Starting phenix.real_space_refine on Thu Jul 2 12:41:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8bc1_15959/07_2026/8bc1_15959.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bc1_15959/07_2026/8bc1_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_15959/07_2026/8bc1_15959.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bc1_15959/07_2026/8bc1_15959.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8bc1_15959/07_2026/8bc1_15959.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8bc1_15959/07_2026/8bc1_15959.cif" model { file = "/net/cci-nas-00/data/ceres_data/8bc1_15959/07_2026/8bc1_15959.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bc1_15959/07_2026/8bc1_15959.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.82, per 1000 atoms: 0.32 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 413.6 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: 0.17 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: 1.08 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: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.930 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:7.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5167 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 are 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/Z covalent geometry : bond 0.00194 / 0.11 ( 8928) covalent geometry : angle 0.45784 / 0.26 (12130) SS BOND : bond 0.00181 / 0.12 ( 8) SS BOND : angle 0.74170 / 0.51 ( 16) hydrogen bonds : bond 0.10487 / 6.48 ( 579) hydrogen bonds : angle 5.31130 / 3.85 ( 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 : 0.251 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: 0.3750 time to fit residues: 114.1801 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 : 0.340 ------------------------------------------------------------------------------- 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: 0.4980 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: 6.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.5215 r_free = 0.5215 target = 0.266705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.5002 r_free = 0.5002 target = 0.244325 restraints weight = 14432.852| |-----------------------------------------------------------------------------| r_work (start): 0.5013 rms_B_bonded: 2.67 r_work: 0.4916 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.4916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5358 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 8936 Z= 0.198 Angle : 0.677 10.199 12146 Z= 0.353 Chirality : 0.043 0.158 1332 Planarity : 0.005 0.048 1486 Dihedral : 4.348 41.420 1172 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.85 % Allowed : 14.78 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.25), residues: 1026 helix: 1.51 (0.18), residues: 740 sheet: None (None), residues: 0 loop : -0.52 (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 0.013 0.002 PHE B 377 TRP 0.025 0.002 TRP A 408 HIS 0.022 0.003 HIS B 844 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.20 ( 8928) covalent geometry : angle 0.66980 / 0.35 (12130) SS BOND : bond 0.00626 / 0.32 ( 8) SS BOND : angle 2.83817 / 1.41 ( 16) hydrogen bonds : bond 0.05071 / 3.21 ( 579) hydrogen bonds : angle 4.76206 / 3.45 ( 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 226 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 190 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 381 ILE cc_start: 0.6416 (mt) cc_final: 0.6213 (mt) REVERT: A 386 MET cc_start: 0.5199 (mmp) cc_final: 0.4947 (mmm) REVERT: A 553 MET cc_start: 0.6786 (tmt) cc_final: 0.6345 (tmm) REVERT: A 595 GLU cc_start: 0.4791 (mp0) cc_final: 0.3696 (tm-30) REVERT: A 608 GLN cc_start: 0.6191 (tp40) cc_final: 0.5363 (tt0) REVERT: A 611 ILE cc_start: 0.7666 (mm) cc_final: 0.7466 (mm) REVERT: A 613 MET cc_start: 0.7118 (mtp) cc_final: 0.6428 (ttm) REVERT: A 638 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7061 (tmmt) REVERT: A 813 ARG cc_start: 0.4990 (mtt90) cc_final: 0.3410 (ppt170) REVERT: B 381 ILE cc_start: 0.6470 (mt) cc_final: 0.6259 (mt) REVERT: B 386 MET cc_start: 0.5195 (mmp) cc_final: 0.4945 (mmm) REVERT: B 553 MET cc_start: 0.6805 (tmt) cc_final: 0.6322 (tmm) REVERT: B 595 GLU cc_start: 0.4677 (mp0) cc_final: 0.3664 (tm-30) REVERT: B 608 GLN cc_start: 0.6135 (tp40) cc_final: 0.5257 (tt0) REVERT: B 611 ILE cc_start: 0.7707 (mm) cc_final: 0.7497 (mm) REVERT: