Starting phenix.real_space_refine on Tue Feb 11 07:12:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oof_17012/02_2025/8oof_17012.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oof_17012/02_2025/8oof_17012.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8oof_17012/02_2025/8oof_17012.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oof_17012/02_2025/8oof_17012.map" model { file = "/net/cci-nas-00/data/ceres_data/8oof_17012/02_2025/8oof_17012.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oof_17012/02_2025/8oof_17012.cif" } resolution = 2.9 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= 0.001 sd= 0.013 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 20 5.16 5 C 2837 2.51 5 N 799 2.21 5 O 819 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 4479 Number of models: 1 Model: "" Number of chains: 3 Chain: "I" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 873 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain breaks: 1 Chain: "J" Number of atoms: 3574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3574 Classifications: {'peptide': 447} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 418} Chain breaks: 3 Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.40, per 1000 atoms: 0.98 Number of scatterers: 4479 At special positions: 0 Unit cell: (89.598, 87.132, 85.488, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 20 16.00 P 3 15.00 Mg 1 11.99 O 819 8.00 N 799 7.00 C 2837 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 562.6 milliseconds 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1036 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 6 sheets defined 41.7% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'I' and resid 7 through 21 Processing helix chain 'I' and resid 43 through 52 Processing helix chain 'I' and resid 190 through 199 Processing helix chain 'I' and resid 203 through 211 removed outlier: 3.931A pdb=" N GLN I 207 " --> pdb=" O GLY I 203 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 52 removed outlier: 3.743A pdb=" N ARG J 46 " --> pdb=" O GLN J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 128 through 143 Processing helix chain 'J' and resid 165 through 179 Processing helix chain 'J' and resid 190 through 198 Processing helix chain 'J' and resid 225 through 228 Processing helix chain 'J' and resid 234 through 250 Processing helix chain 'J' and resid 259 through 271 Processing helix chain 'J' and resid 276 through 283 removed outlier: 4.193A pdb=" N GLY J 283 " --> pdb=" O ARG J 279 " (cutoff:3.500A) Processing helix chain 'J' and resid 289 through 294 Processing helix chain 'J' and resid 603 through 606 Processing helix chain 'J' and resid 607 through 615 removed outlier: 3.597A pdb=" N ALA J 611 " --> pdb=" O SER J 607 " (cutoff:3.500A) Processing helix chain 'J' and resid 634 through 639 Processing helix chain 'J' and resid 640 through 643 Processing helix chain 'J' and resid 645 through 650 Processing helix chain 'J' and resid 656 through 667 Processing helix chain 'J' and resid 679 through 684 Processing helix chain 'J' and resid 690 through 694 Processing helix chain 'J' and resid 697 through 708 removed outlier: 3.648A pdb=" N ALA J 708 " --> pdb=" O GLN J 704 " (cutoff:3.500A) Processing helix chain 'J' and resid 726 through 736 Processing helix chain 'J' and resid 738 through 743 Processing helix chain 'J' and resid 748 through 755 removed outlier: 3.610A pdb=" N GLU J 753 " --> pdb=" O GLU J 749 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 179 through 180 removed outlier: 3.791A pdb=" N TYR I 179 " --> pdb=" O TYR I 188 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 27 through 29 Processing sheet with id=AA3, first strand: chain 'J' and resid 80 through 82 removed outlier: 4.598A pdb=" N ASN J 63 " --> pdb=" O THR J 159 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 97 through 100 Processing sheet with id=AA5, first strand: chain 'J' and resid 222 through 223 Processing sheet with id=AA6, first strand: chain 'J' and resid 222 through 223 removed outlier: 6.269A pdb=" N VAL J 686 " --> pdb=" O ARG J 719 " (cutoff:3.500A) 175 hydrogen bonds defined for protein. 