Starting phenix.real_space_refine on Thu Jul 2 06:36:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8i88_35241/07_2026/8i88_35241.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i88_35241/07_2026/8i88_35241.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8i88_35241/07_2026/8i88_35241.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8i88_35241/07_2026/8i88_35241.cif" model { file = "/net/cci-nas-00/data/ceres_data/8i88_35241/07_2026/8i88_35241.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i88_35241/07_2026/8i88_35241.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8i88_35241/07_2026/8i88_35241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i88_35241/07_2026/8i88_35241.map" } resolution = 3.7 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= 0.003 sd= 1.000 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 23 5.16 5 C 4714 2.51 5 N 1210 2.21 5 O 1338 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7287 Number of models: 1 Model: "" Number of chains: 3 Chain: "L" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Classifications: {'RNA': 2} Modifications used: {'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "B" Number of atoms: 3731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3731 Classifications: {'peptide': 462} Link IDs: {'PTRANS': 23, 'TRANS': 438} Chain breaks: 1 Chain: "C" Number of atoms: 3511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3511 Classifications: {'peptide': 421} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 408} Time building chain proxies: 1.35, per 1000 atoms: 0.19 Number of scatterers: 7287 At special positions: 0 Unit cell: (78.2, 93.5, 125.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 23 16.00 P 2 15.00 O 1338 8.00 N 1210 7.00 C 4714 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: 0.51 Conformation dependent library (CDL) restraints added in 367.8 milliseconds 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1682 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 12 sheets defined 38.2% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 22 through 30 Processing helix chain 'B' and resid 46 through 60 Processing helix chain 'B' and resid 77 through 82 Processing helix chain 'B' and resid 97 through 106 removed outlier: 3.537A pdb=" N PHE B 104 " --> pdb=" O ASP B 100 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR B 106 " --> pdb=" O GLY B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 132 removed outlier: 4.081A pdb=" N LYS B 124 " --> pdb=" O LEU B 120 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 150 removed outlier: 3.733A pdb=" N TYR B 148 " --> pdb=" O PRO B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 214 removed outlier: 3.780A pdb=" N LEU B 214 " --> pdb=" O PHE B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 217 No H-bonds generated for 'chain 'B' and resid 215 through 217' Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 248 through 265 removed outlier: 3.676A pdb=" N GLY B 265 " --> pdb=" O PHE B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 350 Processing helix chain 'B' and resid 366 through 377 removed outlier: 3.990A pdb=" N VAL B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR B 377 " --> pdb=" O PHE B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 462 Processing helix chain 'B' and resid 477 through 482 removed outlier: 4.164A pdb=" N PHE B 482 " --> pdb=" O VAL B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 493 removed outlier: 4.058A pdb=" N SER B 493 " --> pdb=" O ILE B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 506 No H-bonds generated for 'chain 'B' and resid 504 through 506' Processing helix chain 'C' and resid 14 through 29 removed outlier: 3.608A pdb=" N THR C 18 " --> pdb=" O ASP C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 56 Processing helix chain 'C' and resid 66 through 70 removed outlier: 3.675A pdb=" N ASN C 69 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLN C 70 " --> pdb=" O TYR C 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 66 through 70' Processing helix chain 'C' and resid 71 through 89 Processing helix chain 'C' and resid 109 through 114 removed outlier: 4.259A pdb=" N ARG C 114 " --> pdb=" O ILE C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 139 Processing helix chain 'C' and resid 146 through 158 removed outlier: 4.155A pdb=" N SER C 150 " --> pdb=" O ASP C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 203 removed outlier: 3.520A pdb=" N GLU C 202 " --> pdb=" O ASP C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 231 removed outlier: 3.533A pdb=" N GLU C 231 " --> pdb=" O PRO C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 249 Processing helix chain 'C' and resid 257 through 279 Processing helix chain 'C' and resid 300 through 302 No H-bonds generated for 'chain 'C' and