B 613 MET cc_start: 0.7110 (mtp) cc_final: 0.6426 (ttm) REVERT: B 638 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7092 (tmmt) REVERT: B 813 ARG cc_start: 0.5130 (mtt90) cc_final: 0.3438 (ppt170) outliers start: 36 outliers final: 9 residues processed: 210 average time/residue: 0.3664 time to fit residues: 83.4192 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 : 0.323 ------------------------------------------------------------------------------- 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: 0.4980 chunk 39 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 345 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 = 0.5205 r_free = 0.5205 target = 0.264350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4998 r_free = 0.4998 target = 0.242806 restraints weight = 13886.340| |-----------------------------------------------------------------------------| r_work (start): 0.5034 rms_B_bonded: 2.61 r_work: 0.4949 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.4949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5350 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 8936 Z= 0.167 Angle : 0.666 9.531 12146 Z= 0.336 Chirality : 0.042 0.151 1332 Planarity : 0.005 0.050 1486 Dihedral : 4.449 42.906 1170 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.93 % Allowed : 17.02 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.25), residues: 1026 helix: 1.35 (0.18), residues: 740 sheet: None (None), residues: 0 loop : -0.61 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 810 TYR 0.016 0.001 TYR B 528 PHE 0.025 0.001 PHE A 558 TRP 0.017 0.002 TRP B 408 HIS 0.012 0.002 HIS A 844 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 ( 8928) covalent geometry : angle 0.65909 / 0.33 (12130) SS BOND : bond 0.00257 / 0.15 ( 8) SS BOND : angle 2.71802 / 1.34 ( 16) hydrogen bonds : bond 0.04702 / 3.00 ( 579) hydrogen bonds : angle 4.64144 / 3.36 ( 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 211 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 165 time to evaluate : 0.343 Fit side-chains REVERT: A 294 GLU cc_start: 0.4425 (mm-30) cc_final: 0.4071 (mp0) REVERT: A 312 LEU cc_start: 0.7243 (OUTLIER) cc_final: 0.6714 (tp) REVERT: A 381 ILE cc_start: 0.6308 (mt) cc_final: 0.6016 (mt) REVERT: A 386 MET cc_start: 0.5383 (mmp) cc_final: 0.5098 (mmm) REVERT: A 553 MET cc_start: 0.6764 (tmt) cc_final: 0.6269 (tmm) REVERT: A 595 GLU cc_start: 0.4665 (mp0) cc_final: 0.3180 (tm-30) REVERT: A 604 GLU cc_start: 0.7611 (tm-30) cc_final: 0.6985 (mt-10) REVERT: A 611 ILE cc_start: 0.7720 (mm) cc_final: 0.7514 (mm) REVERT: A 613 MET cc_start: 0.7052 (mtp) cc_final: 0.6323 (mtp) REVERT: A 638 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7153 (tmmt) REVERT: A 699 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.6995 (tp30) REVERT: A 813 ARG cc_start: 0.4971 (mtt90) cc_final: 0.3425 (ppt170) REVERT: B 289 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.7175 (tmt90) REVERT: B 294 GLU cc_start: 0.4482 (mm-30) cc_final: 0.4271 (mp0) REVERT: B 381 ILE cc_start: 0.6409 (mt) cc_final: 0.6121 (mt) REVERT: B 386 MET cc_start: 0.5367 (mmp) cc_final: 0.5102 (mmm) REVERT: B 553 MET cc_start: 0.6762 (tmt) cc_final: 0.6242 (tmm) REVERT: B 595 GLU cc_start: 0.4657 (mp0) cc_final: 0.3236 (tm-30) REVERT: B 604 GLU cc_start: 0.7514 (tm-30) cc_final: 0.6831 (mt-10) REVERT: B 613 MET cc_start: 0.7048 (mtp) cc_final: 0.6324 (mtp) REVERT: B 638 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7226 (tmmt) REVERT: B 699 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.6831 (tp30) REVERT: B 813 ARG cc_start: 0.5093 (mtt90) cc_final: 0.3418 (ppt170) outliers start: 46 outliers final: 15 residues processed: 198 average time/residue: 0.3404 time to fit residues: 74.2301 Evaluate side-chains 169 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 694 VAL 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 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 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: 0.0040 chunk 80 optimal weight: 5.9990 chunk 62 optimal weight: 0.5980 chunk 94 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 45 optimal weight: 0.0010 chunk 87 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5212 r_free = 0.5212 target = 0.266008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.5008 r_free = 0.5008 target = 0.244574 restraints weight = 