Starting phenix.real_space_refine on Tue Feb 3 22:28:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o65_70159/02_2026/9o65_70159.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o65_70159/02_2026/9o65_70159.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9o65_70159/02_2026/9o65_70159.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o65_70159/02_2026/9o65_70159.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9o65_70159/02_2026/9o65_70159.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o65_70159/02_2026/9o65_70159.map" } resolution = 3.0 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= 0.014 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: 7 Type Number sf(0) Gaussians Mn 2 7.51 5 P 3 5.49 5 Mg 1 5.21 5 S 37 5.16 5 C 4638 2.51 5 N 1262 2.21 5 O 1405 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 7348 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3592 Classifications: {'peptide': 455} Link IDs: {'PTRANS': 19, 'TRANS': 435} Chain breaks: 1 Chain: "B" Number of atoms: 1352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1352 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 4, 'TRANS': 164} Chain: "C" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2369 Classifications: {'peptide': 294} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 281} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb="MN MN C 402 " occ=0.45 Time building chain proxies: 1.35, per 1000 atoms: 0.18 Number of scatterers: 7348 At special positions: 0 Unit cell: (78.57, 90.792, 104.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 2 24.99 S 37 16.00 P 3 15.00 Mg 1 11.99 O 1405 8.00 N 1262 7.00 C 4638 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.52 Conformation dependent library (CDL) restraints added in 274.3 milliseconds 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1734 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 6 sheets defined 35.9% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 87 through 101 removed outlier: 3.574A pdb=" N ILE A 91 " --> pdb=" O ASN A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 122 removed outlier: 3.572A pdb=" N ILE A 119 " --> pdb=" O PRO A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 145 Processing helix chain 'A' and resid 162 through 168 Processing helix chain 'A' and resid 185 through 191 Processing helix chain 'A' and resid 208 through 214 removed outlier: 3.843A pdb=" N ILE A 211 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 237 removed outlier: 3.542A pdb=" N ILE A 234 " --> pdb=" O PRO A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 260 removed outlier: 3.603A pdb=" N GLY A 258 " --> pdb=" O LYS A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 283 Processing helix chain 'A' and resid 300 through 306 Processing helix chain 'A' and resid 325 through 330 removed outlier: 3.694A pdb=" N SER A 329 " --> pdb=" O SER A 325 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 325 through 330' Processing helix chain 'A' and resid 350 through 355 Processing helix chain 'A' and resid 395 through 401 removed outlier: 4.528A pdb=" N GLY A 399 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP A 401 " --> pdb=" O PHE A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 424 removed outlier: 3.604A pdb=" N SER A 422 " --> pdb=" O GLU A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 447 removed outlier: 3.996A pdb=" N GLY A 445 " --> pdb=" O HIS A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 470 Processing helix chain 'A' and resid 487 through 493 removed outlier: 3.512A pdb=" N LEU A 493 " --> pdb=" O ILE A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 516 Processing helix chain 'B' and resid 15 through 26 Processing helix chain 'B' and resid 61 through 65 Processing helix chain 'B' and resid 67 through 75 removed outlier: 3.657A pdb=" N TYR B 71 " --> pdb=" O MET B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 92 removed outlier: 3.642A pdb=" N PHE B 90 " --> pdb=" O ASN B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 105 removed outlier: 3.511A pdb=" N TYR B 96 " --> pdb=" O ASP B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 138 Processing helix chain 'B' and resid 151 through 167 removed outlier: 3.598A pdb=" N ALA B 155 " --> pdb=" O GLY B 151 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE B 156 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS B 167 " --> pdb=" O ILE B 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 19 removed outlier: 4.364A pdb=" N VAL C 19 " --> pdb=" O ARG C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 22 No H-bonds generated for 'chain 'C' and resid 20 through 22' Processing helix chain 'C' and resid 31 through 48 removed outlier: 3.527A pdb=" N ILE C 35 " --> pdb=" O THR C 31 