Starting phenix.real_space_refine on Tue Nov 19 09:06:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9chp_45597/11_2024/9chp_45597.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9chp_45597/11_2024/9chp_45597.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9chp_45597/11_2024/9chp_45597.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9chp_45597/11_2024/9chp_45597.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9chp_45597/11_2024/9chp_45597.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9chp_45597/11_2024/9chp_45597.cif" } resolution = 3.3 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= -0.000 sd= 0.004 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 S 48 5.16 5 C 6292 2.51 5 N 1568 2.21 5 O 1600 1.98 5 H 9596 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 19104 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 4776 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 11, 'TRANS': 281} Chain breaks: 3 Restraints were copied for chains: C, B, D Time building chain proxies: 10.84, per 1000 atoms: 0.57 Number of scatterers: 19104 At special positions: 0 Unit cell: (122.85, 122.85, 96.6, 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) S 48 16.00 O 1600 8.00 N 1568 7.00 C 6292 6.00 H 9596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.87 Conformation dependent library (CDL) restraints added in 1.3 seconds 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2208 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 0 sheets defined 81.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 404 through 432 Proline residue: A 426 - end of helix Processing helix chain 'A' and resid 450 through 472 removed outlier: 3.692A pdb=" N ILE A 467 " --> pdb=" O PHE A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 496 removed outlier: 3.635A pdb=" N HIS A 492 " --> pdb=" O ARG A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 504 Processing helix chain 'A' and resid 507 through 512 Processing helix chain 'A' and resid 517 through 525 removed outlier: 3.726A pdb=" N LYS A 525 " --> pdb=" O ILE A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 530 Processing helix chain 'A' and resid 531 through 538 removed outlier: 3.928A pdb=" N VAL A 535 " --> pdb=" O ARG A 531 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS A 538 " --> pdb=" O ARG A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 543 Processing helix chain 'A' and resid 545 through 575 Processing helix chain 'A' and resid 584 through 593 removed outlier: 3.571A pdb=" N ASN A 588 " --> pdb=" O GLY A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 623 Processing helix chain 'A' and resid 634 through 667 removed outlier: 3.709A pdb=" N PHE A 656 " --> pdb=" O TYR A 652 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLY A 657 " --> pdb=" O ALA A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 687 Processing helix chain 'A' and resid 690 through 709 Processing helix chain 'B' and resid 404 through 432 Proline residue: B 426 - end of helix Processing helix chain 'B' and resid 450 through 472 removed outlier: 3.692A pdb=" N ILE B 467 " --> pdb=" O PHE B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 496 removed outlier: 3.635A pdb=" N HIS B 492 " --> pdb=" O ARG B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 504 Processing helix chain 'B' and resid 507 through 512 Processing helix chain 'B' and resid 517 through 525 removed outlier: 3.726A pdb=" N LYS B 525 " --> pdb=" O ILE B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 530 Processing helix chain 'B' and resid 531 through 538 removed outlier: 3.928A pdb=" N VAL B 535 " --> pdb=" O ARG B 531 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS B 538 " --> pdb=" O ARG B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 543 Processing helix chain 'B' and resid 545 through 575 Processing helix chain 'B' and resid 584 through 593 removed outlier: 3.571A pdb=" N ASN B 588 " --> pdb=" O GLY B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 623 Processing helix chain 'B' and resid 634 through 667 removed