Starting phenix.real_space_refine on Thu Jul 2 07:24:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o65_70159/07_2026/9o65_70159.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o65_70159/07_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_70159/07_2026/9o65_70159.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o65_70159/07_2026/9o65_70159.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9o65_70159/07_2026/9o65_70159.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o65_70159/07_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-dev-6108/lib/python3.11/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, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb="MN MN C 402 " occ=0.45 Time building chain proxies: 1.29, 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: 0.41 Conformation dependent library (CDL) restraints added in 330.1 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: 0.71 Time building geometry restraints manager: 0.57 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 3.140 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: 1.000 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 6.580 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 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/Z covalent geometry : bond 0.00531 / 0.24 ( 7467) covalent geometry : angle 0.82095 / 0.43 (10103) hydrogen bonds : bond 0.23231 / 14.46 ( 244) hydrogen bonds : angle 6.54199 / 4.60 ( 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 : 0.218 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: 0.5004 time to fit residues: 60.8877 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 : 0.326 ------------------------------------------------------------------------------- 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... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.090812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.065502 restraints weight = 20743.490| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 4.06 r_work: 0.2893 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2901 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 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 = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 422 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (12 function evaluations) r_final: 0.2881 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1839 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= 0.175 Angle : 0.630 8.060 10103 Z= 0.321 Chirality : 0.043 0.171 1167 Planarity : 0.004 0.035 1297 Dihedral : 5.926 85.596 1027 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.40 % Allowed : 22.12 % Favored : 75.48 % 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: -1.38 (0.26), residues: 910 helix: -0.73 (0.31), residues: 288 sheet: -0.63 (0.38), residues: 183 loop : -1.06 (0.27), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 366 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/Z covalent geometry : bond 0.00411 / 0.17 ( 7467) covalent geometry : angle 0.63037 / 0.32 (10103) hydrogen bonds : bond 0.05142 / 3.15 ( 244) hydrogen bonds : angle 5.09816 / 3.63 ( 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 86 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.9007 (mp) REVERT: A 363 GLU cc_start: 0.9079 (pt0) cc_final: 0.8843 (tt0) REVERT: A 388 ASP cc_start: 0.8300 (t0) cc_final: 0.8019 (t70) REVERT: A 420 ASP cc_start: 0.8823 (m-30) cc_final: 0.8493 (t0) REVERT: A 427 LEU cc_start: 0.9146 (tp) cc_final: 0.8913 (mm) REVERT: A 447 LEU cc_start: 0.9232 (mm) cc_final: 0.8977 (mm) REVERT: A 469 TYR cc_start: 0.6952 (t80) cc_final: 0.6715 (t80) REVERT: B 31 GLU cc_start: 0.6776 (tp30) cc_final: 0.6521 (tp30) REVERT: B 67 MET cc_start: 0.5984 (mtp) cc_final: 0.5705 (mtm) REVERT: C 17 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9108 (mp) outliers start: 20 outliers final: 7 residues processed: 76 average time/residue: 0.3965 time to fit residues: 32.4017 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 : 0.235 ------------------------------------------------------------------------------- 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: 0.5980 chunk 37 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 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: 0.8980 chunk 26 optimal weight: 0.5980 chunk 33 optimal weight: 10.