Starting phenix.real_space_refine on Wed Jun 4 15:19:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u3d_41858/06_2025/8u3d_41858.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u3d_41858/06_2025/8u3d_41858.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u3d_41858/06_2025/8u3d_41858.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u3d_41858/06_2025/8u3d_41858.map" model { file = "/net/cci-nas-00/data/ceres_data/8u3d_41858/06_2025/8u3d_41858.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u3d_41858/06_2025/8u3d_41858.cif" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.089 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: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 2230 2.51 5 N 522 2.21 5 O 571 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 3338 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3338 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 18, 'TRANS': 408} Chain breaks: 1 Time building chain proxies: 2.66, per 1000 atoms: 0.80 Number of scatterers: 3338 At special positions: 0 Unit cell: (57.27, 71.38, 81.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 571 8.00 N 522 7.00 C 2230 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 385.8 milliseconds 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 776 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 0 sheets defined 87.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 37 through 68 removed outlier: 4.982A pdb=" N LEU A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N SER A 61 " --> pdb=" O ARG A 57 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL A 65 " --> pdb=" O SER A 61 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 120 removed outlier: 4.874A pdb=" N PHE A 115 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N PHE A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR A 117 " --> pdb=" O GLY A 113 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 134 removed outlier: 3.893A pdb=" N GLY A 127 " --> pdb=" O GLN A 123 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR A 128 " --> pdb=" O ILE A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 151 removed outlier: 3.911A pdb=" N LEU A 138 " --> pdb=" O GLY A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 160 removed outlier: 3.884A pdb=" N ASP A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY A 160 " --> pdb=" O ALA A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 177 removed outlier: 3.502A pdb=" N LEU A 164 " --> pdb=" O GLY A 160 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 190 removed outlier: 3.678A pdb=" N ALA A 181 " --> pdb=" O VAL A 177 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER A 188 " --> pdb=" O ALA A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 193 No H-bonds generated for 'chain 'A' and resid 191 through 193' Processing helix chain 'A' and resid 194 through 224 removed outlier: 4.223A pdb=" N GLY A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ALA A 206 " --> pdb=" O SER A 202 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLN A 207 " --> pdb=" O TYR A 203 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) Proline residue: A 215 - end of helix Processing helix chain 'A' and resid 226 through 248 removed outlier: 4.134A pdb=" N PHE A 230 " --> pdb=" O TRP A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 271 Processing helix chain 'A' and resid 288 through 319 removed outlier: 4.115A pdb=" N ILE A 294 " --> pdb=" O PRO A 290 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR A 304 " --> pdb=" O SER A 300 " (cutoff:3.500A) Proline residue: A 313 - end of helix Processing helix chain 'A' and resid 323 through 356 removed outlier: 3.836A pdb=" N LEU A 333 " --> pdb=" O PHE A 329 " (cutoff:3.500A) Proline residue: A 334 - end of helix removed outlier: 3.661A pdb=" N GLY A 346 " --> pdb=" O MET A 342 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLN A 347 " --> pdb=" O ILE A 343 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP A 350 " --> pdb=" O GLY A 346 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TRP A 356 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 385 Proline residue: A 375 - end of helix Processing helix chain 'A' and resid 388 through 403 removed outlier: 3.889A pdb=" N THR A 400 " --> pdb=" O LEU A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 Processing helix chain 'A' and resid 409 through 412 removed outlier: 3.539A pdb=" N ILE A 412 " --> pdb=" O GLY A 409 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 409 through 412' Processing helix chain 'A' and resid 413 through 418 removed outlier: 3.581A pdb=" N ALA A 418 " --> pdb=" O HIS A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 434 Processing helix chain 'A' and resid 434 through 448 Proline residue: A 441 - end of helix Processing helix chain 'A' and resid 452 through 478 removed outlier: 3.629A pdb=" N TRP A 456 " --> pdb=" O THR A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 487 239 hydrogen bonds defined for protein. 