Starting phenix.real_space_refine on Tue Feb 11 10:18:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p76_17519/02_2025/8p76_17519.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p76_17519/02_2025/8p76_17519.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p76_17519/02_2025/8p76_17519.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p76_17519/02_2025/8p76_17519.map" model { file = "/net/cci-nas-00/data/ceres_data/8p76_17519/02_2025/8p76_17519.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p76_17519/02_2025/8p76_17519.cif" } resolution = 2.0 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= -0.000 sd= 0.001 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 31 5.16 5 C 3296 2.51 5 N 870 2.21 5 O 1064 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 5261 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 512 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 5, 'TRANS': 59} Chain: "I" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2281 Unusual residues: {'ACE': 1} Classifications: {'peptide': 279, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 264} Chain breaks: 1 Chain: "J" Number of atoms: 2283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2283 Classifications: {'peptide': 286} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 267} Chain breaks: 2 Chain: "J" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'X1W': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "I" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 66 Classifications: {'water': 66} Link IDs: {None: 65} Chain: "J" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 63 Classifications: {'water': 63} Link IDs: {None: 62} Time building chain proxies: 4.69, per 1000 atoms: 0.89 Number of scatterers: 5261 At special positions: 0 Unit cell: (84.7875, 93.3375, 68.4, 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 31 16.00 O 1064 8.00 N 870 7.00 C 3296 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: 1.38 Conformation dependent library (CDL) restraints added in 586.7 milliseconds 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1196 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 3 sheets defined 62.1% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'H' and resid 262 through 275 removed outlier: 4.474A pdb=" N GLY H 267 " --> pdb=" O GLU H 264 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY H 270 " --> pdb=" O GLY H 267 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N TYR H 271 " --> pdb=" O ARG H 268 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU H 272 " --> pdb=" O LEU H 269 " (cutoff:3.500A) Processing helix chain 'H' and resid 279 through 286 Processing helix chain 'H' and resid 288 through 302 removed outlier: 3.872A pdb=" N ALA H 292 " --> pdb=" O THR H 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 1 through 4 Processing helix chain 'I' and resid 5 through 11 Processing helix chain 'I' and resid 15 through 36 Processing helix chain 'I' and resid 49 through 70 Processing helix chain 'I' and resid 76 through 93 removed outlier: 3.899A pdb=" N ASN I 93 " --> pdb=" O ARG I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 117 Processing helix chain 'I' and resid 121 through 127 Processing helix chain 'I' and resid 132 through 154 removed outlier: 4.706A pdb=" N LEU I 148 " --> pdb=" O LEU I 144 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LEU I 149 " --> pdb=" O GLU I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 163 through 178 Processing helix chain 'I' and resid 183 through 187 Processing helix chain 'I' and resid 188 through 201 removed outlier: 3.640A pdb=" N THR I 201 " --> pdb=" O ARG I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 206 Processing helix chain 'I' and resid 208 through 224 Processing helix chain 'I' and resid 228 through 234 removed outlier: 3.502A pdb=" N LEU I 232 " --> pdb=" O MET I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 240 Processing helix chain 'I' and resid 241 through 261 Processing helix chain 'I' and resid 266 through 283 Processing helix chain 'J' and resid 56 through 67 Processing helix chain 'J' and resid 98 through 104 Processing helix chain 'J' and resid 110 through 131 Processing helix chain 'J' and resid 175 through 179 Processing helix chain 'J' and resid 180 through 185 Processing helix chain 'J' and resid 192 through 209 Processing helix chain 'J' and resid 217 through 230 Processing helix chain 'J' and resid 239 through 243 Processing helix chain 'J' and resid 256 through 261 Processing helix chain 'J' and resid 265 through 276 Processing helix chain 'J' and resid 285 through 292 Processing helix chain 'J' and resid 292 through 297 removed outlier: 3.877A pdb=" N SER J 296 " --> pdb=" O MET