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3568 r_free = 0.3568 target = 0.089574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.064396 restraints weight = 20322.968| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 4.06 r_work: 0.2889 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2899 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 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 = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 422 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.2901 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7467 Z= 0.114 Angle : 0.545 6.879 10103 Z= 0.278 Chirality : 0.040 0.141 1167 Planarity : 0.003 0.032 1297 Dihedral : 5.501 86.342 1024 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.64 % Allowed : 22.60 % Favored : 74.76 % 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: -0.45 (0.32), residues: 282 sheet: -0.64 (0.38), residues: 183 loop : -0.99 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 23 TYR 0.012 0.001 TYR C 70 PHE 0.009 0.001 PHE A 66 TRP 0.005 0.001 TRP C 149 HIS 0.005 0.001 HIS A 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 ( 7467) covalent geometry : angle 0.54495 / 0.28 (10103) hydrogen bonds : bond 0.04037 / 2.49 ( 244) hydrogen bonds : angle 4.78283 / 3.42 ( 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 87 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 65 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8116 (mt-10) REVERT: A 165 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8964 (mp) REVERT: A 411 THR cc_start: 0.9376 (m) cc_final: 0.9167 (p) REVERT: A 420 ASP cc_start: 0.8845 (m-30) cc_final: 0.8490 (t0) REVERT: A 427 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.9066 (mm) REVERT: A 447 LEU cc_start: 0.9238 (mm) cc_final: 0.8883 (mm) REVERT: B 31 GLU cc_start: 0.6822 (tp30) cc_final: 0.6574 (tp30) REVERT: B 67 MET cc_start: 0.5815 (mtp) cc_final: 0.5599 (mtm) REVERT: C 17 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9091 (mp) REVERT: C 179 ASP cc_start: 0.9359 (m-30) cc_final: 0.9059 (m-30) REVERT: C 181 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7464 (mp10) outliers start: 22 outliers final: 6 residues processed: 78 average time/residue: 0.4213 time to fit residues: 35.4130 Evaluate side-chains 74 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.253 ------------------------------------------------------------------------------- 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 C residue 17 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 52 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 117 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.089439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.064309 restraints weight = 20715.324| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 4.08 r_work: 0.2889 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2898 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2898 r_free = 0.2898 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 = 0.2898 r_free = 0.2898 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 422 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2898 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7467 Z= 0.113 Angle : 0.528 8.229 10103 Z= 0.267 Chirality : 0.039 0.138 1167 Planarity : 0.003 0.032 1297 Dihedral : 5.454 86.518 1024 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.37 % Allowed : 22.60 % Favored : 74.04 % 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: -1.12 (0.27), residues: 910 helix: -0.31 (0.33), residues: 281 sheet: -0.62 (0.38), residues: 183 loop : -0.99 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 23 TYR 0.030 0.001 TYR A 469 PHE 0.009 0.001 PHE A 66 TRP 0.004 0.001 TRP C 206 HIS 0.002 0.000 HIS A 270 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 ( 7467) covalent geometry : angle 0.52750 / 0.27 (10103) hydrogen bonds : bond 0.03729 / 2.30 ( 244) hydrogen bonds : angle 4.63106 / 3.32 ( 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 93 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 65 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8043 (mt-10) REVERT: A 165 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8949 (mp) REVERT: A 411 THR cc_start: 0.9336 (m) cc_final: 0.9114 (p) REVERT: A 420 ASP cc_start: 0.8840 (m-30) cc_final: 0.8481 (t0) REVERT: A 427 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.9014 (mm) REVERT: A 447 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8893 (mm) REVERT: B 31 GLU cc_start: 0.6792 (tp30) cc_final: 0.6535 (tp30) REVERT: C 179 ASP cc_start: 0.9373 (m-30) cc_final: 0.9065 (m-30) REVERT: C 181 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.7491 (mp10) outliers start: 28 outliers final: 7 residues processed: 81 average time/residue: 0.4147 time to fit residues: 36.3288 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 : 0.301 ------------------------------------------------------------------------------- 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 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 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: 2.9990 chunk 76 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 27 optimal weight: 0.5980 chunk 73 optimal weight: 0.0970 chunk 67 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 49 optimal weight: 0.0070 chunk 86 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.090245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.065301 restraints weight = 20556.262| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 4.04 r_work: 0.2915 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2928 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2928 r_free = 0.2928 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 422 