Starting phenix.real_space_refine on Tue Feb 13 04:48:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cyh_30500/02_2024/7cyh_30500.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cyh_30500/02_2024/7cyh_30500.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cyh_30500/02_2024/7cyh_30500.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cyh_30500/02_2024/7cyh_30500.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cyh_30500/02_2024/7cyh_30500.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cyh_30500/02_2024/7cyh_30500.pdb" } resolution = 3.9 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= 0.210 sd= 1.412 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 14 5.16 5 C 2057 2.51 5 N 551 2.21 5 O 619 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 23": "NH1" <-> "NH2" Residue "D ARG 48": "NH1" <-> "NH2" Residue "E ARG 19": "NH1" <-> "NH2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 100": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 3241 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 11, 'TRANS': 182} Chain: "D" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 806 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 101} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 899 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 114} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 2.26, per 1000 atoms: 0.70 Number of scatterers: 3241 At special positions: 0 Unit cell: (72.45, 61.95, 92.4, 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 14 16.00 O 619 8.00 N 551 7.00 C 2057 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 91 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 610.3 milliseconds 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 762 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 11 sheets defined 9.5% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.554A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 390 removed outlier: 3.911A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.841A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'D' and resid 51 through 55 Processing helix chain 'E' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 356 through 357 Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.024A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 400 through 403 removed outlier: 3.650A pdb=" N ARG A 509 " --> pdb=" O TRP A 436 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE A 434 " --> pdb=" O VAL A 511 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA5, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA6, first strand: chain 'D' and resid 4 through 6 removed outlier: 3.885A pdb=" N CYS D 22 " --> pdb=" O PHE D 74 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER D 70 " --> pdb=" O ASP D 73 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 39 through 41 removed outlier: 4.021A pdb=" N VAL D 88 " --> pdb=" O GLN D 41 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 3 through 6 removed outlier: 3.785A pdb=" N LYS E 3 " --> pdb=" O SER E 25 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 11 through 12 Processing sheet with id=AB1, first strand: chain 'E' and resid 45 through 50 removed outlier: 6.383A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N GLU E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N MET E 34 " --> pdb=" O GLU E 50 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N CYS E 96 " --> pdb=" O TRP E 110 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N TRP E 110 " --> pdb=" O CYS E 96 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ARG E 98 " --> pdb=" O ASP E 108 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 45 through 50 removed outlier: 6.383A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N GLU E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N MET E 34 " --> pdb=" O GLU E 50 " (cutoff:3.500A) 71 hydrogen bonds defined for protein. 