Starting phenix.real_space_refine on Sat Aug 23 00:17:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bc1_15959/08_2025/8bc1_15959.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bc1_15959/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8bc1_15959/08_2025/8bc1_15959.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bc1_15959/08_2025/8bc1_15959.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bc1_15959/08_2025/8bc1_15959.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bc1_15959/08_2025/8bc1_15959.map" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 3.34, per 1000 atoms: 0.38 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: 0.69 Conformation dependent library (CDL) restraints added in 449.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.23 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: 1.27 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 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: 0.02 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.850 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.800 ------------------------------------------------------------------------------- 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 8936 Z= 0.112 Angle : 0.458 5.542 12146 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG B 592 TYR 0.011 0.001 TYR A 580 PHE 0.011 0.001 PHE B 393 TRP 0.013 0.001 TRP A 397 HIS 0.002 0.001 HIS A 830 Details of bonding type rmsd covalent geometry : bond 0.00194 ( 8928) covalent geometry : angle 0.45784 (12130) SS BOND : bond 0.00181 ( 8) SS BOND : angle 0.74170 ( 16) hydrogen bonds : bond 0.10487 ( 579) hydrogen bonds : angle 5.31130 ( 1713) *********************** 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 : 0.332 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: 0.5806 (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: 0.4177 (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: 0.3330 (ppt170) outliers start: 32 outliers final: 3 residues processed: 280 average time/residue: 0.3889 time to fit residues: 118.1957 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 : 0.218 ------------------------------------------------------------------------------- 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 49 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.0770 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 0.4980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 overall best weight: 1.0340 ------------------------------------------------------------------------------- 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 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5220 r_free = 0.5220 target = 0.267228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.5008 r_free = 0.5008 target = 0.244972 restraints weight = 14425.316| |-----------------------------------------------------------------------------| r_work (start): 0.5012 rms_B_bonded: 2.67 r_work: 0.4917 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.4917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5396 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 8936 Z= 0.194 Angle : 0.670 9.963 12146 Z= 0.350 Chirality : 0.043 0.169 1332 Planarity : 0.005 0.048 1486 Dihedral : 4.334 41.559 1172 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.53 % Allowed : 15.20 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.25), residues: 1026 helix: 1.52 (0.18), residues: 740 sheet: None (None), residues: 0 loop : -0.51 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 701 TYR 0.016 0.002 TYR A 668 PHE 0.012 0.002 PHE B 558 TRP 0.025 0.002 TRP A 408 HIS 0.018 0.002 HIS B 844 Details of bonding type rmsd covalent geometry : bond 0.00442 ( 8928) covalent geometry : angle 0.66410 (12130) SS BOND : bond 0.00513 ( 8) SS BOND : angle 2.59957 ( 16) hydrogen bonds : bond 0.05012 ( 579) hydrogen bonds : angle 4.74139 ( 1713) *********************** 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 224 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 191 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 381 ILE cc_start: 0.6387 (mt) cc_final: 0.6182 (mt) REVERT: A 386 MET cc_start: 0.5200 (mmp) cc_final: 0.4982 (mmm) REVERT: A 553 MET cc_start: 0.6783 (tmt) cc_final: 0.6346 (tmm) REVERT: A 595 GLU cc_start: 0.4784 (mp0) cc_final: 0.3609 (tm-30) REVERT: A 608 GLN cc_start: 0.6161 (tp40) cc_final: 0.5304 (tt0) REVERT: A 613 MET cc_start: 0.7093 (mtp) cc_final: 0.6399 (ttm) REVERT: A 638 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7077 (tmmt) REVERT: A 813 