705 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: 0.86 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 973 1.34 - 1.45: 684 1.45 - 1.57: 1759 1.57 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 3440 Sorted by residual: bond pdb=" N ILE A 44 " pdb=" CA ILE A 44 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.32e-02 5.74e+03 7.33e+00 bond pdb=" N LEU A 45 " pdb=" CA LEU A 45 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.37e+00 bond pdb=" CB THR A 400 " pdb=" CG2 THR A 400 " ideal model delta sigma weight residual 1.521 1.446 0.075 3.30e-02 9.18e+02 5.13e+00 bond pdb=" N ALA A 43 " pdb=" CA ALA A 43 " ideal model delta sigma weight residual 1.457 1.482 -0.025 1.33e-02 5.65e+03 3.55e+00 bond pdb=" CA ALA A 43 " pdb=" CB ALA A 43 " ideal model delta sigma weight residual 1.530 1.499 0.031 1.68e-02 3.54e+03 3.42e+00 ... (remaining 3435 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 4418 1.53 - 3.06: 236 3.06 - 4.59: 32 4.59 - 6.12: 7 6.12 - 7.65: 1 Bond angle restraints: 4694 Sorted by residual: angle pdb=" C THR A 434 " pdb=" N ILE A 435 " pdb=" CA ILE A 435 " ideal model delta sigma weight residual 120.24 122.92 -2.68 6.30e-01 2.52e+00 1.81e+01 angle pdb=" C ILE A 435 " pdb=" CA ILE A 435 " pdb=" CB ILE A 435 " ideal model delta sigma weight residual 114.35 110.35 4.00 1.06e+00 8.90e-01 1.42e+01 angle pdb=" N LEU A 45 " pdb=" CA LEU A 45 " pdb=" C LEU A 45 " ideal model delta sigma weight residual 112.90 108.56 4.34 1.31e+00 5.83e-01 1.10e+01 angle pdb=" N VAL A 177 " pdb=" CA VAL A 177 " pdb=" CB VAL A 177 " ideal model delta sigma weight residual 111.23 105.88 5.35 1.65e+00 3.67e-01 1.05e+01 angle pdb=" C PRO A 449 " pdb=" N ASP A 450 " pdb=" CA ASP A 450 " ideal model delta sigma weight residual 121.54 116.13 5.41 1.91e+00 2.74e-01 8.01e+00 ... (remaining 4689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.10: 1772 17.10 - 34.19: 140 34.19 - 51.29: 20 51.29 - 68.38: 2 68.38 - 85.48: 3 Dihedral angle restraints: 1937 sinusoidal: 716 harmonic: 1221 Sorted by residual: dihedral pdb=" CA PHE A 358 " pdb=" C PHE A 358 " pdb=" N SER A 359 " pdb=" CA SER A 359 " ideal model delta harmonic sigma weight residual 180.00 158.49 21.51 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA ASP A 450 " pdb=" C ASP A 450 " pdb=" N ASN A 451 " pdb=" CA ASN A 451 " ideal model delta harmonic sigma weight residual 180.00 160.74 19.26 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA TRP A 246 " pdb=" C TRP A 246 " pdb=" N LEU A 247 " pdb=" CA LEU A 247 " ideal model delta harmonic sigma weight residual -180.00 -162.32 -17.68 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 1934 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 335 0.044 - 0.089: 154 0.089 - 0.133: 38 0.133 - 0.177: 5 0.177 - 0.221: 1 Chirality restraints: 533 Sorted by residual: chirality pdb=" CB VAL A 177 " pdb=" CA VAL A 177 " pdb=" CG1 VAL A 177 " pdb=" CG2 VAL A 177 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA LEU A 289 " pdb=" N LEU A 289 " pdb=" C LEU A 289 " pdb=" CB LEU A 289 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.47e-01 chirality pdb=" CA ILE A 44 " pdb=" N ILE A 44 " pdb=" C ILE A 44 " pdb=" CB ILE A 44 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.06e-01 ... (remaining 530 not shown) Planarity restraints: 569 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 289 " -0.037 5.00e-02 4.00e+02 5.52e-02 4.88e+00 pdb=" N PRO A 290 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 290 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 290 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 374 " 0.031 5.00e-02 4.00e+02 4.60e-02 3.39e+00 pdb=" N PRO A 375 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 375 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 375 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 162 " -0.029 5.00e-02 4.00e+02 4.39e-02 3.09e+00 