Starting phenix.real_space_refine on Thu Mar 13 07:45:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bc1_15959/03_2025/8bc1_15959.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bc1_15959/03_2025/8bc1_15959.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bc1_15959/03_2025/8bc1_15959.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bc1_15959/03_2025/8bc1_15959.map" model { file = "/net/cci-nas-00/data/ceres_data/8bc1_15959/03_2025/8bc1_15959.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bc1_15959/03_2025/8bc1_15959.cif" } resolution = 2.93 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= -0.001 sd= 0.019 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 Ca 6 9.91 5 S 62 5.16 5 C 5758 2.51 5 N 1366 2.21 5 O 1492 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8684 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4339 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 25, 'TRANS': 501} Chain breaks: 6 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: B Time building chain proxies: 7.72, per 1000 atoms: 0.89 Number of scatterers: 8684 At special positions: 0 Unit cell: (123.69, 79.422, 98.952, 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) Ca 6 19.99 S 62 16.00 O 1492 8.00 N 1366 7.00 C 5758 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 372 " distance=2.03 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 365 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 807 " distance=2.03 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 601 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 372 " distance=2.03 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 365 " distance=2.03 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 807 " distance=2.03 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 601 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.40 Conformation dependent library (CDL) restraints added in 940.5 milliseconds 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2000 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 0 sheets defined 74.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 276 through 281 removed outlier: 4.612A pdb=" N TYR A 280 " --> pdb=" O ARG A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 292 Processing helix chain 'A' and resid 293 through 328 removed outlier: 3.619A pdb=" N LEU A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 338 Processing helix chain 'A' and resid 342 through 346 Processing helix chain 'A' and resid 360 through 363 removed outlier: 3.648A pdb=" N ILE A 363 " --> pdb=" O ARG A 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 360 through 363' Processing helix chain 'A' and resid 364 through 372 Processing helix chain 'A' and resid 376 through 409 removed outlier: 3.671A pdb=" N LEU A 394 " --> pdb=" O VAL A 390 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU A 395 " --> pdb=" O THR A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 426 removed outlier: 3.697A pdb=" N GLN A 426 " --> pdb=" O GLU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 487 removed outlier: 4.235A pdb=" N ILE A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 539 removed outlier: 3.924A pdb=" N THR A 526 " --> pdb=" O MET A 522 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE A 527 " --> pdb=" O ILE A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 573 removed outlier: 4.760A pdb=" N SER A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N CYS A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 639 Proline residue: A 628 - end of helix removed outlier: 3.687A pdb=" N ARG A 639 " --> pdb=" O GLY A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 655 removed outlier: 3.513A pdb=" N HIS A 655 " --> pdb=" O GLU A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 681 removed outlier: 3.780A pdb=" N PHE A 681 " --> pdb=" O PHE A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 709 removed outlier: 3.659A pdb=" N LEU A 691 " --> pdb=" O LEU A 687 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG A 701 " --> pdb=" O ILE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 746 removed outlier: 4.159A pdb=" N VAL A 738 " --> pdb=" O ILE A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 760 Processing helix chain 'A' and resid 796 through 802 removed outlier: 4.416A pdb=" N GLY A 800 " --> pdb=" O ASN A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 857 removed outlier: 3.553A pdb=" N TRP A 829 " --> pdb=" O ASN A 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 272 Processing helix chain 'B' and resid 276 through 281 removed outlier: 4.614A pdb=" N TYR B 280 " --> pdb=" O ARG B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 292 Processing helix chain 'B' and resid 293 through 328 removed outlier: 3.619A pdb=" N LEU B 312 " --> pdb=" O GLN B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 338 Processing helix chain 'B' and resid 342 through 346 Processing helix chain 'B' and resid 360 through 363 removed outlier: 3.647A pdb=" N ILE B 363 " --> pdb=" O ARG B 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 360 through 363' Processing helix chain 'B' and resid 364 through 372 Processing helix chain 'B' and resid 376 through 409 removed outlier: 3.672A pdb=" N LEU B 394 " --> pdb=" O VAL B 390 