resid 300 through 302' Processing helix chain 'C' and resid 353 through 366 Processing helix chain 'C' and resid 369 through 384 removed outlier: 3.593A pdb=" N LEU C 384 " --> pdb=" O PHE C 380 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 2 through 3 removed outlier: 6.464A pdb=" N LYS B 2 " --> pdb=" O LYS C 411 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 5 through 6 Processing sheet with id=AA3, first strand: chain 'B' and resid 19 through 20 removed outlier: 3.599A pdb=" N LYS B 270 " --> pdb=" O LEU B 13 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 92 through 95 removed outlier: 6.685A pdb=" N GLY B 42 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ILE B 142 " --> pdb=" O GLY B 42 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE B 44 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N TRP B 139 " --> pdb=" O GLN B 222 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N PHE B 224 " --> pdb=" O TRP B 139 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N VAL B 141 " --> pdb=" O PHE B 224 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 318 through 319 removed outlier: 7.136A pdb=" N CYS B 279 " --> pdb=" O PHE B 358 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N HIS B 360 " --> pdb=" O CYS B 279 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU B 281 " --> pdb=" O HIS B 360 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N VAL B 357 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL B 386 " --> pdb=" O VAL B 357 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ILE B 359 " --> pdb=" O VAL B 386 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ILE B 388 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ALA B 361 " --> pdb=" O ILE B 388 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N THR B 387 " --> pdb=" O ILE B 445 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ILE B 445 " --> pdb=" O THR B 387 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N SER B 389 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ILE B 443 " --> pdb=" O SER B 389 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N PHE B 419 " --> pdb=" O VAL B 412 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N VAL B 412 " --> pdb=" O PHE B 419 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 318 through 319 Processing sheet with id=AA7, first strand: chain 'C' and resid 31 through 33 removed outlier: 5.988A pdb=" N ILE C 5 " --> pdb=" O TRP C 33 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N LYS C 4 " --> pdb=" O CYS C 58 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N PHE C 60 " --> pdb=" O LYS C 4 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N PHE C 6 " --> pdb=" O PHE C 60 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N LEU C 62 " --> pdb=" O PHE C 6 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N SER C 8 " --> pdb=" O LEU C 62 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N ILE C 118 " --> pdb=" O ILE C 94 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 175 through 177 removed outlier: 4.462A pdb=" N GLY C 325 " --> pdb=" O THR C 291 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N THR C 291 " --> pdb=" O GLY C 325 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 175 through 177 Processing sheet with id=AB1, first strand: chain 'C' and resid 207 through 210 removed outlier: 3.514A pdb=" N LEU C 214 " --> pdb=" O HIS C 188 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 304 through 305 Processing sheet with id=AB3, first strand: chain 'C' and resid 390 through 394 300 hydrogen bonds defined for protein. 840 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: 0.96 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2276 1.34 - 1.46: 1811 1.46 - 1.58: 3349 1.58 - 1.70: 4 1.70 - 1.81: 35 Bond restraints: 7475 Sorted by residual: bond pdb=" CB PRO C 182 " pdb=" CG PRO C 182 " ideal model delta sigma weight residual 1.492 1.579 -0.087 5.00e-02 4.00e+02 3.01e+00 bond pdb=" CG PRO C 182 " pdb=" CD PRO C 182 " ideal model delta sigma weight residual 1.503 1.551 -0.048 3.40e-02 8.65e+02 2.01e+00 bond pdb=" CA ASP C 100 " pdb=" CB ASP C 100 " ideal model delta sigma weight residual 1.534 1.557 -0.023 1.76e-02 3.23e+03 1.77e+00 bond pdb=" C PHE C 332 " pdb=" N PRO C 333 " ideal model delta sigma weight residual 1.330 1.345 -0.015 1.19e-02 7.06e+03 1.50e+00 bond pdb=" CB ASP C 107 " pdb=" CG ASP C 107 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.21e+00 ... (remaining 7470 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.02: 10076 4.02 - 8.05: 28 8.05 - 12.07: 2 12.07 - 16.10: 0 16.10 - 20.12: 1 Bond angle restraints: 10107 Sorted by residual: angle pdb=" C PRO C 331 " pdb=" N PHE C 332 " pdb=" CA PHE C 332 " ideal model delta sigma weight residual 121.80 141.92 -20.12 2.44e+00 1.68e-01 6.80e+01 angle pdb=" C LYS