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER C 48 " --> pdb=" O GLU C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 80 Processing helix chain 'C' and resid 99 through 114 Processing helix chain 'C' and resid 127 through 135 removed outlier: 3.582A pdb=" N ILE C 133 " --> pdb=" O SER C 129 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY C 135 " --> pdb=" O ASN C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 144 Processing helix chain 'C' and resid 145 through 157 removed outlier: 3.937A pdb=" N TRP C 149 " --> pdb=" O ASN C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 188 removed outlier: 4.285A pdb=" N ILE C 186 " --> pdb=" O SER C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 207 Processing helix chain 'C' and resid 228 through 240 Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 66 removed outlier: 6.607A pdb=" N ALA A 65 " --> pdb=" O CYS C 291 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N PHE C 293 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY C 280 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 105 through 106 removed outlier: 3.648A pdb=" N TYR A 129 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU A 220 " --> pdb=" O ASP A 244 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LEU A 243 " --> pdb=" O ASP A 267 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 311 through 313 removed outlier: 6.742A pdb=" N LEU A 312 " --> pdb=" O THR A 337 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU A 336 " --> pdb=" O ASN A 361 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU A 430 " --> pdb=" O ASP A 454 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU A 453 " --> pdb=" O VAL A 477 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 38 through 46 removed outlier: 6.722A pdb=" N THR B 2 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ASP B 54 " --> pdb=" O THR B 2 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TYR B 4 " --> pdb=" O ASP B 54 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N LEU B 56 " --> pdb=" O TYR B 4 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU B 6 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N PHE B 78 " --> pdb=" O VAL B 112 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N VAL B 114 " --> pdb=" O PHE B 78 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N CYS B 80 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ASN B 116 " --> pdb=" O CYS B 80 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N PHE B 82 " --> pdb=" O ASN B 116 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 52 through 55 removed outlier: 6.659A pdb=" N PHE C 170 " --> pdb=" O CYS C 245 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL C 264 " --> pdb=" O ILE C 244 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 208 through 209 removed outlier: 7.186A pdb=" N ASP C 208 " --> pdb=" O PHE C 227 " (cutoff:3.500A) 244 hydrogen bonds defined for protein. 549 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: 0.89 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2443 1.34 - 1.46: 845 1.46 - 1.57: 4123 1.57 - 1.69: 2 1.69 - 1.81: 54 Bond restraints: 7467 Sorted by residual: bond pdb=" O5' GNP B 201 " pdb=" PA GNP B 201 " ideal model delta sigma weight residual 1.660 1.799 -0.139 2.00e-02 2.50e+03 4.81e+01 bond pdb=" C5' GNP B 201 " pdb=" O5' GNP B 201 " ideal model delta sigma weight residual 1.403 1.294 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" N3B GNP B 201 " pdb=" PB GNP B 201 " ideal model delta sigma weight residual 1.681 1.595 0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" O3A GNP B 201 " pdb=" PA GNP B 201 " ideal model delta sigma weight residual 1.627 1.554 0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C4 GNP B 201 " pdb=" N3 GNP B 201 " ideal model delta sigma weight residual 1.341 1.400 -0.059 2.00e-02 2.50e+03 8.81e+00 ... (remaining 7462 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.25: 10021 3.25 - 6.50: 70 6.50 - 9.74: 8 9.74 - 12.99: 2 12.99 - 16.24: 2 Bond angle restraints: 10103 Sorted by residual: angle pdb=" O2B GNP B 201 " pdb=" PB GNP B 201 " pdb=" O3A GNP B 201 " ideal model delta sigma weight residual 107.69 91.45 16.24 3.00e+00 1.11e-01 2.93e+01 angle pdb=" O2A GNP B 201 " pdb=" PA GNP B 201 " pdb=" O5' GNP B 201 " ideal model delta sigma weight residual 108.80 93.46 15.34 3.00e+00 1.11e-01 2.62e+01 angle pdb=" C VAL C 94 " pdb=" N ASP C 95 " pdb=" CA ASP C 95 " ideal model delta sigma weight residual 122.81 116.89 5.92 1.68e+00 3.54e-01 1.24e+01 angle pdb=" CA ILE C 244 " pdb=" CB ILE C 244 " pdb=" CG1 ILE C 244 " ideal model delta sigma weight residual 110.40 116.30 -5.90 1.70e+00 3.46e-01 1.21e+01 angle pdb=" N GLY C 135 " pdb=" CA GLY C 135 " pdb=" C GLY C 135 " ideal model delta sigma weight