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU B 395 " --> pdb=" O THR B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 426 removed outlier: 3.696A pdb=" N GLN B 426 " --> pdb=" O GLU B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 487 removed outlier: 4.234A pdb=" N ILE B 483 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 539 removed outlier: 3.923A pdb=" N THR B 526 " --> pdb=" O MET B 522 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE B 527 " --> pdb=" O ILE B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 573 removed outlier: 4.760A pdb=" N SER B 566 " --> pdb=" O ASN B 562 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N CYS B 567 " --> pdb=" O TYR B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 639 Proline residue: B 628 - end of helix removed outlier: 3.687A pdb=" N ARG B 639 " --> pdb=" O GLY B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 655 removed outlier: 3.513A pdb=" N HIS B 655 " --> pdb=" O GLU B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 681 removed outlier: 3.780A pdb=" N PHE B 681 " --> pdb=" O PHE B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 709 removed outlier: 3.660A pdb=" N LEU B 691 " --> pdb=" O LEU B 687 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG B 701 " --> pdb=" O ILE B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 746 removed outlier: 4.159A pdb=" N VAL B 738 " --> pdb=" O ILE B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 760 Processing helix chain 'B' and resid 796 through 802 removed outlier: 4.417A pdb=" N GLY B 800 " --> pdb=" O ASN B 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 857 removed outlier: 3.552A pdb=" N TRP B 829 " --> pdb=" O ASN B 825 " (cutoff:3.500A) 579 hydrogen bonds defined for protein. 1713 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: 2.45 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2590 1.35 - 1.46: 2389 1.46 - 1.58: 3853 1.58 - 1.70: 0 1.70 - 1.82: 96 Bond restraints: 8928 Sorted by residual: bond pdb=" CA VAL B 411 " pdb=" CB VAL B 411 " ideal model delta sigma weight residual 1.530 1.541 -0.010 1.05e-02 9.07e+03 9.92e-01 bond pdb=" CA VAL A 411 " pdb=" CB VAL A 411 " ideal model delta sigma weight residual 1.530 1.540 -0.010 1.05e-02 9.07e+03 8.51e-01 bond pdb=" CA ILE B 751 " pdb=" CB ILE B 751 " ideal model delta sigma weight residual 1.539 1.534 0.005 5.40e-03 3.43e+04 7.43e-01 bond pdb=" CA ILE A 700 " pdb=" C ILE A 700 " ideal model delta sigma weight residual 1.524 1.514 0.010 1.22e-02 6.72e+03 6.40e-01 bond pdb=" CA PHE A 685 " pdb=" CB PHE A 685 " ideal model delta sigma weight residual 1.532 1.544 -0.013 1.67e-02 3.59e+03 6.00e-01 ... (remaining 8923 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 11780 1.11 - 2.22: 263 2.22 - 3.32: 71 3.32 - 4.43: 8 4.43 - 5.54: 8 Bond angle restraints: 12130 Sorted by residual: angle pdb=" N PRO A 763 " pdb=" CA PRO A 763 " pdb=" C PRO A 763 " ideal model delta sigma weight residual 110.70 113.26 -2.56 1.22e+00 6.72e-01 4.40e+00 angle pdb=" N PRO B 763 " pdb=" CA PRO B 763 " pdb=" C PRO B 763 " ideal model delta sigma weight residual 110.70 113.23 -2.53 1.22e+00 6.72e-01 4.29e+00 angle pdb=" C TYR B 580 " pdb=" CA TYR B 580 " pdb=" CB TYR B 580 " ideal model delta sigma weight residual 109.22 112.23 -3.01 1.52e+00 4.33e-01 3.92e+00 angle pdb=" C TYR A 580 " pdb=" CA TYR A 580 " pdb=" CB TYR A 580 " ideal model delta sigma weight residual 109.22 112.20 -2.98 1.52e+00 4.33e-01 3.85e+00 angle pdb=" CA PRO B 763 " pdb=" C PRO B 763 " pdb=" N PRO B 764 " ideal model delta sigma weight residual 117.93 120.18 -2.25 1.20e+00 6.94e-01 3.51e+00 ... (remaining 12125 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.66: 4748 12.66 - 25.33: 336 25.33 - 37.99: 96 37.99 - 50.65: 32 50.65 - 63.31: 8 Dihedral angle restraints: 5220 sinusoidal: 2106 harmonic: 3114 Sorted by residual: dihedral pdb=" CA VAL A 625 " pdb=" C VAL A 625 " pdb=" N LEU A 626 " pdb=" CA LEU A 626 " ideal model delta harmonic sigma weight residual -180.00 -164.06 -15.94 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CA VAL B 625 " pdb=" C VAL B 625 " pdb=" N LEU B 626 " pdb=" CA LEU B 626 " ideal model delta harmonic sigma weight residual -180.00 -164.07 -15.93 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" N GLU B 395 " pdb=" CA GLU B 395 " pdb=" CB GLU B 395 " pdb=" CG GLU B 395 " ideal model delta sinusoidal sigma weight residual -60.00 -117.63 57.63 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 5217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 812 0.025 - 0.050: 276 0.050 - 0.075: 173 0.075 - 0.100: 63 0.100 - 0.125: 8 Chirality restraints: 1332 Sorted by residual: chirality pdb=" CA VAL B 715 " pdb=" N VAL B 715 " pdb=" C VAL B 715 " pdb=" CB VAL B 715 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.89e-01 chirality pdb=" CA VAL A 715 " pdb=" N VAL A 715 " pdb=" C VAL A 715 " pdb=" CB VAL A 715 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.80e-01 chirality pdb=" CA PRO A 689 " pdb=" N PRO A 689 " pdb=" C PRO A 689 " pdb=" CB PRO A 689 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.05e-01 ... (remaining 1329 not shown) Planarity restraints: 1486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 700 " -0.007 2.00e-02 2.50e+03 1.43e-02 2.05e+00 pdb=" C ILE A 700 " 0.025 