Starting phenix.real_space_refine on Wed Jul 23 08:31:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xbi_38219/07_2025/8xbi_38219.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xbi_38219/07_2025/8xbi_38219.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xbi_38219/07_2025/8xbi_38219.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xbi_38219/07_2025/8xbi_38219.map" model { file = "/net/cci-nas-00/data/ceres_data/8xbi_38219/07_2025/8xbi_38219.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xbi_38219/07_2025/8xbi_38219.cif" } resolution = 3.06 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 ------------------------------------------------------------------------------- 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= -0.028 sd= 0.435 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 1 5.49 5 S 22 5.16 5 C 1641 2.51 5 N 399 2.21 5 O 404 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 2467 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2424 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 5, 'TRANS': 292} Chain: "R" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'KW3': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.26, per 1000 atoms: 0.92 Number of scatterers: 2467 At special positions: 0 Unit cell: (64.55, 73.587, 77.46, 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 22 16.00 P 1 15.00 O 404 8.00 N 399 7.00 C 1641 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 299 " distance=2.04 Simple disulfide: pdb=" SG CYS R 127 " - pdb=" SG CYS R 204 " distance=2.08 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: 0.71 Conformation dependent library (CDL) restraints added in 289.9 milliseconds 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 570 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 0 sheets defined 84.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'R' and resid 50 through 82 removed outlier: 3.686A pdb=" N ILE R 82 " --> pdb=" O VAL R 78 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 117 Proline residue: R 108 - end of helix removed outlier: 4.189A pdb=" N GLN R 117 " --> pdb=" O TYR R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 123 through 157 removed outlier: 3.561A pdb=" N CYS R 127 " --> pdb=" O GLY R 123 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR R 135 " --> pdb=" O GLY R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 197 removed outlier: 3.702A pdb=" N LYS R 195 " --> pdb=" O ILE R 191 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 252 removed outlier: 4.088A pdb=" N ALA R 217 " --> pdb=" O ALA R 213 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG R 252 " --> pdb=" O ILE R 248 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 294 Proline residue: R 281 - end of helix removed outlier: 3.919A pdb=" N PHE R 287 " --> pdb=" O HIS R 283 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ILE R 288 " --> pdb=" O ALA R 284 " (cutoff:3.500A) Processing helix chain 'R' and resid 298 through 331 removed outlier: 3.809A pdb=" N LYS R 302 " --> pdb=" O SER R 298 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE R 304 " --> pdb=" O TYR R 300 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN R 319 " --> pdb=" O LEU R 315 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER R 320 " --> pdb=" O SER R 316 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N CYS R 321 " --> pdb=" O SER R 317 " (cutoff:3.500A) Proline residue: R 324 - end of helix removed outlier: 3.641A pdb=" N TYR R 327 " --> pdb=" O ASP R 323 " (cutoff:3.500A) Processing helix chain 'R' and resid 331 through 342 196 hydrogen bonds defined for protein. 588 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.68 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 623 1.33 - 1.45: 447 1.45 - 1.58: 1417 1.58 - 1.71: 2 1.71 - 1.83: 34 Bond restraints: 2523 Sorted by residual: bond pdb=" C ALA R 265 " pdb=" O ALA R 265 " ideal model delta sigma weight residual 1.237 1.284 -0.047 1.17e-02 7.31e+03 1.61e+01 bond pdb=" N ILE R 82 " pdb=" CA ILE R 82 " ideal model delta sigma weight residual 1.459 1.491 -0.033 9.10e-03 1.21e+04 1.28e+01 bond pdb=" C ILE R 270 " pdb=" O ILE R 270 " ideal model delta sigma weight residual 1.237 1.276 -0.040 1.13e-02 7.83e+03 1.23e+01 bond pdb=" CA ALA R 265 " pdb=" CB ALA R 265 " ideal model delta sigma weight residual 1.528 1.477 0.051 1.56e-02 4.11e+03 1.08e+01 bond pdb=" N LEU R 103 " pdb=" CA LEU R 103 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.21e-02 6.83e+03 1.04e+01 ... (remaining 2518 