Starting phenix.real_space_refine on Fri Dec 27 10:39:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sk2_25170/12_2024/7sk2_25170.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sk2_25170/12_2024/7sk2_25170.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sk2_25170/12_2024/7sk2_25170.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sk2_25170/12_2024/7sk2_25170.map" model { file = "/net/cci-nas-00/data/ceres_data/7sk2_25170/12_2024/7sk2_25170.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sk2_25170/12_2024/7sk2_25170.cif" } resolution = 3.82 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= 0.019 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 35 5.16 5 C 2788 2.51 5 N 651 2.21 5 O 703 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 4177 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4152 Classifications: {'peptide': 532} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 22, 'TRANS': 509} Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 37 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'TGI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.15, per 1000 atoms: 0.75 Number of scatterers: 4177 At special positions: 0 Unit cell: (83.739, 73.17, 77.235, 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 35 16.00 O 703 8.00 N 651 7.00 C 2788 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 173 " distance=2.03 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: 1.02 Conformation dependent library (CDL) restraints added in 478.8 milliseconds 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 972 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 1 sheets defined 75.6% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 47 through 57 removed outlier: 3.559A pdb=" N MET A 55 " --> pdb=" O PHE A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 68 Processing helix chain 'A' and resid 68 through 78 Processing helix chain 'A' and resid 85 through 93 Processing helix chain 'A' and resid 93 through 109 Processing helix chain 'A' and resid 113 through 118 removed outlier: 3.927A pdb=" N LEU A 118 " --> pdb=" O VAL A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 153 removed outlier: 4.167A pdb=" N GLY A 126 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU A 151 " --> pdb=" O ALA A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'A' and resid 211 through 230 removed outlier: 3.758A pdb=" N CYS A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TRP A 230 " --> pdb=" O TYR A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 237 removed outlier: 3.646A pdb=" N TRP A 235 " --> pdb=" O GLY A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 259 removed outlier: 3.791A pdb=" N ILE A 252 " --> pdb=" O TYR A 248 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE A 253 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU A 254 " --> pdb=" O MET A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 273 removed outlier: 3.940A pdb=" N GLY A 267 " --> pdb=" O GLY A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 280 removed outlier: 4.106A pdb=" N SER A 280 " --> pdb=" O ARG A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 296 removed outlier: 3.585A pdb=" N ILE A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 310 Processing helix chain 'A' and resid 315 through 349 removed outlier: 3.501A pdb=" N ASP A 319 " --> pdb=" O ASN A 315 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE A 322 " --> pdb=" O ARG A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 358 removed outlier: 3.522A pdb=" N VAL A 356 " --> pdb=" O SER A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 362 No H-bonds generated for 'chain 'A' and resid 360 through 362' Processing helix chain 'A' and resid 363 