outlier: 3.709A pdb=" N PHE B 656 " --> pdb=" O TYR B 652 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLY B 657 " --> pdb=" O ALA B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 687 Processing helix chain 'B' and resid 690 through 709 Processing helix chain 'C' and resid 404 through 432 Proline residue: C 426 - end of helix Processing helix chain 'C' and resid 450 through 472 removed outlier: 3.692A pdb=" N ILE C 467 " --> pdb=" O PHE C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 496 removed outlier: 3.635A pdb=" N HIS C 492 " --> pdb=" O ARG C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 504 Processing helix chain 'C' and resid 507 through 512 Processing helix chain 'C' and resid 517 through 525 removed outlier: 3.726A pdb=" N LYS C 525 " --> pdb=" O ILE C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 530 Processing helix chain 'C' and resid 531 through 538 removed outlier: 3.928A pdb=" N VAL C 535 " --> pdb=" O ARG C 531 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS C 538 " --> pdb=" O ARG C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 543 Processing helix chain 'C' and resid 545 through 575 Processing helix chain 'C' and resid 584 through 593 removed outlier: 3.571A pdb=" N ASN C 588 " --> pdb=" O GLY C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 606 through 623 Processing helix chain 'C' and resid 634 through 667 removed outlier: 3.709A pdb=" N PHE C 656 " --> pdb=" O TYR C 652 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLY C 657 " --> pdb=" O ALA C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 687 Processing helix chain 'C' and resid 690 through 709 Processing helix chain 'D' and resid 404 through 432 Proline residue: D 426 - end of helix Processing helix chain 'D' and resid 450 through 472 removed outlier: 3.692A pdb=" N ILE D 467 " --> pdb=" O PHE D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 496 removed outlier: 3.635A pdb=" N HIS D 492 " --> pdb=" O ARG D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 504 Processing helix chain 'D' and resid 507 through 512 Processing helix chain 'D' and resid 517 through 525 removed outlier: 3.726A pdb=" N LYS D 525 " --> pdb=" O ILE D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 530 Processing helix chain 'D' and resid 531 through 538 removed outlier: 3.928A pdb=" N VAL D 535 " --> pdb=" O ARG D 531 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS D 538 " --> pdb=" O ARG D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 543 Processing helix chain 'D' and resid 545 through 575 Processing helix chain 'D' and resid 584 through 593 removed outlier: 3.571A pdb=" N ASN D 588 " --> pdb=" O GLY D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 606 through 623 Processing helix chain 'D' and resid 634 through 667 removed outlier: 3.709A pdb=" N PHE D 656 " --> pdb=" O TYR D 652 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLY D 657 " --> pdb=" O ALA D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 667 through 687 Processing helix chain 'D' and resid 690 through 709 680 hydrogen bonds defined for protein. 2016 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: 6.90 Time building geometry restraints manager: 5.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 9580 1.13 - 1.30: 1520 1.30 - 1.48: 4040 1.48 - 1.65: 4152 1.65 - 1.82: 80 Bond restraints: 19372 Sorted by residual: bond pdb=" CE2 PHE B 686 " pdb=" HE2 PHE B 686 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" CE2 PHE D 686 " pdb=" HE2 PHE D 686 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" CE2 PHE C 686 " pdb=" HE2 PHE C 686 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" CE2 PHE A 686 " pdb=" HE2 PHE A 686 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N ASN A 691 " pdb=" H ASN A 691 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 ... (remaining 19367 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 29473 2.54 - 5.08: 4211 5.08 - 7.62: 1164 7.62 - 10.16: 48 10.16 - 12.70: 16 Bond angle restraints: 34912 Sorted by residual: angle pdb=" CB HIS