2.00e-02 2.50e+03 pdb=" O ILE A 700 " -0.009 2.00e-02 2.50e+03 pdb=" N ARG A 701 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 697 " 0.007 2.00e-02 2.50e+03 1.42e-02 2.03e+00 pdb=" C ILE B 697 " -0.025 2.00e-02 2.50e+03 pdb=" O ILE B 697 " 0.009 2.00e-02 2.50e+03 pdb=" N LEU B 698 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 697 " -0.007 2.00e-02 2.50e+03 1.42e-02 2.01e+00 pdb=" C ILE A 697 " 0.025 2.00e-02 2.50e+03 pdb=" O ILE A 697 " -0.009 2.00e-02 2.50e+03 pdb=" N LEU A 698 " -0.008 2.00e-02 2.50e+03 ... (remaining 1483 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2201 2.79 - 3.32: 9052 3.32 - 3.85: 14674 3.85 - 4.37: 16711 4.37 - 4.90: 28388 Nonbonded interactions: 71026 Sorted by model distance: nonbonded pdb=" O LEU B 626 " pdb=" N VAL B 630 " model vdw 2.265 3.120 nonbonded pdb=" O LEU A 626 " pdb=" N VAL A 630 " model vdw 2.265 3.120 nonbonded pdb=" O THR B 364 " pdb=" OG SER B 367 " model vdw 2.273 3.040 nonbonded pdb=" O THR A 364 " pdb=" OG SER A 367 " model vdw 2.273 3.040 nonbonded pdb=" O SER A 376 " pdb=" OG1 THR A 379 " model vdw 2.281 3.040 ... (remaining 71021 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.840 Find NCS groups from input model: 0.160 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:42.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5220 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 : 0.002 0.018 8928 Z= 0.122 Angle : 0.458 5.542 12130 Z= 0.261 Chirality : 0.036 0.125 1332 Planarity : 0.004 0.032 1486 Dihedral : 10.381 63.314 3196 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.43 % Allowed : 5.25 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.53 (0.26), residues: 1026 helix: 1.62 (0.19), residues: 738 sheet: None (None), residues: 0 loop : -0.51 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 397 HIS 0.002 0.001 HIS A 830 PHE 0.011 0.001 PHE B 393 TYR 0.011 0.001 TYR A 580 ARG 0.002 0.000 ARG B 592 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 252 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 LEU cc_start: 0.8370 (mt) cc_final: 0.8006 (tp) REVERT: A 381 ILE cc_start: 0.6080 (mt) cc_final: 0.5828 (mt) REVERT: A 386 MET cc_start: 0.5095 (mmp) cc_final: 0.4500 (mmp) REVERT: A 530 LYS cc_start: 0.6932 (mmtm) cc_final: 0.6593 (mmmm) REVERT: A 595 GLU cc_start: 0.5110 (mp0) cc_final: 0.3651 (tm-30) REVERT: A 613 MET cc_start: 0.6979 (mtp) cc_final: 0.6312 (mtp) REVERT: A 638 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7104 (tmmt) REVERT: A 813 ARG cc_start: 0.4596 (mtt90) cc_final: 0.3334 (ppt170) REVERT: B 285 LEU cc_start: 0.8377 (mt) cc_final: 0.8019 (tp) REVERT: B 381 ILE cc_start: 0.6065 (mt) cc_final: 0.5805 (mt) REVERT: B 386 MET cc_start: 0.5120 (mmp) cc_final: 0.4486 (mmp) REVERT: B 507 MET cc_start: 0.5033 (ttm) cc_final: 0.4176 (tpp) REVERT: B 530 LYS cc_start: 0.6927 (mmtm) cc_final: 0.6587 (mmmm) REVERT: B 595 GLU cc_start: 0.5123 (mp0) cc_final: 0.3668 (tm-30) REVERT: B 613 MET cc_start: 0.6980 (mtp) cc_final: 0.6311 (mtp) REVERT: B 638 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7140 (tmmt) REVERT: B 813 ARG cc_start: 0.4723 (mtt90) cc_final: 0.3329 (ppt170) outliers start: 32 outliers final: 3 residues processed: 280 average time/residue: 0.8959 time to fit residues: 272.8583 Evaluate side-chains 170 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 165 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 638 LYS Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 826 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 chunk 43 optimal weight: 0.0020 chunk 26 optimal weight: 0.5980 chunk 53 optimal weight: 5.9990 chunk 42 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 GLN ** A 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 632 ASN A 730 GLN A 814 ASN A 830 HIS B 401 GLN B 559 GLN B 632 ASN B 730 GLN B 814 ASN B 830 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5248 r_free = 0.5248 target = 0.269961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.5059 r_free = 0.5059 target = 0.248916 restraints weight = 14181.110| |-----------------------------------------------------------------------------| r_work (start): 0.5064 rms_B_bonded: 2.53 r_work: 0.4976 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.4976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5305 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 8928 Z= 0.236 Angle : 0.647 10.985 12130 Z= 0.335 Chirality : 0.042 0.163 1332 Planarity : 0.005 0.045 1486 Dihedral : 4.291 42.945 1172 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.64 % Allowed : 14.99 % Favored : 81.37 % 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: 1.56 (0.26), residues: 1026 helix: 1.61 (0.18), residues: 740 sheet: None (None), residues: 0 loop : -0.41 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 408 HIS 0.020 0.002 HIS B 844 PHE 0.013 0.001 PHE B 558 TYR 0.015 0.001 TYR A 668 ARG 0.004 0.001 ARG B 592 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 180 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 381 ILE cc_start: 0.6319 (mt) cc_final: 0.6032 (mt) REVERT: A 553 MET cc_start: 0.6826 (tmt) cc_final: 0.6372 (tmm) REVERT: A 595 GLU cc_start: 0.4783 (mp0) cc_final: 0.3307 (tm-30) REVERT: A 613 MET cc_start: 0.6999 (mtp) cc_final: 0.6279 (ttm) REVERT: A 638 