through 374 Proline residue: A 369 - end of helix Processing helix chain 'A' and resid 377 through 410 removed outlier: 3.919A pdb=" N SER A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 418 Processing helix chain 'A' and resid 423 through 431 Processing helix chain 'A' and resid 431 through 440 removed outlier: 6.303A pdb=" N SER A 437 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ASN A 438 " --> pdb=" O ILE A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 454 Processing helix chain 'A' and resid 457 through 472 Processing helix chain 'A' and resid 476 through 489 removed outlier: 4.423A pdb=" N ASP A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 502 Processing helix chain 'A' and resid 502 through 518 Processing helix chain 'A' and resid 530 through 559 removed outlier: 3.559A pdb=" N SER A 543 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER A 544 " --> pdb=" O MET A 540 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ILE A 548 " --> pdb=" O SER A 544 " (cutoff:3.500A) Proline residue: A 549 - end of helix Processing helix chain 'A' and resid 562 through 569 removed outlier: 4.235A pdb=" N ARG A 566 " --> pdb=" O SER A 562 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE A 567 " --> pdb=" O LEU A 563 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 523 through 524 256 hydrogen bonds defined for protein. 750 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.97 Time building geometry restraints manager: 1.14 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: 1211 1.34 - 1.46: 1142 1.46 - 1.58: 1904 1.58 - 1.70: 4 1.70 - 1.82: 52 Bond restraints: 4313 Sorted by residual: bond pdb=" C03 TGI A 601 " pdb=" C07 TGI A 601 " ideal model delta sigma weight residual 1.468 1.538 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C03 TGI A 601 " pdb=" S04 TGI A 601 " ideal model delta sigma weight residual 1.744 1.690 0.054 2.00e-02 2.50e+03 7.17e+00 bond pdb=" C07 TGI A 601 " pdb=" C20 TGI A 601 " ideal model delta sigma weight residual 1.480 1.531 -0.051 2.00e-02 2.50e+03 6.49e+00 bond pdb=" C20 TGI A 601 " pdb=" S24 TGI A 601 " ideal model delta sigma weight residual 1.737 1.687 0.050 2.00e-02 2.50e+03 6.16e+00 bond pdb=" C14 TGI A 601 " pdb=" C15 TGI A 601 " ideal model delta sigma weight residual 1.539 1.494 0.045 2.00e-02 2.50e+03 4.98e+00 ... (remaining 4308 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 5608 2.19 - 4.38: 209 4.38 - 6.58: 43 6.58 - 8.77: 16 8.77 - 10.96: 7 Bond angle restraints: 5883 Sorted by residual: angle pdb=" C ILE A 377 " pdb=" N SER A 378 " pdb=" CA SER A 378 " ideal model delta sigma weight residual 120.58 127.09 -6.51 1.32e+00 5.74e-01 2.43e+01 angle pdb=" CB LYS A 350 " pdb=" CG LYS A 350 " pdb=" CD LYS A 350 " ideal model delta sigma weight residual 111.30 122.26 -10.96 2.30e+00 1.89e-01 2.27e+01 angle pdb=" CA VAL A 58 " pdb=" CB VAL A 58 " pdb=" CG1 VAL A 58 " ideal model delta sigma weight residual 110.40 117.16 -6.76 1.70e+00 3.46e-01 1.58e+01 angle pdb=" C SER A 302 " pdb=" N LEU A 303 " pdb=" CA LEU A 303 " ideal model delta sigma weight residual 121.54 129.03 -7.49 1.91e+00 2.74e-01 1.54e+01 angle pdb=" C LEU A 416 " pdb=" N ARG A 417 " pdb=" CA ARG A 417 " ideal model delta sigma weight residual 122.06 115.23 6.83 1.86e+00 2.89e-01 1.35e+01 ... (remaining 5878 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.93: 2204 16.93 - 33.86: 179 33.86 - 50.80: 45 50.80 - 67.73: 4 67.73 - 84.66: 4 Dihedral angle restraints: 2436 sinusoidal: 906 harmonic: 1530 Sorted by residual: dihedral pdb=" CA PHE A 480 " pdb=" C PHE A 480 " pdb=" N TYR A 481 " pdb=" CA TYR A 481 " ideal model delta harmonic sigma weight residual 180.00 155.99 24.01 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA GLN A 199 " pdb=" C GLN A 199 " pdb=" N MET A 200 " pdb=" CA MET A 200 " ideal model delta harmonic sigma weight residual -180.00 -159.15 -20.85 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA ALA A 130 " pdb=" C ALA A 130 " pdb=" N VAL A 131 " pdb=" CA VAL A 131 " ideal model delta harmonic sigma weight residual -180.00 -159.94 -20.06 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 2433 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 379 0.039 - 0.079: 170 0.079 - 0.118: 60 0.118 - 0.157: 24 0.157 - 0.197: 9 Chirality restraints: 642 Sorted by residual: chirality pdb=" CB VAL A 546 " pdb=" CA VAL A 546 " pdb=" CG1 VAL A 546 " pdb=" CG2 VAL A 546 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.66e-01 chirality pdb=" CB ILE A 341 " pdb=" CA ILE A 341 " pdb=" CG1 ILE A 341 " pdb=" CG2 ILE A 341 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.43e-01 chirality pdb=" CA SER A 378 " pdb=" N SER A 378 " pdb=" C SER A 378 " pdb=" CB SER A 378 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.06e-01 ... (remaining 639 not shown) Planarity restraints: 722 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 137 " -0.016 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C ASN A 137 " 0.057 2.00e-02 2.50e+03 pdb=" O ASN A 137 " -0.022 2.00e-02 2.50e+03 pdb=" N ILE A 138 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 136 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.17e+00 pdb=" C LEU A 136 " -0.052 2.00e-02 2.50e+03 pdb=" O LEU A 136 " 0.020 2.00e-02 2.50e+03 pdb=" N ASN A 137 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 138 " 0.015 2.00e-02 2.50e+03 3.02e-02 9.09e+00 pdb=" C ILE A 138 " -0.052 2.00e-02 2.50e+03 pdb=" O ILE A 138 " 0.020 2.00e-02 2.50e+03 pdb=" N TYR A 139 " 0.017 2.00e-02 2.50e+03 ... (remaining 719 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 815 2.77 - 3.30: 4247 3.30 - 3.83: 7327 3.83 - 4.37: 8299 4.37 - 4.90: 13716 Nonbonded interactions: 34404 Sorted by model distance: nonbonded pdb=" OH TYR A 296 " pdb=" OG SER A 328 " model vdw 2.235 3.040 nonbonded pdb=" O VAL A 142 " pdb=" OG SER A 145 " model vdw 2.250 3.040 nonbonded pdb=" O PHE A 92 " pdb=" OG1 THR A 504 " model vdw 2.264 3.040 nonbonded pdb=" O PHE A 450 " pdb=" OG SER A 454 " model vdw 2.265 3.040 nonbonded pdb=" O SER A 437 " pdb=" OG1 THR A 440 " model vdw 2.285 3.040 ... (remaining 34399 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.750 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 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 0.070 4313 Z= 0.338 Angle : 1.059 10.959 5883 Z= 0.545 Chirality : 0.055 0.197 642 Planarity : 0.006 0.044 722 Dihedral : 13.666 84.661 1461 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.34), residues: 530 helix: -1.32 (0.26), residues: 346 sheet: None (None), residues: 0 loop : -2.27 (0.44), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 230 HIS 0.001 0.000 HIS A 347 PHE 0.037 0.003 PHE A 480 TYR 0.039 0.003 TYR A 452 ARG 0.005 0.001 ARG A 195 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 MET cc_start: 0.7822 (tmm) cc_final: 0.7527 (tmm) REVERT: A 283 GLU cc_start: 0.8133 (pp20) cc_final: 0.7926 (pp20) REVERT: A 292 ILE cc_start: 0.8583 (mm) cc_final: 0.8317 (mm) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.1420 time to fit residues: 24.5489 Evaluate side-chains 110 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 4.9990 chunk 40 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 GLN A 196 ASN A 483 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4313 Z= 0.234 Angle : 0.719 7.802 5883 Z= 0.374 Chirality : 0.043 0.146 642 Planarity : 0.005 0.031 722 Dihedral : 6.675 44.938 599 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.82 % Allowed : 11.74 