C 315 " pdb=" CA LYS C 315 " pdb=" CB LYS C 315 " ideal model delta sigma weight residual 117.23 110.21 7.02 1.36e+00 5.41e-01 2.66e+01 angle pdb=" CA PRO C 182 " pdb=" N PRO C 182 " pdb=" CD PRO C 182 " ideal model delta sigma weight residual 112.00 105.21 6.79 1.40e+00 5.10e-01 2.35e+01 angle pdb=" CA LYS C 315 " pdb=" C LYS C 315 " pdb=" N ASP C 316 " ideal model delta sigma weight residual 119.98 116.99 2.99 8.50e-01 1.38e+00 1.24e+01 angle pdb=" N LEU C 37 " pdb=" CA LEU C 37 " pdb=" C LEU C 37 " ideal model delta sigma weight residual 114.75 110.45 4.30 1.26e+00 6.30e-01 1.17e+01 ... (remaining 10102 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.65: 3771 16.65 - 33.31: 513 33.31 - 49.96: 147 49.96 - 66.61: 27 66.61 - 83.26: 7 Dihedral angle restraints: 4465 sinusoidal: 1862 harmonic: 2603 Sorted by residual: dihedral pdb=" CA TYR C 330 " pdb=" C TYR C 330 " pdb=" N PRO C 331 " pdb=" CA PRO C 331 " ideal model delta harmonic sigma weight residual 180.00 121.04 58.96 0 5.00e+00 4.00e-02 1.39e+02 dihedral pdb=" CA ASN C 191 " pdb=" C ASN C 191 " pdb=" N TRP C 192 " pdb=" CA TRP C 192 " ideal model delta harmonic sigma weight residual 180.00 157.94 22.06 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA MET C 193 " pdb=" C MET C 193 " pdb=" N LEU C 194 " pdb=" CA LEU C 194 " ideal model delta harmonic sigma weight residual 180.00 161.13 18.87 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 4462 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 742 0.035 - 0.070: 239 0.070 - 0.105: 67 0.105 - 0.140: 34 0.140 - 0.175: 4 Chirality restraints: 1086 Sorted by residual: chirality pdb=" CG LEU C 275 " pdb=" CB LEU C 275 " pdb=" CD1 LEU C 275 " pdb=" CD2 LEU C 275 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.67e-01 chirality pdb=" CB ILE B 60 " pdb=" CA ILE B 60 " pdb=" CG1 ILE B 60 " pdb=" CG2 ILE B 60 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.16e-01 chirality pdb=" CG LEU B 214 " pdb=" CB LEU B 214 " pdb=" CD1 LEU B 214 " pdb=" CD2 LEU B 214 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.17 2.00e-01 2.50e+01 6.83e-01 ... (remaining 1083 not shown) Planarity restraints: 1268 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 181 " -0.078 5.00e-02 4.00e+02 1.15e-01 2.12e+01 pdb=" N PRO C 182 " 0.199 5.00e-02 4.00e+02 pdb=" CA PRO C 182 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO C 182 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 330 " -0.059 5.00e-02 4.00e+02 9.09e-02 1.32e+01 pdb=" N PRO C 331 " 0.157 5.00e-02 4.00e+02 pdb=" CA PRO C 331 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO C 331 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 241 " 0.057 5.00e-02 4.00e+02 8.63e-02 1.19e+01 pdb=" N PRO C 242 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO C 242 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO C 242 " 0.047 5.00e-02 4.00e+02 ... (remaining 1265 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 81 2.64 - 3.21: 6343 3.21 - 3.77: 10772 3.77 - 4.34: 14363 4.34 - 4.90: 24114 Nonbonded interactions: 55673 Sorted by model distance: nonbonded pdb=" O PRO C 206 " pdb=" OG1 THR C 216 " model vdw 2.077 3.040 nonbonded pdb=" OG1 THR C 344 " pdb=" O LYS C 349 " model vdw 2.154 3.040 nonbonded pdb=" O VAL C 52 " pdb=" OG1 THR C 57 " model vdw 2.168 3.040 nonbonded pdb=" OD1 ASP C 40 " pdb=" N LYS C 41 " model vdw 2.172 3.120 nonbonded pdb=" OH TYR B 280 " pdb=" OD1 ASP B 458 " model vdw 2.214 3.040 ... (remaining 55668 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.200 Find NCS groups from input model: 0.030 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:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 7475 Z= 0.128 Angle : 0.656 20.119 10107 Z= 0.353 Chirality : 0.042 0.175 1086 Planarity : 0.006 0.115 1268 Dihedral : 16.389 83.263 2783 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.99 % Favored : 95.90 % Rotamer: Outliers : 0.38 % Allowed : 23.01 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: 0.14 (0.29), residues: 877 helix: 1.64 (0.32), residues: 277 sheet: 0.64 (0.43), residues: 157 loop : -1.17 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 416 TYR 0.014 0.001 TYR B 37 PHE 0.011 0.001 PHE C 391 TRP 0.049 0.002 TRP C 20 HIS 0.006 0.001 HIS C 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 7475) covalent geometry : angle 0.65589 / 0.35 (10107) hydrogen bonds : bond 0.12229 / 6.86 ( 284) hydrogen bonds : angle 5.46972 / 3.93 ( 840) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 109 time to evaluate : 0.233 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 111 average time/residue: 0.0697 time to fit residues: 11.0969 Evaluate side-chains 96 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 ASN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.178669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.136233 restraints weight = 9725.