Starting phenix.real_space_refine on Tue Aug 4 22:47:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8i88_35241/08_2026/8i88_35241.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i88_35241/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8i88_35241/08_2026/8i88_35241.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i88_35241/08_2026/8i88_35241.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8i88_35241/08_2026/8i88_35241.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8i88_35241/08_2026/8i88_35241.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8i88_35241/08_2026/8i88_35241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i88_35241/08_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'RNAv2': 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: 1.44, per 1000 atoms: 0.20 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: 0.50 Conformation dependent library (CDL) restraints added in 301.5 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: 0.15 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: 1.01 Time building geometry restraints manager: 0.67 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: 3769 16.65 - 33.31: 513 33.31 - 49.96: 148 49.96 - 66.61: 28 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 - 0.049: 868 0.049 - 0.099: 167 0.099 - 0.148: 45 0.148 - 0.197: 4 0.197 - 0.247: 2 Chirality restraints: 1086 Sorted by residual: chirality pdb=" P A L 3 " pdb=" OP1 A L 3 " pdb=" OP2 A L 3 " pdb=" O5' A L 3 " both_signs ideal model delta sigma weight residual True 2.17 -2.42 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" P G L 2 " pdb=" OP1 G L 2 " pdb=" OP2 G L 2 " pdb=" O5' G L 2 " both_signs ideal model delta sigma weight residual True 2.17 -2.40 -0.23 2.00e-01 2.50e+01 1.32e+00 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 ... (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: 0.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.850 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.350 ------------------------------------------------------------------------------- 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 : 0.659 20.119 10107 Z= 0.353 Chirality : 0.043 0.247 1086 Planarity : 0.006 0.115 1268 Dihedral : 16.438 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 0.65853 / 0.35 (10107) hydrogen bonds : bond 0.12229 / 6.65 ( 284) hydrogen bonds : angle 5.46972 / 3.90 ( 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 : 0.274 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 111 average time/residue: 0.0708 time to fit residues: 11.4149 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 : 0.279 ------------------------------------------------------------------------------- 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 = 0.4109 r_free = 0.4109 target = 0.178344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.136535 restraints weight = 9659.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.134687 restraints weight = 7736.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.136388 restraints weight = 7511.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.137151 restraints weight = 5476.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.138041 restraints weight = 5290.144| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 7475 Z= 0.201 Angle : 0.613 9.109 10107 Z= 0.319 Chirality : 0.044 0.154 1086 Planarity : 0.006 0.084 1268 Dihedral : 5.928 62.703 978 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.90 % Favored : 94.98 % Rotamer: Outliers : 4.80 % Allowed : 21.74 % Favored : 73.45 % 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: -0.05 (0.28), residues: 877 helix: 1.33 (0.31), residues: 282 sheet: 0.40 (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 19 TYR 0.011 0.001 TYR C 171 PHE 0.016 0.002 PHE C 17 TRP 0.031 0.002 TRP C 20 HIS 0.007 0.001 HIS C 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.20 ( 7475) covalent geometry : angle 0.61306 / 0.32 (10107) hydrogen bonds : bond 0.04406 / 2.66 ( 284) hydrogen bonds : angle 4.78688 / 3.35 ( 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 140 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 102 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: C 107 ASP cc_start: 0.7575 (t0) cc_final: 0.7223 (t0) REVERT: C 138 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7592 (mp10) REVERT: C 192 TRP cc_start: 0.6290 (p90) cc_final: 0.6006 (p90) REVERT: C 193 MET cc_start: 0.5676 (mmt) cc_final: 0.5387 (ttp) REVERT: C 225 TYR cc_start: 0.7283 (OUTLIER) cc_final: 0.6441 (p90) REVERT: C 276 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.6494 (mmm-85) outliers start: 38 outliers final: 28 residues processed: 127 average time/residue: 0.0687 time to fit residues: 12.6264 Evaluate side-chains 129 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 98 time to evaluate : 0.280 ------------------------------------------------------------------------------- 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 412 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain C residue 36 ILE 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: 3.9990 chunk 1 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 53 optimal weight: 9.9990 chunk 26 optimal weight: 0.7980 chunk 75 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 80 optimal weight: 0.9990 chunk 82 optimal weight: 20.