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2928 r_free = 0.2928 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 425 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2928 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7467 Z= 0.093 Angle : 0.531 8.080 10103 Z= 0.267 Chirality : 0.039 0.138 1167 Planarity : 0.003 0.040 1297 Dihedral : 5.304 85.433 1024 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.16 % Allowed : 24.04 % 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: -1.08 (0.27), residues: 910 helix: -0.27 (0.33), residues: 282 sheet: -0.63 (0.38), residues: 183 loop : -0.96 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 23 TYR 0.026 0.001 TYR A 469 PHE 0.013 0.001 PHE A 66 TRP 0.003 0.001 TRP C 149 HIS 0.005 0.001 HIS A 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.09 ( 7467) covalent geometry : angle 0.53098 / 0.27 (10103) hydrogen bonds : bond 0.03216 / 2.00 ( 244) hydrogen bonds : angle 4.51443 / 3.23 ( 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 84 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 GLU cc_start: 0.8493 (mt-10) cc_final: 0.7960 (mt-10) REVERT: A 165 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8971 (mp) REVERT: A 411 THR cc_start: 0.9308 (m) cc_final: 0.9092 (p) REVERT: A 420 ASP cc_start: 0.8809 (m-30) cc_final: 0.8458 (t0) REVERT: A 447 LEU cc_start: 0.9189 (mm) cc_final: 0.8926 (mm) REVERT: B 31 GLU cc_start: 0.6903 (tp30) cc_final: 0.6666 (tp30) REVERT: C 179 ASP cc_start: 0.9353 (m-30) cc_final: 0.9139 (m-30) outliers start: 18 outliers final: 4 residues processed: 76 average time/residue: 0.4297 time to fit residues: 35.3171 Evaluate side-chains 65 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.294 ------------------------------------------------------------------------------- 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 C residue 153 THR 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: 1.9990 chunk 40 optimal weight: 9.9990 chunk 65 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 42 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 84 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.088784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.063797 restraints weight = 20586.158| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 4.05 r_work: 0.2881 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2886 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2886 r_free = 0.2886 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 425 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2886 r_free = 0.2886 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 423 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2886 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7467 Z= 0.126 Angle : 0.560 8.204 10103 Z= 0.276 Chirality : 0.040 0.137 1167 Planarity : 0.003 0.039 1297 Dihedral : 5.416 84.848 1024 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.52 % Allowed : 24.76 % Favored : 72.72 % 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: -1.07 (0.27), residues: 910 helix: -0.17 (0.33), residues: 281 sheet: -0.65 (0.38), residues: 183 loop : -1.01 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 23 TYR 0.027 0.001 TYR A 469 PHE 0.014 0.001 PHE A 66 TRP 0.004 0.001 TRP C 206 HIS 0.005 0.001 HIS A 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 7467) covalent geometry : angle 0.55993 / 0.28 (10103) hydrogen bonds : bond 0.03710 / 2.26 ( 244) hydrogen bonds : angle 4.62569 / 3.32 ( 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 83 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 62 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8004 (mt-10) REVERT: A 165 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8958 (mp) REVERT: A 219 MET cc_start: 0.7674 (tpp) cc_final: 0.7417 (tpt) REVERT: A 267 ASP cc_start: 0.8235 (t0) cc_final: 0.8013 (t0) REVERT: A 420 ASP cc_start: 0.8807 (m-30) cc_final: 0.8449 (t0) REVERT: A 447 LEU cc_start: 0.9130 (mm) cc_final: 0.8855 (mm) REVERT: B 31 GLU cc_start: 0.6938 (tp30) cc_final: 0.6714 (tp30) REVERT: B 63 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7450 (pm20) REVERT: C 179 ASP cc_start: 0.9371 (m-30) cc_final: 0.9144 (m-30) outliers start: 21 outliers final: 9 residues processed: 76 average time/residue: 0.4366 time to fit residues: 35.7993 Evaluate side-chains 72 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.309 ------------------------------------------------------------------------------- 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 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 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: 0.9990 chunk 70 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3555 r_free = 0.3555 target = 0.088677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.063815 restraints weight = 20638.370| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 4.04 r_work: 0.2882 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2889 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 423 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 424 