residual 113.18 121.33 -8.15 2.37e+00 1.78e-01 1.18e+01 ... (remaining 10098 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.87: 4012 16.87 - 33.74: 414 33.74 - 50.61: 135 50.61 - 67.48: 32 67.48 - 84.35: 7 Dihedral angle restraints: 4600 sinusoidal: 1923 harmonic: 2677 Sorted by residual: dihedral pdb=" CG ARG C 50 " pdb=" CD ARG C 50 " pdb=" NE ARG C 50 " pdb=" CZ ARG C 50 " ideal model delta sinusoidal sigma weight residual -90.00 -133.13 43.13 2 1.50e+01 4.44e-03 9.97e+00 dihedral pdb=" N ARG C 187 " pdb=" CA ARG C 187 " pdb=" CB ARG C 187 " pdb=" CG ARG C 187 " ideal model delta sinusoidal sigma weight residual -60.00 -117.16 57.16 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" CB ARG C 187 " pdb=" CG ARG C 187 " pdb=" CD ARG C 187 " pdb=" NE ARG C 187 " ideal model delta sinusoidal sigma weight residual -180.00 -123.29 -56.71 3 1.50e+01 4.44e-03 9.41e+00 ... (remaining 4597 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1000 0.068 - 0.136: 155 0.136 - 0.204: 9 0.204 - 0.272: 2 0.272 - 0.340: 1 Chirality restraints: 1167 Sorted by residual: chirality pdb=" C4' GNP B 201 " pdb=" C3' GNP B 201 " pdb=" C5' GNP B 201 " pdb=" O4' GNP B 201 " both_signs ideal model delta sigma weight residual False -2.44 -2.78 0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" C2' GNP B 201 " pdb=" C1' GNP B 201 " pdb=" C3' GNP B 201 " pdb=" O2' GNP B 201 " both_signs ideal model delta sigma weight residual False -2.55 -2.81 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA ARG B 68 " pdb=" N ARG B 68 " pdb=" C ARG B 68 " pdb=" CB ARG B 68 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 1164 not shown) Planarity restraints: 1297 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 448 " -0.219 9.50e-02 1.11e+02 9.89e-02 7.84e+00 pdb=" NE ARG A 448 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG A 448 " -0.022 2.00e-02 2.50e+03 pdb=" NH1 ARG A 448 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG A 448 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 346 " -0.007 2.00e-02 2.50e+03 1.94e-02 7.52e+00 pdb=" CG TYR A 346 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR A 346 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR A 346 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 346 " 0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR A 346 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 346 " 0.029 2.00e-02 2.50e+03 pdb=" OH TYR A 346 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 246 " 0.219 9.50e-02 1.11e+02 9.88e-02 7.13e+00 pdb=" NE ARG C 246 " -0.020 2.00e-02 2.50e+03 pdb=" CZ ARG C 246 " 0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG C 246 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG C 246 " 0.002 2.00e-02 2.50e+03 ... (remaining 1294 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 48 2.56 - 3.14: 5727 3.14 - 3.73: 10615 3.73 - 4.31: 14937 4.31 - 4.90: 25071 Nonbonded interactions: 56398 Sorted by model distance: nonbonded pdb=" OG SER B 17 " pdb="MG MG B 202 " model vdw 1.973 2.170 nonbonded pdb=" O2B GNP B 201 " pdb="MG MG B 202 " model vdw 1.986 2.170 nonbonded pdb=" OG1 THR B 35 " pdb="MG MG B 202 " model vdw 2.004 2.170 nonbonded pdb=" ND2 ASN C 124 " pdb="MN MN C 401 " model vdw 2.141 2.400 nonbonded pdb=" OE1 GLU A 127 " pdb=" OH TYR A 129 " model vdw 2.311 3.040 ... (remaining 56393 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.93 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: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.500 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:5.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 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 : 0.005 0.139 7467 Z= 0.240 Angle : 0.821 16.238 10103 Z= 0.429 Chirality : 0.048 0.340 1167 Planarity : 0.009 0.099 1297 Dihedral : 15.628 84.350 2866 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.60 % Allowed : 22.72 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -1.53 (0.27), residues: 910 helix: -1.05 (0.30), residues: 295 sheet: -0.72 (0.39), residues: 180 loop : -0.97 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.004 ARG A 448 TYR 0.030 0.005 TYR A 346 PHE 0.017 0.002 PHE C 81 TRP 0.017 0.003 TRP C 206 HIS 0.003 0.001 HIS A 442 Details of bonding type rmsd covalent geometry : bond 0.00531 ( 7467) covalent geometry : angle 0.82095 (10103) hydrogen bonds : bond 0.23231 ( 244) hydrogen bonds : angle 6.54199 ( 549) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 111 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7070 (pm20) REVERT: B 160 VAL cc_start: 0.9234 (t) cc_final: 0.8816 (p) outliers start: 5 outliers final: 1 residues processed: 115 average time/residue: 0.4581 time to fit residues: 55.8161 Evaluate side-chains 58 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain C residue 223 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.090331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.065463 restraints weight = 20848.360| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 4.01 r_work: 0.2896 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2904 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 413 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2884 r_free = 0.2884 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 420 | |-----------------------------------------------------------------------------| r_final: 0.2884 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7467 Z= 0.174 Angle : 0.630 8.049 10103 Z= 0.322 Chirality : 0.043 0.172 1167 Planarity : 0.004 0.035 1297 Dihedral : 5.923 85.315 1027 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.40 % Allowed : 22.24 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -1.40 (0.26), residues: 910 helix: -0.73 (0.31), residues: 288 sheet: -0.75 (0.38), residues: 188 loop : -1.03 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 448 TYR 0.013 0.001 TYR C 70 PHE 0.013 0.001 PHE C 170 TRP 0.007 0.001 TRP C 206 HIS 0.005 0.001 HIS A 498 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 7467) covalent geometry : angle 0.63033 (10103) hydrogen bonds : bond 0.05215 ( 244) hydrogen bonds : angle 5.10221 ( 549) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.9011 (mp) REVERT: A 363 GLU cc_start: 0.9061 (pt0) cc_final: 0.8830 (tt0) REVERT: A 388 ASP cc_start: 0.8260 (t0) cc_final: 0.7973 (t70) REVERT: A 420 ASP cc_start: 0.8820 (m-30) cc_final: 0.8499 (t0) REVERT: A 427 LEU cc_start: 0.9146 (tp) cc_final: 0.8909 (mm) REVERT: A 447 LEU cc_start: 0.9241 (mm) cc_final: 0.8988 (mm) REVERT: A 469 TYR cc_start: 0.6946 (t80) cc_final: 0.6713 (t80) REVERT: B 31 GLU cc_start: 0.6769 (tp30) cc_final: 0.6523 (tp30) REVERT: B 67 MET cc_start: 0.5999 (mtp) cc_final: 0.5721 (mtm) REVERT: C 17 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9115 (mp) outliers start: 20 outliers final: 7 residues processed: 77 average time/residue: 0.3640 time to fit residues: 30.0395 Evaluate side-chains 65 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 442 HIS Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 296 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 44 optimal weight: 9.9990 chunk 57 optimal weight: 8.9990 chunk 61 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 33 optimal weight: 9.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 ASN ** 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 = 0.3536 r_free = 0.3536 target = 0.087768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.062814 restraints weight = 20537.730| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 4.01 r_work: 0.2850 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2862 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 420 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 423 | |-----------------------------------------------------------------------------| r_final: 0.2863 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7467 Z= 0.171 Angle : 0.578 7.447 10103 Z= 0.296 Chirality : 0.041 0.141 1167 Planarity : 0.003 0.032 1297 Dihedral : 5.702 88.080 1024 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.88 % Allowed : 22.72 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -1.40 (0.27), residues: 910 helix: -0.60 (0.31), residues: 288 sheet: -0.66 (0.39), residues: 183 loop : -1.18 (0.27), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 366 TYR 0.013 0.001 TYR C 70 PHE 0.010 0.001 PHE C 170 TRP 0.006 0.001 TRP C 206 HIS 0.002 0.001 HIS A 270 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 7467) covalent geometry : angle 0.57764 (10103) hydrogen bonds : bond 0.04644 ( 244) hydrogen bonds : angle 4.92491 ( 549) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 58 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8096 (mt-10) REVERT: A 165 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8957 (mp) REVERT: A 219 MET cc_start: 0.8305 (ttt) cc_final: 0.8082 (tpp) REVERT: A 388 ASP cc_start: 0.8336 (t0) cc_final: 0.8066 (t70) REVERT: A 420 ASP cc_start: 0.8800 (m-30) cc_final: 0.8473 (t0) REVERT: A 447 LEU cc_start: 0.9261 (mm) cc_final: 0.8871 (mm) REVERT: A 469 TYR cc_start: 0.7121 (t80) cc_final: 0.6914 (t80) REVERT: B 67 MET cc_start: 0.5996 (mtp) cc_final: 0.5769 (mtm) REVERT: C 17 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9105 (mp) REVERT: C 181 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.7547 (mp10) outliers start: 24 outliers final: 7 residues processed: 74 average time/residue: 0.3845 time to fit residues: 30.4801 Evaluate side-chains 66 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 442 HIS Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 296 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 52 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 16 optimal weight: 0.0770 chunk 82 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 overall best weight: 1.