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7065 (tmmt) REVERT: A 813 ARG cc_start: 0.4741 (mtt90) cc_final: 0.3251 (ppt170) REVERT: B 381 ILE cc_start: 0.6359 (mt) cc_final: 0.6068 (mt) REVERT: B 553 MET cc_start: 0.6807 (tmt) cc_final: 0.6355 (tmm) REVERT: B 595 GLU cc_start: 0.4800 (mp0) cc_final: 0.3322 (tm-30) REVERT: B 613 MET cc_start: 0.6988 (mtp) cc_final: 0.6296 (ttm) REVERT: B 638 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7087 (tmmt) REVERT: B 813 ARG cc_start: 0.4799 (mtt90) cc_final: 0.3311 (ppt170) outliers start: 34 outliers final: 8 residues processed: 205 average time/residue: 1.0808 time to fit residues: 240.0448 Evaluate side-chains 148 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 138 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 638 LYS Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 840 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 33 optimal weight: 0.3980 chunk 24 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 GLN ** A 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5223 r_free = 0.5223 target = 0.266862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.5027 r_free = 0.5027 target = 0.245935 restraints weight = 14141.493| |-----------------------------------------------------------------------------| r_work (start): 0.5020 rms_B_bonded: 2.63 r_work: 0.4930 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.4930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5351 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 8928 Z= 0.232 Angle : 0.650 9.655 12130 Z= 0.331 Chirality : 0.041 0.150 1332 Planarity : 0.005 0.049 1486 Dihedral : 4.431 42.315 1172 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 4.18 % Allowed : 18.31 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.36 (0.25), residues: 1026 helix: 1.51 (0.18), residues: 740 sheet: None (None), residues: 0 loop : -0.62 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 408 HIS 0.013 0.002 HIS A 844 PHE 0.026 0.001 PHE A 558 TYR 0.015 0.001 TYR B 528 ARG 0.013 0.001 ARG B 810 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 168 time to evaluate : 0.870 Fit side-chains REVERT: A 294 GLU cc_start: 0.4475 (mm-30) cc_final: 0.4141 (mp0) REVERT: A 381 ILE cc_start: 0.6364 (mt) cc_final: 0.6071 (mt) REVERT: A 553 MET cc_start: 0.6717 (tmt) cc_final: 0.6212 (tmm) REVERT: A 595 GLU cc_start: 0.5016 (mp0) cc_final: 0.3514 (tm-30) REVERT: A 604 GLU cc_start: 0.7546 (tm-30) cc_final: 0.6957 (mt-10) REVERT: A 613 MET cc_start: 0.7174 (mtp) cc_final: 0.6465 (mtp) REVERT: A 638 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7234 (tmmt) REVERT: A 813 ARG cc_start: 0.4695 (mtt90) cc_final: 0.3272 (ppt170) REVERT: B 294 GLU cc_start: 0.4469 (mm-30) cc_final: 0.4136 (mp0) REVERT: B 310 LEU cc_start: 0.5076 (mt) cc_final: 0.4805 (mt) REVERT: B 381 ILE cc_start: 0.6363 (mt) cc_final: 0.6069 (mt) REVERT: B 553 MET cc_start: 0.6711 (tmt) cc_final: 0.6209 (tmm) REVERT: B 595 GLU cc_start: 0.4994 (mp0) cc_final: 0.3502 (tm-30) REVERT: B 604 GLU cc_start: 0.7397 (tm-30) cc_final: 0.6806 (mt-10) REVERT: B 613 MET cc_start: 0.7177 (mtp) cc_final: 0.6605 (mtp) REVERT: B 638 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7268 (tmmt) REVERT: B 813 ARG cc_start: 0.4852 (mtt90) cc_final: 0.3302 (ppt170) outliers start: 39 outliers final: 17 residues processed: 193 average time/residue: 0.8653 time to fit residues: 182.1253 Evaluate side-chains 163 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 638 LYS Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 826 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 14 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 51 optimal weight: 0.2980 chunk 64 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 15 optimal weight: 9.9990 chunk 8 optimal weight: 0.0370 chunk 24 optimal weight: 4.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5236 r_free = 0.5236 target = 0.268501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.5035 r_free = 0.5035 target = 0.247288 restraints weight = 14123.561| |-----------------------------------------------------------------------------| r_work (start): 0.5034 rms_B_bonded: 2.70 r_work: 0.4938 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.4938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5318 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8928 Z= 0.206 Angle : 0.658 13.540 12130 Z= 0.324 Chirality : 0.041 0.144 1332 Planarity : 0.005 0.049 1486 Dihedral : 4.400 42.699 1172 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 5.14 % Allowed : 17.77 % Favored : 77.09 % 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: 1.25 (0.25), residues: 1026 helix: 1.42 (0.18), residues: 740 sheet: None (None), residues: 0 loop : -0.64 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 408 HIS 0.008 0.001 HIS A 844 PHE 0.027 0.001 PHE A 558 TYR 0.018 0.001 TYR A 306 ARG 0.008 0.000 ARG B 810 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 171 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 289 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.6940 (tmt90) REVERT: A 306 TYR cc_start: 0.6707 (t80) cc_final: 0.6500 (t80) REVERT: A 381 ILE cc_start: 0.6341 (mt) cc_final: 0.6040 (mt) REVERT: A 553 MET cc_start: 0.6686 (tmt) cc_final: 0.6177 (tmm) REVERT: A 595 