A 587 " pdb=" CG HIS A 587 " pdb=" CD2 HIS A 587 " ideal model delta sigma weight residual 131.20 124.72 6.48 1.30e+00 5.92e-01 2.49e+01 angle pdb=" CB HIS D 587 " pdb=" CG HIS D 587 " pdb=" CD2 HIS D 587 " ideal model delta sigma weight residual 131.20 124.72 6.48 1.30e+00 5.92e-01 2.49e+01 angle pdb=" CB HIS C 587 " pdb=" CG HIS C 587 " pdb=" CD2 HIS C 587 " ideal model delta sigma weight residual 131.20 124.72 6.48 1.30e+00 5.92e-01 2.49e+01 angle pdb=" CB HIS B 587 " pdb=" CG HIS B 587 " pdb=" CD2 HIS B 587 " ideal model delta sigma weight residual 131.20 124.72 6.48 1.30e+00 5.92e-01 2.49e+01 angle pdb=" CA ASP A 540 " pdb=" CB ASP A 540 " pdb=" CG ASP A 540 " ideal model delta sigma weight residual 112.60 117.30 -4.70 1.00e+00 1.00e+00 2.21e+01 ... (remaining 34907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.62: 8412 15.62 - 31.24: 456 31.24 - 46.86: 152 46.86 - 62.48: 92 62.48 - 78.10: 12 Dihedral angle restraints: 9124 sinusoidal: 4760 harmonic: 4364 Sorted by residual: dihedral pdb=" CA HIS B 578 " pdb=" C HIS B 578 " pdb=" N MET B 579 " pdb=" CA MET B 579 " ideal model delta harmonic sigma weight residual 180.00 -151.10 -28.90 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA HIS C 578 " pdb=" C HIS C 578 " pdb=" N MET C 579 " pdb=" CA MET C 579 " ideal model delta harmonic sigma weight residual -180.00 -151.10 -28.90 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA HIS D 578 " pdb=" C HIS D 578 " pdb=" N MET D 579 " pdb=" CA MET D 579 " ideal model delta harmonic sigma weight residual -180.00 -151.10 -28.90 0 5.00e+00 4.00e-02 3.34e+01 ... (remaining 9121 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 948 0.081 - 0.163: 448 0.163 - 0.244: 76 0.244 - 0.326: 20 0.326 - 0.407: 4 Chirality restraints: 1496 Sorted by residual: chirality pdb=" CA SER A 624 " pdb=" N SER A 624 " pdb=" C SER A 624 " pdb=" CB SER A 624 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.14e+00 chirality pdb=" CA SER B 624 " pdb=" N SER B 624 " pdb=" C SER B 624 " pdb=" CB SER B 624 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.14e+00 chirality pdb=" CA SER D 624 " pdb=" N SER D 624 " pdb=" C SER D 624 " pdb=" CB SER D 624 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.14e+00 ... (remaining 1493 not shown) Planarity restraints: 2732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 534 " 0.508 9.50e-02 1.11e+02 1.85e-01 1.52e+02 pdb=" NE ARG A 534 " 0.038 2.00e-02 2.50e+03 pdb=" CZ ARG A 534 " 0.028 2.00e-02 2.50e+03 pdb=" NH1 ARG A 534 " 0.080 2.00e-02 2.50e+03 pdb=" NH2 ARG A 534 " -0.035 2.00e-02 2.50e+03 pdb="HH11 ARG A 534 " -0.171 2.00e-02 2.50e+03 pdb="HH12 ARG A 534 " 0.093 2.00e-02 2.50e+03 pdb="HH21 ARG A 534 " -0.029 2.00e-02 2.50e+03 pdb="HH22 ARG A 534 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 534 " 0.508 9.50e-02 1.11e+02 1.85e-01 1.52e+02 pdb=" NE ARG D 534 " 0.038 2.00e-02 2.50e+03 pdb=" CZ ARG D 534 " 0.028 2.00e-02 2.50e+03 pdb=" NH1 ARG D 534 " 0.080 2.00e-02 2.50e+03 pdb=" NH2 ARG D 534 " -0.035 2.00e-02 2.50e+03 pdb="HH11 ARG D 534 " -0.171 2.00e-02 2.50e+03 pdb="HH12 ARG D 534 " 0.093 2.00e-02 2.50e+03 pdb="HH21 ARG D 534 " -0.029 2.00e-02 2.50e+03 pdb="HH22 ARG D 534 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 534 " 0.508 9.50e-02 1.11e+02 1.85e-01 1.52e+02 pdb=" NE ARG C 534 " 0.038 2.00e-02 2.50e+03 pdb=" CZ ARG C 534 " 0.028 2.00e-02 2.50e+03 pdb=" NH1 ARG C 534 " 0.080 2.00e-02 2.50e+03 pdb=" NH2 ARG C 534 " -0.035 2.00e-02 2.50e+03 pdb="HH11 ARG C 534 " -0.171 2.00e-02 2.50e+03 pdb="HH12 ARG C 534 " 0.093 2.00e-02 2.50e+03 pdb="HH21 ARG C 534 " -0.029 2.00e-02 2.50e+03 pdb="HH22 ARG C 534 " -0.026 2.00e-02 2.50e+03 ... (remaining 2729 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 1016 2.21 - 2.81: 34968 2.81 - 3.41: 52855 3.41 - 4.00: 68966 4.00 - 4.60: 99356 Nonbonded interactions: 257161 Sorted by model distance: nonbonded pdb=" OE2 GLU A 575 " pdb=" HG SER A 636 " model vdw 1.614 2.450 nonbonded pdb=" OE2 GLU B 575 " pdb=" HG SER B 636 " model vdw 1.614 2.450 nonbonded pdb=" OE2 GLU C 575 " pdb=" HG SER C 636 " model vdw 