486 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: 1.19 Time building geometry restraints manager: 1.29 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: 1484 1.34 - 1.46: 727 1.46 - 1.57: 2346 1.57 - 1.69: 3 1.69 - 1.81: 34 Bond restraints: 4594 Sorted by residual: bond pdb=" CB THR J 689 " pdb=" CG2 THR J 689 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.73e+00 bond pdb=" CB LEU J 683 " pdb=" CG LEU J 683 " ideal model delta sigma weight residual 1.530 1.508 0.022 2.00e-02 2.50e+03 1.19e+00 bond pdb=" N ALA I 160 " pdb=" CA ALA I 160 " ideal model delta sigma weight residual 1.455 1.477 -0.022 2.40e-02 1.74e+03 8.12e-01 bond pdb=" CG ARG J 636 " pdb=" CD ARG J 636 " ideal model delta sigma weight residual 1.520 1.493 0.027 3.00e-02 1.11e+03 8.03e-01 bond pdb=" O3B ATP J 801 " pdb=" PB ATP J 801 " ideal model delta sigma weight residual 1.592 1.566 0.026 3.00e-02 1.11e+03 7.49e-01 ... (remaining 4589 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 5833 1.35 - 2.70: 339 2.70 - 4.05: 49 4.05 - 5.39: 10 5.39 - 6.74: 2 Bond angle restraints: 6233 Sorted by residual: angle pdb=" CA GLU J 17 " pdb=" C GLU J 17 " pdb=" N PRO J 18 " ideal model delta sigma weight residual 116.90 121.49 -4.59 1.50e+00 4.44e-01 9.35e+00 angle pdb=" N THR J 627 " pdb=" CA THR J 627 " pdb=" C THR J 627 " ideal model delta sigma weight residual 110.19 107.25 2.94 1.24e+00 6.50e-01 5.61e+00 angle pdb=" N VAL J 634 " pdb=" CA VAL J 634 " pdb=" C VAL J 634 " ideal model delta sigma weight residual 111.05 113.96 -2.91 1.25e+00 6.40e-01 5.41e+00 angle pdb=" N ALA I 160 " pdb=" CA ALA I 160 " pdb=" C ALA I 160 " ideal model delta sigma weight residual 107.37 114.11 -6.74 2.96e+00 1.14e-01 5.19e+00 angle pdb=" CA ARG J 295 " pdb=" CB ARG J 295 " pdb=" CG ARG J 295 " ideal model delta sigma weight residual 114.10 109.68 4.42 2.00e+00 2.50e-01 4.88e+00 ... (remaining 6228 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.44: 2518 16.44 - 32.88: 187 32.88 - 49.32: 51 49.32 - 65.76: 8 65.76 - 82.20: 6 Dihedral angle restraints: 2770 sinusoidal: 1160 harmonic: 1610 Sorted by residual: dihedral pdb=" CA GLU J 626 " pdb=" C GLU J 626 " pdb=" N THR J 627 " pdb=" CA THR J 627 " ideal model delta harmonic sigma weight residual 180.00 150.59 29.41 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA ASP J 104 " pdb=" C ASP J 104 " pdb=" N CYS J 105 " pdb=" CA CYS J 105 " ideal model delta harmonic sigma weight residual 180.00 151.04 28.96 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA ARG J 90 " pdb=" C ARG J 90 " pdb=" N ASP J 91 " pdb=" CA ASP J 91 " ideal model delta harmonic sigma weight residual 180.00 153.67 26.33 0 5.00e+00 4.00e-02 2.77e+01 ... (remaining 2767 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 417 0.041 - 0.083: 170 0.083 - 0.124: 62 0.124 - 0.165: 2 0.165 - 0.206: 3 Chirality restraints: 654 Sorted by residual: chirality pdb=" CB ILE J 39 " pdb=" CA ILE J 39 " pdb=" CG1 ILE J 39 " pdb=" CG2 ILE J 39 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA GLU J 635 " pdb=" N GLU J 635 " pdb=" C GLU J 635 " pdb=" CB GLU J 635 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.75e-01 chirality pdb=" CA ARG I 185 " pdb=" N ARG I 185 " pdb=" C ARG I 185 " pdb=" CB ARG I 185 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.87e-01 ... (remaining 651 not shown) Planarity restraints: 811 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG J 293 " -0.210 9.50e-02 1.11e+02 9.48e-02 6.86e+00 pdb=" NE ARG J 293 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG J 293 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG J 293 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG J 293 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR J 284 " -0.007 2.00e-02 2.50e+03 1.46e-02 4.28e+00 pdb=" CG TYR J 284 " 0.008 2.00e-02 2.50e+03 pdb=" CD1 TYR J 284 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR J 284 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR J 284 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR J 284 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR J 284 " 0.020 2.00e-02 2.50e+03 pdb=" OH TYR J 284 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 636 " 0.165 9.50e-02 1.11e+02 7.45e-02 4.03e+00 pdb=" NE ARG J 636 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG J 636 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG J 636 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG J 636 " 0.001 2.00e-02 2.50e+03 ... (remaining 808 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 35 2.61 - 3.19: 3966 3.19 - 3.76: 6776 3.76 - 4.33: 10095 4.33 - 4.90: 16176 Nonbonded interactions: 37048 Sorted by model distance: nonbonded pdb=" OD2 ASP J 190 " pdb="MG MG J 802 " model vdw 2.043 2.170 nonbonded pdb=" O1B ATP J 801 " pdb="MG MG J 802 " model vdw 2.087 2.170 nonbonded pdb=" O1G ATP J 801 " pdb="MG MG J 802 " model vdw 2.096 2.170 nonbonded pdb=" OE2 GLU J 264 " pdb=" NH2 ARG J 268 " model vdw 2.231 3.120 nonbonded pdb=" NZ LYS I 42 " pdb=" OE1 GLU I 50 " model vdw 2.305 3.120 ... (remaining 37043 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.750 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:15.