156 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: 0.76 Time building geometry restraints manager: 1.41 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: 1045 1.34 - 1.46: 891 1.46 - 1.59: 1370 1.59 - 1.71: 0 1.71 - 1.83: 16 Bond restraints: 3322 Sorted by residual: bond pdb=" C PHE A 497 " pdb=" N GLN A 498 " ideal model delta sigma weight residual 1.329 1.256 0.073 1.86e-02 2.89e+03 1.53e+01 bond pdb=" CA VAL A 512 " pdb=" C VAL A 512 " ideal model delta sigma weight residual 1.525 1.503 0.022 9.00e-03 1.23e+04 6.10e+00 bond pdb=" C GLN A 498 " pdb=" N PRO A 499 " ideal model delta sigma weight residual 1.336 1.307 0.029 1.25e-02 6.40e+03 5.50e+00 bond pdb=" CB PHE A 429 " pdb=" CG PHE A 429 " ideal model delta sigma weight residual 1.502 1.449 0.053 2.30e-02 1.89e+03 5.27e+00 bond pdb=" CB PHE A 377 " pdb=" CG PHE A 377 " ideal model delta sigma weight residual 1.502 1.449 0.053 2.30e-02 1.89e+03 5.24e+00 ... (remaining 3317 not shown) Histogram of bond angle deviations from ideal: 99.89 - 106.76: 115 106.76 - 113.63: 1730 113.63 - 120.50: 1338 120.50 - 127.37: 1298 127.37 - 134.23: 34 Bond angle restraints: 4515 Sorted by residual: angle pdb=" C PHE A 497 " pdb=" N GLN A 498 " pdb=" CA GLN A 498 " ideal model delta sigma weight residual 121.48 105.12 16.36 2.04e+00 2.40e-01 6.44e+01 angle pdb=" N VAL A 512 " pdb=" CA VAL A 512 " pdb=" C VAL A 512 " ideal model delta sigma weight residual 108.53 99.98 8.55 1.22e+00 6.72e-01 4.91e+01 angle pdb=" N GLY E 105 " pdb=" CA GLY E 105 " pdb=" C GLY E 105 " ideal model delta sigma weight residual 111.42 103.58 7.84 1.51e+00 4.39e-01 2.69e+01 angle pdb=" C PHE D 35 " pdb=" N MET D 36 " pdb=" CA MET D 36 " ideal model delta sigma weight residual 121.53 131.27 -9.74 2.25e+00 1.98e-01 1.87e+01 angle pdb=" C ARG D 99 " pdb=" N ILE D 100 " pdb=" CA ILE D 100 " ideal model delta sigma weight residual 121.97 128.15 -6.18 1.80e+00 3.09e-01 1.18e+01 ... (remaining 4510 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 15.72: 1830 15.72 - 31.43: 108 31.43 - 47.14: 7 47.14 - 62.85: 1 62.85 - 78.56: 1 Dihedral angle restraints: 1947 sinusoidal: 738 harmonic: 1209 Sorted by residual: dihedral pdb=" CA THR E 63 " pdb=" C THR E 63 " pdb=" N VAL E 64 " pdb=" CA VAL E 64 " ideal model delta harmonic sigma weight residual 180.00 146.98 33.02 0 5.00e+00 4.00e-02 4.36e+01 dihedral pdb=" CA GLN D 92 " pdb=" C GLN D 92 " pdb=" N GLN D 93 " pdb=" CA GLN D 93 " ideal model delta harmonic sigma weight residual 180.00 149.00 31.00 0 5.00e+00 4.00e-02 3.84e+01 dihedral pdb=" CA SER A 383 " pdb=" C SER A 383 " pdb=" N PRO A 384 " pdb=" CA PRO A 384 " ideal model delta harmonic sigma weight residual 180.00 -149.34 -30.66 0 5.00e+00 4.00e-02 3.76e+01 ... (remaining 1944 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 263 0.042 - 0.084: 136 0.084 - 0.127: 55 0.127 - 0.169: 27 0.169 - 0.211: 3 Chirality restraints: 484 Sorted by residual: chirality pdb=" CA HIS A 519 " pdb=" N HIS A 519 " pdb=" C HIS A 519 " pdb=" CB HIS A 519 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CB VAL A 511 " pdb=" CA VAL A 511 " pdb=" CG1 VAL A 511 " pdb=" CG2 VAL A 511 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.19 2.00e-01 2.50e+01 9.43e-01 chirality pdb=" CA THR E 58 " pdb=" N THR E 58 " pdb=" C THR E 58 " pdb=" CB THR E 58 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.42e-01 ... (remaining 481 not shown) Planarity restraints: 589 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 526 " 0.056 5.00e-02 4.00e+02 8.50e-02 1.16e+01 pdb=" N PRO A 527 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO A 527 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 527 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 398 " -0.015 2.00e-02 2.50e+03 3.05e-02 9.31e+00 pdb=" C ASP A 398 " 0.053 2.00e-02 2.50e+03 pdb=" O ASP A 398 " -0.020 2.00e-02 2.50e+03 pdb=" N SER A 399 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR E 60 " -0.037 5.00e-02 4.00e+02 5.53e-02 4.89e+00 pdb=" N PRO E 61 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO E 61 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 61 " -0.030 5.00e-02 4.00e+02 ... (remaining 586 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 107 2.65 - 3.21: 3284 3.21 - 3.77: 4889 3.77 - 4.34: 6489 4.34 - 4.90: 10557 Nonbonded interactions: 25326 Sorted by model distance: nonbonded pdb=" OG1 THR A 393 " pdb=" OE1 GLU A 516 " model vdw 2.087 2.440 nonbonded pdb=" O THR E 30 " pdb=" OG SER E 53 " model vdw 2.093 2.440 nonbonded pdb=" O SER E 52 " pdb=" NH1 ARG E 72 " model vdw 2.145 2.520 nonbonded pdb=" O LEU A 513 " pdb=" OG SER A 514 " model vdw 2.165 2.440 nonbonded pdb=" NH1 ARG A 457 " pdb=" OG SER A 459 " model vdw 2.169 2.520 ... (remaining 25321 