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.4141 r_free = 0.4141 target = 0.181569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.140121 restraints weight = 9300.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.138580 restraints weight = 7783.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.140284 restraints weight = 7706.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.140659 restraints weight = 5652.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.141277 restraints weight = 5931.143| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7475 Z= 0.124 Angle : 0.546 10.296 10107 Z= 0.280 Chirality : 0.041 0.140 1086 Planarity : 0.005 0.075 1268 Dihedral : 5.641 60.843 978 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.10 % Favored : 95.78 % Rotamer: Outliers : 4.17 % Allowed : 23.01 % Favored : 72.82 % 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: 0.12 (0.28), residues: 877 helix: 1.60 (0.31), residues: 282 sheet: 0.43 (0.42), residues: 159 loop : -1.11 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 407 TYR 0.007 0.001 TYR B 346 PHE 0.011 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 0.00291 / 0.12 ( 7475) covalent geometry : angle 0.54639 / 0.28 (10107) hydrogen bonds : bond 0.03700 / 2.26 ( 284) hydrogen bonds : angle 4.49793 / 3.14 ( 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: 33 poor density : 106 time to evaluate : 0.287 Fit side-chains revert: symmetry clash REVERT: C 1 MET cc_start: 0.7045 (tpp) cc_final: 0.6609 (ttp) REVERT: C 107 ASP cc_start: 0.7607 (t0) cc_final: 0.7313 (t0) REVERT: C 138 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7742 (mp10) REVERT: C 174 ASN cc_start: 0.8357 (OUTLIER) cc_final: 0.7971 (p0) REVERT: C 225 TYR cc_start: 0.7179 (OUTLIER) cc_final: 0.6309 (p90) REVERT: C 276 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.6781 (mmm-85) REVERT: C 393 LEU cc_start: 0.8147 (tp) cc_final: 0.7839 (tp) outliers start: 33 outliers final: 20 residues processed: 127 average time/residue: 0.0745 time to fit residues: 13.3149 Evaluate side-chains 120 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 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 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 320 HIS Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 370 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 45 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 chunk 60 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 = 0.4095 r_free = 0.4095 target = 0.177281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.136830 restraints weight = 9792.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.135370 restraints weight = 10350.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.136472 restraints weight = 12204.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.137565 restraints weight = 7078.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.138194 restraints weight = 6199.563| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 7475 Z= 0.202 Angle : 0.601 9.397 10107 Z= 0.312 Chirality : 0.043 0.141 1086 Planarity : 0.005 0.077 1268 Dihedral : 5.533 61.317 975 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.13 % Favored : 94.75 % Rotamer: Outliers : 4.80 % Allowed : 23.89 % Favored : 71.30 % 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: -0.04 (0.28), residues: 877 helix: 1.40 (0.31), residues: 283 sheet: 0.33 (0.43), residues: 149 loop : -1.12 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 275 TYR 0.012 0.001 TYR B 280 PHE 0.015 0.001 PHE C 17 TRP 0.038 0.002 TRP C 20 HIS 0.005 0.001 HIS C 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.20 ( 7475) covalent geometry : angle 0.60052 / 0.31 (10107) hydrogen bonds : bond 0.04296 / 2.61 ( 284) hydrogen bonds : angle 4.67910 / 3.28 ( 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 143 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 105 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: B 56 TYR cc_start: 0.9051 (t80) cc_final: 0.8790 (t80) REVERT: C 40 ASP cc_start: 0.8765 (p0) cc_final: 0.8554 (p0) REVERT: C 107 ASP cc_start: 0.7728 (t0) cc_final: 0.7231 (t0) REVERT: C 138 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7571 (mp10) REVERT: C 174 ASN cc_start: 0.8497 (OUTLIER) cc_final: 0.8159 (p0) REVERT: C 225 TYR cc_start: 0.7272 (OUTLIER) cc_final: 0.6351 (p90) REVERT: C 276 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.6749 (mmm-85) REVERT: C 318 ASN cc_start: 0.6262 (m-40) cc_final: 0.6022 (m-40) REVERT: C 393 LEU cc_start: 0.8124 (tp) cc_final: 0.7853 (tp) outliers start: 38 outliers final: 31 residues processed: 132 average time/residue: 0.0619 time to fit residues: 11.7893 Evaluate side-chains 135 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 100 time to evaluate : 0.280 ------------------------------------------------------------------------------- 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 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 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 B residue 491 THR Chi-restraints excluded: chain C residue 37 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 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 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: 0.8980 chunk 11 optimal weight: 0.0770 chunk 48 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 58 optimal weight: 10.0000 chunk 71 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 85 optimal weight: 9.9990 overall best weight: 0.7142 ------------------------------------------------------------------------------- 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 = 0.4166 r_free = 0.4166 target = 0.184704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.143217 restraints weight = 9218.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.141868 restraints weight = 7870.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.143451 restraints weight = 8176.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.144355 restraints weight = 6074.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.144881 restraints weight = 5525.900| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7475 Z= 0.100 Angle : 0.536 10.711 10107 Z= 0.274 Chirality : 0.041 0.146 1086 Planarity : 0.005 0.075 1268 Dihedral : 5.175 59.213 975 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.76 % Favored : 96.12 % Rotamer: Outliers : 4.17 % Allowed : 25.16 % Favored : 70.67 % 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: 0.19 (0.29), residues: 877 helix: 1.72 (0.31), residues: 282 sheet: 0.31 (0.41), residues: 167 loop : -1.06 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 407 TYR 0.009 0.001 TYR C 213 PHE 0.010 0.001 PHE C 332 TRP 0.034 0.002 TRP C 192 HIS 0.005 0.001 HIS C 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 ( 7475) covalent geometry : angle 0.53611 / 0.27 (10107) hydrogen bonds : bond 0.03288 / 2.03 ( 284) hydrogen bonds : angle 4.33298 / 3.03 ( 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 145 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 0.272 Fit side-chains REVERT: C 1 MET cc_start: 0.6870 (tpp) cc_final: 0.6415 (ttp) REVERT: C 40 ASP cc_start: 0.8776 (p0) cc_final: 0.8572 (p0) REVERT: C 107 ASP cc_start: 0.7652 (t0) cc_final: 0.7302 (t0) REVERT: C 138 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.7941 (mp10) REVERT: C 174 ASN cc_start: 0.8259 (OUTLIER) cc_final: 0.7881 (p0) REVERT: C 216 THR cc_start: 0.8120 (m) cc_final: 0.7718 (p) REVERT: C 225 TYR cc_start: 0.7197 (OUTLIER) cc_final: 0.6303 (p90) REVERT: C 276 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.6546 (mmm-85) REVERT: C 393 LEU cc_start: 0.7988 (tp) cc_final: 0.7760 (tp) outliers start: 33 outliers final: 21 residues processed: 134 average time/residue: 0.0671 time to fit residues: 12.8664 Evaluate side-chains 120 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 0.178 ------------------------------------------------------------------------------- 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 202 TYR 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 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 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 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: 0.8980 chunk 60 optimal weight: 0.9990 chunk 87 optimal weight: 8.9990 chunk 20 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 74 optimal weight: 9.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 ASN C 116 ASN C 174 ASN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.182390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.141507 restraints weight = 9255.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.139780 restraints weight = 7530.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.141602 restraints weight = 7654.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.141796 restraints weight = 5716.