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.134359 restraints weight = 7886.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.136450 restraints weight = 7650.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.136692 restraints weight = 5541.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.137348 restraints weight = 5706.455| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 7475 Z= 0.200 Angle : 0.607 9.509 10107 Z= 0.316 Chirality : 0.043 0.151 1086 Planarity : 0.006 0.084 1268 Dihedral : 5.580 62.527 978 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.02 % Favored : 94.87 % Rotamer: Outliers : 4.68 % Allowed : 21.74 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -0.02 (0.28), residues: 877 helix: 1.37 (0.31), residues: 282 sheet: 0.42 (0.43), residues: 157 loop : -1.13 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 276 TYR 0.011 0.001 TYR C 171 PHE 0.015 0.002 PHE C 17 TRP 0.029 0.002 TRP C 20 HIS 0.007 0.001 HIS C 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.20 ( 7475) covalent geometry : angle 0.60671 / 0.32 (10107) hydrogen bonds : bond 0.04491 / 2.74 ( 284) hydrogen bonds : angle 4.79336 / 3.38 ( 840) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 101 time to evaluate : 0.285 Fit side-chains REVERT: C 107 ASP cc_start: 0.7552 (t0) cc_final: 0.7198 (t0) REVERT: C 138 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.7626 (mp10) REVERT: C 192 TRP cc_start: 0.6249 (p90) cc_final: 0.5941 (p90) REVERT: C 193 MET cc_start: 0.5647 (mmt) cc_final: 0.5382 (ttp) REVERT: C 225 TYR cc_start: 0.7285 (OUTLIER) cc_final: 0.6441 (p90) REVERT: C 276 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.6539 (mmm-85) outliers start: 37 outliers final: 26 residues processed: 124 average time/residue: 0.0707 time to fit residues: 12.6668 Evaluate side-chains 126 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 48 GLN Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 58 CYS Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 225 TYR Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 276 ARG Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 378 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 40 optimal weight: 4.9990 chunk 1 optimal weight: 0.0270 chunk 48 optimal weight: 0.0870 chunk 53 optimal weight: 10.0000 chunk 26 optimal weight: 0.8980 chunk 75 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 80 optimal weight: 0.7980 chunk 82 optimal weight: 20.0000 overall best weight: 0.9618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.183092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.140891 restraints weight = 9258.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.140429 restraints weight = 7755.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.142110 restraints weight = 7531.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.142524 restraints weight = 5404.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.142886 restraints weight = 5705.804| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7475 Z= 0.108 Angle : 0.539 10.583 10107 Z= 0.275 Chirality : 0.041 0.138 1086 Planarity : 0.005 0.075 1268 Dihedral : 5.203 63.098 978 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.76 % Favored : 96.12 % Rotamer: Outliers : 3.92 % Allowed : 23.14 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: 0.15 (0.29), residues: 877 helix: 1.66 (0.31), residues: 282 sheet: 0.39 (0.42), residues: 161 loop : -1.11 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 276 TYR 0.007 0.001 TYR B 346 PHE 0.010 0.001 PHE C 60 TRP 0.033 0.002 TRP C 20 HIS 0.006 0.001 HIS C 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 7475) covalent geometry : angle 0.53921 / 0.28 (10107) hydrogen bonds : bond 0.03607 / 2.25 ( 284) hydrogen bonds : angle 4.44016 / 3.12 ( 840) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 108 time to evaluate : 0.282 Fit side-chains REVERT: B 305 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.7219 (mm) REVERT: C 1 MET cc_start: 0.6953 (tpp) cc_final: 0.6560 (ttp) REVERT: C 107 ASP cc_start: 0.7501 (t0) cc_final: 0.7231 (t0) REVERT: C 138 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7922 (mp10) REVERT: C 225 TYR cc_start: 0.7177 (OUTLIER) cc_final: 0.6320 (p90) REVERT: C 276 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.6488 (mmm-85) outliers start: 31 outliers final: 18 residues processed: 129 average time/residue: 0.0742 time to fit residues: 13.4467 Evaluate side-chains 121 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 225 TYR Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 276 ARG Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 384 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 45 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 60 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 ASN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.181565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.141319 restraints weight = 9344.