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.350 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: 1.810 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.960 Find NCS groups from input model: 0.090 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6059 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 : 0.011 0.073 3322 Z= 0.702 Angle : 1.176 16.365 4515 Z= 0.656 Chirality : 0.062 0.211 484 Planarity : 0.008 0.085 589 Dihedral : 9.756 78.558 1170 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 28.64 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.83 % Favored : 89.69 % Rotamer: Outliers : 0.87 % Allowed : 0.87 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % Twisted Proline : 4.76 % Twisted General : 0.75 % 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: -4.10 (0.33), residues: 417 helix: -4.58 (0.31), residues: 26 sheet: -2.91 (0.39), residues: 108 loop : -2.59 (0.31), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.004 TRP A 353 HIS 0.000 0.000 HIS A 519 PHE 0.036 0.005 PHE A 497 TYR 0.032 0.004 TYR A 495 ARG 0.007 0.001 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 109 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 365 TYR cc_start: 0.8298 (m-80) cc_final: 0.8050 (m-80) REVERT: A 493 GLN cc_start: 0.7362 (tt0) cc_final: 0.7029 (tt0) outliers start: 3 outliers final: 3 residues processed: 112 average time/residue: 0.2112 time to fit residues: 27.1657 Evaluate side-chains 73 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 70 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 515 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 chunk 17 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5941 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 3322 Z= 0.234 Angle : 0.787 9.821 4515 Z= 0.407 Chirality : 0.051 0.163 484 Planarity : 0.006 0.047 589 Dihedral : 7.926 54.606 474 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.43 % Favored : 92.09 % Rotamer: Outliers : 3.49 % Allowed : 10.17 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % 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: -2.86 (0.37), residues: 417 helix: -4.16 (0.55), residues: 25 sheet: -2.31 (0.42), residues: 111 loop : -1.53 (0.35), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 353 HIS 0.001 0.001 HIS A 519 PHE 0.025 0.002 PHE A 497 TYR 0.028 0.003 TYR A 495 ARG 0.004 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 100 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 493 GLN cc_start: 0.7284 (tt0) cc_final: 0.7012 (tt0) REVERT: D 56 ASN cc_start: 0.5858 (m110) cc_final: 0.5578 (m110) REVERT: E 83 MET cc_start: 0.4794 (tpp) cc_final: 0.4481 (tpp) outliers start: 12 outliers final: 7 residues processed: 104 average time/residue: 0.1655 time to fit residues: 20.6951 Evaluate side-chains 79 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 72 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain E residue 96 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 7.9990 chunk 11 optimal weight: 0.6980 chunk 30 optimal weight: 20.0000 chunk 25 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 36 optimal weight: 0.0670 chunk 12 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5870 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3322 Z= 0.199 Angle : 0.777 12.030 4515 Z= 0.394 Chirality : 0.050 0.194 484 Planarity : 0.005 0.057 589 Dihedral : 7.222 59.153 473 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.95 % Favored : 92.57 % Rotamer: Outliers : 3.49 % Allowed : 13.95 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % 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: -2.42 (0.39), residues: 417 helix: -3.94 (0.58), residues: 25 sheet: -2.00 (0.43), residues: 117 loop : -1.18 (0.37), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 47 HIS 0.001 0.001 HIS A 519 PHE 0.023 0.002 PHE D 101 TYR 0.021 0.002 TYR A 495 ARG 0.009 0.001 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 90 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 ARG cc_start: 0.7863 (ttt90) cc_final: 0.7512 (ttt90) REVERT: A 376 THR cc_start: 0.8532 (t) cc_final: 0.8197 (p) REVERT: A 401 VAL cc_start: 0.9445 (t) cc_final: 0.9226 (p) REVERT: A 506 GLN cc_start: 0.6477 (mt0) cc_final: 0.6136 (mt0) outliers start: 12 outliers final: 10 residues processed: 94 average