GLU cc_start: 0.5071 (mp0) cc_final: 0.3395 (tm-30) REVERT: A 604 GLU cc_start: 0.7530 (tm-30) cc_final: 0.6889 (mt-10) REVERT: A 613 MET cc_start: 0.7202 (mtp) cc_final: 0.6616 (mtp) REVERT: A 638 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7134 (tmmt) REVERT: A 699 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.6618 (tp30) REVERT: A 813 ARG cc_start: 0.4766 (mtt90) cc_final: 0.3237 (ppt170) REVERT: B 294 GLU cc_start: 0.4767 (mm-30) cc_final: 0.4277 (mp0) REVERT: B 381 ILE cc_start: 0.6340 (mt) cc_final: 0.6037 (mt) REVERT: B 408 TRP cc_start: 0.6552 (m-10) cc_final: 0.6347 (m-10) REVERT: B 553 MET cc_start: 0.6683 (tmt) cc_final: 0.6391 (tmt) REVERT: B 595 GLU cc_start: 0.4787 (mp0) cc_final: 0.3257 (tm-30) REVERT: B 604 GLU cc_start: 0.7466 (tm-30) cc_final: 0.6841 (mt-10) REVERT: B 613 MET cc_start: 0.7204 (mtp) cc_final: 0.6608 (mtp) REVERT: B 638 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7170 (tmmt) REVERT: B 699 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6655 (tp30) REVERT: B 813 ARG cc_start: 0.5065 (mtt90) cc_final: 0.3381 (ppt170) outliers start: 48 outliers final: 13 residues processed: 205 average time/residue: 0.8686 time to fit residues: 194.6592 Evaluate side-chains 164 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 638 LYS Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 826 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 64 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 59 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 45 optimal weight: 0.0010 chunk 70 optimal weight: 8.9990 chunk 42 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 549 ASN ** A 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5225 r_free = 0.5225 target = 0.267204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.5017 r_free = 0.5017 target = 0.245079 restraints weight = 14188.748| |-----------------------------------------------------------------------------| r_work (start): 0.5023 rms_B_bonded: 2.76 r_work: 0.4924 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.4924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5390 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 8928 Z= 0.227 Angle : 0.680 12.449 12130 Z= 0.337 Chirality : 0.042 0.148 1332 Planarity : 0.005 0.052 1486 Dihedral : 4.348 41.306 1170 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.28 % Allowed : 19.70 % Favored : 76.02 % 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: 1.23 (0.25), residues: 1026 helix: 1.43 (0.18), residues: 740 sheet: None (None), residues: 0 loop : -0.74 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 408 HIS 0.005 0.001 HIS B 844 PHE 0.032 0.002 PHE A 558 TYR 0.016 0.001 TYR B 306 ARG 0.004 0.000 ARG B 810 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 163 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.4636 (mm-30) cc_final: 0.4387 (mp0) REVERT: A 381 ILE cc_start: 0.6408 (mt) cc_final: 0.6096 (mt) REVERT: A 534 MET cc_start: 0.6721 (mmt) cc_final: 0.6483 (mmt) REVERT: A 553 MET cc_start: 0.6780 (tmt) cc_final: 0.6285 (tmm) REVERT: A 595 GLU cc_start: 0.4484 (mp0) cc_final: 0.3173 (tm-30) REVERT: A 604 GLU cc_start: 0.7531 (tm-30) cc_final: 0.6908 (mt-10) REVERT: A 611 ILE cc_start: 0.7520 (mm) cc_final: 0.7312 (mm) REVERT: A 613 MET cc_start: 0.6931 (mtp) cc_final: 0.6343 (mtp) REVERT: A 638 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7132 (tmmt) REVERT: A 699 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6737 (tp30) REVERT: A 813 ARG cc_start: 0.4676 (mtt90) cc_final: 0.3116 (ppt170) REVERT: B 289 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.7076 (tmt90) REVERT: B 294 GLU cc_start: 0.4642 (mm-30) cc_final: 0.4394 (mp0) REVERT: B 381 ILE cc_start: 0.6367 (mt) cc_final: 0.6063 (mt) REVERT: B 534 MET cc_start: 0.6756 (mmt) cc_final: 0.6518 (mmt) REVERT: B 553 MET cc_start: 0.6757 (tmt) cc_final: 0.6251 (tmm) REVERT: B 592 ARG cc_start: 0.5696 (OUTLIER) cc_final: 0.5374 (tmm-80) REVERT: B 595 GLU cc_start: 0.4805 (mp0) cc_final: 0.3097 (tm-30) REVERT: B 604 GLU cc_start: 0.7457 (tm-30) cc_final: 0.6815 (mt-10) REVERT: B 613 MET cc_start: 0.7171 (mtp) cc_final: 0.6623 (mtp) REVERT: B 638 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7190 (tmmt) REVERT: B 699 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6669 (tp30) REVERT: B 813 ARG cc_start: 0.4796 (mtt90) cc_final: 0.3134 (ppt170) outliers start: 40 outliers final: 15 residues processed: 189 average time/residue: 0.8589 time to fit residues: 176.6920 Evaluate side-chains 167 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 638 LYS Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 592 ARG Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 826 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 82 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 89 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 67 optimal weight: 0.0170 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5226 r_free = 0.5226 target = 0.267583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.5017 r_free = 0.5017 target = 0.245229 restraints weight = 13987.535| |-----------------------------------------------------------------------------| r_work (start): 0.5030 rms_B_bonded: 2.76 r_work: 0.4929 