Starting phenix.real_space_refine on Wed Feb 12 04:57:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i88_35241/02_2025/8i88_35241.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i88_35241/02_2025/8i88_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8i88_35241/02_2025/8i88_35241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i88_35241/02_2025/8i88_35241.map" model { file = "/net/cci-nas-00/data/ceres_data/8i88_35241/02_2025/8i88_35241.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i88_35241/02_2025/8i88_35241.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7287 Number of models: 1 Model: "" Number of chains: 3 Chain: "L" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Classifications: {'RNA': 2} Modifications used: {'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "B" Number of atoms: 3731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3731 Classifications: {'peptide': 462} Link IDs: {'PTRANS': 23, 'TRANS': 438} Chain breaks: 1 Chain: "C" Number of atoms: 3511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3511 Classifications: {'peptide': 421} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 408} Time building chain proxies: 4.29, per 1000 atoms: 0.59 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: 1.64 Conformation dependent library (CDL) restraints added in 972.9 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: 0.89 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: 2.01 Time building geometry restraints manager: 1.91 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: 3773 16.65 - 33.31: 513 33.31 - 49.96: 149 49.96 - 66.61: 29 66.61 - 83.26: 7 Dihedral angle restraints: 4471 sinusoidal: 1868 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 4468 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 742 0.035 - 0.070: 239 0.070 - 0.105: 67 0.105 - 0.140: 34 0.140 - 0.175: 4 Chirality restraints: 1086 Sorted by residual: chirality pdb=" CG LEU C 275 " pdb=" CB LEU C 275 " pdb=" CD1 LEU C 275 " pdb=" CD2 LEU C 275 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.67e-01 chirality pdb=" CB ILE B 60 " pdb=" CA ILE B 60 " pdb=" CG1 ILE B 60 " pdb=" CG2 ILE B 60 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.16e-01 chirality pdb=" CG LEU B 214 " pdb=" CB LEU B 214 " pdb=" CD1 LEU B 214 " pdb=" CD2 LEU B 214 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.17 2.00e-01 2.50e+01 6.83e-01 ... (remaining 1083 not shown) Planarity restraints: 1268 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 181 " -0.078 5.00e-02 4.00e+02 1.15e-01 2.12e+01 pdb=" N PRO C 182 " 0.199 5.00e-02 4.00e+02 pdb=" CA PRO C 182 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO C 182 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 330 " -0.059 5.00e-02 4.00e+02 9.09e-02 1.32e+01 pdb=" N PRO C 331 " 0.157 5.00e-02 4.00e+02 pdb=" CA PRO C 331 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO C 331 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 241 " 0.057 5.00e-02 4.00e+02 8.63e-02 1.19e+01 pdb=" N PRO C 242 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO C 242 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO C 242 " 0.047 5.00e-02 4.00e+02 ... (remaining 1265 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 81 2.64 - 3.21: 6343 3.21 - 3.77: 10772 3.77 - 4.34: 14363 4.34 - 4.90: 24114 Nonbonded interactions: 55673 Sorted by model distance: nonbonded pdb=" O PRO C 206 " pdb=" OG1 THR C 216 " model vdw 2.077 3.040 nonbonded pdb=" OG1 THR C 344 " pdb=" O LYS C 349 " model vdw 2.154 3.040 nonbonded pdb=" O VAL C 52 " pdb=" OG1 THR C 57 " model vdw 2.168 3.040 nonbonded pdb=" OD1 ASP C 40 " pdb=" N LYS C 41 " model vdw 2.172 3.120 nonbonded pdb=" OH TYR B 280 " pdb=" OD1 ASP B 458 " model vdw 2.214 3.040 ... (remaining 55668 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.540 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 18.990 Find NCS groups from input model: 0.080 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: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 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= 0.185 Angle : 0.656 20.119 10107 Z= 0.353 Chirality : 0.042 0.175 1086 Planarity : 0.006 0.115 1268 Dihedral : 16.500 83.263 2789 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 9.42 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.049 0.002 TRP C 20 HIS 0.006 0.001 HIS C 160 PHE 0.011 0.001 PHE C 391 TYR 0.014 0.001 TYR B 37 ARG 0.006 0.000 ARG B 416 *********************** 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 : 0.939 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 111 average time/residue: 0.1759 time to fit residues: 27.5491 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 : 0.882 ------------------------------------------------------------------------------- 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 75 optimal weight: 8.9990 chunk 67 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4104 r_free = 0.4104 target = 0.177801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.137136 restraints weight = 9476.