Starting phenix.real_space_refine on Thu Aug 6 10:52:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zjn_74329/08_2026/9zjn_74329_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zjn_74329/08_2026/9zjn_74329.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zjn_74329/08_2026/9zjn_74329_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zjn_74329/08_2026/9zjn_74329_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zjn_74329/08_2026/9zjn_74329.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zjn_74329/08_2026/9zjn_74329.map" } resolution = 3.2 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= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 S 50 5.16 5 C 4535 2.51 5 N 1227 2.21 5 O 1364 1.98 5 H 7386 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14564 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 5643 Classifications: {'peptide': 357} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 345} Chain breaks: 1 Chain: "B" Number of atoms: 7708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 7708 Classifications: {'peptide': 485} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 470} Chain breaks: 2 Chain: "C" Number of atoms: 1201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1201 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 4, 'TRANS': 66} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 11 Unusual residues: {' ZN': 1, 'SAL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1688 SG CYS A 150 28.849 65.477 37.844 1.00 0.00 S ATOM 1750 SG CYS A 155 25.070 65.961 37.578 1.00 0.00 S ATOM 1815 SG CYS A 160 26.396 63.480 39.825 1.00 0.00 S ATOM 7331 SG CYS B 150 17.580 60.419 108.188 1.00 0.00 S ATOM 7393 SG CYS B 155 14.554 62.488 108.976 1.00 0.00 S ATOM 7458 SG CYS B 160 17.234 63.645 106.634 1.00 0.00 S Time building chain proxies: 1.99, per 1000 atoms: 0.14 Number of scatterers: 14564 At special positions: 0 Unit cell: (67.149, 103.625, 156.681, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 50 16.00 O 1364 8.00 N 1227 7.00 C 4535 6.00 H 7386 1.00 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: 0.92 Conformation dependent library (CDL) restraints added in 378.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 900 " pdb="ZN ZN A 900 " - pdb=" ND1 HIS A 157 " pdb="ZN ZN A 900 " - pdb=" SG CYS A 160 " pdb="ZN ZN A 900 " - pdb=" SG CYS A 155 " pdb="ZN ZN A 900 " - pdb=" SG CYS A 150 " pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" ND1 HIS B 157 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 150 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 160 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 155 " Number of angles added : 6 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1774 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 2 sheets defined 70.9% alpha, 2.0% 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 42 through 59 Processing helix chain 'A' and resid 80 through 88 removed outlier: 4.018A pdb=" N ALA A 86 " --> pdb=" O CYS A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 102 Processing helix chain 'A' and resid 115 through 117 No H-bonds generated for 'chain 'A' and resid 115 through 117' Processing helix chain 'A' and resid 124 through 138 removed outlier: 3.575A pdb=" N VAL A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 178 Processing helix chain 'A' and resid 179 through 194 removed outlier: 3.592A pdb=" N LEU A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL A 193 " --> pdb=" O HIS A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 212 removed outlier: 3.603A pdb=" N VAL A 204 " --> pdb=" O GLU A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 230 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.567A pdb=" N LYS A 239 " --> pdb=" O VAL A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 256 Processing helix chain 'A' and resid 265 through 276 Processing helix chain 'A' and resid 278 through 289 Processing helix chain 'A' and resid 292 through 297 Processing helix chain 'A' and resid 297 through 305 Processing helix chain 'A' and resid 307 through 318 removed outlier: 3.528A pdb=" N ALA A 311 " --> pdb=" O ASN A 307 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP A 318 " --> pdb=" O LEU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 339 Processing helix chain 'A' and resid 341 through 351 Processing helix chain 'A' and resid 364 through 372 Processing helix chain 'A' and resid 374 through 379 Processing helix chain 'A' and resid 389 through 404 removed outlier: 3.546A pdb=" N GLU A 401 " --> pdb=" O ILE A 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 59 Processing helix chain 