Starting phenix.real_space_refine on Thu Jul 2 00:18:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kvy_62604/07_2026/9kvy_62604.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kvy_62604/07_2026/9kvy_62604.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kvy_62604/07_2026/9kvy_62604.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kvy_62604/07_2026/9kvy_62604.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kvy_62604/07_2026/9kvy_62604.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kvy_62604/07_2026/9kvy_62604.map" } resolution = 3.34 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: 5 Type Number sf(0) Gaussians Mn 1 7.51 5 S 31 5.16 5 C 2909 2.51 5 N 727 2.21 5 O 786 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4454 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2197 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 13, 'TRANS': 274} Chain breaks: 2 Chain: "B" Number of atoms: 2256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2256 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 11, 'TRANS': 283} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' MN': 1} Chain breaks: 1 Time building chain proxies: 0.96, per 1000 atoms: 0.22 Number of scatterers: 4454 At special positions: 0 Unit cell: (74.56, 59.648, 113.704, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Mn 1 24.99 S 31 16.00 O 786 8.00 N 727 7.00 C 2909 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 273 " - pdb=" SG CYS A 277 " distance=2.05 Simple disulfide: pdb=" SG CYS A 404 " - pdb=" SG CYS A 409 " distance=2.03 Simple disulfide: pdb=" SG CYS B 273 " - pdb=" SG CYS B 277 " distance=2.05 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: 0.25 Conformation dependent library (CDL) restraints added in 133.2 milliseconds 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1092 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 4 sheets defined 67.8% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 10 through 33 removed outlier: 3.600A pdb=" N TYR A 30 " --> pdb=" O LEU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 62 Processing helix chain 'A' and resid 73 through 75 No H-bonds generated for 'chain 'A' and resid 73 through 75' Processing helix chain 'A' and resid 76 through 106 Processing helix chain 'A' and resid 112 through 133 removed outlier: 3.928A pdb=" N GLY A 130 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LEU A 131 " --> pdb=" O ASN A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 264 removed outlier: 3.689A pdb=" N GLY A 251 " --> pdb=" O GLY A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 307 removed outlier: 3.913A pdb=" N TYR A 278 " --> pdb=" O ASN A 274 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE A 279 " --> pdb=" O TRP A 275 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ASP A 280 " --> pdb=" O GLN A 276 " (cutoff:3.500A) Proline residue: A 281 - end of helix Proline residue: A 297 - end of helix Processing helix chain 'A' and resid 315 through 325 Processing helix chain 'A' and resid 359 through 374 Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.517A pdb=" N ALA A 410 " --> pdb=" O LYS A 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 23 Processing helix chain 'B' and resid 24 through 26 No H-bonds generated for 'chain 'B' and resid 24 through 26' Processing helix chain 'B' and resid 33 through 37 removed outlier: 4.421A pdb=" N ALA B 36 " --> pdb=" O ASN B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 62 removed outlier: 3.643A pdb=" N LEU B 45 " --> pdb=" O SER B 41 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASP B 47 " --> pdb=" O ASN B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 75 No H-bonds generated for 'chain 'B' and resid 73 through 75' Processing helix chain 'B' and resid 76 through 106 Processing helix chain 'B' and resid 112 through 132 removed outlier: 3.723A pdb=" N VAL B 116 " --> pdb=" O ASP B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 265 Processing helix chain 'B' and resid 274 through 306 removed outlier: 3.585A pdb=" N TYR B 278 " --> pdb=" O ASN B 274 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASP B 280 " --> pdb=" O GLN B 276 " (cutoff:3.500A) Proline residue: B 281 - end of helix Proline residue: B 297 - end of helix removed outlier: 3.735A pdb=" N ALA B 304 " --> pdb=" O LYS B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 326 removed outlier: 3.922A pdb=" N SER B 321 " --> pdb=" O GLU B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 373 removed outlier: 3.898A pdb=" N THR B 364 " --> pdb=" O GLN B 360 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS B 365 " --> pdb=" O ASP B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 412 removed outlier: 3.641A pdb=" N LYS B 411 " --> pdb=" O GLY B 408 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 331 through 341 removed outlier: 6.452A pdb=" N VAL A 332 " --> pdb=" O LYS A 352 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N LYS A 352 " --> pdb=" O VAL A 332 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N GLU A 334 " --> pdb=" O HIS A 350 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N HIS A 350 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LYS A 344 " --> pdb=" O LEU A 340 