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.142203 restraints weight = 6117.547| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7475 Z= 0.146 Angle : 0.586 9.988 10107 Z= 0.297 Chirality : 0.043 0.153 1086 Planarity : 0.005 0.074 1268 Dihedral : 5.247 60.366 975 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.33 % Favored : 95.55 % Rotamer: Outliers : 5.06 % Allowed : 25.28 % Favored : 69.66 % 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: 0.18 (0.29), residues: 877 helix: 1.61 (0.31), residues: 284 sheet: 0.31 (0.42), residues: 165 loop : -1.00 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 19 TYR 0.010 0.001 TYR C 213 PHE 0.016 0.001 PHE C 45 TRP 0.045 0.002 TRP C 20 HIS 0.004 0.001 HIS C 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 ( 7475) covalent geometry : angle 0.58572 / 0.30 (10107) hydrogen bonds : bond 0.03738 / 2.30 ( 284) hydrogen bonds : angle 4.41010 / 3.07 ( 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 137 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 97 time to evaluate : 0.240 Fit side-chains REVERT: C 1 MET cc_start: 0.6869 (tpp) cc_final: 0.6540 (ttp) REVERT: C 40 ASP cc_start: 0.8836 (p0) cc_final: 0.8616 (p0) REVERT: C 107 ASP cc_start: 0.7738 (t0) cc_final: 0.7381 (t0) REVERT: C 138 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7852 (mp10) REVERT: C 174 ASN cc_start: 0.8420 (OUTLIER) cc_final: 0.8033 (p0) REVERT: C 216 THR cc_start: 0.8281 (m) cc_final: 0.7801 (p) REVERT: C 225 TYR cc_start: 0.7223 (OUTLIER) cc_final: 0.6355 (p90) REVERT: C 276 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8172 (tpt-90) REVERT: C 393 LEU cc_start: 0.8068 (tp) cc_final: 0.7809 (tp) outliers start: 40 outliers final: 31 residues processed: 125 average time/residue: 0.0649 time to fit residues: 11.4927 Evaluate side-chains 127 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 92 time to evaluate : 0.268 ------------------------------------------------------------------------------- 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 227 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 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 25 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 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: 3.9990 chunk 42 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.4154 r_free = 0.4154 target = 0.183570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.142373 restraints weight = 9220.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.141091 restraints weight = 7366.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.142712 restraints weight = 7645.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.143441 restraints weight = 5339.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.144028 restraints weight = 5198.741| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7475 Z= 0.126 Angle : 0.585 11.273 10107 Z= 0.294 Chirality : 0.043 0.206 1086 Planarity : 0.005 0.072 1268 Dihedral : 5.203 60.093 975 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.68 % Favored : 95.21 % Rotamer: Outliers : 4.42 % Allowed : 25.54 % 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: 0.21 (0.29), residues: 877 helix: 1.64 (0.31), residues: 284 sheet: 0.28 (0.42), residues: 166 loop : -0.96 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 275 TYR 0.009 0.001 TYR C 213 PHE 0.019 0.001 PHE C 45 TRP 0.052 0.002 TRP C 20 HIS 0.004 0.001 HIS C 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 7475) covalent geometry : angle 0.58535 / 0.29 (10107) hydrogen bonds : bond 0.03526 / 2.17 ( 284) hydrogen bonds : angle 4.37340 / 3.03 ( 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 132 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 97 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: C 1 MET cc_start: 0.6850 (tpp) cc_final: 0.6506 (ttp) REVERT: C 107 ASP cc_start: 0.7455 (t0) cc_final: 0.7044 (t0) REVERT: C 138 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7841 (mp10) REVERT: C 174 ASN cc_start: 0.8355 (OUTLIER) cc_final: 0.7978 (p0) REVERT: C 225 TYR cc_start: 0.7287 (OUTLIER) cc_final: 0.6381 (p90) REVERT: C 276 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.6669 (mmm-85) REVERT: C 393 LEU cc_start: 0.8048 (tp) cc_final: 0.7813 (tp) outliers start: 35 outliers final: 26 residues processed: 121 average time/residue: 0.0788 time to fit residues: 13.5085 Evaluate side-chains 122 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 92 time to evaluate : 0.282 ------------------------------------------------------------------------------- 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 227 SER 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 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 9 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 20 optimal weight: 0.2980 chunk 81 optimal weight: 7.9990 chunk 83 optimal weight: 8.9990 chunk 46 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 72 optimal weight: 0.0770 overall best weight: 0.6340 ------------------------------------------------------------------------------- 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 = 0.4186 r_free = 0.4186 target = 0.186752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.144915 restraints weight = 9271.