J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 303 through 307 Processing sheet with id=AA1, first strand: chain 'J' and resid 13 through 20 removed outlier: 6.042A pdb=" N LYS J 14 " --> pdb=" O ARG J 30 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ARG J 30 " --> pdb=" O LYS J 14 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N VAL J 26 " --> pdb=" O LEU J 18 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ASP J 92 " --> pdb=" O LEU J 77 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N LEU J 77 " --> pdb=" O ASP J 92 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 96 through 97 Processing sheet with id=AA3, first strand: chain 'J' and resid 133 through 134 279 hydrogen bonds defined for protein. 765 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: 1.34 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1642 1.34 - 1.46: 1183 1.46 - 1.58: 2358 1.58 - 1.70: 3 1.70 - 1.82: 49 Bond restraints: 5235 Sorted by residual: bond pdb=" C08 X1W J 401 " pdb=" N09 X1W J 401 " ideal model delta sigma weight residual 1.337 1.490 -0.153 2.00e-02 2.50e+03 5.86e+01 bond pdb=" C26 X1W J 401 " pdb=" C27 X1W J 401 " ideal model delta sigma weight residual 1.502 1.610 -0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" C02 X1W J 401 " pdb=" C04 X1W J 401 " ideal model delta sigma weight residual 1.498 1.600 -0.102 2.00e-02 2.50e+03 2.61e+01 bond pdb=" C18 X1W J 401 " pdb=" N19 X1W J 401 " ideal model delta sigma weight residual 1.356 1.454 -0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" C20 X1W J 401 " pdb=" C24 X1W J 401 " ideal model delta sigma weight residual 1.528 1.621 -0.093 2.00e-02 2.50e+03 2.17e+01 ... (remaining 5230 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 6917 1.63 - 3.25: 128 3.25 - 4.88: 27 4.88 - 6.51: 8 6.51 - 8.14: 5 Bond angle restraints: 7085 Sorted by residual: angle pdb=" CG ARG I 279 " pdb=" CD ARG I 279 " pdb=" NE ARG I 279 " ideal model delta sigma weight residual 112.00 118.65 -6.65 2.20e+00 2.07e-01 9.15e+00 angle pdb=" CA MET I 237 " pdb=" CB MET I 237 " pdb=" CG MET I 237 " ideal model delta sigma weight residual 114.10 119.90 -5.80 2.00e+00 2.50e-01 8.42e+00 angle pdb=" CB MET I 237 " pdb=" CG MET I 237 " pdb=" SD MET I 237 " ideal model delta sigma weight residual 112.70 120.84 -8.14 3.00e+00 1.11e-01 7.35e+00 angle pdb=" CB MET J 94 " pdb=" CG MET J 94 " pdb=" SD MET J 94 " ideal model delta sigma weight residual 112.70 120.06 -7.36 3.00e+00 1.11e-01 6.01e+00 angle pdb=" CA GLU I 137 " pdb=" CB GLU I 137 " pdb=" CG GLU I 137 " ideal model delta sigma weight residual 114.10 118.98 -4.88 2.00e+00 2.50e-01 5.96e+00 ... (remaining 7080 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 2751 17.71 - 35.43: 317 35.43 - 53.14: 72 53.14 - 70.86: 23 70.86 - 88.57: 8 Dihedral angle restraints: 3171 sinusoidal: 1324 harmonic: 1847 Sorted by residual: dihedral pdb=" CA TYR I 91 " pdb=" C TYR I 91 " pdb=" N LEU I 92 " pdb=" CA LEU I 92 " ideal model delta harmonic sigma weight residual 180.00 161.45 18.55 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CG ARG I 279 " pdb=" CD ARG I 279 " pdb=" NE ARG I 279 " pdb=" CZ ARG I 279 " ideal model delta sinusoidal sigma weight residual 90.00 39.27 50.73 2 1.50e+01 4.44e-03 1.28e+01 dihedral pdb=" CB GLU I 141 " pdb=" CG GLU I 141 " pdb=" CD GLU I 141 " pdb=" OE1 GLU I 141 " ideal model delta sinusoidal sigma weight residual 0.00 -88.57 88.57 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 3168 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 612 0.045 - 0.090: 129 0.090 - 0.136: 33 0.136 - 0.181: 1 0.181 - 0.226: 2 Chirality restraints: 777 Sorted by residual: chirality pdb=" C20 X1W J 401 " pdb=" C21 X1W J 401 " pdb=" C24 X1W J 401 " pdb=" N19 X1W J 401 " both_signs ideal model delta sigma weight residual False -2.45 -2.68 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" C24 X1W J 401 " pdb=" C20 X1W J 401 " pdb=" C23 X1W J 401 " pdb=" O25 X1W J 401 " both_signs ideal model delta sigma weight residual False -2.71 -2.90 0.19 2.00e-01 2.50e+01 9.16e-01 chirality pdb=" CA MET I 237 " pdb=" N MET I 237 " pdb=" C MET I 237 " pdb=" CB MET I 237 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.75e-01 ... (remaining 774 not shown) Planarity restraints: 904 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP I 116 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" CG ASP I 116 " 0.029 2.00e-02 2.50e+03 pdb=" OD1 ASP I 116 " -0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP I 116 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG I 165 " 0.024 5.00e-02 4.00e+02 3.60e-02 2.07e+00 pdb=" N PRO I 166 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO I 166 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO