Starting phenix.real_space_refine on Fri Jul 3 02:51:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7b5c_12025/07_2026/7b5c_12025.cif Found real_map, /net/cci-nas-00/data/ceres_data/7b5c_12025/07_2026/7b5c_12025.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7b5c_12025/07_2026/7b5c_12025.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7b5c_12025/07_2026/7b5c_12025.cif" model { file = "/net/cci-nas-00/data/ceres_data/7b5c_12025/07_2026/7b5c_12025.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7b5c_12025/07_2026/7b5c_12025.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7b5c_12025/07_2026/7b5c_12025.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7b5c_12025/07_2026/7b5c_12025.map" } resolution = 3.7 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= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 74 5.16 5 C 7684 2.51 5 N 1936 2.21 5 O 2072 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 82 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: 11770 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5883 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 31, 'TRANS': 686} Chain breaks: 4 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B Time building chain proxies: 5.57, per 1000 atoms: 0.47 Number of scatterers: 11770 At special positions: 0 Unit cell: (116.38, 112.332, 114.356, 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 4 19.99 S 74 16.00 O 2072 8.00 N 1936 7.00 C 7684 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 395 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 836 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 386 " distance=2.03 Simple disulfide: pdb=" SG CYS A 625 " - pdb=" SG CYS A 630 " distance=2.04 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 395 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 836 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 386 " distance=2.03 Simple disulfide: pdb=" SG CYS B 625 " - pdb=" SG CYS B 630 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 562.6 milliseconds 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2752 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 4 sheets defined 63.4% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 166 through 181 Proline residue: A 177 - end of helix Processing helix chain 'A' and resid 205 through 211 Processing helix chain 'A' and resid 242 through 257 Processing helix chain 'A' and resid 268 through 275 Processing helix chain 'A' and resid 296 through 305 Processing helix chain 'A' and resid 307 through 311 removed outlier: 3.597A pdb=" N PHE A 311 " --> pdb=" O TYR A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 325 Processing helix chain 'A' and resid 325 through 360 Proline residue: A 344 - end of helix Processing helix chain 'A' and resid 363 through 368 removed outlier: 4.247A pdb=" N MET A 367 " --> pdb=" O ASN A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 393 Processing helix chain 'A' and resid 394 through 405 removed outlier: 4.045A pdb=" N ALA A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU A 403 " --> pdb=" O ARG A 399 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE A 404 " --> pdb=" O ALA A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 438 removed outlier: 4.081A pdb=" N VAL A 410 " --> pdb=" O ASN A 406 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE A 411 " --> pdb=" O PRO A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 466 Processing helix chain 'A' and resid 490 through 519 Processing helix chain 'A' and resid 536 through 568 removed outlier: 3.747A pdb=" N ALA A 540 " --> pdb=" O VAL A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 601 Proline residue: A 595 - end of helix Processing helix chain 'A' and resid 617 through 619 No H-bonds generated for 'chain 'A' and resid 617 through 619' Processing helix chain 'A' and resid 630 through 644 Processing helix chain 'A' and resid 648 through 667 Proline residue: A 658 - end of helix Processing helix chain 'A' and resid 685 through 690 Processing helix chain 'A' and resid 699 through 716 removed outlier: 4.078A pdb=" N PHE A 716 " --> pdb=" O PHE A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 744 removed outlier: 3.501A pdb=" N PHE A 726 " --> pdb=" O LEU A 722 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ARG A 736 " --> pdb=" O ILE A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 782 removed outlier: 4.114A pdb=" N VAL A 772 " --> pdb=" O GLY A 768 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ILE A 773 " --> pdb=" O LYS A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 795 Processing helix chain 'A' and resid 803 through 809 Processing helix chain 'A' and resid 813 through 817 removed outlier: 4.115A pdb=" N PHE A 817 " --> pdb=" O VAL A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 886 removed outlier: 3.922A pdb=" N TRP A 858 " --> pdb=" O SER A 854 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE A 886 " --> pdb=" O VAL A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 909 Processing helix chain 'B' and resid 166 through 181 Proline residue: B 177 - end of helix Processing helix chain 'B' and resid 205 through 211 Processing helix chain 'B' and resid 242 through 257 Processing helix chain 'B' and resid 268 through 275 Processing helix chain 'B' and resid 296 through 305 Processing helix chain 'B' and resid 307 through 311 removed outlier: 3.597A pdb=" N PHE B 311 " --> pdb=" O TYR B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 325 Processing helix chain 'B' and resid 325 through 360 Proline residue: B 344 - end of helix