pdb=" N PRO A 163 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 163 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 163 " -0.025 5.00e-02 4.00e+02 ... (remaining 566 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 988 2.81 - 3.33: 3269 3.33 - 3.85: 5720 3.85 - 4.38: 7053 4.38 - 4.90: 11807 Nonbonded interactions: 28837 Sorted by model distance: nonbonded pdb=" OG1 THR A 304 " pdb=" OD1 ASN A 467 " model vdw 2.284 3.040 nonbonded pdb=" O SER A 213 " pdb=" OG SER A 217 " model vdw 2.301 3.040 nonbonded pdb=" O THR A 452 " pdb=" N GLU A 455 " model vdw 2.315 3.120 nonbonded pdb=" OH TYR A 40 " pdb=" OE2 GLU A 194 " model vdw 2.329 3.040 nonbonded pdb=" NZ LYS A 317 " pdb=" OE2 GLU A 318 " model vdw 2.345 3.120 ... (remaining 28832 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.380 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:10.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 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 : 0.009 0.075 3440 Z= 0.365 Angle : 0.781 7.654 4694 Z= 0.461 Chirality : 0.052 0.221 533 Planarity : 0.006 0.055 569 Dihedral : 12.533 85.479 1161 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % 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: -2.36 (0.35), residues: 423 helix: -1.21 (0.25), residues: 326 sheet: None (None), residues: 0 loop : -2.21 (0.55), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 244 HIS 0.011 0.003 HIS A 298 PHE 0.016 0.002 PHE A 299 TYR 0.021 0.002 TYR A 335 ARG 0.006 0.001 ARG A 168 Details of bonding type rmsd hydrogen bonds : bond 0.12343 ( 239) hydrogen bonds : angle 5.70207 ( 705) covalent geometry : bond 0.00902 ( 3440) covalent geometry : angle 0.78113 ( 4694) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.337 Fit side-chains REVERT: A 239 PHE cc_start: 0.7041 (t80) cc_final: 0.6678 (m-10) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.8772 time to fit residues: 33.0877 Evaluate side-chains 32 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 38 optimal weight: 0.0980 chunk 11 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 HIS A 351 ASN A 414 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.125774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.097353 restraints weight = 3797.134| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.86 r_work: 0.3005 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3440 Z= 0.136 Angle : 0.576 8.400 4694 Z= 0.303 Chirality : 0.042 0.120 533 Planarity : 0.006 0.045 569 Dihedral : 4.833 20.803 455 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.99 % Allowed : 9.09 % Favored : 88.92 % 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: -0.42 (0.39), residues: 423 helix: 0.26 (0.28), residues: 327 sheet: None (None), residues: 0 loop : -1.88 (0.55), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 244 HIS 0.005 0.001 HIS A 298 PHE 0.014 0.001 PHE A 232 TYR 0.015 0.001 TYR A 335 ARG 0.002 0.000 ARG A 168 Details of bonding type rmsd hydrogen bonds : bond 0.03989 ( 239) hydrogen bonds : angle 4.62303 ( 705) covalent geometry : bond 0.00315 ( 3440) covalent geometry : angle 0.57595 ( 4694) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.347 Fit side-chains REVERT: A 194 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8444 (mt-10) REVERT: A 239 PHE cc_start: 0.7272 (t80) cc_final: 0.6360 (m-10) outliers start: 7 outliers final: 1 residues processed: 39 average time/residue: 0.7559 time to fit residues: 31.0892 Evaluate side-chains 30 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 194 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 40 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 3 optimal weight: 0.0670 chunk 4 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 HIS A 467 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.125349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.097292 restraints weight = 3741.345| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.83 r_work: 0.3007 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3440 Z= 0.133 Angle : 0.559 8.277 4694 Z= 0.292 Chirality : 0.042 0.131 533 Planarity : 0.006 0.052 569 Dihedral : 4.567 17.248 455 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.99 % Allowed : 11.08 % Favored : 86.93 % 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: 0.44 (0.40), residues: 423 helix: 0.88 (0.29), residues: 331 sheet: None (None), residues: 0 loop : -1.71 (0.54), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 