time/residue: 0.1850 time to fit residues: 20.7743 Evaluate side-chains 86 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 115 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 19 optimal weight: 7.9990 chunk 4 optimal weight: 0.0270 chunk 17 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5845 moved from start: 0.5058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3322 Z= 0.186 Angle : 0.739 9.275 4515 Z= 0.370 Chirality : 0.047 0.198 484 Planarity : 0.005 0.059 589 Dihedral : 6.684 54.228 473 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.48 % Allowed : 5.52 % Favored : 94.00 % Rotamer: Outliers : 4.36 % Allowed : 15.70 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % 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: -2.32 (0.39), residues: 417 helix: -3.88 (0.60), residues: 25 sheet: -1.83 (0.41), residues: 131 loop : -1.10 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP E 47 HIS 0.001 0.001 HIS A 519 PHE 0.024 0.002 PHE E 29 TYR 0.016 0.002 TYR A 495 ARG 0.005 0.000 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 83 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 ARG cc_start: 0.7848 (ttt90) cc_final: 0.7485 (ttt90) REVERT: A 376 THR cc_start: 0.8367 (t) cc_final: 0.8086 (p) REVERT: A 389 ASP cc_start: 0.7312 (t70) cc_final: 0.6813 (t0) outliers start: 15 outliers final: 10 residues processed: 90 average time/residue: 0.1775 time to fit residues: 19.0171 Evaluate side-chains 81 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 71 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 84 ASN Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 115 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 16 optimal weight: 8.9990 chunk 33 optimal weight: 0.0030 chunk 27 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 7 optimal weight: 0.9990 overall best weight: 3.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6014 moved from start: 0.5171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 3322 Z= 0.338 Angle : 0.793 11.045 4515 Z= 0.408 Chirality : 0.049 0.207 484 Planarity : 0.005 0.059 589 Dihedral : 6.588 33.125 471 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.59 % Favored : 89.93 % Rotamer: Outliers : 6.40 % Allowed : 14.24 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % 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: -2.24 (0.39), residues: 417 helix: -3.85 (0.55), residues: 25 sheet: -1.79 (0.41), residues: 137 loop : -0.99 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP E 47 HIS 0.003 0.002 HIS A 519 PHE 0.023 0.003 PHE A 400 TYR 0.024 0.002 TYR D 52 ARG 0.003 0.001 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 76 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 ARG cc_start: 0.7985 (ttt90) cc_final: 0.7484 (ttt90) REVERT: A 376 THR cc_start: 0.8418 (t) cc_final: 0.7878 (p) REVERT: A 389 ASP cc_start: 0.7349 (t70) cc_final: 0.6815 (t0) REVERT: A 506 GLN cc_start: 0.6214 (mt0) cc_final: 0.5562 (mt0) REVERT: E 83 MET cc_start: 0.4223 (tpt) cc_final: 0.3504 (tpp) outliers start: 22 outliers final: 13 residues processed: 88 average time/residue: 0.1784 time to fit residues: 18.6371 Evaluate side-chains 76 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 63 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 84 ASN Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 115 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 0.0980 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 20.0000 chunk 38 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5918 moved from start: 0.5541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3322 Z= 0.201 Angle : 0.731 9.788 4515 Z= 0.371 Chirality : 0.049 0.232 484 Planarity : 0.004 0.062 589 Dihedral : 6.087 33.736 471 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.95 % Favored : 92.57 % Rotamer: Outliers : 4.65 % Allowed : 16.86 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % 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: -1.95 (0.40), residues: 417 helix: -3.74 (0.62), residues: 25 sheet: -1.52 (0.44), residues: 126 loop : -0.88 (0.39), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP E 47 HIS 0.002 0.001 HIS A 519 PHE 0.015 0.002 PHE E 29 TYR 0.016 0.002 TYR D 52 ARG 0.004 0.000 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 79 