Processing helix chain 'B' and resid 363 through 368 removed outlier: 4.248A pdb=" N MET B 367 " --> pdb=" O ASN B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 393 Processing helix chain 'B' and resid 394 through 405 removed outlier: 4.044A pdb=" N ALA B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU B 403 " --> pdb=" O ARG B 399 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE B 404 " --> pdb=" O ALA B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 438 removed outlier: 4.080A pdb=" N VAL B 410 " --> pdb=" O ASN B 406 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE B 411 " --> pdb=" O PRO B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 466 Processing helix chain 'B' and resid 490 through 519 Processing helix chain 'B' and resid 536 through 568 removed outlier: 3.747A pdb=" N ALA B 540 " --> pdb=" O VAL B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 601 Proline residue: B 595 - end of helix Processing helix chain 'B' and resid 617 through 619 No H-bonds generated for 'chain 'B' and resid 617 through 619' Processing helix chain 'B' and resid 630 through 644 Processing helix chain 'B' and resid 648 through 667 Proline residue: B 658 - end of helix Processing helix chain 'B' and resid 685 through 690 Processing helix chain 'B' and resid 699 through 716 removed outlier: 4.078A pdb=" N PHE B 716 " --> pdb=" O PHE B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 744 removed outlier: 3.501A pdb=" N PHE B 726 " --> pdb=" O LEU B 722 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ARG B 736 " --> pdb=" O ILE B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 782 removed outlier: 4.113A pdb=" N VAL B 772 " --> pdb=" O GLY B 768 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE B 773 " --> pdb=" O LYS B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 795 Processing helix chain 'B' and resid 803 through 809 Processing helix chain 'B' and resid 813 through 817 removed outlier: 4.116A pdb=" N PHE B 817 " --> pdb=" O VAL B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 854 through 886 removed outlier: 3.921A pdb=" N TRP B 858 " --> pdb=" O SER B 854 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE B 886 " --> pdb=" O VAL B 882 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 909 Processing sheet with id=AA1, first strand: chain 'A' and resid 217 through 218 Processing sheet with id=AA2, first strand: chain 'A' and resid 615 through 616 removed outlier: 3.514A pdb=" N ILE A 616 " --> pdb=" O PHE A 620 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE A 620 " --> pdb=" O ILE A 616 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 217 through 218 Processing sheet with id=AA4, first strand: chain 'B' and resid 615 through 616 removed outlier: 3.514A pdb=" N ILE B 616 " --> pdb=" O PHE B 620 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE B 620 " --> pdb=" O ILE B 616 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 642 hydrogen bonds defined for protein. 1902 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: 1.80 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3642 1.35 - 1.47: 3075 1.47 - 1.59: 5225 1.59 - 1.71: 0 1.71 - 1.83: 122 Bond restraints: 12064 Sorted by residual: bond pdb=" C MET A 378 " pdb=" N CYS A 379 " ideal model delta sigma weight residual 1.333 1.292 0.041 1.59e-02 3.96e+03 6.55e+00 bond pdb=" C MET B 378 " pdb=" N CYS B 379 " ideal model delta sigma weight residual 1.333 1.292 0.040 1.59e-02 3.96e+03 6.48e+00 bond pdb=" C SER A 527 " pdb=" N PRO A 528 " ideal model delta sigma weight residual 1.334 1.371 -0.037 2.34e-02 1.83e+03 2.50e+00 bond pdb=" CA ILE A 343 " pdb=" C ILE A 343 " ideal model delta sigma weight residual 1.523 1.538 -0.014 9.20e-03 1.18e+04 2.48e+00 bond pdb=" CA ILE B 343 " pdb=" C ILE B 343 " ideal model delta sigma weight residual 1.523 1.537 -0.014 9.20e-03 1.18e+04 2.43e+00 ... (remaining 12059 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 16014 2.65 - 5.29: 263 5.29 - 7.94: 39 7.94 - 10.59: 2 10.59 - 13.23: 2 Bond angle restraints: 16320 Sorted by residual: angle pdb=" N VAL B 536 " pdb=" CA VAL B 536 " pdb=" C VAL B 536 " ideal model delta sigma weight residual 113.53 106.75 6.78 9.80e-01 1.04e+00 4.79e+01 angle pdb=" N VAL A 536 " pdb=" CA VAL A 536 " pdb=" C VAL A 536 " ideal model delta sigma weight residual 113.53 106.75 6.78 9.80e-01 1.04e+00 4.79e+01 angle pdb=" C THR B 235 " pdb=" N ASP B 236 " pdb=" CA ASP B 236 " ideal model delta sigma weight residual 121.54 129.35 -7.81 1.91e+00 2.74e-01 1.67e+01 angle pdb=" C THR A 235 " pdb=" N ASP A 236 " pdb=" CA ASP A 236 " ideal model delta sigma weight residual 121.54 129.34 -7.80 1.91e+00 2.74e-01 1.67e+01 angle pdb=" CA LEU B 722 " pdb=" CB LEU B 722 " pdb=" CG LEU B 722 " ideal model delta sigma weight residual 116.30 129.53 -13.23 3.50e+00 8.16e-02 1.43e+01 ... (remaining 16315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 6340 17.88 - 35.77: 720 35.77 - 53.65: 130 53.65 - 71.54: 18 71.54 - 89.42: 10 Dihedral angle restraints: 7218 sinusoidal: 2966 harmonic: 4252 Sorted by residual: dihedral pdb=" CB CYS A 382 " pdb=" SG CYS A 382 " pdb=" SG CYS A 386 " pdb=" CB CYS A 386 " ideal model delta sinusoidal sigma weight residual 93.00 47.69 45.31 1 1.00e+01 1.00e-02 2.85e+01 dihedral pdb=" CB CYS B 382 " pdb=" SG CYS B 382 " pdb=" SG CYS B 386 " pdb=" CB CYS B 386 " ideal model delta sinusoidal sigma weight residual 93.00 47.70 45.30 1 1.00e+01 1.00e-02 2.85e+01 dihedral pdb=" CA CYS A 370 " pdb=" C CYS A 370 " pdb=" N ASP A 371 " pdb=" CA ASP A 371 " ideal model delta harmonic sigma weight residual 