Starting phenix.real_space_refine on Tue Mar 3 11:36:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wp1_32666/03_2026/7wp1_32666.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wp1_32666/03_2026/7wp1_32666.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wp1_32666/03_2026/7wp1_32666.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wp1_32666/03_2026/7wp1_32666.map" model { file = "/net/cci-nas-00/data/ceres_data/7wp1_32666/03_2026/7wp1_32666.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wp1_32666/03_2026/7wp1_32666.cif" } resolution = 3.77 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= 0.009 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 15 5.16 5 C 2096 2.51 5 N 551 2.21 5 O 643 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3305 Number of models: 1 Model: "" Number of chains: 4 Chain: "L" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 796 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain: "H" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1017 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "F" Number of atoms: 1464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1464 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 9, 'TRANS': 173} Chain: "A" 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: 0.94, per 1000 atoms: 0.28 Number of scatterers: 3305 At special positions: 0 Unit cell: (87.914, 63.018, 81.69, 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 15 16.00 O 643 8.00 N 551 7.00 C 2096 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " 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 BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN F 343 " Time building additional restraints: 0.28 Conformation dependent library (CDL) restraints added in 131.3 milliseconds 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 756 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 7 sheets defined 4.3% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'L' and resid 28 through 32 removed outlier: 3.536A pdb=" N GLY L 32 " --> pdb=" O ILE L 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.853A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 403 through 410 removed outlier: 4.734A pdb=" N ARG F 408 " --> pdb=" O ASP F 405 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE F 410 " --> pdb=" O VAL F 407 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.941A pdb=" N THR L 109 " --> pdb=" O VAL L 10 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY L 12 " --> pdb=" O THR L 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'L' and resid 17 through 18 Processing sheet with id=AA3, first strand: chain 'L' and resid 47 through 50 removed outlier: 6.500A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 6 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.636A pdb=" N THR H 125 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR H 94 " --> pdb=" O THR H 125 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA H 92 " --> pdb=" O VAL H 127 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR H 59 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 376 through 378 removed outlier: 3.575A pdb=" N THR F 376 " --> pdb=" O ALA F 435 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA F 435 " --> pdb=" O THR F 376 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 452 through 454 57 hydrogen bonds defined for protein. 123 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: 0.54 Time building geometry restraints manager: 0.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1021 1.34 - 1.46: 851 1.46 - 1.58: 1498 1.58 - 1.70: 0 1.70 - 1.82: 19 Bond restraints: 3389 Sorted by residual: bond pdb=" CB ASN F 370 " pdb=" CG ASN F 370 " ideal model delta sigma weight residual 1.516 1.575 -0.059 2.50e-02 1.60e+03 5.61e+00 bond pdb=" CA ASN F 370 " pdb=" CB ASN F 370 " ideal model delta sigma weight residual 1.532 1.566 -0.034 1.43e-02 4.89e+03 5.60e+00 bond pdb=" C LEU F 425 " pdb=" N PRO F 426 " ideal model delta sigma weight residual 1.330 1.353 -0.023 1.25e-02 6.40e+03 3.51e+00 bond pdb=" C GLY L 12 " pdb=" N ALA L 13 " ideal model delta sigma weight residual 1.330 1.304 0.026 1.47e-02 4.63e+03 3.23e+00 bond pdb=" CA CYS F 336 " pdb=" C CYS F 336 " ideal model delta sigma weight residual 1.525 1.562 -0.037 2.10e-02 2.27e+03 3.10e+00 ... (remaining 3384 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 4396 2.47 - 4.94: 170 4.94 - 7.41: 30 7.41 - 9.88: 6 9.88 - 12.34: 1 Bond angle restraints: 4603 Sorted by residual: angle pdb=" N VAL F 367 " pdb=" CA VAL F 367 " pdb=" C VAL F 367 " ideal model delta sigma weight