ARG cc_start: 0.4971 (mtt90) cc_final: 0.3409 (ppt170) REVERT: B 381 ILE cc_start: 0.6453 (mt) cc_final: 0.6234 (mt) REVERT: B 386 MET cc_start: 0.5184 (mmp) cc_final: 0.4946 (mmm) REVERT: B 553 MET cc_start: 0.6797 (tmt) cc_final: 0.6317 (tmm) REVERT: B 595 GLU cc_start: 0.4668 (mp0) cc_final: 0.3578 (tm-30) REVERT: B 608 GLN cc_start: 0.6118 (tp40) cc_final: 0.5252 (tt0) REVERT: B 611 ILE cc_start: 0.7702 (mm) cc_final: 0.7492 (mm) REVERT: B 613 MET cc_start: 0.7098 (mtp) cc_final: 0.6406 (ttm) REVERT: B 638 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7097 (tmmt) REVERT: B 813 ARG cc_start: 0.5103 (mtt90) cc_final: 0.3433 (ppt170) outliers start: 33 outliers final: 9 residues processed: 210 average time/residue: 0.3916 time to fit residues: 88.9559 Evaluate side-chains 158 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 147 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 453 VAL Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 826 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 78 optimal weight: 0.7980 chunk 39 optimal weight: 0.2980 chunk 3 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 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 328 GLN B 328 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5211 r_free = 0.5211 target = 0.265644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4997 r_free = 0.4997 target = 0.242653 restraints weight = 14063.148| |-----------------------------------------------------------------------------| r_work (start): 0.5006 rms_B_bonded: 2.74 r_work: 0.4908 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.4908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5406 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 8936 Z= 0.164 Angle : 0.664 9.451 12146 Z= 0.334 Chirality : 0.041 0.146 1332 Planarity : 0.005 0.050 1486 Dihedral : 4.409 42.650 1170 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.50 % Allowed : 18.09 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.25), residues: 1026 helix: 1.38 (0.18), residues: 740 sheet: None (None), residues: 0 loop : -0.56 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 420 TYR 0.015 0.001 TYR B 528 PHE 0.026 0.001 PHE A 558 TRP 0.016 0.002 TRP B 408 HIS 0.012 0.002 HIS A 844 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 8928) covalent geometry : angle 0.65611 (12130) SS BOND : bond 0.00462 ( 8) SS BOND : angle 2.80040 ( 16) hydrogen bonds : bond 0.04713 ( 579) hydrogen bonds : angle 4.63585 ( 1713) *********************** 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 202 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 160 time to evaluate : 0.389 Fit side-chains REVERT: A 294 GLU cc_start: 0.4524 (mm-30) cc_final: 0.4156 (mp0) REVERT: A 312 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.6723 (tp) REVERT: A 381 ILE cc_start: 0.6313 (mt) cc_final: 0.6021 (mt) REVERT: A 386 MET cc_start: 0.5321 (mmp) cc_final: 0.5020 (mmm) REVERT: A 553 MET cc_start: 0.6795 (tmt) cc_final: 0.6310 (tmm) REVERT: A 595 GLU cc_start: 0.4721 (mp0) cc_final: 0.3473 (tm-30) REVERT: A 604 GLU cc_start: 0.7605 (tm-30) cc_final: 0.6963 (mt-10) REVERT: A 613 MET cc_start: 0.7078 (mtp) cc_final: 0.6344 (mtp) REVERT: A 638 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7153 (tmmt) REVERT: A 699 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.6836 (tp30) REVERT: A 813 ARG cc_start: 0.5028 (mtt90) cc_final: 0.3435 (ppt170) REVERT: B 294 GLU cc_start: 0.4607 (mm-30) cc_final: 0.4188 (mp0) REVERT: B 381 ILE cc_start: 0.6400 (mt) cc_final: 0.6107 (mt) REVERT: B 386 MET cc_start: 0.5258 (mmp) cc_final: 0.5045 (mmm) REVERT: B 553 MET cc_start: 0.6768 (tmt) cc_final: 0.6259 (tmm) REVERT: B 595 GLU cc_start: 0.4735 (mp0) cc_final: 0.3378 (tm-30) REVERT: B 604 GLU cc_start: 0.7512 (tm-30) cc_final: 0.6884 (mt-10) REVERT: B 613 MET cc_start: 0.7081 (mtp) cc_final: 0.6349 (mtp) REVERT: B 638 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7204 (tmmt) REVERT: B 699 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.6769 (tp30) REVERT: B 813 ARG cc_start: 0.5122 (mtt90) cc_final: 0.3413 (ppt170) outliers start: 42 outliers final: 14 residues processed: 190 average time/residue: 0.3307 time to fit residues: 69.2876 Evaluate side-chains 164 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 LEU 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 668 TYR 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 13 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 80 optimal weight: 4.9990 chunk 62 optimal weight: 0.1980 chunk 