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 3148 2.12 - 4.25: 248 4.25 - 6.37: 9 6.37 - 8.49: 1 8.49 - 10.61: 1 Bond angle restraints: 3407 Sorted by residual: angle pdb=" O GLN R 161 " pdb=" C GLN R 161 " pdb=" N GLN R 162 " ideal model delta sigma weight residual 121.76 126.04 -4.28 1.15e+00 7.56e-01 1.39e+01 angle pdb=" N GLU R 303 " pdb=" CA GLU R 303 " pdb=" CB GLU R 303 " ideal model delta sigma weight residual 110.16 115.17 -5.01 1.48e+00 4.57e-01 1.14e+01 angle pdb=" CD LYS R 254 " pdb=" CE LYS R 254 " pdb=" NZ LYS R 254 " ideal model delta sigma weight residual 111.90 101.29 10.61 3.20e+00 9.77e-02 1.10e+01 angle pdb=" CG LYS R 254 " pdb=" CD LYS R 254 " pdb=" CE LYS R 254 " ideal model delta sigma weight residual 111.30 118.44 -7.14 2.30e+00 1.89e-01 9.63e+00 angle pdb=" N ILE R 166 " pdb=" CA ILE R 166 " pdb=" C ILE R 166 " ideal model delta sigma weight residual 112.17 109.26 2.91 9.50e-01 1.11e+00 9.39e+00 ... (remaining 3402 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.76: 1414 24.76 - 49.51: 83 49.51 - 74.27: 8 74.27 - 99.02: 6 99.02 - 123.78: 3 Dihedral angle restraints: 1514 sinusoidal: 632 harmonic: 882 Sorted by residual: dihedral pdb=" O2 KW3 R 401 " pdb=" C4 KW3 R 401 " pdb=" C5 KW3 R 401 " pdb=" O6 KW3 R 401 " ideal model delta sinusoidal sigma weight residual 296.46 172.68 123.78 1 3.00e+01 1.11e-03 1.66e+01 dihedral pdb=" N1 KW3 R 401 " pdb=" C28 KW3 R 401 " pdb=" C29 KW3 R 401 " pdb=" O9 KW3 R 401 " ideal model delta sinusoidal sigma weight residual 57.01 -55.00 112.01 1 3.00e+01 1.11e-03 1.47e+01 dihedral pdb=" C1 KW3 R 401 " pdb=" C2 KW3 R 401 " pdb=" O1 KW3 R 401 " pdb=" C3 KW3 R 401 " ideal model delta sinusoidal sigma weight residual 71.30 -178.59 -110.11 1 3.00e+01 1.11e-03 1.43e+01 ... (remaining 1511 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 163 0.038 - 0.075: 119 0.075 - 0.113: 66 0.113 - 0.150: 43 0.150 - 0.188: 10 Chirality restraints: 401 Sorted by residual: chirality pdb=" CA ILE R 148 " pdb=" N ILE R 148 " pdb=" C ILE R 148 " pdb=" CB ILE R 148 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.80e-01 chirality pdb=" CA ILE R 156 " pdb=" N ILE R 156 " pdb=" C ILE R 156 " pdb=" CB ILE R 156 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.28e-01 chirality pdb=" CA ILE R 98 " pdb=" N ILE R 98 " pdb=" C ILE R 98 " pdb=" CB ILE R 98 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.50e-01 ... (remaining 398 not shown) Planarity restraints: 399 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE R 269 " 0.039 2.00e-02 2.50e+03 2.60e-02 1.19e+01 pdb=" CG PHE R 269 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE R 269 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE R 269 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE R 269 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE R 269 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE R 269 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 238 " 0.032 2.00e-02 2.50e+03 2.31e-02 1.07e+01 pdb=" CG TYR R 238 " -0.004 2.00e-02 2.50e+03 pdb=" CD1 TYR R 238 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR R 238 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR R 238 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR R 238 " -0.021 2.00e-02 2.50e+03 pdb=" CZ TYR R 238 " -0.019 2.00e-02 2.50e+03 pdb=" OH TYR R 238 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 279 " 0.024 2.00e-02 2.50e+03 2.21e-02 8.53e+00 pdb=" CG PHE R 279 " -0.005 2.00e-02 2.50e+03 pdb=" CD1 PHE R 279 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE R 279 " -0.043 2.00e-02 2.50e+03 pdb=" CE1 PHE R 279 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE R 279 " 0.029 2.00e-02 2.50e+03 pdb=" CZ PHE R 279 " 0.009 2.00e-02 2.50e+03 ... (remaining 396 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 186 2.76 - 3.29: 2780 3.29 - 3.83: 3984 3.83 - 4.36: 4780 4.36 - 4.90: 8162 Nonbonded interactions: 19892 Sorted by model distance: nonbonded pdb=" OH TYR R 282 " pdb=" NH2 ARG R 286 " model vdw 2.221 3.120 nonbonded pdb=" O LYS R 155 " pdb=" OG SER R 159 " model vdw 2.232 3.040 nonbonded pdb=" OG SER R 54 " pdb=" O HIS R 114 " model vdw 2.239 3.040 nonbonded pdb=" OG SER R 331 " pdb=" OD1 ASN R 333 " model vdw 2.276 3.040 nonbonded pdb=" O VAL R 78 " pdb=" ND1 HIS R 83 " model vdw 2.339 3.120 ... (remaining 19887 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.680 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6462 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 : 0.013 0.056 2525 Z= 0.934 Angle : 1.206 10.611 3411 