residual 113.47 107.26 6.21 1.01e+00 9.80e-01 3.78e+01 angle pdb=" N ILE F 468 " pdb=" CA ILE F 468 " pdb=" C ILE F 468 " ideal model delta sigma weight residual 112.12 107.84 4.28 8.40e-01 1.42e+00 2.60e+01 angle pdb=" CA ASN F 370 " pdb=" CB ASN F 370 " pdb=" CG ASN F 370 " ideal model delta sigma weight residual 112.60 117.12 -4.52 1.00e+00 1.00e+00 2.04e+01 angle pdb=" N CYS F 391 " pdb=" CA CYS F 391 " pdb=" C CYS F 391 " ideal model delta sigma weight residual 113.23 118.58 -5.35 1.22e+00 6.72e-01 1.92e+01 angle pdb=" N TYR F 473 " pdb=" CA TYR F 473 " pdb=" C TYR F 473 " ideal model delta sigma weight residual 111.69 116.53 -4.84 1.23e+00 6.61e-01 1.55e+01 ... (remaining 4598 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 1758 17.43 - 34.86: 196 34.86 - 52.29: 32 52.29 - 69.72: 4 69.72 - 87.15: 2 Dihedral angle restraints: 1992 sinusoidal: 783 harmonic: 1209 Sorted by residual: dihedral pdb=" CA LEU F 390 " pdb=" C LEU F 390 " pdb=" N CYS F 391 " pdb=" CA CYS F 391 " ideal model delta harmonic sigma weight residual 180.00 145.06 34.94 0 5.00e+00 4.00e-02 4.88e+01 dihedral pdb=" CA ASP H 113 " pdb=" C ASP H 113 " pdb=" N TYR H 114 " pdb=" CA TYR H 114 " ideal model delta harmonic sigma weight residual -180.00 -146.69 -33.31 0 5.00e+00 4.00e-02 4.44e+01 dihedral pdb=" CA TYR F 380 " pdb=" C TYR F 380 " pdb=" N GLY F 381 " pdb=" CA GLY F 381 " ideal model delta harmonic sigma weight residual 180.00 -148.09 -31.91 0 5.00e+00 4.00e-02 4.07e+01 ... (remaining 1989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.138: 474 0.138 - 0.277: 15 0.277 - 0.415: 0 0.415 - 0.553: 0 0.553 - 0.691: 1 Chirality restraints: 490 Sorted by residual: chirality pdb=" C1 NAG A 1 " pdb=" ND2 ASN F 343 " pdb=" C2 NAG A 1 " pdb=" O5 NAG A 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.71 -0.69 2.00e-01 2.50e+01 1.19e+01 chirality pdb=" C1 NAG A 2 " pdb=" O4 NAG A 1 " pdb=" C2 NAG A 2 " pdb=" O5 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.47 0.07 2.00e-02 2.50e+03 1.18e+01 chirality pdb=" CA ASN F 370 " pdb=" N ASN F 370 " pdb=" C ASN F 370 " pdb=" CB ASN F 370 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 487 not shown) Planarity restraints: 596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 1 " 0.284 2.00e-02 2.50e+03 2.43e-01 7.36e+02 pdb=" C7 NAG A 1 " -0.072 2.00e-02 2.50e+03 pdb=" C8 NAG A 1 " 0.172 2.00e-02 2.50e+03 pdb=" N2 NAG A 1 " -0.421 2.00e-02 2.50e+03 pdb=" O7 NAG A 1 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 2 " -0.274 2.00e-02 2.50e+03 2.28e-01 6.52e+02 pdb=" C7 NAG A 2 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG A 2 " -0.182 2.00e-02 2.50e+03 pdb=" N2 NAG A 2 " 0.384 2.00e-02 2.50e+03 pdb=" O7 NAG A 2 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN H 13 " -0.043 5.00e-02 4.00e+02 6.47e-02 6.70e+00 pdb=" N PRO H 14 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO H 14 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO H 14 " -0.036 5.00e-02 4.00e+02 ... (remaining 593 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 1171 2.85 - 3.36: 2769 3.36 - 3.88: 5198 3.88 - 4.39: 5643 4.39 - 4.90: 10286 Nonbonded interactions: 25067 Sorted by model distance: nonbonded pdb=" O SER F 366 " pdb=" OG SER F 366 " model vdw 2.338 3.040 nonbonded pdb=" O SER H 85 " pdb=" OG SER H 85 " model vdw 2.345 3.040 nonbonded pdb=" NE2 HIS L 36 " pdb=" O ASN H 115 " model vdw 2.360 3.120 nonbonded pdb=" OG1 THR F 393 " pdb=" O GLU F 516 " model vdw 2.364 3.040 nonbonded pdb=" OH TYR L 38 " pdb=" OE1 GLN L 91 " model vdw 2.370 3.040 ... (remaining 25062 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 14.080 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.400 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 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 : 0.006 0.059 3394 Z= 0.297 Angle : 1.181 12.344 4615 Z= 0.686 Chirality : 0.068 0.691 490 Planarity : 0.016 0.243 595 Dihedral : 14.456 87.147 1227 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.23 % Favored : 87.53 % Rotamer: Outliers : 0.00 % Allowed : 15.01 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.75 % 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: -5.40 (0.31), residues: 417 helix: -5.32 (0.22), residues: 20 sheet: -3.25 (0.37), residues: 145 loop : -3.79 (0.28), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 87 TYR 0.018 0.002 TYR H 104 PHE 0.021 0.002 PHE F 338 TRP 0.011 0.002 TRP F 436 HIS 0.006 0.003 HIS L 36 Details of bonding type rmsd covalent geometry : bond 0.00583 ( 3389) covalent geometry : angle 1.16953 ( 4603) SS BOND : bond 0.00338 ( 3) SS BOND : angle 0.79268 ( 6) hydrogen bonds : bond 0.27535 ( 57) hydrogen bonds : angle 10.86817 ( 123) link_BETA1-4 : bond 0.00371 ( 1) link_BETA1-4 : angle 3.81629 ( 3) link_NAG-ASN : bond 0.03583 ( 1) link_NAG-ASN : angle 5.53440 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.140 Fit side-chains REVERT: H 18 LEU cc_start: 0.6969 (tp) cc_final: 0.6738 (tp) REVERT: H 67 ARG cc_start: 0.7095 (mpt-90) cc_final: 0.6689 (mpt-90) REVERT: F 457 ARG cc_start: 0.8434 (ttt-90) cc_final: 0.7902 (ttt-90) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1030 time to fit residues: 10.1402 Evaluate side-chains 67 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.4980 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.0870 chunk 37 optimal weight: 0.8980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 39 GLN H 74 ASN F 388 ASN ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.151770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.135913 restraints weight = 5278.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.139103 restraints weight = 3272.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.141343 restraints weight = 2275.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.142820 restraints weight = 1698.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.143972 restraints weight = 1348.557| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3622 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3622 r_free = 0.3622 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3621 r_free = 0.3621 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3621 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 3394 Z= 0.205 Angle : 0.769 7.418 4615 Z= 0.406 Chirality : 0.051 0.327 490 Planarity : 0.006 0.053 595 Dihedral : 7.935 51.050 516 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.95 % Favored : 86.81 % Rotamer: Outliers : 4.25 % Allowed : 17.56 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % 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: -4.71 (0.35), residues: 417 helix: -5.28 (0.23), residues: 20 sheet: -2.73 (0.36), residues: 166 loop : -3.29 (0.34), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 87 TYR 0.013 0.002 TYR H 104 PHE 0.019 0.002 PHE F 338 TRP 0.014 0.002 TRP F 353 HIS 0.004 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00462 ( 3389) covalent geometry : angle 0.76088 ( 4603) SS BOND : bond 0.00282 ( 3) SS BOND : angle 0.88353 ( 6) hydrogen bonds : bond 0.03601 ( 57) hydrogen bonds : angle 7.52800 ( 123) link_BETA1-4 : bond 0.00450 ( 1) link_BETA1-4 : angle 2.50853 ( 3) link_NAG-ASN : bond 0.01010 ( 1) link_NAG-ASN : angle 3.68448 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.123 Fit side-chains REVERT: L 17 ARG cc_start: 0.7063 (OUTLIER) cc_final: 0.6410 (ttp-110) REVERT: L 38 TYR cc_start: 0.9329 (m-80) cc_final: 0.9113 (m-80) REVERT: L 81 GLN cc_start: 0.7972 (mp10) cc_final: 0.7738 (mp10) REVERT: F 457 ARG cc_start: 0.8407 (ttt-90) cc_final: 0.7945 (ttt-90) outliers start: 15 outliers final: 12 residues processed: 78 average time/residue: 0.1010 time to fit residues: 9.0645 Evaluate side-chains 79 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 17 ARG Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 376 THR Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 467 ASP Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 478 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 38 optimal weight: 0.0570 chunk 22 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 HIS H 115 ASN F 409 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.150109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.133227 restraints weight = 5358.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.136547 restraints weight = 3242.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.138921 restraints weight = 2224.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.140608 restraints weight = 1652.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.141463 restraints weight = 1294.080| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3583 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3583 r_free = 0.3583 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3583 r_free = 0.3583 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3583 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 3394 Z= 0.218 Angle : 0.767 7.428 4615 Z= 0.400 Chirality : 0.051 0.328 490 Planarity : 0.006 0.057 595 Dihedral : 7.624 49.978 516 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.24 % Allowed : 13.67 % Favored : 86.09 % Rotamer: Outliers : 6.80 % Allowed : 18.13 