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN A 377 " --> pdb=" O ILE A 345 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 331 through 341 removed outlier: 6.452A pdb=" N VAL A 332 " --> pdb=" O LYS A 352 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N LYS A 352 " --> pdb=" O VAL A 332 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N GLU A 334 " --> pdb=" O HIS A 350 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N HIS A 350 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LYS A 344 " --> pdb=" O LEU A 340 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 331 through 332 removed outlier: 4.356A pdb=" N SER B 331 " --> pdb=" O LYS B 352 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 337 through 341 removed outlier: 5.515A pdb=" N GLU B 339 " --> pdb=" O ILE B 346 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE B 346 " --> pdb=" O GLU B 339 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL B 341 " --> pdb=" O LYS B 344 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN B 377 " --> pdb=" O ILE B 345 " (cutoff:3.500A) 301 hydrogen bonds defined for protein. 885 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: 0.65 Time building geometry restraints manager: 0.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1047 1.33 - 1.46: 1041 1.46 - 1.58: 2401 1.58 - 1.71: 0 1.71 - 1.83: 45 Bond restraints: 4534 Sorted by residual: bond pdb=" N ILE A 279 " pdb=" CA ILE A 279 " ideal model delta sigma weight residual 1.459 1.508 -0.049 1.30e-02 5.92e+03 1.40e+01 bond pdb=" C ALA A 410 " pdb=" N LYS A 411 " ideal model delta sigma weight residual 1.335 1.293 0.042 1.38e-02 5.25e+03 9.29e+00 bond pdb=" N VAL A 98 " pdb=" CA VAL A 98 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.17e-02 7.31e+03 7.35e+00 bond pdb=" N ASP B 280 " pdb=" CA ASP B 280 " ideal model delta sigma weight residual 1.462 1.439 0.023 8.50e-03 1.38e+04 7.30e+00 bond pdb=" N CYS A 277 " pdb=" CA CYS A 277 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.26e-02 6.30e+03 6.65e+00 ... (remaining 4529 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 5964 1.86 - 3.72: 159 3.72 - 5.58: 28 5.58 - 7.44: 8 7.44 - 9.30: 6 Bond angle restraints: 6165 Sorted by residual: angle pdb=" C LYS A 411 " pdb=" CA LYS A 411 " pdb=" CB LYS A 411 " ideal model delta sigma weight residual 110.67 101.37 9.30 1.92e+00 2.71e-01 2.35e+01 angle pdb=" C CYS A 277 " pdb=" CA CYS A 277 " pdb=" CB CYS A 277 " ideal model delta sigma weight residual 110.70 101.86 8.84 1.83e+00 2.99e-01 2.33e+01 angle pdb=" N TRP A 275 " pdb=" CA TRP A 275 " pdb=" C TRP A 275 " ideal model delta sigma weight residual 111.28 106.77 4.51 1.09e+00 8.42e-01 1.71e+01 angle pdb=" C CYS A 273 " pdb=" CA CYS A 273 " pdb=" CB CYS A 273 " ideal model delta sigma weight residual 109.54 116.96 -7.42 1.84e+00 2.95e-01 1.63e+01 angle pdb=" C ASN A 274 " pdb=" N TRP A 275 " pdb=" CA TRP A 275 " ideal model delta sigma weight residual 120.28 115.23 5.05 1.34e+00 5.57e-01 1.42e+01 ... (remaining 6160 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 2298 17.13 - 34.25: 319 34.25 - 51.38: 80 51.38 - 68.50: 17 68.50 - 85.63: 9 Dihedral angle restraints: 2723 sinusoidal: 1038 harmonic: 1685 Sorted by residual: dihedral pdb=" CB CYS A 404 " pdb=" SG CYS A 404 " pdb=" SG CYS A 409 " pdb=" CB CYS A 409 " ideal model delta sinusoidal sigma weight residual -86.00 -7.62 -78.38 1 1.00e+01 1.00e-02 7.67e+01 dihedral pdb=" C CYS A 273 " pdb=" N CYS A 273 " pdb=" CA CYS A 273 " pdb=" CB CYS A 273 " ideal model delta harmonic sigma weight residual -122.60 -134.63 12.03 0 2.50e+00 1.60e-01 2.32e+01 dihedral pdb=" CA ASN B 33 " pdb=" C ASN B 33 " pdb=" N SER B 34 " pdb=" CA SER B 34 " ideal model delta harmonic sigma weight residual 180.00 157.07 22.93 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 2720 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 705 0.085 - 0.170: 60 0.170 - 0.255: 5 0.255 - 0.340: 0 0.340 - 0.425: 1 Chirality restraints: 771 Sorted by residual: chirality pdb=" CA CYS A 273 " pdb=" N CYS A 273 " pdb=" C CYS A 273 " pdb=" CB CYS A 273 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.43 2.00e-01 2.50e+01 4.52e+00 chirality pdb=" CA LYS A 411 " pdb=" N LYS A 411 " pdb=" C LYS A 411 " pdb=" CB LYS A 411 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA CYS A 277 " pdb=" N CYS A 277 " pdb=" C CYS A 277 " pdb=" CB CYS A 277 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 768 not shown) Planarity restraints: 755 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 353 " -0.056 5.00e-02 4.00e+02 8.50e-02 1.15e+01 pdb=" N PRO B 354 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO B 354 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 354 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 275 " -0.023 2.00e-02 2.50e+03 1.55e-02 6.00e+00 pdb=" CG TRP A 275 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP A 275 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP A 275 " 0.010 2.00e-02 2.50e+03 pdb=" NE1 TRP A 275 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 275 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 275 " 0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 275 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 275 