Z= 0.876 Chirality : 0.071 0.188 401 Planarity : 0.006 0.027 399 Dihedral : 16.804 123.776 938 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.92 (0.45), residues: 296 helix: 2.03 (0.31), residues: 237 sheet: None (None), residues: 0 loop : -1.99 (0.66), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.006 TRP R 179 HIS 0.007 0.002 HIS R 206 PHE 0.053 0.007 PHE R 269 TYR 0.045 0.008 TYR R 238 ARG 0.012 0.002 ARG R 110 Details of bonding type rmsd hydrogen bonds : bond 0.10752 ( 196) hydrogen bonds : angle 4.74204 ( 588) SS BOND : bond 0.03479 ( 2) SS BOND : angle 1.31959 ( 4) covalent geometry : bond 0.01281 ( 2523) covalent geometry : angle 1.20601 ( 3407) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: R 247 ARG cc_start: 0.7415 (ptm-80) cc_final: 0.6991 (tpp-160) REVERT: R 251 ARG cc_start: 0.7236 (mtm110) cc_final: 0.6919 (ptt180) REVERT: R 303 GLU cc_start: 0.7252 (pm20) cc_final: 0.6944 (pt0) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.1761 time to fit residues: 13.1784 Evaluate side-chains 48 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 24 optimal weight: 6.9990 chunk 21 optimal weight: 0.0170 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 11 optimal weight: 0.0270 chunk 22 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.214091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.180817 restraints weight = 2605.392| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 1.58 r_work: 0.3742 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2525 Z= 0.129 Angle : 0.520 5.326 3411 Z= 0.287 Chirality : 0.039 0.138 401 Planarity : 0.003 0.027 399 Dihedral : 16.009 126.560 363 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.09 % Allowed : 12.00 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 2.45 (0.47), residues: 296 helix: 2.44 (0.32), residues: 238 sheet: None (None), residues: 0 loop : -2.09 (0.63), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 228 HIS 0.004 0.001 HIS R 206 PHE 0.010 0.001 PHE R 134 TYR 0.009 0.001 TYR R 139 ARG 0.004 0.000 ARG R 286 Details of bonding type rmsd hydrogen bonds : bond 0.04403 ( 196) hydrogen bonds : angle 3.86490 ( 588) SS BOND : bond 0.00213 ( 2) SS BOND : angle 0.45798 ( 4) covalent geometry : bond 0.00245 ( 2523) covalent geometry : angle 0.51957 ( 3407) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.267 Fit side-chains REVERT: R 51 LYS cc_start: 0.7220 (mppt) cc_final: 0.6783 (tttt) outliers start: 3 outliers final: 2 residues processed: 62 average time/residue: 0.1875 time to fit residues: 13.5774 Evaluate side-chains 55 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain R residue 181 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 17 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 21 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.203731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.171591 restraints weight = 2635.444| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 1.51 r_work: 0.3679 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3553 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2525 Z= 0.154 Angle : 0.556 5.416 3411 Z= 0.301 Chirality : 0.040 0.132 401 Planarity : 0.004 0.038 399 Dihedral : 15.649 124.947 363 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.82 % Allowed : 14.18 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.90 (0.46), residues: 296 helix: 2.08 (0.32), residues: 233 sheet: None (None), residues: 0 loop : -2.05 (0.60), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 228 HIS 0.004 0.001 HIS R 306 PHE 0.017 0.002 PHE R 227 TYR 0.016 0.002 TYR R 282 ARG 0.006 0.001 ARG R 286 Details of bonding type rmsd hydrogen bonds : bond 0.04902 ( 196) hydrogen bonds : angle 3.86057 ( 588) SS BOND : bond 0.00101 ( 2) SS BOND : angle 0.47538 ( 4) covalent geometry : bond 0.00329 ( 2523) covalent geometry : angle 0.55628 ( 3407) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.267 Fit side-chains REVERT: R 51 LYS cc_start: 0.7265 (mppt) cc_final: 0.7025 (tttt) REVERT: R 318 PHE cc_start: 0.7562 (t80) cc_final: 0.7243 (t80) outliers start: 5 outliers final: 3 residues processed: 61 average time/residue: 0.1646 time to fit residues: 11.6897 Evaluate side-chains 59 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 151 ASP Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain R residue 181 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 0.4980 chunk 0 optimal weight: 30.0000 chunk 15 optimal weight: 20.0000 chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 13 