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.133992 restraints weight = 9072.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.136061 restraints weight = 9526.065| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7475 Z= 0.335 Angle : 0.626 8.905 10107 Z= 0.327 Chirality : 0.044 0.154 1086 Planarity : 0.006 0.085 1268 Dihedral : 6.402 63.754 984 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.90 % Favored : 94.98 % Rotamer: Outliers : 5.06 % Allowed : 21.74 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.28), residues: 877 helix: 1.27 (0.31), residues: 283 sheet: 0.35 (0.43), residues: 157 loop : -1.15 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 20 HIS 0.007 0.001 HIS C 160 PHE 0.017 0.002 PHE C 17 TYR 0.012 0.002 TYR C 171 ARG 0.002 0.001 ARG C 276 *********************** 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 141 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 101 time to evaluate : 0.844 Fit side-chains revert: symmetry clash REVERT: B 56 TYR cc_start: 0.9074 (t80) cc_final: 0.8788 (t80) REVERT: B 74 MET cc_start: 0.7963 (ppp) cc_final: 0.7755 (ppp) REVERT: C 107 ASP cc_start: 0.7600 (t0) cc_final: 0.7251 (t0) REVERT: C 138 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7635 (mp10) REVERT: C 174 ASN cc_start: 0.8398 (OUTLIER) cc_final: 0.8006 (p0) REVERT: C 192 TRP cc_start: 0.6276 (p90) cc_final: 0.5997 (p90) REVERT: C 193 MET cc_start: 0.5591 (mmt) cc_final: 0.5378 (ttp) REVERT: C 225 TYR cc_start: 0.7218 (OUTLIER) cc_final: 0.6397 (p90) REVERT: C 276 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.6471 (mmm-85) outliers start: 40 outliers final: 29 residues processed: 128 average time/residue: 0.1600 time to fit residues: 29.7294 Evaluate side-chains 130 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 97 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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 25 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 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 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 42 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 81 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4153 r_free = 0.4153 target = 0.182646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.140662 restraints weight = 9461.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.139380 restraints weight = 7749.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.141096 restraints weight = 7760.869| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7475 Z= 0.156 Angle : 0.538 10.485 10107 Z= 0.276 Chirality : 0.041 0.137 1086 Planarity : 0.005 0.075 1268 Dihedral : 6.008 63.737 984 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.65 % Favored : 96.24 % Rotamer: Outliers : 3.79 % Allowed : 23.51 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.29), residues: 877 helix: 1.62 (0.31), residues: 283 sheet: 0.46 (0.42), residues: 159 loop : -1.08 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 20 HIS 0.006 0.001 HIS C 160 PHE 0.010 0.001 PHE C 60 TYR 0.007 0.001 TYR B 346 ARG 0.002 0.000 ARG B 407 *********************** 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 138 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 108 time to evaluate : 0.794 Fit side-chains revert: symmetry clash REVERT: B 305 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.7155 (mm) REVERT: C 1 MET cc_start: 0.7052 (tpp) cc_final: 0.6611 (ttp) REVERT: C 107 ASP cc_start: 0.7534 (t0) cc_final: 0.7254 (t0) REVERT: C 138 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7904 (mp10) REVERT: C 174 ASN cc_start: 0.8334 (OUTLIER) cc_final: 0.7895 (p0) REVERT: C 225 TYR cc_start: 0.7200 (OUTLIER) cc_final: 0.6323 (p90) REVERT: C 276 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.6784 (mmm-85) REVERT: C 393 LEU cc_start: 0.8148 (tp) cc_final: 0.7856 (tp) outliers start: 30 outliers final: 18 residues processed: 126 average time/residue: 0.1926 time to fit residues: 33.1373 Evaluate side-chains 122 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 0.947 ------------------------------------------------------------------------------- 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 305 LEU 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 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 75 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 20 optimal weight: 8.9990 chunk 70 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 50 optimal weight: 0.0670 chunk 86 optimal weight: 9.9990 overall best weight: 2.