14019.745| |-----------------------------------------------------------------------------| r_work (start): 0.5020 rms_B_bonded: 2.64 r_work: 0.4924 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.4924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5331 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 8936 Z= 0.146 Angle : 0.687 13.785 12146 Z= 0.334 Chirality : 0.041 0.141 1332 Planarity : 0.005 0.051 1486 Dihedral : 4.431 42.656 1170 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.25), residues: 1026 helix: 1.35 (0.18), residues: 740 sheet: None (None), residues: 0 loop : -0.67 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 810 TYR 0.017 0.001 TYR A 528 PHE 0.028 0.001 PHE A 558 TRP 0.019 0.001 TRP A 408 HIS 0.008 0.001 HIS A 844 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 ( 8928) covalent geometry : angle 0.67597 / 0.33 (12130) SS BOND : bond 0.00354 / 0.20 ( 8) SS BOND : angle 3.46119 / 1.80 ( 16) hydrogen bonds : bond 0.04602 / 2.95 ( 579) hydrogen bonds : angle 4.64714 / 3.37 ( 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 217 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 169 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: A 312 LEU cc_start: 0.7148 (OUTLIER) cc_final: 0.6605 (tp) REVERT: A 381 ILE cc_start: 0.6266 (mt) cc_final: 0.5969 (mt) REVERT: A 386 MET cc_start: 0.5332 (mmp) cc_final: 0.4989 (mmm) REVERT: A 553 MET cc_start: 0.6764 (tmt) cc_final: 0.6256 (tmm) REVERT: A 595 GLU cc_start: 0.4741 (mp0) cc_final: 0.3228 (tm-30) REVERT: A 604 GLU cc_start: 0.7499 (tm-30) cc_final: 0.6911 (mt-10) REVERT: A 613 MET cc_start: 0.7028 (mtp) cc_final: 0.6445 (mtp) REVERT: A 638 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7164 (tmmt) REVERT: A 699 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.6866 (tp30) REVERT: A 813 ARG cc_start: 0.5028 (mtt90) cc_final: 0.3435 (ppt170) REVERT: B 294 GLU cc_start: 0.4574 (mm-30) cc_final: 0.4172 (mp0) REVERT: B 381 ILE cc_start: 0.6340 (mt) cc_final: 0.6031 (mt) REVERT: B 386 MET cc_start: 0.5339 (mmp) cc_final: 0.5074 (mmm) REVERT: B 553 MET cc_start: 0.6771 (tmt) cc_final: 0.6253 (tmm) REVERT: B 595 GLU cc_start: 0.4747 (mp0) cc_final: 0.3237 (tm-30) REVERT: B 604 GLU cc_start: 0.7583 (tm-30) cc_final: 0.6903 (mt-10) REVERT: B 613 MET cc_start: 0.7018 (mtp) cc_final: 0.6437 (mtp) REVERT: B 638 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7200 (tmmt) REVERT: B 699 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6648 (tp30) REVERT: B 813 ARG cc_start: 0.4979 (mtt90) cc_final: 0.3417 (ppt170) outliers start: 48 outliers final: 18 residues processed: 204 average time/residue: 0.3573 time to fit residues: 79.9248 Evaluate side-chains 166 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 0.200 ------------------------------------------------------------------------------- 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 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 286 ASP 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 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: 0.9980 chunk 102 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 67 optimal weight: 0.5980 chunk 30 optimal weight: 4.9990 chunk 100 optimal weight: 0.0670 chunk 60 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 549 ASN B 549 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5208 r_free = 0.5208 target = 0.265725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.5008 r_free = 0.5008 target = 0.244062 restraints weight = 14232.248| |-----------------------------------------------------------------------------| r_work (start): 0.5012 rms_B_bonded: 2.66 r_work: 0.4907 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.4907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5372 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8936 Z= 0.146 Angle : 0.696 12.768 12146 Z= 0.338 Chirality : 0.042 0.144 1332 Planarity : 0.005 0.051 1486 Dihedral : 4.403 41.597 1170 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 4.82 % Allowed : 20.02 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.25), residues: 1026 helix: 1.33 (0.18), residues: 740 sheet: None (None), residues: 0 loop : -0.63 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 420 TYR 0.016 0.001 TYR A 528 PHE 0.031 0.002 PHE A 558 TRP 0.020 0.001 TRP A 408 HIS 0.005 0.001 HIS A 844 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 ( 8928) covalent geometry : angle 0.69477 / 0.34 (12130) SS BOND : bond 0.00249 / 0.14 ( 8) SS BOND : angle 1.46200 / 0.73 ( 16) hydrogen bonds : bond 0.04550 / 2.90 ( 579) hydrogen bonds : angle 4.63472 / 3.36 ( 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 203 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 158 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 294 GLU cc_start: 0.4461 (mm-30) cc_final: 0.4101 (mp0) REVERT: A 381 ILE cc_start: 0.6259 (mt) cc_final: 0.5973 (mt) REVERT: A 386 MET cc_start: 0.5207 (mmp) cc_final: 0.4927 (mmm) REVERT: A 408 TRP cc_start: 0.6494 (m-10) cc_final: 0.6261 (m-10) REVERT: A 553 MET cc_start: 0.6844 (tmt) cc_final: 0.6344 (tmm) REVERT: A 595 GLU cc_start: 0.4567 (mp0) cc_final: 0.2803 (tm-30) REVERT: A 604 GLU cc_start: 0.7456 (tm-30) cc_final: 0.6933 (mt-10) REVERT: A 613 MET cc_start: 0.7016 (mtp) cc_final: 0.6427 (mtp) REVERT: A 638 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7244 (tmmt) REVERT: A 699 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7053 (tp30) REVERT: A 813 ARG cc_start: 0.5316 (mtt90) cc_final: 0.3580 (ppt170) REVERT: B 294 GLU cc_start: 0.4516 (mm-30) cc_final: 0.4111 (mp0) REVERT: B 381 ILE cc_start: 0.6406 (mt) cc_final: 0.6102 (mt) REVERT: B 386 MET cc_start: 0.5184 (mmp) cc_final: 0.4891 (mmm) REVERT: B 553 MET cc_start: 0.6868 (tmt) cc_final: 0.6361 (tmm) REVERT: B 595 GLU cc_start: 0.4577 (mp0) cc_final: 0.2784 (tm-30) REVERT: B 604 GLU cc_start: 0.7507 (tm-30) cc_final: 0.6735 (mp0) REVERT: B 613 MET cc_start: 0.7005 (mtp) cc_final: 0.6418 (mtp) REVERT: B 638 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7262 (tmmt) REVERT: B 699 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.6984 (tp30) REVERT: B 813 ARG cc_start: 0.4998 (mtt90) cc_final: 0.3429 (ppt170) outliers start: 45 outliers final: 16 residues processed: 189 average time/residue: 0.3262 time to fit residues: 67.8888 Evaluate side-chains 163 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 0.258 ------------------------------------------------------------------------------- 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 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 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 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: 7.9990 chunk 64 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 23 optimal weight: 0.0020 chunk 61 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 674 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5205 r_free = 0.5205 target = 0.265407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.5003 r_free = 0.5003 target = 0.243647 restraints weight = 14035.950| |-----------------------------------------------------------------------------| r_work (start): 0.5004 rms_B_bonded: 2.64 r_work: 0.4902 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.4902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5371 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 8936 Z= 0.155 Angle : 0.737 15.211 12146 Z= 0.357 Chirality : 0.043 0.189 1332 Planarity : 0.005 0.067 1486 Dihedral : 4.552 41.274 1170 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.28 % Allowed : 21.52 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.25), residues: 1026 helix: 1.29 (0.18), residues: 740 sheet: None (None), residues: 0 loop : -0.71 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 592 TYR 0.018 0.001 TYR A 528 PHE 0.031 0.002 PHE A 558 TRP 0.023 0.001 TRP B 408 HIS 0.005 0.001 HIS B 844 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 ( 8928) covalent geometry : angle 0.72409 / 0.35 (12130) SS BOND : bond 0.00186 / 0.12 ( 8) SS BOND : angle 3.83823 / 1.91 ( 16) hydrogen bonds : bond 0.04626 / 2.95 ( 579) hydrogen bonds : angle 4.71127 / 3.42 ( 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 194 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 154 time to evaluate : 0.200 Fit side-chains REVERT: A 294 GLU cc_start: 0.4485 (mm-30) cc_final: 0.4097 (mp0) REVERT: A 381 ILE cc_start: 0.6286 (mt) cc_final: 0.6002 (mt) REVERT: A 386 MET cc_start: 0.5088 (mmp) cc_final: 0.4818 (mmm) REVERT: A 530 LYS cc_start: 0.6171 (mmtp) cc_final: 0.5772 (mptm) REVERT: A 534 MET cc_start: 0.6669 (mmt) cc_final: 0.6370 (mmt) REVERT: A 553 MET cc_start: 0.6862 (tmt) cc_final: 0.6355 (tmm) REVERT: A 595 GLU cc_start: 0.3490 (mp0) cc_final: 0.2479 (tm-30) REVERT: A 604 GLU cc_start: 0.7460 (tm-30) cc_final: 0.6905 (mt-10) REVERT: A 613 MET cc_start: 0.6890 (mtp) cc_final: 0.6325 (mtp) REVERT: A 638 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7169 (tmmt) REVERT: A 699 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7088 (tp30) REVERT: A 813 ARG cc_start: 0.5246 (mtt90) cc_final: 0.3520 (ppt170) REVERT: B 381 ILE cc_start: 0.6390 (mt) cc_final: 0.6084 (mt) REVERT: B 386 MET cc_start: 0.4904 (mmp) cc_final: 0.4637 (mmm) REVERT: B 530 LYS cc_start: 0.6113 (mmtp) cc_final: 0.5830 (mmtt) REVERT: B 534 MET cc_start: 0.6696 (mmt) cc_final: 0.6486 (mmt) REVERT: B 553 MET cc_start: 0.6884 (tmt) cc_final: 0.6377 (tmm) REVERT: B 595 GLU cc_start: 0.3460 (mp0) cc_final: 0.2572 (tm-30) REVERT: B 604 GLU cc_start: 0.7473 (tm-30) cc_final: 0.6892 (mt-10) REVERT: B 613 MET cc_start: 0.6882 (mtp) cc_final: 0.6330 (mtp) REVERT: B 638 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7259 (tmmt) REVERT: B 699 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.6904 (tp30) REVERT: B 813 ARG cc_start: 0.5055 (mtt90) cc_final: 0.3387 (ppt170) outliers start: 40 outliers final: 14 residues processed: 179 average time/residue: 0.3217 time to fit residues: 63.3551 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 : 0.339 ------------------------------------------------------------------------------- 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 668 TYR Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 738 VAL 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 61 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 chunk 39 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 50 optimal weight: 0.2980 chunk 26 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 330 ASN A 674 GLN B 330 ASN B 674 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5200 r_free = 0.5200 target = 0.265221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4999 r_free = 0.4999 target = 0.243273 restraints weight = 14416.079| |-----------------------------------------------------------------------------| r_work (start): 0.5030 rms_B_bonded: 2.68 r_work: 0.4945 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.4945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5362 moved from start: 0.4413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8936 Z= 0.154 Angle : 0.727 15.938 12146 Z= 0.354 Chirality : 0.044 0.293 1332 Planarity : 0.005 0.054 1486 Dihedral : 4.283 21.579 1166 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.85 % Allowed : 21.95 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.26), residues: 1026 helix: 1.19 (0.18), residues: 740 sheet: None (None), residues: 0 loop : -0.72 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 592 TYR 0.016 0.001 TYR A 528 PHE 0.033 0.002 PHE A 558 TRP 0.028 0.002 TRP B 408 HIS 0.005 0.001 HIS A 844 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 ( 8928) covalent geometry : angle 0.72178 / 0.35 (12130) SS BOND : bond 0.00257 / 0.17 ( 8) SS BOND : angle 2.49271 / 1.25 ( 16) hydrogen bonds : bond 0.04559 / 2.91 ( 579) hydrogen bonds : angle 4.73287 / 3.43 ( 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 186 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 150 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 294 GLU cc_start: 0.4748 (mm-30) cc_final: 0.4186 (mp0) REVERT: A 381 ILE cc_start: 0.6428 (mt) cc_final: 0.6139 (mt) REVERT: A 386 MET cc_start: 0.4866 (mmp) cc_final: 0.4599 (mmm) REVERT: A 530 LYS cc_start: 0.6263 (mmtp) cc_final: 0.5889 (mptm) REVERT: A 534 MET cc_start: 0.6753 (mmt) cc_final: 0.6545 (mmt) REVERT: A 553 MET cc_start: 0.6842 (tmt) cc_final: 0.6321 (tmm) REVERT: A 595 GLU cc_start: 0.3541 (mp0) cc_final: 0.2566 (tm-30) REVERT: A 604 GLU cc_start: 0.7552 (tm-30) cc_final: 0.6844 (mt-10) REVERT: A 613 MET cc_start: 0.6927 (mtp) cc_final: 0.6199 (mtp) REVERT: A 638 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7051 (tmmt) REVERT: A 699 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.6240 (tp30) REVERT: A 813 ARG cc_start: 0.5100 (mtt90) cc_final: 0.3500 (ppt170) REVERT: B 381 ILE cc_start: 0.6452 (mt) cc_final: 0.6172 (mt) REVERT: B 386 MET cc_start: 0.5249 (mmp) cc_final: 0.4972 (mmm) REVERT: B 530 LYS cc_start: 0.6166 (mmtp) cc_final: 0.5943 (mmtt) REVERT: B 553 MET cc_start: 0.6830 (tmt) cc_final: 0.6299 (tmm) REVERT: B 595 GLU cc_start: 0.3555 (mp0) cc_final: 0.2566 (tm-30) REVERT: B 604 GLU cc_start: 0.7552 (tm-30) cc_final: 0.6871 (mt-10) REVERT: B 613 MET cc_start: 0.6943 (mtp) cc_final: 0.6315 (ttm) REVERT: B 638 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7163 (tmmt) REVERT: B 699 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6783 (tp30) REVERT: B 813 ARG cc_start: 0.5312 (mtt90) cc_final: 0.3491 (ppt170) REVERT: B 842 MET cc_start: 0.7930 (OUTLIER) cc_final: 0.7480 (mpp) outliers start: 36 outliers final: 15 residues processed: 171 average time/residue: 0.2864 time to fit residues: 54.4929 Evaluate side-chains 163 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 0.242 ------------------------------------------------------------------------------- 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 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 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: 0.1980 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 79 optimal weight: 0.0050 chunk 22 optimal weight: 0.5980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 674 GLN 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 = 0.5207 r_free = 0.5207 target = 0.265904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.5007 r_free = 0.5007 target = 0.244194 restraints weight = 14326.132| |-----------------------------------------------------------------------------| r_work (start): 0.5039 rms_B_bonded: 2.67 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: 0.5341 moved from start: 0.4557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 8936 Z= 0.153 Angle : 0.732 15.931 12146 Z= 0.356 Chirality : 0.044 0.321 1332 Planarity : 0.005 0.054 1486 Dihedral : 4.401 43.795 1166 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % 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 : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.26), residues: 1026 helix: 1.22 (0.18), residues: 738 sheet: None (None), residues: 0 loop : -0.61 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 592 TYR 0.017 0.001 TYR A 528 PHE 0.034 0.001 PHE A 558 TRP 0.031 0.002 TRP B 408 HIS 0.004 0.001 HIS A 844 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 ( 8928) covalent geometry : angle 0.72575 / 0.35 (12130) SS BOND : bond 0.00145 / 0.09 ( 8) SS BOND : angle 2.72347 / 1.44 ( 16) hydrogen bonds : bond 0.04590 / 2.91 ( 579) hydrogen bonds : angle 4.77450 / 3.47 ( 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 184 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 0.334 Fit side-chains REVERT: A 381 ILE cc_start: 0.6383 (mt) cc_final: 0.6110 (mt) REVERT: A 386 MET cc_start: 0.4827 (mmp) cc_final: 0.4598 (mmm) REVERT: A 530 LYS cc_start: 0.6268 (mmtp) cc_final: 0.5865 (mptm) REVERT: A 534 MET cc_start: 0.6766 (mmt) cc_final: 0.6533 (mmt) REVERT: A 553 MET cc_start: 0.6835 (tmt) cc_final: 0.6308 (tmm) REVERT: A 595 GLU cc_start: 0.3576 (mp0) cc_final: 0.2562 (tm-30) REVERT: A 604 GLU cc_start: 0.7423 (tm-30) cc_final: 0.6667 (mt-10) REVERT: A 613 MET cc_start: 0.6920 (mtp) cc_final: 0.6363 (mtp) REVERT: A 638 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7134 (tmmt) REVERT: A 659 MET cc_start: 0.6554 (OUTLIER) cc_final: 0.6326 (mtp) REVERT: A 699 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6816 (tp30) REVERT: A 813 ARG cc_start: 0.5106 (mtt90) cc_final: 0.3487 (ppt170) REVERT: B 381 ILE cc_start: 0.6429 (mt) cc_final: 0.6160 (mt) REVERT: B 386 MET cc_start: 0.5222 (mmp) cc_final: 0.4869 (mmm) REVERT: B 530 LYS cc_start: 0.6072 (mmtp) cc_final: 0.5866 (mmtt) REVERT: B 553 MET cc_start: 0.6842 (tmt) cc_final: 0.6306 (tmm) REVERT: B 555 MET cc_start: 0.7371 (mmm) cc_final: 0.6966 (tpt) REVERT: B 595 GLU cc_start: 0.3651 (mp0) cc_final: 0.2619 (tm-30) REVERT: B 604 GLU cc_start: 0.7555 (tm-30) cc_final: 0.6731 (mp0) REVERT: B 613 MET cc_start: 0.6935 (mtp) cc_final: 0.6295 (ttm) REVERT: B 638 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7125 (tmmt) REVERT: B 659 MET cc_start: 0.6834 (OUTLIER) cc_final: 0.6624 (mtp) REVERT: B 671 MET cc_start: 0.7654 (mmt) cc_final: 0.7438 (mmp) REVERT: B 699 GLU cc_start: 0.6758 (OUTLIER) cc_final: 0.6110 (tp30) REVERT: B 813 ARG cc_start: 0.5338 (mtt90) cc_final: 0.3482 (ppt170) outliers start: 25 outliers final: 10 residues processed: 173 average time/residue: 0.2981 time to fit residues: 57.1218 Evaluate side-chains 162 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 