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 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 : 0.004 0.043 4594 Z= 0.273 Angle : 0.706 6.743 6233 Z= 0.407 Chirality : 0.049 0.206 654 Planarity : 0.009 0.095 811 Dihedral : 13.651 82.195 1734 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.80 (0.34), residues: 544 helix: -1.27 (0.33), residues: 197 sheet: 0.92 (0.80), residues: 46 loop : -0.10 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP J 735 HIS 0.008 0.002 HIS J 197 PHE 0.019 0.002 PHE J 612 TYR 0.023 0.004 TYR J 284 ARG 0.021 0.003 ARG J 293 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: I 48 LEU cc_start: 0.8993 (mt) cc_final: 0.8675 (mt) REVERT: I 191 LYS cc_start: 0.8398 (pttt) cc_final: 0.7010 (mmtt) REVERT: J 677 ASP cc_start: 0.7923 (t0) cc_final: 0.7552 (t0) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 1.6104 time to fit residues: 164.0271 Evaluate side-chains 67 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 199 ASN J 52 GLN J 628 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.091085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.073529 restraints weight = 7429.638| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.79 r_work: 0.3001 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4594 Z= 0.263 Angle : 0.614 5.786 6233 Z= 0.327 Chirality : 0.045 0.147 654 Planarity : 0.005 0.045 811 Dihedral : 8.112 81.955 649 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.14 % Allowed : 11.56 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.28 (0.35), residues: 544 helix: 0.01 (0.34), residues: 217 sheet: 0.73 (0.82), residues: 46 loop : 0.44 (0.36), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP J 129 HIS 0.004 0.001 HIS I 189 PHE 0.014 0.002 PHE J 612 TYR 0.014 0.002 TYR J 180 ARG 0.005 0.001 ARG J 748 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.400 Fit side-chains REVERT: I 48 LEU cc_start: 0.9134 (mt) cc_final: 0.8876 (mt) REVERT: I 158 GLU cc_start: 0.6732 (mt-10) cc_final: 0.6476 (mt-10) REVERT: I 191 LYS cc_start: 0.8336 (pttt) cc_final: 0.6916 (mmtt) REVERT: J 242 MET cc_start: 0.8762 (tpp) cc_final: 0.8547 (tpp) REVERT: J 635 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.6776 (pm20) REVERT: J 677 ASP cc_start: 0.8107 (t0) cc_final: 0.7894 (t0) outliers start: 10 outliers final: 2 residues processed: 80 average time/residue: 1.6196 time to fit residues: 133.6756 Evaluate side-chains 65 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 635 GLU Chi-restraints excluded: chain J residue 689 THR Chi-restraints excluded: chain J residue 712 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 40 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 42 optimal weight: 0.0770 chunk 11 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 12 optimal weight: 0.0040 chunk 4 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 overall best weight: 0.5750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 199 ASN ** J 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.089214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.071689 restraints weight = 7610.370| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.82 r_work: 0.2958 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4594 Z= 0.241 Angle : 0.570 5.326 6233 Z= 0.302 Chirality : 0.044 0.136 654 Planarity : 0.005 0.044 811 Dihedral : 7.704 82.101 649 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.57 % Allowed : 12.21 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.48 (0.36), residues: 544 helix: 0.41 (0.35), residues: 217 sheet: 0.03 (0.78), residues: 45 loop : 0.48 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 287 HIS 0.004 0.001 HIS I 189 PHE 0.014 0.002 PHE J 612 TYR 0.012 0.001 TYR J 180 ARG 0.003 0.000 ARG J 602 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 48 LEU cc_start: 0.9106 (mt) cc_final: 0.8834 (mt) REVERT: I 191 LYS cc_start: 0.8329 (pttt) cc_final: 0.6892 (mmtt) REVERT: J 174 GLU cc_start: 0.7710 (tt0) cc_final: 0.7502 (tt0) REVERT: J 626 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8220 (mt-10) outliers start: 12 outliers final: 5 residues processed: 68 average time/residue: 1.5471 time to fit residues: 108.8052 Evaluate side-chains 64 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 257 LYS Chi-restraints excluded: chain J residue 