1.614 2.450 nonbonded pdb=" OE2 GLU D 575 " pdb=" HG SER D 636 " model vdw 1.614 2.450 nonbonded pdb=" HH TYR B 420 " pdb=" OD1 ASP B 456 " model vdw 1.625 2.450 ... (remaining 257156 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.830 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: 0.340 Extract box with map and model: 0.770 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 41.900 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.030 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.042 9776 Z= 0.825 Angle : 1.747 8.061 13288 Z= 1.208 Chirality : 0.092 0.407 1496 Planarity : 0.018 0.163 1620 Dihedral : 11.611 78.104 3420 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.91 (0.24), residues: 1140 helix: -0.82 (0.15), residues: 904 sheet: None (None), residues: 0 loop : 1.22 (0.52), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.107 0.019 TRP B 705 HIS 0.010 0.003 HIS B 587 PHE 0.069 0.014 PHE C 701 TYR 0.136 0.023 TYR B 652 ARG 0.008 0.001 ARG A 531 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 1.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 502 MET cc_start: 0.7094 (tpt) cc_final: 0.6808 (tpt) REVERT: A 688 GLN cc_start: 0.8171 (mt0) cc_final: 0.7498 (tm-30) REVERT: B 502 MET cc_start: 0.7023 (tpt) cc_final: 0.6745 (tpt) REVERT: B 688 GLN cc_start: 0.8118 (mt0) cc_final: 0.7488 (tm-30) REVERT: C 502 MET cc_start: 0.7079 (tpt) cc_final: 0.6797 (tpt) REVERT: C 688 GLN cc_start: 0.8181 (mt0) cc_final: 0.7479 (tm-30) REVERT: D 502 MET cc_start: 0.7103 (tpt) cc_final: 0.6819 (tpt) REVERT: D 688 GLN cc_start: 0.8177 (mt0) cc_final: 0.7494 (tm-30) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.5766 time to fit residues: 147.0385 Evaluate side-chains 156 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 HIS A 687 HIS B 674 HIS B 687 HIS C 674 HIS C 687 HIS D 674 HIS D 687 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9776 Z= 0.219 Angle : 0.584 7.216 13288 Z= 0.322 Chirality : 0.040 0.127 1496 Planarity : 0.005 0.058 1620 Dihedral : 4.835 24.507 1280 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.78 % Allowed : 2.84 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.12 (0.25), residues: 1140 helix: 0.66 (0.16), residues: 908 sheet: None (None), residues: 0 loop : 1.70 (0.51), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 585 HIS 0.003 0.001 HIS A 687 PHE 0.014 0.002 PHE A 656 TYR 0.015 0.002 TYR A 611 ARG 0.003 0.001 ARG D 665 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 148 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 502 MET cc_start: 0.7145 (tpt) cc_final: 0.6725 (tpt) REVERT: B 502 MET cc_start: 0.7086 (tpt) cc_final: 0.6665 (tpt) REVERT: C 502 MET cc_start: 0.7142 (tpt) cc_final: 0.6718 (tpt) REVERT: D 502 MET cc_start: 0.7166 (tpt) cc_final: 0.6742 (tpt) outliers start: 8 outliers final: 0 residues processed: 156 average time/residue: 0.6213 time to fit residues: 127.3330 Evaluate side-chains 144 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9776 Z= 0.349 Angle : 0.593 8.154 13288 Z= 0.329 Chirality : 0.041 0.131 1496 Planarity : 0.004 0.048 1620 Dihedral : 4.615 23.636 1280 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.39 % Allowed : 6.37 % Favored : 93.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.18 (0.24), residues: 1140 helix: 0.81 (0.16), residues: 904 sheet: None (None), residues: 0 loop : 1.24 (0.46), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 585 HIS 0.004 0.001 HIS A 402 PHE 0.013 0.002 PHE B 656 TYR 0.015 0.002 TYR D 616 ARG 0.003 0.000 ARG B 679 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 148 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 502 MET cc_start: 0.7337 (tpt) cc_final: 0.6906 (tpt) REVERT: B 502 MET cc_start: 0.7270 (tpt) cc_final: 0.6841 (tpt) REVERT: C 502 MET cc_start: 0.7330 (tpt) cc_final: 0.6898 (tpt) REVERT: D 502 MET cc_start: 0.7354 (tpt) cc_final: 0.6922 (tpt) outliers start: 4 outliers final: 4 residues processed: 148 average time/residue: 0.6323 time to fit residues: 122.9246 Evaluate side-chains 144 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 