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 275 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 411 " 0.011 2.00e-02 2.50e+03 2.35e-02 5.53e+00 pdb=" C LYS A 411 " -0.041 2.00e-02 2.50e+03 pdb=" O LYS A 411 " 0.015 2.00e-02 2.50e+03 pdb=" N GLN A 412 " 0.014 2.00e-02 2.50e+03 ... (remaining 752 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 22 2.55 - 3.14: 3623 3.14 - 3.73: 7114 3.73 - 4.31: 8983 4.31 - 4.90: 15401 Nonbonded interactions: 35143 Sorted by model distance: nonbonded pdb=" OD1 ASP A 40 " pdb="MN MN A 501 " model vdw 1.968 3.060 nonbonded pdb=" OG SER A 252 " pdb="MN MN A 501 " model vdw 1.990 3.060 nonbonded pdb=" OD1 ASN A 127 " pdb="MN MN A 501 " model vdw 2.189 3.060 nonbonded pdb=" NH1 ARG A 103 " pdb=" OE1 GLU A 108 " model vdw 2.244 3.120 nonbonded pdb=" O SER B 34 " pdb=" OG SER B 34 " model vdw 2.301 3.040 ... (remaining 35138 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 385 or resid 398 or resid 405 through 416)) selection = (chain 'B' and (resid 10 through 133 or resid 243 through 385 or resid 387 throu \ gh 416)) } 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: 0.900 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: 0.050 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.400 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 4537 Z= 0.247 Angle : 0.773 9.305 6171 Z= 0.419 Chirality : 0.050 0.425 771 Planarity : 0.006 0.085 755 Dihedral : 17.440 85.626 1622 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.00 % Allowed : 26.65 % Favored : 72.34 % Cbeta Deviations : 0.37 % 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: 1.53 (0.37), residues: 571 helix: 2.32 (0.28), residues: 342 sheet: -0.81 (0.75), residues: 50 loop : -1.07 (0.49), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 367 TYR 0.006 0.001 TYR B 278 PHE 0.016 0.001 PHE A 21 TRP 0.032 0.004 TRP A 275 HIS 0.007 0.002 HIS A 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.25 ( 4534) covalent geometry : angle 0.77091 / 0.42 ( 6165) SS BOND : bond 0.01478 / 0.76 ( 3) SS BOND : angle 1.90233 / 1.16 ( 6) hydrogen bonds : bond 0.12743 / 7.29 ( 296) hydrogen bonds : angle 4.95680 / 3.54 ( 885) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 298 time to evaluate : 0.113 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 ASN cc_start: 0.7298 (m110) cc_final: 0.6598 (m110) REVERT: A 349 LEU cc_start: 0.8516 (tt) cc_final: 0.8262 (tt) REVERT: B 33 ASN cc_start: 0.7960 (p0) cc_final: 0.7735 (p0) outliers start: 5 outliers final: 1 residues processed: 299 average time/residue: 0.0637 time to fit residues: 23.8373 Evaluate side-chains 211 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 210 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 243 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 54 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.2980 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 381 GLN B 127 ASN B 276 GLN B 360 GLN ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.107414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.088742 restraints weight = 10830.315| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 5.11 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4537 Z= 0.156 Angle : 0.747 12.865 6171 Z= 0.364 Chirality : 0.043 0.167 771 Planarity : 0.005 0.043 755 Dihedral : 4.856 53.519 616 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.61 % Allowed : 30.66 % Favored : 64.73 % 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: 1.72 (0.36), residues: 571 helix: 2.23 (0.27), residues: 351 sheet: -0.39 (0.75), residues: 50 loop : -0.72 (0.50), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 367 TYR 0.021 0.002 TYR A 353 PHE 0.013 0.001 PHE A 88 TRP 0.016 0.001 TRP A 275 HIS 0.003 0.001 HIS B 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 4534) covalent geometry : angle 0.74705 / 0.36 ( 6165) SS BOND : bond 0.00136 / 0.07 ( 3) SS BOND : angle 1.08772 / 0.60 ( 6) hydrogen bonds : bond 0.04112 / 2.72 ( 296) hydrogen bonds : angle 4.30897 / 3.09 ( 885) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 215 time to evaluate : 0.165 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8558 (mt-10) REVERT: A 34 SER cc_start: 0.9532 (t) cc_final: 0.9157 (t) REVERT: A 99 GLU cc_start: 0.9112 (tp30) cc_final: 0.8873 (tp30) REVERT: A 109 ARG cc_start: 0.7730 (ttp-110) cc_final: 0.7529 (ptm160) REVERT: A 114 GLU cc_start: 0.8096 (pt0) cc_final: 0.7353 (pm20) REVERT: A 268 LYS cc_start: 0.9136 (tptp) cc_final: 0.8448 (tptp) REVERT: A 308 GLN cc_start: 0.9223 (mp10) cc_final: 0.8535 (mp10) REVERT: A 316 MET cc_start: 0.9067 (tmm) cc_final: 0.8747 (tmm) REVERT: B 33 ASN cc_start: 0.7982 (p0) cc_final: 0.7425 (p0) REVERT: B 108 GLU cc_start: 0.9072 (tp30) cc_final: 0.8847 (tp30) REVERT: B 292 LEU cc_start: 0.9346 (mt) cc_final: 0.9139 (mm) REVERT: B 309 MET cc_start: 0.9369 (mtm) cc_final: 0.9132 (mtm) REVERT: B 315 ASN cc_start: 0.8016 (p0) cc_final: 0.7804 (p0) REVERT: B 334 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8103 (mt-10) REVERT: B 355 LYS cc_start: 0.9557 (tptm) cc_final: 0.9290 (tppp) REVERT: B 379 THR cc_start: 0.9503 (m) cc_final: 0.9100 (p) outliers start: 23 outliers final: 17 residues processed: 227 average time/residue: 0.0585 time to fit residues: 17.1435 