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.37), residues: 530 helix: -0.66 (0.26), residues: 361 sheet: None (None), residues: 0 loop : -1.82 (0.52), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 230 HIS 0.009 0.003 HIS A 347 PHE 0.017 0.002 PHE A 462 TYR 0.024 0.002 TYR A 139 ARG 0.004 0.001 ARG A 566 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 ASN cc_start: 0.8306 (m-40) cc_final: 0.7730 (m-40) REVERT: A 174 PHE cc_start: 0.5961 (p90) cc_final: 0.5733 (p90) REVERT: A 179 MET cc_start: 0.4264 (pmm) cc_final: 0.4047 (pmm) REVERT: A 200 MET cc_start: 0.6736 (tpt) cc_final: 0.6335 (mmm) REVERT: A 283 GLU cc_start: 0.8233 (pp20) cc_final: 0.7497 (pp20) REVERT: A 287 ASP cc_start: 0.8021 (m-30) cc_final: 0.7727 (m-30) REVERT: A 321 ILE cc_start: 0.8289 (pt) cc_final: 0.8082 (pt) REVERT: A 479 ARG cc_start: 0.7656 (ptt180) cc_final: 0.7405 (ptt180) REVERT: A 527 TYR cc_start: 0.7636 (t80) cc_final: 0.7383 (t80) REVERT: A 545 MET cc_start: 0.8383 (mmt) cc_final: 0.8144 (mmt) outliers start: 12 outliers final: 10 residues processed: 133 average time/residue: 0.1287 time to fit residues: 22.6675 Evaluate side-chains 128 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 526 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 26 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4313 Z= 0.237 Angle : 0.698 7.876 5883 Z= 0.360 Chirality : 0.043 0.192 642 Planarity : 0.004 0.029 722 Dihedral : 6.355 43.528 599 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.05 % Allowed : 18.08 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.37), residues: 530 helix: -0.43 (0.26), residues: 362 sheet: None (None), residues: 0 loop : -1.53 (0.53), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 168 HIS 0.008 0.003 HIS A 347 PHE 0.024 0.002 PHE A 385 TYR 0.021 0.002 TYR A 139 ARG 0.004 0.001 ARG A 566 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 0.452 Fit side-chains REVERT: A 77 ASN cc_start: 0.8382 (m-40) cc_final: 0.7869 (m-40) REVERT: A 198 HIS cc_start: 0.7859 (m90) cc_final: 0.7144 (m90) REVERT: A 283 GLU cc_start: 0.8260 (pp20) cc_final: 0.7547 (pp20) REVERT: A 287 ASP cc_start: 0.8119 (m-30) cc_final: 0.7484 (m-30) REVERT: A 321 ILE cc_start: 0.8357 (pt) cc_final: 0.8055 (pt) REVERT: A 452 TYR cc_start: 0.8026 (t80) cc_final: 0.7594 (t80) REVERT: A 479 ARG cc_start: 0.7613 (ptt180) cc_final: 0.7355 (ptt180) REVERT: A 527 TYR cc_start: 0.7764 (t80) cc_final: 0.7556 (t80) outliers start: 13 outliers final: 11 residues processed: 132 average time/residue: 0.1303 time to fit residues: 22.5505 Evaluate side-chains 131 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 523 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 47 optimal weight: 5.9990 chunk 36 optimal weight: 0.0070 chunk 25 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 77 ASN A 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4313 Z= 0.213 Angle : 0.691 7.899 5883 Z= 0.354 Chirality : 0.042 0.161 642 Planarity : 0.004 0.026 722 Dihedral : 6.218 42.154 599 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 3.29 % Allowed : 19.95 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.37), residues: 530 helix: -0.29 (0.27), residues: 362 sheet: None (None), residues: 0 loop : -1.46 (0.53), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 168 HIS 0.008 0.002 HIS A 347 PHE 0.018 0.002 PHE A 385 TYR 0.020 0.002 TYR A 139 ARG 0.002 0.000 ARG A 479 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.460 Fit side-chains REVERT: A 77 ASN cc_start: 0.8287 (m110) cc_final: 0.7864 (m-40) REVERT: A 168 TRP cc_start: 0.6193 (p90) cc_final: 0.5976 (p90) REVERT: A 174 PHE cc_start: 0.6826 (p90) cc_final: 0.5736 (p90) REVERT: A 283 GLU cc_start: 0.8256 (pp20) cc_final: 0.7550 (pp20) REVERT: A 287 ASP cc_start: 