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.4929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5376 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 8928 Z= 0.225 Angle : 0.692 15.537 12130 Z= 0.338 Chirality : 0.041 0.168 1332 Planarity : 0.005 0.053 1486 Dihedral : 4.465 41.974 1170 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.53 % Allowed : 21.63 % Favored : 74.84 % 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: 1.17 (0.25), residues: 1026 helix: 1.39 (0.18), residues: 740 sheet: None (None), residues: 0 loop : -0.78 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 408 HIS 0.004 0.001 HIS B 844 PHE 0.030 0.002 PHE A 558 TYR 0.017 0.001 TYR A 528 ARG 0.006 0.001 ARG A 592 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 153 time to evaluate : 0.951 Fit side-chains REVERT: A 294 GLU cc_start: 0.4692 (mm-30) cc_final: 0.4298 (mp0) REVERT: A 381 ILE cc_start: 0.6412 (mt) cc_final: 0.6104 (mt) REVERT: A 408 TRP cc_start: 0.6572 (m-10) cc_final: 0.6336 (m100) REVERT: A 553 MET cc_start: 0.6780 (tmt) cc_final: 0.6271 (tmm) REVERT: A 595 GLU cc_start: 0.4111 (mp0) cc_final: 0.2932 (tm-30) REVERT: A 604 GLU cc_start: 0.7506 (tm-30) cc_final: 0.6901 (mt-10) REVERT: A 613 MET cc_start: 0.6832 (mtp) cc_final: 0.6272 (mtp) REVERT: A 638 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7171 (tmmt) REVERT: A 699 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6584 (tp30) REVERT: A 813 ARG cc_start: 0.4969 (mtt90) cc_final: 0.3237 (ppt170) REVERT: B 294 GLU cc_start: 0.4811 (mm-30) cc_final: 0.4323 (mp0) REVERT: B 381 ILE cc_start: 0.6452 (mt) cc_final: 0.6136 (mt) REVERT: B 408 TRP cc_start: 0.6518 (m-10) cc_final: 0.6236 (m100) REVERT: B 553 MET cc_start: 0.6758 (tmt) cc_final: 0.6233 (tmm) REVERT: B 595 GLU cc_start: 0.4417 (mp0) cc_final: 0.3043 (tm-30) REVERT: B 604 GLU cc_start: 0.7485 (tm-30) cc_final: 0.6801 (mt-10) REVERT: B 613 MET cc_start: 0.7183 (mtp) cc_final: 0.6631 (mtp) REVERT: B 638 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7158 (tmmt) REVERT: B 699 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6634 (tp30) REVERT: B 813 ARG cc_start: 0.4790 (mtt90) cc_final: 0.3103 (ppt170) outliers start: 33 outliers final: 14 residues processed: 177 average time/residue: 0.8691 time to fit residues: 167.9014 Evaluate side-chains 163 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 638 LYS Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 826 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 75 optimal weight: 3.9990 chunk 33 optimal weight: 0.0770 chunk 57 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 6 optimal weight: 0.2980 chunk 90 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 559 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5207 r_free = 0.5207 target = 0.265864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.5007 r_free = 0.5007 target = 0.244248 restraints weight = 14406.796| |-----------------------------------------------------------------------------| r_work (start): 0.5024 rms_B_bonded: 2.74 r_work: 0.4922 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.4922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5412 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 8928 Z= 0.215 Angle : 0.671 16.161 12130 Z= 0.333 Chirality : 0.042 0.161 1332 Planarity : 0.005 0.053 1486 Dihedral : 4.476 41.194 1170 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.78 % Allowed : 22.70 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1026 helix: 1.36 (0.18), residues: 740 sheet: None (None), residues: 0 loop : -0.81 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 408 HIS 0.004 0.001 HIS B 844 PHE 0.034 0.002 PHE A 558 TYR 0.018 0.001 TYR A 528 ARG 0.007 0.000 ARG A 592 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 1.102 Fit side-chains revert: symmetry clash REVERT: A 381 ILE cc_start: 0.6352 (mt) cc_final: 0.6041 (mt) REVERT: A 530 LYS cc_start: 0.6170 (mmtp) cc_final: 0.5779 (mptm) REVERT: A 534 MET cc_start: 0.6660 (mmt) cc_final: 0.6377 (mmt) REVERT: A 553 MET cc_start: 0.6841 (tmt) cc_final: 0.6330 (tmm) REVERT: A 595 GLU cc_start: 0.4162 (mp0) cc_final: 0.2923 (tm-30) REVERT: A 604 GLU cc_start: 0.7535 (tm-30) cc_final: 0.6882 (mt-10) REVERT: A 613 MET cc_start: 0.6919 (mtp) cc_final: 0.6247 (mtp) REVERT: A 638 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7204 (tmmt) REVERT: A 813 ARG cc_start: 0.4673 (mtt90) cc_final: 0.3100 (ppt170) REVERT: B 381 ILE cc_start: 0.6383 (mt) cc_final: 0.6078 (mt) REVERT: B 530 LYS cc_start: 0.6111 (mmtp) cc_final: 0.5861 (mmtt) REVERT: B 553 MET cc_start: 0.6894 (tmt) cc_final: 0.6352 (tmm) REVERT: B 595 GLU cc_start: 0.4126 (mp0) cc_final: 0.2945 (tm-30) REVERT: B 604 GLU cc_start: 0.7327 (tm-30) cc_final: 0.6644 (mt-10) REVERT: B 613 MET cc_start: 0.6994 (mtp) cc_final: 0.6434 (mtp) REVERT: B 638 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7221 (tmmt) REVERT: B 699 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.6731 (tp30) REVERT: B 813 ARG cc_start: 0.4793 (mtt90) cc_final: 0.3106 (ppt170) outliers start: 26 outliers final: 15 residues processed: 172 average time/residue: 0.9395 time to fit residues: 178.3918 Evaluate side-chains 157 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 638 LYS Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 826 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 84 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 32 optimal weight: 0.5980 chunk 82 optimal weight: 0.4980 chunk 8 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 16 optimal weight: 8.