I 166 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS J 139 " 0.022 5.00e-02 4.00e+02 3.36e-02 1.80e+00 pdb=" N PRO J 140 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO J 140 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO J 140 " 0.019 5.00e-02 4.00e+02 ... (remaining 901 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1258 2.79 - 3.32: 5206 3.32 - 3.84: 9884 3.84 - 4.37: 11771 4.37 - 4.90: 18853 Nonbonded interactions: 46972 Sorted by model distance: nonbonded pdb=" O TRP J 177 " pdb=" O HOH J 501 " model vdw 2.258 3.040 nonbonded pdb=" O GLY H 286 " pdb=" O HOH H 401 " model vdw 2.261 3.040 nonbonded pdb=" O ARG I 89 " pdb=" O HOH I 401 " model vdw 2.287 3.040 nonbonded pdb=" O HOH J 504 " pdb=" O HOH J 549 " model vdw 2.304 3.040 nonbonded pdb=" O HOH J 554 " pdb=" O HOH J 557 " model vdw 2.306 3.040 ... (remaining 46967 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: 3.690 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 16.830 Find NCS groups from input model: 0.060 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:14.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.153 5235 Z= 0.287 Angle : 0.615 8.136 7085 Z= 0.298 Chirality : 0.041 0.226 777 Planarity : 0.004 0.036 904 Dihedral : 16.638 88.570 1975 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 0.90 % Allowed : 16.43 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.34), residues: 618 helix: 2.09 (0.29), residues: 335 sheet: 2.90 (1.24), residues: 14 loop : 0.29 (0.39), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 132 HIS 0.003 0.001 HIS J 131 PHE 0.019 0.002 PHE I 30 TYR 0.016 0.001 TYR I 60 ARG 0.009 0.001 ARG I 279 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 98 time to evaluate : 0.577 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 103 average time/residue: 1.5994 time to fit residues: 170.1649 Evaluate side-chains 96 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 92 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 145 GLU Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 228 THR Chi-restraints excluded: chain J residue 302 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 26 optimal weight: 0.6980 chunk 16 optimal weight: 7.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 36 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN I 136 GLN I 142 GLN I 155 ASN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.169027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.151422 restraints weight = 4813.226| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 0.87 r_work: 0.3721 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.3632 rms_B_bonded: 2.30 restraints_weight: 0.2500 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.0627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5235 Z= 0.210 Angle : 0.590 6.964 7085 Z= 0.302 Chirality : 0.042 0.139 777 Planarity : 0.005 0.034 904 Dihedral : 6.449 82.183 720 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 1.62 % Allowed : 14.44 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.35), residues: 618 helix: 1.93 (0.29), residues: 341 sheet: 2.29 (1.35), residues: 15 loop : 0.31 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 132 HIS 0.006 0.001 HIS J 131 PHE 0.020 0.002 PHE I 30 TYR 0.017 0.002 TYR I 2 ARG 0.006 0.001 ARG I 23 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.607 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 104 average time/residue: 1.5805 time to fit residues: 170.0981 Evaluate side-chains 98 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 95 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain J residue 292 MET Chi-restraints excluded: chain J residue 302 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 28 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 25 optimal weight: 0.3980 chunk 49 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN I 18 GLN I 142 GLN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.169961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.152234 restraints weight = 4867.049| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 0.88 r_work: 0.3733 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.3644 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.0703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5235 Z= 0.178 Angle : 0.552 6.575 7085 Z= 0.283 Chirality : 0.040 0.139 777 Planarity : 0.004 0.036 904 Dihedral : 5.251 55.771 714 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 0.72 % Allowed : 16.06 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.35), residues: 618 helix: 1.99 (0.28), residues: 343 sheet: 2.26 (1.40), residues: 15 loop : 0.23 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 132 HIS 