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.144272 restraints weight = 7390.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.145883 restraints weight = 7617.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.146764 restraints weight = 5353.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.147156 restraints weight = 5340.641| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7475 Z= 0.103 Angle : 0.571 10.853 10107 Z= 0.286 Chirality : 0.042 0.180 1086 Planarity : 0.004 0.072 1268 Dihedral : 5.002 59.712 975 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.10 % Favored : 95.78 % Rotamer: Outliers : 4.05 % Allowed : 26.17 % 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: 0.37 (0.29), residues: 877 helix: 1.79 (0.31), residues: 284 sheet: 0.27 (0.41), residues: 173 loop : -0.86 (0.30), residues: 420 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 0.020 0.001 PHE C 45 TRP 0.042 0.002 TRP C 20 HIS 0.005 0.001 HIS C 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.10 ( 7475) covalent geometry : angle 0.57146 / 0.29 (10107) hydrogen bonds : bond 0.03211 / 2.00 ( 284) hydrogen bonds : angle 4.25093 / 2.94 ( 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 127 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 95 time to evaluate : 0.291 Fit side-chains REVERT: C 107 ASP cc_start: 0.7243 (t0) cc_final: 0.6832 (t0) REVERT: C 138 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8010 (mp10) REVERT: C 174 ASN cc_start: 0.8269 (OUTLIER) cc_final: 0.7932 (p0) REVERT: C 225 TYR cc_start: 0.7198 (OUTLIER) cc_final: 0.6314 (p90) REVERT: C 276 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.6602 (mmm-85) REVERT: C 393 LEU cc_start: 0.7975 (tp) cc_final: 0.7702 (tp) outliers start: 32 outliers final: 24 residues processed: 118 average time/residue: 0.0736 time to fit residues: 12.4476 Evaluate side-chains 119 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 91 time to evaluate : 0.217 ------------------------------------------------------------------------------- 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 44 ILE 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 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 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 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 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: 0.9990 chunk 70 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 22 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.4186 r_free = 0.4186 target = 0.186659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.145130 restraints weight = 9172.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.143785 restraints weight = 8321.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.145851 restraints weight = 7610.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.146370 restraints weight = 5389.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.147753 restraints weight = 4977.653| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7475 Z= 0.107 Angle : 0.576 10.561 10107 Z= 0.286 Chirality : 0.042 0.206 1086 Planarity : 0.004 0.071 1268 Dihedral : 4.958 59.620 975 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.33 % Favored : 95.55 % 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: 0.43 (0.29), residues: 877 helix: 1.77 (0.31), residues: 291 sheet: 0.31 (0.42), residues: 171 loop : -0.80 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 275 TYR 0.008 0.001 TYR C 213 PHE 0.019 0.001 PHE C 45 TRP 0.039 0.002 TRP C 192 HIS 0.004 0.001 HIS C 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 7475) covalent geometry : angle 0.57561 / 0.29 (10107) hydrogen bonds : bond 0.03214 / 2.00 ( 284) hydrogen bonds : angle 4.18526 / 2.89 ( 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 130 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 96 time to evaluate : 0.287 Fit side-chains REVERT: C 107 ASP cc_start: 0.7243 (t0) cc_final: 0.6856 (t0) REVERT: C 138 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.8032 (mp10) REVERT: C 174 ASN cc_start: 0.8278 (OUTLIER) cc_final: 0.7869 (p0) REVERT: C 225 TYR cc_start: 0.7210 (OUTLIER) cc_final: 0.6338 (p90) REVERT: C 276 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.6521 (mmm-85) REVERT: C 388 ASP cc_start: 0.8418 (m-30) cc_final: 0.8136 (p0) REVERT: C 393 LEU cc_start: 0.7894 (tp) cc_final: 0.7683 (tp) outliers start: 34 