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.5206 r_free = 0.5206 target = 0.265624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.5003 r_free = 0.5003 target = 0.243877 restraints weight = 14402.163| |-----------------------------------------------------------------------------| r_work (start): 0.5037 rms_B_bonded: 2.75 r_work: 0.4952 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.4952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5411 moved from start: 0.4611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8928 Z= 0.238 Angle : 0.689 15.780 12130 Z= 0.342 Chirality : 0.042 0.163 1332 Planarity : 0.005 0.055 1486 Dihedral : 4.508 40.555 1170 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.46 % Allowed : 23.77 % Favored : 73.77 % 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: 1.00 (0.25), residues: 1026 helix: 1.28 (0.18), residues: 740 sheet: None (None), residues: 0 loop : -0.86 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP B 408 HIS 0.003 0.001 HIS B 844 PHE 0.035 0.002 PHE A 558 TYR 0.018 0.001 TYR B 306 ARG 0.007 0.001 ARG A 592 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 289 ARG cc_start: 0.7277 (OUTLIER) cc_final: 0.6995 (ttt90) REVERT: A 381 ILE cc_start: 0.6413 (mt) cc_final: 0.6130 (mt) REVERT: A 530 LYS cc_start: 0.6187 (mmtp) cc_final: 0.5839 (mptm) REVERT: A 553 MET cc_start: 0.6784 (tmt) cc_final: 0.6252 (tmm) REVERT: A 595 GLU cc_start: 0.3898 (mp0) cc_final: 0.2840 (tm-30) REVERT: A 604 GLU cc_start: 0.7582 (tm-30) cc_final: 0.6876 (mt-10) REVERT: A 613 MET cc_start: 0.6880 (mtp) cc_final: 0.6173 (mtp) REVERT: A 638 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7062 (tmmt) REVERT: A 671 MET cc_start: 0.7588 (mmt) cc_final: 0.7346 (mmp) REVERT: A 813 ARG cc_start: 0.4694 (mtt90) cc_final: 0.3098 (ppt170) REVERT: B 381 ILE cc_start: 0.6424 (mt) cc_final: 0.6128 (mt) REVERT: B 553 MET cc_start: 0.6861 (tmt) cc_final: 0.6303 (tmm) REVERT: B 595 GLU cc_start: 0.3883 (mp0) cc_final: 0.2825 (tm-30) REVERT: B 604 GLU cc_start: 0.7389 (tm-30) cc_final: 0.6603 (mt-10) REVERT: B 613 MET cc_start: 0.6846 (mtp) cc_final: 0.6302 (mtp) REVERT: B 638 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7188 (tmmt) REVERT: B 668 TYR cc_start: 0.7692 (OUTLIER) cc_final: 0.7352 (m-10) REVERT: B 671 MET cc_start: 0.7650 (mmt) cc_final: 0.7427 (mmp) REVERT: B 813 ARG cc_start: 0.4682 (mtt90) cc_final: 0.3082 (ppt170) outliers start: 23 outliers final: 13 residues processed: 160 average time/residue: 0.8692 time to fit residues: 152.6423 Evaluate side-chains 156 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 638 LYS Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 738 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 59 optimal weight: 0.3980 chunk 0 optimal weight: 5.9990 chunk 74 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.3980 chunk 94 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN A 608 GLN B 525 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5215 r_free = 0.5215 target = 0.266403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.5011 r_free = 0.5011 target = 0.245156 restraints weight = 14292.958| |-----------------------------------------------------------------------------| r_work (start): 0.5043 rms_B_bonded: 2.68 r_work: 0.4962 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.4962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5412 moved from start: 0.4762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8928 Z= 0.229 Angle : 0.702 16.279 12130 Z= 0.350 Chirality : 0.043 0.258 1332 Planarity : 0.005 0.056 1486 Dihedral : 4.274 19.129 1166 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.89 % Allowed : 23.23 % Favored : 73.88 % 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: 0.85 (0.26), residues: 1026 helix: 1.15 (0.18), residues: 740 sheet: None (None), residues: 0 loop : -0.88 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 408 HIS 0.003 0.001 HIS B 844 PHE 0.038 0.002 PHE A 558 TYR 0.018 0.001 TYR A 528 ARG 0.006 0.000 ARG A 592 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 0.827 Fit side-chains revert: symmetry clash REVERT: A 289 ARG cc_start: 0.7266 (OUTLIER) cc_final: 0.6960 (ttt90) REVERT: A 381 ILE cc_start: 0.6380 (mt) cc_final: 0.6117 (mt) REVERT: A 530 LYS cc_start: 0.6122 (mmtp) cc_final: 0.5901 (mmtt) REVERT: A 534 MET cc_start: 0.6705 (mmt) cc_final: 0.6467 (mmt) REVERT: A 553 MET cc_start: 0.6831 (tmt) cc_final: 0.6298 (tmm) REVERT: A 595 GLU cc_start: 0.3591 (mp0) cc_final: 0.2508 (tm-30) REVERT: A 604 GLU cc_start: 0.7420 (tm-30) cc_final: 0.6698 (mt-10) REVERT: A 608 GLN cc_start: 0.6424 (OUTLIER) cc_final: 0.5531 (tt0) REVERT: A 613 MET cc_start: 0.6905 (mtp) cc_final: 0.6373 (mtp) REVERT: A 638 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7064 (tmmt) REVERT: A 671 MET cc_start: 0.7576 (mmt) cc_final: 0.7177 (mmp) REVERT: A 813 ARG cc_start: 0.4678 (mtt90) cc_final: 0.3070 (ppt170) REVERT: B 381 ILE cc_start: 0.6333 (mt) cc_final: 0.6095 (mt) REVERT: B 530 LYS cc_start: 0.5963 (mmtt) cc_final: 