94 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 45 optimal weight: 0.0770 chunk 87 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 549 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5227 r_free = 0.5227 target = 0.268482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.5017 r_free = 0.5017 target = 0.246343 restraints weight = 14384.881| |-----------------------------------------------------------------------------| r_work (start): 0.5018 rms_B_bonded: 2.72 r_work: 0.4922 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.4922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5381 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 8936 Z= 0.145 Angle : 0.664 12.669 12146 Z= 0.326 Chirality : 0.041 0.152 1332 Planarity : 0.005 0.051 1486 Dihedral : 4.410 42.687 1170 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 4.82 % Allowed : 18.31 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.25), residues: 1026 helix: 1.36 (0.18), residues: 740 sheet: None (None), residues: 0 loop : -0.64 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 810 TYR 0.014 0.001 TYR A 528 PHE 0.027 0.001 PHE A 558 TRP 0.020 0.001 TRP B 408 HIS 0.008 0.001 HIS A 844 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 8928) covalent geometry : angle 0.65225 (12130) SS BOND : bond 0.00346 ( 8) SS BOND : angle 3.42704 ( 16) hydrogen bonds : bond 0.04585 ( 579) hydrogen bonds : angle 4.62513 ( 1713) *********************** 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 216 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 171 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: A 294 GLU cc_start: 0.4699 (mm-30) cc_final: 0.4240 (mp0) REVERT: A 312 LEU cc_start: 0.7127 (OUTLIER) cc_final: 0.6613 (tp) REVERT: A 381 ILE cc_start: 0.6314 (mt) cc_final: 0.6006 (mt) REVERT: A 386 MET cc_start: 0.5319 (mmp) cc_final: 0.5054 (mmm) REVERT: A 553 MET cc_start: 0.6786 (tmt) cc_final: 0.6276 (tmm) REVERT: A 595 GLU cc_start: 0.4848 (mp0) cc_final: 0.3466 (tm-30) REVERT: A 604 GLU cc_start: 0.7541 (tm-30) cc_final: 0.6921 (mt-10) REVERT: A 613 MET cc_start: 0.7064 (mtp) cc_final: 0.6481 (mtp) REVERT: A 638 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7222 (tmmt) REVERT: A 699 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6883 (tp30) REVERT: A 813 ARG cc_start: 0.5046 (mtt90) cc_final: 0.3435 (ppt170) REVERT: B 294 GLU cc_start: 0.4671 (mm-30) cc_final: 0.4218 (mp0) REVERT: B 381 ILE cc_start: 0.6439 (mt) cc_final: 0.6121 (mt) REVERT: B 386 MET cc_start: 0.5291 (mmp) cc_final: 0.5079 (mmm) REVERT: B 553 MET cc_start: 0.6788 (tmt) cc_final: 0.6282 (tmm) REVERT: B 595 GLU cc_start: 0.4865 (mp0) cc_final: 0.3499 (tm-30) REVERT: B 604 GLU cc_start: 0.7466 (tm-30) cc_final: 0.6633 (mp0) REVERT: B 613 MET cc_start: 0.7064 (mtp) cc_final: 0.6300 (mtp) REVERT: B 638 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7237 (tmmt) REVERT: B 699 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.6757 (tp30) REVERT: B 813 ARG cc_start: 0.5006 (mtt90) cc_final: 0.3423 (ppt170) outliers start: 45 outliers final: 15 residues processed: 204 average time/residue: 0.3612 time to fit residues: 80.8823 Evaluate side-chains 161 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 638 LYS Chi-restraints excluded: chain A residue 668 TYR 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 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 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 Chi-restraints excluded: chain B residue 840 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 19 optimal weight: 0.9990 chunk 102 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 100 optimal weight: 0.0980 chunk 60 optimal weight: 0.2980 chunk 78 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.5229 r_free = 0.5229 target = 0.268641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.5021 r_free = 0.5021 target = 0.246717 restraints weight = 14397.820| |-----------------------------------------------------------------------------| r_work (start): 0.5019 rms_B_bonded: 2.69 r_work: 0.4919 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.4919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5372 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 8936 Z= 0.145 Angle : 0.694 15.014 12146 Z= 0.336 Chirality : 0.041 0.145 1332 Planarity : 0.005 0.051 1486 Dihedral : 4.352 41.908 1170 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.39 % Allowed : 19.81 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.25), residues: 1026 helix: 1.34 (0.18), residues: 740 sheet: None (None), residues: 0 loop : -0.64 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 420 TYR 0.014 0.001 TYR A 528 PHE 0.031 0.001 PHE A 558 TRP 0.023 0.001 TRP B 408 HIS 0.005 0.001 HIS A 844 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 8928) covalent geometry : angle 0.69208 (12130) SS BOND : bond 0.00250 ( 8) SS BOND : angle 1.52682 ( 16) hydrogen bonds : bond 0.04527 ( 579) hydrogen bonds : angle 4.60534 ( 1713) *********************** 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 191 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 150 time to evaluate : 0.214 Fit side-chains revert: symmetry clash REVERT: A 381 ILE cc_start: 0.6328 (mt) cc_final: 0.6050 (mt) REVERT: A 386 MET cc_start: 0.5275 (mmp) cc_final: 0.4920 (mmm) REVERT: A 553 MET cc_start: 0.6715 (tmt) cc_final: 0.6225 (tmm) REVERT: A 595 GLU cc_start: 0.4696 (mp0) cc_final: 0.3430 (tm-30) REVERT: A 604 GLU cc_start: 0.7524 (tm-30) cc_final: 0.6942 (mt-10) REVERT: A 613 MET cc_start: 0.6975 (mtp) cc_final: 0.6401 (mtp) REVERT: A 638 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7199 (tmmt) REVERT: A 699 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6777 (tp30) REVERT: A 813 ARG cc_start: 0.5366 (mtt90) cc_final: 0.3576 (ppt170) REVERT: B 381 ILE cc_start: 0.6405 (mt) cc_final: 0.6115 (mt) REVERT: B 386 MET cc_start: 0.5083 (mmp) cc_final: 0.4830 (mmm) REVERT: B 553 MET cc_start: 0.6771 (tmt) cc_final: 0.6278 (tmm) REVERT: B 595 GLU cc_start: 0.4699 (mp0) cc_final: 0.3438 (tm-30) REVERT: B 604 GLU cc_start: 0.7452 (tm-30) cc_final: 0.6802 (mt-10) REVERT: B 613 MET cc_start: 0.7038 (mtp) cc_final: 0.6441 (mtp) REVERT: B 638 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7191 (tmmt) REVERT: B 699 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6620 (tp30) REVERT: B 813 ARG cc_start: 0.5037 (mtt90) cc_final: 0.3419 (ppt170) outliers start: 41 outliers final: 18 residues processed: 177 average time/residue: 0.3388 time to fit residues: 65.8337 Evaluate side-chains 159 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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 638 LYS Chi-restraints excluded: chain A residue 668 TYR 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 307 THR Chi-restraints excluded: chain B residue 310 LEU 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 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 37 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 61 optimal weight: 0.4980 chunk 68 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 59 optimal weight: 0.0270 chunk 94 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 overall best weight: 0.5840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 549 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5217 r_free = 0.5217 target = 0.266553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.5008 r_free = 0.5008 target = 0.243842 restraints weight = 14261.695| |-----------------------------------------------------------------------------| r_work (start): 0.5009 rms_B_bonded: 2.74 r_work: 0.4904 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.4904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5401 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 8936 Z= 0.151 Angle : 0.717 14.594 12146 Z= 0.345 Chirality : 0.042 0.168 1332 Planarity : 0.005 0.052 1486 Dihedral : 4.423 41.363 1170 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.96 % Allowed : 21.09 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.25), residues: 1026 helix: 1.29 (0.18), residues: 740 sheet: None (None), residues: 0 loop : -0.71 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 420 TYR 0.018 0.001 TYR A 306 PHE 0.030 0.001 PHE A 558 TRP 0.025 0.001 TRP A 408 HIS 0.005 0.001 HIS B 844 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 8928) covalent geometry : angle 0.70690 (12130) SS BOND : bond 0.00334 ( 8) SS BOND : angle 3.44223 ( 16) hydrogen bonds : bond 0.04584 ( 579) hydrogen bonds : angle 4.65355 ( 1713) *********************** 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 184 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 147 time to evaluate : 0.344 Fit side-chains REVERT: A 289 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.7000 (ttt90) REVERT: A 381 ILE cc_start: 0.6348 (mt) cc_final: 0.6071 (mt) REVERT: A 386 MET cc_start: 0.5186 (mmp) cc_final: 0.4936 (mmm) REVERT: A 534 MET cc_start: 0.6733 (mmt) cc_final: 0.6502 (mmt) REVERT: A 553 MET cc_start: 0.6755 (tmt) cc_final: 0.6249 (tmm) REVERT: A 595 GLU