Starting phenix.real_space_refine on Thu Mar 13 18:26:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8csz_26976/03_2025/8csz_26976.cif Found real_map, /net/cci-nas-00/data/ceres_data/8csz_26976/03_2025/8csz_26976.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8csz_26976/03_2025/8csz_26976.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8csz_26976/03_2025/8csz_26976.map" model { file = "/net/cci-nas-00/data/ceres_data/8csz_26976/03_2025/8csz_26976.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8csz_26976/03_2025/8csz_26976.cif" } resolution = 3.2 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= -0.001 sd= 0.028 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 236 5.49 5 Mg 2 5.21 5 S 27 5.16 5 C 4741 2.51 5 N 1654 2.21 5 O 2287 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8948 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 3950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3950 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 472} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 3937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 3937 Classifications: {'RNA': 184} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 13, 'rna3p_pur': 91, 'rna3p_pyr': 67} Link IDs: {'rna2p': 25, 'rna3p': 158} Chain breaks: 2 Chain: "B" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 661 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "E" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 397 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2125 SG CYS D 265 82.445 57.202 49.318 1.00 89.87 S Time building chain proxies: 6.44, per 1000 atoms: 0.72 Number of scatterers: 8948 At special positions: 0 Unit cell: (99.51, 111.28, 131.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 27 16.00 P 236 15.00 Mg 2 11.99 O 2287 8.00 N 1654 7.00 C 4741 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: 2.40 Conformation dependent library (CDL) restraints added in 506.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 503 " pdb="ZN ZN D 503 " - pdb=" SG CYS D 265 " pdb="ZN ZN D 503 " - pdb=" NE2 HIS D 268 " 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 922 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 7 sheets defined 34.8% alpha, 17.8% beta 82 base pairs and 139 stacking pairs defined. Time for finding SS restraints: 4.37 Creating SS restraints... Processing helix chain 'D' and resid 21 through 29 Processing helix chain 'D' and resid 85 through 87 No H-bonds generated for 'chain 'D' and resid 85 through 87' Processing helix chain 'D' and resid 88 through 109 removed outlier: 4.413A pdb=" N LYS D 92 " --> pdb=" O LYS D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 121 Processing helix chain 'D' and resid 163 through 184 removed outlier: 3.723A pdb=" N ILE D 183 " --> pdb=" O LYS D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 212 Processing helix chain 'D' and resid 221 through 230 Processing helix chain 'D' and resid 265 through 275 Processing helix chain 'D' and resid 275 through 286 removed outlier: 3.715A pdb=" N GLU D 279 " --> pdb=" O ASP D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 314 removed outlier: 3.870A pdb=" N VAL D 298 " --> pdb=" O HIS D 294 " (cutoff:3.500A) Proline residue: D 304 - end of helix Processing helix chain 'D' and resid 323 through 334 Processing helix chain 'D' and resid 340 through 351 removed outlier: 3.692A pdb=" N TYR D 344 " --> pdb=" O TYR D 340 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA D 350 " --> pdb=" O ILE D 346 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU D 351 " --> pdb=" O ALA D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 416 Processing helix chain 'D' and resid 417 through 423 Processing helix chain 'D' and resid 480 through 482 No H-bonds generated for 'chain 'D' and resid 480 through 482' Processing sheet with id=AA1, first strand: chain 'D' and resid 13 through 17 removed outlier: 5.180A pdb=" N MET D 15 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N VAL D 6 " --> pdb=" O MET D 15 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N TYR D 5 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N LEU D 44 " --> pdb=" O TYR D 5 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE D 7 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N THR D 41 " --> pdb=" O VAL D 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 318 through 322 removed outlier: 3.988A pdb=" N MET D 68 " --> pdb=" O ALA D 81 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE D 79 " --> pdb=" O VAL D 70 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 129 through 131 Processing sheet with id=AA4, first strand: chain 'D' and resid 243 through 246 Processing sheet with id=AA5, first strand: chain 'D' and resid 378 through 380 removed outlier: 6.593A pdb=" N GLN D 432 " --> pdb=" O HIS D 379 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 392 through 395 removed outlier: 5.883A pdb=" N LEU D 393 " --> pdb=" O MET D 389 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N MET D 389 " --> pdb=" O LEU D 393 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA D 395 " --> pdb=" O TYR D 387 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER D 386 " --> pdb=" O LYS D 427 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 476 through 478 removed outlier: 6.997A pdb=" N GLY D 460 " --> pdb=" O ASN D 467 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N PHE D 469 " --> pdb=" O SER D 458 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N SER D 458 " --> pdb=" O PHE D 469 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N SER D 471 " --> pdb=" O SER D 456 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N SER D 456 " --> pdb=" O SER D 471 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE D 444 " --> pdb=" O LEU D 485 " (cutoff:3.500A) 156 hydrogen bonds defined for protein. 429 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 208 hydrogen bonds 388 hydrogen bond angles 0 basepair planarities 82 basepair parallelities 139 stacking parallelities Total time for adding SS restraints: 4.11 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1542 1.33 - 1.45: 3518 1.45 - 1.57: 4051 1.57 - 1.69: 467 1.69 - 1.80: 42 Bond restraints: 9620 Sorted by residual: bond pdb=" O5' G C 172 " pdb=" C5' G C 172 " ideal model delta sigma weight residual 1.420 1.443 -0.023 1.50e-02 4.44e+03 2.29e+00 bond pdb=" O5' A C 78 " pdb=" C5' A C 78 " ideal model delta sigma weight residual 1.420 1.440 -0.020 1.50e-02 4.44e+03 1.73e+00 bond pdb=" CB ARG D 101 " pdb=" CG ARG D 101 " ideal model delta sigma weight residual 1.520 1.484 0.036 3.00e-02 1.11e+03 1.47e+00 bond pdb=" N ASN D 203 " pdb=" CA ASN D 203 " ideal model delta sigma weight residual 1.463 1.451 0.011 9.30e-03 1.16e+04 1.47e+00 bond pdb=" O5' U C 205 " pdb=" C5' U C 205 " ideal model delta sigma weight residual 1.420 1.438 -0.018 1.50e-02 4.44e+03 1.47e+00 ... (remaining 9615 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 13569 1.54 - 3.08: 460 3.08 - 4.62: 57 4.62 - 6.16: 11 6.16 - 7.70: 5 Bond angle restraints: 14102 Sorted by residual: angle pdb=" O3' DG E 127 " pdb=" C3' DG E 127 " pdb=" C2' DG E 127 " ideal model delta sigma weight residual 111.50 104.54 6.96 1.50e+00 4.44e-01 2.15e+01 angle pdb=" C4' U C 206 " pdb=" C3' U C 206 " pdb=" O3' U C 206 " ideal model delta sigma weight residual 109.40 114.83 -5.43 1.50e+00 4.44e-01 1.31e+01 angle pdb=" O3' DA B 10 " pdb=" C3' DA B 10 " pdb=" C2' DA B 10 " ideal model delta sigma weight residual 111.50 106.22 5.28 1.50e+00 4.44e-01 1.24e+01 angle pdb=" C3' A C 128 " pdb=" O3' A C 128 " pdb=" P U C 129 " ideal model delta sigma weight residual 120.20 124.99 -4.79 1.50e+00 4.44e-01 1.02e+01 angle pdb=" C4' A C 128 " pdb=" C3' A C 128 " pdb=" O3' A C 128 " ideal model delta sigma weight residual 109.40 114.19 -4.79 1.50e+00 4.44e-01 1.02e+01 ... (remaining 14097 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.92: 5157 34.92 - 69.84: 614 69.84 - 104.77: 59 104.77 - 139.69: 6 139.69 - 174.61: 8 Dihedral angle restraints: 5844 sinusoidal: 4409 harmonic: 1435 Sorted by residual: dihedral pdb=" O4' C C 60 " pdb=" C1' C C 60 " pdb=" N1 C C 60 " pdb=" C2 C C 60 " ideal model delta sinusoidal sigma weight residual 200.00 40.92 159.08 1 1.50e+01 4.44e-03 8.25e+01 dihedral pdb=" O4' C C 94 " pdb=" C1' C C 94 " pdb=" N1 C C 94 " pdb=" C2 C C 94 " ideal model delta sinusoidal sigma weight residual 232.00 57.39 174.61 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' U C 107 " pdb=" C1' U C 107 " pdb=" N1 U C 107 " pdb=" C2 U C 107 " ideal model delta sinusoidal sigma weight residual -128.00 39.42 -167.42 1 1.70e+01 3.46e-03 6.56e+01 ... (remaining 5841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1544 0.062 - 0.124: 138 0.124 - 0.185: 15 0.185 - 0.247: 7 0.247 - 0.309: 1 Chirality restraints: 1705 Sorted by residual: chirality pdb=" C3' U C 206 " pdb=" C4' U C 206 " pdb=" O3' U C 206 " pdb=" C2' U C 206 " both_signs ideal model delta sigma weight residual False -2.74 -2.44 -0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" C3' A C 78 " pdb=" C4' A C 78 " pdb=" O3' A C 78 " pdb=" C2' A C 78 " both_signs ideal model delta sigma weight residual False -2.48 -2.72 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" C3' A C 128 " pdb=" C4' A C 128 " pdb=" O3' A C 128 " pdb=" C2' A C 128 " both_signs ideal model delta sigma weight residual False -2.74 -2.52 -0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 1702 not shown) Planarity restraints: 938 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A C 122 " 0.036 2.00e-02 2.50e+03 1.63e-02 7.31e+00 pdb=" N9 A C 122 " -0.038 2.00e-02 2.50e+03 pdb=" C8 A C 122 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A C 122 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A C 122 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A C 122 " 0.005 2.00e-02 2.50e+03 pdb=" N6 A C 122 " 0.007 2.00e-02 2.50e+03 pdb=" N1 A C 122 " 0.003 2.00e-02 2.50e+03 pdb=" C2 A C 122 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A C 122 " -0.006 2.00e-02 2.50e+03 pdb=" C4 A C 122 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G C 91 " -0.032 2.00e-02 2.50e+03 1.40e-02 5.86e+00 pdb=" N9 G C 91 " 0.034 2.00e-02 2.50e+03 pdb=" C8 G C 91 " 0.003 2.00e-02 2.50e+03 pdb=" N7 G C 91 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G C 91 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G C 91 " -0.002 2.00e-02 2.50e+03 pdb=" O6 G C 91 " -0.009 2.00e-02 2.50e+03 pdb=" N1 G C 91 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G C 91 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G C 91 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G C 91 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G C 91 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C C 127 " -0.030 2.00e-02 2.50e+03 1.56e-02 5.47e+00 pdb=" N1 C C 127 " 0.034 2.00e-02 2.50e+03 pdb=" C2 C C 127 " 0.002 2.00e-02 2.50e+03 pdb=" O2 C C 127 " 0.004 2.00e-02 2.50e+03 pdb=" N3 C C 127 " -0.002 2.00e-02 2.50e+03 pdb=" C4 C C 127 " -0.003 2.00e-02 2.50e+03 pdb=" N4 C C 127 " -0.010 2.00e-02 2.50e+03 pdb=" C5 C C 127 " 0.004 2.00e-02 2.50e+03 pdb=" C6 C C 127 " 0.003 2.00e-02 2.50e+03 ... (remaining 935 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 61 2.55 - 3.14: 6562 3.14 - 3.72: 16549 3.72 - 4.31: 23135 4.31 - 4.90: 32429 Nonbonded interactions: 78736 Sorted by model distance: nonbonded pdb=" ND1 HIS D 245 " pdb="MG MG D 501 " model vdw 1.962 2.250 nonbonded pdb=" NE2 HIS D 269 " pdb="MG MG D 501 " model vdw 2.018 2.250 nonbonded pdb=" OP2 DC E 111 " pdb="MG MG D 502 " model vdw 2.021 2.170 nonbonded pdb=" ND1 HIS D 273 " pdb="MG MG D 501 " model vdw 2.071 2.250 nonbonded pdb=" O2' U C 180 " pdb=" OP1 C C 181 " model vdw 2.127 3.040 ... (remaining 78731 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.840 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 30.330 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 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 : 0.005 0.037 9620 Z= 0.317 Angle : 0.672 7.704 14102 Z= 0.385 Chirality : 0.040 0.309 1705 Planarity : 0.004 0.053 938 Dihedral : 23.812 174.610 4922 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.97 (0.37), residues: 492 helix: 0.82 (0.42), residues: 152 sheet: -1.55 (0.65), residues: 65 loop : -1.27 (0.35), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 478 HIS 0.007 0.001 HIS D 273 PHE 0.007 0.001 PHE D 453 TYR 0.011 0.002 TYR D 340 ARG 0.008 0.001 ARG D 363 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.646 Fit side-chains REVERT: D 353 ASP cc_start: 0.7944 (m-30) cc_final: 0.7581 (p0) REVERT: D 403 ASP cc_start: 0.7862 (m-30) cc_final: 0.7354 (m-30) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.3310 time to fit residues: 15.4506 Evaluate side-chains 27 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 59 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 29 optimal weight: 0.5980 chunk 18 optimal weight: 0.3980 chunk 36 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.081581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.059340 restraints weight = 23987.115| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 1.60 r_work: 0.2840 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.0835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9620 Z= 0.319 Angle : 0.645 11.032 14102 Z= 0.347 Chirality : 0.038 0.260 1705 Planarity : 0.005 0.048 938 Dihedral : 24.809 175.625 3920 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.47 % Allowed : 5.18 % Favored : 94.