0.8085 (m-30) cc_final: 0.7432 (m-30) REVERT: A 321 ILE cc_start: 0.8331 (pt) cc_final: 0.8018 (pt) REVERT: A 450 PHE cc_start: 0.8035 (m-10) cc_final: 0.7755 (m-10) REVERT: A 452 TYR cc_start: 0.8005 (t80) cc_final: 0.7582 (t80) outliers start: 14 outliers final: 11 residues processed: 127 average time/residue: 0.1330 time to fit residues: 22.1241 Evaluate side-chains 130 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 523 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 0.0370 chunk 21 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.6064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 77 ASN A 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4313 Z= 0.258 Angle : 0.720 8.162 5883 Z= 0.368 Chirality : 0.043 0.149 642 Planarity : 0.004 0.029 722 Dihedral : 6.220 40.082 599 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.76 % Allowed : 22.30 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.37), residues: 530 helix: -0.33 (0.27), residues: 367 sheet: None (None), residues: 0 loop : -1.34 (0.54), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 193 HIS 0.009 0.003 HIS A 347 PHE 0.023 0.002 PHE A 404 TYR 0.023 0.002 TYR A 152 ARG 0.001 0.000 ARG A 351 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 ASN cc_start: 0.8413 (m-40) cc_final: 0.8044 (m-40) REVERT: A 283 GLU cc_start: 0.8311 (pp20) cc_final: 0.7613 (pp20) REVERT: A 287 ASP cc_start: 0.8143 (m-30) cc_final: 0.7432 (m-30) REVERT: A 321 ILE cc_start: 0.8298 (pt) cc_final: 0.7960 (pt) REVERT: A 452 TYR cc_start: 0.8035 (t80) cc_final: 0.7595 (t80) outliers start: 16 outliers final: 15 residues processed: 128 average time/residue: 0.1472 time to fit residues: 24.6185 Evaluate side-chains 132 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 417 ARG Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 538 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 10 optimal weight: 0.3980 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 51 optimal weight: 0.0030 chunk 42 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 16 optimal weight: 0.3980 chunk 26 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 77 ASN A 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4313 Z= 0.177 Angle : 0.684 9.042 5883 Z= 0.345 Chirality : 0.042 0.136 642 Planarity : 0.004 0.027 722 Dihedral : 5.920 39.449 599 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.99 % Allowed : 23.47 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.37), residues: 530 helix: -0.01 (0.27), residues: 354 sheet: None (None), residues: 0 loop : -1.25 (0.51), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 168 HIS 0.008 0.002 HIS A 347 PHE 0.020 0.002 PHE A 385 TYR 0.020 0.001 TYR A 139 ARG 0.002 0.000 ARG A 211 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 ASN cc_start: 0.8241 (m110) cc_final: 0.7877 (m-40) REVERT: A 146 TRP cc_start: 0.8416 (m-10) cc_final: 0.8053 (m-10) REVERT: A 283 GLU cc_start: 0.8239 (pp20) cc_final: 0.7582 (pp20) REVERT: A 287 ASP cc_start: 0.8046 (m-30) cc_final: 0.7389 (m-30) REVERT: A 321 ILE cc_start: 0.8260 (pt) cc_final: 0.7993 (pt) REVERT: A 452 TYR cc_start: 0.8002 (t80) cc_final: 0.7572 (t80) REVERT: A 462 PHE cc_start: 0.8529 (t80) cc_final: 0.8298 (t80) REVERT: A 479 ARG cc_start: 0.7640 (ptt180) cc_final: 0.7373 (ptt180) outliers start: 17 outliers final: 12 residues processed: 130 average time/residue: 0.1428 time to fit residues: 24.0104 Evaluate side-chains 132 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 417 ARG Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 538 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 0.7980 chunk 37 optimal weight: 0.0170 chunk 43 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 51 optimal weight: 0.0020 chunk 