Starting phenix.real_space_refine on Fri Aug 22 13:00:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jsw_36628/08_2025/8jsw_36628.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jsw_36628/08_2025/8jsw_36628.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jsw_36628/08_2025/8jsw_36628.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jsw_36628/08_2025/8jsw_36628.map" model { file = "/net/cci-nas-00/data/ceres_data/8jsw_36628/08_2025/8jsw_36628.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jsw_36628/08_2025/8jsw_36628.cif" } resolution = 2.84 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= -0.002 sd= 0.123 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 27 5.16 5 C 1906 2.51 5 N 443 2.21 5 O 483 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2859 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2846 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 23, 'TRANS': 360} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'SRO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.94, per 1000 atoms: 0.33 Number of scatterers: 2859 At special positions: 0 Unit cell: (57.8, 63.75, 71.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 27 16.00 O 483 8.00 N 443 7.00 C 1906 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.33 Conformation dependent library (CDL) restraints added in 128.4 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 692 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 0 sheets defined 92.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 19 through 54 removed outlier: 3.608A pdb=" N LEU A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Proline residue: A 42 - end of helix Proline residue: A 45 - end of helix Processing helix chain 'A' and resid 129 through 157 removed outlier: 4.508A pdb=" N LYS A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ALA A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Proline residue: A 147 - end of helix removed outlier: 3.988A pdb=" N ASN A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 179 Processing helix chain 'A' and resid 181 through 211 Processing helix chain 'A' and resid 213 through 246 removed outlier: 3.661A pdb=" N GLY A 218 " --> pdb=" O ASP A 214 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A 223 " --> pdb=" O ASN A 219 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 249 through 270 Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 291 through 323 removed outlier: 3.857A pdb=" N ILE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Proline residue: A 313 - end of helix Proline residue: A 316 - end of helix removed outlier: 3.511A pdb=" N GLU A 321 " --> pdb=" O ILE A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 333 removed outlier: 3.681A pdb=" N GLY A 331 " --> pdb=" O LYS A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 356 removed outlier: 3.687A pdb=" N SER A 338 " --> pdb=" O PHE A 334 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ILE A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N HIS A 353 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LYS A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 375 Processing helix chain 'A' and resid 376 through 378 No H-bonds generated for 'chain 'A' and resid 376 through 378' Processing helix chain 'A' and resid 380 through 414 removed outlier: 4.604A pdb=" N ALA A 386 " --> pdb=" O TYR A 382 " (cutoff:3.500A) Proline residue: A 387 - end of helix Proline residue: A 404 - end of helix removed outlier: 3.855A pdb=" N GLY A 407 " --> pdb=" O MET A 403 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL A 410 " --> pdb=" O MET A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 447 removed outlier: 3.653A pdb=" N ILE A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) Proline residue: A 437 - end of helix Processing helix chain 'A' and resid 448 through 464 Processing helix chain 'A' and resid 465 through 471 removed outlier: 3.542A pdb=" N ARG A 471 " --> pdb=" O PHE A 468 " (cutoff:3.500A) 243 hydrogen bonds defined for protein. 720 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: 0.50 Time building geometry restraints manager: 0.