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % 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: -4.30 (0.37), residues: 417 helix: -5.26 (0.24), residues: 20 sheet: -2.47 (0.38), residues: 167 loop : -2.96 (0.37), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 19 TYR 0.022 0.002 TYR H 80 PHE 0.019 0.002 PHE F 338 TRP 0.016 0.002 TRP F 353 HIS 0.005 0.003 HIS L 36 Details of bonding type rmsd covalent geometry : bond 0.00497 ( 3389) covalent geometry : angle 0.75758 ( 4603) SS BOND : bond 0.00383 ( 3) SS BOND : angle 0.80042 ( 6) hydrogen bonds : bond 0.03188 ( 57) hydrogen bonds : angle 7.00932 ( 123) link_BETA1-4 : bond 0.00209 ( 1) link_BETA1-4 : angle 2.90841 ( 3) link_NAG-ASN : bond 0.00818 ( 1) link_NAG-ASN : angle 3.80805 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 71 time to evaluate : 0.115 Fit side-chains REVERT: L 17 ARG cc_start: 0.7167 (OUTLIER) cc_final: 0.6417 (ttp-110) REVERT: F 369 TYR cc_start: 0.7811 (OUTLIER) cc_final: 0.7192 (t80) REVERT: F 457 ARG cc_start: 0.8447 (ttt-90) cc_final: 0.7825 (ttt-90) outliers start: 24 outliers final: 16 residues processed: 86 average time/residue: 0.0890 time to fit residues: 8.8394 Evaluate side-chains 86 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 17 ARG Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 369 TYR Chi-restraints excluded: chain F residue 376 THR Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 478 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 12 optimal weight: 0.0060 chunk 35 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 498 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.148524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.131924 restraints weight = 5307.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.135168 restraints weight = 3246.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.137487 restraints weight = 2242.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.139090 restraints weight = 1667.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.140231 restraints weight = 1316.527| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3579 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3579 r_free = 0.3579 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3579 r_free = 0.3579 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3579 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 3394 Z= 0.223 Angle : 0.777 7.811 4615 Z= 0.402 Chirality : 0.051 0.319 490 Planarity : 0.005 0.048 595 Dihedral : 7.617 46.765 516 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.24 % Allowed : 14.63 % Favored : 85.13 % Rotamer: Outliers : 6.80 % Allowed : 19.55 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % 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: -4.20 (0.38), residues: 417 helix: -5.18 (0.29), residues: 20 sheet: -2.44 (0.38), residues: 169 loop : -2.85 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 98 TYR 0.014 0.002 TYR H 104 PHE 0.018 0.002 PHE F 338 TRP 0.018 0.002 TRP F 353 HIS 0.005 0.003 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00510 ( 3389) covalent geometry : angle 0.76715 ( 4603) SS BOND : bond 0.00358 ( 3) SS BOND : angle 0.82174 ( 6) hydrogen bonds : bond 0.02847 ( 57) hydrogen bonds : angle 6.84889 ( 123) link_BETA1-4 : bond 0.00110 ( 1) link_BETA1-4 : angle 3.14745 ( 3) link_NAG-ASN : bond 0.00797 ( 1) link_NAG-ASN : angle 3.89036 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 66 time to evaluate : 0.101 Fit side-chains REVERT: L 17 ARG cc_start: 0.7143 (OUTLIER) cc_final: 0.6287 (ttp-110) REVERT: F 369 TYR cc_start: 0.7850 (OUTLIER) cc_final: 0.7207 (t80) REVERT: F 457 ARG cc_start: 0.8370 (ttt-90) cc_final: 0.7862 (ttt-90) outliers start: 24 outliers final: 20 residues processed: 83 average time/residue: 0.0961 time to fit residues: 9.2609 Evaluate side-chains 86 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 64 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 17 ARG Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 36 HIS Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 369 TYR Chi-restraints excluded: chain F residue 376 THR Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 478 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 18 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 6 optimal weight: 0.3980 chunk 1 optimal weight: 0.2980 chunk 31 optimal weight: 0.0980 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 498 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.151687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.135693 restraints weight = 5257.