cc_start: 0.4749 (mp0) cc_final: 0.3387 (tm-30) REVERT: A 604 GLU cc_start: 0.7563 (tm-30) cc_final: 0.6896 (mt-10) REVERT: A 613 MET cc_start: 0.7210 (mtp) cc_final: 0.6638 (mtp) REVERT: A 638 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7171 (tmmt) REVERT: A 699 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6950 (tp30) REVERT: A 813 ARG cc_start: 0.5254 (mtt90) cc_final: 0.3612 (ppt170) REVERT: B 381 ILE cc_start: 0.6462 (mt) cc_final: 0.6161 (mt) REVERT: B 386 MET cc_start: 0.4968 (mmp) cc_final: 0.4727 (mmm) REVERT: B 530 LYS cc_start: 0.6091 (mmtp) cc_final: 0.5815 (mmtt) REVERT: B 534 MET cc_start: 0.6748 (mmt) cc_final: 0.6531 (mmt) REVERT: B 553 MET cc_start: 0.6793 (tmt) cc_final: 0.6266 (tmm) REVERT: B 595 GLU cc_start: 0.4748 (mp0) cc_final: 0.3386 (tm-30) REVERT: B 604 GLU cc_start: 0.7474 (tm-30) cc_final: 0.6780 (mt-10) REVERT: B 613 MET cc_start: 0.6985 (mtp) cc_final: 0.6398 (mtp) REVERT: B 638 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7194 (tmmt) REVERT: B 699 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.6848 (tp30) REVERT: B 813 ARG cc_start: 0.5362 (mtt90) cc_final: 0.3576 (ppt170) outliers start: 37 outliers final: 13 residues processed: 174 average time/residue: 0.3527 time to fit residues: 68.1807 Evaluate side-chains 158 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.528 ------------------------------------------------------------------------------- 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 453 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 638 LYS Chi-restraints excluded: chain A residue 668 TYR 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 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 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 805 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 61 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 39 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 2 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 330 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5204 r_free = 0.5204 target = 0.265613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4990 r_free = 0.4990 target = 0.242179 restraints weight = 14357.068| |-----------------------------------------------------------------------------| r_work (start): 0.4995 rms_B_bonded: 2.77 r_work: 0.4892 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.4892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5436 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 8936 Z= 0.162 Angle : 0.708 15.440 12146 Z= 0.346 Chirality : 0.043 0.246 1332 Planarity : 0.005 0.054 1486 Dihedral : 4.136 19.044 1166 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.64 % Allowed : 21.52 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.26), residues: 1026 helix: 1.21 (0.18), residues: 740 sheet: None (None), residues: 0 loop : -0.76 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 420 TYR 0.016 0.001 TYR B 305 PHE 0.033 0.002 PHE A 558 TRP 0.028 0.002 TRP B 408 HIS 0.003 0.001 HIS B 844 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 8928) covalent geometry : angle 0.70287 (12130) SS BOND : bond 0.00292 ( 8) SS BOND : angle 2.53114 ( 16) hydrogen bonds : bond 0.04619 ( 579) hydrogen bonds : angle 4.72630 ( 1713) *********************** 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: 34 poor density : 145 time to evaluate : 0.340 Fit side-chains REVERT: A 289 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.7059 (tmt90) REVERT: A 381 ILE cc_start: 0.6407 (mt) cc_final: 0.6147 (mt) REVERT: A 386 MET cc_start: 0.5148 (mmp) cc_final: 0.4807 (mmm) REVERT: A 553 MET cc_start: 0.6841 (tmt) cc_final: 0.6331 (tmm) REVERT: A 595 GLU cc_start: 0.4565 (mp0) cc_final: 0.3485 (tm-30) REVERT: A 604 GLU cc_start: 0.7539 (tm-30) cc_final: 0.6841 (mt-10) REVERT: A 613 MET cc_start: 0.6916 (mtp) cc_final: 0.6371 (mtp) REVERT: A 638 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7112 (tmmt) REVERT: A 699 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7095 (tp30) REVERT: A 705 TRP cc_start: 0.5222 (t60) cc_final: 0.4979 (t60) REVERT: A 813 ARG cc_start: 0.5327 (mtt90) cc_final: 0.3511 (ppt170) REVERT: B 289 ARG cc_start: 0.7482 (OUTLIER) cc_final: 0.7040 (tmt90) REVERT: B 381 ILE cc_start: 0.6484 (mt) cc_final: 0.6194 (mt) REVERT: B 386 MET cc_start: 0.5174 (mmp) cc_final: 0.4915 (mmm) REVERT: B 553 MET cc_start: 0.6836 (tmt) cc_final: 0.6297 (tmm) REVERT: B 595 GLU cc_start: 0.4553 (mp0) cc_final: 0.3492 (tm-30) REVERT: B 604 GLU cc_start: 0.7476 (tm-30) cc_final: 