'B' and resid 80 through 88 Processing helix chain 'B' and resid 88 through 102 Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'B' and resid 124 through 138 removed outlier: 3.523A pdb=" N VAL B 128 " --> pdb=" O GLY B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 177 Processing helix chain 'B' and resid 179 through 194 removed outlier: 3.962A pdb=" N LEU B 185 " --> pdb=" O GLU B 181 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG B 188 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL B 193 " --> pdb=" O HIS B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 212 removed outlier: 4.234A pdb=" N VAL B 204 " --> pdb=" O GLU B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 229 removed outlier: 3.598A pdb=" N LYS B 229 " --> pdb=" O GLU B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 241 Processing helix chain 'B' and resid 242 through 256 Processing helix chain 'B' and resid 267 through 276 Processing helix chain 'B' and resid 278 through 289 Processing helix chain 'B' and resid 297 through 305 Processing helix chain 'B' and resid 307 through 318 removed outlier: 3.622A pdb=" N ASP B 318 " --> pdb=" O LEU B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 340 Processing helix chain 'B' and resid 341 through 351 Processing helix chain 'B' and resid 364 through 371 Processing helix chain 'B' and resid 374 through 379 Processing helix chain 'B' and resid 389 through 404 removed outlier: 3.670A pdb=" N GLU B 401 " --> pdb=" O ILE B 397 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASP B 402 " --> pdb=" O LEU B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 440 Processing helix chain 'B' and resid 440 through 452 Processing helix chain 'B' and resid 487 through 508 Processing helix chain 'B' and resid 508 through 520 Processing helix chain 'B' and resid 523 through 529 Processing helix chain 'B' and resid 537 through 558 Processing helix chain 'C' and resid 29 through 46 removed outlier: 3.845A pdb=" N LYS C 33 " --> pdb=" O ASP C 29 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N HIS C 45 " --> pdb=" O THR C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 72 Processing helix chain 'C' and resid 74 through 89 Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 79 Processing sheet with id=AA2, first strand: chain 'B' and resid 76 through 79 443 hydrogen bonds defined for protein. 1314 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.54 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7357 1.03 - 1.23: 29 1.23 - 1.42: 2832 1.42 - 1.61: 4367 1.61 - 1.81: 71 Bond restraints: 14656 Sorted by residual: bond pdb=" N GLY B 40 " pdb=" H1 GLY B 40 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" N GLY A 40 " pdb=" H1 GLY A 40 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" CB VAL A 170 " pdb=" CG2 VAL A 170 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.23e-01 bond pdb=" CB ILE C 38 " pdb=" CG2 ILE C 38 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.90e-01 bond pdb=" CB ILE A 205 " pdb=" CG2 ILE A 205 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.61e-01 ... (remaining 14651 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 25379 1.20 - 2.39: 1212 2.39 - 3.59: 71 3.59 - 4.79: 6 4.79 - 5.98: 7 Bond angle restraints: 26675 Sorted by residual: angle pdb=" N SER A 356 " pdb=" CA SER A 356 " pdb=" C SER A 356 " ideal model delta sigma weight residual 114.39 110.72 3.67 1.45e+00 4.76e-01 6.40e+00 angle pdb=" N ALA A 355 " pdb=" CA ALA A 355 " pdb=" C ALA A 355 " ideal model delta sigma weight residual 112.97 110.61 2.36 1.06e+00 8.90e-01 4.96e+00 angle pdb=" C CYS A 160 " pdb=" CA CYS A 160 " pdb=" CB CYS A 160 " ideal model delta sigma weight residual 113.33 108.38 4.95 2.26e+00 1.96e-01 4.80e+00 angle pdb=" CA ALA A 355 " pdb=" C ALA A 355 " pdb=" N SER A 356 " ideal model delta sigma weight residual 117.92 115.05 2.87 1.35e+00 5.49e-01 4.53e+00 angle pdb=" CG MET A 234 " pdb=" SD MET A 234 " pdb=" CE MET A 234 " ideal model delta sigma weight residual 100.90 96.24 4.66 2.20e+00 2.07e-01 4.49e+00 ... (remaining 26670 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 6263 17.07 - 34.13: 400 34.13 - 51.20: 94 51.20 - 68.26: 25 68.26 - 85.33: 6 Dihedral angle restraints: 6788 sinusoidal: 3798 harmonic: 2990 Sorted by residual: dihedral pdb=" CA CYS B 155 " pdb=" C CYS B 155 " pdb=" N CYS B 156 " pdb=" CA CYS B 156 " ideal model delta harmonic sigma weight residual 180.00 160.90 19.10 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA ALA B 118 " pdb=" C ALA B 118 " pdb=" N LYS B 119 " pdb=" CA LYS B 119 " ideal model delta harmonic sigma weight residual -180.00 -161.67 -18.33 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA LYS A 111 " pdb=" C LYS A 111 " pdb=" N LEU A 112 " pdb=" CA LEU A 112 " ideal model delta harmonic sigma weight residual 180.00 163.39 16.61 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 6785 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 765 0.028 - 0.056: 285 0.056 - 0.084: 64 0.084 - 0.112: 37 0.112 - 0.140: 11 Chirality restraints: 1162 Sorted by residual: chirality pdb=" CA ILE B 179 " pdb=" N ILE B 179 " pdb=" C ILE B 179 " pdb=" CB ILE B 179 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA ILE B 381 " pdb=" N ILE B 381 " pdb=" C ILE B 381 " pdb=" CB ILE B 381 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.18e-01 chirality pdb=" CA VAL B 260 " pdb=" N VAL B 260 " pdb=" C VAL B 260 " pdb=" CB VAL B 260 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.85e-01 ... (remaining 1159 not shown) Planarity restraints: 2125 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 186 " -0.011 2.00e-02 2.50e+03 9.19e-03 2.53e+00 pdb=" CG TYR A 186 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR A 186 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A 186 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR A 186 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 186 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 186 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 186 " 0.004 2.00e-02 2.50e+03 pdb=" HD1 TYR A 186 " 0.007 2.00e-02 2.50e+03 pdb=" HD2 TYR A 186 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 TYR A 186 " -0.006 2.00e-02 2.50e+03 pdb=" HE2 TYR A 186 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 59 " -0.132 9.50e-02 1.11e+02 4.42e-02 2.27e+00 pdb=" NE ARG C 59 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG C 59 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG C 59 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG C 59 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG C 59 " 0.004 2.00e-02 2.50e+03 pdb="HH12 ARG C 59 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG C 59 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG C 59 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 186 " -0.006 2.00e-02 2.50e+03 1.26e-02 1.58e+00 pdb=" C TYR A 186 " 0.022 2.00e-02 2.50e+03 pdb=" O TYR A 186 " -0.008 2.00e-02 2.50e+03 pdb=" N GLN A 187 " -0.007 2.00e-02 2.50e+03 ... (remaining 2122 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.39: 6123 2.39 - 2.94: 35006 2.94 - 3.49: 38393 3.49 - 4.05: 50306 4.05 - 4.60: 77011 Nonbonded interactions: 206839 Sorted by model distance: nonbonded pdb=" HD1 PHE C 64 " pdb=" HZ2 LYS C 85 " model vdw 1.833 2.100 nonbonded pdb=" H ILE A 205 " pdb="HG22 ILE A 205 " model vdw 1.852 2.270 nonbonded pdb=" HG SER B 88 " pdb=" HD2 PHE B 91 " model vdw 1.861 2.100 nonbonded pdb=" HG2 ARG C 59 " pdb="HH11 ARG C 59 " model vdw 1.876 2.270 nonbonded pdb=" HD2 HIS B 80 " pdb=" HE2 TYR B 136 " model vdw 1.884 2.100 ... (remaining 206834 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.440 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 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 : 0.004 0.111 7278 Z= 0.147 Angle : 0.567 9.825 9800 Z= 0.317 Chirality : 0.035 0.140 1162 Planarity : 0.004 0.058 1247 Dihedral : 12.925 85.330 2788 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.50 % Allowed : 8.56 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.28), residues: 901 helix: 0.82 (0.21), residues: 639 sheet: -3.35 (0.76), residues: 20 loop : -0.17 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 59 TYR 0.026 0.002 TYR A 186 PHE 0.014 0.002 PHE A 53 TRP 0.005 0.001 TRP C 22 HIS 0.003 0.001 HIS B 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 7270) covalent geometry : angle 0.54402 / 0.31 ( 9794) hydrogen bonds : bond 0.15594 / 11.12 ( 443) hydrogen bonds : angle 6.29454 / 4.75 ( 1314) metal coordination : bond 0.04350 / 3.81 ( 8) metal coordination : angle 6.52390 / 3.27 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 109 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 SER cc_start: 0.8484 (t) cc_final: 0.8253 (p) REVERT: B 137 SER cc_start: 0.9001 (OUTLIER) cc_final: 0.8782 (p) REVERT: B 217 MET cc_start: 0.7482 (tpp) cc_final: 0.6749 (tpt) outliers start: 4 outliers final: 3 residues processed: 110 average time/residue: 0.1577 time to fit residues: 23.8696 Evaluate side-chains 108 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 104 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 78 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.0870 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.4980 chunk 74 