244 HIS 0.004 0.001 HIS A 298 PHE 0.013 0.001 PHE A 232 TYR 0.009 0.001 TYR A 335 ARG 0.002 0.000 ARG A 353 Details of bonding type rmsd hydrogen bonds : bond 0.03816 ( 239) hydrogen bonds : angle 4.47625 ( 705) covalent geometry : bond 0.00313 ( 3440) covalent geometry : angle 0.55906 ( 4694) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.359 Fit side-chains REVERT: A 194 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8469 (mt-10) REVERT: A 207 GLN cc_start: 0.8463 (mp10) cc_final: 0.8168 (mm-40) REVERT: A 239 PHE cc_start: 0.7260 (t80) cc_final: 0.6355 (m-10) outliers start: 7 outliers final: 5 residues processed: 39 average time/residue: 0.9028 time to fit residues: 36.8933 Evaluate side-chains 38 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 342 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.5980 chunk 14 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 34 optimal weight: 0.1980 chunk 6 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.125933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.097845 restraints weight = 3859.227| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.87 r_work: 0.3014 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3440 Z= 0.129 Angle : 0.548 8.018 4694 Z= 0.285 Chirality : 0.042 0.136 533 Planarity : 0.006 0.054 569 Dihedral : 4.439 15.451 455 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.56 % Allowed : 11.65 % Favored : 85.80 % 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: 0.92 (0.41), residues: 423 helix: 1.22 (0.29), residues: 331 sheet: None (None), residues: 0 loop : -1.51 (0.55), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 244 HIS 0.003 0.001 HIS A 298 PHE 0.015 0.001 PHE A 384 TYR 0.008 0.001 TYR A 40 ARG 0.001 0.000 ARG A 353 Details of bonding type rmsd hydrogen bonds : bond 0.03659 ( 239) hydrogen bonds : angle 4.41211 ( 705) covalent geometry : bond 0.00304 ( 3440) covalent geometry : angle 0.54795 ( 4694) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.346 Fit side-chains REVERT: A 194 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8504 (mt-10) REVERT: A 207 GLN cc_start: 0.8490 (mp10) cc_final: 0.8194 (mm-40) REVERT: A 239 PHE cc_start: 0.7259 (t80) cc_final: 0.6359 (m-10) REVERT: A 417 ILE cc_start: 0.7678 (tp) cc_final: 0.7308 (tp) outliers start: 9 outliers final: 3 residues processed: 40 average time/residue: 0.8832 time to fit residues: 37.0069 Evaluate side-chains 35 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 332 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 0.0370 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.125955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.097904 restraints weight = 3826.859| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.85 r_work: 0.3022 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3440 Z= 0.130 Angle : 0.551 7.898 4694 Z= 0.285 Chirality : 0.042 0.119 533 Planarity : 0.006 0.054 569 Dihedral : 4.384 14.995 455 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.56 % Allowed : 12.78 % Favored : 84.66 % 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: 1.19 (0.41), residues: 423 helix: 1.42 (0.29), residues: 330 sheet: None (None), residues: 0 loop : -1.41 (0.56), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 244 HIS 0.003 0.001 HIS A 298 PHE 0.018 0.001 PHE A 384 TYR 0.008 0.001 TYR A 40 ARG 0.001 0.000 ARG A 353 Details of bonding type rmsd hydrogen bonds : bond 0.03675 ( 239) hydrogen bonds : angle 4.37062 ( 705) covalent geometry : bond 0.00309 ( 3440) covalent geometry : angle 0.55149 ( 4694) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.484 Fit side-chains REVERT: A 207 GLN cc_start: 0.8429 (mp10) cc_final: 0.8118 (mm-40) REVERT: A 239 PHE cc_start: 0.7121 (t80) cc_final: 0.6245 (m-10) REVERT: A 417 ILE cc_start: 0.7655 (tp) cc_final: 0.7423 (tt) outliers start: 9 outliers final: 4 residues processed: 38 average time/residue: 0.8510 time to fit residues: 33.9706 Evaluate side-chains 36 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 332 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 21 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.125830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.097540 restraints weight = 3902.721| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.88 r_work: 0.3016 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3440 Z= 0.134 Angle : 0.556 7.845 4694 Z= 0.286 Chirality : 0.042 0.118 533 