140 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain C residue 682 GLU Chi-restraints excluded: chain D residue 682 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 GLN B 576 GLN C 576 GLN D 576 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9776 Z= 0.282 Angle : 0.534 6.900 13288 Z= 0.294 Chirality : 0.039 0.132 1496 Planarity : 0.004 0.044 1620 Dihedral : 4.406 23.187 1280 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.78 % Allowed : 7.55 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.35 (0.24), residues: 1140 helix: 0.93 (0.16), residues: 908 sheet: None (None), residues: 0 loop : 1.28 (0.45), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 585 HIS 0.002 0.001 HIS D 492 PHE 0.013 0.001 PHE A 656 TYR 0.015 0.002 TYR D 616 ARG 0.007 0.001 ARG D 528 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 152 time to evaluate : 1.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 502 MET cc_start: 0.7409 (tpt) cc_final: 0.6958 (tpt) REVERT: B 502 MET cc_start: 0.7344 (tpt) cc_final: 0.6890 (tpt) REVERT: C 502 MET cc_start: 0.7394 (tpt) cc_final: 0.6944 (tpt) REVERT: D 502 MET cc_start: 0.7419 (tpt) cc_final: 0.6967 (tpt) outliers start: 8 outliers final: 8 residues processed: 152 average time/residue: 0.6201 time to fit residues: 123.7660 Evaluate side-chains 152 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 144 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 682 GLU Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 682 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 9776 Z= 0.253 Angle : 0.491 4.632 13288 Z= 0.273 Chirality : 0.038 0.133 1496 Planarity : 0.004 0.042 1620 Dihedral : 4.247 21.843 1280 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.57 % Allowed : 7.55 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.55 (0.24), residues: 1140 helix: 1.08 (0.17), residues: 908 sheet: None (None), residues: 0 loop : 1.29 (0.45), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 585 HIS 0.002 0.001 HIS D 674 PHE 0.011 0.002 PHE A 656 TYR 0.014 0.002 TYR B 616 ARG 0.006 0.001 ARG A 528 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 481 GLU cc_start: 0.2668 (tp30) cc_final: 0.2458 (tp30) REVERT: A 502 MET cc_start: 0.7447 (tpt) cc_final: 0.6949 (tpt) REVERT: A 652 TYR cc_start: 0.7763 (OUTLIER) cc_final: 0.6741 (m-80) REVERT: B 481 GLU cc_start: 0.2583 (tp30) cc_final: 0.2359 (tp30) REVERT: B 502 MET cc_start: 0.7389 (tpt) cc_final: 0.6894 (tpt) REVERT: B 652 TYR cc_start: 0.7704 (OUTLIER) cc_final: 0.6663 (m-80) REVERT: C 481 GLU cc_start: 0.2632 (tp30) cc_final: 0.2420 (tp30) REVERT: C 502 MET cc_start: 0.7441 (tpt) cc_final: 0.6942 (tpt) REVERT: C 652 TYR cc_start: 0.7754 (OUTLIER) cc_final: 0.6724 (m-80) REVERT: D 481 GLU cc_start: 0.2655 (tp30) cc_final: 0.2437 (tp30) REVERT: D 502 MET cc_start: 0.7465 (tpt) cc_final: 0.6969 (tpt) REVERT: D 652 TYR cc_start: 0.7760 (OUTLIER) cc_final: 0.6730 (m-80) outliers start: 16 outliers final: 8 residues processed: 156 average time/residue: 0.5356 time to fit residues: 112.0458 Evaluate side-chains 159 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 652 TYR Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 652 TYR Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 652 TYR Chi-restraints excluded: chain C residue 682 GLU Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 652 TYR Chi-restraints excluded: chain D residue 682 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 9776 Z= 0.181 Angle : 0.453 4.554 13288 Z= 0.249 Chirality : 0.037 0.136 1496 Planarity : 0.004 0.041 1620 Dihedral : 4.050 21.191 1280 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.18 % Allowed : 7.94 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.83 (0.25), residues: 1140 helix: 1.23 (0.17), residues: 916 sheet: None (None), residues: 0 loop : 1.62 (0.47), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 568 HIS 0.002 0.001 HIS D 674 PHE 0.010 0.001 PHE B 656 TYR 0.014 0.001 TYR D 616 ARG 0.006 0.000 ARG A 528 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 