optimal weight: 0.8980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 517 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.223848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.144997 restraints weight = 22604.464| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.58 r_work: 0.3510 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.0682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 7278 Z= 0.153 Angle : 0.538 11.130 9800 Z= 0.286 Chirality : 0.035 0.131 1162 Planarity : 0.004 0.029 1247 Dihedral : 4.730 43.006 979 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.12 % Allowed : 8.06 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.28), residues: 901 helix: 1.08 (0.21), residues: 645 sheet: -2.33 (0.76), residues: 20 loop : -0.02 (0.39), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 404 TYR 0.017 0.002 TYR A 186 PHE 0.014 0.001 PHE A 53 TRP 0.002 0.001 TRP C 22 HIS 0.003 0.001 HIS B 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 ( 7270) covalent geometry : angle 0.51098 / 0.28 ( 9794) hydrogen bonds : bond 0.05170 / 3.63 ( 443) hydrogen bonds : angle 4.90861 / 3.63 ( 1314) metal coordination : bond 0.04456 / 3.86 ( 8) metal coordination : angle 6.77733 / 3.35 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 137 SER cc_start: 0.9392 (OUTLIER) cc_final: 0.9178 (p) REVERT: B 217 MET cc_start: 0.8164 (tpp) cc_final: 0.7745 (tpt) REVERT: B 264 LYS cc_start: 0.8425 (ptpt) cc_final: 0.8093 (ptpp) REVERT: B 438 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7598 (mmp80) outliers start: 9 outliers final: 4 residues processed: 102 average time/residue: 0.1533 time to fit residues: 21.9112 Evaluate side-chains 101 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 438 ARG Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 78 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 79 optimal weight: 0.0040 chunk 88 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 13 optimal weight: 0.4980 chunk 2 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 71 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 overall best weight: 0.5392 ------------------------------------------------------------------------------- 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 = 0.4496 r_free = 0.4496 target = 0.223168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.144224 restraints weight = 22601.444| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.69 r_work: 0.3478 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 7278 Z= 0.143 Angle : 0.518 10.555 9800 Z= 0.267 Chirality : 0.035 0.133 1162 Planarity : 0.003 0.027 1247 Dihedral : 4.521 45.530 977 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.24 % Allowed : 8.68 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.28), residues: 901 helix: 1.30 (0.21), residues: 646 sheet: -1.76 (0.86), residues: 20 loop : -0.03 (0.39), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 328 TYR 0.015 0.002 TYR A 186 PHE 0.013 0.001 PHE A 53 TRP 0.002 0.001 TRP C 22 HIS 0.003 0.001 HIS B 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 7270) covalent geometry : angle 0.49075 / 0.26 ( 9794) hydrogen bonds : bond 0.04332 / 3.00 ( 443) hydrogen bonds : angle 4.49610 / 3.33 ( 1314) metal coordination : bond 0.04483 / 3.87 ( 8) metal coordination : angle 6.76080 / 3.41 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 GLU cc_start: 0.7934 (tt0) cc_final: 0.7717 (tp30) REVERT: B 217 MET cc_start: 0.8194 (tpp) cc_final: 0.7784 (tpt) REVERT: B 264 LYS cc_start: 0.8408 (ptpt) cc_final: 0.8133 (ptpp) outliers start: 10 outliers final: 8 residues processed: 108 average time/residue: 0.1620 time to fit residues: 23.7571 Evaluate side-chains 106 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 78 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 4 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 14 optimal weight: 0.0370 chunk 55 optimal weight: 0.1980 chunk 28 optimal weight: 6.9990 chunk 64 optimal weight: 0.1980 chunk 49 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 231 ASN B 437 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.223161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.144769 restraints weight = 22467.772| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 3.02 r_work: 0.3409 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 7278 Z= 0.121 Angle : 0.500 10.117 9800 Z= 0.258 Chirality : 0.034 0.130 1162 Planarity : 0.003 0.028 1247 Dihedral : 4.366 46.513 976 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.99 % Allowed : 8.93 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.54 (0.28), residues: 901 