Starting phenix.real_space_refine on Wed Mar 5 17:30:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gs9_34226/03_2025/8gs9_34226.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gs9_34226/03_2025/8gs9_34226.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gs9_34226/03_2025/8gs9_34226.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gs9_34226/03_2025/8gs9_34226.map" model { file = "/net/cci-nas-00/data/ceres_data/8gs9_34226/03_2025/8gs9_34226.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gs9_34226/03_2025/8gs9_34226.cif" } resolution = 2.66 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.041 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 12 5.16 5 C 1984 2.51 5 N 531 2.21 5 O 589 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3116 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1462 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 171} Chain: "H" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 881 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain: "K" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 773 Classifications: {'peptide': 102} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 96} Time building chain proxies: 3.25, per 1000 atoms: 1.04 Number of scatterers: 3116 At special positions: 0 Unit cell: (67.545, 58.995, 94.905, 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 12 16.00 O 589 8.00 N 531 7.00 C 1984 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 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: 0.77 Conformation dependent library (CDL) restraints added in 381.3 milliseconds 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 724 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 9 sheets defined 12.1% alpha, 38.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 371 removed outlier: 4.143A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 371' Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.515A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.017A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'H' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.954A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.687A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N TYR H 33 " --> pdb=" O SER H 98 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE H 105 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.687A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N TYR H 33 " --> pdb=" O SER H 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AA8, first strand: chain 'K' and resid 11 through 12 removed outlier: 6.535A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 11 through 12 130 hydrogen bonds defined for protein. 300 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: 0.88 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1009 1.34 - 1.46: 845 1.46 - 1.58: 1326 1.58 - 1.70: 0 1.70 - 1.82: 14 Bond restraints: 3194 Sorted by residual: bond pdb=" N VAL A 362 " pdb=" CA VAL A 362 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.19e-02 7.06e+03 8.98e+00 bond pdb=" N ASN A 360 " pdb=" CA ASN A 360 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.29e-02 6.01e+03 8.39e+00 bond pdb=" N CYS A 361 " pdb=" CA CYS A 361 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.26e-02 6.30e+03 6.87e+00 bond pdb=" N SER A 359 " pdb=" CA SER A 359 " ideal model delta sigma weight residual 1.457 1.486 -0.028 1.29e-02 6.01e+03 4.81e+00 bond pdb=" N ALA A 363 " pdb=" CA ALA A 363 " ideal model delta sigma weight residual 1.457 1.482 -0.025 1.24e-02 6.50e+03 4.10e+00 ... (remaining 3189 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.92: 4007 0.92 - 1.84: 260 1.84 - 2.76: 45 2.76 - 3.68: 18 3.68 - 4.60: 5 Bond angle restraints: 4335 Sorted by residual: angle pdb=" CA VAL A 362 " pdb=" C VAL A 362 " pdb=" O VAL A 362 " ideal model delta sigma weight residual 121.36 117.47 3.89 1.10e+00 8.26e-01 1.25e+01 angle pdb=" N ALA K 51 " pdb=" CA ALA K 51 " pdb=" CB ALA K 51 " ideal model delta sigma weight residual 114.17 110.62 3.55 1.14e+00 7.69e-01 9.68e+00 angle pdb=" CA SER A 359 " pdb=" C SER A 359 " pdb=" O SER A 359 " ideal model delta sigma weight residual 120.51 116.68 3.83 1.43e+00 4.89e-01 7.17e+00 angle pdb=" C ASN A 450 " pdb=" N TYR A 451 " pdb=" CA TYR A 451 " ideal model delta sigma weight residual 121.54 126.14 -4.60 1.91e+00 2.74e-01 5.80e+00 angle pdb=" CA ALA A 363 " pdb=" C ALA A 363 " pdb=" O ALA A 363 " ideal model delta sigma weight residual 120.32 117.78 2.54 1.11e+00 8.12e-01 5.25e+00 ... (remaining 4330 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.49: 1681 13.49 - 26.98: 138 26.98 - 40.48: 38 40.48 - 53.97: 9 53.97 - 67.46: 6 Dihedral angle restraints: 1872 sinusoidal: 729 harmonic: 1143 Sorted by residual: dihedral pdb=" CA PHE A 490 " pdb=" C PHE A 490 " pdb=" N PRO A 491 " pdb=" CA PRO A 491 " ideal model delta harmonic sigma weight residual -180.00 -162.67 -17.33 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA GLN H 13 " pdb=" C GLN H 13 " pdb=" N PRO H 14 " pdb=" CA PRO H 14 " ideal model delta harmonic sigma weight residual 180.00 -163.10 -16.90 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA LYS A 478 " pdb=" C LYS A 478 " pdb=" N PRO A 479 " pdb=" CA PRO A 479 " ideal model delta harmonic sigma weight residual -180.00 -163.49 -16.51 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 1869 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 300 0.035 - 0.070: 109 0.070 - 0.105: 30 0.105 - 0.140: 20 0.140 - 0.175: 2 Chirality restraints: 461 Sorted by residual: chirality pdb=" CA VAL A 362 " pdb=" N VAL A 362 " pdb=" C VAL A 362 " pdb=" CB VAL A 362 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.17 2.00e-01 2.50e+01 7.63e-01 chirality pdb=" CA VAL H 37 " pdb=" N VAL H 37 " pdb=" C VAL H 37 " pdb=" CB VAL H 37 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.98e-01 chirality pdb=" CA ILE K 21 " pdb=" N ILE K 21 " pdb=" C ILE K 21 " pdb=" CB ILE K 21 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.79e-01 ... (remaining 458 not shown) Planarity restraints: 564 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 358 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.29e+00 pdb=" C ILE A 358 " -0.031 2.00e-02 2.50e+03 pdb=" O ILE A 358 " 0.012 2.00e-02 2.50e+03 pdb=" N SER A 359 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 478 " 0.022 5.00e-02 4.00e+02 3.38e-02 1.83e+00 pdb=" N PRO A 479 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 479 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 479 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN H 32 " -0.006 2.00e-02 2.50e+03 1.16e-02 1.34e+00 pdb=" C ASN H 32 " 0.020 2.00e-02 2.50e+03 pdb=" O ASN H 32 " -0.008 2.00e-02 2.50e+03 pdb=" N TYR H 33 " -0.007 2.00e-02 2.50e+03 ... (remaining 561 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 940 2.82 - 3.34: 2496 3.34 - 3.86: 4712 3.86 - 4.38: 5702 4.38 - 4.90: 10174 Nonbonded interactions: 24024 Sorted by model distance: nonbonded pdb=" NE2 GLN K 89 " pdb=" O GLU K 91 " model vdw 2.297 3.120 nonbonded pdb=" N GLU H 6 " pdb=" OE1 GLU H 6 " model vdw 2.347 3.120 nonbonded pdb=" OH TYR A 473 " pdb=" O ARG H 31 " model vdw 2.378 3.040 nonbonded pdb=" NE ARG H 38 " pdb=" OE1 GLU H 46 " model vdw 2.428 3.120 nonbonded pdb=" N GLY H 15 " pdb=" O LEU H 85 " model vdw 2.437 3.120 ... (remaining 24019 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.750 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.350 Find NCS groups from input model: 0.030 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:12.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 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 : 0.003 0.037 3194 Z= 0.216 Angle : 0.547 4.601 4335 Z= 0.320 Chirality : 0.045 0.175 461 Planarity : 0.003 0.034 564 Dihedral : 11.977 67.459 1136 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.64 % Favored : 93.85 % Rotamer: Outliers : 0.60 % Allowed : 5.37 % Favored : 94.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.40), residues: 390 helix: -3.37 (0.74), residues: 27 sheet: 0.37 (0.44), residues: 124 loop : -0.30 (0.37), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.001 0.000 HIS A 505 PHE 0.008 0.001 PHE A 456 TYR 0.007 0.001 TYR H 52 ARG 0.002 0.000 ARG K 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 88 time to evaluate : 0.363 Fit side-chains REVERT: A 456 PHE cc_start: 0.7267 (OUTLIER) cc_final: 0.6797 (p90) REVERT: A 516 GLU cc_start: 0.6176 (mt-10) cc_final: 0.5760 (mt-10) REVERT: K 83 PHE cc_start: 0.5818 (m-80) cc_final: 0.5538 (m-80) outliers start: 2 outliers final: 0 residues processed: 90 average time/residue: 1.0678 time to fit residues: 99.0277 Evaluate side-chains 52 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 16 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 30 optimal weight: 0.0570 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 ASN H 108 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.148671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.136953 restraints weight = 6897.891| |-----------------------------------------------------------------------------| r_work (start): 0.4114 rms_B_bonded: 2.23 r_work: 0.4026 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 3194 Z= 0.171 Angle : 0.541 7.273 4335 Z= 0.296 Chirality : 0.045 0.157 461 Planarity : 0.004 0.025 564 Dihedral : 4.637 32.022 444 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.33 % Favored : 96.41 % Rotamer: Outliers : 4.78 % Allowed : 15.22 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.41), residues: 390 helix: -3.33 (0.73), residues: 26 sheet: 0.59 (0.48), residues: 113 loop : -0.28 (0.37), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.001 0.000 HIS K 90 PHE 0.008 0.001 PHE A 456 TYR 0.009 0.001 TYR H 52 ARG 0.005 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.369 Fit side-chains REVERT: A 456 PHE cc_start: 0.7352 (OUTLIER) cc_final: 0.6698 (p90) REVERT: K 18 ARG cc_start: 0.6879 (OUTLIER) cc_final: 0.5916 (ttp-170) REVERT: K 83 PHE cc_start: 0.6169 (m-80) cc_final: 0.5875 (m-80) outliers start: 16 outliers final: 7 residues processed: 64 average time/residue: 0.9762 time to fit residues: 64.6830 Evaluate side-chains 57 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 20 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.146286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.134163 restraints weight = 6856.946| |-----------------------------------------------------------------------------| r_work (start): 0.4066 rms_B_bonded: 2.19 r_work: 0.3990 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 3194 Z= 0.393 Angle : 0.742 8.946 4335 Z= 0.390 Chirality : 0.050 0.276 461 Planarity : 0.005 0.036 564 Dihedral : 5.691 47.226 444 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.64 % Favored : 94.10 % Rotamer: Outliers : 5.37 % Allowed : 17.01 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.41), residues: 390 helix: -3.48 (0.72), residues: 26 sheet: -0.00 (0.45), residues: 140 loop : -0.47 (0.38), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 353 HIS 0.001 0.000 HIS K 90 PHE 0.016 0.002 PHE H 105 TYR 0.022 0.002 TYR H 52 ARG 0.006 0.001 ARG K 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 53 time to evaluate : 0.364 Fit side-chains REVERT: A 456 PHE cc_start: 0.7733 (OUTLIER) cc_final: 0.6754 (p90) REVERT: H 20 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7238 (mm) REVERT: K 18 ARG cc_start: 0.6946 (OUTLIER) cc_final: 0.5877 (ttp-170) outliers start: 18 outliers final: 8 residues processed: 64 average time/residue: 1.1225 time to fit residues: 74.1302 Evaluate side-chains 56 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 72 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 27 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 29 optimal weight: 20.0000 chunk 32 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 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 = 0.4220 r_free = 0.4220 target = 0.145936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.133885 restraints weight = 6911.966| |-----------------------------------------------------------------------------| r_work (start): 0.4065 rms_B_bonded: 2.18 r_work: 0.3991 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 3194 Z= 0.295 Angle : 0.674 13.503 4335 Z= 0.353 Chirality : 0.047 0.270 461 Planarity : 0.004 0.032 564 Dihedral : 5.603 52.464 444 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 6.27 % Allowed : 18.81 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.41), residues: 390 helix: -3.48 (0.76), residues: 26 sheet: 0.14 (0.46), residues: 138 loop : -0.55 (0.38), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 436 HIS 0.001 0.000 HIS K 90 PHE 0.014 0.001 PHE A 456 TYR 0.018 0.002 TYR H 52 ARG 0.007 0.001 ARG K 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 51 time to evaluate : 0.345 Fit side-chains REVERT: H 20 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7298 (mm) REVERT: K 18 ARG cc_start: 0.6953 (OUTLIER) cc_final: 0.5890 (ttp-170) REVERT: K 38 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7732 (tt0) outliers start: 21 outliers final: 10 residues processed: 64 average time/residue: 1.0547 time to fit residues: 69.8486 Evaluate side-chains 58 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 105 PHE Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 72 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 14 optimal weight: 0.0970 chunk 1 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 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 = 0.4228 r_free = 0.4228 target = 0.146290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.134275 restraints weight = 6913.059| |-----------------------------------------------------------------------------| r_work (start): 0.4075 rms_B_bonded: 2.21 r_work: 0.4001 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 3194 Z= 0.212 Angle : 0.605 9.804 4335 Z= 0.315 Chirality : 0.045 0.228 461 Planarity : 0.004 0.028 564 Dihedral : 5.189 52.866 444 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.78 % Allowed : 21.79 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.42), residues: 390 helix: -3.38 (0.81), residues: 26 sheet: 0.34 (0.47), residues: 133 loop : -0.51 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.001 0.000 HIS K 90 PHE 0.013 0.001 PHE A 456 TYR 0.013 