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 450 1.32 - 1.45: 734 1.45 - 1.57: 1696 1.57 - 1.69: 2 1.69 - 1.81: 46 Bond restraints: 2928 Sorted by residual: bond pdb=" CE2 SRO A 501 " pdb=" CZ2 SRO A 501 " ideal model delta sigma weight residual 1.393 1.576 -0.183 2.00e-02 2.50e+03 8.33e+01 bond pdb=" CD2 SRO A 501 " pdb=" CE3 SRO A 501 " ideal model delta sigma weight residual 1.404 1.575 -0.171 2.00e-02 2.50e+03 7.29e+01 bond pdb=" CZ2 SRO A 501 " pdb=" CH2 SRO A 501 " ideal model delta sigma weight residual 1.386 1.506 -0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" CE3 SRO A 501 " pdb=" CZ3 SRO A 501 " ideal model delta sigma weight residual 1.385 1.505 -0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" CZ3 SRO A 501 " pdb=" CH2 SRO A 501 " ideal model delta sigma weight residual 1.407 1.486 -0.079 2.00e-02 2.50e+03 1.58e+01 ... (remaining 2923 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 3562 1.34 - 2.69: 320 2.69 - 4.03: 78 4.03 - 5.38: 22 5.38 - 6.72: 6 Bond angle restraints: 3988 Sorted by residual: angle pdb=" N PRO A 473 " pdb=" CA PRO A 473 " pdb=" C PRO A 473 " ideal model delta sigma weight residual 110.70 116.98 -6.28 1.22e+00 6.72e-01 2.65e+01 angle pdb=" CA ILE A 44 " pdb=" C ILE A 44 " pdb=" N PRO A 45 " ideal model delta sigma weight residual 120.83 123.61 -2.78 6.10e-01 2.69e+00 2.08e+01 angle pdb=" CA VAL A 41 " pdb=" C VAL A 41 " pdb=" N PRO A 42 " ideal model delta sigma weight residual 120.83 123.41 -2.58 6.10e-01 2.69e+00 1.79e+01 angle pdb=" CA PRO A 473 " pdb=" C PRO A 473 " pdb=" N PRO A 474 " ideal model delta sigma weight residual 117.93 122.87 -4.94 1.20e+00 6.94e-01 1.70e+01 angle pdb=" CA ILE A 381 " pdb=" C ILE A 381 " pdb=" O ILE A 381 " ideal model delta sigma weight residual 121.05 116.88 4.17 1.04e+00 9.25e-01 1.61e+01 ... (remaining 3983 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 1532 17.78 - 35.56: 139 35.56 - 53.34: 33 53.34 - 71.12: 3 71.12 - 88.90: 2 Dihedral angle restraints: 1709 sinusoidal: 623 harmonic: 1086 Sorted by residual: dihedral pdb=" C ILE A 44 " pdb=" N ILE A 44 " pdb=" CA ILE A 44 " pdb=" CB ILE A 44 " ideal model delta harmonic sigma weight residual -122.00 -131.84 9.84 0 2.50e+00 1.60e-01 1.55e+01 dihedral pdb=" N ILE A 44 " pdb=" C ILE A 44 " pdb=" CA ILE A 44 " pdb=" CB ILE A 44 " ideal model delta harmonic sigma weight residual 123.40 131.84 -8.44 0 2.50e+00 1.60e-01 1.14e+01 dihedral pdb=" CB GLU A 244 " pdb=" CG GLU A 244 " pdb=" CD GLU A 244 " pdb=" OE1 GLU A 244 " ideal model delta sinusoidal sigma weight residual 0.00 88.90 -88.90 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 1706 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 317 0.043 - 0.086: 108 0.086 - 0.129: 40 0.129 - 0.173: 8 0.173 - 0.216: 6 Chirality restraints: 479 Sorted by residual: chirality pdb=" CA PRO A 473 " pdb=" N PRO A 473 " pdb=" C PRO A 473 " pdb=" CB PRO A 473 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA ILE A 44 " pdb=" N ILE A 44 " pdb=" C ILE A 44 " pdb=" CB ILE A 44 " both_signs ideal model delta sigma weight residual False 2.43 2.22 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA ILE A 443 " pdb=" N ILE A 443 " pdb=" C ILE A 443 " pdb=" CB ILE A 443 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 476 not shown) Planarity restraints: 489 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 400 " 0.011 2.00e-02 2.50e+03 2.12e-02 4.50e+00 pdb=" C SER A 400 " -0.037 2.00e-02 2.50e+03 pdb=" O SER A 400 " 0.014 2.00e-02 2.50e+03 pdb=" N SER A 401 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 401 " 0.010 2.00e-02 2.50e+03 2.04e-02 4.15e+00 pdb=" C SER A 401 " -0.035 2.00e-02 2.50e+03 pdb=" O SER A 401 " 0.013 2.00e-02 2.50e+03 pdb=" N MET A 402 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 186 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.52e+00 pdb=" C LEU A 186 " 0.032 2.00e-02 2.50e+03 pdb=" O LEU A 186 " -0.012 2.00e-02 2.50e+03 pdb=" N ILE A 187 " -0.011 2.00e-02 2.50e+03 ... (remaining 486 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 688 2.80 - 3.33: 2847 3.33 - 3.85: 4502 3.85 - 4.38: 5222 4.38 - 4.90: 9244 Nonbonded interactions: 22503 Sorted by model distance: nonbonded pdb=" O PRO A 336 " pdb=" OG SER A 340 " model vdw 2.277 3.040 nonbonded pdb=" O TRP A 318 " pdb=" OG1 THR A 322 " model vdw 2.296 3.040 nonbonded pdb=" O SER A 180 " pdb=" OG SER A 180 " model vdw 2.430 3.040 nonbonded pdb=" N ASN A 128 " pdb=" OD1 ASN A 128 " model vdw 2.437 3.120 nonbonded pdb=" O ILE A 367 " pdb=" OG SER A 371 " model vdw 2.469 3.040 ... (remaining 22498 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 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: 1.