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 ASN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 364 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.178242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.137840 restraints weight = 9685.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.136423 restraints weight = 10253.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.137569 restraints weight = 12016.715| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7475 Z= 0.277 Angle : 0.582 9.674 10107 Z= 0.302 Chirality : 0.042 0.139 1086 Planarity : 0.005 0.077 1268 Dihedral : 5.828 63.751 981 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.90 % Favored : 94.98 % Rotamer: Outliers : 4.80 % Allowed : 24.27 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.28), residues: 877 helix: 1.50 (0.31), residues: 282 sheet: 0.30 (0.42), residues: 157 loop : -1.07 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 20 HIS 0.005 0.001 HIS C 160 PHE 0.014 0.001 PHE C 17 TYR 0.012 0.001 TYR B 280 ARG 0.002 0.000 ARG B 275 *********************** 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 144 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 106 time to evaluate : 0.888 Fit side-chains REVERT: C 40 ASP cc_start: 0.8759 (p0) cc_final: 0.8541 (p0) REVERT: C 107 ASP cc_start: 0.7657 (t0) cc_final: 0.7159 (t0) REVERT: C 138 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7735 (mp10) REVERT: C 174 ASN cc_start: 0.8405 (OUTLIER) cc_final: 0.8038 (p0) REVERT: C 225 TYR cc_start: 0.7199 (OUTLIER) cc_final: 0.6315 (p90) REVERT: C 276 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.6696 (mmm-85) REVERT: C 393 LEU cc_start: 0.8136 (tp) cc_final: 0.7869 (tp) outliers start: 38 outliers final: 28 residues processed: 130 average time/residue: 0.1772 time to fit residues: 32.3366 Evaluate side-chains 135 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 103 time to evaluate : 0.906 ------------------------------------------------------------------------------- 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 202 TYR 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 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 265 ILE Chi-restraints excluded: chain C residue 276 ARG Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 370 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 52 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 74 optimal weight: 8.9990 chunk 87 optimal weight: 8.9990 chunk 36 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 ASN C 174 ASN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.179175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.136551 restraints weight = 9482.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.135567 restraints weight = 7559.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.137095 restraints weight = 7954.363| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7475 Z= 0.241 Angle : 0.576 9.905 10107 Z= 0.297 Chirality : 0.042 0.139 1086 Planarity : 0.005 0.076 1268 Dihedral : 5.800 63.747 981 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.56 % Favored : 95.32 % Rotamer: Outliers : 4.93 % Allowed : 24.27 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.28), residues: 877 helix: 1.46 (0.31), residues: 284 sheet: 0.35 (0.42), residues: 157 loop : -1.09 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 192 HIS 0.005 0.001 HIS C 160 PHE 0.012 0.001 PHE C 17 TYR 0.010 0.001 TYR C 213 ARG 0.002 0.000 ARG B 275 *********************** 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 143 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 104 time to evaluate : 0.828 Fit side-chains REVERT: C 1 MET cc_start: 0.7073 (tpp) cc_final: 0.6639 (ttp) REVERT: C 107 ASP cc_start: 0.7708 (t0) cc_final: 0.7177 (t0) REVERT: C 138 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7557 (mp10) REVERT: C 174 ASN cc_start: 0.8419 (OUTLIER) cc_final: 0.8024 (p0) REVERT: C 225 TYR cc_start: 0.7275 (OUTLIER) cc_final: 0.6401 (p90) REVERT: C 276 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.6685 (mmm-85) REVERT: C 393 LEU cc_start: 0.8199 (tp) cc_final: 0.7951 (tp) outliers start: 39 outliers final: 29 residues processed: 131 average time/residue: 0.1667 time to fit residues: 30.5295 Evaluate side-chains 128 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 95 time to evaluate : 0.815 ------------------------------------------------------------------------------- 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 202 TYR Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 63 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 68 optimal weight: 0.5980 chunk 55 optimal weight: 6.9990 chunk 82 optimal weight: 7.9990 chunk 54 optimal weight: 8.9990 chunk 81 optimal weight: 0.4980 chunk 76 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4096 r_free = 0.4096 target = 0.176981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.136595 restraints weight = 9588.