0.001 TYR H 33 ARG 0.004 0.000 ARG K 42 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.380 Fit side-chains REVERT: H 20 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7337 (mm) REVERT: K 18 ARG cc_start: 0.6839 (OUTLIER) cc_final: 0.5831 (ttp-170) outliers start: 16 outliers final: 9 residues processed: 62 average time/residue: 1.0000 time to fit residues: 64.1530 Evaluate side-chains 56 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 105 PHE Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 72 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 29 optimal weight: 0.3980 chunk 22 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 14 optimal weight: 0.0770 chunk 38 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 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 = 0.4240 r_free = 0.4240 target = 0.146846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.134591 restraints weight = 7063.008| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 2.25 r_work: 0.4005 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 3194 Z= 0.227 Angle : 0.625 12.284 4335 Z= 0.324 Chirality : 0.044 0.203 461 Planarity : 0.004 0.027 564 Dihedral : 5.217 53.812 444 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.48 % Allowed : 22.99 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.41), residues: 390 helix: -3.32 (0.73), residues: 29 sheet: 0.38 (0.48), residues: 133 loop : -0.53 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.001 0.000 HIS K 90 PHE 0.013 0.001 PHE A 456 TYR 0.012 0.001 TYR H 33 ARG 0.004 0.000 ARG K 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.339 Fit side-chains REVERT: H 20 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7338 (mm) REVERT: K 18 ARG cc_start: 0.6791 (OUTLIER) cc_final: 0.5751 (ttp-170) REVERT: K 38 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7790 (tt0) outliers start: 15 outliers final: 9 residues processed: 58 average time/residue: 1.0492 time to fit residues: 62.8840 Evaluate side-chains 56 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 72 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 chunk 4 optimal weight: 0.0070 chunk 36 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 chunk 8 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.2804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 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 = 0.4231 r_free = 0.4231 target = 0.146086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.133803 restraints weight = 6830.697| |-----------------------------------------------------------------------------| r_work (start): 0.4070 rms_B_bonded: 2.24 r_work: 0.3994 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 3194 Z= 0.243 Angle : 0.661 13.155 4335 Z= 0.343 Chirality : 0.046 0.239 461 Planarity : 0.004 0.026 564 Dihedral : 5.526 59.765 444 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.78 % Allowed : 23.28 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.41), residues: 390 helix: -3.40 (0.69), residues: 29 sheet: 0.37 (0.48), residues: 133 loop : -0.73 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 47 HIS 0.001 0.000 HIS K 90 PHE 0.014 0.001 PHE A 456 TYR 0.014 0.001 TYR H 33 ARG 0.004 0.000 ARG K 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 45 time to evaluate : 0.349 Fit side-chains REVERT: A 389 ASP cc_start: 0.7662 (m-30) cc_final: 0.7402 (m-30) REVERT: H 20 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7308 (mm) REVERT: K 18 ARG cc_start: 0.6894 (OUTLIER) cc_final: 0.5874 (ttp-170) REVERT: K 38 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7755 (tt0) outliers start: 16 outliers final: 11 residues processed: 56 average time/residue: 1.0816 time to fit residues: 62.5503 Evaluate side-chains 56 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 105 PHE Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 9 SER Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 72 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 14 optimal weight: 0.0970 chunk 12 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 108 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.147123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.134624 restraints weight = 6859.067| |-----------------------------------------------------------------------------| r_work (start): 0.4083 rms_B_bonded: 2.27 r_work: 0.4007 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 3194 Z= 0.192 Angle : 0.633 12.207 4335 Z= 0.330 Chirality : 0.044 0.216 461 Planarity : 0.004 0.026 564 Dihedral : 5.217 57.541 444 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.78 % Allowed : 23.88 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.41), residues: 390 helix: -3.43 (0.69), residues: 29 sheet: 0.46 (0.48), residues: 133 loop : -0.74 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.001 0.000 HIS K 90 PHE 0.013 0.001 PHE A 456 TYR 0.012 0.001 TYR H 33 ARG 0.006 0.000 ARG K 42 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 42 time to evaluate : 0.380 Fit side-chains REVERT: H 20 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7320 (mm) REVERT: K 18 ARG cc_start: 0.6794 (OUTLIER) cc_final: 0.5760 (ttp-170) REVERT: K 38 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7787 (tt0) outliers start: 16 outliers final: 10 residues processed: 55 average time/residue: 1.1456 time to fit residues: 65.0259 Evaluate side-chains 54 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 9 SER Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 72 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 8 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.145580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.133080 restraints weight = 6866.240| |-----------------------------------------------------------------------------| r_work (start): 0.4061 rms_B_bonded: 2.27 r_work: 0.3983 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 3194 Z= 0.291 Angle : 0.712 12.338 4335 Z= 0.369 Chirality : 0.046 0.233 461 Planarity : 0.004 0.028 564 Dihedral : 5.432 49.165 444 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.48 % Allowed : 23.58 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.41), residues: 390 helix: -3.48 (0.68), residues: 29 sheet: 0.34 (0.48), residues: 133 loop : -0.88 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 47 HIS 0.001 0.000 HIS K 90 PHE 0.016 0.001 PHE A 456 TYR 0.015 0.002 TYR H 33 ARG 0.005 0.001 ARG K 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.370 Fit side-chains REVERT: H 20 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7330 (mm) REVERT: K 18 ARG cc_start: 0.6890 (OUTLIER) cc_final: 0.5901 (ttp-170) REVERT: K 38 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7756 (tt0) outliers start: 15 outliers final: 9 residues processed: 54 average time/residue: 1.1302 time to fit residues: 62.9750 Evaluate side-chains 53 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 9 SER Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 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 = 0.4236 r_free = 0.4236 target = 0.146535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.134112 restraints weight = 6750.005| |-----------------------------------------------------------------------------| r_work (start): 0.4073 rms_B_bonded: 2.25 r_work: 0.3996 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 3194 Z= 0.210 Angle : 0.661 11.967 4335 Z= 0.347 Chirality : 0.045 0.222 461 Planarity : 0.004 0.027 564 Dihedral : 5.016 43.159 444 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.18 % Allowed : 24.18 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.41), residues: 390 helix: -3.26 (0.75), residues: 29 sheet: 0.39 (0.49), residues: 133 loop : -0.79 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.001 0.000 HIS K 90 PHE 0.013 0.001 PHE A 456 TYR 0.012 0.001 TYR H 33 ARG 0.006 0.000 ARG K 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 20 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7294 (mm) REVERT: K 18 ARG cc_start: 0.6784 (OUTLIER) cc_final: 0.5750 (ttp-170) REVERT: K 38 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7775 (tt0) outliers start: 14 outliers final: 10 residues processed: 55 average time/residue: 1.1513 time to fit residues: 65.3877 Evaluate side-chains 56 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 9 SER Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 36 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 34 optimal weight: 0.3980 chunk 27 optimal weight: 0.7980 chunk 20 optimal weight: 0.0870 chunk 13 optimal weight: 0.0070 chunk 12 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.147900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.135374 restraints weight = 6869.636| |-----------------------------------------------------------------------------| r_work (start): 0.4090 rms_B_bonded: 2.30 r_work: 0.4011 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 3194 Z= 0.183 Angle : 0.627 11.685 4335 Z= 0.329 Chirality : 0.044 0.211 461 Planarity : 0.004 0.026 564 Dihedral : 4.561 37.485 444 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.88 % Allowed : 25.67 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.41), residues: 390 helix: -3.16 (0.79), residues: 29 sheet: 0.84 (0.50), residues: 123 loop : -0.79 (0.36), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.001 0.000 HIS K 90 PHE 0.010 0.001 PHE A 456 TYR 0.010 0.001 TYR H 33 ARG 0.006 0.000 ARG K 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2704.02 seconds wall clock time: 46 minutes 55.77 seconds (2815.77 seconds total)