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2889 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7467 Z= 0.124 Angle : 0.568 9.142 10103 Z= 0.280 Chirality : 0.040 0.134 1167 Planarity : 0.003 0.048 1297 Dihedral : 5.434 84.984 1024 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.40 % Allowed : 24.88 % Favored : 72.72 % 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: -1.06 (0.27), residues: 910 helix: -0.12 (0.33), residues: 281 sheet: -0.66 (0.38), residues: 183 loop : -1.02 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 23 TYR 0.026 0.001 TYR A 469 PHE 0.011 0.001 PHE A 66 TRP 0.004 0.001 TRP C 206 HIS 0.005 0.001 HIS A 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 ( 7467) covalent geometry : angle 0.56820 / 0.28 (10103) hydrogen bonds : bond 0.03632 / 2.22 ( 244) hydrogen bonds : angle 4.61679 / 3.32 ( 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 79 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 59 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8034 (mt-10) REVERT: A 165 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8965 (mp) REVERT: A 388 ASP cc_start: 0.8082 (t0) cc_final: 0.7840 (t70) REVERT: A 420 ASP cc_start: 0.8775 (m-30) cc_final: 0.8439 (t0) REVERT: A 447 LEU cc_start: 0.9130 (mm) cc_final: 0.8827 (mm) outliers start: 20 outliers final: 9 residues processed: 73 average time/residue: 0.4332 time to fit residues: 34.1605 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 : 0.303 ------------------------------------------------------------------------------- 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 454 ASP Chi-restraints excluded: chain A residue 477 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 37 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 458 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.089074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.064127 restraints weight = 20715.025| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 4.04 r_work: 0.2888 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2896 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 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 = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 424 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2896 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7467 Z= 0.113 Angle : 0.578 8.174 10103 Z= 0.282 Chirality : 0.040 0.135 1167 Planarity : 0.003 0.058 1297 Dihedral : 5.411 84.364 1024 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.68 % Allowed : 25.72 % 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: -1.07 (0.27), residues: 910 helix: -0.10 (0.33), residues: 282 sheet: -0.77 (0.38), residues: 188 loop : -1.00 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 23 TYR 0.027 0.001 TYR A 469 PHE 0.009 0.001 PHE C 170 TRP 0.004 0.001 TRP C 206 HIS 0.004 0.000 HIS A 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 ( 7467) covalent geometry : angle 0.57798 / 0.28 (10103) hydrogen bonds : bond 0.03513 / 2.14 ( 244) hydrogen bonds : angle 4.59347 / 3.29 ( 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 72 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 PHE cc_start: 0.7628 (m-10) cc_final: 0.7400 (m-10) REVERT: A 127 GLU cc_start: 0.8500 (mt-10) cc_final: 0.7977 (mt-10) REVERT: A 165 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8944 (mp) REVERT: A 388 ASP cc_start: 0.8154 (t0) cc_final: 0.7904 (t70) REVERT: A 420 ASP cc_start: 0.8771 (m-30) cc_final: 0.8426 (t0) REVERT: A 447 LEU cc_start: 0.9093 (mm) cc_final: 0.8787 (mm) outliers start: 14 outliers final: 8 residues processed: 67 average time/residue: 0.4261 time to fit residues: 30.9552 Evaluate side-chains 66 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 442 HIS 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 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: 2.9990 chunk 9 optimal weight: 0.0970 chunk 65 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3541 r_free = 0.3541 target = 0.087775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.062944 restraints weight = 20593.470| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 4.01 r_work: 0.2860 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2866 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 424 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 424 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2866 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7467 Z= 0.170 Angle : 0.618 9.827 10103 Z= 0.303 Chirality : 0.041 0.134 1167 Planarity : 0.004 0.074 1297 Dihedral : 5.573 85.423 1024 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.04 % Allowed : 25.72 % Favored : 72.24 % 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: -1.26 (0.27), residues: 910 helix: -0.24 (0.32), residues: 289 sheet: -0.71 (0.38), residues: 186 loop : -1.22 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG C 23 TYR 0.027 0.002 TYR A 469 PHE 0.012 0.001 PHE C 170 TRP 0.005 0.001 TRP C 206 HIS 0.005 0.001 HIS A 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 ( 