helix: 1.54 (0.21), residues: 641 sheet: -1.72 (0.82), residues: 25 loop : 0.05 (0.40), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 404 TYR 0.016 0.002 TYR A 186 PHE 0.012 0.001 PHE A 53 TRP 0.001 0.000 TRP C 22 HIS 0.003 0.001 HIS B 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 7270) covalent geometry : angle 0.47375 / 0.25 ( 9794) hydrogen bonds : bond 0.03891 / 2.69 ( 443) hydrogen bonds : angle 4.33151 / 3.21 ( 1314) metal coordination : bond 0.04234 / 3.67 ( 8) metal coordination : angle 6.45182 / 3.22 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 GLU cc_start: 0.7921 (tt0) cc_final: 0.7680 (tp30) REVERT: B 217 MET cc_start: 0.8177 (tpp) cc_final: 0.7834 (tpt) REVERT: B 264 LYS cc_start: 0.8412 (ptpt) cc_final: 0.8157 (ptpp) outliers start: 8 outliers final: 7 residues processed: 102 average time/residue: 0.1763 time to fit residues: 24.4827 Evaluate side-chains 101 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 78 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 88 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 54 optimal weight: 0.3980 chunk 60 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 25 optimal weight: 20.0000 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 = 0.4428 r_free = 0.4428 target = 0.215546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.141167 restraints weight = 22479.584| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 3.06 r_work: 0.3323 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.125 7278 Z= 0.257 Angle : 0.620 15.467 9800 Z= 0.323 Chirality : 0.039 0.210 1162 Planarity : 0.005 0.048 1247 Dihedral : 4.746 48.010 976 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.36 % Allowed : 9.80 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.28), residues: 901 helix: 1.13 (0.20), residues: 639 sheet: -2.18 (0.85), residues: 25 loop : -0.20 (0.39), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 87 TYR 0.026 0.002 TYR B 186 PHE 0.022 0.002 PHE A 53 TRP 0.003 0.001 TRP C 22 HIS 0.009 0.002 HIS B 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00609 / 0.26 ( 7270) covalent geometry : angle 0.58371 / 0.32 ( 9794) hydrogen bonds : bond 0.04815 / 3.28 ( 443) hydrogen bonds : angle 4.48950 / 3.29 ( 1314) metal coordination : bond 0.04826 / 4.29 ( 8) metal coordination : angle 8.48308 / 4.67 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 GLU cc_start: 0.8159 (tt0) cc_final: 0.7947 (tp30) REVERT: B 264 LYS cc_start: 0.8422 (ptpt) cc_final: 0.8214 (ptpp) REVERT: B 295 ASP cc_start: 0.8360 (m-30) cc_final: 0.8070 (m-30) REVERT: B 510 ARG cc_start: 0.7788 (ttp80) cc_final: 0.7567 (ttp80) outliers start: 11 outliers final: 9 residues processed: 96 average time/residue: 0.2025 time to fit residues: 25.4805 Evaluate side-chains 98 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 78 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 16 optimal weight: 0.3980 chunk 41 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 44 optimal weight: 0.0670 chunk 5 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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 = 0.4454 r_free = 0.4454 target = 0.218254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.139024 restraints weight = 22514.737| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.47 r_work: 0.3336 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.118 7278 Z= 0.134 Angle : 0.516 10.794 9800 Z= 0.265 Chirality : 0.034 0.132 1162 Planarity : 0.004 0.034 1247 Dihedral : 4.517 48.628 976 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.87 % Allowed : 10.42 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.28), residues: 901 helix: 1.45 (0.21), residues: 638 sheet: -2.11 (0.86), residues: 25 loop : -0.02 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 404 TYR 0.017 0.002 TYR A 186 PHE 0.014 0.001 PHE A 53 TRP 0.001 0.000 TRP C 22 HIS 0.004 0.001 HIS B 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 7270) covalent geometry : angle 0.48671 / 0.26 ( 9794) hydrogen bonds : bond 0.03956 / 2.71 ( 443) hydrogen bonds : angle 4.31101 / 3.17 ( 1314) metal coordination : bond 0.04600 / 4.03 ( 8) metal coordination : angle 6.95042 / 3.53 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 GLU cc_start: 0.8019 (tt0) cc_final: 0.7777 (tp30) REVERT: B 66 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.7898 (m-30) REVERT: B 264 LYS cc_start: 0.8361 (ptpt) cc_final: 0.8160 (ptpp) REVERT: B 295 ASP cc_start: 0.8293 (m-30) cc_final: 0.7983 (m-30) REVERT: B 510 ARG cc_start: 0.7638 (ttp80) cc_final: 0.7416 (ttp80) REVERT: C 86 MET cc_start: 0.8828 (mmm) cc_final: 0.8572 (mmm) outliers start: 7 outliers final: 6 residues processed: 95 average time/residue: 0.2010 time to fit residues: 25.1500 Evaluate side-chains 97 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain C residue 78 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 29 optimal weight: 2.9990 chunk 8 optimal weight: 0.0980 chunk 47 optimal weight: 0.1980 chunk 50 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 89 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 25 optimal weight: 20.0000 chunk 83 optimal weight: 9.