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.138743 restraints weight = 3260.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.140913 restraints weight = 2269.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.142331 restraints weight = 1704.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.143532 restraints weight = 1364.159| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3622 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3622 r_free = 0.3622 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3622 r_free = 0.3622 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3622 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3394 Z= 0.162 Angle : 0.727 7.597 4615 Z= 0.373 Chirality : 0.049 0.310 490 Planarity : 0.005 0.051 595 Dihedral : 7.170 43.495 516 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.23 % Favored : 87.53 % Rotamer: Outliers : 6.52 % Allowed : 21.81 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -4.04 (0.39), residues: 417 helix: -5.04 (0.31), residues: 20 sheet: -2.38 (0.39), residues: 169 loop : -2.71 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 98 TYR 0.012 0.001 TYR F 421 PHE 0.014 0.001 PHE F 392 TRP 0.017 0.002 TRP F 353 HIS 0.005 0.003 HIS L 36 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 3389) covalent geometry : angle 0.71618 ( 4603) SS BOND : bond 0.00251 ( 3) SS BOND : angle 0.73191 ( 6) hydrogen bonds : bond 0.02576 ( 57) hydrogen bonds : angle 6.55545 ( 123) link_BETA1-4 : bond 0.00098 ( 1) link_BETA1-4 : angle 3.02844 ( 3) link_NAG-ASN : bond 0.00857 ( 1) link_NAG-ASN : angle 3.99551 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 0.109 Fit side-chains REVERT: L 38 TYR cc_start: 0.9305 (m-80) cc_final: 0.9098 (m-80) REVERT: H 101 GLN cc_start: 0.7365 (tm-30) cc_final: 0.7050 (tm-30) REVERT: F 369 TYR cc_start: 0.7847 (OUTLIER) cc_final: 0.7192 (t80) REVERT: F 440 ASN cc_start: 0.8331 (p0) cc_final: 0.8082 (p0) REVERT: F 457 ARG cc_start: 0.8245 (ttt-90) cc_final: 0.7807 (ttt-90) outliers start: 23 outliers final: 16 residues processed: 85 average time/residue: 0.1015 time to fit residues: 9.9565 Evaluate side-chains 82 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 369 TYR Chi-restraints excluded: chain F residue 376 THR Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 470 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 25 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 15 optimal weight: 0.0010 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 0.1980 chunk 0 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 498 GLN F 506 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.150933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.133848 restraints weight = 5261.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.137242 restraints weight = 3181.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.139525 restraints weight = 2178.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.141093 restraints weight = 1626.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.142371 restraints weight = 1293.792| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3592 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3592 r_free = 0.3592 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3591 r_free = 0.3591 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3591 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 3394 Z= 0.179 Angle : 0.724 6.896 4615 Z= 0.374 Chirality : 0.049 0.306 490 Planarity : 0.005 0.049 595 Dihedral : 7.175 43.032 516 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.24 % Allowed : 13.19 % Favored : 86.57 % Rotamer: Outliers : 6.80 % Allowed : 20.68 % Favored : 72.52 % 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: -3.92 (0.39), residues: 417 helix: -4.96 (0.34), residues: 20 sheet: -2.32 (0.39), residues: 169 loop : -2.59 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 17 TYR 0.029 0.002 TYR H 80 PHE 0.014 0.001 PHE F 392 TRP 0.013 0.002 TRP F 353 HIS 0.005 0.003 HIS L 36 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 3389) covalent geometry : angle 0.71308 ( 4603) SS BOND : bond 0.00239 ( 3) SS BOND : angle 0.78684 ( 6) hydrogen bonds : bond 0.02643 ( 57) hydrogen bonds : angle 6.51665 ( 123) link_BETA1-4 : bond 0.00125 ( 1) link_BETA1-4 : angle 3.11096 ( 3) link_NAG-ASN : bond 0.00798 ( 1) link_NAG-ASN : angle 3.95793 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 66 time to evaluate : 0.120 Fit side-chains REVERT: L 17 ARG cc_start: 0.7018 (OUTLIER) cc_final: 0.6182 (ttp-110) REVERT: F 369 TYR cc_start: 0.7824 (OUTLIER) cc_final: 0.7247 (t80) REVERT: F 440 ASN cc_start: 0.8363 (p0) cc_final: 0.8134 (p0) REVERT: F 457 ARG cc_start: 0.8326 (ttt-90) cc_final: 0.7805 (ttt-90) outliers start: 24 outliers final: 20 residues processed: 83 average time/residue: 0.0968 time to fit residues: 9.2860 Evaluate side-chains 85 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 63 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 17 ARG Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 369 TYR Chi-restraints excluded: chain F residue 376 THR Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 478 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 0.1980 chunk 30 optimal weight: 0.3980 chunk 20 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 498 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.150006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.132764 restraints weight = 5321.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.136141 restraints weight = 3225.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.138436 restraints weight = 2209.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.140138 restraints weight = 1644.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.141348 restraints weight = 1293.849| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3598 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3598 r_free = 0.3598 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3598 r_free = 0.3598 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3598 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 3394 Z= 0.197 Angle : 0.748 7.749 4615 Z= 0.388 Chirality : 0.050 0.304 490 Planarity : 0.005 0.050 595 Dihedral : 7.382 42.941 516 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.95 % Favored : 86.81 % Rotamer: Outliers : 7.65 % Allowed : 20.40 % Favored : 71.95 % 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: -3.91 (0.39), residues: 417 helix: -4.89 (0.38), residues: 20 sheet: -2.36 (0.39), residues: 169 loop : -2.55 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 98 TYR 0.028 0.002 TYR H 80 PHE 0.015 0.001 PHE F 392 TRP 0.020 0.002 TRP F 353 HIS 0.005 0.003 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 3389) covalent geometry : angle 0.73671 ( 4603) SS BOND : bond 0.00268 ( 3) SS BOND : angle 0.87965 ( 6) hydrogen bonds : bond 0.02663 ( 57) hydrogen bonds : angle 6.65498 ( 123) link_BETA1-4 : bond 0.00150 ( 1) link_BETA1-4 : angle 3.22783 ( 3) link_NAG-ASN : bond 0.00760 ( 1) link_NAG-ASN : angle 3.89703 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 65 time to evaluate : 0.206 Fit side-chains REVERT: L 85 GLU cc_start: 0.8382 (pm20) cc_final: 0.7992 (pm20) REVERT: H 3 GLN cc_start: 0.8466 (pt0) cc_final: 0.8178 (pt0) REVERT: H 72 ARG cc_start: 0.8495 (ptm160) cc_final: 0.7752 (ptm160) REVERT: F 369 TYR cc_start: 0.7814 (OUTLIER) cc_final: 0.7241 (t80) REVERT: F 440 ASN cc_start: 0.8361 (p0) cc_final: 0.8152 (p0) outliers start: 27 outliers final: 20 residues processed: 85 average time/residue: 0.0945 time to fit residues: 9.3139 Evaluate side-chains 86 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 369 TYR Chi-restraints excluded: chain F residue 376 THR Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 478 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 0.0980 chunk 22 optimal weight: 0.6980 chunk 17 optimal weight: 0.1980 chunk 10 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 12 optimal weight: 0.1980 chunk 26 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 498 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.152278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.135592 restraints weight = 5282.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.138846 restraints weight = 3242.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.141034 restraints weight = 2226.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.142709 restraints weight = 1670.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.143830 restraints weight = 1312.128| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3621 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3621 r_free = 0.3621 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3621 r_free = 0.3621 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3621 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3394 Z= 0.157 Angle : 0.728 6.378 4615 Z= 0.375 Chirality : 0.049 0.303 490 Planarity : 0.005 0.049 595 Dihedral : 7.180 41.222 516 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.47 % Favored : 87.29 % Rotamer: Outliers : 6.52 % Allowed : 21.81 % Favored : 71.67 % 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 are not related in