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 HIS C 117 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.088507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.063339 restraints weight = 20722.607| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 4.09 r_work: 0.2868 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 423 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 424 | |-----------------------------------------------------------------------------| r_final: 0.2877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7467 Z= 0.119 Angle : 0.531 7.942 10103 Z= 0.269 Chirality : 0.040 0.141 1167 Planarity : 0.003 0.033 1297 Dihedral : 5.542 88.184 1024 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.88 % Allowed : 23.44 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -1.23 (0.27), residues: 910 helix: -0.35 (0.33), residues: 281 sheet: -0.66 (0.38), residues: 183 loop : -1.11 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 23 TYR 0.013 0.001 TYR C 70 PHE 0.010 0.001 PHE A 66 TRP 0.004 0.001 TRP C 149 HIS 0.003 0.000 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 7467) covalent geometry : angle 0.53069 (10103) hydrogen bonds : bond 0.03903 ( 244) hydrogen bonds : angle 4.73600 ( 549) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 60 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8064 (mt-10) REVERT: A 155 GLU cc_start: 0.8528 (mp0) cc_final: 0.8323 (mp0) REVERT: A 165 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8940 (mp) REVERT: A 267 ASP cc_start: 0.8287 (t0) cc_final: 0.8057 (t0) REVERT: A 363 GLU cc_start: 0.8939 (pt0) cc_final: 0.8738 (tt0) REVERT: A 420 ASP cc_start: 0.8810 (m-30) cc_final: 0.8475 (t0) REVERT: A 447 LEU cc_start: 0.9237 (mm) cc_final: 0.8762 (mm) REVERT: B 31 GLU cc_start: 0.6700 (tp30) cc_final: 0.6428 (tp30) REVERT: C 181 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.7501 (mp10) outliers start: 24 outliers final: 8 residues processed: 76 average time/residue: 0.3957 time to fit residues: 32.3584 Evaluate side-chains 66 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 442 HIS Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 296 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 48 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 27 optimal weight: 0.0670 chunk 73 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 49 optimal weight: 0.0980 chunk 86 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 41 optimal weight: 20.0000 overall best weight: 0.5922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.089607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.064654 restraints weight = 20507.974| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 4.02 r_work: 0.2894 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2909 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 424 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 424 | |-----------------------------------------------------------------------------| r_final: 0.2910 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7467 Z= 0.095 Angle : 0.530 8.270 10103 Z= 0.264 Chirality : 0.039 0.137 1167 Planarity : 0.003 0.040 1297 Dihedral : 5.379 86.706 1024 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.00 % Allowed : 23.20 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -1.14 (0.27), residues: 910 helix: -0.29 (0.33), residues: 282 sheet: -0.66 (0.38), residues: 183 loop : -1.01 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 23 TYR 0.033 0.001 TYR A 469 PHE 0.013 0.001 PHE A 66 TRP 0.004 0.001 TRP C 149 HIS 0.005 0.000 HIS A 498 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 7467) covalent geometry : angle 0.53029 (10103) hydrogen bonds : bond 0.03336 ( 244) hydrogen bonds : angle 4.54969 ( 549) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 67 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 GLU cc_start: 0.8509 (mt-10) cc_final: 0.7984 (mt-10) REVERT: A 149 MET cc_start: 0.8604 (ttt) cc_final: 0.8399 (ttm) REVERT: A 155 GLU cc_start: 0.8579 (mp0) cc_final: 0.8341 (mp0) REVERT: A 165 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8959 (mp) REVERT: A 267 ASP cc_start: 0.8259 (t0) cc_final: 0.8032 (t0) REVERT: A 388 ASP cc_start: 0.8103 (t70) cc_final: 0.7872 (t70) REVERT: A 420 ASP cc_start: 0.8840 (m-30) cc_final: 0.8476 (t0) REVERT: A 447 LEU cc_start: 0.9225 (mm) cc_final: 0.8887 (mm) REVERT: B 31 GLU cc_start: 0.6794 (tp30) cc_final: 0.6475 (tp30) REVERT: B 63 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7524 (pm20) REVERT: C 