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.133570 restraints weight = 9378.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.134900 restraints weight = 11153.499| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7475 Z= 0.317 Angle : 0.622 10.032 10107 Z= 0.323 Chirality : 0.044 0.214 1086 Planarity : 0.005 0.075 1268 Dihedral : 5.964 63.755 981 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.36 % Favored : 94.53 % Rotamer: Outliers : 6.19 % Allowed : 23.01 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.28), residues: 877 helix: 1.19 (0.31), residues: 290 sheet: 0.23 (0.43), residues: 152 loop : -1.16 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP C 20 HIS 0.004 0.001 HIS C 160 PHE 0.014 0.001 PHE C 17 TYR 0.013 0.001 TYR C 213 ARG 0.003 0.000 ARG B 275 *********************** 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 152 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 103 time to evaluate : 0.837 Fit side-chains REVERT: C 1 MET cc_start: 0.7063 (tpp) cc_final: 0.6658 (ttp) REVERT: C 107 ASP cc_start: 0.7822 (t0) cc_final: 0.7338 (t0) REVERT: C 138 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7552 (mp10) REVERT: C 174 ASN cc_start: 0.8370 (OUTLIER) cc_final: 0.8016 (p0) REVERT: C 225 TYR cc_start: 0.7352 (OUTLIER) cc_final: 0.6460 (p90) REVERT: C 276 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.6741 (mmm-85) REVERT: C 318 ASN cc_start: 0.6387 (m-40) cc_final: 0.6074 (m-40) REVERT: C 393 LEU cc_start: 0.8164 (tp) cc_final: 0.7900 (tp) outliers start: 49 outliers final: 37 residues processed: 138 average time/residue: 0.1661 time to fit residues: 32.5261 Evaluate side-chains 138 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 97 time to evaluate : 0.798 ------------------------------------------------------------------------------- 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 227 SER Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 491 THR 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 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 355 SER Chi-restraints excluded: chain C residue 370 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 59 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 41 optimal weight: 0.0570 chunk 25 optimal weight: 0.0570 overall best weight: 2.0222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4108 r_free = 0.4108 target = 0.177892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.134332 restraints weight = 9621.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.133549 restraints weight = 7347.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.134643 restraints weight = 7782.495| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7475 Z= 0.245 Angle : 0.590 9.778 10107 Z= 0.305 Chirality : 0.043 0.207 1086 Planarity : 0.005 0.074 1268 Dihedral : 5.865 63.747 981 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.90 % Favored : 94.98 % Rotamer: Outliers : 5.31 % Allowed : 25.66 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.29), residues: 877 helix: 1.31 (0.31), residues: 290 sheet: 0.25 (0.43), residues: 152 loop : -1.12 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP C 192 HIS 0.003 0.001 HIS B 207 PHE 0.011 0.001 PHE C 332 TYR 0.008 0.001 TYR B 280 ARG 0.002 0.000 ARG B 275 *********************** 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 146 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 104 time to evaluate : 0.877 Fit side-chains REVERT: B 243 ARG cc_start: 0.7870 (mtt-85) cc_final: 0.7587 (mtt180) REVERT: C 1 MET cc_start: 0.7186 (tpp) cc_final: 0.6857 (ttp) REVERT: C 107 ASP cc_start: 0.7810 (t0) cc_final: 0.7321 (t0) REVERT: C 108 ILE cc_start: 0.7480 (mt) cc_final: 0.7249 (mp) REVERT: C 138 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7523 (mp10) REVERT: C 174 ASN cc_start: 0.8431 (OUTLIER) cc_final: 0.8067 (p0) REVERT: C 225 TYR cc_start: 0.7323 (OUTLIER) cc_final: 0.6484 (p90) REVERT: C 276 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.6601 (mmm-85) REVERT: C 318 ASN cc_start: 0.6485 (m-40) cc_final: 0.6157 (m-40) REVERT: C 388 ASP cc_start: 0.8732 (m-30) cc_final: 0.8299 (p0) outliers start: 42 outliers final: 33 residues processed: 134 average time/residue: 0.1776 time to fit residues: 33.3036 Evaluate side-chains 139 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 102 time to evaluate : 0.885 ------------------------------------------------------------------------------- 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 46 THR Chi-restraints excluded: chain B residue 48 GLN 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 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 489 ILE Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 491 THR 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 227 LEU Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 276 ARG Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 370 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 61 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 14 optimal weight: 0.3980 chunk 9 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.176835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.132504 restraints weight = 9656.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.133034 restraints weight = 7397.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.134237 restraints weight = 7333.457| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7475 Z= 0.287 Angle : 0.614 9.532 10107 Z= 0.318 Chirality : 0.044 0.200 1086 Planarity : 0.005 0.074 1268 Dihedral : 5.931 63.751 981 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.13 % Favored : 94.75 % Rotamer: Outliers : 5.44 % Allowed : 25.41 % Favored : 69.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.29), residues: 877 helix: 1.26 (0.31), residues: 291 sheet: -0.21 (0.41), residues: 173 loop : -1.04 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP C 20 HIS 0.003 0.001 HIS C 226 PHE 0.013 0.001 PHE C 17 TYR 0.008 0.001 TYR C 293 ARG 0.003 0.000 ARG B 275 *********************** 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 144 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 101 time to evaluate : 0.819 Fit side-chains REVERT: B 74 MET cc_start: 0.8111 (ppp) cc_final: 0.7872 (ppp) REVERT: B 243 ARG cc_start: 0.7932 (mtt-85) cc_final: 0.7546 (mtt180) REVERT: C 107 ASP cc_start: 0.7842 (t0) cc_final: 0.7394 (t0) REVERT: C 138 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7480 (mp10) REVERT: C 174 ASN cc_start: 0.8382 (OUTLIER) cc_final: 0.8050 (p0) REVERT: C 225 TYR cc_start: 0.7375 (OUTLIER) cc_final: 0.6526 (p90) REVERT: C 276 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.6128 (mmm-85) REVERT: C 318 ASN cc_start: 0.6466 (m-40) cc_final: 0.6184 (m-40) REVERT: C 388 ASP cc_start: 0.8756 (m-30) cc_final: 0.8327 (p0) outliers start: 43 outliers final: 37 residues processed: 132 average time/residue: 0.1697 time to fit residues: 31.7465 Evaluate side-chains 138 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 97 time to evaluate : 0.996 ------------------------------------------------------------------------------- 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 46 THR Chi-restraints excluded: chain B residue 48 GLN 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 281 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 389 SER 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 489 ILE Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain C residue 25 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 227 LEU Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 276 ARG Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 370 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 64 optimal weight: 4.9990 chunk 57 optimal weight: 9.9990 chunk 8 optimal weight: 0.7980 chunk 34 optimal weight: 0.3980 chunk 66 optimal weight: 0.0980 chunk 75 optimal weight: 9.9990 chunk 39 optimal weight: 0.4980 chunk 44 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4159 r_free = 0.4159 target = 0.183318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.143176 restraints weight = 9511.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.140154 restraints weight = 10580.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.142360 restraints weight = 10437.516| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 7475 Z= 0.153 Angle : 0.579 11.358 10107 Z= 0.293 Chirality : 0.042 0.188 1086 Planarity : 0.005 0.072 1268 Dihedral : 5.510 63.734 981 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.10 % Favored : 95.78 % Rotamer: Outliers : 4.30 % Allowed : 26.93 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.29), residues: 877 helix: 1.58 (0.31), residues: 291 sheet: -0.22 (0.39), residues: 188 loop : -0.90 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP C 20 HIS 0.002 0.000 HIS C 226 PHE 0.011 0.001 PHE C 332 TYR 0.009 0.001 TYR B 280 ARG 0.003 0.000 ARG C 276 *********************** 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 136 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 102 time to evaluate : 0.871 Fit side-chains revert: symmetry clash REVERT: B 243 ARG