180.00 154.90 25.10 0 5.00e+00 4.00e-02 2.52e+01 ... (remaining 7215 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1301 0.051 - 0.103: 388 0.103 - 0.154: 89 0.154 - 0.206: 14 0.206 - 0.257: 4 Chirality restraints: 1796 Sorted by residual: chirality pdb=" CB VAL B 310 " pdb=" CA VAL B 310 " pdb=" CG1 VAL B 310 " pdb=" CG2 VAL B 310 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB VAL A 310 " pdb=" CA VAL A 310 " pdb=" CG1 VAL A 310 " pdb=" CG2 VAL A 310 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CB VAL B 569 " pdb=" CA VAL B 569 " pdb=" CG1 VAL B 569 " pdb=" CG2 VAL B 569 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 1793 not shown) Planarity restraints: 2044 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 203 " -0.055 5.00e-02 4.00e+02 8.18e-02 1.07e+01 pdb=" N PRO B 204 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO B 204 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 204 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 203 " 0.054 5.00e-02 4.00e+02 8.17e-02 1.07e+01 pdb=" N PRO A 204 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO A 204 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 204 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 723 " 0.051 5.00e-02 4.00e+02 7.65e-02 9.37e+00 pdb=" N PRO A 724 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 724 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 724 " 0.043 5.00e-02 4.00e+02 ... (remaining 2041 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2381 2.77 - 3.30: 11383 3.30 - 3.84: 19670 3.84 - 4.37: 21569 4.37 - 4.90: 37092 Nonbonded interactions: 92095 Sorted by model distance: nonbonded pdb=" O LYS A 740 " pdb=" OG1 THR A 744 " model vdw 2.239 3.040 nonbonded pdb=" O LYS B 740 " pdb=" OG1 THR B 744 " model vdw 2.239 3.040 nonbonded pdb=" O ALA A 600 " pdb=" OG1 THR A 782 " model vdw 2.242 3.040 nonbonded pdb=" O ALA B 600 " pdb=" OG1 THR B 782 " model vdw 2.242 3.040 nonbonded pdb=" OH TYR A 791 " pdb=" O HIS A 802 " model vdw 2.257 3.040 ... (remaining 92090 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: 0.03 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 group one per residue 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: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.540 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 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:1.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 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 : 0.005 0.048 12072 Z= 0.231 Angle : 0.870 13.232 16336 Z= 0.491 Chirality : 0.052 0.257 1796 Planarity : 0.008 0.082 2044 Dihedral : 15.211 89.423 4442 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.78 % Allowed : 8.75 % Favored : 90.47 % 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: -3.64 (0.18), residues: 1416 helix: -1.58 (0.15), residues: 838 sheet: -2.47 (0.87), residues: 32 loop : -3.72 (0.20), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 321 TYR 0.018 0.002 TYR A 222 PHE 0.019 0.002 PHE B 589 TRP 0.028 0.002 TRP B 427 HIS 0.007 0.001 HIS A 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.23 (12064) covalent geometry : angle 0.85675 / 0.49 (16320) SS BOND : bond 0.00914 / 0.50 ( 8) SS BOND : angle 4.87638 / 2.86 ( 16) hydrogen bonds : bond 0.07470 / 4.81 ( 642) hydrogen bonds : angle 5.54449 / 3.71 ( 1902) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 250 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 PHE cc_start: 0.5415 (t80) cc_final: 0.5122 (t80) REVERT: A 446 GLU cc_start: 0.5564 (OUTLIER) cc_final: 0.5343 (mm-30) REVERT: A 524 MET cc_start: 0.2652 (ptt) cc_final: 0.1590 (ttt) REVERT: A 560 ILE cc_start: 0.8464 (tp) cc_final: 0.8245 (tt) REVERT: B 341 MET cc_start: 0.7809 (mmm) cc_final: 0.7602 (mmm) REVERT: B 351 ILE cc_start: 0.8798 (tp) cc_final: 0.8465 (pt) REVERT: B 418 LEU cc_start: 0.8079 (tt) cc_final: 0.7478 (mp) REVERT: B 446 GLU cc_start: 0.5953 (OUTLIER) cc_final: 0.5631 (mm-30) REVERT: B 515 ARG cc_start: 0.6786 (tpm170) cc_final: 0.6103 (ttt180) REVERT: B 524 MET cc_start: 0.2614 (ptt) cc_final: 0.1569 (ttt) REVERT: B 666 TYR cc_start: 0.3989 (t80) cc_final: 0.3436 (m-80) outliers start: 10 outliers final: 1 residues processed: 258 average time/residue: 0.1207 time to fit residues: 41.6686 Evaluate side-chains 164 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 161 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain B residue 446 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 0.1980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.1980 chunk 55 optimal weight: 6.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 340 GLN A 431 GLN A 709 GLN A 731 ASN B 709 GLN B 731 ASN B 895 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.146263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.119151 restraints weight = 18057.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.119640 restraints weight = 13850.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.119832 restraints weight = 11041.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.120556 restraints weight = 10454.