Starting phenix.real_space_refine on Wed Mar 4 08:00:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zk3_14753/03_2026/7zk3_14753_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zk3_14753/03_2026/7zk3_14753.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zk3_14753/03_2026/7zk3_14753.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zk3_14753/03_2026/7zk3_14753.map" model { file = "/net/cci-nas-00/data/ceres_data/7zk3_14753/03_2026/7zk3_14753_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zk3_14753/03_2026/7zk3_14753_trim.cif" } resolution = 2.85 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= 0.002 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: 6 Type Number sf(0) Gaussians Ca 6 9.91 5 S 74 5.16 5 C 7770 2.51 5 N 1962 2.21 5 O 2080 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11898 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5926 Classifications: {'peptide': 721} Link IDs: {'PTRANS': 31, 'TRANS': 689} Chain breaks: 5 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 23 Unusual residues: {' CA': 3, 'JRF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Restraints were copied for chains: B Time building chain proxies: 5.42, per 1000 atoms: 0.46 Number of scatterers: 11898 At special positions: 0 Unit cell: (91.977, 123.625, 114.724, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 6 19.99 S 74 16.00 F 6 9.00 O 2080 8.00 N 1962 7.00 C 7770 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 395 " distance=2.03 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=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 707.4 milliseconds 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2764 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 10 sheets defined 66.7% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 166 through 180 removed outlier: 3.669A pdb=" N LYS A 173 " --> pdb=" O ALA A 169 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Proline residue: A 177 - end of helix Processing helix chain 'A' and resid 204 through 211 removed outlier: 3.674A pdb=" N LYS A 208 " --> pdb=" O PRO A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 257 removed outlier: 3.553A pdb=" N THR A 257 " --> pdb=" O ILE A 253 " (cutoff:3.500A) 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: 3.507A pdb=" N VAL A 310 " --> pdb=" O SER A 307 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE A 311 " --> pdb=" O TYR A 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 307 through 311' 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 371 Processing helix chain 'A' and resid 394 through 403 removed outlier: 3.739A pdb=" N LEU A 403 " --> pdb=" O ARG A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 439 Processing helix chain 'A' and resid 452 through 466 Processing helix chain 'A' and resid 486 through 525 removed outlier: 3.667A pdb=" N ASN A 525 " --> pdb=" O ALA A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 533 Processing helix chain 'A' and resid 533 through 569 removed outlier: 3.699A pdb=" N VAL A 569 " --> pdb=" O THR A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 602 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 629 through 644 removed outlier: 4.402A pdb=" N GLU A 633 " --> pdb=" O GLY A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 668 Proline residue: A 658 - end of helix Processing helix chain 'A' and resid 685 through 693 Processing helix chain 'A' and resid 699 through 716 removed outlier: 3.659A pdb=" N PHE A 716 " --> pdb=" O PHE A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 745 removed outlier: 4.063A pdb=" N ARG A 736 " --> pdb=" O ILE A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 removed outlier: 4.150A pdb=" N ASN A 762 " --> pdb=" O GLY A 758 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL A 772 " --> pdb=" O GLY A 768 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE A 773 " --> pdb=" O LYS A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 795 removed outlier: 3.681A pdb=" N ARG A 788 " --> pdb=" O ASP A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 809 Processing helix chain 'A' and resid 815 through 817 No H-bonds generated for 'chain 'A' and resid 815 through 817' Processing helix chain 'A' and resid 854 through 886 removed outlier: 3.659A pdb=" N TRP A 858 " --> pdb=" O SER A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 910 Processing helix chain 'B' and resid 166 through 180 removed outlier: 3.669A pdb=" N LYS B 173 " --> pdb=" O ALA B 169 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Proline residue: B 177 - end of helix Processing helix chain 'B' and resid 204 through 211 removed outlier: 3.674A pdb=" N LYS B 208 " --> pdb=" O PRO B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 257 removed outlier: 3.552A pdb=" N THR B 257 " --> pdb=" O ILE B 253 " (cutoff:3.500A) 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: 3.507A pdb=" N VAL B 310 " --> pdb=" O SER B 307 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE B 311 " --> pdb=" O TYR B 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 307 through 311' 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 371 Processing helix chain 'B' and resid 394 through 403 removed outlier: 3.739A pdb=" N LEU B 403 " --> pdb=" O ARG B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 