TYR 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 659 MET Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain B residue 310 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 659 MET 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: 0.6980 chunk 17 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 21 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 674 GLN 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 = 0.5190 r_free = 0.5190 target = 0.264287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4989 r_free = 0.4989 target = 0.242257 restraints weight = 14214.372| |-----------------------------------------------------------------------------| r_work (start): 0.5021 rms_B_bonded: 2.64 r_work: 0.4937 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.4937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5388 moved from start: 0.4697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8936 Z= 0.168 Angle : 0.761 16.695 12146 Z= 0.368 Chirality : 0.045 0.222 1332 Planarity : 0.005 0.056 1486 Dihedral : 4.382 41.510 1166 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.57 % Allowed : 24.73 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.26), residues: 1026 helix: 1.17 (0.18), residues: 740 sheet: None (None), residues: 0 loop : -0.67 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 592 TYR 0.017 0.001 TYR A 528 PHE 0.035 0.002 PHE A 558 TRP 0.048 0.002 TRP B 408 HIS 0.003 0.001 HIS A 844 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 ( 8928) covalent geometry : angle 0.75968 / 0.37 (12130) SS BOND : bond 0.00674 / 0.34 ( 8) SS BOND : angle 1.41044 / 0.82 ( 16) hydrogen bonds : bond 0.04703 / 2.99 ( 579) hydrogen bonds : angle 4.82027 / 3.50 ( 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 166 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 381 ILE cc_start: 0.6371 (mt) cc_final: 0.6153 (mt) REVERT: A 386 MET cc_start: 0.5244 (mmp) cc_final: 0.4892 (mmm) REVERT: A 553 MET cc_start: 0.6814 (tmt) cc_final: 0.6292 (tmm) REVERT: A 595 GLU cc_start: 0.3737 (mp0) cc_final: 0.2675 (tm-30) REVERT: A 604 GLU cc_start: 0.7451 (tm-30) cc_final: 0.6661 (mt-10) REVERT: A 613 MET cc_start: 0.6817 (mtp) cc_final: 0.6371 (ttm) REVERT: A 638 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7074 (tmmt) REVERT: A 699 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7188 (tp30) REVERT: A 813 ARG cc_start: 0.5459 (mtt90) cc_final: 0.3519 (ppt170) REVERT: B 381 ILE cc_start: 0.6389 (mt) cc_final: 0.6169 (mt) REVERT: B 386 MET cc_start: 0.5136 (mmp) cc_final: 0.4874 (mmm) REVERT: B 553 MET cc_start: 0.6868 (tmt) cc_final: 0.6327 (tmm) REVERT: B 555 MET cc_start: 0.7349 (mmm) cc_final: 0.7022 (mmm) REVERT: B 595 GLU cc_start: 0.3783 (mp0) cc_final: 0.2835 (tm-30) REVERT: B 604 GLU cc_start: 0.7580 (tm-30) cc_final: 0.6834 (mt-10) REVERT: B 613 MET cc_start: 0.6854 (mtp) cc_final: 0.6318 (mtp) REVERT: B 638 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7157 (tmmt) REVERT: B 671 MET cc_start: 0.7663 (mmt) cc_final: 0.7035 (mmt) REVERT: B 813 ARG cc_start: 0.5416 (mtt90) cc_final: 0.3507 (ppt170) outliers start: 24 outliers final: 12 residues processed: 158 average time/residue: 0.3112 time to fit residues: 54.3704 Evaluate side-chains 153 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 699 GLU Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 826 ILE 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 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: 0.6980 chunk 9 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 80 optimal weight: 0.0170 chunk 4 optimal weight: 0.8980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 674 GLN B 674 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5229 r_free = 0.5229 target = 0.272895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.5038 r_free = 0.5038 target = 0.248783 restraints weight = 14135.623| |-----------------------------------------------------------------------------| r_work (start): 0.5028 rms_B_bonded: 2.80 r_work: 0.4941 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.4941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5363 moved from start: 0.4785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 8936 Z= 0.157 Angle : 0.766 16.976 12146 Z= 0.369 Chirality : 0.045 0.272 1332 Planarity : 0.005 0.056 1486 Dihedral : 4.404 38.784 1166 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.36 % Allowed : 25.91 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.26), residues: 1026 helix: 1.17 (0.19), residues: 738 sheet: None (None), residues: 0 loop : -0.74 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 289 TYR 0.016 0.001 TYR A 528 PHE 0.036 0.002 PHE A 558 TRP 0.058 0.002 TRP A 408 HIS 0.003 0.001 HIS A 844 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 ( 8928) covalent geometry : angle 0.76473 / 0.37 (12130) SS BOND : bond 0.00582 / 0.29 ( 8) SS BOND : angle 1.42559 / 0.82 ( 16) hydrogen bonds : bond 0.04697 / 3.00 ( 579) hydrogen bonds : angle 4.83929 / 3.50 ( 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 157 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.206 Fit side-chains REVERT: A 381 ILE cc_start: 0.6399 (mt) cc_final: 0.6190 (mt) REVERT: A 386 MET cc_start: 0.5181 (mmp) cc_final: 0.4880 (mmm) REVERT: A 530 LYS cc_start: 0.6123 (mmtp) cc_final: 0.5821 (mptm) REVERT: A 534 MET cc_start: 0.6714 (mmt) cc_final: 0.6488 (mmt) REVERT: A 553 MET cc_start: 0.6811 (tmt) cc_final: 0.6287 (tmm) REVERT: A 595 GLU cc_start: 0.3756 (mp0) cc_final: 0.2648 (tm-30) REVERT: A 604 GLU cc_start: 0.7445 (tm-30) cc_final: 0.6657 (mt-10) REVERT: A 613 MET cc_start: 0.6925 (mtp) cc_final: 0.6275 (ttm) REVERT: A 638 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7146 (tmmt) REVERT: A 699 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7236 (tp30) REVERT: A 813 ARG cc_start: 0.5464 (mtt90) cc_final: 0.3460 (ppt170) REVERT: B 289 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.6825 (ttm-80) REVERT: B 553 MET cc_start: 0.6841 (tmt) cc_final: 0.6303 (tmm) REVERT: B 555 MET cc_start: 0.7364 (mmm) cc_final: 0.7030 (tpt) REVERT: B 595 GLU cc_start: 0.3790 (mp0) cc_final: 0.2810 (tm-30) REVERT: B 604 GLU cc_start: 0.7578 (tm-30) cc_final: 0.6837 (mt-10) REVERT: B 613 MET cc_start: 0.6857 (mtp) cc_final: 0.6307 (mtp) REVERT: B 638 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7149 (tmmt) REVERT: B 671 MET cc_start: 0.7574 (mmt) cc_final: 0.7034 (mmt) REVERT: B 813 ARG cc_start: 0.5273 (mtt90) cc_final: 0.3373 (ppt170) REVERT: B 842 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7412 (mpp) outliers start: 22 outliers final: 11 residues processed: 151 average time/residue: 0.3374 time to fit residues: 55.7220 Evaluate side-chains 146 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 699 GLU Chi-restraints excluded: chain A residue 738 VAL 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 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 826 ILE Chi-restraints excluded: chain B residue 842 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 55 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 99 optimal weight: 0.0870 chunk 21 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 22 optimal weight: 0.3980 chunk 101 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 674 GLN B 674 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5209 r_free = 0.5209 target = 0.266531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.5009 r_free = 0.5009 target = 0.244697 restraints weight = 14154.841| |-----------------------------------------------------------------------------| r_work (start): 0.5047 rms_B_bonded: 2.68 r_work: 0.4965 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.4965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5363 moved from start: 0.4906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8936 Z= 0.156 Angle : 0.771 16.997 12146 Z= 0.374 Chirality : 0.044 0.208 1332 Planarity : 0.005 0.056 1486 Dihedral : 4.466 37.739 1166 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.03 % Allowed : 26.12 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.26), residues: 1026 helix: 1.15 (0.19), residues: 738 sheet: None (None), residues: 0 loop : -0.74 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 592 TYR 0.016 0.001 TYR A 528 PHE 0.036 0.001 PHE A 558 TRP 0.093 0.003 TRP A 408 HIS 0.002 0.000 HIS A 844 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 ( 8928) covalent geometry : angle 0.76783 / 0.37 (12130) SS BOND : bond 0.00535 / 0.26 ( 8) SS BOND : angle 2.01861 / 1.22 ( 16) hydrogen bonds : bond 0.04647 / 2.96 ( 579) hydrogen bonds : angle 4.89193 / 3.52 ( 1713) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2426.02 seconds wall clock time: 42 minutes 7.49 seconds (2527.49 seconds total)