Evaluate side-chains 219 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 202 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 407 LYS Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 409 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 27 optimal weight: 0.0570 chunk 17 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 85 ASN B 237 ASN B 381 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.108664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.089659 restraints weight = 10766.495| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 5.14 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 4537 Z= 0.147 Angle : 0.686 10.814 6171 Z= 0.338 Chirality : 0.042 0.156 771 Planarity : 0.004 0.041 755 Dihedral : 4.295 22.909 614 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 7.21 % Allowed : 31.66 % Favored : 61.12 % 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: 1.75 (0.36), residues: 571 helix: 2.26 (0.27), residues: 351 sheet: -0.92 (0.67), residues: 48 loop : -0.51 (0.50), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 367 TYR 0.016 0.002 TYR B 72 PHE 0.009 0.001 PHE A 21 TRP 0.010 0.002 TRP A 338 HIS 0.006 0.001 HIS B 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 4534) covalent geometry : angle 0.68493 / 0.34 ( 6165) SS BOND : bond 0.01072 / 0.56 ( 3) SS BOND : angle 1.32158 / 0.70 ( 6) hydrogen bonds : bond 0.03879 / 2.59 ( 296) hydrogen bonds : angle 4.18498 / 3.01 ( 885) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 214 time to evaluate : 0.168 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.9173 (mt-10) cc_final: 0.8918 (mt-10) REVERT: A 34 SER cc_start: 0.9414 (t) cc_final: 0.9092 (t) REVERT: A 99 GLU cc_start: 0.9188 (tp30) cc_final: 0.8931 (tp30) REVERT: A 109 ARG cc_start: 0.7926 (ttp-110) cc_final: 0.7718 (ptm160) REVERT: A 268 LYS cc_start: 0.9038 (tptp) cc_final: 0.8540 (tptp) REVERT: A 276 GLN cc_start: 0.9186 (mt0) cc_final: 0.8660 (tt0) REVERT: A 308 GLN cc_start: 0.9346 (mp10) cc_final: 0.8676 (mp10) REVERT: A 309 MET cc_start: 0.9138 (mmm) cc_final: 0.8764 (mmm) REVERT: A 316 MET cc_start: 0.9268 (tmm) cc_final: 0.8660 (tmm) REVERT: A 412 GLN cc_start: 0.9010 (mp10) cc_final: 0.8745 (mp10) REVERT: B 33 ASN cc_start: 0.8170 (p0) cc_final: 0.7538 (p0) REVERT: B 108 GLU cc_start: 0.9063 (tp30) cc_final: 0.8810 (tp30) REVERT: B 307 LEU cc_start: 0.9425 (tp) cc_final: 0.9059 (tt) REVERT: B 309 MET cc_start: 0.9338 (mtm) cc_final: 0.8659 (mtm) REVERT: B 315 ASN cc_start: 0.8144 (p0) cc_final: 0.7816 (p0) REVERT: B 317 GLU cc_start: 0.8653 (pm20) cc_final: 0.8388 (pm20) REVERT: B 331 SER cc_start: 0.8417 (t) cc_final: 0.8178 (m) REVERT: B 334 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8133 (mt-10) REVERT: B 355 LYS cc_start: 0.9587 (tptm) cc_final: 0.9311 (tppp) outliers start: 36 outliers final: 22 residues processed: 226 average time/residue: 0.0610 time to fit residues: 17.6708 Evaluate side-chains 224 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 202 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 407 LYS Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 326 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 21 optimal weight: 0.0670 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 381 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.109047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.090856 restraints weight = 10561.198| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 4.93 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.4694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 4537 Z= 0.138 Angle : 0.679 9.994 6171 Z= 0.335 Chirality : 0.043 0.165 771 Planarity : 0.004 0.043 755 Dihedral : 4.321 22.603 614 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 5.01 % Allowed : 36.27 % Favored : 58.72 % 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: 1.71 (0.36), residues: 571 helix: 2.11 (0.27), residues: 355 sheet: -0.96 (0.67), residues: 48 loop : -0.30 (0.52), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 239 TYR 0.020 0.002 TYR A 353 PHE 0.009 0.001 PHE A 13 TRP 0.009 0.001 TRP A 275 HIS 0.004 0.001 HIS B 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 4534) covalent geometry : angle 0.67838 / 0.34 ( 6165) SS BOND : bond 0.00496 / 0.25 ( 3) SS BOND : angle 0.87645 / 0.47 ( 6) hydrogen bonds : bond 0.03779 / 2.56 ( 296) hydrogen bonds : angle 4.13799 / 2.99 ( 885) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 206 time to evaluate : 0.166 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.9102 (mt-10) cc_final: 0.8780 (tt0) REVERT: A 34 SER cc_start: 0.9384 (t) cc_final: 0.8956 (t) REVERT: A 40 ASP cc_start: 0.9264 (t70) cc_final: 0.8470 (t70) REVERT: A 99 GLU cc_start: 0.9252 (tp30) cc_final: 0.8925 (tp30) REVERT: A 109 ARG cc_start: 0.7979 (ttp-110) cc_final: 0.7719 (ptm160) REVERT: A 114 GLU cc_start: 0.7938 (pt0) cc_final: 0.7200 (pm20) REVERT: A 268 LYS cc_start: 0.9012 (tptp) cc_final: 0.8365 (tptp) REVERT: A 276 GLN cc_start: 0.9138 (mt0) cc_final: 0.8660 (tt0) REVERT: A 308 GLN cc_start: 0.9396 (mp10) cc_final: 0.8613 (mp10) REVERT: A 309 MET cc_start: 0.9163 (mmm) cc_final: 0.8821 (mmm) REVERT: A 316 MET cc_start: 0.9303 (tmm) cc_final: 0.8710 (tmm) REVERT: A 339 GLU cc_start: 0.8361 (tt0) cc_final: 0.8152 (tt0) REVERT: A 352 LYS cc_start: 0.8882 (mttt) cc_final: 0.8652 (mttt) REVERT: A 368 GLU cc_start: 0.9151 (tt0) cc_final: 0.8641 (tm-30) REVERT: A 412 GLN cc_start: 0.8992 (mp10) cc_final: 0.8738 (mp10) REVERT: B 33 ASN cc_start: 0.8153 (p0) cc_final: 0.7524 (p0) REVERT: B 108 GLU cc_start: 0.9045 (tp30) cc_final: 0.8812 (tp30) REVERT: B 287 MET cc_start: 0.8833 (tmm) cc_final: 0.8610 (tmm) REVERT: B 309 MET cc_start: 0.9312 (mtm) cc_final: 0.8997 (mtm) REVERT: B 315 ASN cc_start: 0.8156 (p0) cc_final: 0.7699 (p0) REVERT: B 317 GLU cc_start: 0.8647 (pm20) cc_final: 0.8220 (pm20) REVERT: B 331 SER cc_start: 0.8401 (t) cc_final: 0.8172 (m) REVERT: B 334 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8148 (mt-10) outliers start: 25 outliers final: 13 residues processed: 217 average time/residue: 0.0612 time to fit residues: 16.9980 Evaluate side-chains 214 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 201 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 407 LYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 326 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 44 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 ASN B 127 ASN B 384 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.105368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.086978 restraints weight = 10912.134| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 4.90 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.4896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 4537 Z= 0.182 Angle : 0.721 10.272 6171 Z= 0.360 Chirality : 0.044 0.215 771 Planarity : 0.004 0.045 755 Dihedral : 4.391 23.372 614 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 6.01 % Allowed : 34.87 % Favored : 59.12 % 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: 1.52 (0.36), residues: 571 helix: 1.90 (0.27), residues: 358 sheet: -0.95 (0.69), residues: 48 loop : -0.26 (0.55), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 357 TYR 0.021 0.002 TYR A 72 PHE 0.012 0.001 PHE A 21 TRP 0.019 0.002 TRP A 275 HIS 0.006 0.001 HIS B 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.18 ( 4534) covalent geometry : angle 0.72081 / 0.36 ( 6165) SS BOND : bond 0.00772 / 0.40 ( 3) SS BOND : angle 0.86594 / 0.50 ( 6) hydrogen bonds : bond 0.03978 / 2.68 ( 296) hydrogen bonds : angle 4.38792 / 3.19 ( 885) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 199 time to evaluate : 0.168 Fit side-chains revert: symmetry clash REVERT: A 99 GLU cc_start: 0.9270 (tp30) cc_final: 0.8966 (tp30) REVERT: A 103 ARG cc_start: 0.8447 (mtp85) cc_final: 0.8234 (mtp85) REVERT: A 109 ARG cc_start: 0.8113 (ttp-110) cc_final: 0.7873 (ptm160) REVERT: A 111 ASP cc_start: 0.8162 (m-30) cc_final: 0.7919 (m-30) REVERT: A 268 LYS cc_start: 0.9045 (tptp) cc_final: 0.8306 (tptp) REVERT: A 271 ASP cc_start: 0.8934 (OUTLIER) cc_final: 0.8493 (m-30) REVERT: A 276 GLN cc_start: 0.9100 (mt0) cc_final: 0.8614 (tt0) REVERT: A 309 MET cc_start: 0.9221 (mmm) cc_final: 0.8855 (mmm) REVERT: A 315 ASN cc_start: 0.8750 (t0) cc_final: 0.8315 (t0) REVERT: A 317 GLU cc_start: 0.9461 (tp30) cc_final: 0.9152 (tp30) REVERT: A 339 GLU cc_start: 0.8401 (tt0) cc_final: 0.8163 (tt0) REVERT: A 352 LYS cc_start: 0.8786 (mttt) cc_final: 0.8570 (mttt) REVERT: A 368 GLU cc_start: 0.9151 (tt0) cc_final: 0.8584 (tm-30) REVERT: B 33 ASN cc_start: 0.8266 (p0) cc_final: 0.7641 (p0) REVERT: B 287 MET cc_start: 0.8881 (tmm) cc_final: 0.8576 (tmm) REVERT: B 309 MET cc_start: 0.9413 (mtm) cc_final: 0.9061 (mtm) REVERT: B 315 ASN cc_start: 0.8306 (p0) cc_final: 0.7770 (p0) REVERT: B 317 GLU cc_start: 0.8696 (pm20) cc_final: 0.8209 (pm20) REVERT: B 334 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8167 (mt-10) outliers start: 30 outliers final: 18 residues processed: 210 average time/residue: 0.0596 time to fit residues: 15.8600 Evaluate side-chains 210 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 191 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 407 LYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 384 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 26 optimal weight: 0.1980 chunk 32 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 8.9990 chunk 22 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 127 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.107267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.088837 restraints weight = 10980.122| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 5.03 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.5116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4537 Z= 0.148 Angle : 0.723 9.771 6171 Z= 0.357 Chirality : 0.044 0.181 771 Planarity : 0.004 0.040 755 Dihedral : 4.382 22.175 614 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.01 % Allowed : 36.67 % Favored : 59.32 % 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: 1.51 (0.37), residues: 571 helix: 1.90 (0.27), residues: 358 sheet: -1.20 (0.68), residues: 49 loop : -0.21 (0.55), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 367 TYR 0.024 0.002 TYR A 353 PHE 0.023 0.001 PHE A 88 TRP 0.014 0.002 TRP A 275 HIS 0.004 0.001 HIS B 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 ( 4534) covalent geometry : angle 0.72228 / 0.36 ( 6165) SS BOND : bond 0.00373 / 0.19 ( 3) SS BOND : angle 0.92577 / 0.52 ( 6) hydrogen bonds : bond 0.03833 / 2.60 ( 296) hydrogen bonds : angle 4.28727 / 3.12 ( 885) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 199 time to evaluate : 0.132 Fit side-chains revert: symmetry clash REVERT: A 99 GLU cc_start: 0.9272 (tp30) cc_final: 0.8942 (tp30) REVERT: A 106 ARG cc_start: 0.8080 (mtm-85) cc_final: 0.7879 (mtt-85) REVERT: A 114 GLU cc_start: 0.7846 (pt0) cc_final: 0.7137 (pm20) REVERT: A 260 ILE cc_start: 0.8646 (mp) cc_final: 0.8405 (mp) REVERT: A 268 LYS cc_start: 0.8996 (tptp) cc_final: 0.8291 (tptp) REVERT: A 271 ASP cc_start: 0.8970 (OUTLIER) cc_final: 0.8322 (m-30) REVERT: A 276 GLN cc_start: 0.9122 (mt0) cc_final: 0.8638 (tt0) REVERT: A 309 MET cc_start: 0.9207 (mmm) cc_final: 0.8859 (mmm) REVERT: A 315 ASN cc_start: 0.8650 (t0) cc_final: 0.8257 (t0) REVERT: A 317 GLU cc_start: 0.9479 (tp30) cc_final: 0.9164 (tp30) REVERT: A 339 GLU cc_start: 0.8418 (tt0) cc_final: 0.8173 (tt0) REVERT: A 352 LYS cc_start: 0.8765 (mttt) cc_final: 0.8561 (mttt) REVERT: A 368 GLU cc_start: 0.9111 (tt0) cc_final: 0.8584 (tm-30) REVERT: A 377 ASN cc_start: 0.8789 (m-40) cc_final: 0.8426 (m110) REVERT: A 412 GLN cc_start: 0.9110 (mp10) cc_final: 0.8696 (mp10) REVERT: B 33 ASN cc_start: 0.8247 (p0) cc_final: 0.7614 (p0) REVERT: B 236 LEU cc_start: 0.9634 (mm) cc_final: 0.9394 (mp) REVERT: B 287 MET cc_start: 0.8904 (tmm) cc_final: 0.8552 (tmm) REVERT: B 309 MET cc_start: 0.9395 (mtm) cc_final: 0.9099 (mtm) REVERT: B 315 ASN cc_start: 0.8308 (p0) cc_final: 0.7734 (p0) REVERT: B 317 GLU cc_start: 0.8755 (pm20) cc_final: 0.8370 (pm20) outliers start: 20 outliers final: 15 residues processed: 209 average time/residue: 0.0559 time to fit residues: 14.9768 Evaluate side-chains 206 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 190 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 407 LYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 326 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 52 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 15 optimal weight: 0.2980 chunk 30 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.107911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.089645 restraints weight = 10989.089| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 5.01 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.5334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4537 Z= 0.148 Angle : 0.744 11.349 6171 Z= 0.364 Chirality : 0.044 0.177 771 Planarity : 0.004 0.038 755 Dihedral : 4.337 22.648 614 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.01 % Allowed : 38.28 % Favored : 57.72 % 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: 1.56 (0.37), residues: 571 helix: 1.92 (0.27), residues: 357 sheet: -1.17 (0.69), residues: 49 loop : -0.12 (0.56), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 357 TYR 0.013 0.001 TYR B 72 PHE 0.018 0.001 PHE A 88 TRP 0.013 0.001 TRP A 275 HIS 0.006 0.001 HIS B 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 4534) covalent geometry : angle 0.74375 / 0.36 ( 6165) SS BOND : bond 0.00353 / 0.18 ( 3) SS BOND : angle 0.95010 / 0.52 ( 6) hydrogen bonds : bond 0.03856 / 2.61 ( 296) hydrogen bonds : angle 4.30635 / 3.11 ( 885) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 194 time to evaluate : 0.147 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.9202 (mt-10) cc_final: 0.8967 (tt0) REVERT: A 106 ARG cc_start: 0.8133 (mtm-85) cc_final: 0.7910 (mtt-85) REVERT: A 114 GLU cc_start: 0.7796 (pt0) cc_final: 0.7051 (pm20) REVERT: A 260 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8378 (mp) REVERT: A 276 GLN cc_start: 0.9088 (mt0) cc_final: 0.8669 (tt0) REVERT: A 287 MET cc_start: 0.9738 (tpp) cc_final: 0.9369 (mmt) REVERT: A 309 MET cc_start: 0.9196 (OUTLIER) cc_final: 0.8896 (mmm) REVERT: A 315 ASN cc_start: 0.8661 (t0) cc_final: 0.8247 (t0) REVERT: A 317 GLU cc_start: 0.9442 (tp30) cc_final: 0.8944 (tp30) REVERT: A 339 GLU cc_start: 0.8374 (tt0) cc_final: 0.8114 (tt0) REVERT: A 355 LYS cc_start: 0.9194 (tptp) cc_final: 0.8872 (tppt) REVERT: A 368 GLU cc_start: 0.9090 (tt0) cc_final: 0.8621 (tm-30) REVERT: A 377 ASN cc_start: 0.8759 (m-40) cc_final: 0.8540 (m110) REVERT: A 412 GLN cc_start: 0.9106 (mp10) cc_final: 0.8717 (mp10) REVERT: B 33 ASN cc_start: 0.8246 (p0) cc_final: 0.7605 (p0) REVERT: B 236 LEU cc_start: 0.9626 (mm) cc_final: 0.9391 (mp) REVERT: B 287 MET cc_start: 0.8875 (tmm) cc_final: 0.8501 (tmm) REVERT: B 309 MET cc_start: 0.9402 (mtm) cc_final: 0.9108 (mtm) REVERT: B 315 ASN cc_start: 0.8325 (p0) cc_final: 0.7783 (p0) REVERT: B 317 GLU cc_start: 0.8787 (pm20) cc_final: 0.8459 (pm20) outliers start: 20 outliers final: 15 residues processed: 203 average time/residue: 0.0515 time to fit residues: 13.5326 Evaluate side-chains 207 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 190 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 407 LYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 326 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 29 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 16 optimal weight: 0.2980 chunk 45 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.108850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.090305 restraints weight = 