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.120699 restraints weight = 9232.733| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12072 Z= 0.129 Angle : 0.624 10.145 16336 Z= 0.324 Chirality : 0.041 0.150 1796 Planarity : 0.006 0.077 2044 Dihedral : 5.926 69.970 1591 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.42 % Allowed : 14.84 % Favored : 82.73 % 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: -2.14 (0.20), residues: 1416 helix: -0.14 (0.17), residues: 838 sheet: -2.09 (0.92), residues: 32 loop : -3.50 (0.22), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 213 TYR 0.017 0.001 TYR A 251 PHE 0.028 0.001 PHE B 617 TRP 0.022 0.001 TRP B 427 HIS 0.009 0.001 HIS B 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (12064) covalent geometry : angle 0.61460 / 0.32 (16320) SS BOND : bond 0.00444 / 0.23 ( 8) SS BOND : angle 3.58455 / 2.12 ( 16) hydrogen bonds : bond 0.04615 / 3.07 ( 642) hydrogen bonds : angle 4.86671 / 3.29 ( 1902) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 196 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 PHE cc_start: 0.5157 (t80) cc_final: 0.4940 (t80) REVERT: A 391 MET cc_start: 0.8093 (tpt) cc_final: 0.7892 (tpt) REVERT: A 418 LEU cc_start: 0.8079 (tt) cc_final: 0.7655 (mp) REVERT: A 446 GLU cc_start: 0.5625 (OUTLIER) cc_final: 0.5383 (mm-30) REVERT: A 491 PHE cc_start: 0.4734 (t80) cc_final: 0.4482 (t80) REVERT: A 524 MET cc_start: 0.2346 (ptt) cc_final: 0.1428 (ttt) REVERT: A 560 ILE cc_start: 0.8559 (tp) cc_final: 0.8254 (tt) REVERT: A 617 PHE cc_start: 0.6081 (OUTLIER) cc_final: 0.5508 (m-80) REVERT: A 904 MET cc_start: 0.6339 (mtp) cc_final: 0.5746 (mtp) REVERT: B 215 GLN cc_start: 0.7458 (tp40) cc_final: 0.7244 (tm-30) REVERT: B 381 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.6636 (pp) REVERT: B 418 LEU cc_start: 0.7949 (tt) cc_final: 0.7492 (mp) REVERT: B 446 GLU cc_start: 0.5944 (OUTLIER) cc_final: 0.5583 (mm-30) REVERT: B 515 ARG cc_start: 0.6670 (tpm170) cc_final: 0.5994 (ttt180) REVERT: B 524 MET cc_start: 0.2217 (ptt) cc_final: 0.1345 (ttt) REVERT: B 560 ILE cc_start: 0.8618 (tp) cc_final: 0.8283 (tt) REVERT: B 666 TYR cc_start: 0.3973 (t80) cc_final: 0.3322 (m-80) REVERT: B 731 ASN cc_start: 0.8554 (m-40) cc_final: 0.8255 (m-40) outliers start: 31 outliers final: 9 residues processed: 217 average time/residue: 0.1090 time to fit residues: 33.3138 Evaluate side-chains 180 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 167 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 431 GLN Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 617 PHE Chi-restraints excluded: chain A residue 849 HIS Chi-restraints excluded: chain A residue 883 ASP Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 849 HIS Chi-restraints excluded: chain B residue 883 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 56 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 15 optimal weight: 0.4980 chunk 93 optimal weight: 0.9980 chunk 102 optimal weight: 10.0000 chunk 105 optimal weight: 9.9990 chunk 7 optimal weight: 0.1980 chunk 60 optimal weight: 7.9990 chunk 18 optimal weight: 0.0570 chunk 95 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 overall best weight: 0.4698 ------------------------------------------------------------------------------- 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 = 0.3995 r_free = 0.3995 target = 0.147078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.119608 restraints weight = 18308.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.120084 restraints weight = 13876.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.120324 restraints weight = 11290.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.120988 restraints weight = 10527.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.121095 restraints weight = 9368.878| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12072 Z= 0.123 Angle : 0.618 10.477 16336 Z= 0.313 Chirality : 0.040 0.145 1796 Planarity : 0.005 0.076 2044 Dihedral : 5.718 70.270 1590 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.27 % Allowed : 16.88 % Favored : 80.86 % 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: -1.39 (0.21), residues: 1416 helix: 0.48 (0.17), residues: 848 sheet: -2.01 (0.88), residues: 32 loop : -3.28 (0.23), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 748 TYR 0.022 0.001 TYR B 182 PHE 0.019 0.001 PHE A 696 TRP 0.021 0.001 TRP A 427 HIS 0.007 0.001 HIS B 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (12064) covalent geometry : angle 0.60740 / 0.31 (16320) SS BOND : bond 0.00256 / 0.15 ( 8) SS BOND : angle 3.72491 / 2.18 ( 16) hydrogen bonds : bond 0.04372 / 2.90 ( 642) hydrogen bonds : angle 4.74571 / 3.20 ( 1902) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 MET cc_start: 0.7885 (tpp) cc_final: 0.7597 (ttt) REVERT: A 418 LEU cc_start: 0.7998 (tt) cc_final: 0.7686 (mp) REVERT: A 446 GLU cc_start: 0.5729 (OUTLIER) cc_final: 0.5456 (mm-30) REVERT: A 491 PHE cc_start: 0.4843 (t80) cc_final: 0.4602 (t80) REVERT: A 524 MET cc_start: 0.2204 (ptt) cc_final: 0.1499 (ttt) REVERT: A 560 ILE cc_start: 0.8571 (tp) cc_final: 0.8248 (tt) REVERT: B 381 LEU cc_start: 0.7095 (OUTLIER) cc_final: 0.6661 (pp) REVERT: B 418 LEU cc_start: 0.7862 (tt) cc_final: 0.7551 (mp) REVERT: B 446 GLU cc_start: 0.5775 (OUTLIER) cc_final: 0.5428 (mm-30) REVERT: B 515 ARG cc_start: 0.6714 (tpm170) cc_final: 0.6098 (ttt180) REVERT: B 524 MET cc_start: 0.1968 (ptt) cc_final: 0.1178 (ttt) REVERT: B 560 ILE cc_start: 0.8593 (tp) cc_final: 0.8224 (tt) REVERT: B 666 TYR cc_start: 0.3973 (t80) cc_final: 0.3291 (m-80) REVERT: B 731 ASN cc_start: 0.8456 (m-40) cc_final: 0.8228 (m-40) outliers start: 29 outliers final: 13 residues processed: 210 average time/residue: 0.1030 time to fit residues: 31.1911 Evaluate side-chains 185 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 169 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 849 HIS Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 411 PHE Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 849 HIS Chi-restraints excluded: chain B residue 883 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 43 optimal weight: 7.9990 chunk 107 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 64 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 15 optimal weight: 0.0170 chunk 45 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 overall best weight: 2.5624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 GLN A 431 GLN B 215 GLN B 431 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.141403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.114290 restraints weight = 18515.