a simple way. whole: -3.85 (0.39), residues: 417 helix: -4.83 (0.50), residues: 19 sheet: -2.34 (0.38), residues: 171 loop : -2.50 (0.39), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 98 TYR 0.016 0.001 TYR H 80 PHE 0.013 0.001 PHE F 392 TRP 0.017 0.002 TRP F 353 HIS 0.005 0.003 HIS L 36 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 3389) covalent geometry : angle 0.71720 ( 4603) SS BOND : bond 0.00207 ( 3) SS BOND : angle 0.75519 ( 6) hydrogen bonds : bond 0.02586 ( 57) hydrogen bonds : angle 6.52452 ( 123) link_BETA1-4 : bond 0.00317 ( 1) link_BETA1-4 : angle 3.14152 ( 3) link_NAG-ASN : bond 0.00796 ( 1) link_NAG-ASN : angle 3.89966 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 63 time to evaluate : 0.130 Fit side-chains REVERT: L 85 GLU cc_start: 0.8315 (pm20) cc_final: 0.7933 (pm20) REVERT: H 3 GLN cc_start: 0.8377 (pt0) cc_final: 0.8125 (pt0) REVERT: H 72 ARG cc_start: 0.8443 (ptm160) cc_final: 0.7829 (ptm160) REVERT: F 353 TRP cc_start: 0.7550 (p90) cc_final: 0.6945 (p90) REVERT: F 369 TYR cc_start: 0.7836 (OUTLIER) cc_final: 0.7251 (t80) REVERT: F 440 ASN cc_start: 0.8295 (p0) cc_final: 0.8083 (p0) outliers start: 23 outliers final: 20 residues processed: 80 average time/residue: 0.0888 time to fit residues: 8.3615 Evaluate side-chains 82 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 61 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 369 TYR Chi-restraints excluded: chain F residue 376 THR Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 478 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 38 optimal weight: 0.0060 chunk 24 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 11 optimal weight: 0.3980 chunk 3 optimal weight: 0.0870 chunk 14 optimal weight: 0.9990 chunk 37 optimal weight: 0.1980 overall best weight: 0.2974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 498 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.154117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.137123 restraints weight = 5196.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.140540 restraints weight = 3101.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.142828 restraints weight = 2100.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.144534 restraints weight = 1559.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.145691 restraints weight = 1216.803| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3643 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3643 r_free = 0.3643 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3643 r_free = 0.3643 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3643 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3394 Z= 0.143 Angle : 0.712 6.097 4615 Z= 0.365 Chirality : 0.048 0.301 490 Planarity : 0.005 0.050 595 Dihedral : 6.859 38.579 516 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.23 % Favored : 87.53 % Rotamer: Outliers : 5.95 % Allowed : 22.10 % Favored : 71.95 % 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: -3.74 (0.39), residues: 417 helix: -4.70 (0.61), residues: 19 sheet: -2.29 (0.39), residues: 171 loop : -2.42 (0.39), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 98 TYR 0.015 0.001 TYR H 80 PHE 0.011 0.001 PHE F 392 TRP 0.017 0.001 TRP F 353 HIS 0.005 0.003 HIS L 36 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 3389) covalent geometry : angle 0.70080 ( 4603) SS BOND : bond 0.00197 ( 3) SS BOND : angle 0.71648 ( 6) hydrogen bonds : bond 0.02516 ( 57) hydrogen bonds : angle 6.34806 ( 123) link_BETA1-4 : bond 0.00318 ( 1) link_BETA1-4 : angle 3.01448 ( 3) link_NAG-ASN : bond 0.00804 ( 1) link_NAG-ASN : angle 3.91763 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.142 Fit side-chains REVERT: L 38 TYR cc_start: 0.9257 (m-80) cc_final: 0.8889 (m-80) REVERT: H 3 GLN cc_start: 0.8400 (pt0) cc_final: 0.8148 (pt0) REVERT: F 353 TRP cc_start: 0.7525 (p90) cc_final: 0.6907 (p90) REVERT: F 369 TYR cc_start: 0.7775 (OUTLIER) cc_final: 0.7264 (t80) outliers start: 21 outliers final: 18 residues processed: 78 average time/residue: 0.0852 time to fit residues: 7.8499 Evaluate side-chains 79 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 60 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 369 TYR Chi-restraints excluded: chain F residue 376 THR Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 478 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 13 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 40 optimal weight: 0.3980 chunk 34 optimal weight: 1.9990 chunk 31 optimal weight: 0.1980 chunk 27 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 26 optimal weight: 0.0980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 498 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.152229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.134932 restraints weight = 5316.