0.6764 (mt-10) REVERT: B 613 MET cc_start: 0.6985 (mtp) cc_final: 0.6382 (ttm) REVERT: B 638 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7191 (tmmt) REVERT: B 699 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7075 (tp30) REVERT: B 813 ARG cc_start: 0.5102 (mtt90) cc_final: 0.3361 (ppt170) REVERT: B 842 MET cc_start: 0.7926 (OUTLIER) cc_final: 0.7518 (mpp) outliers start: 34 outliers final: 14 residues processed: 169 average time/residue: 0.3725 time to fit residues: 69.4624 Evaluate side-chains 154 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 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 307 THR Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 453 VAL 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 Chi-restraints excluded: chain B residue 842 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 37 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 34 optimal weight: 0.0270 chunk 49 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN B 525 ASN B 674 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5200 r_free = 0.5200 target = 0.265291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.5000 r_free = 0.5000 target = 0.243503 restraints weight = 13955.134| |-----------------------------------------------------------------------------| r_work (start): 0.5036 rms_B_bonded: 2.64 r_work: 0.4952 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.4952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5416 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8936 Z= 0.154 Angle : 0.722 16.011 12146 Z= 0.351 Chirality : 0.043 0.235 1332 Planarity : 0.005 0.054 1486 Dihedral : 4.130 19.450 1166 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.53 % Allowed : 22.70 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.26), residues: 1026 helix: 1.18 (0.18), residues: 740 sheet: None (None), residues: 0 loop : -0.82 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 420 TYR 0.013 0.001 TYR B 528 PHE 0.034 0.002 PHE A 558 TRP 0.022 0.001 TRP B 408 HIS 0.003 0.001 HIS B 844 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 8928) covalent geometry : angle 0.71914 (12130) SS BOND : bond 0.00317 ( 8) SS BOND : angle 1.87291 ( 16) hydrogen bonds : bond 0.04616 ( 579) hydrogen bonds : angle 4.75179 ( 1713) *********************** 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 174 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 141 time to evaluate : 0.346 Fit side-chains REVERT: A 289 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.7102 (tmt90) REVERT: A 381 ILE cc_start: 0.6295 (mt) cc_final: 0.6084 (mt) REVERT: A 386 MET cc_start: 0.4616 (mmp) cc_final: 0.4409 (mmm) REVERT: A 553 MET cc_start: 0.6835 (tmt) cc_final: 0.6315 (tmm) REVERT: A 595 GLU cc_start: 0.4588 (mp0) cc_final: 0.3466 (tm-30) REVERT: A 604 GLU cc_start: 0.7523 (tm-30) cc_final: 0.6836 (mt-10) REVERT: A 613 MET cc_start: 0.6891 (mtp) cc_final: 0.6356 (mtp) REVERT: A 638 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7093 (tmmt) REVERT: A 699 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6922 (tp30) REVERT: A 705 TRP cc_start: 0.5052 (t60) cc_final: 0.4761 (t60) REVERT: A 813 ARG cc_start: 0.5171 (mtt90) cc_final: 0.3511 (ppt170) REVERT: A 842 MET cc_start: 0.8035 (OUTLIER) cc_final: 0.7335 (mpp) REVERT: B 289 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.7099 (tmt90) REVERT: B 381 ILE cc_start: 0.6435 (mt) cc_final: 0.6180 (mt) REVERT: B 386 MET cc_start: 0.5169 (mmp) cc_final: 0.4929 (mmm) REVERT: B 553 MET cc_start: 0.6836 (tmt) cc_final: 0.6290 (tmm) REVERT: B 555 MET cc_start: 0.7360 (mmm) cc_final: 0.7006 (tpt) REVERT: B 595 GLU cc_start: 0.4573 (mp0) cc_final: 0.3447 (tm-30) REVERT: B 604 GLU cc_start: 0.7374 (tm-30) cc_final: 0.6590 (mt-10) REVERT: B 611 ILE cc_start: 0.7545 (mm) cc_final: 0.7344 (mm) REVERT: B 613 MET cc_start: 0.6927 (mtp) cc_final: 0.6279 (ttm) REVERT: B 638 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7148 (tmmt) REVERT: B 699 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7065 (tp30) REVERT: B 813 ARG cc_start: 0.5408 (mtt90) cc_final: 0.3507 (ppt170) outliers start: 33 outliers final: 10 residues processed: 161 average time/residue: 0.3864 time to fit residues: 68.4983 Evaluate side-chains 150 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 638 LYS Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain B residue 289 ARG 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 526 THR Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 699 GLU 