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.114226 restraints weight = 13849.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.114365 restraints weight = 12065.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.114723 restraints weight = 11155.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.115076 restraints weight = 10310.971| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12072 Z= 0.205 Angle : 0.689 9.846 16336 Z= 0.355 Chirality : 0.044 0.156 1796 Planarity : 0.006 0.073 2044 Dihedral : 5.836 71.251 1590 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 2.97 % Allowed : 17.73 % Favored : 79.30 % 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: -1.36 (0.22), residues: 1416 helix: 0.48 (0.17), residues: 848 sheet: -1.57 (0.95), residues: 32 loop : -3.25 (0.23), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 125 TYR 0.017 0.002 TYR B 182 PHE 0.020 0.002 PHE A 696 TRP 0.016 0.002 TRP B 760 HIS 0.008 0.001 HIS A 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.21 (12064) covalent geometry : angle 0.67178 / 0.35 (16320) SS BOND : bond 0.00710 / 0.36 ( 8) SS BOND : angle 4.90379 / 2.79 ( 16) hydrogen bonds : bond 0.04877 / 3.24 ( 642) hydrogen bonds : angle 4.81212 / 3.23 ( 1902) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 183 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 446 GLU cc_start: 0.5810 (OUTLIER) cc_final: 0.5583 (tm-30) REVERT: A 491 PHE cc_start: 0.5102 (t80) cc_final: 0.4878 (t80) REVERT: A 515 ARG cc_start: 0.6759 (tpm170) cc_final: 0.5973 (ttt180) REVERT: A 524 MET cc_start: 0.2375 (ptt) cc_final: 0.1606 (ttt) REVERT: A 560 ILE cc_start: 0.8594 (tp) cc_final: 0.8261 (tt) REVERT: A 622 MET cc_start: 0.3221 (mmm) cc_final: 0.2911 (mmm) REVERT: B 381 LEU cc_start: 0.7076 (OUTLIER) cc_final: 0.6613 (pp) REVERT: B 418 LEU cc_start: 0.8275 (tt) cc_final: 0.7671 (mp) REVERT: B 515 ARG cc_start: 0.6755 (tpm170) cc_final: 0.6079 (ttt180) REVERT: B 524 MET cc_start: 0.2413 (ptt) cc_final: 0.1414 (ttt) REVERT: B 560 ILE cc_start: 0.8600 (tp) cc_final: 0.8253 (tt) REVERT: B 666 TYR cc_start: 0.3942 (t80) cc_final: 0.3269 (m-80) REVERT: B 731 ASN cc_start: 0.8729 (m-40) cc_final: 0.8420 (m-40) outliers start: 38 outliers final: 21 residues processed: 210 average time/residue: 0.1054 time to fit residues: 31.5188 Evaluate side-chains 192 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 169 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 849 HIS Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 849 HIS Chi-restraints excluded: chain B residue 883 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 116 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 136 optimal weight: 0.4980 chunk 35 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 GLN A 431 GLN A 546 ASN B 215 GLN B 431 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.141498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.113863 restraints weight = 18480.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.114080 restraints weight = 13673.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.114311 restraints weight = 12125.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.114746 restraints weight = 11049.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.114904 restraints weight = 10052.818| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12072 Z= 0.189 Angle : 0.667 10.037 16336 Z= 0.345 Chirality : 0.043 0.153 1796 Planarity : 0.006 0.072 2044 Dihedral : 5.462 72.775 1587 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 3.59 % Allowed : 18.91 % Favored : 77.50 % 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 (0.22), residues: 1416 helix: 0.59 (0.18), residues: 844 sheet: -1.35 (0.99), residues: 32 loop : -3.10 (0.23), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 748 TYR 0.028 0.002 TYR B 251 PHE 0.018 0.002 PHE B 617 TRP 0.020 0.001 TRP B 427 HIS 0.008 0.001 HIS B 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 (12064) covalent geometry : angle 0.65169 / 0.34 (16320) SS BOND : bond 0.00619 / 0.33 ( 8) SS BOND : angle 4.65011 / 2.68 ( 16) hydrogen bonds : bond 0.04851 / 3.25 ( 642) hydrogen bonds : angle 4.78927 / 3.23 ( 1902) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 169 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 446 GLU cc_start: 0.5719 (OUTLIER) cc_final: 0.5509 (tm-30) REVERT: A 515 ARG cc_start: 0.6827 (tpm170) cc_final: 0.6089 (ttt180) REVERT: A 524 MET cc_start: 0.2289 (ptt) cc_final: 0.1529 (ttt) REVERT: A 560 ILE cc_start: 0.8585 (tp) cc_final: 0.8249 (tt) REVERT: A 617 PHE cc_start: 0.5836 (m-80) cc_final: 0.5563 (m-80) REVERT: B 381 LEU cc_start: 0.7072 (OUTLIER) cc_final: 0.6567 (pp) REVERT: B 418 LEU cc_start: 0.8203 (tt) cc_final: 0.7625 (mp) REVERT: B 515 ARG cc_start: 0.6716 (tpm170) cc_final: 0.6091 (ttt180) REVERT: B 524 MET cc_start: 0.2665 (ptt) cc_final: 0.1561 (ttt) REVERT: B 560 ILE cc_start: 0.8580 (tp) cc_final: 0.8242 (tt) REVERT: B 731 ASN cc_start: 0.8664 (m-40) cc_final: 0.8385 (m-40) outliers start: 46 outliers final: 24 residues processed: 201 average time/residue: 0.1100 time to fit residues: 31.0595 Evaluate side-chains 188 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 162 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 849 HIS Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 431 GLN Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 794 MET Chi-restraints excluded: chain B residue 849 HIS Chi-restraints excluded: chain B residue 883 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 126 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 133 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 124 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 52 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3969 r_free = 0.3969 target = 0.144884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.117583 restraints weight = 18427.