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.860 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 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 : 0.009 0.183 2928 Z= 0.544 Angle : 0.913 6.722 3988 Z= 0.632 Chirality : 0.054 0.216 479 Planarity : 0.006 0.046 489 Dihedral : 14.545 88.899 1017 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.67 % Allowed : 21.67 % Favored : 77.67 % 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 aren not related in a simple way. whole: -0.02 (0.42), residues: 380 helix: 0.54 (0.28), residues: 323 sheet: None (None), residues: 0 loop : -2.82 (0.71), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 19 TYR 0.012 0.001 TYR A 422 PHE 0.016 0.002 PHE A 238 TRP 0.008 0.001 TRP A 318 HIS 0.002 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00868 ( 2928) covalent geometry : angle 0.91326 ( 3988) hydrogen bonds : bond 0.14787 ( 243) hydrogen bonds : angle 6.52591 ( 720) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.115 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 47 average time/residue: 0.4726 time to fit residues: 22.9397 Evaluate side-chains 45 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 24 optimal weight: 0.4980 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.144621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.122734 restraints weight = 3046.917| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.26 r_work: 0.3134 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.0811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 2928 Z= 0.173 Angle : 0.690 8.786 3988 Z= 0.338 Chirality : 0.043 0.152 479 Planarity : 0.006 0.047 489 Dihedral : 4.448 20.544 407 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.33 % Allowed : 19.67 % Favored : 77.00 % 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 aren not related in a simple way. whole: 0.69 (0.43), residues: 380 helix: 0.99 (0.28), residues: 325 sheet: None (None), residues: 0 loop : -2.52 (0.74), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 19 TYR 0.012 0.001 TYR A 422 PHE 0.017 0.001 PHE A 238 TRP 0.007 0.001 TRP A 318 HIS 0.003 0.002 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 2928) covalent geometry : angle 0.69049 ( 3988) hydrogen bonds : bond 0.05848 ( 243) hydrogen bonds : angle 4.68034 ( 720) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.112 Fit side-chains REVERT: A 379 LYS cc_start: 0.7040 (tppp) cc_final: 0.6484 (mtmm) outliers start: 10 outliers final: 2 residues processed: 49 average time/residue: 0.5243 time to fit residues: 26.4407 Evaluate side-chains 45 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 286 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 0.0470 chunk 15 optimal weight: 0.9990 chunk 8 optimal weight: 0.3980 chunk 32 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.5880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.145107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.122789 restraints weight = 3046.202| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.32 r_work: 0.3230 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2928 Z= 0.152 Angle : 0.654 9.089 3988 Z= 0.317 Chirality : 0.042 0.149 479 Planarity : 0.006 0.046 489 Dihedral : 4.116 16.965 405 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.00 % Allowed : 20.00 % Favored : 77.00 % 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 aren not related in a simple way. whole: 1.08 (0.43), residues: 380 helix: 1.26 (0.29), residues: 330 sheet: None (None), residues: 0 loop : -2.79 (0.79), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 19 TYR 0.011 0.001 TYR A 422 PHE 0.016 0.001 PHE A 238 TRP 0.006 0.001 TRP A 318 HIS 0.003 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 2928) covalent geometry : angle 0.65386 ( 3988) hydrogen bonds : bond 0.05132 ( 243) hydrogen bonds : angle 4.41324 ( 720) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.118 Fit side-chains REVERT: A 317 ILE cc_start: 0.8324 (OUTLIER) cc_final: 0.7997 (mt) REVERT: A 379 LYS cc_start: 0.6823 (tppp) cc_final: 0.6342 (mtmm) REVERT: A 435 ILE cc_start: 0.7386 (OUTLIER) cc_final: 0.7160 (mt) outliers start: 9 outliers final: 5 residues processed: 46 average time/residue: 0.4982 time to fit residues: 23.6186 Evaluate side-chains 48 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 435 