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 87 optimal weight: 0.1980 chunk 17 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 53 optimal weight: 0.4980 chunk 91 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 chunk 29 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5203 r_free = 0.5203 target = 0.265795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.5009 r_free = 0.5009 target = 0.244203 restraints weight = 14123.764| |-----------------------------------------------------------------------------| r_work (start): 0.5039 rms_B_bonded: 2.61 r_work: 0.4957 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.4957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5407 moved from start: 0.4692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8936 Z= 0.155 Angle : 0.744 16.735 12146 Z= 0.360 Chirality : 0.044 0.216 1332 Planarity : 0.005 0.056 1486 Dihedral : 4.173 19.336 1166 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.89 % Allowed : 24.41 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.26), residues: 1026 helix: 1.16 (0.18), residues: 738 sheet: None (None), residues: 0 loop : -0.91 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 420 TYR 0.014 0.001 TYR A 528 PHE 0.034 0.002 PHE A 558 TRP 0.020 0.002 TRP B 408 HIS 0.003 0.001 HIS A 844 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 8928) covalent geometry : angle 0.74174 (12130) SS BOND : bond 0.00315 ( 8) SS BOND : angle 1.85340 ( 16) hydrogen bonds : bond 0.04605 ( 579) hydrogen bonds : angle 4.76700 ( 1713) *********************** 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 165 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 0.332 Fit side-chains REVERT: A 289 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.7137 (tmt90) REVERT: A 386 MET cc_start: 0.5141 (mmp) cc_final: 0.4872 (mmm) REVERT: A 553 MET cc_start: 0.6841 (tmt) cc_final: 0.6309 (tmm) REVERT: A 555 MET cc_start: 0.7434 (mmm) cc_final: 0.7103 (tpt) REVERT: A 595 GLU cc_start: 0.4593 (mp0) cc_final: 0.3445 (tm-30) REVERT: A 604 GLU cc_start: 0.7400 (tm-30) cc_final: 0.6628 (mt-10) REVERT: A 613 MET cc_start: 0.6895 (mtp) cc_final: 0.6364 (mtp) REVERT: A 638 LYS cc_start: 0.8102 (OUTLIER) cc_final: 0.7195 (tmmt) REVERT: A 699 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6818 (tp30) REVERT: A 813 ARG cc_start: 0.5315 (mtt90) cc_final: 0.3502 (ppt170) REVERT: A 842 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.7347 (mpp) REVERT: B 381 ILE cc_start: 0.6426 (mt) cc_final: 0.6196 (mt) REVERT: B 386 MET cc_start: 0.5147 (mmp) cc_final: 0.4839 (mmm) REVERT: B 553 MET cc_start: 0.6838 (tmt) cc_final: 0.6292 (tmm) REVERT: B 555 MET cc_start: 0.7347 (mmm) cc_final: 0.7037 (mmm) REVERT: B 595 GLU cc_start: 0.4583 (mp0) cc_final: 0.3447 (tm-30) REVERT: B 604 GLU cc_start: 0.7346 (tm-30) cc_final: 0.6583 (mt-10) REVERT: B 608 GLN cc_start: 0.6136 (tp40) cc_final: 0.5323 (tt0) REVERT: B 611 ILE cc_start: 0.7535 (mm) cc_final: 0.7327 (mm) REVERT: B 613 MET cc_start: 0.6927 (mtp) cc_final: 0.6264 (ttm) REVERT: B 638 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7157 (tmmt) REVERT: B 699 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6665 (tp30) REVERT: B 813 ARG cc_start: 0.5432 (mtt90) cc_final: 0.3513 (ppt170) outliers start: 27 outliers final: 12 residues processed: 158 average time/residue: 0.4043 time to fit residues: 69.9594 Evaluate side-chains 154 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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 453 VAL Chi-restraints excluded: chain A residue 467 ILE 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 A residue 842 MET Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 638 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 96 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 80 optimal weight: 0.1980 chunk 4 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 674 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 = 0.266262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.5012 r_free = 0.5012 target = 0.244300 restraints weight = 14057.099| |-----------------------------------------------------------------------------| r_work (start): 0.5024 rms_B_bonded: 2.61 r_work: 0.4930 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.4930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5447 moved from start: 0.4834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8936 Z= 0.161 Angle : 0.760 16.777 12146 Z= 0.369 Chirality : 0.044 0.203 1332 Planarity : 0.005 0.057 1486 Dihedral : 4.213 19.602 1166 