31 optimal weight: 0.0060 chunk 23 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.2842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 438 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4313 Z= 0.170 Angle : 0.703 9.121 5883 Z= 0.351 Chirality : 0.042 0.217 642 Planarity : 0.003 0.026 722 Dihedral : 5.787 39.378 599 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.52 % Allowed : 24.65 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.37), residues: 530 helix: 0.05 (0.27), residues: 363 sheet: None (None), residues: 0 loop : -1.24 (0.52), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 193 HIS 0.010 0.003 HIS A 347 PHE 0.021 0.001 PHE A 385 TYR 0.019 0.001 TYR A 139 ARG 0.003 0.000 ARG A 195 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ASN cc_start: 0.8092 (m110) cc_final: 0.7860 (m-40) REVERT: A 283 GLU cc_start: 0.8220 (pp20) cc_final: 0.7605 (pp20) REVERT: A 287 ASP cc_start: 0.7953 (m-30) cc_final: 0.7288 (m-30) REVERT: A 321 ILE cc_start: 0.8206 (pt) cc_final: 0.7971 (pt) REVERT: A 391 MET cc_start: 0.7850 (mtt) cc_final: 0.7597 (mtt) REVERT: A 452 TYR cc_start: 0.7979 (t80) cc_final: 0.7564 (t80) REVERT: A 462 PHE cc_start: 0.8414 (t80) cc_final: 0.8180 (t80) REVERT: A 479 ARG cc_start: 0.7555 (ptt180) cc_final: 0.7276 (ptt180) outliers start: 15 outliers final: 12 residues processed: 130 average time/residue: 0.1377 time to fit residues: 23.2353 Evaluate side-chains 131 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 417 ARG Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 538 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 9 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4313 Z= 0.197 Angle : 0.729 9.973 5883 Z= 0.365 Chirality : 0.043 0.216 642 Planarity : 0.003 0.025 722 Dihedral : 5.719 39.142 599 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.05 % Allowed : 26.29 % Favored : 70.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.37), residues: 530 helix: 0.07 (0.27), residues: 364 sheet: None (None), residues: 0 loop : -1.17 (0.53), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 193 HIS 0.008 0.002 HIS A 347 PHE 0.023 0.002 PHE A 385 TYR 0.020 0.001 TYR A 139 ARG 0.002 0.000 ARG A 211 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: A 77 ASN cc_start: 0.8212 (m110) cc_final: 0.7885 (m-40) REVERT: A 283 GLU cc_start: 0.8264 (pp20) cc_final: 0.7596 (pp20) REVERT: A 287 ASP cc_start: 0.8011 (m-30) cc_final: 0.7412 (m-30) REVERT: A 321 ILE cc_start: 0.8218 (pt) cc_final: 0.7970 (pt) REVERT: A 391 MET cc_start: 0.7893 (mtt) cc_final: 0.7653 (mtt) REVERT: A 452 TYR cc_start: 0.8020 (t80) cc_final: 0.7580 (t80) REVERT: A 479 ARG cc_start: 0.7579 (ptt180) cc_final: 0.7294 (ptt180) outliers start: 13 outliers final: 12 residues processed: 127 average time/residue: 0.1387 time to fit residues: 22.9339 Evaluate side-chains 131 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 417 ARG Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 538 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 20 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 45 optimal weight: 0.0970 chunk 47 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4313 Z= 0.193 Angle : 0.737 10.617 5883 Z= 0.368 Chirality : 0.044 0.211 642 Planarity : 0.004 0.025 722 Dihedral : 5.672 38.785 599 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.76 % Allowed : 26.06 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.38), residues: 530 helix: 0.23 (0.28), residues: 353 sheet: None (None), residues: 0 loop : -1.12 (0.52), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 168 HIS 0.009 0.002 HIS A 347 PHE 0.028 0.002 PHE A 404 TYR 0.025 0.001 TYR A 551 ARG 0.003 0.000 ARG A 419 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.470 