626 GLU Chi-restraints excluded: chain J residue 635 GLU Chi-restraints excluded: chain J residue 689 THR Chi-restraints excluded: chain J residue 712 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.0270 chunk 39 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 9 optimal weight: 0.0060 chunk 1 optimal weight: 0.4980 chunk 12 optimal weight: 5.9990 chunk 40 optimal weight: 0.0570 chunk 46 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 overall best weight: 0.2572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 199 ASN ** J 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.091204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.074026 restraints weight = 7643.020| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.82 r_work: 0.3001 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4594 Z= 0.159 Angle : 0.512 6.259 6233 Z= 0.268 Chirality : 0.041 0.134 654 Planarity : 0.004 0.044 811 Dihedral : 7.089 83.820 649 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.36 % Allowed : 13.70 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.85 (0.37), residues: 544 helix: 0.80 (0.36), residues: 223 sheet: 0.57 (0.85), residues: 40 loop : 0.54 (0.38), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 129 HIS 0.005 0.001 HIS J 628 PHE 0.007 0.001 PHE J 612 TYR 0.014 0.001 TYR J 167 ARG 0.002 0.000 ARG J 21 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 48 LEU cc_start: 0.9078 (mt) cc_final: 0.8824 (mt) REVERT: I 191 LYS cc_start: 0.8266 (pttt) cc_final: 0.6853 (mmtt) REVERT: J 165 LEU cc_start: 0.8712 (mt) cc_final: 0.8511 (mp) REVERT: J 174 GLU cc_start: 0.7757 (tt0) cc_final: 0.7556 (tt0) outliers start: 11 outliers final: 5 residues processed: 71 average time/residue: 1.4134 time to fit residues: 103.8064 Evaluate side-chains 65 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 43 LEU Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 635 GLU Chi-restraints excluded: chain J residue 689 THR Chi-restraints excluded: chain J residue 712 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 8 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 53 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 199 ASN ** J 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 237 HIS J 633 ASN J 697 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.088429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.070671 restraints weight = 7796.963| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.88 r_work: 0.2930 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 4594 Z= 0.293 Angle : 0.590 6.116 6233 Z= 0.308 Chirality : 0.044 0.132 654 Planarity : 0.005 0.043 811 Dihedral : 7.601 80.674 649 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.14 % Allowed : 14.35 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.36), residues: 544 helix: 0.77 (0.36), residues: 217 sheet: -0.27 (0.74), residues: 45 loop : 0.41 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J 287 HIS 0.004 0.001 HIS I 189 PHE 0.016 0.002 PHE J 612 TYR 0.013 0.002 TYR J 180 ARG 0.009 0.001 ARG J 293 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 48 LEU cc_start: 0.9034 (mt) cc_final: 0.8772 (mt) REVERT: I 191 LYS cc_start: 0.8310 (pttt) cc_final: 0.6889 (mmtt) outliers start: 10 outliers final: 7 residues processed: 67 average time/residue: 1.5141 time to fit residues: 104.8636 Evaluate side-chains 67 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 99 SER Chi-restraints excluded: chain J residue 257 LYS Chi-restraints excluded: chain J residue 635 GLU Chi-restraints excluded: chain J residue 689 THR Chi-restraints excluded: chain J residue 700 GLU Chi-restraints excluded: chain J residue 712 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 32 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 9 optimal weight: 0.4980 chunk 39 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 199 ASN J 128 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.088847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.071301 restraints weight = 7694.247| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.84 r_work: 0.2951 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4594 Z= 0.246 Angle : 0.563 5.968 6233 Z= 0.294 Chirality : 0.043 0.134 654 Planarity : 0.004 0.042 811 Dihedral : 7.421 82.998 649 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.28 % Allowed : 12.63 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.63 (0.36), residues: 544 helix: 0.80 (0.36), residues: 217 sheet: -0.35 (0.73), residues: 45 loop : 0.41 