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.138980 restraints weight = 7856.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.140759 restraints weight = 7956.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.141105 restraints weight = 5949.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.141696 restraints weight = 6101.679| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7475 Z= 0.165 Angle : 0.570 9.741 10107 Z= 0.295 Chirality : 0.043 0.137 1086 Planarity : 0.005 0.077 1268 Dihedral : 4.959 60.898 975 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.45 % Favored : 95.44 % Rotamer: Outliers : 4.55 % Allowed : 23.89 % Favored : 71.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: 0.10 (0.28), residues: 877 helix: 1.53 (0.31), residues: 282 sheet: 0.36 (0.42), residues: 157 loop : -1.04 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 275 TYR 0.012 0.001 TYR B 280 PHE 0.013 0.001 PHE C 17 TRP 0.044 0.002 TRP C 20 HIS 0.005 0.001 HIS C 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 ( 7475) covalent geometry : angle 0.56991 / 0.30 (10107) hydrogen bonds : bond 0.04026 / 2.50 ( 284) hydrogen bonds : angle 4.52775 / 3.20 ( 840) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 100 time to evaluate : 0.334 Fit side-chains REVERT: C 107 ASP cc_start: 0.7637 (t0) cc_final: 0.7131 (t0) REVERT: C 138 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.7780 (mp10) REVERT: C 174 ASN cc_start: 0.8371 (OUTLIER) cc_final: 0.8011 (p0) REVERT: C 225 TYR cc_start: 0.7152 (OUTLIER) cc_final: 0.6282 (p90) REVERT: C 232 THR cc_start: 0.8262 (p) cc_final: 0.8002 (t) REVERT: C 276 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.6399 (mmm-85) outliers start: 36 outliers final: 26 residues processed: 122 average time/residue: 0.0763 time to fit residues: 13.2821 Evaluate side-chains 131 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 101 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 48 GLN Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 174 ASN Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 225 TYR Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 276 ARG Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 370 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 48 optimal weight: 0.5980 chunk 6 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 58 optimal weight: 0.0870 chunk 71 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 85 optimal weight: 7.9990 overall best weight: 1.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.184673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.142992 restraints weight = 9139.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.141287 restraints weight = 8171.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.143096 restraints weight = 8709.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.143666 restraints weight = 6025.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.144521 restraints weight = 5311.475| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7475 Z= 0.113 Angle : 0.537 10.463 10107 Z= 0.276 Chirality : 0.041 0.134 1086 Planarity : 0.005 0.075 1268 Dihedral : 4.718 59.643 975 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.99 % Favored : 95.90 % Rotamer: Outliers : 4.17 % Allowed : 24.27 % Favored : 71.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: 0.23 (0.29), residues: 877 helix: 1.64 (0.31), residues: 283 sheet: 0.43 (0.41), residues: 165 loop : -1.00 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 276 TYR 0.010 0.001 TYR C 213 PHE 0.011 0.001 PHE C 332 TRP 0.047 0.002 TRP C 20 HIS 0.005 0.001 HIS C 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 ( 7475) covalent geometry : angle 0.53718 / 0.28 (10107) hydrogen bonds : bond 0.03482 / 2.17 ( 284) hydrogen bonds : angle 4.34112 / 3.06 ( 840) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 111 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: C 1 MET cc_start: 0.6812 (tpp) cc_final: 0.6381 (ttp) REVERT: C 107 ASP cc_start: 0.7617 (t0) cc_final: 0.7267 (t0) REVERT: C 138 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7700 (mp10) REVERT: C 192 TRP cc_start: 0.6071 (p90) cc_final: 0.5653 (p90) REVERT: C 225 TYR cc_start: 0.7221 (OUTLIER) cc_final: 0.6323 (p90) REVERT: C 276 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.7845 (tpt-90) outliers start: 33 outliers final: 23 residues processed: 131 average time/residue: 0.0747 time to fit residues: 13.8980 Evaluate side-chains 121 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 48 GLN Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 225 TYR Chi-restraints excluded: chain C residue 276 ARG Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 384 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 67 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 chunk 22 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 ASN C 174 ASN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.183492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.141611 restraints weight = 9243.