0.006 0.001 HIS J 131 PHE 0.018 0.002 PHE I 30 TYR 0.016 0.002 TYR I 91 ARG 0.005 0.001 ARG I 279 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 100 time to evaluate : 0.585 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 102 average time/residue: 1.5778 time to fit residues: 166.3131 Evaluate side-chains 94 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 91 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain J residue 292 MET Chi-restraints excluded: chain J residue 302 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN I 142 GLN I 155 ASN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 297 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.166503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.148563 restraints weight = 4942.162| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 0.88 r_work: 0.3688 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.3597 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.0950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5235 Z= 0.344 Angle : 0.708 7.400 7085 Z= 0.362 Chirality : 0.046 0.148 777 Planarity : 0.006 0.041 904 Dihedral : 5.554 57.754 714 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.73 % Rotamer: Outliers : 1.62 % Allowed : 15.52 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.34), residues: 618 helix: 1.39 (0.28), residues: 347 sheet: 0.72 (1.05), residues: 25 loop : -0.02 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP J 132 HIS 0.009 0.002 HIS J 131 PHE 0.022 0.003 PHE I 30 TYR 0.025 0.003 TYR I 2 ARG 0.013 0.001 ARG I 23 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.577 Fit side-chains REVERT: I 33 LYS cc_start: 0.7253 (ttpp) cc_final: 0.6793 (mptt) REVERT: J 227 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6949 (tt0) outliers start: 9 outliers final: 6 residues processed: 94 average time/residue: 1.6246 time to fit residues: 157.8482 Evaluate side-chains 96 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 145 GLU Chi-restraints excluded: chain I residue 239 LYS Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain J residue 292 MET Chi-restraints excluded: chain J residue 302 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 57 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 36 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 60 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 18 GLN I 142 GLN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.170239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.152475 restraints weight = 4862.150| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 0.88 r_work: 0.3738 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.3648 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.0798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5235 Z= 0.165 Angle : 0.554 7.397 7085 Z= 0.283 Chirality : 0.040 0.141 777 Planarity : 0.004 0.036 904 Dihedral : 5.249 55.223 714 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 1.44 % Allowed : 15.70 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.34), residues: 618 helix: 1.96 (0.28), residues: 342 sheet: 2.30 (1.43), residues: 15 loop : 0.12 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 132 HIS 0.005 0.001 HIS J 131 PHE 0.017 0.002 PHE I 30 TYR 0.017 0.002 TYR I 60 ARG 0.006 0.001 ARG I 279 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.668 Fit side-chains REVERT: J 227 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6918 (tt0) outliers start: 8 outliers final: 4 residues processed: 100 average time/residue: 1.5808 time to fit residues: 163.4227 Evaluate side-chains 95 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain J residue 251 SER Chi-restraints excluded: chain J residue 292 MET Chi-restraints excluded: chain J residue 302 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 14 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 35 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 39 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN I 18 GLN I 142 GLN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.169423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.151541 restraints weight = 4887.483| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 0.88 r_work: 0.3725 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.3635 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5235 Z= 0.190 Angle : 0.570 7.638 7085 Z= 0.291 Chirality : 0.041 0.140 777 Planarity : 0.004 0.035 904 Dihedral : 5.257 55.715 714 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.73 % Rotamer: Outliers : 1.26 % Allowed : 15.70 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.34), residues: 618 helix: 1.94 (0.28), residues: 343 sheet: 2.34 (1.43), residues: 15 loop : 0.14 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 132 HIS 0.006 0.001 HIS J 131 PHE 0.017 0.002 PHE I 30 TYR 0.016 0.002 TYR I 91 ARG 0.006 0.001 ARG I 279 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.604 Fit side-chains REVERT: H 268 ARG cc_start: 0.7080 (ptp90) cc_final: 0.6865 (ptp90) REVERT: I 33 LYS cc_start: 0.7316 (ttpp) cc_final: 0.6825 (mptt) REVERT: J 227 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6928 (tt0) outliers start: 7 outliers final: 6 residues processed: 101 average time/residue: 1.5867 time to fit residues: 165.6983 Evaluate side-chains 98 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 145 GLU Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain J residue 251 SER Chi-restraints excluded: chain J residue 292 MET Chi-restraints excluded: chain J residue 302 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 7 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 54 optimal weight: 0.5980 chunk 45 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 44 optimal weight: 0.0870 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 overall best weight: 1.1160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN I 18 GLN I 142 GLN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.169396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.151739 restraints weight = 4806.924| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 0.87 r_work: 0.3726 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3636 rms_B_bonded: 2.32 restraints_weight: 0.2500 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.0849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5235 Z= 0.195 Angle : 0.586 7.954 7085 Z= 0.299 Chirality : 0.041 0.141 777 Planarity : 0.005 0.035 904 Dihedral : 5.253 55.889 714 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 1.26 % Allowed : 16.06 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.34), residues: 618 helix: 1.93 (0.28), residues: 343 sheet: 2.28 (1.41), residues: 15 loop : 0.12 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 132 HIS 0.006 0.001 HIS J 131 PHE 0.017 0.002 PHE I 30 TYR 0.016 0.002 TYR I 91 ARG 0.007 0.001 ARG I 279 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.569 Fit side-chains REVERT: H 268 ARG cc_start: 0.7117 (ptp90) cc_final: 0.6885 (ptp90) REVERT: I 33 LYS cc_start: 0.7271 (ttpp) cc_final: 0.6790 (mptt) REVERT: J 227 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6935 (tt0) outliers start: 7 outliers final: 5 residues processed: 95 average time/residue: 1.6440 time to fit residues: 161.5409 Evaluate side-chains 95 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain J residue 251 SER Chi-restraints excluded: chain J residue 292 MET Chi-restraints excluded: chain J residue 302 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 26 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 4 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 142 GLN I 155 ASN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.169003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.151154 restraints weight = 4863.634| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 0.88 r_work: 0.3719 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.3629 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.0851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5235 Z= 0.218 Angle : 0.622 8.271 7085 Z= 0.316 Chirality : 0.042 0.142 777 Planarity : 0.005 0.034 904 Dihedral : 5.299 56.191 714 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.27 % Favored : 97.57 % Rotamer: Outliers : 1.62 % Allowed : 15.88 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.34), residues: 618 helix: 1.86 (0.28), residues: 343 sheet: 0.49 (1.05), residues: 26 loop : 0.06 (0.41), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 132 HIS 0.007 0.001 HIS J 131 PHE 0.017 0.002 PHE I 30 TYR 0.017 0.002 TYR I 2 ARG 0.007 0.001 ARG I 279 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.636 Fit side-chains REVERT: H 268 ARG cc_start: 0.7148 (ptp90) cc_final: 0.6902 (ptp90) REVERT: I 33 LYS cc_start: 0.7275 (ttpp) cc_final: 0.6779 (mptt) REVERT: J 227 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6951 (tt0) outliers start: 9 outliers final: 4 residues processed: 97 average time/residue: 1.6609 time to fit residues: 166.4471 Evaluate side-chains 94 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain J residue 251 SER Chi-restraints excluded: chain J residue 292 MET Chi-restraints excluded: chain J residue 302 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 0 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 GLN I 142 GLN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.167543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.149689 