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 287 HIS 0.003 0.001 HIS I 189 PHE 0.013 0.001 PHE J 612 TYR 0.010 0.001 TYR J 180 ARG 0.008 0.000 ARG J 293 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 60 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 48 LEU cc_start: 0.9077 (mt) cc_final: 0.8808 (mt) REVERT: I 191 LYS cc_start: 0.8302 (pttt) cc_final: 0.6920 (mmtt) REVERT: J 48 ARG cc_start: 0.7874 (mtt-85) cc_final: 0.7489 (mtp180) outliers start: 20 outliers final: 13 residues processed: 74 average time/residue: 1.3851 time to fit residues: 106.1974 Evaluate side-chains 70 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 94 MET Chi-restraints excluded: chain J residue 99 SER Chi-restraints excluded: chain J residue 127 SER Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 225 LEU Chi-restraints excluded: chain J residue 257 LYS Chi-restraints excluded: chain J residue 635 GLU Chi-restraints excluded: chain J residue 689 THR Chi-restraints excluded: chain J residue 700 GLU Chi-restraints excluded: chain J residue 712 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 47 optimal weight: 0.1980 chunk 18 optimal weight: 0.6980 chunk 9 optimal weight: 0.3980 chunk 8 optimal weight: 0.8980 chunk 4 optimal weight: 0.4980 chunk 46 optimal weight: 0.4980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.089833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.072360 restraints weight = 7646.694| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.81 r_work: 0.2976 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4594 Z= 0.211 Angle : 0.555 6.166 6233 Z= 0.289 Chirality : 0.042 0.131 654 Planarity : 0.004 0.043 811 Dihedral : 7.242 84.619 649 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.78 % Allowed : 14.99 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.55 (0.37), residues: 544 helix: 0.74 (0.36), residues: 223 sheet: -0.35 (0.73), residues: 45 loop : 0.34 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 287 HIS 0.004 0.001 HIS J 628 PHE 0.010 0.001 PHE J 612 TYR 0.021 0.001 TYR J 167 ARG 0.008 0.000 ARG J 293 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 48 LEU cc_start: 0.9097 (mt) cc_final: 0.8848 (mt) REVERT: I 191 LYS cc_start: 0.8303 (pttt) cc_final: 0.6946 (mmtt) REVERT: J 48 ARG cc_start: 0.7892 (mtt-85) cc_final: 0.7529 (mtp180) outliers start: 13 outliers final: 10 residues processed: 68 average time/residue: 1.4745 time to fit residues: 103.7319 Evaluate side-chains 68 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 94 MET Chi-restraints excluded: chain J residue 99 SER Chi-restraints excluded: chain J residue 127 SER Chi-restraints excluded: chain J residue 635 GLU Chi-restraints excluded: chain J residue 689 THR Chi-restraints excluded: chain J residue 700 GLU Chi-restraints excluded: chain J residue 712 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 3 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 25 optimal weight: 0.2980 chunk 32 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.089234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.071897 restraints weight = 7622.612| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.79 r_work: 0.2964 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4594 Z= 0.231 Angle : 0.559 6.306 6233 Z= 0.292 Chirality : 0.043 0.135 654 Planarity : 0.004 0.044 811 Dihedral : 7.269 84.035 649 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.57 % Allowed : 15.63 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.51 (0.37), residues: 544 helix: 0.69 (0.36), residues: 223 sheet: -0.26 (0.73), residues: 45 loop : 0.31 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 287 HIS 0.004 0.001 HIS J 628 PHE 0.012 0.001 PHE J 612 TYR 0.009 0.001 TYR J 167 ARG 0.007 0.000 ARG J 293 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 48 LEU cc_start: 0.9109 (mt) cc_final: 0.8877 (mt) REVERT: I 191 LYS cc_start: 0.8314 (pttt) cc_final: 0.6958 (mmtt) outliers start: 12 outliers final: 10 residues processed: 64 average time/residue: 1.4375 time to fit residues: 95.4345 Evaluate side-chains 65 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 94 MET Chi-restraints excluded: chain J residue 99 SER Chi-restraints excluded: chain J residue 635 GLU Chi-restraints excluded: chain J residue 689 THR Chi-restraints excluded: chain J residue 700 GLU Chi-restraints excluded: chain J residue 712 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 10 optimal weight: 0.0670 chunk 40 optimal weight: 0.0670 chunk 46 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 33 