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 ARG cc_start: 0.7833 (ttt90) cc_final: 0.7463 (ttt90) REVERT: A 376 THR cc_start: 0.8400 (t) cc_final: 0.8003 (p) REVERT: A 389 ASP cc_start: 0.7325 (t70) cc_final: 0.6832 (t0) REVERT: A 452 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.7631 (mt) outliers start: 16 outliers final: 14 residues processed: 82 average time/residue: 0.2047 time to fit residues: 19.6321 Evaluate side-chains 80 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 65 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 84 ASN Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 115 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 18 optimal weight: 0.0870 chunk 15 optimal weight: 4.9990 chunk 23 optimal weight: 0.5980 chunk 11 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 overall best weight: 2.1364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 GLN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5973 moved from start: 0.5737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3322 Z= 0.261 Angle : 0.751 10.088 4515 Z= 0.384 Chirality : 0.049 0.231 484 Planarity : 0.005 0.063 589 Dihedral : 6.106 32.550 471 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.63 % Favored : 90.89 % Rotamer: Outliers : 6.10 % Allowed : 15.12 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % 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: -1.89 (0.41), residues: 417 helix: -3.85 (0.55), residues: 25 sheet: -1.51 (0.43), residues: 126 loop : -0.80 (0.40), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.004 TRP E 36 HIS 0.002 0.001 HIS A 519 PHE 0.015 0.002 PHE A 400 TYR 0.031 0.002 TYR D 52 ARG 0.008 0.001 ARG D 48 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 67 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 ARG cc_start: 0.7905 (ttt90) cc_final: 0.7468 (ttt90) REVERT: A 376 THR cc_start: 0.8363 (t) cc_final: 0.7847 (p) REVERT: A 389 ASP cc_start: 0.7284 (t70) cc_final: 0.6773 (t0) REVERT: A 452 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.7624 (mt) REVERT: E 83 MET cc_start: 0.3702 (tpt) cc_final: 0.3350 (tpp) outliers start: 21 outliers final: 17 residues processed: 76 average time/residue: 0.1821 time to fit residues: 16.5595 Evaluate side-chains 80 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 62 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 84 ASN Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 115 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 30.0000 chunk 19 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 31 optimal weight: 30.0000 chunk 35 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6039 moved from start: 0.5656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 3322 Z= 0.353 Angle : 0.818 10.259 4515 Z= 0.418 Chirality : 0.051 0.204 484 Planarity : 0.005 0.063 589 Dihedral : 6.427 32.405 471 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.72 % Allowed : 10.07 % Favored : 89.21 % Rotamer: Outliers : 6.10 % Allowed : 15.41 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % 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: -1.93 (0.41), residues: 417 helix: -4.16 (0.38), residues: 25 sheet: -1.45 (0.45), residues: 126 loop : -0.84 (0.40), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP E 36 HIS 0.002 0.001 HIS A 519 PHE 0.022 0.003 PHE A 400 TYR 0.015 0.002 TYR A 495 ARG 0.008 0.001 ARG D 48 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 63 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 ARG cc_start: 0.7902 (ttt90) cc_final: 0.7356 (ttt90) REVERT: A 376 THR cc_start: 0.8366 (t) cc_final: 0.7951 (m) REVERT: A 389 ASP cc_start: 0.7157 (t70) cc_final: 0.6553 (t0) REVERT: E 83 MET cc_start: 0.3982 (tpt) cc_final: 0.3281 (tpp) outliers start: 21 outliers final: 19 residues processed: 72 average time/residue: 0.1717 time to fit residues: 14.8676 Evaluate side-chains 80 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 61 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 84 ASN Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 115 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6007 moved from start: 0.5825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3322 Z= 0.283 Angle : 0.773 9.430 4515 Z= 0.391 Chirality : 0.049 0.206 484 Planarity : 0.005 0.063 589 Dihedral : 6.264 32.759 471 