Starting phenix.real_space_refine on Tue Feb 3 12:33:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cwp_45969/02_2026/9cwp_45969.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cwp_45969/02_2026/9cwp_45969.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cwp_45969/02_2026/9cwp_45969.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cwp_45969/02_2026/9cwp_45969.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cwp_45969/02_2026/9cwp_45969.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cwp_45969/02_2026/9cwp_45969.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.044 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 10 5.16 5 C 1310 2.51 5 N 343 2.21 5 O 363 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2026 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1496 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 13, 'TRANS': 179} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "K" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 502 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'TRANS': 69} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 11, 'GLN:plan1': 1, 'ASP:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 69 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 0.72, per 1000 atoms: 0.36 Number of scatterers: 2026 At special positions: 0 Unit cell: (48, 57, 75, 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 10 16.00 O 363 8.00 N 343 7.00 C 1310 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.10 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " 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 Links applied NAG-ASN " NAG C 601 " - " ASN C 343 " " NAG C 602 " - " ASN C 354 " Time building additional restraints: 0.17 Conformation dependent library (CDL) restraints added in 79.6 milliseconds 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 498 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 4 sheets defined 41.8% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.896A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 369 Processing helix chain 'C' and resid 386 through 389 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.734A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'K' and resid 2 through 20 Processing helix chain 'K' and resid 21 through 23 No H-bonds generated for 'chain 'K' and resid 21 through 23' Processing helix chain 'K' and resid 25 through 49 removed outlier: 3.696A pdb=" N ALA K 32 " --> pdb=" O GLU K 28 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ILE K 47 " --> pdb=" O MET K 43 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS K 48 " --> pdb=" O LEU K 44 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 70 Processing sheet with id=AA1, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AA3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'C' and resid 473 through 474 97 hydrogen bonds defined for protein. 252 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: 0.28 Time building geometry restraints manager: 0.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 496 1.33 - 1.45: 518 1.45 - 1.57: 1060 1.57 - 1.70: 0 1.70 - 1.82: 12 Bond restraints: 2086 Sorted by residual: bond pdb=" N PRO C 337 " pdb=" CA PRO C 337 " ideal model delta sigma weight residual 1.474 1.440 0.034 1.24e-02 6.50e+03 7.73e+00 bond pdb=" C5 NAG C 602 " pdb=" O5 NAG C 602 " ideal model delta sigma weight residual 1.413 1.467 -0.054 2.00e-02 2.50e+03 7.24e+00 bond pdb=" C5 NAG C 601 " pdb=" O5 NAG C 601 " ideal model delta sigma weight residual 1.413 1.465 -0.052 2.00e-02 2.50e+03 6.65e+00 bond pdb=" CG ASP K 11 " pdb=" OD2 ASP K 11 " ideal model delta sigma weight residual 1.249 1.201 0.048 1.90e-02 2.77e+03 6.29e+00 bond pdb=" N PRO C 412 " pdb=" CA PRO C 412 " ideal model delta sigma weight residual 1.467 1.438 0.029 1.21e-02 6.83e+03 5.69e+00 ... (remaining 2081 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 2461 1.62 - 3.25: 333 3.25 - 4.87: 29 4.87 - 6.50: 21 6.50 - 8.12: 6 Bond angle restraints: 2850 Sorted by residual: angle pdb=" C GLY C 485 " pdb=" N PRO C 486 " pdb=" CA PRO C 486 " ideal model delta sigma weight residual 119.32 127.44 -8.12 1.14e+00 7.69e-01 5.07e+01 angle pdb=" C PHE C 490 " pdb=" N PRO C 491 " pdb=" CA