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.62 (0.37), residues: 492 helix: 1.13 (0.42), residues: 152 sheet: -1.41 (0.65), residues: 61 loop : -1.06 (0.36), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 161 HIS 0.011 0.001 HIS D 268 PHE 0.009 0.001 PHE D 453 TYR 0.012 0.002 TYR D 5 ARG 0.005 0.001 ARG D 155 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.623 Fit side-chains REVERT: D 208 ARG cc_start: 0.7494 (mpp80) cc_final: 0.6544 (mtp180) REVERT: D 273 HIS cc_start: 0.8208 (OUTLIER) cc_final: 0.7257 (t70) REVERT: D 353 ASP cc_start: 0.8645 (m-30) cc_final: 0.7917 (p0) REVERT: D 403 ASP cc_start: 0.8294 (m-30) cc_final: 0.7423 (m-30) outliers start: 2 outliers final: 0 residues processed: 33 average time/residue: 0.2821 time to fit residues: 12.6067 Evaluate side-chains 30 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 273 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 59 optimal weight: 5.9990 chunk 42 optimal weight: 0.0980 chunk 50 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 65 optimal weight: 20.0000 chunk 46 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 31 optimal weight: 0.5980 chunk 39 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.082025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.059954 restraints weight = 24172.488| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 1.65 r_work: 0.2813 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9620 Z= 0.222 Angle : 0.581 9.330 14102 Z= 0.314 Chirality : 0.035 0.210 1705 Planarity : 0.004 0.046 938 Dihedral : 24.651 177.977 3920 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.41 % Allowed : 7.53 % Favored : 91.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.35 (0.37), residues: 492 helix: 1.43 (0.42), residues: 154 sheet: -1.00 (0.68), residues: 55 loop : -1.04 (0.35), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 478 HIS 0.003 0.001 HIS D 273 PHE 0.007 0.001 PHE D 453 TYR 0.010 0.001 TYR D 5 ARG 0.004 0.001 ARG D 155 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.592 Fit side-chains REVERT: D 353 ASP cc_start: 0.8667 (m-30) cc_final: 0.7997 (p0) REVERT: D 389 MET cc_start: 0.8328 (tpp) cc_final: 0.8120 (tpp) outliers start: 6 outliers final: 3 residues processed: 38 average time/residue: 0.2864 time to fit residues: 14.4407 Evaluate side-chains 31 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 426 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 51 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.079775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.057639 restraints weight = 24158.452| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 1.74 r_work: 0.2757 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 9620 Z= 0.367 Angle : 0.648 10.293 14102 Z= 0.347 Chirality : 0.039 0.278 1705 Planarity : 0.005 0.041 938 Dihedral : 24.667 177.920 3920 Min Nonbonded Distance : 1.544 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.41 % Allowed : 8.47 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.53 (0.37), residues: 492 helix: 1.24 (0.42), residues: 152 sheet: -1.19 (0.67), residues: 55 loop : -1.08 (0.35), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 161 HIS 0.006 0.001 HIS D 273 PHE 0.010 0.001 PHE D 453 TYR 0.011 0.002 TYR D 5 ARG 0.005 0.001 ARG D 101 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.591 Fit side-chains REVERT: D 208 ARG cc_start: 0.7476 (mpp80) cc_final: 0.6512 (mtp180) REVERT: D 353 ASP cc_start: 0.8689 (m-30) cc_final: 0.7799 (p0) outliers start: 6 outliers final: 4 residues processed: 35 average time/residue: 0.2765 time to fit residues: 13.0407 Evaluate side-chains 32 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 426 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 34 optimal weight: 0.6980 chunk 59 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.078863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.056764 restraints weight = 24195.915| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 1.75 r_work: 0.2738 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 9620 Z= 0.436 Angle : 0.683 10.901 14102 Z= 0.364 Chirality : 0.041 0.312 1705 Planarity : 0.005 0.039 938 Dihedral : 24.671 177.708 3920 Min Nonbonded Distance : 1.561 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.65 % Allowed : 10.12 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.76 (0.37), residues: 492 helix: 1.02 (0.42), residues: 152 sheet: -1.02 (0.60), residues: 70 loop : -1.28 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 