179 ASP cc_start: 0.9363 (m-30) cc_final: 0.9044 (m-30) REVERT: C 181 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.7435 (mp10) outliers start: 25 outliers final: 7 residues processed: 84 average time/residue: 0.3996 time to fit residues: 36.0782 Evaluate side-chains 68 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 442 HIS Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 223 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 38 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 42 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 HIS ** A 482 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 = 0.3515 r_free = 0.3515 target = 0.086423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.061469 restraints weight = 20842.290| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 4.03 r_work: 0.2820 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2833 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 424 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 424 | |-----------------------------------------------------------------------------| r_final: 0.2833 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7467 Z= 0.223 Angle : 0.628 8.534 10103 Z= 0.311 Chirality : 0.042 0.138 1167 Planarity : 0.004 0.038 1297 Dihedral : 5.766 87.834 1024 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.88 % Allowed : 24.52 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -1.28 (0.27), residues: 910 helix: -0.28 (0.33), residues: 280 sheet: -0.82 (0.38), residues: 193 loop : -1.15 (0.27), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 23 TYR 0.025 0.002 TYR A 469 PHE 0.016 0.001 PHE A 66 TRP 0.007 0.001 TRP C 206 HIS 0.005 0.001 HIS A 498 Details of bonding type rmsd covalent geometry : bond 0.00528 ( 7467) covalent geometry : angle 0.62802 (10103) hydrogen bonds : bond 0.04752 ( 244) hydrogen bonds : angle 4.96420 ( 549) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 56 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 MET cc_start: 0.8632 (OUTLIER) cc_final: 0.8420 (ttm) REVERT: A 155 GLU cc_start: 0.8739 (mp0) cc_final: 0.8459 (mp0) REVERT: A 165 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8945 (mp) REVERT: A 388 ASP cc_start: 0.7970 (t70) cc_final: 0.7727 (t70) REVERT: A 420 ASP cc_start: 0.8758 (m-30) cc_final: 0.8437 (t0) REVERT: A 447 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8824 (mm) REVERT: B 31 GLU cc_start: 0.6843 (tp30) cc_final: 0.6603 (tp30) REVERT: B 63 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7553 (pm20) REVERT: C 181 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.7538 (mp10) outliers start: 24 outliers final: 13 residues processed: 70 average time/residue: 0.4181 time to fit residues: 31.3594 Evaluate side-chains 73 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 55 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 442 HIS Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 296 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 9 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 72 optimal weight: 0.4980 chunk 79 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 0.0870 chunk 62 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 overall best weight: 0.9164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.088225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.063195 restraints weight = 20589.750| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 4.05 r_work: 0.2867 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 424 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 422 | |-----------------------------------------------------------------------------| r_final: 0.2877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7467 Z= 0.112 Angle : 0.577 8.528 10103 Z= 0.287 Chirality : 0.041 0.138 1167 Planarity : 0.003 0.039 1297 Dihedral : 5.524 87.363 1024 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.88 % Allowed : 24.76 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -1.15 (0.27), residues: 910 helix: -0.15 (0.33), residues: 280 sheet: -0.78 (0.38), residues: 193 loop : -1.07 (0.27), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 23 TYR 0.026 0.001 TYR A 469 PHE 0.013 0.001 PHE A 66 TRP 0.004 0.001 TRP C 149 HIS 0.007 0.001 HIS A 498 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 7467) covalent geometry : angle 0.57702 (10103) hydrogen bonds : bond 0.03652 ( 244) hydrogen bonds : angle 4.71232 ( 549) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 60 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8048 (mt-10) REVERT: A 155 GLU cc_start: 0.8738 (mp0) cc_final: 0.8470 (mp0) REVERT: A 165 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8943 (mp) REVERT: A 388 ASP cc_start: 0.8058 (t70) cc_final: 0.7759 (t70) REVERT: A 420 ASP cc_start: 