Planarity : 0.006 0.055 569 Dihedral : 4.369 14.953 455 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.56 % Allowed : 13.35 % Favored : 84.09 % 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: 1.41 (0.40), residues: 423 helix: 1.58 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -1.23 (0.54), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 244 HIS 0.003 0.001 HIS A 298 PHE 0.020 0.002 PHE A 384 TYR 0.009 0.001 TYR A 40 ARG 0.001 0.000 ARG A 353 Details of bonding type rmsd hydrogen bonds : bond 0.03680 ( 239) hydrogen bonds : angle 4.35929 ( 705) covalent geometry : bond 0.00322 ( 3440) covalent geometry : angle 0.55565 ( 4694) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.352 Fit side-chains REVERT: A 207 GLN cc_start: 0.8514 (mp10) cc_final: 0.8205 (mm-40) REVERT: A 239 PHE cc_start: 0.7262 (t80) cc_final: 0.6350 (m-10) REVERT: A 417 ILE cc_start: 0.7731 (tp) cc_final: 0.7362 (tp) outliers start: 9 outliers final: 6 residues processed: 37 average time/residue: 0.7874 time to fit residues: 30.6782 Evaluate side-chains 38 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 342 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 14 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 11 optimal weight: 0.0970 chunk 17 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 37 optimal weight: 0.2980 chunk 24 optimal weight: 0.5980 chunk 38 optimal weight: 0.3980 chunk 0 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.128307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.100174 restraints weight = 3808.075| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.86 r_work: 0.3053 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3440 Z= 0.114 Angle : 0.535 7.876 4694 Z= 0.273 Chirality : 0.041 0.116 533 Planarity : 0.005 0.055 569 Dihedral : 4.226 14.553 455 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.70 % Allowed : 14.77 % Favored : 83.52 % 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: 1.51 (0.41), residues: 423 helix: 1.69 (0.29), residues: 327 sheet: None (None), residues: 0 loop : -1.42 (0.53), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 244 HIS 0.002 0.000 HIS A 298 PHE 0.022 0.001 PHE A 384 TYR 0.007 0.001 TYR A 40 ARG 0.001 0.000 ARG A 353 Details of bonding type rmsd hydrogen bonds : bond 0.03308 ( 239) hydrogen bonds : angle 4.27427 ( 705) covalent geometry : bond 0.00259 ( 3440) covalent geometry : angle 0.53462 ( 4694) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.439 Fit side-chains REVERT: A 239 PHE cc_start: 0.7255 (t80) cc_final: 0.6347 (m-10) REVERT: A 417 ILE cc_start: 0.7733 (tp) cc_final: 0.7386 (tp) outliers start: 6 outliers final: 3 residues processed: 37 average time/residue: 0.7948 time to fit residues: 31.1140 Evaluate side-chains 34 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 342 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 19 optimal weight: 0.0070 chunk 8 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.126585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.098808 restraints weight = 3949.155| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 1.83 r_work: 0.2918 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3440 Z= 0.123 Angle : 0.540 7.824 4694 Z= 0.278 Chirality : 0.041 0.116 533 Planarity : 0.005 0.055 569 Dihedral : 4.230 14.891 455 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.42 % Allowed : 15.62 % Favored : 82.95 % 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: 1.52 (0.41), residues: 423 helix: 1.67 (0.29), residues: 329 sheet: None (None), residues: 0 loop : -1.37 (0.54), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 244 HIS 0.002 0.000 HIS A 298 PHE 0.024 0.001 PHE A 384 TYR 0.008 0.001 TYR A 40 ARG 0.001 0.000 ARG A 353 Details of bonding type rmsd hydrogen bonds : bond 0.03479 ( 239) hydrogen bonds : angle 4.28363 ( 705) covalent geometry : bond 0.00287 ( 3440) covalent geometry : angle 0.54041 ( 4694) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.370 Fit side-chains REVERT: A 239 PHE cc_start: 0.7259 (t80) cc_final: 0.6324 (m-10) REVERT: A 417 ILE cc_start: 0.7729 (tp) cc_final: 0.7375 (tp) outliers start: 5 outliers final: 3 residues processed: 37 average time/residue: 0.6530 time to fit residues: 25.7601 Evaluate side-chains 34 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 342 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 19 optimal weight: 0.0770 chunk 16 optimal weight: 0.9990 chunk 