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.140177 restraints weight = 7965.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.141754 restraints weight = 8308.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.142754 restraints weight = 5862.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.143033 restraints weight = 5653.218| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7475 Z= 0.134 Angle : 0.596 12.826 10107 Z= 0.295 Chirality : 0.043 0.219 1086 Planarity : 0.005 0.074 1268 Dihedral : 4.824 60.437 975 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.22 % Favored : 95.67 % Rotamer: Outliers : 5.06 % Allowed : 24.53 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: 0.24 (0.29), residues: 877 helix: 1.63 (0.31), residues: 284 sheet: 0.36 (0.41), residues: 166 loop : -0.95 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 276 TYR 0.008 0.001 TYR B 280 PHE 0.011 0.001 PHE C 332 TRP 0.037 0.002 TRP C 20 HIS 0.004 0.001 HIS C 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.13 ( 7475) covalent geometry : angle 0.59623 / 0.30 (10107) hydrogen bonds : bond 0.03642 / 2.27 ( 284) hydrogen bonds : angle 4.40617 / 3.08 ( 840) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 95 time to evaluate : 0.275 Fit side-chains REVERT: C 1 MET cc_start: 0.6744 (tpp) cc_final: 0.6469 (ttp) REVERT: C 107 ASP cc_start: 0.7672 (t0) cc_final: 0.7314 (t0) REVERT: C 138 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.7795 (mp10) REVERT: C 174 ASN cc_start: 0.8391 (OUTLIER) cc_final: 0.8023 (p0) REVERT: C 225 TYR cc_start: 0.7252 (OUTLIER) cc_final: 0.6368 (p90) REVERT: C 232 THR cc_start: 0.8153 (p) cc_final: 0.7628 (t) REVERT: C 276 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.6327 (mmm-85) outliers start: 40 outliers final: 29 residues processed: 124 average time/residue: 0.0734 time to fit residues: 13.0613 Evaluate side-chains 123 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 90 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 174 ASN Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 225 TYR Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 276 ARG Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 384 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 84 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 19 optimal weight: 0.0060 chunk 83 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.185702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.144089 restraints weight = 9174.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.142116 restraints weight = 8150.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.143702 restraints weight = 8336.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.144763 restraints weight = 6227.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.145144 restraints weight = 5642.720| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7475 Z= 0.111 Angle : 0.585 11.330 10107 Z= 0.288 Chirality : 0.042 0.197 1086 Planarity : 0.005 0.072 1268 Dihedral : 4.655 59.946 975 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.99 % Favored : 95.90 % Rotamer: Outliers : 4.55 % Allowed : 25.03 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: 0.36 (0.29), residues: 877 helix: 1.76 (0.31), residues: 284 sheet: 0.29 (0.41), residues: 171 loop : -0.85 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 276 TYR 0.008 0.001 TYR C 213 PHE 0.012 0.001 PHE C 332 TRP 0.051 0.002 TRP C 20 HIS 0.004 0.001 HIS C 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 ( 7475) covalent geometry : angle 0.58476 / 0.29 (10107) hydrogen bonds : bond 0.03356 / 2.10 ( 284) hydrogen bonds : angle 4.32157 / 3.01 ( 840) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 98 time to evaluate : 0.316 Fit side-chains REVERT: C 1 MET cc_start: 0.6690 (tpp) cc_final: 0.6334 (ttp) REVERT: C 107 ASP cc_start: 0.7656 (t0) cc_final: 0.7309 (t0) REVERT: C 138 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7830 (mp10) REVERT: C 225 TYR cc_start: 0.7251 (OUTLIER) cc_final: 0.6424 (p90) REVERT: C 276 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.6273 (mmm-85) outliers start: 36 outliers final: 29 residues processed: 124 average time/residue: 0.0745 time to fit residues: 13.3741 Evaluate side-chains 119 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 87 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 225 TYR Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 276 ARG Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 355 SER Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 384 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 9 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 83 optimal weight: 0.0060 chunk 46 optimal weight: 0.6980 chunk 6 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 overall best weight: 1.