outliers final: 28 residues processed: 121 average time/residue: 0.0705 time to fit residues: 12.3785 Evaluate side-chains 122 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 90 time to evaluate : 0.219 ------------------------------------------------------------------------------- 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 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 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 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 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: 7.9990 chunk 15 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 83 optimal weight: 10.0000 chunk 84 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 = 0.4158 r_free = 0.4158 target = 0.184174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.141622 restraints weight = 9233.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.139610 restraints weight = 7670.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.141810 restraints weight = 7733.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.142214 restraints weight = 5553.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.143565 restraints weight = 4931.115| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2177 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= 0.133 Angle : 0.595 10.490 10107 Z= 0.298 Chirality : 0.043 0.205 1086 Planarity : 0.004 0.072 1268 Dihedral : 5.071 62.792 975 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.90 % Favored : 94.98 % Rotamer: Outliers : 3.92 % Allowed : 25.79 % Favored : 70.29 % 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: 0.43 (0.29), residues: 877 helix: 1.73 (0.31), residues: 290 sheet: 0.26 (0.42), residues: 171 loop : -0.73 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 275 TYR 0.019 0.001 TYR C 213 PHE 0.020 0.001 PHE C 45 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 0.00317 / 0.13 ( 7475) covalent geometry : angle 0.59506 / 0.30 (10107) hydrogen bonds : bond 0.03520 / 2.18 ( 284) hydrogen bonds : angle 4.25968 / 2.93 ( 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 121 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 90 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: C 107 ASP cc_start: 0.7413 (t0) cc_final: 0.7005 (t0) REVERT: C 138 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.7852 (mp10) REVERT: C 174 ASN cc_start: 0.8334 (OUTLIER) cc_final: 0.8007 (p0) REVERT: C 225 TYR cc_start: 0.7271 (OUTLIER) cc_final: 0.6399 (p90) REVERT: C 276 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.7611 (tpt-90) REVERT: C 388 ASP cc_start: 0.8543 (m-30) cc_final: 0.8209 (p0) REVERT: C 393 LEU cc_start: 0.8044 (tp) cc_final: 0.7818 (tp) outliers start: 31 outliers final: 27 residues processed: 112 average time/residue: 0.0719 time to fit residues: 11.7213 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 : 0.291 ------------------------------------------------------------------------------- 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 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 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 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 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 47 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 50 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.4176 r_free = 0.4176 target = 0.185959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.144717 restraints weight = 9209.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.142971 restraints weight = 8149.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.144515 restraints weight = 7894.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.145390 restraints weight = 5984.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.146241 restraints weight = 5178.545| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7475 Z= 0.109 Angle : 0.573 10.727 10107 Z= 0.286 Chirality : 0.042 0.202 1086 Planarity : 0.004 0.072 1268 Dihedral : 4.977 61.822 975 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.45 % Favored : 95.44 % Rotamer: Outliers : 4.05 % Allowed : 25.79 % Favored : 70.16 % 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: 0.48 (0.29), residues: 877 helix: 1.77 (0.31), residues: 296 sheet: 0.34 (0.42), residues: 169 loop : -0.76 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 275 TYR 0.016 0.001 TYR C 213 PHE 0.021 0.001 PHE C 45 TRP 0.048 0.002 TRP C 20 HIS 0.004 0.001 HIS C 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 7475) covalent geometry : angle 0.57326 / 0.29 (10107) hydrogen bonds : bond 0.03233 / 2.02 ( 284) hydrogen bonds : angle 4.19074 / 2.88 ( 840) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1138.61 seconds wall clock time: 20 minutes 25.10 seconds (1225.10 seconds total)