0.8771 (m-30) cc_final: 0.8432 (t0) REVERT: A 447 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8842 (mm) REVERT: B 31 GLU cc_start: 0.6838 (tp30) cc_final: 0.6618 (tp30) REVERT: C 179 ASP cc_start: 0.9372 (m-30) cc_final: 0.9049 (m-30) REVERT: C 181 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.7487 (mp10) outliers start: 24 outliers final: 10 residues processed: 77 average time/residue: 0.3822 time to fit residues: 31.6175 Evaluate side-chains 68 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 442 HIS Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 296 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 37 optimal weight: 8.9990 chunk 88 optimal weight: 9.9990 chunk 65 optimal weight: 0.0040 chunk 36 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.087355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.062416 restraints weight = 20873.073| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 4.04 r_work: 0.2850 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 422 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 422 | |-----------------------------------------------------------------------------| r_final: 0.2857 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 7467 Z= 0.160 Angle : 0.610 9.177 10103 Z= 0.300 Chirality : 0.041 0.145 1167 Planarity : 0.004 0.064 1297 Dihedral : 5.599 87.482 1024 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.16 % Allowed : 25.48 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -1.31 (0.27), residues: 910 helix: -0.29 (0.32), residues: 287 sheet: -0.76 (0.38), residues: 188 loop : -1.23 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 23 TYR 0.027 0.001 TYR A 469 PHE 0.011 0.001 PHE C 170 TRP 0.005 0.001 TRP C 206 HIS 0.003 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 7467) covalent geometry : angle 0.60962 (10103) hydrogen bonds : bond 0.03978 ( 244) hydrogen bonds : angle 4.77665 ( 549) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 55 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 PHE cc_start: 0.7628 (m-10) cc_final: 0.7407 (m-10) REVERT: A 155 GLU cc_start: 0.8766 (mp0) cc_final: 0.8534 (mp0) REVERT: A 165 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8945 (mp) REVERT: A 388 ASP cc_start: 0.8047 (t70) cc_final: 0.7757 (t70) REVERT: A 420 ASP cc_start: 0.8773 (m-30) cc_final: 0.8431 (t0) REVERT: A 447 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8771 (mm) REVERT: A 457 GLU cc_start: 0.9253 (tm-30) cc_final: 0.8957 (tp30) REVERT: B 31 GLU cc_start: 0.6850 (tp30) cc_final: 0.6641 (tp30) REVERT: C 181 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.7520 (mp10) outliers start: 18 outliers final: 10 residues processed: 67 average time/residue: 0.3837 time to fit residues: 27.7706 Evaluate side-chains 69 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 442 HIS Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 296 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 37 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 36 optimal weight: 0.7980 chunk 27 optimal weight: 0.0010 chunk 61 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 51 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 GLN ** A 498 HIS ** 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 = 0.3558 r_free = 0.3558 target = 0.088910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.063982 restraints weight = 20476.667| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 4.03 r_work: 0.2883 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2895 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 422 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 423 | |-----------------------------------------------------------------------------| r_final: 0.2895 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 7467 Z= 0.101 Angle : 0.588 8.999 10103 Z= 0.286 Chirality : 0.040 0.181 1167 Planarity : 0.004 0.073 1297 Dihedral : 5.448 87.065 1024 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.04 % Allowed : 25.36 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -1.22 (0.27), residues: 910 helix: -0.24 (0.33), residues: 288 sheet: -0.64 (0.38), residues: 186 loop : -1.19 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 23 TYR 0.028 0.001 TYR A 469 PHE 0.008 0.001 PHE C 170 TRP 0.004 0.001 TRP C 149 HIS 0.002 0.000 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 7467) covalent geometry : angle 0.58764 (10103) hydrogen bonds : bond 0.03328 ( 244) hydrogen bonds : angle 4.59150 ( 549) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 PHE cc_start: 0.7536 (m-10) cc_final: 0.7314 (m-10) REVERT: A 155 GLU cc_start: 0.8773 (mp0) cc_final: 0.8568 (mp0) REVERT: A 165 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8987 (mp) REVERT: A 219 MET cc_start: 0.7502 (tpp) cc_final: 0.7298 (tpt) REVERT: A 388 ASP cc_start: 0.8081 (t70) cc_final: 0.7774 (t70) REVERT: A 420 ASP cc_start: 0.8780 (m-30) cc_final: 0.8441 (t0) REVERT: A 447 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8763 (mm) REVERT: A 457 GLU cc_start: 0.9236 (tm-30) cc_final: 0.9001 (tp30) REVERT: B 31 GLU cc_start: 0.6853 (tp30) cc_final: 0.6613 (tp30) REVERT: C 179 ASP cc_start: 0.9357 (m-30) cc_final: 0.9034 (m-30) REVERT: C 181 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7399 (mp10) REVERT: C 286 ASP cc_start: 0.8697 (OUTLIER) cc_final: 0.8351 (p0) outliers start: 17 outliers final: 7 residues processed: 68 average time/residue: 0.3779 time to fit residues: 27.7456 Evaluate side-chains 68 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 442 HIS Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 296 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 62 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 68 optimal weight: 0.0670 chunk 42 optimal weight: 20.0000 chunk 55 optimal weight: 1.9990 overall best weight: 2.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.087250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.062376 restraints weight = 20608.732| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 4.02 r_work: 0.2848 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2861 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 423 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 424 | |-----------------------------------------------------------------------------| r_final: 0.2860 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 7467 Z= 0.175 Angle : 0.627 10.124 10103 Z= 0.306 Chirality : 0.042 0.212 1167 Planarity : 0.004 0.077 1297 Dihedral : 5.598 86.506 1024 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.68 % Allowed : 25.96 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -1.30 (0.27), residues: 910 helix: -0.25 (0.33), residues: 287 sheet: -0.68 (0.39), residues: 186 loop : -1.29 (0.27), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG C 23 TYR 0.028 0.002 TYR A 469 PHE 0.012 0.001 PHE C 170 TRP 0.006 0.001 TRP C 206 HIS 0.003 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 7467) covalent geometry : angle 0.62661 (10103) hydrogen bonds : bond 0.04094 ( 244) hydrogen bonds : angle 4.78877 ( 549) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 GLU cc_start: 0.8796 (mp0) cc_final: 0.8535 (mp0) REVERT: A 165 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8952 (mp) REVERT: A 388 ASP cc_start: 0.8130 (t70) cc_final: 0.7831 (t70) REVERT: A 420 ASP cc_start: 0.8742 (m-30) cc_final: 0.8463 (t0) REVERT: A 447 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8727 (mm) REVERT: A 457 GLU cc_start: 0.9251 (tm-30) cc_final: 0.9037 (tp30) REVERT: C 181 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.7500 (mp10) REVERT: C 286 ASP cc_start: 0.8737 (OUTLIER) cc_final: 0.8397 (p0) outliers start: 14 outliers final: 7 residues processed: 62 average time/residue: 0.4426 time to fit residues: 29.3374 Evaluate side-chains 61 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 442 HIS Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 296 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 38 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 51 optimal weight: 0.3980 chunk 65 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 29 optimal weight: 0.2980 chunk 24 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.089311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.064445 restraints weight = 20376.790| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 4.01 r_work: 0.2896 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2907 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 424 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 424 | |-----------------------------------------------------------------------------| r_final: 0.2908 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7467 Z= 0.101 Angle : 0.592 11.213 10103 Z= 0.287 Chirality : 0.040 0.173 1167 Planarity : 0.004 0.058 1297 Dihedral : 5.422 86.655 1024 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.32 % Allowed : 26.32 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -1.19 (0.27), residues: 910 helix: -0.21 (0.33), residues: 288 sheet: -0.62 (0.39), residues: 186 loop : -1.18 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 23 TYR 0.028 0.001 TYR A 469 PHE 0.006 0.001 PHE C 170 TRP 0.004 0.000 TRP C 149 HIS 0.002 0.000 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 7467) covalent geometry : angle 0.59231 (10103) hydrogen bonds : bond 0.03193 ( 244) hydrogen bonds : angle 4.55370 ( 549) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1874.15 seconds wall clock time: 32 minutes 39.03 seconds (1959.03 seconds total)