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.117159 restraints weight = 14544.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.117602 restraints weight = 12846.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.117833 restraints weight = 11657.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.119295 restraints weight = 10688.730| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12072 Z= 0.137 Angle : 0.638 10.096 16336 Z= 0.327 Chirality : 0.041 0.166 1796 Planarity : 0.005 0.074 2044 Dihedral : 5.414 73.570 1587 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.58 % Allowed : 21.02 % Favored : 76.41 % 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 are not related in a simple way. whole: -0.84 (0.22), residues: 1416 helix: 0.88 (0.18), residues: 836 sheet: -1.08 (1.01), residues: 32 loop : -2.92 (0.24), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 213 TYR 0.027 0.001 TYR B 251 PHE 0.013 0.001 PHE A 585 TRP 0.024 0.001 TRP B 427 HIS 0.007 0.001 HIS B 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (12064) covalent geometry : angle 0.62041 / 0.32 (16320) SS BOND : bond 0.00873 / 0.42 ( 8) SS BOND : angle 4.80672 / 2.64 ( 16) hydrogen bonds : bond 0.04548 / 3.03 ( 642) hydrogen bonds : angle 4.67924 / 3.16 ( 1902) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 181 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 LEU cc_start: 0.8080 (tt) cc_final: 0.7691 (mp) REVERT: A 491 PHE cc_start: 0.5130 (t80) cc_final: 0.4863 (t80) REVERT: A 515 ARG cc_start: 0.6712 (tpm170) cc_final: 0.6054 (ttt180) REVERT: A 524 MET cc_start: 0.2221 (ptt) cc_final: 0.1465 (ttt) REVERT: A 560 ILE cc_start: 0.8569 (tp) cc_final: 0.8232 (tt) REVERT: A 617 PHE cc_start: 0.5925 (m-80) cc_final: 0.5552 (m-80) REVERT: B 418 LEU cc_start: 0.8088 (tt) cc_final: 0.7658 (mp) REVERT: B 515 ARG cc_start: 0.6670 (tpm170) cc_final: 0.6032 (ttt180) REVERT: B 524 MET cc_start: 0.2429 (ptt) cc_final: 0.1599 (ttt) REVERT: B 560 ILE cc_start: 0.8585 (tp) cc_final: 0.8237 (tt) REVERT: B 731 ASN cc_start: 0.8536 (m-40) cc_final: 0.8311 (m-40) outliers start: 33 outliers final: 21 residues processed: 207 average time/residue: 0.1098 time to fit residues: 32.4374 Evaluate side-chains 178 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 157 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 849 HIS Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 367 MET Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 849 HIS Chi-restraints excluded: chain B residue 883 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 86 optimal weight: 0.7980 chunk 120 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 130 optimal weight: 0.1980 chunk 110 optimal weight: 8.9990 chunk 56 optimal weight: 0.2980 chunk 10 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.147098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.119710 restraints weight = 18376.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.119730 restraints weight = 14052.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.120209 restraints weight = 12009.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.120455 restraints weight = 11520.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.120671 restraints weight = 10286.997| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12072 Z= 0.128 Angle : 0.633 9.974 16336 Z= 0.322 Chirality : 0.041 0.152 1796 Planarity : 0.005 0.075 2044 Dihedral : 4.799 25.277 1584 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.34 % Allowed : 21.33 % Favored : 76.33 % 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: -0.52 (0.22), residues: 1416 helix: 1.09 (0.18), residues: 842 sheet: -0.76 (1.04), residues: 32 loop : -2.77 (0.24), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 213 TYR 0.026 0.001 TYR B 251 PHE 0.020 0.001 PHE B 617 TRP 0.023 0.001 TRP A 427 HIS 0.005 0.001 HIS B 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (12064) covalent geometry : angle 0.62018 / 0.32 (16320) SS BOND : bond 0.00565 / 0.28 ( 8) SS BOND : angle 4.10783 / 2.31 ( 16) hydrogen bonds : bond 0.04350 / 2.88 ( 642) hydrogen bonds : angle 4.60856 / 3.12 ( 1902) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 174 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 LEU cc_start: 0.7952 (tt) cc_final: 0.7620 (mp) REVERT: A 491 PHE cc_start: 0.5089 (t80) cc_final: 0.4838 (t80) REVERT: A 515 ARG cc_start: 0.6651 (tpm170) cc_final: 0.5942 (ttt180) REVERT: A 524 MET cc_start: 0.2291 (ptt) cc_final: 0.1782 (ttt) REVERT: A 560 ILE cc_start: 0.8572 (tp) cc_final: 0.8206 (tt) REVERT: B 341 MET cc_start: 0.7552 (mmm) cc_final: 0.7309 (mmm) REVERT: B 418 LEU cc_start: 0.7984 (tt) cc_final: 0.7701 (mp) REVERT: B 515 ARG cc_start: 0.6744 (tpm170) cc_final: 0.6113 (ttt180) REVERT: B 524 