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4542 r_free = 0.4542 target = 0.227330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.147528 restraints weight = 22486.223| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.69 r_work: 0.3509 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.116 7278 Z= 0.185 Angle : 0.546 12.957 9800 Z= 0.279 Chirality : 0.036 0.188 1162 Planarity : 0.004 0.037 1247 Dihedral : 4.384 49.086 973 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.36 % Allowed : 10.30 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.35 (0.28), residues: 901 helix: 1.44 (0.21), residues: 638 sheet: -2.12 (0.88), residues: 25 loop : -0.09 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 404 TYR 0.019 0.002 TYR B 186 PHE 0.015 0.002 PHE A 53 TRP 0.002 0.001 TRP C 22 HIS 0.006 0.001 HIS B 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.18 ( 7270) covalent geometry : angle 0.51379 / 0.27 ( 9794) hydrogen bonds : bond 0.04101 / 2.81 ( 443) hydrogen bonds : angle 4.31756 / 3.17 ( 1314) metal coordination : bond 0.04483 / 3.97 ( 8) metal coordination : angle 7.45028 / 4.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 ASP cc_start: 0.8273 (OUTLIER) cc_final: 0.7850 (m-30) REVERT: B 295 ASP cc_start: 0.8342 (m-30) cc_final: 0.8080 (m-30) outliers start: 11 outliers final: 8 residues processed: 104 average time/residue: 0.1712 time to fit residues: 23.8222 Evaluate side-chains 100 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 187 GLN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain C residue 78 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 7.9990 chunk 58 optimal weight: 0.9980 chunk 83 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 chunk 55 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4537 r_free = 0.4537 target = 0.226598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.147295 restraints weight = 22531.542| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.73 r_work: 0.3495 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.118 7278 Z= 0.181 Angle : 0.543 12.483 9800 Z= 0.277 Chirality : 0.036 0.134 1162 Planarity : 0.004 0.039 1247 Dihedral : 4.369 49.395 973 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.49 % Allowed : 10.55 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.37 (0.28), residues: 901 helix: 1.45 (0.21), residues: 638 sheet: -2.06 (0.90), residues: 25 loop : -0.09 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 404 TYR 0.017 0.002 TYR B 186 PHE 0.015 0.002 PHE A 53 TRP 0.001 0.001 TRP C 22 HIS 0.005 0.001 HIS B 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.18 ( 7270) covalent geometry : angle 0.51216 / 0.27 ( 9794) hydrogen bonds : bond 0.04055 / 2.78 ( 443) hydrogen bonds : angle 4.29385 / 3.15 ( 1314) metal coordination : bond 0.04585 / 4.03 ( 8) metal coordination : angle 7.36037 / 3.90 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 ASP cc_start: 0.8269 (OUTLIER) cc_final: 0.7834 (m-30) REVERT: B 295 ASP cc_start: 0.8340 (m-30) cc_final: 0.8097 (m-30) outliers start: 12 outliers final: 11 residues processed: 96 average time/residue: 0.1508 time to fit residues: 19.8142 Evaluate side-chains 97 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 82 CYS Chi-restraints excluded: chain B residue 187 GLN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain C residue 78 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 79 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 36 optimal weight: 0.4980 chunk 41 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 31 optimal weight: 8.