 ( 223) hydrogen bonds : angle 6.42994 ( 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 169 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 0.389 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: 0.8344 (p0) cc_final: 0.7918 (p0) REVERT: A 198 THR cc_start: 0.6809 (p) cc_final: 0.6384 (m) REVERT: A 230 GLN cc_start: 0.8016 (mp10) cc_final: 0.7596 (mp10) REVERT: A 255 GLU cc_start: 0.7587 (tm-30) cc_final: 0.7369 (tm-30) REVERT: A 272 TYR cc_start: 0.7777 (OUTLIER) cc_final: 0.7165 (t80) REVERT: A 302 GLU cc_start: 0.6677 (mt-10) cc_final: 0.6017 (mt-10) REVERT: A 318 MET cc_start: 0.7070 (mmt) cc_final: 0.6615 (mmt) REVERT: B 176 SER cc_start: 0.7985 (OUTLIER) cc_final: 0.7325 (p) outliers start: 29 outliers final: 24 residues processed: 159 average time/residue: 0.2024 time to fit residues: 42.3930 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 : 0.383 ------------------------------------------------------------------------------- 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 347 ASN Chi-restraints excluded: chain A residue 423 ASP 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 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 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: 0.5980 chunk 79 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 83 optimal weight: 0.3980 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.160894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.141673 restraints weight = 30333.282| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 2.22 r_work: 0.3787 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3649 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 7612 Z= 0.233 Angle : 0.578 6.419 10325 Z= 0.313 Chirality : 0.046 0.157 1128 Planarity : 0.005 0.040 1362 Dihedral : 6.006 50.782 1050 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 2.94 % Allowed : 18.04 % 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: -1.77 (0.27), residues: 956 helix: -0.55 (0.55), residues: 86 sheet: -1.21 (0.29), residues: 311 loop : -1.22 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 263 TYR 0.017 0.002 TYR A 195 PHE 0.015 0.002 PHE A 273 TRP 0.015 0.002 TRP A 33 HIS 0.007 0.001 HIS B 212 Details of bonding type rmsd covalent geometry : bond 0.00515 ( 7603) covalent geometry : angle 0.57290 (10307) SS BOND : bond 0.00245 ( 9) SS BOND : angle 1.86570 ( 18) hydrogen bonds : bond 0.03959 ( 223) hydrogen bonds : angle 6.68958 ( 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 169 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 145 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: symmetry clash REVERT: A 2 ASN cc_start: 0.8336 (p0) cc_final: 0.7835 (p0) REVERT: A 230 GLN cc_start: 0.8025 (mp10) cc_final: 0.7605 (mp10) REVERT: A 272 TYR cc_start: 0.7861 (OUTLIER) cc_final: 0.7316 (t80) REVERT: A 302 GLU cc_start: 0.6502 (mt-10) cc_final: 0.5834 (mt-10) REVERT: A 467 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7471 (mp) REVERT: B 176 SER cc_start: 0.8024 (OUTLIER) cc_final: 0.7643 (p) outliers start: 24 outliers final: 21 residues processed: 161 average time/residue: 0.2025 time to fit residues: 42.9473 Evaluate side-chains 167 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 347 ASN 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 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 236 LEU Chi-restraints excluded: chain B residue 349 VAL 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: 0.9990 chunk 68 optimal weight: 0.3980 chunk 11 optimal weight: 0.6980 chunk 70 optimal weight: 0.1980 chunk 64 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 20 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: 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 = 0.164410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.145276 restraints weight = 30323.610| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 2.21 r_work: 0.3801 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3660 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7612 Z= 0.199 Angle : 0.560 6.201 10325 Z= 0.302 Chirality : 0.046 0.153 1128 Planarity : 0.004 0.039 1362 Dihedral : 5.956 50.698 1050 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 3.07 % Allowed : 18.16 % Favored : 78.77 % 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: -1.75 (0.27), residues: 956 helix: -0.58 (0.54), residues: 86 sheet: -1.21 (0.29), residues: 311 loop : -1.20 (0.27), residues: 559 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 0.014 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 covalent geometry : bond 0.00439 ( 7603) covalent geometry : angle 0.55553 (10307) SS BOND : bond 0.00226 ( 9) SS BOND : angle 1.75399 ( 18) hydrogen bonds : bond 0.03699 ( 223) hydrogen bonds : angle 6.56266 ( 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 167 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.400 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: 0.8356 (p0) cc_final: 0.7875 (p0) REVERT: A 198 THR cc_start: 0.6818 (p) cc_final: 0.6395 (m) REVERT: A 230 GLN cc_start: 0.8064 (mp10) cc_final: 0.7616 (mp10) REVERT: A 255 GLU cc_start: 0.7638 (tm-30) cc_final: 0.7329 (tm-30) REVERT: A 272 TYR cc_start: 0.7799 (OUTLIER) cc_final: 0.7184 (t80) REVERT: A 302 GLU cc_start: 0.6704 (mt-10) cc_final: 0.6051 (mt-10) REVERT: A 318 MET cc_start: 0.7112 (mmt) cc_final: 0.6647 (mmm) REVERT: A 440 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8295 (mt) REVERT: A 467 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7326 (mp) REVERT: B 176 SER cc_start: 0.7996 (OUTLIER) cc_final: 0.7611 (p) outliers start: 25 outliers final: 21 residues processed: 158 average time/residue: 0.2109 time to fit residues: 43.6310 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 : 0.383 ------------------------------------------------------------------------------- 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 347 ASN 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 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 236 LEU Chi-restraints excluded: chain B residue 349 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 0 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 82 optimal weight: 0.2980 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 0.1980 chunk 21 optimal weight: 0.4980 chunk 54 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4164 r_free = 0.4164 target = 0.164131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.145262 restraints weight = 30517.840| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 2.19 r_work: 0.3805 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3665 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7612 Z= 0.201 Angle : 0.561 6.561 10325 Z= 0.303 Chirality : 0.046 0.153 1128 Planarity : 0.004 0.041 1362 Dihedral : 5.941 50.497 1050 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 3.31 % Allowed : 18.28 % 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: -1.75 (0.27), residues: 956 helix: -0.55 (0.54), residues: 86 sheet: -1.24 (0.29), residues: 315 loop : -1.17 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 259 TYR 0.015 0.002 TYR A 195 PHE 0.014 0.002 PHE A 273 TRP 0.013 0.002 TRP A 33 HIS 0.006 0.001 HIS B 212 Details of bonding type rmsd covalent geometry : bond 0.00442 ( 7603) covalent geometry : angle 0.55755 (10307) SS BOND : bond 0.00208 ( 9) SS BOND : angle 1.60752 ( 18) hydrogen bonds : bond 0.03692 ( 223) hydrogen bonds : angle 6.57207 ( 624) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4361.76 seconds wall clock time: 74 minutes 51.65 seconds (4491.65 seconds total)