restraints weight = 4800.326| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 0.87 r_work: 0.3704 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3613 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.0963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5235 Z= 0.297 Angle : 0.706 9.820 7085 Z= 0.358 Chirality : 0.044 0.145 777 Planarity : 0.005 0.036 904 Dihedral : 5.451 56.949 714 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.27 % Favored : 97.57 % Rotamer: Outliers : 1.81 % Allowed : 15.88 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.34), residues: 618 helix: 1.62 (0.28), residues: 342 sheet: 0.39 (1.03), residues: 26 loop : -0.07 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP J 132 HIS 0.009 0.002 HIS J 131 PHE 0.019 0.002 PHE I 30 TYR 0.023 0.003 TYR I 2 ARG 0.011 0.001 ARG I 23 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.645 Fit side-chains REVERT: H 268 ARG cc_start: 0.7134 (ptp90) cc_final: 0.6891 (ptp90) REVERT: I 33 LYS cc_start: 0.7304 (ttpp) cc_final: 0.6814 (mptt) REVERT: I 63 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.7332 (mmm160) REVERT: J 227 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6964 (tt0) outliers start: 10 outliers final: 5 residues processed: 99 average time/residue: 1.6018 time to fit residues: 164.0856 Evaluate side-chains 99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 102 ARG Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain J residue 251 SER Chi-restraints excluded: chain J residue 292 MET Chi-restraints excluded: chain J residue 302 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 41 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 32 optimal weight: 0.3980 chunk 56 optimal weight: 0.3980 chunk 36 optimal weight: 7.9990 chunk 59 optimal weight: 0.0770 chunk 28 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 18 GLN I 142 GLN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.170599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.152839 restraints weight = 4897.780| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 0.88 r_work: 0.3741 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.3651 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.0891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5235 Z= 0.173 Angle : 0.598 8.629 7085 Z= 0.304 Chirality : 0.041 0.144 777 Planarity : 0.004 0.036 904 Dihedral : 5.284 55.040 714 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 1.08 % Allowed : 16.43 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.34), residues: 618 helix: 2.06 (0.28), residues: 337 sheet: 0.50 (1.06), residues: 26 loop : 0.05 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 132 HIS 0.005 0.001 HIS J 131 PHE 0.015 0.002 PHE I 30 TYR 0.020 0.002 TYR H 287 ARG 0.009 0.001 ARG I 279 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.616 Fit side-chains REVERT: I 33 LYS cc_start: 0.7255 (ttpp) cc_final: 0.6754 (mptt) REVERT: I 63 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.7237 (mmm160) REVERT: J 94 MET cc_start: 0.7624 (mmm) cc_final: 0.7389 (mmm) REVERT: J 227 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6970 (tt0) outliers start: 6 outliers final: 4 residues processed: 96 average time/residue: 1.5766 time to fit residues: 156.5442 Evaluate side-chains 96 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain J residue 251 SER Chi-restraints excluded: chain J residue 292 MET Chi-restraints excluded: chain J residue 302 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 15 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 35 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 22 optimal weight: 0.0980 chunk 47 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN I 142 GLN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.171416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.153730 restraints weight = 4914.996| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 0.88 r_work: 0.3753 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.3664 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5235 Z= 0.173 Angle : 0.596 8.598 7085 Z= 0.303 Chirality : 0.041 0.141 777 Planarity : 0.004 0.037 904 Dihedral : 5.217 54.609 714 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 0.90 % Allowed : 16.79 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.35), residues: 618 helix: 2.13 (0.29), residues: 337 sheet: 0.46 (1.05), residues: 26 loop : 0.10 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 132 HIS 0.004 0.001 HIS J 131 PHE 0.014 0.002 PHE I 30 TYR 0.020 0.002 TYR H 287 ARG 0.008 0.001 ARG I 279 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5685.67 seconds wall clock time: 100 minutes 45.26 seconds (6045.26 seconds total)