439 Processing helix chain 'B' and resid 452 through 466 Processing helix chain 'B' and resid 486 through 525 removed outlier: 3.666A pdb=" N ASN B 525 " --> pdb=" O ALA B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 533 Processing helix chain 'B' and resid 533 through 569 removed outlier: 3.699A pdb=" N VAL B 569 " --> pdb=" O THR B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 602 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 629 through 644 removed outlier: 4.401A pdb=" N GLU B 633 " --> pdb=" O GLY B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 668 Proline residue: B 658 - end of helix Processing helix chain 'B' and resid 685 through 693 Processing helix chain 'B' and resid 699 through 716 removed outlier: 3.660A pdb=" N PHE B 716 " --> pdb=" O PHE B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 745 removed outlier: 4.065A pdb=" N ARG B 736 " --> pdb=" O ILE B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 782 removed outlier: 4.150A pdb=" N ASN B 762 " --> pdb=" O GLY B 758 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL B 772 " --> pdb=" O GLY B 768 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE B 773 " --> pdb=" O LYS B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 795 removed outlier: 3.682A pdb=" N ARG B 788 " --> pdb=" O ASP B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 809 Processing helix chain 'B' and resid 815 through 817 No H-bonds generated for 'chain 'B' and resid 815 through 817' Processing helix chain 'B' and resid 854 through 886 removed outlier: 3.659A pdb=" N TRP B 858 " --> pdb=" O SER B 854 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 910 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 189 removed outlier: 3.524A pdb=" N ASP A 123 " --> pdb=" O GLN A 199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 217 through 218 Processing sheet with id=AA3, first strand: chain 'A' and resid 377 through 378 Processing sheet with id=AA4, first strand: chain 'A' and resid 615 through 616 Processing sheet with id=AA5, first strand: chain 'A' and resid 810 through 813 Processing sheet with id=AA6, first strand: chain 'B' and resid 185 through 189 removed outlier: 3.524A pdb=" N ASP B 123 " --> pdb=" O GLN B 199 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 217 through 218 Processing sheet with id=AA8, first strand: chain 'B' and resid 377 through 378 Processing sheet with id=AA9, first strand: chain 'B' and resid 615 through 616 Processing sheet with id=AB1, first strand: chain 'B' and resid 810 through 813 732 hydrogen bonds defined for protein. 2154 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: 1.82 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1858 1.29 - 1.43: 3376 1.43 - 1.56: 6840 1.56 - 1.70: 2 1.70 - 1.83: 122 Bond restraints: 12198 Sorted by residual: bond pdb=" C08 JRF B1003 " pdb=" C09 JRF B1003 " ideal model delta sigma weight residual 1.418 1.515 -0.097 2.00e-02 2.50e+03 2.35e+01 bond pdb=" C08 JRF A1003 " pdb=" C09 JRF A1003 " ideal model delta sigma weight residual 1.418 1.515 -0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" C13 JRF A1003 " pdb=" N06 JRF A1003 " ideal model delta sigma weight residual 1.367 1.440 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C13 JRF B1003 " pdb=" N06 JRF B1003 " ideal model delta sigma weight residual 1.367 1.439 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" C08 JRF B1003 " pdb=" N05 JRF B1003 " ideal model delta sigma weight residual 1.401 1.471 -0.070 2.00e-02 2.50e+03 1.24e+01 ... (remaining 12193 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.97: 16407 2.97 - 5.93: 82 5.93 - 8.90: 11 8.90 - 11.86: 2 11.86 - 14.83: 4 Bond angle restraints: 16506 Sorted by residual: angle pdb=" CA GLU A 186 " pdb=" CB GLU A 186 " pdb=" CG GLU A 186 " ideal model delta sigma weight residual 114.10 128.93 -14.83 2.00e+00 2.50e-01 5.50e+01 angle pdb=" CA GLU B 186 " pdb=" CB GLU B 186 " pdb=" CG GLU B 186 " ideal model delta sigma weight residual 114.10 128.91 -14.81 2.00e+00 2.50e-01 5.48e+01 angle pdb=" CB MET B 424 " pdb=" CG MET B 424 " pdb=" SD MET B 424 " ideal model delta sigma weight residual 112.70 127.13 -14.43 3.00e+00 1.11e-01 2.31e+01 angle pdb=" CB MET A 424 " pdb=" CG MET A 424 " pdb=" SD MET A 424 " ideal model delta sigma weight residual 112.70 127.08 -14.38 3.00e+00 1.11e-01 2.30e+01 angle pdb=" CB GLU B 186 " pdb=" CG GLU B 186 " pdb=" CD GLU B 186 " ideal model delta sigma weight residual 112.60 120.73 -8.13 1.70e+00 3.46e-01 2.29e+01 ... (remaining 16501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.14: 6586 16.14 - 32.28: 533 32.28 - 48.42: 97 48.42 - 64.56: 52 64.56 - 80.70: 12 Dihedral angle restraints: 7280 sinusoidal: 3012 harmonic: 4268 Sorted by residual: 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 -86.00 -166.70 80.70 1 1.00e+01 1.00e-02 8.05e+01 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 -86.00 -166.68 80.68 1 1.00e+01 1.00e-02 8.05e+01 dihedral pdb=" CA ARG B 621 " pdb=" C ARG B 621 " pdb=" N MET B 622 " pdb=" CA MET B 622 " ideal model delta harmonic sigma weight residual -180.00 -161.16 -18.84 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 7277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1162 0.027 - 0.054: 380 0.054 - 0.081: 173 0.081 - 0.108: 