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 ASN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.182976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.142390 restraints weight = 9401.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.140281 restraints weight = 7999.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.141857 restraints weight = 8341.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.142541 restraints weight = 6070.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.143042 restraints weight = 5871.392| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7475 Z= 0.142 Angle : 0.598 10.705 10107 Z= 0.298 Chirality : 0.043 0.209 1086 Planarity : 0.005 0.072 1268 Dihedral : 4.792 60.329 975 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.68 % Favored : 95.21 % Rotamer: Outliers : 4.30 % Allowed : 25.66 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: 0.35 (0.29), residues: 877 helix: 1.80 (0.31), residues: 284 sheet: 0.25 (0.41), residues: 171 loop : -0.86 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 276 TYR 0.007 0.001 TYR B 280 PHE 0.013 0.001 PHE C 332 TRP 0.044 0.002 TRP C 20 HIS 0.004 0.001 HIS C 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 ( 7475) covalent geometry : angle 0.59773 / 0.30 (10107) hydrogen bonds : bond 0.03589 / 2.25 ( 284) hydrogen bonds : angle 4.32561 / 3.02 ( 840) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 91 time to evaluate : 0.275 Fit side-chains REVERT: B 243 ARG cc_start: 0.7646 (mtt-85) cc_final: 0.7414 (mtt180) REVERT: C 1 MET cc_start: 0.6707 (tpp) cc_final: 0.6372 (ttp) REVERT: C 107 ASP cc_start: 0.7712 (t0) cc_final: 0.7371 (t0) REVERT: C 138 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.7783 (mp10) REVERT: C 225 TYR cc_start: 0.7291 (OUTLIER) cc_final: 0.6463 (p90) REVERT: C 276 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.6153 (mmm-85) outliers start: 34 outliers final: 31 residues processed: 116 average time/residue: 0.0740 time to fit residues: 12.2784 Evaluate side-chains 120 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 86 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 225 TYR Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 276 ARG Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 355 SER Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 384 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 35 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 62 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.180576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.137517 restraints weight = 9493.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.136300 restraints weight = 7949.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.137900 restraints weight = 8276.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.138623 restraints weight = 5861.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.139672 restraints weight = 5234.600| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7475 Z= 0.154 Angle : 0.603 10.414 10107 Z= 0.303 Chirality : 0.043 0.206 1086 Planarity : 0.005 0.072 1268 Dihedral : 4.920 60.579 975 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.56 % Favored : 95.32 % Rotamer: Outliers : 4.68 % Allowed : 25.41 % Favored : 69.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: 0.29 (0.29), residues: 877 helix: 1.74 (0.31), residues: 284 sheet: 0.32 (0.42), residues: 166 loop : -0.95 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 275 TYR 0.008 0.001 TYR C 171 PHE 0.012 0.001 PHE C 332 TRP 0.052 0.002 TRP C 20 HIS 0.005 0.001 HIS C 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.15 ( 7475) covalent geometry : angle 0.60280 / 0.30 (10107) hydrogen bonds : bond 0.03755 / 2.35 ( 284) hydrogen bonds : angle 4.37732 / 3.05 ( 840) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 91 time to evaluate : 0.289 Fit side-chains REVERT: B 243 ARG cc_start: 0.7790 (mtt-85) cc_final: 0.7504 (mtt180) REVERT: C 1 MET cc_start: 0.6891 (tpp) cc_final: 0.6580 (ttp) REVERT: C 107 ASP cc_start: 0.7440 (t0) cc_final: 0.7033 (t0) REVERT: C 138 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7646 (mp10) REVERT: C 225 TYR cc_start: 0.7332 (OUTLIER) cc_final: 0.6551 (p90) REVERT: C 276 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.6036 (mmm-85) REVERT: C 318 ASN cc_start: 0.6300 (m-40) cc_final: 0.6007 (m-40) REVERT: C 388 ASP cc_start: 0.8611 (m-30) cc_final: 0.8226 (p0) outliers start: 37 outliers final: 32 residues processed: 118 average time/residue: 0.0740 time to fit residues: 12.5147 Evaluate side-chains 120 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 85 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 225 TYR Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 276 ARG Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 355 SER Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 384 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 9 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 76 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 83 optimal weight: 8.9990 chunk 84 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.177513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.135020 restraints weight = 9602.