10849.797| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 5.16 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.5469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4537 Z= 0.150 Angle : 0.761 11.007 6171 Z= 0.375 Chirality : 0.044 0.201 771 Planarity : 0.004 0.034 755 Dihedral : 4.332 22.963 614 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.01 % Allowed : 39.28 % Favored : 56.71 % 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: 1.52 (0.37), residues: 571 helix: 1.88 (0.27), residues: 357 sheet: -1.19 (0.69), residues: 49 loop : -0.12 (0.56), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 103 TYR 0.012 0.002 TYR B 72 PHE 0.015 0.001 PHE A 88 TRP 0.012 0.001 TRP A 275 HIS 0.005 0.001 HIS B 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 ( 4534) covalent geometry : angle 0.76133 / 0.37 ( 6165) SS BOND : bond 0.00294 / 0.15 ( 3) SS BOND : angle 0.87159 / 0.48 ( 6) hydrogen bonds : bond 0.03891 / 2.63 ( 296) hydrogen bonds : angle 4.37052 / 3.16 ( 885) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 192 time to evaluate : 0.163 Fit side-chains revert: symmetry clash REVERT: A 99 GLU cc_start: 0.9065 (tp30) cc_final: 0.8656 (tp30) REVERT: A 106 ARG cc_start: 0.8062 (mtm-85) cc_final: 0.7844 (mtt-85) REVERT: A 114 GLU cc_start: 0.7785 (pt0) cc_final: 0.7037 (pm20) REVERT: A 260 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8389 (mp) REVERT: A 276 GLN cc_start: 0.9053 (mt0) cc_final: 0.8577 (tt0) REVERT: A 309 MET cc_start: 0.9195 (OUTLIER) cc_final: 0.8898 (mmm) REVERT: A 315 ASN cc_start: 0.8675 (t0) cc_final: 0.8261 (t0) REVERT: A 339 GLU cc_start: 0.8379 (tt0) cc_final: 0.8153 (tt0) REVERT: A 368 GLU cc_start: 0.9078 (tt0) cc_final: 0.8623 (tm-30) REVERT: A 377 ASN cc_start: 0.8740 (m-40) cc_final: 0.8515 (m110) REVERT: A 412 GLN cc_start: 0.9105 (mp10) cc_final: 0.8701 (mp10) REVERT: B 33 ASN cc_start: 0.8277 (p0) cc_final: 0.7616 (p0) REVERT: B 236 LEU cc_start: 0.9634 (mm) cc_final: 0.9401 (mp) REVERT: B 287 MET cc_start: 0.8904 (tmm) cc_final: 0.8516 (tmm) REVERT: B 309 MET cc_start: 0.9423 (mtm) cc_final: 0.9109 (mtm) REVERT: B 315 ASN cc_start: 0.8315 (p0) cc_final: 0.7745 (p0) REVERT: B 317 GLU cc_start: 0.8774 (pm20) cc_final: 0.8510 (pm20) REVERT: B 355 LYS cc_start: 0.9566 (tppt) cc_final: 0.9325 (tppt) outliers start: 20 outliers final: 16 residues processed: 200 average time/residue: 0.0534 time to fit residues: 13.9971 Evaluate side-chains 207 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 189 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 407 LYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 326 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 15 optimal weight: 0.2980 chunk 46 optimal weight: 0.0770 chunk 30 optimal weight: 0.0980 chunk 54 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.109956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.091920 restraints weight = 10736.857| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 4.99 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.5680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4537 Z= 0.143 Angle : 0.785 12.146 6171 Z= 0.381 Chirality : 0.044 0.182 771 Planarity : 0.004 0.034 755 Dihedral : 4.252 22.417 614 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.01 % Allowed : 40.88 % Favored : 56.11 % 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: 1.60 (0.37), residues: 571 helix: 1.94 (0.27), residues: 357 sheet: -0.88 (0.70), residues: 51 loop : -0.18 (0.57), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 103 TYR 0.015 0.001 TYR A 353 PHE 0.013 0.001 PHE A 88 TRP 0.008 0.001 TRP A 275 HIS 0.004 0.001 HIS B 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 4534) covalent geometry : angle 0.78510 / 0.38 ( 6165) SS BOND : bond 0.00341 / 0.18 ( 3) SS BOND : angle 0.90326 / 0.49 ( 6) hydrogen bonds : bond 0.03805 / 2.58 ( 296) hydrogen bonds : angle 4.35753 / 3.15 ( 885) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 194 time to evaluate : 0.136 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.8841 (tt0) cc_final: 0.8517 (tt0) REVERT: A 69 SER cc_start: 0.9132 (p) cc_final: 0.8851 (t) REVERT: A 99 GLU cc_start: 0.9109 (tp30) cc_final: 0.8596 (tp30) REVERT: A 109 ARG cc_start: 0.7531 (ptm160) cc_final: 0.7055 (ptm160) REVERT: A 114 GLU cc_start: 0.7749 (pt0) cc_final: 0.7026 (pm20) REVERT: A 260 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8364 (mp) REVERT: A 276 GLN cc_start: 0.9013 (mt0) cc_final: 0.8590 (tt0) REVERT: A 309 MET cc_start: 0.9174 (OUTLIER) cc_final: 0.8903 (mmm) REVERT: A 315 ASN cc_start: 0.8678 (t0) cc_final: 0.8202 (t0) REVERT: A 318 GLU cc_start: 0.9035 (tm-30) cc_final: 0.8738 (tm-30) REVERT: A 339 GLU cc_start: 0.8377 (tt0) cc_final: 0.8147 (tt0) REVERT: A 355 LYS cc_start: 0.9251 (tptp) cc_final: 0.8967 (tppt) REVERT: A 368 GLU cc_start: 0.9062 (tt0) cc_final: 0.8638 (tm-30) REVERT: A 377 ASN cc_start: 0.8679 (m-40) cc_final: 0.8441 (m110) REVERT: A 412 GLN cc_start: 0.9091 (mp10) cc_final: 0.8686 (mp10) REVERT: B 33 ASN cc_start: 0.8280 (p0) cc_final: 0.7620 (p0) REVERT: B 236 LEU cc_start: 0.9607 (mm) cc_final: 0.9351 (mp) REVERT: B 287 MET cc_start: 0.8881 (tmm) cc_final: 0.8477 (tmm) REVERT: B 309 MET cc_start: 0.9397 (mtm) cc_final: 0.9004 (mtm) REVERT: B 315 ASN