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 2 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 6 optimal weight: 0.4980 chunk 25 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN A 280 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.146035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.123687 restraints weight = 3031.236| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.32 r_work: 0.3104 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2928 Z= 0.161 Angle : 0.661 9.248 3988 Z= 0.320 Chirality : 0.042 0.146 479 Planarity : 0.006 0.045 489 Dihedral : 4.101 17.051 405 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.33 % Allowed : 20.67 % Favored : 76.00 % 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 aren not related in a simple way. whole: 1.12 (0.44), residues: 380 helix: 1.29 (0.29), residues: 330 sheet: None (None), residues: 0 loop : -2.88 (0.78), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 19 TYR 0.014 0.001 TYR A 422 PHE 0.016 0.001 PHE A 238 TRP 0.006 0.001 TRP A 318 HIS 0.003 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 2928) covalent geometry : angle 0.66098 ( 3988) hydrogen bonds : bond 0.05370 ( 243) hydrogen bonds : angle 4.39947 ( 720) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.092 Fit side-chains REVERT: A 317 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7842 (mt) outliers start: 10 outliers final: 6 residues processed: 46 average time/residue: 0.5285 time to fit residues: 25.0593 Evaluate side-chains 46 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 445 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 19 optimal weight: 0.9990 chunk 3 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 2 optimal weight: 0.0870 chunk 13 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.145494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.123213 restraints weight = 3001.860| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.30 r_work: 0.3258 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2928 Z= 0.144 Angle : 0.641 9.147 3988 Z= 0.308 Chirality : 0.041 0.146 479 Planarity : 0.006 0.045 489 Dihedral : 4.034 16.612 405 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.33 % Allowed : 20.33 % Favored : 76.33 % 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 aren not related in a simple way. whole: 1.41 (0.44), residues: 380 helix: 1.48 (0.29), residues: 332 sheet: None (None), residues: 0 loop : -2.93 (0.79), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 19 TYR 0.011 0.001 TYR A 422 PHE 0.016 0.001 PHE A 238 TRP 0.004 0.001 TRP A 318 HIS 0.002 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 2928) covalent geometry : angle 0.64074 ( 3988) hydrogen bonds : bond 0.04775 ( 243) hydrogen bonds : angle 4.26694 ( 720) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.118 Fit side-chains REVERT: A 317 ILE cc_start: 0.8305 (OUTLIER) cc_final: 0.7963 (mt) REVERT: A 379 LYS cc_start: 0.6682 (tppp) cc_final: 0.6075 (mtmm) outliers start: 10 outliers final: 7 residues processed: 50 average time/residue: 0.4739 time to fit residues: 24.3671 Evaluate side-chains 49 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 445 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 28 optimal weight: 0.0270 chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 23 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.144998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.122449 restraints weight = 3061.371| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.33 r_work: 0.3118 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2928 Z= 0.151 Angle : 0.651 9.186 3988 Z= 0.312 Chirality : 0.041 0.144 479 Planarity : 0.006 0.045 489 Dihedral : 4.022 16.845 405 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 4.00 % Allowed : 19.00 % Favored : 77.00 % 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 aren not related in a simple way. whole: 1.30 (0.44), residues: 380 helix: 1.44 (0.29), residues: 331 sheet: None (None), residues: 0 loop : -3.14 (0.78), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 19 TYR 0.013 0.001 TYR A 422 PHE 0.016 0.001 PHE A 238 TRP 0.005 0.001 TRP A 318 HIS 0.003 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 2928) covalent geometry : angle 0.65064 ( 3988) hydrogen bonds : bond 0.04980 ( 243) hydrogen bonds : angle 4.27335 ( 720) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.113 