MET cc_start: 0.2239 (ptt) cc_final: 0.1460 (ttt) REVERT: B 560 ILE cc_start: 0.8586 (tp) cc_final: 0.8185 (tt) REVERT: B 706 MET cc_start: 0.8695 (mmp) cc_final: 0.8324 (mmt) REVERT: B 731 ASN cc_start: 0.8488 (m-40) cc_final: 0.8192 (m-40) outliers start: 30 outliers final: 21 residues processed: 197 average time/residue: 0.1119 time to fit residues: 30.7988 Evaluate side-chains 177 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 849 HIS Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 367 MET Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 794 MET Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 849 HIS Chi-restraints excluded: chain B residue 883 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 88 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 126 optimal weight: 0.0670 chunk 74 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 chunk 53 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 overall best weight: 0.9524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 431 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.146704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.119860 restraints weight = 18400.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.119797 restraints weight = 13994.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.120805 restraints weight = 12175.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.121060 restraints weight = 10846.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.121161 restraints weight = 9591.555| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12072 Z= 0.135 Angle : 0.643 13.578 16336 Z= 0.323 Chirality : 0.041 0.150 1796 Planarity : 0.005 0.075 2044 Dihedral : 4.700 23.880 1584 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.34 % Allowed : 21.64 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.44 (0.22), residues: 1416 helix: 1.13 (0.18), residues: 844 sheet: -0.62 (1.06), residues: 32 loop : -2.70 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 213 TYR 0.031 0.001 TYR A 251 PHE 0.013 0.001 PHE B 589 TRP 0.020 0.001 TRP A 427 HIS 0.005 0.001 HIS B 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (12064) covalent geometry : angle 0.63244 / 0.32 (16320) SS BOND : bond 0.00494 / 0.26 ( 8) SS BOND : angle 3.71582 / 2.14 ( 16) hydrogen bonds : bond 0.04359 / 2.89 ( 642) hydrogen bonds : angle 4.60138 / 3.09 ( 1902) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 160 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 LEU cc_start: 0.7966 (tt) cc_final: 0.7610 (mp) REVERT: A 491 PHE cc_start: 0.5036 (t80) cc_final: 0.4777 (t80) REVERT: A 515 ARG cc_start: 0.6647 (tpm170) cc_final: 0.6008 (ttt180) REVERT: A 524 MET cc_start: 0.2287 (ptt) cc_final: 0.1797 (ttt) REVERT: A 560 ILE cc_start: 0.8577 (tp) cc_final: 0.8203 (tt) REVERT: B 418 LEU cc_start: 0.8015 (tt) cc_final: 0.7745 (mp) REVERT: B 515 ARG cc_start: 0.6756 (tpm170) cc_final: 0.6125 (ttt180) REVERT: B 524 MET cc_start: 0.2159 (ptt) cc_final: 0.1417 (ttt) REVERT: B 560 ILE cc_start: 0.8531 (tp) cc_final: 0.8145 (tt) REVERT: B 706 MET cc_start: 0.8733 (mmp) cc_final: 0.8386 (mmp) REVERT: B 731 ASN cc_start: 0.8533 (m-40) cc_final: 0.8237 (m-40) outliers start: 30 outliers final: 22 residues processed: 182 average time/residue: 0.0999 time to fit residues: 26.1246 Evaluate side-chains 179 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 849 HIS Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 367 MET Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 431 GLN Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 783 SER Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 849 HIS Chi-restraints excluded: chain B residue 883 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 136 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 431 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.147239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.119911 restraints weight = 18131.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.119668 restraints weight = 15403.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.120218 restraints weight = 12611.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.120520 restraints weight = 11232.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.121044 restraints weight = 10412.654| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12072 Z= 0.134 Angle : 0.651 14.641 16336 Z= 0.327 Chirality : 0.041 0.148 1796 Planarity : 0.005 0.075 2044 Dihedral : 4.674 23.032 1584 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.27 % Allowed : 22.27 % Favored : 75.47 % 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: -0.38 (0.23), residues: 1416 helix: 1.12 (0.18), residues: 852 sheet: -0.59 (1.06), residues: 32 loop : -2.64 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 125 TYR 0.028 0.002 TYR B 251 PHE 0.031 0.001 PHE A 617 TRP 0.021 0.001 TRP A 427 HIS 0.006 0.001 HIS B 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (12064) covalent geometry : angle 0.64170 / 0.32 (16320) SS BOND : bond 0.00500 / 0.26 ( 8) SS BOND : angle 3.53718 / 2.04 ( 16) hydrogen bonds : bond 0.04366 / 2.88 ( 642) hydrogen bonds : angle 4.60847 / 3.10 ( 1902) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 418 LEU cc_start: 0.7924 (tt) cc_final: 0.7600 (mp) REVERT: A 491 PHE cc_start: 0.5024 (t80) cc_final: 0.4761 (t80) REVERT: A 515 ARG cc_start: 0.6668 (tpm170) cc_final: 0.6049 (ttt180) REVERT: A 524 MET cc_start: 0.2495 (ptt) cc_final: 0.1894 (ttt) REVERT: A 560 ILE cc_start: 0.8583 (tp) cc_final: 0.8200 (tt) REVERT: B 418 LEU cc_start: 0.8025 (tt) cc_final: 0.7763 (mp) REVERT: B 515 ARG cc_start: 0.6803 (tpm170) cc_final: 0.6171 (ttt180) REVERT: B 524 MET cc_start: 0.2105 (ptt) cc_final: 0.1415 (ttt) REVERT: B 560 ILE cc_start: 0.8524 (tp) cc_final: 0.8138 (tt) REVERT: B 706 MET cc_start: 0.8698 (mmp) cc_final: 0.8316 (mmp) REVERT: B 731 ASN cc_start: 0.8530 (m-40) cc_final: 0.8239 (m-40) outliers start: 29 outliers final: 23 residues processed: 179 average time/residue: 0.0923 time to fit residues: 23.5882 Evaluate side-chains 175 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 849 HIS Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 367 MET Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 431 GLN Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 783 SER Chi-restraints excluded: chain B residue 794 MET Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 849 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 51 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 chunk 128 optimal weight: 0.9980 chunk 35 optimal weight: 20.0000 chunk 61 optimal weight: 7.9990 chunk 41 optimal weight: 0.6980 chunk 72 optimal weight: 10.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3985 r_free = 0.3985 target = 0.146381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.118097 restraints weight = 18395.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.118623 restraints weight = 15232.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.118977 restraints weight = 12317.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.119455 restraints weight = 11023.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.119649 restraints weight = 9905.528| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12072 Z= 0.146 Angle : 0.649 13.802 16336 Z= 0.328 Chirality : 0.041 0.150 1796 Planarity : 0.005 0.074 2044 Dihedral : 4.662 22.716 1584 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.95 % Allowed : 22.19 % Favored : 75.86 % 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: -0.38 (0.23), residues: 1416 helix: 1.10 (0.18), residues: 852 sheet: -0.64 (1.05), residues: 32 loop : -2.59 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 213 TYR 0.026 0.001 TYR A 251 PHE 0.031 0.001 PHE A 617 TRP 0.019 0.001 TRP A 427 HIS 0.006 0.001 HIS B 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (12064) covalent geometry : angle 0.63903 / 0.32 (16320) SS BOND : bond 0.00501 / 0.26 ( 8) SS BOND : angle 3.71354 / 2.14 ( 16) hydrogen bonds : bond 0.04409 / 2.92 ( 642) hydrogen bonds : angle 4.62683 / 3.09 ( 1902) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 LEU cc_start: 0.7943 (tt) cc_final: 0.7534 (mp) REVERT: A 491 PHE cc_start: 0.5113 (t80) cc_final: 0.4896 (t80) REVERT: A 515 ARG cc_start: 0.6754 (tpm170) cc_final: 0.6103 (ttt180) REVERT: A 524 MET cc_start: 0.2462 (ptt) cc_final: 0.1872 (ttt) REVERT: A 560 ILE cc_start: 0.8575 (tp) cc_final: 0.8198 (tt) REVERT: B 391 MET cc_start: 0.8534 (tpp) cc_final: 0.8302 (tpp) REVERT: B 418 LEU cc_start: 0.8106 (tt) cc_final: 0.7798 (mp) REVERT: B 515 ARG cc_start: 0.6845 (tpm170) cc_final: 0.6184 (ttt180) REVERT: B 524 MET cc_start: 0.2259 (ptt) cc_final: 0.1497 (ttt) REVERT: B 560 ILE cc_start: 0.8524 (tp) cc_final: 0.8141 (tt) REVERT: B 706 MET cc_start: 0.8725 (mmp) cc_final: 0.8386 (mmt) REVERT: B 731 ASN cc_start: 0.8585 (m-40) cc_final: 0.8291 (m-40) outliers start: 25 outliers final: 22 residues processed: 173 average time/residue: 0.1094 time to fit residues: 26.8516 Evaluate side-chains 173 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 849 HIS Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 367 MET Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 783 SER Chi-restraints excluded: chain B residue 794 MET Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 849 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 37 optimal weight: 6.9990 chunk 6 optimal weight: 20.0000 chunk 21 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 chunk 139 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 chunk 74 optimal weight: 7.9990 chunk 73 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 215 GLN B 431 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.142608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.115041 restraints weight = 18459.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.114571 restraints weight = 14571.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.114872 restraints weight = 12468.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.115270 restraints weight = 11894.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.115561 restraints weight = 10611.755| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12072 Z= 0.198 Angle : 0.717 14.558 16336 Z= 0.366 Chirality : 0.044 0.156 1796 Planarity : 0.006 0.076 2044 Dihedral : 4.931 24.960 1584 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 2.11 % Allowed : 22.42 % Favored : 75.47 % 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: -0.60 (0.23), residues: 1416 helix: 0.89 (0.18), residues: 860 sheet: -0.70 (1.04), residues: 32 loop : -2.67 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG A 125 TYR 0.027 0.002 TYR A 251 PHE 0.033 0.002 PHE A 617 TRP 0.016 0.002 TRP A 427 HIS 0.007 0.001 HIS A 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.20 (12064) covalent geometry : angle 0.70611 / 0.36 (16320) SS BOND : bond 0.00627 / 0.33 ( 8) SS BOND : angle 4.09772 / 2.46 ( 16) hydrogen bonds : bond 0.04847 / 3.22 ( 642) hydrogen bonds : angle 4.76549 / 3.18 ( 1902) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1637.06 seconds wall clock time: 29 minutes 5.66 seconds (1745.66 seconds total)