502 MET cc_start: 0.7385 (tpt) cc_final: 0.6881 (tpt) REVERT: B 502 MET cc_start: 0.7322 (tpt) cc_final: 0.6820 (tpt) REVERT: C 502 MET cc_start: 0.7379 (tpt) cc_final: 0.6872 (tpt) REVERT: D 502 MET cc_start: 0.7404 (tpt) cc_final: 0.6900 (tpt) outliers start: 12 outliers final: 8 residues processed: 149 average time/residue: 0.5610 time to fit residues: 111.4913 Evaluate side-chains 153 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 145 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 682 GLU Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 682 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 9776 Z= 0.172 Angle : 0.440 4.574 13288 Z= 0.240 Chirality : 0.037 0.137 1496 Planarity : 0.004 0.040 1620 Dihedral : 3.897 20.240 1280 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.18 % Allowed : 8.73 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.17 (0.25), residues: 1140 helix: 1.47 (0.17), residues: 916 sheet: None (None), residues: 0 loop : 1.72 (0.47), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 568 HIS 0.002 0.001 HIS D 674 PHE 0.010 0.001 PHE D 656 TYR 0.014 0.001 TYR C 616 ARG 0.006 0.000 ARG A 528 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 502 MET cc_start: 0.7415 (tpt) cc_final: 0.6785 (tpt) REVERT: B 502 MET cc_start: 0.7353 (tpt) cc_final: 0.6717 (tpt) REVERT: C 502 MET cc_start: 0.7409 (tpt) cc_final: 0.6777 (tpt) REVERT: D 502 MET cc_start: 0.7434 (tpt) cc_final: 0.6806 (tpt) outliers start: 12 outliers final: 12 residues processed: 147 average time/residue: 0.5630 time to fit residues: 111.2433 Evaluate side-chains 147 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 554 MET Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 554 MET Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 554 MET Chi-restraints excluded: chain C residue 682 GLU Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 554 MET Chi-restraints excluded: chain D residue 682 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 107 optimal weight: 0.3980 chunk 97 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 9776 Z= 0.264 Angle : 0.492 4.601 13288 Z= 0.272 Chirality : 0.038 0.135 1496 Planarity : 0.004 0.040 1620 Dihedral : 4.012 20.208 1280 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.57 % Allowed : 8.14 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.94 (0.25), residues: 1140 helix: 1.31 (0.17), residues: 912 sheet: None (None), residues: 0 loop : 1.66 (0.48), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 585 HIS 0.003 0.001 HIS D 674 PHE 0.013 0.001 PHE B 656 TYR 0.016 0.002 TYR B 616 ARG 0.007 0.000 ARG D 679 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 502 MET cc_start: 0.7486 (tpt) cc_final: 0.6859 (tpt) REVERT: A 538 LYS cc_start: 0.8158 (mttt) cc_final: 0.7851 (mttt) REVERT: B 502 MET cc_start: 0.7418 (tpt) cc_final: 0.6787 (tpt) REVERT: B 538 LYS cc_start: 0.8193 (mttt) cc_final: 0.7893 (mttt) REVERT: C 502 MET cc_start: 0.7475 (tpt) cc_final: 0.6848 (tpt) REVERT: C 538 LYS cc_start: 0.8141 (mttt) cc_final: 0.7836 (mttt) REVERT: D 502 MET cc_start: 0.7502 (tpt) cc_final: 0.6877 (tpt) REVERT: D 538 LYS cc_start: 0.8149 (mttt) cc_final: 0.7843 (mttt) REVERT: D 677 MET cc_start: 0.8106 (tpp) cc_final: 0.7883 (tpp) outliers start: 16 outliers final: 12 residues processed: 152 average time/residue: 0.6127 time to fit residues: 124.4810 Evaluate side-chains 159 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 554 MET Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 554 MET Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 554 MET Chi-restraints excluded: chain C residue 682 GLU Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 554 MET Chi-restraints excluded: chain D residue 682 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 110 optimal weight: 0.0060 chunk 67 optimal weight: 3.