Fit side-chains REVERT: A 317 ILE cc_start: 0.8140 (OUTLIER) cc_final: 0.7827 (mt) REVERT: A 351 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7149 (mp) REVERT: A 379 LYS cc_start: 0.6583 (tppp) cc_final: 0.5948 (mtmm) outliers start: 12 outliers final: 8 residues processed: 49 average time/residue: 0.5111 time to fit residues: 25.8231 Evaluate side-chains 51 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 445 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 29 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 28 optimal weight: 0.0970 chunk 30 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 26 optimal weight: 0.1980 chunk 11 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.145615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.123064 restraints weight = 3043.262| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.33 r_work: 0.3144 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2928 Z= 0.141 Angle : 0.627 9.198 3988 Z= 0.301 Chirality : 0.041 0.144 479 Planarity : 0.006 0.045 489 Dihedral : 3.980 16.619 405 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 4.33 % Allowed : 19.33 % Favored : 76.33 % 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 aren not related in a simple way. whole: 1.46 (0.45), residues: 380 helix: 1.55 (0.29), residues: 331 sheet: None (None), residues: 0 loop : -3.11 (0.79), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 19 TYR 0.011 0.001 TYR A 422 PHE 0.015 0.001 PHE A 238 TRP 0.004 0.001 TRP A 318 HIS 0.002 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 2928) covalent geometry : angle 0.62748 ( 3988) hydrogen bonds : bond 0.04661 ( 243) hydrogen bonds : angle 4.22371 ( 720) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.110 Fit side-chains REVERT: A 169 MET cc_start: 0.7576 (OUTLIER) cc_final: 0.7009 (ttt) REVERT: A 317 ILE cc_start: 0.8126 (OUTLIER) cc_final: 0.7819 (mt) REVERT: A 351 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7132 (mp) REVERT: A 379 LYS cc_start: 0.6531 (tppp) cc_final: 0.5924 (mtmm) outliers start: 13 outliers final: 9 residues processed: 48 average time/residue: 0.5089 time to fit residues: 25.1648 Evaluate side-chains 52 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 445 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 37 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 18 optimal weight: 0.0050 chunk 11 optimal weight: 0.7980 chunk 2 optimal weight: 0.0060 chunk 32 optimal weight: 0.0970 overall best weight: 0.3408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.148294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.125848 restraints weight = 3076.995| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.33 r_work: 0.3266 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2928 Z= 0.128 Angle : 0.605 9.169 3988 Z= 0.288 Chirality : 0.040 0.143 479 Planarity : 0.006 0.044 489 Dihedral : 3.870 15.756 405 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 4.00 % Allowed : 19.00 % Favored : 77.00 % 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 aren not related in a simple way. whole: 1.81 (0.45), residues: 380 helix: 1.77 (0.29), residues: 332 sheet: None (None), residues: 0 loop : -2.96 (0.81), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 19 TYR 0.009 0.001 TYR A 422 PHE 0.014 0.001 PHE A 238 TRP 0.004 0.001 TRP A 358 HIS 0.001 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 2928) covalent geometry : angle 0.60477 ( 3988) hydrogen bonds : bond 0.04161 ( 243) hydrogen bonds : angle 4.11089 ( 720) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.113 Fit side-chains REVERT: A 169 MET cc_start: 0.7738 (OUTLIER) cc_final: 0.7159 (ttt) REVERT: A 351 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7167 (mp) outliers start: 12 outliers final: 6 residues processed: 47 average time/residue: 0.4686 time to fit residues: 22.7032 Evaluate side-chains 49 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 445 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 6 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 19 optimal weight: 0.0980 chunk 13 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3620 r_free = 0.3620 target = 0.145486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.123391 restraints weight = 3097.627| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.28 r_work: 0.3220 