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.206063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.170412 restraints weight = 2655.810| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 1.70 r_work: 0.3684 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2525 Z= 0.121 Angle : 0.487 4.967 3411 Z= 0.269 Chirality : 0.038 0.128 401 Planarity : 0.003 0.025 399 Dihedral : 15.874 129.196 363 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.91 % Allowed : 15.27 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.16 (0.47), residues: 296 helix: 2.21 (0.32), residues: 238 sheet: None (None), residues: 0 loop : -2.06 (0.64), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 228 HIS 0.004 0.001 HIS R 206 PHE 0.011 0.001 PHE R 227 TYR 0.012 0.001 TYR R 139 ARG 0.003 0.000 ARG R 286 Details of bonding type rmsd hydrogen bonds : bond 0.04235 ( 196) hydrogen bonds : angle 3.80059 ( 588) SS BOND : bond 0.00219 ( 2) SS BOND : angle 0.37338 ( 4) covalent geometry : bond 0.00230 ( 2523) covalent geometry : angle 0.48735 ( 3407) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.284 Fit side-chains REVERT: R 167 THR cc_start: 0.5860 (OUTLIER) cc_final: 0.5641 (p) REVERT: R 272 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.7717 (tp) outliers start: 8 outliers final: 4 residues processed: 64 average time/residue: 0.1754 time to fit residues: 13.0588 Evaluate side-chains 59 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 151 ASP Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain R residue 167 THR Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 323 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 27 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 10 optimal weight: 8.9990 chunk 15 optimal weight: 30.0000 chunk 16 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 118 ASN ** R 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 206 HIS ** 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 = 0.4123 r_free = 0.4123 target = 0.198031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.165570 restraints weight = 2678.118| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 1.52 r_work: 0.3580 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3457 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 2525 Z= 0.288 Angle : 0.728 6.668 3411 Z= 0.387 Chirality : 0.049 0.254 401 Planarity : 0.005 0.067 399 Dihedral : 16.483 119.881 363 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 4.00 % Allowed : 18.18 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.38 (0.44), residues: 296 helix: 0.91 (0.31), residues: 233 sheet: None (None), residues: 0 loop : -2.12 (0.64), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 228 HIS 0.006 0.002 HIS R 306 PHE 0.026 0.003 PHE R 227 TYR 0.023 0.003 TYR R 282 ARG 0.008 0.001 ARG R 286 Details of bonding type rmsd hydrogen bonds : bond 0.06406 ( 196) hydrogen bonds : angle 4.21555 ( 588) SS BOND : bond 0.00178 ( 2) SS BOND : angle 0.87566 ( 4) covalent geometry : bond 0.00674 ( 2523) covalent geometry : angle 0.72774 ( 3407) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.242 Fit side-chains REVERT: R 94 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7591 (tp) REVERT: R 272 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8288 (tp) REVERT: R 318 PHE cc_start: 0.8180 (t80) cc_final: 0.7841 (t80) outliers start: 11 outliers final: 5 residues processed: 65 average time/residue: 0.1484 time to fit residues: 11.3589 Evaluate side-chains 62 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 151 ASP Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 323 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 0 optimal weight: 30.0000 chunk 9 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.203381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.169008 restraints weight = 2611.917| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 1.61 r_work: 0.3638 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3511 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2525 Z= 0.136 Angle : 0.521 5.190 3411 Z= 0.288 Chirality : 0.041 0.165 401 Planarity : 0.003 0.024 399 Dihedral : 15.987 124.262 363 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 4.00 % Allowed : 20.00 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.38 (0.47), residues: 296 helix: 1.63 (0.32), residues: 234 sheet: None (None), residues: 0 loop : -1.91 (0.67), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 228 HIS 0.004 0.001 HIS R 206 PHE 0.011 0.001 PHE R 227 TYR 0.014 0.001 