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 635 ASN C 635 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 9776 Z= 0.153 Angle : 0.429 4.591 13288 Z= 0.232 Chirality : 0.036 0.138 1496 Planarity : 0.004 0.039 1620 Dihedral : 3.812 19.986 1280 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.18 % Allowed : 8.73 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.36 (0.25), residues: 1140 helix: 1.61 (0.17), residues: 908 sheet: None (None), residues: 0 loop : 1.78 (0.48), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 568 HIS 0.002 0.001 HIS D 674 PHE 0.009 0.001 PHE D 656 TYR 0.013 0.001 TYR C 616 ARG 0.007 0.001 ARG D 679 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 137 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 502 MET cc_start: 0.7429 (tpt) cc_final: 0.6785 (tpt) REVERT: B 502 MET cc_start: 0.7360 (tpt) cc_final: 0.6711 (tpt) REVERT: C 502 MET cc_start: 0.7420 (tpt) cc_final: 0.6774 (tpt) REVERT: D 502 MET cc_start: 0.7445 (tpt) cc_final: 0.6803 (tpt) outliers start: 12 outliers final: 12 residues processed: 137 average time/residue: 0.5628 time to fit residues: 103.0545 Evaluate side-chains 145 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 133 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 554 MET Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 554 MET Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 554 MET Chi-restraints excluded: chain C residue 682 GLU Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 554 MET Chi-restraints excluded: chain D residue 682 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 2.9990 chunk 76 optimal weight: 0.1980 chunk 115 optimal weight: 0.9980 chunk 106 optimal weight: 0.0670 chunk 92 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 635 ASN B 635 ASN C 635 ASN D 635 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 9776 Z= 0.147 Angle : 0.427 4.536 13288 Z= 0.229 Chirality : 0.036 0.139 1496 Planarity : 0.004 0.039 1620 Dihedral : 3.698 19.325 1280 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.18 % Allowed : 9.41 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.57 (0.25), residues: 1140 helix: 1.75 (0.17), residues: 908 sheet: None (None), residues: 0 loop : 1.87 (0.49), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 705 HIS 0.002 0.000 HIS D 674 PHE 0.009 0.001 PHE A 656 TYR 0.014 0.001 TYR B 616 ARG 0.006 0.000 ARG D 679 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 137 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 502 MET cc_start: 0.7423 (tpt) cc_final: 0.6779 (tpt) REVERT: B 502 MET cc_start: 0.7356 (tpt) cc_final: 0.6704 (tpt) REVERT: C 502 MET cc_start: 0.7409 (tpt) cc_final: 0.6765 (tpt) REVERT: D 502 MET cc_start: 0.7437 (tpt) cc_final: 0.6797 (tpt) outliers start: 12 outliers final: 12 residues processed: 137 average time/residue: 0.5840 time to fit residues: 106.5554 Evaluate side-chains 148 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 136 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 554 MET Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 554 MET Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 554 MET Chi-restraints excluded: chain C residue 682 GLU Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 554 MET Chi-restraints excluded: chain D residue 682 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 635 ASN D 635 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.184735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.128246 restraints weight = 28314.593| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.97 r_work: 0.3004 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 9776 Z= 0.276 Angle : 0.496 4.648 13288 Z= 0.273 Chirality : 0.039 0.136 1496 Planarity : 0.004 0.040 1620 Dihedral : 3.922 19.477 1280 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.18 % Allowed : 9.31 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.07 (0.25), residues: 1140 helix: 1.44 (0.17), residues: 908 sheet: None (None), residues: 0 loop : 1.53 (0.48), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 585 HIS 0.003 0.001 HIS D 674 PHE 0.012 0.002 PHE D 656 TYR 0.017 0.002 TYR C 616 ARG 0.005 0.000 ARG D 679 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4269.60 seconds wall clock time: 77 minutes 19.33 seconds (4639.33 seconds total)