7467) covalent geometry : angle 0.61758 / 0.30 (10103) hydrogen bonds : bond 0.04055 / 2.45 ( 244) hydrogen bonds : angle 4.76282 / 3.41 ( 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 73 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 PHE cc_start: 0.7590 (m-10) cc_final: 0.7356 (m-10) REVERT: A 127 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8065 (mt-10) REVERT: A 165 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8959 (mp) REVERT: A 219 MET cc_start: 0.7820 (tpp) cc_final: 0.7569 (tpt) REVERT: A 388 ASP cc_start: 0.8220 (t0) cc_final: 0.7948 (t70) REVERT: A 420 ASP cc_start: 0.8777 (m-30) cc_final: 0.8440 (t0) REVERT: A 447 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8746 (mm) REVERT: B 31 GLU cc_start: 0.6484 (tp30) cc_final: 0.6218 (tp30) outliers start: 17 outliers final: 10 residues processed: 68 average time/residue: 0.4337 time to fit residues: 32.0524 Evaluate side-chains 66 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.311 ------------------------------------------------------------------------------- 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 442 HIS Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 458 ASN Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 223 VAL 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: 3.9990 chunk 23 optimal weight: 0.0270 chunk 39 optimal weight: 1.9990 chunk 88 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 68 optimal weight: 0.0060 chunk 42 optimal weight: 20.0000 chunk 55 optimal weight: 0.9990 overall best weight: 0.5856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 458 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.089684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.064902 restraints weight = 20286.679| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 4.03 r_work: 0.2910 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2918 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 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 = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 424 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2918 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 7467 Z= 0.099 Angle : 0.593 8.948 10103 Z= 0.287 Chirality : 0.040 0.136 1167 Planarity : 0.003 0.058 1297 Dihedral : 5.396 84.134 1024 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.56 % Allowed : 26.32 % Favored : 72.12 % 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: -0.19 (0.33), residues: 290 sheet: -0.62 (0.39), residues: 186 loop : -1.13 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG C 23 TYR 0.028 0.001 TYR A 469 PHE 0.008 0.001 PHE C 170 TRP 0.003 0.000 TRP C 149 HIS 0.004 0.000 HIS A 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 ( 7467) covalent geometry : angle 0.59277 / 0.29 (10103) hydrogen bonds : bond 0.03231 / 1.98 ( 244) hydrogen bonds : angle 4.54567 / 3.26 ( 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 72 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 GLU cc_start: 0.8487 (mt-10) cc_final: 0.7975 (mt-10) REVERT: A 219 MET cc_start: 0.7396 (tpp) cc_final: 0.7154 (tpt) REVERT: A 388 ASP cc_start: 0.8176 (t0) cc_final: 0.7901 (t70) REVERT: A 420 ASP cc_start: 0.8752 (m-30) cc_final: 0.8451 (t0) REVERT: A 447 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8738 (mm) outliers start: 13 outliers final: 8 residues processed: 67 average time/residue: 0.4393 time to fit residues: 31.8177 Evaluate side-chains 62 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 427 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 223 VAL 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: 6.9990 chunk 46 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3541 r_free = 0.3541 target = 0.087856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.062957 restraints weight = 20506.178| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 4.01 r_work: 0.2868 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2867 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 424 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 425 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2867 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 7467 Z= 0.183 Angle : 0.642 9.939 10103 Z= 0.314 Chirality : 0.042 0.135 1167 Planarity : 0.004 0.078 1297 Dihedral : 5.591 84.555 1024 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.56 % Allowed : 26.68 % Favored : 71.75 % 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: -1.25 (0.27), residues: 910 helix: -0.21 (0.33), residues: 289 sheet: -0.65 (0.39), residues: 186 loop : -1.26 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG C 23 TYR 0.027 0.001 TYR A 469 PHE 0.013 0.001 PHE C 170 TRP 0.006 0.001 TRP C 206 HIS 0.005 0.001 HIS A 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.18 ( 7467) covalent geometry : angle 0.64194 / 0.31 (10103) hydrogen bonds : bond 0.04087 / 2.46 ( 244) hydrogen bonds : angle 4.76668 / 3.41 ( 549) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2146.56 seconds wall clock time: 37 minutes 30.05 seconds (2250.05 seconds total)