TYR R 139 ARG 0.003 0.001 ARG R 286 Details of bonding type rmsd hydrogen bonds : bond 0.04713 ( 196) hydrogen bonds : angle 4.00325 ( 588) SS BOND : bond 0.00307 ( 2) SS BOND : angle 0.47171 ( 4) covalent geometry : bond 0.00273 ( 2523) covalent geometry : angle 0.52130 ( 3407) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: R 94 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7452 (tp) REVERT: R 272 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8245 (tp) REVERT: R 318 PHE cc_start: 0.7892 (t80) cc_final: 0.7599 (t80) outliers start: 11 outliers final: 7 residues processed: 64 average time/residue: 0.1699 time to fit residues: 12.6946 Evaluate side-chains 64 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 151 ASP Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 250 LYS Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 323 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.201519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.165632 restraints weight = 2739.391| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 1.70 r_work: 0.3608 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2525 Z= 0.143 Angle : 0.547 6.145 3411 Z= 0.296 Chirality : 0.041 0.170 401 Planarity : 0.003 0.022 399 Dihedral : 15.887 121.814 363 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.91 % Allowed : 20.00 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.49 (0.46), residues: 296 helix: 1.71 (0.32), residues: 234 sheet: None (None), residues: 0 loop : -1.87 (0.68), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 228 HIS 0.004 0.001 HIS R 206 PHE 0.014 0.001 PHE R 227 TYR 0.019 0.001 TYR R 282 ARG 0.004 0.001 ARG R 286 Details of bonding type rmsd hydrogen bonds : bond 0.04807 ( 196) hydrogen bonds : angle 4.03054 ( 588) SS BOND : bond 0.00114 ( 2) SS BOND : angle 0.49881 ( 4) covalent geometry : bond 0.00301 ( 2523) covalent geometry : angle 0.54680 ( 3407) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: R 48 MET cc_start: 0.4820 (ptp) cc_final: 0.4486 (mtm) REVERT: R 318 PHE cc_start: 0.7737 (t80) cc_final: 0.7440 (t80) outliers start: 8 outliers final: 7 residues processed: 61 average time/residue: 0.1438 time to fit residues: 10.4665 Evaluate side-chains 63 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 151 ASP Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 250 LYS Chi-restraints excluded: chain R residue 323 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 28 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 5 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 chunk 23 optimal weight: 0.0670 chunk 22 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.202574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.166861 restraints weight = 2710.788| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 1.70 r_work: 0.3635 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2525 Z= 0.133 Angle : 0.518 5.232 3411 Z= 0.284 Chirality : 0.041 0.172 401 Planarity : 0.003 0.022 399 Dihedral : 15.656 120.699 363 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.91 % Allowed : 20.73 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.64 (0.47), residues: 296 helix: 1.81 (0.32), residues: 233 sheet: None (None), residues: 0 loop : -1.74 (0.67), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 228 HIS 0.004 0.001 HIS R 206 PHE 0.013 0.001 PHE R 227 TYR 0.020 0.001 TYR R 282 ARG 0.003 0.000 ARG R 286 Details of bonding type rmsd hydrogen bonds : bond 0.04566 ( 196) hydrogen bonds : angle 3.95217 ( 588) SS BOND : bond 0.00138 ( 2) SS BOND : angle 0.40806 ( 4) covalent geometry : bond 0.00274 ( 2523) covalent geometry : angle 0.51764 ( 3407) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: R 48 MET cc_start: 0.4810 (ptp) cc_final: 0.4527 (mtm) REVERT: R 318 PHE cc_start: 0.7543 (t80) cc_final: 0.7239 (t80) outliers start: 8 outliers final: 8 residues processed: 62 average time/residue: 0.1712 time to fit residues: 12.3929 Evaluate side-chains 64 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 151 ASP Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 250 LYS Chi-restraints excluded: chain R residue 292 SER Chi-restraints excluded: chain R residue 323 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 9 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 15 optimal weight: 20.0000 chunk 17 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 6 optimal weight: 0.8980 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.200027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.164135 