0.5713 (mmtt) REVERT: B 534 MET cc_start: 0.6814 (mmt) cc_final: 0.6556 (mmt) REVERT: B 553 MET cc_start: 0.6859 (tmt) cc_final: 0.6303 (tmm) REVERT: B 595 GLU cc_start: 0.3051 (mp0) cc_final: 0.2220 (tm-30) REVERT: B 604 GLU cc_start: 0.7366 (tm-30) cc_final: 0.6607 (mt-10) REVERT: B 611 ILE cc_start: 0.7523 (mm) cc_final: 0.7321 (mm) REVERT: B 613 MET cc_start: 0.6874 (mtp) cc_final: 0.6336 (mtp) REVERT: B 638 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7189 (tmmt) REVERT: B 668 TYR cc_start: 0.7721 (OUTLIER) cc_final: 0.7401 (m-10) REVERT: B 671 MET cc_start: 0.7613 (mmt) cc_final: 0.7313 (mmp) REVERT: B 813 ARG cc_start: 0.4685 (mtt90) cc_final: 0.3103 (ppt170) outliers start: 27 outliers final: 12 residues processed: 161 average time/residue: 0.7956 time to fit residues: 140.4945 Evaluate side-chains 156 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 608 GLN Chi-restraints excluded: chain A residue 638 LYS Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 738 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 79 optimal weight: 0.0970 chunk 49 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 59 optimal weight: 0.3980 chunk 9 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 23 optimal weight: 0.0670 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 GLN B 525 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5220 r_free = 0.5220 target = 0.267565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.5024 r_free = 0.5024 target = 0.246713 restraints weight = 14099.374| |-----------------------------------------------------------------------------| r_work (start): 0.5062 rms_B_bonded: 2.59 r_work: 0.4981 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.4981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5391 moved from start: 0.4912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8928 Z= 0.227 Angle : 0.718 16.903 12130 Z= 0.357 Chirality : 0.044 0.286 1332 Planarity : 0.005 0.056 1486 Dihedral : 4.347 21.263 1166 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.68 % Allowed : 23.98 % Favored : 73.34 % 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: 0.80 (0.26), residues: 1026 helix: 1.15 (0.18), residues: 738 sheet: None (None), residues: 0 loop : -1.01 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP B 408 HIS 0.003 0.001 HIS A 844 PHE 0.037 0.002 PHE A 558 TYR 0.016 0.001 TYR A 528 ARG 0.006 0.000 ARG A 592 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: A 289 ARG cc_start: 0.7272 (OUTLIER) cc_final: 0.6980 (ttt90) REVERT: A 381 ILE cc_start: 0.6318 (mt) cc_final: 0.6079 (mt) REVERT: A 553 MET cc_start: 0.6813 (tmt) cc_final: 0.6277 (tmm) REVERT: A 595 GLU cc_start: 0.3104 (mp0) cc_final: 0.2269 (tm-30) REVERT: A 604 GLU cc_start: 0.7396 (tm-30) cc_final: 0.6649 (mt-10) REVERT: A 608 GLN cc_start: 0.6551 (OUTLIER) cc_final: 0.5597 (tt0) REVERT: A 613 MET cc_start: 0.6944 (mtp) cc_final: 0.6405 (mtp) REVERT: A 638 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7231 (tmmt) REVERT: A 813 ARG cc_start: 0.4923 (mtt90) cc_final: 0.3140 (ppt170) REVERT: B 381 ILE cc_start: 0.6369 (mt) cc_final: 0.6134 (mt) REVERT: B 553 MET cc_start: 0.6822 (tmt) cc_final: 0.6259 (tmm) REVERT: B 595 GLU cc_start: 0.3035 (mp0) cc_final: 0.2214 (tm-30) REVERT: B 604 GLU cc_start: 0.7326 (tm-30) cc_final: 0.6605 (mt-10) REVERT: B 613 MET cc_start: 0.6829 (mtp) cc_final: 0.6303 (mtp) REVERT: B 638 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7205 (tmmt) REVERT: B 813 ARG cc_start: 0.5086 (mtt90) cc_final: 0.3183 (ppt170) outliers start: 25 outliers final: 16 residues processed: 155 average time/residue: 0.8866 time to fit residues: 150.3539 Evaluate side-chains 151 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 305 TYR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 608 GLN Chi-restraints excluded: chain A residue 638 LYS Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 738 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 33 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 102 optimal weight: 0.1980 chunk 39 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5233 r_free = 0.5233 target = 0.273481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.5045 r_free = 0.5045 target = 0.248779 restraints weight = 13868.698| |-----------------------------------------------------------------------------| r_work (start): 0.5037 rms_B_bonded: 2.83 r_work: 0.4953 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.4953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5427 moved from start: 0.5003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8928 Z= 0.240 Angle : 0.716 16.769 12130 Z= 0.360 Chirality : 0.044 0.242 1332 Planarity : 0.005 0.056 1486 Dihedral : 4.340 20.611 1166 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.46 % Allowed : 24.84 % Favored : 72.70 % 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: 0.77 (0.26), residues: 1026 helix: 1.14 (0.19), residues: 738 sheet: None (None), residues: 0 loop : -1.03 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP B 408 HIS 0.002 0.000 HIS A 844 PHE 0.038 0.002 PHE A 558 TYR 0.020 0.001 TYR B 668 ARG 0.006 0.000 ARG A 592 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5868.10 seconds wall clock time: 104 minutes 29.89 seconds (6269.89 seconds total)