PRO C 491 " ideal model delta sigma weight residual 119.56 126.56 -7.00 1.02e+00 9.61e-01 4.71e+01 angle pdb=" C ARG C 498 " pdb=" N PRO C 499 " pdb=" CA PRO C 499 " ideal model delta sigma weight residual 119.47 127.18 -7.71 1.16e+00 7.43e-01 4.41e+01 angle pdb=" C SER C 383 " pdb=" N PRO C 384 " pdb=" CA PRO C 384 " ideal model delta sigma weight residual 119.28 126.27 -6.99 1.10e+00 8.26e-01 4.03e+01 angle pdb=" C GLN C 506 " pdb=" N PRO C 507 " pdb=" CA PRO C 507 " ideal model delta sigma weight residual 119.76 125.87 -6.11 1.00e+00 1.00e+00 3.74e+01 ... (remaining 2845 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.79: 1170 16.79 - 33.57: 51 33.57 - 50.36: 9 50.36 - 67.14: 6 67.14 - 83.93: 2 Dihedral angle restraints: 1238 sinusoidal: 463 harmonic: 775 Sorted by residual: dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 172.25 -79.25 1 1.00e+01 1.00e-02 7.81e+01 dihedral pdb=" CA ALA C 372 " pdb=" C ALA C 372 " pdb=" N PRO C 373 " pdb=" CA PRO C 373 " ideal model delta harmonic sigma weight residual 180.00 162.37 17.63 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " pdb=" SG CYS C 525 " pdb=" CB CYS C 525 " ideal model delta sinusoidal sigma weight residual 93.00 120.06 -27.06 1 1.00e+01 1.00e-02 1.05e+01 ... (remaining 1235 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 218 0.059 - 0.118: 74 0.118 - 0.177: 9 0.177 - 0.236: 6 0.236 - 0.295: 2 Chirality restraints: 309 Sorted by residual: chirality pdb=" C2 NAG C 602 " pdb=" C1 NAG C 602 " pdb=" C3 NAG C 602 " pdb=" N2 NAG C 602 " both_signs ideal model delta sigma weight residual False -2.49 -2.79 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" C2 NAG C 601 " pdb=" C1 NAG C 601 " pdb=" C3 NAG C 601 " pdb=" N2 NAG C 601 " both_signs ideal model delta sigma weight residual False -2.49 -2.78 0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" C5 NAG C 601 " pdb=" C4 NAG C 601 " pdb=" C6 NAG C 601 " pdb=" O5 NAG C 601 " both_signs ideal model delta sigma weight residual False -2.41 -2.61 0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 306 not shown) Planarity restraints: 373 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 501 " 0.027 2.00e-02 2.50e+03 1.38e-02 3.82e+00 pdb=" CG TYR C 501 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR C 501 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR C 501 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR C 501 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR C 501 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR C 501 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 501 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 489 " 0.022 2.00e-02 2.50e+03 1.25e-02 3.15e+00 pdb=" CG TYR C 489 " -0.007 2.00e-02 2.50e+03 pdb=" CD1 TYR C 489 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR C 489 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR C 489 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR C 489 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR C 489 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR C 489 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 495 " -0.024 2.00e-02 2.50e+03 1.25e-02 3.11e+00 pdb=" CG TYR C 495 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR C 495 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR C 495 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR C 495 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR C 495 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR C 495 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 495 " -0.016 2.00e-02 2.50e+03 ... (remaining 370 not shown) Histogram of nonbonded interaction distances: 2.57 - 3.04: 1216 3.04 - 3.50: 1938 3.50 - 3.97: 3291 3.97 - 4.43: 3973 4.43 - 4.90: 6005 Nonbonded interactions: 16423 Sorted by model distance: nonbonded pdb=" N TYR C 495 " pdb=" O TYR C 495 " model vdw 2.570 2.496 nonbonded pdb=" O LEU K 29 " pdb=" C GLU K 30 " model vdw 2.597 3.270 nonbonded pdb=" NE2 HIS C 505 " pdb=" OD2 ASP K 11 " model vdw 2.600 3.120 nonbonded pdb=" N ASN C 370 " pdb=" N PHE C 371 " model vdw 2.601 2.560 nonbonded pdb=" N GLY C 526 " pdb=" O GLY C 526 " model vdw 2.609 2.496 ... (remaining 16418 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: 11.180 