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.72 % Allowed : 9.59 % Favored : 89.69 % Rotamer: Outliers : 6.10 % Allowed : 15.99 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % 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: -1.79 (0.42), residues: 417 helix: -4.13 (0.39), residues: 25 sheet: -1.22 (0.47), residues: 124 loop : -0.83 (0.40), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP E 47 HIS 0.002 0.001 HIS A 519 PHE 0.024 0.003 PHE A 392 TYR 0.025 0.002 TYR D 52 ARG 0.005 0.001 ARG D 48 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 66 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 ARG cc_start: 0.7876 (ttt90) cc_final: 0.7367 (ttt90) REVERT: A 376 THR cc_start: 0.8454 (t) cc_final: 0.7900 (m) REVERT: A 389 ASP cc_start: 0.7069 (t70) cc_final: 0.6485 (t0) REVERT: E 83 MET cc_start: 0.4010 (tpt) cc_final: 0.3632 (tpp) outliers start: 21 outliers final: 19 residues processed: 76 average time/residue: 0.1655 time to fit residues: 15.1176 Evaluate side-chains 81 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 62 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 84 ASN Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 115 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 0.3980 chunk 19 optimal weight: 0.0570 chunk 34 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 45 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5901 moved from start: 0.6160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3322 Z= 0.187 Angle : 0.741 8.354 4515 Z= 0.371 Chirality : 0.047 0.192 484 Planarity : 0.005 0.065 589 Dihedral : 5.784 29.602 471 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.91 % Favored : 91.61 % Rotamer: Outliers : 5.23 % Allowed : 17.73 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % 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: -1.58 (0.43), residues: 417 helix: -4.00 (0.46), residues: 25 sheet: -1.03 (0.47), residues: 125 loop : -0.70 (0.42), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP E 47 HIS 0.001 0.001 HIS A 519 PHE 0.020 0.002 PHE A 392 TYR 0.021 0.001 TYR D 52 ARG 0.004 0.000 ARG E 72 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 69 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 355 ARG cc_start: 0.7756 (ttt90) cc_final: 0.7460 (tpp80) REVERT: A 376 THR cc_start: 0.8433 (t) cc_final: 0.8046 (p) REVERT: A 452 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.7621 (mt) REVERT: D 39 PHE cc_start: 0.5375 (m-10) cc_final: 0.5156 (m-10) REVERT: E 11 LEU cc_start: 0.5629 (tp) cc_final: 0.5323 (mp) REVERT: E 76 LYS cc_start: 0.6148 (ptpt) cc_final: 0.5528 (mtmt) REVERT: E 83 MET cc_start: 0.4087 (tpt) cc_final: 0.3717 (tpp) outliers start: 18 outliers final: 14 residues processed: 75 average time/residue: 0.1848 time to fit residues: 16.5008 Evaluate side-chains 75 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 60 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 84 ASN Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 115 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 8.9990 chunk 24 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN D 37 ASN ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.164764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.118572 restraints weight = 5085.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.121008 restraints weight = 3526.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.122759 restraints weight = 2761.059| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.6251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3322 Z= 0.225 Angle : 0.768 8.863 4515 Z= 0.387 Chirality : 0.050 0.321 484 Planarity : 0.005 0.063 589 Dihedral : 5.812 32.229 471 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.15 % Favored : 91.37 % Rotamer: Outliers : 4.94 % Allowed : 18.02 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % 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: -1.53 (0.43), residues: 417 helix: -3.80 (0.59), residues: 24 sheet: -0.92 (0.48), residues: 124 loop : -0.75 (0.41), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP E 47 HIS 0.002 0.001 HIS A 519 PHE 0.028 0.002 PHE A 392 TYR 0.030 0.002 TYR D 52 ARG 0.004 0.001 ARG D 48 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1144.64 seconds wall clock time: 21 minutes 27.09 seconds (1287.09 seconds total)