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.133669 restraints weight = 7995.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.135288 restraints weight = 8424.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.135978 restraints weight = 5935.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.136291 restraints weight = 5938.357| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7475 Z= 0.215 Angle : 0.652 10.406 10107 Z= 0.330 Chirality : 0.045 0.214 1086 Planarity : 0.005 0.073 1268 Dihedral : 5.257 61.393 975 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.25 % Favored : 94.64 % Rotamer: Outliers : 4.55 % Allowed : 25.66 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: 0.11 (0.29), residues: 877 helix: 1.46 (0.31), residues: 289 sheet: 0.23 (0.42), residues: 158 loop : -0.96 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 275 TYR 0.012 0.001 TYR C 171 PHE 0.015 0.002 PHE C 17 TRP 0.074 0.003 TRP C 20 HIS 0.003 0.001 HIS C 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.21 ( 7475) covalent geometry : angle 0.65183 / 0.33 (10107) hydrogen bonds : bond 0.04246 / 2.65 ( 284) hydrogen bonds : angle 4.62205 / 3.21 ( 840) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 95 time to evaluate : 0.330 Fit side-chains REVERT: B 74 MET cc_start: 0.8007 (ppp) cc_final: 0.7796 (ppp) REVERT: B 243 ARG cc_start: 0.7873 (mtt-85) cc_final: 0.7575 (mtt180) REVERT: C 1 MET cc_start: 0.7067 (tpp) cc_final: 0.6738 (ttp) REVERT: C 107 ASP cc_start: 0.7609 (t0) cc_final: 0.7241 (t0) REVERT: C 138 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7421 (mp10) REVERT: C 225 TYR cc_start: 0.7331 (OUTLIER) cc_final: 0.6585 (p90) REVERT: C 232 THR cc_start: 0.8163 (p) cc_final: 0.7607 (t) REVERT: C 276 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.6016 (mmm-85) REVERT: C 388 ASP cc_start: 0.8691 (m-30) cc_final: 0.8297 (p0) outliers start: 36 outliers final: 28 residues processed: 122 average time/residue: 0.0728 time to fit residues: 12.8429 Evaluate side-chains 122 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 91 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 225 TYR Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 276 ARG Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 355 SER Chi-restraints excluded: chain C residue 370 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 47 optimal weight: 8.9990 chunk 5 optimal weight: 0.8980 chunk 68 optimal weight: 10.0000 chunk 46 optimal weight: 0.1980 chunk 18 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 50 optimal weight: 0.0070 chunk 17 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 66 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 = 0.4165 r_free = 0.4165 target = 0.184306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.143136 restraints weight = 9359.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.141840 restraints weight = 7306.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.143276 restraints weight = 7767.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.144377 restraints weight = 5477.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.144638 restraints weight = 5262.631| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7475 Z= 0.102 Angle : 0.579 11.021 10107 Z= 0.289 Chirality : 0.042 0.202 1086 Planarity : 0.005 0.071 1268 Dihedral : 4.693 59.282 975 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.88 % Favored : 96.01 % Rotamer: Outliers : 3.79 % Allowed : 26.42 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: 0.36 (0.29), residues: 877 helix: 1.87 (0.31), residues: 284 sheet: 0.21 (0.42), residues: 171 loop : -0.90 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 276 TYR 0.008 0.001 TYR C 213 PHE 0.011 0.001 PHE C 332 TRP 0.059 0.002 TRP C 20 HIS 0.003 0.001 HIS C 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 ( 7475) covalent geometry : angle 0.57883 / 0.29 (10107) hydrogen bonds : bond 0.03094 / 1.97 ( 284) hydrogen bonds : angle 4.24662 / 2.94 ( 840) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1166.82 seconds wall clock time: 21 minutes 1.93 seconds (1261.93 seconds total)