cc_start: 0.8217 (p0) cc_final: 0.7709 (p0) REVERT: B 317 GLU cc_start: 0.8824 (pm20) cc_final: 0.8554 (pm20) REVERT: B 355 LYS cc_start: 0.9554 (tppt) cc_final: 0.9296 (tppt) outliers start: 15 outliers final: 9 residues processed: 199 average time/residue: 0.0486 time to fit residues: 12.5032 Evaluate side-chains 201 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 190 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 407 LYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 326 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 4 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 127 ASN ** B 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.108118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.090022 restraints weight = 10943.295| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 4.97 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.5739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4537 Z= 0.160 Angle : 0.810 12.207 6171 Z= 0.394 Chirality : 0.045 0.184 771 Planarity : 0.004 0.033 755 Dihedral : 4.298 22.916 614 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.81 % Allowed : 41.68 % Favored : 55.51 % 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: 1.62 (0.37), residues: 571 helix: 1.92 (0.27), residues: 357 sheet: -1.12 (0.70), residues: 49 loop : 0.01 (0.57), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 357 TYR 0.014 0.002 TYR B 72 PHE 0.012 0.001 PHE A 88 TRP 0.013 0.001 TRP A 275 HIS 0.005 0.001 HIS B 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 ( 4534) covalent geometry : angle 0.80954 / 0.39 ( 6165) SS BOND : bond 0.00388 / 0.20 ( 3) SS BOND : angle 1.05117 / 0.65 ( 6) hydrogen bonds : bond 0.03893 / 2.61 ( 296) hydrogen bonds : angle 4.45515 / 3.22 ( 885) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 188 time to evaluate : 0.112 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.8844 (tt0) cc_final: 0.8500 (tt0) REVERT: A 69 SER cc_start: 0.9216 (p) cc_final: 0.8907 (t) REVERT: A 99 GLU cc_start: 0.9165 (tp30) cc_final: 0.8603 (tp30) REVERT: A 109 ARG cc_start: 0.7579 (ptm160) cc_final: 0.7143 (ptm160) REVERT: A 114 GLU cc_start: 0.7787 (pt0) cc_final: 0.7019 (pm20) REVERT: A 260 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8403 (mp) REVERT: A 276 GLN cc_start: 0.9100 (mt0) cc_final: 0.8635 (tt0) REVERT: A 309 MET cc_start: 0.9217 (OUTLIER) cc_final: 0.8909 (mmm) REVERT: A 315 ASN cc_start: 0.8708 (t0) cc_final: 0.8241 (t0) REVERT: A 318 GLU cc_start: 0.9014 (tm-30) cc_final: 0.8713 (tm-30) REVERT: A 339 GLU cc_start: 0.8368 (tt0) cc_final: 0.8165 (tt0) REVERT: A 368 GLU cc_start: 0.9077 (tt0) cc_final: 0.8637 (tm-30) REVERT: A 377 ASN cc_start: 0.8742 (m-40) cc_final: 0.8516 (m110) REVERT: A 412 GLN cc_start: 0.9064 (mp10) cc_final: 0.8662 (mp10) REVERT: B 33 ASN cc_start: 0.8362 (p0) cc_final: 0.7642 (p0) REVERT: B 108 GLU cc_start: 0.8947 (tp30) cc_final: 0.8738 (tp30) REVERT: B 236 LEU cc_start: 0.9608 (mm) cc_final: 0.9358 (mp) REVERT: B 287 MET cc_start: 0.8881 (tmm) cc_final: 0.8598 (tmm) REVERT: B 309 MET cc_start: 0.9441 (mtm) cc_final: 0.9193 (mtm) REVERT: B 315 ASN cc_start: 0.8248 (p0) cc_final: 0.7755 (p0) REVERT: B 317 GLU cc_start: 0.8809 (pm20) cc_final: 0.8567 (pm20) REVERT: B 355 LYS cc_start: 0.9513 (tppt) cc_final: 0.9236 (tppt) REVERT: B 360 GLN cc_start: 0.9281 (tm-30) cc_final: 0.8786 (tm-30) outliers start: 14 outliers final: 10 residues processed: 195 average time/residue: 0.0506 time to fit residues: 12.8286 Evaluate side-chains 199 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 187 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 407 LYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 326 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 20 optimal weight: 0.8980 chunk 34 optimal weight: 0.3980 chunk 2 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 44 optimal weight: 0.0170 chunk 5 optimal weight: 0.8980 chunk 22 optimal weight: 0.3980 chunk 43 optimal weight: 0.7980 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.110145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.091984 restraints weight = 10820.925| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 4.99 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.5904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4537 Z= 0.144 Angle : 0.808 12.736 6171 Z= 0.392 Chirality : 0.045 0.192 771 Planarity : 0.004 0.034 755 Dihedral : 4.276 21.722 614 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.81 % Allowed : 41.48 % Favored : 55.71 % 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: 1.63 (0.37), residues: 571 helix: 1.91 (0.27), residues: 357 sheet: -1.08 (0.69), residues: 49 loop : 0.06 (0.58), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 357 TYR 0.012 0.001 TYR A 353 PHE 0.012 0.001 PHE A 88 TRP 0.008 0.001 TRP A 275 HIS 0.004 0.001 HIS B 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 ( 4534) covalent geometry : angle 0.80803 / 0.39 ( 6165) SS BOND : bond 0.00348 / 0.18 ( 3) SS BOND : angle 0.94547 / 0.56 ( 6) hydrogen bonds : bond 0.03876 / 2.61 ( 296) hydrogen bonds : angle 4.38765 / 3.18 ( 885) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 914.48 seconds wall clock time: 16 minutes 23.97 seconds (983.97 seconds total)