cc_start: 0.7676 (mtt-85) cc_final: 0.7434 (mtt180) REVERT: C 1 MET cc_start: 0.6787 (tpp) cc_final: 0.6299 (ttp) REVERT: C 107 ASP cc_start: 0.7653 (t0) cc_final: 0.7196 (t0) REVERT: C 138 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.7880 (mp10) REVERT: C 174 ASN cc_start: 0.8271 (OUTLIER) cc_final: 0.7995 (p0) REVERT: C 225 TYR cc_start: 0.7377 (OUTLIER) cc_final: 0.6476 (p90) REVERT: C 276 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.6235 (mmm-85) REVERT: C 388 ASP cc_start: 0.8623 (m-30) cc_final: 0.8276 (p0) REVERT: C 393 LEU cc_start: 0.8115 (tp) cc_final: 0.7876 (tp) outliers start: 34 outliers final: 23 residues processed: 127 average time/residue: 0.1727 time to fit residues: 30.6032 Evaluate side-chains 121 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 0.873 ------------------------------------------------------------------------------- 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 120 LEU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 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 200 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 33 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 35 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 82 optimal weight: 20.0000 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 ASN C 212 ASN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.179987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.136342 restraints weight = 9767.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.135773 restraints weight = 7539.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.136884 restraints weight = 7731.746| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7475 Z= 0.216 Angle : 0.631 11.502 10107 Z= 0.315 Chirality : 0.043 0.206 1086 Planarity : 0.005 0.072 1268 Dihedral : 5.585 63.744 981 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.79 % Favored : 95.10 % Rotamer: Outliers : 4.05 % Allowed : 27.69 % Favored : 68.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.29), residues: 877 helix: 1.54 (0.31), residues: 297 sheet: -0.06 (0.40), residues: 181 loop : -0.89 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP C 20 HIS 0.002 0.001 HIS C 226 PHE 0.012 0.001 PHE C 332 TYR 0.017 0.001 TYR C 213 ARG 0.002 0.000 ARG B 275 ********************** 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 127 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 95 time to evaluate : 0.815 Fit side-chains revert: symmetry clash REVERT: B 243 ARG cc_start: 0.7899 (mtt-85) cc_final: 0.7523 (mtt180) REVERT: C 1 MET cc_start: 0.7027 (tpp) cc_final: 0.6682 (ttp) REVERT: C 107 ASP cc_start: 0.7771 (t0) cc_final: 0.7284 (t0) REVERT: C 138 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.7794 (mp10) REVERT: C 174 ASN cc_start: 0.8401 (OUTLIER) cc_final: 0.8001 (p0) REVERT: C 192 TRP cc_start: 0.5468 (p-90) cc_final: 0.5263 (p90) REVERT: C 225 TYR cc_start: 0.7461 (OUTLIER) cc_final: 0.6618 (p90) REVERT: C 276 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.7931 (tpt-90) REVERT: C 388 ASP cc_start: 0.8751 (m-30) cc_final: 0.8330 (p0) REVERT: C 393 LEU cc_start: 0.8265 (tp) cc_final: 0.8042 (tp) outliers start: 32 outliers final: 26 residues processed: 118 average time/residue: 0.1657 time to fit residues: 27.5546 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 : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 389 SER Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 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 200 VAL 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 69 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 22 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4151 r_free = 0.4151 target = 0.182977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.141123 restraints weight = 9301.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.137694 restraints weight = 8068.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.139568 restraints weight = 7925.205| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7475 Z= 0.168 Angle : 0.609 11.427 10107 Z= 0.303 Chirality : 0.042 0.201 1086 Planarity : 0.004 0.072 1268 Dihedral : 5.458 63.738 981 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.56 % Favored : 95.32 % Rotamer: Outliers : 4.05 % Allowed : 27.69 % Favored : 68.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.29), residues: 877 helix: 1.61 (0.31), residues: 297 sheet: -0.12 (0.40), residues: 186 loop : -0.79 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP C 20 HIS 0.002 0.000 HIS C 226 PHE 0.012 0.001 PHE C 332 TYR 0.017 0.001 TYR C 213 ARG 0.002 0.000 ARG B 275 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2068.02 seconds wall clock time: 38 minutes 8.23 seconds (2288.23 seconds total)