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4534 r_free = 0.4534 target = 0.226215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.147348 restraints weight = 22636.859| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.46 r_work: 0.3525 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.117 7278 Z= 0.176 Angle : 0.538 12.451 9800 Z= 0.274 Chirality : 0.036 0.134 1162 Planarity : 0.004 0.039 1247 Dihedral : 4.364 49.895 973 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.36 % Allowed : 10.67 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.43 (0.28), residues: 901 helix: 1.51 (0.21), residues: 638 sheet: -2.01 (0.91), residues: 25 loop : -0.08 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 404 TYR 0.017 0.002 TYR A 186 PHE 0.014 0.001 PHE A 53 TRP 0.014 0.004 TRP C 22 HIS 0.005 0.001 HIS B 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.17 ( 7270) covalent geometry : angle 0.50630 / 0.27 ( 9794) hydrogen bonds : bond 0.03976 / 2.72 ( 443) hydrogen bonds : angle 4.26994 / 3.14 ( 1314) metal coordination : bond 0.04510 / 4.00 ( 8) metal coordination : angle 7.32089 / 3.89 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 ILE cc_start: 0.8374 (tt) cc_final: 0.7889 (mt) REVERT: B 66 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.7805 (m-30) REVERT: B 295 ASP cc_start: 0.8306 (m-30) cc_final: 0.8051 (m-30) outliers start: 11 outliers final: 10 residues processed: 96 average time/residue: 0.1513 time to fit residues: 20.0439 Evaluate side-chains 99 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 187 GLN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain C residue 78 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 0.0470 chunk 39 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 47 optimal weight: 0.5980 chunk 13 optimal weight: 0.0970 overall best weight: 0.4476 ------------------------------------------------------------------------------- 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 = 0.4543 r_free = 0.4543 target = 0.227568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.148829 restraints weight = 22495.261| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.46 r_work: 0.3474 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.117 7278 Z= 0.125 Angle : 0.507 10.865 9800 Z= 0.259 Chirality : 0.034 0.133 1162 Planarity : 0.004 0.044 1247 Dihedral : 4.266 50.452 973 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.24 % Allowed : 10.92 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.66 (0.28), residues: 901 helix: 1.67 (0.21), residues: 639 sheet: -1.98 (0.90), residues: 25 loop : 0.04 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 404 TYR 0.016 0.002 TYR A 186 PHE 0.012 0.001 PHE A 53 TRP 0.011 0.003 TRP C 22 HIS 0.003 0.001 HIS B 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 7270) covalent geometry : angle 0.47963 / 0.26 ( 9794) hydrogen bonds : bond 0.03693 / 2.54 ( 443) hydrogen bonds : angle 4.20035 / 3.09 ( 1314) metal coordination : bond 0.04545 / 4.00 ( 8) metal coordination : angle 6.71244 / 3.48 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 ILE cc_start: 0.8375 (tt) cc_final: 0.7945 (mt) REVERT: B 66 ASP cc_start: 0.8263 (OUTLIER) cc_final: 0.7831 (m-30) REVERT: B 295 ASP cc_start: 0.8318 (m-30) cc_final: 0.8074 (m-30) REVERT: B 404 ARG cc_start: 0.6447 (ttp80) cc_final: 0.6060 (ptm-80) REVERT: C 86 MET cc_start: 0.8874 (mmm) cc_final: 0.8626 (mmm) REVERT: C 90 GLU cc_start: 0.6688 (pt0) cc_final: 0.6458 (pt0) outliers start: 10 outliers final: 8 residues processed: 96 average time/residue: 0.1566 time to fit residues: 20.0647 Evaluate side-chains 96 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 187 GLN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain C residue 78 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 41 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 16 optimal weight: 0.1980 chunk 7 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4524 r_free = 0.4524 target = 0.225611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.147509 restraints weight = 22387.995| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.43 r_work: 0.3450 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 7278 Z= 0.165 Angle : 0.534 12.612 9800 Z= 0.272 Chirality : 0.036 0.134 1162 Planarity : 0.004 0.044 1247 Dihedral : 4.300 51.473 973 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.12 % Allowed : 11.17 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.28), residues: 901 helix: 1.65 (0.21), residues: 639 sheet: -2.01 (0.86), residues: 27 loop : 0.03 (0.40), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 404 TYR 0.018 0.002 TYR B 186 PHE 0.015 0.001 PHE A 53 TRP 0.009 0.002 TRP C 22 HIS 0.006 0.001 HIS B 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.16 ( 7270) covalent geometry : angle 0.50370 / 0.27 ( 9794) hydrogen bonds : bond 0.03853 / 2.64 ( 443) hydrogen bonds : angle 4.22234 / 3.12 ( 1314) metal coordination : bond 0.04346 / 3.88 ( 8) metal coordination : angle 7.18893 / 3.89 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3787.72 seconds wall clock time: 64 minutes 39.55 seconds (3879.55 seconds total)