Fit side-chains revert: symmetry clash REVERT: A 77 ASN cc_start: 0.8163 (m110) cc_final: 0.7884 (m-40) REVERT: A 200 MET cc_start: 0.6689 (tpt) cc_final: 0.6383 (mmm) REVERT: A 283 GLU cc_start: 0.8253 (pp20) cc_final: 0.7664 (pp20) REVERT: A 287 ASP cc_start: 0.7972 (m-30) cc_final: 0.7322 (m-30) REVERT: A 321 ILE cc_start: 0.8208 (pt) cc_final: 0.7978 (pt) REVERT: A 391 MET cc_start: 0.7836 (mtt) cc_final: 0.7611 (mtt) REVERT: A 452 TYR cc_start: 0.7986 (t80) cc_final: 0.7564 (t80) REVERT: A 479 ARG cc_start: 0.7568 (ptt180) cc_final: 0.7270 (ptt180) outliers start: 16 outliers final: 13 residues processed: 128 average time/residue: 0.1365 time to fit residues: 22.9973 Evaluate side-chains 131 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 417 ARG Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 538 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 52 optimal weight: 0.0870 chunk 48 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 4 optimal weight: 0.3980 chunk 32 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 44 optimal weight: 0.3980 chunk 12 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4313 Z= 0.187 Angle : 0.779 14.015 5883 Z= 0.383 Chirality : 0.044 0.238 642 Planarity : 0.004 0.026 722 Dihedral : 5.566 38.597 599 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.58 % Allowed : 28.17 % Favored : 69.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.38), residues: 530 helix: 0.32 (0.28), residues: 350 sheet: None (None), residues: 0 loop : -1.07 (0.51), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 500 HIS 0.008 0.002 HIS A 347 PHE 0.028 0.002 PHE A 447 TYR 0.022 0.001 TYR A 527 ARG 0.003 0.000 ARG A 419 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: A 77 ASN cc_start: 0.8097 (m110) cc_final: 0.7875 (m-40) REVERT: A 200 MET cc_start: 0.6514 (tpt) cc_final: 0.5995 (mmm) REVERT: A 283 GLU cc_start: 0.8236 (pp20) cc_final: 0.7685 (pp20) REVERT: A 287 ASP cc_start: 0.7951 (m-30) cc_final: 0.7386 (m-30) REVERT: A 321 ILE cc_start: 0.8200 (pt) cc_final: 0.7998 (pt) REVERT: A 391 MET cc_start: 0.7837 (mtt) cc_final: 0.7611 (mtt) REVERT: A 479 ARG cc_start: 0.7548 (ptt180) cc_final: 0.7230 (ptt180) outliers start: 11 outliers final: 11 residues processed: 124 average time/residue: 0.1316 time to fit residues: 21.4481 Evaluate side-chains 132 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 417 ARG Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 538 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 11 optimal weight: 0.0050 chunk 42 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 36 optimal weight: 0.2980 chunk 2 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.164787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.142720 restraints weight = 9208.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.146455 restraints weight = 5662.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.149064 restraints weight = 3971.753| |-----------------------------------------------------------------------------| r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 4313 Z= 0.188 Angle : 0.772 11.701 5883 Z= 0.379 Chirality : 0.044 0.241 642 Planarity : 0.004 0.025 722 Dihedral : 5.554 38.428 599 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.29 % Allowed : 27.93 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.37), residues: 530 helix: 0.21 (0.27), residues: 362 sheet: None (None), residues: 0 loop : -1.17 (0.53), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 500 HIS 0.008 0.002 HIS A 347 PHE 0.025 0.001 PHE A 294 TYR 0.037 0.002 TYR A 551 ARG 0.003 0.000 ARG A 419 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1284.01 seconds wall clock time: 24 minutes 2.51 seconds (1442.51 seconds total)