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.138355 restraints weight = 3202.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.140621 restraints weight = 2189.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.142353 restraints weight = 1638.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.143596 restraints weight = 1290.448| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3609 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3609 r_free = 0.3609 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3609 r_free = 0.3609 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3609 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3394 Z= 0.175 Angle : 0.739 6.224 4615 Z= 0.381 Chirality : 0.049 0.300 490 Planarity : 0.005 0.057 595 Dihedral : 7.074 40.055 516 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.24 % Allowed : 13.19 % Favored : 86.57 % Rotamer: Outliers : 5.67 % Allowed : 22.38 % Favored : 71.95 % 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: -3.66 (0.39), residues: 417 helix: -4.70 (0.62), residues: 19 sheet: -2.24 (0.39), residues: 170 loop : -2.36 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 87 TYR 0.018 0.001 TYR H 80 PHE 0.013 0.001 PHE F 392 TRP 0.017 0.002 TRP F 353 HIS 0.005 0.003 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 3389) covalent geometry : angle 0.72883 ( 4603) SS BOND : bond 0.00214 ( 3) SS BOND : angle 0.80573 ( 6) hydrogen bonds : bond 0.02593 ( 57) hydrogen bonds : angle 6.38426 ( 123) link_BETA1-4 : bond 0.00238 ( 1) link_BETA1-4 : angle 3.09428 ( 3) link_NAG-ASN : bond 0.00744 ( 1) link_NAG-ASN : angle 3.88680 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 0.131 Fit side-chains REVERT: L 85 GLU cc_start: 0.8322 (pm20) cc_final: 0.7940 (pm20) REVERT: H 3 GLN cc_start: 0.8397 (pt0) cc_final: 0.8155 (pt0) REVERT: F 353 TRP cc_start: 0.7546 (p90) cc_final: 0.6965 (p90) REVERT: F 369 TYR cc_start: 0.7799 (OUTLIER) cc_final: 0.7437 (t80) REVERT: F 440 ASN cc_start: 0.8386 (p0) cc_final: 0.8132 (p0) outliers start: 20 outliers final: 17 residues processed: 78 average time/residue: 0.0820 time to fit residues: 7.6037 Evaluate side-chains 81 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 369 TYR Chi-restraints excluded: chain F residue 376 THR Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 478 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 12 optimal weight: 0.0970 chunk 9 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 498 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.150237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.133280 restraints weight = 5288.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.136628 restraints weight = 3191.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.138861 restraints weight = 2177.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.140586 restraints weight = 1624.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.141741 restraints weight = 1271.034| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3604 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3604 r_free = 0.3604 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3604 r_free = 0.3604 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3604 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 3394 Z= 0.210 Angle : 0.768 6.562 4615 Z= 0.397 Chirality : 0.050 0.298 490 Planarity : 0.005 0.056 595 Dihedral : 7.502 49.515 516 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.24 % Allowed : 13.91 % Favored : 85.85 % Rotamer: Outliers : 5.67 % Allowed : 22.10 % Favored : 72.24 % 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: -3.62 (0.39), residues: 417 helix: -4.70 (0.63), residues: 19 sheet: -2.20 (0.39), residues: 168 loop : -2.35 (0.39), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 98 TYR 0.020 0.002 TYR H 80 PHE 0.015 0.001 PHE F 338 TRP 0.018 0.002 TRP F 353 HIS 0.005 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00490 ( 3389) covalent geometry : angle 0.75771 ( 4603) SS BOND : bond 0.00259 ( 3) SS BOND : angle 0.87947 ( 6) hydrogen bonds : bond 0.02661 ( 57) hydrogen bonds : angle 6.58233 ( 123) link_BETA1-4 : bond 0.00331 ( 1) link_BETA1-4 : angle 3.33756 ( 3) link_NAG-ASN : bond 0.00730 ( 1) link_NAG-ASN : angle 3.78798 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1095.20 seconds wall clock time: 19 minutes 31.27 seconds (1171.27 seconds total)