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2928 Z= 0.163 Angle : 0.680 9.288 3988 Z= 0.326 Chirality : 0.042 0.142 479 Planarity : 0.006 0.044 489 Dihedral : 3.998 16.905 405 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.00 % Allowed : 21.00 % Favored : 76.00 % 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 aren not related in a simple way. whole: 1.40 (0.45), residues: 380 helix: 1.51 (0.29), residues: 331 sheet: None (None), residues: 0 loop : -3.05 (0.79), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 19 TYR 0.016 0.001 TYR A 422 PHE 0.017 0.002 PHE A 238 TRP 0.004 0.001 TRP A 318 HIS 0.003 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 2928) covalent geometry : angle 0.67999 ( 3988) hydrogen bonds : bond 0.05190 ( 243) hydrogen bonds : angle 4.27522 ( 720) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.110 Fit side-chains REVERT: A 169 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.7237 (ttt) REVERT: A 351 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7319 (mp) outliers start: 9 outliers final: 6 residues processed: 46 average time/residue: 0.4736 time to fit residues: 22.5055 Evaluate side-chains 48 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 445 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 24 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3614 r_free = 0.3614 target = 0.144919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.122848 restraints weight = 3054.096| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.28 r_work: 0.3113 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2928 Z= 0.173 Angle : 0.699 9.365 3988 Z= 0.336 Chirality : 0.042 0.144 479 Planarity : 0.006 0.045 489 Dihedral : 4.075 16.939 405 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.67 % Allowed : 20.67 % Favored : 75.67 % 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 aren not related in a simple way. whole: 1.26 (0.44), residues: 380 helix: 1.39 (0.29), residues: 331 sheet: None (None), residues: 0 loop : -2.95 (0.81), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 19 TYR 0.016 0.001 TYR A 422 PHE 0.018 0.002 PHE A 238 TRP 0.005 0.001 TRP A 318 HIS 0.003 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 2928) covalent geometry : angle 0.69890 ( 3988) hydrogen bonds : bond 0.05447 ( 243) hydrogen bonds : angle 4.34844 ( 720) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.113 Fit side-chains REVERT: A 169 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.7152 (ttt) REVERT: A 351 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7255 (mp) outliers start: 11 outliers final: 7 residues processed: 47 average time/residue: 0.4879 time to fit residues: 23.6875 Evaluate side-chains 48 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 445 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 17 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 25 optimal weight: 0.0870 chunk 16 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 22 optimal weight: 0.4980 chunk 29 optimal weight: 0.9990 chunk 14 optimal weight: 0.0870 chunk 7 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.3936 ------------------------------------------------------------------------------- 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 = 0.3604 r_free = 0.3604 target = 0.144730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.122469 restraints weight = 3044.420| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.31 r_work: 0.3151 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2928 Z= 0.136 Angle : 0.637 9.235 3988 Z= 0.304 Chirality : 0.040 0.144 479 Planarity : 0.006 0.044 489 Dihedral : 3.946 16.182 405 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.67 % Allowed : 22.33 % Favored : 75.00 % 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 aren not related in a simple way. whole: 1.67 (0.45), residues: 380 helix: 1.68 (0.29), residues: 331 sheet: None (None), residues: 0 loop : -2.85 (0.81), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 19 TYR 0.009 0.001 TYR A 422 PHE 0.015 0.001 PHE A 238 TRP 0.004 0.001 TRP A 358 HIS 0.002 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 2928) covalent geometry : angle 0.63694 ( 3988) hydrogen bonds : bond 0.04372 ( 243) hydrogen bonds : angle 4.17362 ( 720) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1111.60 seconds wall clock time: 19 minutes 38.58 seconds (1178.58 seconds total)