161 HIS 0.008 0.002 HIS D 273 PHE 0.010 0.001 PHE D 453 TYR 0.012 0.002 TYR D 5 ARG 0.006 0.001 ARG D 101 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.601 Fit side-chains REVERT: D 201 MET cc_start: 0.8706 (mtm) cc_final: 0.8254 (ttp) REVERT: D 208 ARG cc_start: 0.7512 (mpp80) cc_final: 0.6552 (mtp180) REVERT: D 353 ASP cc_start: 0.8693 (m-30) cc_final: 0.7884 (p0) outliers start: 7 outliers final: 7 residues processed: 34 average time/residue: 0.2838 time to fit residues: 12.9615 Evaluate side-chains 35 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 237 CYS Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 273 HIS Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 426 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 13 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 42 optimal weight: 0.0000 chunk 55 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.083033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.061104 restraints weight = 23882.532| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 1.62 r_work: 0.2845 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 9620 Z= 0.159 Angle : 0.552 8.094 14102 Z= 0.298 Chirality : 0.034 0.191 1705 Planarity : 0.004 0.040 938 Dihedral : 24.450 179.611 3920 Min Nonbonded Distance : 1.666 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.41 % Allowed : 10.59 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.29 (0.38), residues: 492 helix: 1.51 (0.42), residues: 154 sheet: -1.00 (0.68), residues: 55 loop : -1.01 (0.36), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 478 HIS 0.002 0.001 HIS D 104 PHE 0.008 0.001 PHE D 79 TYR 0.011 0.001 TYR D 484 ARG 0.004 0.000 ARG D 195 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.643 Fit side-chains REVERT: D 201 MET cc_start: 0.8572 (mtm) cc_final: 0.8177 (ttp) REVERT: D 353 ASP cc_start: 0.8684 (m-30) cc_final: 0.7875 (p0) REVERT: D 389 MET cc_start: 0.8261 (tpp) cc_final: 0.7993 (tpp) outliers start: 6 outliers final: 6 residues processed: 35 average time/residue: 0.2661 time to fit residues: 12.8321 Evaluate side-chains 33 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 273 HIS Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 426 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 53 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.081501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.059403 restraints weight = 24304.642| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 1.63 r_work: 0.2802 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 9620 Z= 0.249 Angle : 0.571 7.766 14102 Z= 0.308 Chirality : 0.035 0.206 1705 Planarity : 0.004 0.039 938 Dihedral : 24.404 179.081 3920 Min Nonbonded Distance : 1.606 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.41 % Allowed : 11.06 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.29 (0.38), residues: 492 helix: 1.48 (0.42), residues: 154 sheet: -0.99 (0.69), residues: 55 loop : -0.99 (0.36), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 161 HIS 0.004 0.001 HIS D 273 PHE 0.007 0.001 PHE D 453 TYR 0.011 0.001 TYR D 5 ARG 0.003 0.000 ARG D 101 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.590 Fit side-chains REVERT: D 201 MET cc_start: 0.8680 (mtm) cc_final: 0.8269 (ttp) REVERT: D 353 ASP cc_start: 0.8680 (m-30) cc_final: 0.7867 (p0) outliers start: 6 outliers final: 5 residues processed: 32 average time/residue: 0.2714 time to fit residues: 11.8519 Evaluate side-chains 31 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 273 HIS Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 426 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 69 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.080017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.057858 restraints weight = 24397.003| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 1.74 r_work: 0.2762 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 9620 Z= 0.348 Angle : 0.621 7.980 14102 Z= 0.333 Chirality : 0.038 0.268 1705 Planarity : 0.004 0.037 938 Dihedral : 24.431 179.256 3920 Min Nonbonded Distance : 1.578 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.18 % Allowed : 12.00 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 (0.38), residues: 492 helix: 1.35 (0.42), residues: 152 sheet: -1.04 (0.69), residues: 55 loop : -0.99 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 161 HIS 0.005 0.001 HIS D 273 PHE 0.009 0.001 PHE D 453 TYR 0.012 0.002 TYR D 5 ARG 0.004 0.001 ARG D 101 