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.46 % Allowed : 25.27 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.26), residues: 1026 helix: 1.10 (0.18), residues: 738 sheet: None (None), residues: 0 loop : -0.90 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 420 TYR 0.014 0.001 TYR B 306 PHE 0.035 0.001 PHE A 558 TRP 0.048 0.002 TRP B 408 HIS 0.003 0.001 HIS B 844 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 8928) covalent geometry : angle 0.75660 (12130) SS BOND : bond 0.00258 ( 8) SS BOND : angle 2.08277 ( 16) hydrogen bonds : bond 0.04660 ( 579) hydrogen bonds : angle 4.81207 ( 1713) ********************** 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 154 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.330 Fit side-chains REVERT: A 289 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.7237 (tmt90) REVERT: A 386 MET cc_start: 0.5168 (mmp) cc_final: 0.4926 (mmm) REVERT: A 553 MET cc_start: 0.6911 (tmt) cc_final: 0.6394 (tmm) REVERT: A 555 MET cc_start: 0.7344 (mmm) cc_final: 0.6982 (mmm) REVERT: A 595 GLU cc_start: 0.4641 (mp0) cc_final: 0.3535 (tm-30) REVERT: A 604 GLU cc_start: 0.7366 (tm-30) cc_final: 0.6678 (mt-10) REVERT: A 613 MET cc_start: 0.6870 (mtp) cc_final: 0.6376 (mtp) REVERT: A 638 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7265 (tmmt) REVERT: A 699 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7165 (tp30) REVERT: A 813 ARG cc_start: 0.5428 (mtt90) cc_final: 0.3498 (ppt170) REVERT: A 842 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7228 (mpp) REVERT: B 386 MET cc_start: 0.5093 (mmp) cc_final: 0.4834 (mmm) REVERT: B 553 MET cc_start: 0.6912 (tmt) cc_final: 0.6371 (tmm) REVERT: B 555 MET cc_start: 0.7315 (mmm) cc_final: 0.6960 (tpt) REVERT: B 595 GLU cc_start: 0.4645 (mp0) cc_final: 0.3530 (tm-30) REVERT: B 604 GLU cc_start: 0.7309 (tm-30) cc_final: 0.6617 (mt-10) REVERT: B 608 GLN cc_start: 0.6201 (tp40) cc_final: 0.5383 (tt0) REVERT: B 611 ILE cc_start: 0.7561 (mm) cc_final: 0.7343 (mm) REVERT: B 613 MET cc_start: 0.6882 (mtp) cc_final: 0.6176 (ttm) REVERT: B 638 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7265 (tmmt) REVERT: B 813 ARG cc_start: 0.5349 (mtt90) cc_final: 0.3441 (ppt170) REVERT: B 842 MET cc_start: 0.7923 (OUTLIER) cc_final: 0.7239 (mpp) REVERT: B 857 ILE cc_start: 0.8382 (OUTLIER) cc_final: 0.8010 (tp) outliers start: 23 outliers final: 12 residues processed: 146 average time/residue: 0.4240 time to fit residues: 67.6654 Evaluate side-chains 147 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 453 VAL Chi-restraints excluded: chain A residue 467 ILE 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 842 MET 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 Chi-restraints excluded: chain B residue 842 MET Chi-restraints excluded: chain B residue 857 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 55 optimal weight: 0.5980 chunk 78 optimal weight: 0.3980 chunk 99 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 43 optimal weight: 0.0170 chunk 22 optimal weight: 0.7980 chunk 101 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 674 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5217 r_free = 0.5217 target = 0.267131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.5019 r_free = 0.5019 target = 0.244891 restraints weight = 13985.538| |-----------------------------------------------------------------------------| r_work (start): 0.5044 rms_B_bonded: 2.65 r_work: 0.4962 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.4962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5405 moved from start: 0.4883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8936 Z= 0.153 Angle : 0.755 16.875 12146 Z= 0.369 Chirality : 0.044 0.196 1332 Planarity : 0.005 0.057 1486 Dihedral : 4.226 23.496 1166 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.36 % Allowed : 25.80 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.26), residues: 1026 helix: 1.09 (0.18), residues: 738 sheet: None (None), residues: 0 loop : -0.91 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 289 TYR 0.016 0.001 TYR A 528 PHE 0.032 0.001 PHE A 558 TRP 0.093 0.002 TRP B 408 HIS 0.003 0.001 HIS B 844 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 8928) covalent geometry : angle 0.75272 (12130) SS BOND : bond 0.00265 ( 8) SS BOND : angle 1.84409 ( 16) hydrogen bonds : bond 0.04636 ( 579) hydrogen bonds : angle 4.82062 ( 1713) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2711.82 seconds wall clock time: 47 minutes 6.56 seconds (2826.56 seconds total)