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: 0.020 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 4.310 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 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 : 0.013 0.072 2092 Z= 0.714 Angle : 1.244 8.120 2864 Z= 0.835 Chirality : 0.064 0.295 309 Planarity : 0.005 0.014 371 Dihedral : 11.464 83.928 728 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.54 % Allowed : 1.63 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.47), residues: 259 helix: -1.21 (0.46), residues: 97 sheet: 0.74 (0.71), residues: 45 loop : -0.11 (0.52), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 509 TYR 0.027 0.005 TYR C 501 PHE 0.011 0.003 PHE C 374 TRP 0.014 0.003 TRP C 353 HIS 0.002 0.001 HIS K 68 Details of bonding type rmsd covalent geometry : bond 0.01269 ( 2086) covalent geometry : angle 1.23450 ( 2850) SS BOND : bond 0.03763 ( 4) SS BOND : angle 3.02972 ( 8) hydrogen bonds : bond 0.17410 ( 97) hydrogen bonds : angle 8.74795 ( 252) link_NAG-ASN : bond 0.05410 ( 2) link_NAG-ASN : angle 1.76119 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.046 Fit side-chains revert: symmetry clash REVERT: K 34 TYR cc_start: 0.8285 (t80) cc_final: 0.7795 (t80) outliers start: 1 outliers final: 0 residues processed: 53 average time/residue: 0.0448 time to fit residues: 2.7548 Evaluate side-chains 41 residues out of total 231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 12 optimal weight: 0.3980 chunk 24 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 1 optimal weight: 0.1980 chunk 8 optimal weight: 0.0980 chunk 16 optimal weight: 0.0970 chunk 15 optimal weight: 0.1980 chunk 25 optimal weight: 0.5980 chunk 9 optimal weight: 0.2980 chunk 11 optimal weight: 0.4980 chunk 18 optimal weight: 0.6980 overall best weight: 0.1778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.178661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.146686 restraints weight = 2388.008| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.37 r_work: 0.3447 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2092 Z= 0.127 Angle : 0.569 7.398 2864 Z= 0.287 Chirality : 0.044 0.195 309 Planarity : 0.004 0.032 371 Dihedral : 4.210 15.156 329 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.17 % Allowed : 9.78 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.50), residues: 259 helix: -0.21 (0.51), residues: 103 sheet: 1.01 (0.79), residues: 43 loop : -0.01 (0.53), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 357 TYR 0.015 0.001 TYR C 495 PHE 0.010 0.001 PHE C 490 TRP 0.009 0.001 TRP C 436 HIS 0.001 0.000 HIS K 22 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 2086) covalent geometry : angle 0.55325 ( 2850) SS BOND : bond 0.00377 ( 4) SS BOND : angle 2.16355 ( 8) hydrogen bonds : bond 0.04249 ( 97) hydrogen bonds : angle 6.26323 ( 252) link_NAG-ASN : bond 0.00396 ( 2) link_NAG-ASN : angle 1.70174 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.045 Fit side-chains REVERT: C 451 TYR cc_start: 0.8358 (m-80) cc_final: 0.8139 (m-80) REVERT: C 489 TYR cc_start: 0.7858 (m-80) cc_final: 0.7652 (m-80) REVERT: K 8 HIS cc_start: 0.7250 (OUTLIER) cc_final: 0.6871 (m-70) REVERT: K 34 TYR cc_start: 0.8325 (t80) cc_final: 0.7729 (t80) outliers start: 4 outliers final: 2 residues processed: 50 average time/residue: 0.0392 time to fit residues: 2.2910 Evaluate side-chains 44 residues out of total 231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain K residue 8 HIS Chi-restraints excluded: chain K residue 14 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 9 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 405 ASN K 18 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.171688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.140340 restraints weight = 2433.173| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.32 r_work: 0.3360 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 2092 Z= 0.294 Angle : 0.710 7.785 2864 Z= 0.357 Chirality : 0.048 0.184 309 Planarity : 0.005 0.037 371 Dihedral : 4.956 14.735 329 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.63 % Allowed : 14.67 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.50), residues: 259 helix: -0.42 (0.53), residues: 98 