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.624 Fit side-chains REVERT: D 201 MET cc_start: 0.8704 (mtm) cc_final: 0.8332 (ttp) REVERT: D 208 ARG cc_start: 0.7434 (mpp80) cc_final: 0.6490 (mtp180) REVERT: D 353 ASP cc_start: 0.8710 (m-30) cc_final: 0.7912 (p0) outliers start: 5 outliers final: 5 residues processed: 32 average time/residue: 0.3178 time to fit residues: 13.6439 Evaluate side-chains 32 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 273 HIS Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 426 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 26 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.080987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.058792 restraints weight = 24261.378| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 1.63 r_work: 0.2786 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9620 Z= 0.241 Angle : 0.584 8.103 14102 Z= 0.315 Chirality : 0.035 0.242 1705 Planarity : 0.004 0.037 938 Dihedral : 24.433 179.397 3920 Min Nonbonded Distance : 1.608 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.65 % Allowed : 11.29 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.29 (0.38), residues: 492 helix: 1.40 (0.42), residues: 152 sheet: -0.97 (0.70), residues: 55 loop : -0.93 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 161 HIS 0.004 0.001 HIS D 273 PHE 0.007 0.001 PHE D 79 TYR 0.012 0.001 TYR D 5 ARG 0.005 0.001 ARG D 155 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 1.743 Fit side-chains REVERT: D 201 MET cc_start: 0.8660 (mtm) cc_final: 0.8317 (ttp) REVERT: D 208 ARG cc_start: 0.7350 (mpp80) cc_final: 0.6362 (mtp180) REVERT: D 353 ASP cc_start: 0.8712 (m-30) cc_final: 0.7928 (p0) outliers start: 7 outliers final: 6 residues processed: 34 average time/residue: 0.4550 time to fit residues: 20.1780 Evaluate side-chains 33 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 237 CYS Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 273 HIS Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 426 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 5 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.083156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.061108 restraints weight = 24032.420| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.62 r_work: 0.2847 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9620 Z= 0.165 Angle : 0.537 7.832 14102 Z= 0.290 Chirality : 0.033 0.191 1705 Planarity : 0.004 0.038 938 Dihedral : 24.298 178.208 3920 Min Nonbonded Distance : 1.659 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.41 % Allowed : 11.29 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.14 (0.38), residues: 492 helix: 1.62 (0.43), residues: 154 sheet: -0.88 (0.69), residues: 55 loop : -0.91 (0.37), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 478 HIS 0.002 0.001 HIS D 104 PHE 0.007 0.001 PHE D 198 TYR 0.010 0.001 TYR D 484 ARG 0.003 0.000 ARG D 363 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.635 Fit side-chains REVERT: D 201 MET cc_start: 0.8590 (mtm) cc_final: 0.8306 (ttp) REVERT: D 353 ASP cc_start: 0.8706 (m-30) cc_final: 0.7929 (p0) outliers start: 6 outliers final: 6 residues processed: 32 average time/residue: 0.2913 time to fit residues: 12.8229 Evaluate side-chains 33 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 237 CYS Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 273 HIS Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 426 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 11 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 9 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.080439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.058176 restraints weight = 24028.533| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 1.73 r_work: 0.2768 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 9620 Z= 0.315 Angle : 0.600 7.996 14102 Z= 0.321 Chirality : 0.036 0.242 1705 Planarity : 0.004 0.037 938 Dihedral : 24.354 178.001 3920 Min Nonbonded Distance : 1.581 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.65 % Allowed : 11.29 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.31 (0.38), residues: 492 helix: 1.43 (0.42), residues: 154 sheet: -1.00 (0.69), residues: 55 loop : -0.98 (0.37), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 161 HIS 0.005 0.001 HIS D 273 PHE 0.008 0.001 PHE D 453 TYR 0.012 0.001 TYR D 5 ARG 0.003 0.001 ARG D 155 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4555.94 seconds wall clock time: 81 minutes 48.41 seconds (4908.41 seconds total)