6 optimal weight: 0.0470 chunk 13 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.127674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.099905 restraints weight = 3940.557| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.85 r_work: 0.3020 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3440 Z= 0.117 Angle : 0.536 7.826 4694 Z= 0.275 Chirality : 0.041 0.142 533 Planarity : 0.005 0.055 569 Dihedral : 4.189 14.722 455 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.42 % Allowed : 15.91 % Favored : 82.67 % 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: 1.60 (0.41), residues: 423 helix: 1.76 (0.29), residues: 328 sheet: None (None), residues: 0 loop : -1.42 (0.55), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 244 HIS 0.002 0.000 HIS A 298 PHE 0.028 0.001 PHE A 384 TYR 0.008 0.001 TYR A 40 ARG 0.001 0.000 ARG A 353 Details of bonding type rmsd hydrogen bonds : bond 0.03366 ( 239) hydrogen bonds : angle 4.25725 ( 705) covalent geometry : bond 0.00270 ( 3440) covalent geometry : angle 0.53615 ( 4694) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.367 Fit side-chains REVERT: A 239 PHE cc_start: 0.7318 (t80) cc_final: 0.6427 (m-10) REVERT: A 417 ILE cc_start: 0.7788 (tp) cc_final: 0.7463 (tp) outliers start: 5 outliers final: 3 residues processed: 36 average time/residue: 0.6528 time to fit residues: 25.0661 Evaluate side-chains 35 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 342 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.0030 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 33 optimal weight: 0.3980 chunk 36 optimal weight: 0.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN A 467 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.128900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.101409 restraints weight = 3881.756| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.82 r_work: 0.3020 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3440 Z= 0.120 Angle : 0.538 7.781 4694 Z= 0.276 Chirality : 0.041 0.139 533 Planarity : 0.005 0.055 569 Dihedral : 4.174 14.782 455 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.42 % Allowed : 15.91 % Favored : 82.67 % 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: 1.46 (0.41), residues: 423 helix: 1.66 (0.29), residues: 334 sheet: None (None), residues: 0 loop : -1.71 (0.55), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 244 HIS 0.002 0.000 HIS A 298 PHE 0.027 0.001 PHE A 384 TYR 0.008 0.001 TYR A 40 ARG 0.001 0.000 ARG A 353 Details of bonding type rmsd hydrogen bonds : bond 0.03407 ( 239) hydrogen bonds : angle 4.25058 ( 705) covalent geometry : bond 0.00279 ( 3440) covalent geometry : angle 0.53757 ( 4694) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.361 Fit side-chains REVERT: A 239 PHE cc_start: 0.7320 (t80) cc_final: 0.6430 (m-10) REVERT: A 417 ILE cc_start: 0.7794 (tp) cc_final: 0.7488 (tp) outliers start: 5 outliers final: 3 residues processed: 35 average time/residue: 0.6665 time to fit residues: 24.8538 Evaluate side-chains 35 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 342 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 2 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 22 optimal weight: 0.0270 chunk 3 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 overall best weight: 0.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.126295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.098664 restraints weight = 3952.211| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.83 r_work: 0.3005 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3440 Z= 0.129 Angle : 0.546 7.747 4694 Z= 0.281 Chirality : 0.042 0.129 533 Planarity : 0.005 0.055 569 Dihedral : 4.214 14.961 455 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.70 % Allowed : 15.62 % Favored : 82.67 % 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: 1.65 (0.41), residues: 423 helix: 1.78 (0.29), residues: 327 sheet: None (None), residues: 0 loop : -1.32 (0.55), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 244 HIS 0.002 0.001 HIS A 298 PHE 0.027 0.002 PHE A 384 TYR 0.008 0.001 TYR A 40 ARG 0.001 0.000 ARG A 353 Details of bonding type rmsd hydrogen bonds : bond 0.03564 ( 239) hydrogen bonds : angle 4.28961 ( 705) covalent geometry : bond 0.00309 ( 3440) covalent geometry : angle 0.54619 ( 4694) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2290.71 seconds wall clock time: 40 minutes 26.51 seconds (2426.51 seconds total)