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 199 ASN J 66 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.090203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.072975 restraints weight = 7617.764| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.80 r_work: 0.2986 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4594 Z= 0.188 Angle : 0.537 7.345 6233 Z= 0.278 Chirality : 0.042 0.135 654 Planarity : 0.004 0.041 811 Dihedral : 7.026 85.883 649 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.36 % Allowed : 16.92 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.66 (0.37), residues: 544 helix: 0.82 (0.36), residues: 223 sheet: -0.13 (0.73), residues: 45 loop : 0.39 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 287 HIS 0.004 0.001 HIS J 628 PHE 0.009 0.001 PHE J 612 TYR 0.007 0.001 TYR J 180 ARG 0.007 0.000 ARG J 293 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 48 LEU cc_start: 0.9095 (mt) cc_final: 0.8848 (mt) REVERT: I 191 LYS cc_start: 0.8291 (pttt) cc_final: 0.6942 (mmtt) REVERT: J 48 ARG cc_start: 0.7902 (mtt-85) cc_final: 0.7545 (mtp180) REVERT: J 722 GLN cc_start: 0.7474 (OUTLIER) cc_final: 0.7243 (mt0) outliers start: 11 outliers final: 8 residues processed: 64 average time/residue: 1.3993 time to fit residues: 92.9302 Evaluate side-chains 62 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 99 SER Chi-restraints excluded: chain J residue 635 GLU Chi-restraints excluded: chain J residue 689 THR Chi-restraints excluded: chain J residue 712 VAL Chi-restraints excluded: chain J residue 722 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 0.0470 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 0 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.089288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.071882 restraints weight = 7610.011| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.79 r_work: 0.2962 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4594 Z= 0.243 Angle : 0.585 13.159 6233 Z= 0.300 Chirality : 0.043 0.138 654 Planarity : 0.004 0.044 811 Dihedral : 7.200 84.060 649 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.57 % Allowed : 16.92 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.55 (0.37), residues: 544 helix: 0.68 (0.36), residues: 223 sheet: -0.15 (0.73), residues: 45 loop : 0.37 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 287 HIS 0.004 0.001 HIS I 189 PHE 0.012 0.001 PHE J 612 TYR 0.008 0.001 TYR J 210 ARG 0.007 0.000 ARG J 293 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 48 LEU cc_start: 0.9106 (mt) cc_final: 0.8865 (mt) REVERT: I 191 LYS cc_start: 0.8325 (pttt) cc_final: 0.6977 (mmtt) REVERT: J 48 ARG cc_start: 0.7905 (mtt-85) cc_final: 0.7570 (mtp180) REVERT: J 225 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8486 (mt) REVERT: J 722 GLN cc_start: 0.7518 (OUTLIER) cc_final: 0.7286 (mt0) outliers start: 12 outliers final: 9 residues processed: 61 average time/residue: 1.3154 time to fit residues: 83.3872 Evaluate side-chains 64 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 86 MET Chi-restraints excluded: chain J residue 99 SER Chi-restraints excluded: chain J residue 225 LEU Chi-restraints excluded: chain J residue 635 GLU Chi-restraints excluded: chain J residue 689 THR Chi-restraints excluded: chain J residue 712 VAL Chi-restraints excluded: chain J residue 722 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 1.9990 chunk 2 optimal weight: 0.3980 chunk 34 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 46 optimal weight: 0.4980 chunk 26 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 43 optimal weight: 0.0060 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.090069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.072643 restraints weight = 7620.682| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.82 r_work: 0.2976 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4594 Z= 0.205 Angle : 0.566 14.457 6233 Z= 0.290 Chirality : 0.042 0.140 654 Planarity : 0.004 0.041 811 Dihedral : 7.050 85.803 649 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.14 % Allowed : 17.56 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.63 (0.37), residues: 544 helix: 0.75 (0.36), residues: 223 sheet: -0.12 (0.73), residues: 45 loop : 0.41 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 287 HIS 0.004 0.001 HIS J 628 PHE 0.009 0.001 PHE J 612 TYR 0.021 0.001 TYR J 167 ARG 0.007 0.000 ARG J 293 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4497.37 seconds wall clock time: 79 minutes 42.50 seconds (4782.50 seconds total)