restraints weight = 2688.073| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 1.69 r_work: 0.3602 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2525 Z= 0.160 Angle : 0.559 5.368 3411 Z= 0.303 Chirality : 0.042 0.177 401 Planarity : 0.004 0.026 399 Dihedral : 15.937 119.494 363 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.27 % Allowed : 20.00 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.35 (0.46), residues: 296 helix: 1.59 (0.32), residues: 234 sheet: None (None), residues: 0 loop : -1.79 (0.69), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 228 HIS 0.003 0.001 HIS R 306 PHE 0.016 0.002 PHE R 227 TYR 0.022 0.002 TYR R 282 ARG 0.004 0.001 ARG R 286 Details of bonding type rmsd hydrogen bonds : bond 0.05015 ( 196) hydrogen bonds : angle 3.99421 ( 588) SS BOND : bond 0.00098 ( 2) SS BOND : angle 0.51663 ( 4) covalent geometry : bond 0.00351 ( 2523) covalent geometry : angle 0.55890 ( 3407) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: R 318 PHE cc_start: 0.7752 (t80) cc_final: 0.7448 (t80) outliers start: 9 outliers final: 8 residues processed: 59 average time/residue: 0.1280 time to fit residues: 9.1506 Evaluate side-chains 63 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 151 ASP Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 250 LYS Chi-restraints excluded: chain R residue 292 SER Chi-restraints excluded: chain R residue 323 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 0 optimal weight: 40.0000 chunk 3 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.202954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.167401 restraints weight = 2671.110| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 1.67 r_work: 0.3648 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2525 Z= 0.129 Angle : 0.513 5.063 3411 Z= 0.281 Chirality : 0.040 0.174 401 Planarity : 0.003 0.022 399 Dihedral : 15.595 120.030 363 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.91 % Allowed : 21.09 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.66 (0.47), residues: 296 helix: 1.82 (0.33), residues: 233 sheet: None (None), residues: 0 loop : -1.69 (0.68), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 228 HIS 0.004 0.001 HIS R 206 PHE 0.013 0.001 PHE R 227 TYR 0.020 0.001 TYR R 282 ARG 0.003 0.000 ARG R 286 Details of bonding type rmsd hydrogen bonds : bond 0.04463 ( 196) hydrogen bonds : angle 3.94436 ( 588) SS BOND : bond 0.00287 ( 2) SS BOND : angle 0.48909 ( 4) covalent geometry : bond 0.00259 ( 2523) covalent geometry : angle 0.51319 ( 3407) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: R 120 TRP cc_start: 0.7003 (t-100) cc_final: 0.6519 (t-100) REVERT: R 318 PHE cc_start: 0.7511 (t80) cc_final: 0.7215 (t80) outliers start: 8 outliers final: 8 residues processed: 60 average time/residue: 0.1298 time to fit residues: 9.4202 Evaluate side-chains 62 residues out of total 275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 151 ASP Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 250 LYS Chi-restraints excluded: chain R residue 292 SER Chi-restraints excluded: chain R residue 323 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 2 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 11 optimal weight: 0.0770 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 14 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.203064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.167543 restraints weight = 2684.550| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 1.70 r_work: 0.3644 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2525 Z= 0.130 Angle : 0.517 5.029 3411 Z= 0.282 Chirality : 0.040 0.173 401 Planarity : 0.003 0.022 399 Dihedral : 15.461 117.793 363 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.27 % Allowed : 20.00 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.68 (0.47), residues: 296 helix: 1.82 (0.32), residues: 233 sheet: None (None), residues: 0 loop : -1.60 (0.69), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 228 HIS 0.004 0.001 HIS R 206 PHE 0.012 0.001 PHE R 227 TYR 0.020 0.001 TYR R 282 ARG 0.003 0.000 ARG R 286 Details of bonding type rmsd hydrogen bonds : bond 0.04497 ( 196) hydrogen bonds : angle 3.92263 ( 588) SS BOND : bond 0.00111 ( 2) SS BOND : angle 0.61202 ( 4) covalent geometry : bond 0.00263 ( 2523) covalent geometry : angle 0.51699 ( 3407) =============================================================================== Job complete usr+sys time: 1584.46 seconds wall clock time: 27 minutes 57.75 seconds (1677.75 seconds total)