sheet: 0.73 (0.80), residues: 43 loop : -0.67 (0.51), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 457 TYR 0.024 0.002 TYR C 495 PHE 0.010 0.002 PHE C 515 TRP 0.010 0.002 TRP C 436 HIS 0.003 0.001 HIS K 22 Details of bonding type rmsd covalent geometry : bond 0.00690 ( 2086) covalent geometry : angle 0.68510 ( 2850) SS BOND : bond 0.00758 ( 4) SS BOND : angle 3.27760 ( 8) hydrogen bonds : bond 0.04619 ( 97) hydrogen bonds : angle 6.82778 ( 252) link_NAG-ASN : bond 0.00098 ( 2) link_NAG-ASN : angle 1.84889 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.046 Fit side-chains REVERT: C 451 TYR cc_start: 0.8557 (m-80) cc_final: 0.8357 (m-80) REVERT: C 474 GLN cc_start: 0.8121 (tt0) cc_final: 0.5658 (mm-40) REVERT: K 34 TYR cc_start: 0.8417 (t80) cc_final: 0.7636 (t80) outliers start: 3 outliers final: 3 residues processed: 47 average time/residue: 0.0425 time to fit residues: 2.3774 Evaluate side-chains 46 residues out of total 231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 506 GLN Chi-restraints excluded: chain K residue 14 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 2 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 22 optimal weight: 0.0870 chunk 24 optimal weight: 0.7980 chunk 7 optimal weight: 0.0040 chunk 9 optimal weight: 0.4980 chunk 15 optimal weight: 0.7980 overall best weight: 0.3970 ------------------------------------------------------------------------------- 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 = 0.3917 r_free = 0.3917 target = 0.174594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.144350 restraints weight = 2373.941| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.15 r_work: 0.3400 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 2092 Z= 0.193 Angle : 0.619 8.648 2864 Z= 0.307 Chirality : 0.045 0.170 309 Planarity : 0.004 0.036 371 Dihedral : 4.503 17.083 329 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.63 % Allowed : 14.13 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.50), residues: 259 helix: -0.38 (0.52), residues: 98 sheet: 0.72 (0.80), residues: 43 loop : -0.81 (0.52), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 457 TYR 0.020 0.001 TYR C 495 PHE 0.006 0.001 PHE C 400 TRP 0.008 0.001 TRP C 436 HIS 0.003 0.001 HIS K 22 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 2086) covalent geometry : angle 0.60038 ( 2850) SS BOND : bond 0.01042 ( 4) SS BOND : angle 2.67328 ( 8) hydrogen bonds : bond 0.04027 ( 97) hydrogen bonds : angle 6.46037 ( 252) link_NAG-ASN : bond 0.00087 ( 2) link_NAG-ASN : angle 1.53790 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.077 Fit side-chains REVERT: C 451 TYR cc_start: 0.8559 (m-80) cc_final: 0.8349 (m-80) REVERT: C 474 GLN cc_start: 0.8111 (tt0) cc_final: 0.5622 (mm-40) REVERT: K 34 TYR cc_start: 0.8381 (t80) cc_final: 0.7729 (t80) outliers start: 3 outliers final: 0 residues processed: 45 average time/residue: 0.0686 time to fit residues: 3.5805 Evaluate side-chains 41 residues out of total 231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 1 optimal weight: 0.9990 chunk 0 optimal weight: 0.5980 chunk 4 optimal weight: 0.3980 chunk 12 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 chunk 10 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3902 r_free = 0.3902 target = 0.173184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.142257 restraints weight = 2387.810| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.24 r_work: 0.3358 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 2092 Z= 0.246 Angle : 0.648 8.450 2864 Z= 0.327 Chirality : 0.045 0.157 309 Planarity : 0.005 0.039 371 Dihedral : 4.809 19.063 329 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.26 % Allowed : 13.59 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.49), residues: 259 helix: -0.56 (0.51), residues: 99 sheet: 0.69 (0.80), residues: 43 loop : -1.01 (0.51), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 457 TYR 0.021 0.002 TYR C 495 PHE 0.011 0.002 PHE C 392 TRP 0.006 0.001 TRP C 436 HIS 0.003 0.001 HIS K 22 Details of bonding type rmsd covalent geometry : bond 0.00583 ( 2086) covalent geometry : angle 0.62727 ( 2850) SS BOND : bond 0.00788 ( 4) SS BOND : angle 2.85742 ( 8) hydrogen bonds : bond 0.04281 ( 97) hydrogen bonds : angle 6.64866 ( 252) link_NAG-ASN : bond 0.00078 ( 2) link_NAG-ASN : angle 1.61716 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.076 Fit side-chains REVERT: C 474 GLN cc_start: 0.8131 (tt0) cc_final: 0.5733 (mm-40) REVERT: K 34 TYR cc_start: 0.8360 (t80) cc_final: 0.7683 (t80) outliers start: 6 outliers final: 2 residues processed: 49 average time/residue: 0.0784 time to fit residues: 4.4402 Evaluate side-chains 45 residues out of total 231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 389 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 4 optimal weight: 0.4980 chunk 23 optimal weight: 0.9980 chunk 22 optimal weight: 0.0980 chunk 9 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 6 optimal weight: 0.4980 chunk 16 optimal weight: 0.0670 chunk 8 optimal weight: 0.0980 chunk 7 optimal weight: 0.4980 chunk 2 optimal weight: 0.0980 chunk 14 optimal weight: 0.4980 overall best weight: 0.1718 ------------------------------------------------------------------------------- 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 = 0.3965 r_free = 0.3965 target = 0.178795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.147875 restraints weight = 2371.575| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.28 r_work: 0.3430 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2092 Z= 0.119 Angle : 0.537 7.591 2864 Z= 0.264 Chirality : 0.044 0.161 309 Planarity : 0.004 0.034 371 Dihedral : 4.073 17.404 329 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 4.35 % Allowed : 13.59 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.50), residues: 259 helix: -0.05 (0.54), residues: 92 sheet: 0.94 (0.81), residues: 43 loop : -0.67 (0.51), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 457 TYR 0.012 0.001 TYR C 495 PHE 0.007 0.001 PHE C 392 TRP 0.008 0.001 TRP C 436 HIS 0.003 0.001 HIS K 22 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 2086) covalent geometry : angle 0.52628 ( 2850) SS BOND : bond 0.00602 ( 4) SS BOND : angle 1.84677 ( 8) hydrogen bonds : bond 0.03634 ( 97) hydrogen bonds : angle 6.05266 ( 252) link_NAG-ASN : bond 0.00204 ( 2) link_NAG-ASN : angle 1.32097 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.091 Fit side-chains REVERT: C 369 TYR cc_start: 0.6063 (OUTLIER) cc_final: 0.5007 (m-80) REVERT: C 474 GLN cc_start: 0.8112 (tt0) cc_final: 0.5567 (mm-40) REVERT: K 34 TYR cc_start: 0.8368 (t80) cc_final: 0.8001 (t80) outliers start: 8 outliers final: 3 residues processed: 46 average time/residue: 0.0480 time to fit residues: 2.6256 Evaluate side-chains 43 residues out of total 231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 442 ASP Chi-restraints excluded: chain K residue 36 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 1 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 25 optimal weight: 0.1980 chunk 6 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 334 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.171155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.139741 restraints weight = 2424.327| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.24 r_work: 0.3338 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 2092 Z= 0.294 Angle : 0.692 8.125 2864 Z= 0.348 Chirality : 0.048 0.148 309 Planarity : 0.005 0.040 371 Dihedral : 4.941 20.436 329 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.80 % Allowed : 16.30 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.50), residues: 259 helix: -0.32 (0.53), residues: 92 sheet: 0.58 (0.81), residues: 44 loop : -1.07 (0.52), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 457 TYR 0.020 0.002 TYR C 495 PHE 0.009 0.002 PHE C 400 TRP 0.005 0.002 TRP K 38 HIS 0.003 0.001 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00693 ( 2086) covalent geometry : angle 0.67380 ( 2850) SS BOND : bond 0.00993 ( 4) SS BOND : angle 2.73894 ( 8) hydrogen bonds : bond 0.04538 ( 97) hydrogen bonds : angle 6.81563 ( 252) link_NAG-ASN : bond 0.00095 ( 2) link_NAG-ASN : angle 1.63875 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.076 Fit side-chains REVERT: C 369 TYR cc_start: 0.6269 (OUTLIER) cc_final: 0.5070 (m-80) REVERT: C 439 ASN cc_start: 0.7691 (t0) cc_final: 0.7424 (t0) REVERT: C 474 GLN cc_start: 0.8187 (tt0) cc_final: 0.5753 (mm-40) REVERT: K 34 TYR cc_start: 0.8340 (t80) cc_final: 0.7640 (t80) outliers start: 7 outliers final: 1 residues processed: 51 average time/residue: 0.0640 time to fit residues: 3.7916 Evaluate side-chains 46 residues out of total 231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 369 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 13 optimal weight: 0.9980 chunk 11 optimal weight: 0.0060 chunk 10 optimal weight: 0.1980 chunk 3 optimal weight: 0.4980 chunk 15 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 1 optimal weight: 0.1980 chunk 6 optimal weight: 0.1980 chunk 5 optimal weight: 0.0270 chunk 14 optimal weight: 0.0870 chunk 0 optimal weight: 0.2980 overall best weight: 0.1032 ------------------------------------------------------------------------------- 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 = 0.3974 r_free = 0.3974 target = 0.179412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.148983 restraints weight = 2373.643| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.14 r_work: 0.3460 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2092 Z= 0.106 Angle : 0.523 6.469 2864 Z= 0.260 Chirality : 0.044 0.157 309 Planarity : 0.004 0.035 371 Dihedral : 4.054 17.532 329 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.72 % Allowed : 16.30 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.50), residues: 259 helix: -0.17 (0.54), residues: 92 sheet: 0.92 (0.80), residues: 43 loop : -0.63 (0.53), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 457 TYR 0.009 0.001 TYR C 495 PHE 0.006 0.001 PHE C 392 TRP 0.008 0.001 TRP C 436 HIS 0.002 0.001 HIS K 22 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 2086) covalent geometry : angle 0.51500 ( 2850) SS BOND : bond 0.00865 ( 4) SS BOND : angle 1.53902 ( 8) hydrogen bonds : bond 0.03476 ( 97) hydrogen bonds : angle 6.00213 ( 252) link_NAG-ASN : bond 0.00288 ( 2) link_NAG-ASN : angle 1.27172 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.046 Fit side-chains REVERT: C 369 TYR cc_start: 0.6052 (OUTLIER) cc_final: 0.4800 (m-80) REVERT: C 439 ASN cc_start: 0.7661 (t0) cc_final: 0.7377 (t0) REVERT: C 474 GLN cc_start: 0.8152 (tt0) cc_final: 0.5645 (mm-40) REVERT: K 34 TYR cc_start: 0.8350 (t80) cc_final: 0.7984 (t80) outliers start: 5 outliers final: 1 residues processed: 44 average time/residue: 0.0479 time to fit residues: 2.4949 Evaluate side-chains 43 residues out of total 231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain K residue 36 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 9 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 4 optimal weight: 0.4980 chunk 5 optimal weight: 0.3980 chunk 20 optimal weight: 0.7980 chunk 25 optimal weight: 0.0670 chunk 1 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 overall best weight: 0.4518 ------------------------------------------------------------------------------- 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 = 0.3913 r_free = 0.3913 target = 0.173430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.142423 restraints weight = 2395.980| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.26 r_work: 0.3367 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 2092 Z= 0.212 Angle : 0.631 9.177 2864 Z= 0.311 Chirality : 0.046 0.148 309 Planarity : 0.004 0.040 371 Dihedral : 4.466 19.846 329 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.26 % Allowed : 17.39 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.51), residues: 259 helix: -0.31 (0.53), residues: 93 sheet: 0.98 (0.83), residues: 43 loop : -0.80 (0.54), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 457 TYR 0.018 0.001 TYR C 495 PHE 0.007 0.002 PHE C 429 TRP 0.004 0.001 TRP C 436 HIS 0.002 0.001 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00495 ( 2086) covalent geometry : angle 0.61622 ( 2850) SS BOND : bond 0.00755 ( 4) SS BOND : angle 2.39435 ( 8) hydrogen bonds : bond 0.04032 ( 97) hydrogen bonds : angle 6.51010 ( 252) link_NAG-ASN : bond 0.00147 ( 2) link_NAG-ASN : angle 1.50809 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.079 Fit side-chains REVERT: C 369 TYR cc_start: 0.6161 (OUTLIER) cc_final: 0.4949 (m-80) REVERT: C 439 ASN cc_start: 0.7734 (t0) cc_final: 0.7437 (t0) REVERT: C 474 GLN cc_start: 0.8154 (tt0) cc_final: 0.5754 (mm-40) REVERT: K 34 TYR cc_start: 0.8273 (t80) cc_final: 0.7763 (t80) outliers start: 6 outliers final: 1 residues processed: 46 average time/residue: 0.0715 time to fit residues: 3.7965 Evaluate side-chains 44 residues out of total 231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain K residue 36 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 3 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 13 optimal weight: 0.0170 chunk 11 optimal weight: 0.9980 chunk 14 optimal weight: 0.0870 chunk 17 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 10 optimal weight: 0.4980 chunk 20 optimal weight: 0.5980 chunk 1 optimal weight: 0.0980 overall best weight: 0.2596 ------------------------------------------------------------------------------- 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 = 0.3944 r_free = 0.3944 target = 0.176430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.145974 restraints weight = 2413.419| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.17 r_work: 0.3440 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2092 Z= 0.148 Angle : 0.577 8.645 2864 Z= 0.285 Chirality : 0.045 0.149 309 Planarity : 0.004 0.039 371 Dihedral : 4.268 18.851 329 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.09 % Allowed : 19.02 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.51), residues: 259 helix: -0.28 (0.54), residues: 93 sheet: 0.95 (0.82), residues: 43 loop : -0.68 (0.54), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 457 TYR 0.015 0.001 TYR C 495 PHE 0.005 0.001 PHE C 392 TRP 0.006 0.001 TRP C 436 HIS 0.002 0.001 HIS K 22 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 2086) covalent geometry : angle 0.56559 ( 2850) SS BOND : bond 0.00679 ( 4) SS BOND : angle 2.00444 ( 8) hydrogen bonds : bond 0.03731 ( 97) hydrogen bonds : angle 6.30568 ( 252) link_NAG-ASN : bond 0.00180 ( 2) link_NAG-ASN : angle 1.31818 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.078 Fit side-chains REVERT: C 369 TYR cc_start: 0.5952 (OUTLIER) cc_final: 0.4717 (m-80) REVERT: C 439 ASN cc_start: 0.7653 (t0) cc_final: 0.7336 (t0) REVERT: C 474 GLN cc_start: 0.8178 (tt0) cc_final: 0.5762 (mm-40) REVERT: K 34 TYR cc_start: 0.8365 (t80) cc_final: 0.7915 (t80) outliers start: 2 outliers final: 1 residues processed: 43 average time/residue: 0.0651 time to fit residues: 3.2677 Evaluate side-chains 44 residues out of total 231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain K residue 36 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 5 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 8 optimal weight: 0.4980 chunk 19 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 4 optimal weight: 0.0870 chunk 1 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 0 optimal weight: 0.6980 chunk 15 optimal weight: 0.0770 overall best weight: 0.3916 ------------------------------------------------------------------------------- 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 = 0.3932 r_free = 0.3932 target = 0.175211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.145047 restraints weight = 2419.290| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.21 r_work: 0.3407 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 2092 Z= 0.193 Angle : 0.617 8.731 2864 Z= 0.306 Chirality : 0.045 0.150 309 Planarity : 0.004 0.041 371 Dihedral : 4.478 19.837 329 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.63 % Allowed : 18.48 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.51), residues: 259 helix: -0.35 (0.53), residues: 93 sheet: 0.69 (0.82), residues: 44 loop : -0.67 (0.55), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 457 TYR 0.018 0.001 TYR C 495 PHE 0.006 0.001 PHE C 392 TRP 0.005 0.001 TRP C 436 HIS 0.003 0.001 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 2086) covalent geometry : angle 0.60301 ( 2850) SS BOND : bond 0.00734 ( 4) SS BOND : angle 2.24338 ( 8) hydrogen bonds : bond 0.03968 ( 97) hydrogen bonds : angle 6.49254 ( 252) link_NAG-ASN : bond 0.00124 ( 2) link_NAG-ASN : angle 1.42547 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 953.74 seconds wall clock time: 16 minutes 58.87 seconds (1018.87 seconds total)