79 0.108 - 0.135: 8 Chirality restraints: 1802 Sorted by residual: chirality pdb=" CA MET B 622 " pdb=" N MET B 622 " pdb=" C MET B 622 " pdb=" CB MET B 622 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA MET A 622 " pdb=" N MET A 622 " pdb=" C MET A 622 " pdb=" CB MET A 622 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" CA ILE A 889 " pdb=" N ILE A 889 " pdb=" C ILE A 889 " pdb=" CB ILE A 889 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.80e-01 ... (remaining 1799 not shown) Planarity restraints: 2060 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 314 " 0.017 2.00e-02 2.50e+03 1.39e-02 3.89e+00 pdb=" CG TYR A 314 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR A 314 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR A 314 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR A 314 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 314 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 314 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 314 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 314 " 0.017 2.00e-02 2.50e+03 1.39e-02 3.89e+00 pdb=" CG TYR B 314 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR B 314 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR B 314 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR B 314 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 314 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 314 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 314 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 786 " 0.024 5.00e-02 4.00e+02 3.67e-02 2.15e+00 pdb=" N PRO A 787 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 787 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 787 " 0.021 5.00e-02 4.00e+02 ... (remaining 2057 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 174 2.67 - 3.23: 11784 3.23 - 3.79: 18790 3.79 - 4.34: 24768 4.34 - 4.90: 41353 Nonbonded interactions: 96869 Sorted by model distance: nonbonded pdb=" N GLU A 186 " pdb=" OE1 GLU A 186 " model vdw 2.118 3.120 nonbonded pdb=" N GLU B 186 " pdb=" OE1 GLU B 186 " model vdw 2.119 3.120 nonbonded pdb=" OE1 GLN A 215 " pdb=" NH2 ARG A 753 " model vdw 2.232 3.120 nonbonded pdb=" OE1 GLN B 215 " pdb=" NH2 ARG B 753 " model vdw 2.233 3.120 nonbonded pdb=" O ASN A 406 " pdb=" OG1 THR A 409 " model vdw 2.284 3.040 ... (remaining 96864 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.300 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 14.760 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 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 : 0.003 0.097 12206 Z= 0.162 Angle : 0.585 14.826 16522 Z= 0.286 Chirality : 0.036 0.135 1802 Planarity : 0.003 0.037 2060 Dihedral : 13.318 75.641 4492 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.09 % Allowed : 0.78 % Favored : 98.13 % 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: 1.70 (0.22), residues: 1418 helix: 2.63 (0.16), residues: 898 sheet: -0.61 (0.71), residues: 58 loop : -1.85 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 562 TYR 0.034 0.001 TYR A 314 PHE 0.008 0.001 PHE A 585 TRP 0.017 0.001 TRP A 427 HIS 0.004 0.001 HIS B 402 Details of bonding type rmsd covalent geometry : bond 0.00323 (12198) covalent geometry : angle 0.58482 (16506) SS BOND : bond 0.00099 ( 8) SS BOND : angle 0.27933 ( 16) hydrogen bonds : bond 0.13333 ( 732) hydrogen bonds : angle 6.08122 ( 2154) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 209 time to evaluate : 0.467 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 1 residues processed: 212 average time/residue: 0.6669 time to fit residues: 151.5283 Evaluate side-chains 143 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 664 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.0770 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN A 215 GLN A 709 GLN A 730 ASN ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 GLN B 493 ASN B 533 ASN B 591 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.144245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.102299 restraints weight = 17277.398| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.22 r_work: 0.3118 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12206 Z= 0.175 Angle : 0.590 9.438 16522 Z= 0.308 Chirality : 0.041 0.131 1802 Planarity : 0.004 0.037 2060 Dihedral : 4.242 41.842 1612 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.10 % Allowed : 8.63 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.22), residues: 1418 helix: 2.37 (0.16), residues: 906 sheet: -1.19 (0.62), residues: 58 loop : -1.95 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 461 TYR 0.019 0.002 TYR A 514 PHE 0.015 0.001 PHE B 585 TRP 0.013 0.001 TRP A 427 HIS 0.006 0.001 HIS A 898 Details of bonding type rmsd covalent geometry : bond 0.00405 (12198) covalent geometry : angle 0.58852 (16506) SS BOND : bond 0.00202 ( 8) SS BOND : angle 1.34616 ( 16) hydrogen bonds : bond 0.05265 ( 732) hydrogen bonds : angle 4.87274 ( 2154) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 162 time to evaluate : 0.450 Fit side-chains revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7002 (mp0) REVERT: A 188 ARG cc_start: 0.7317 (mmm-85) cc_final: 0.7006 (mmm-85) REVERT: A 457 GLU cc_start: 0.6424 (mt-10) cc_final: 0.5774 (mp0) REVERT: A 461 ARG cc_start: 0.5947 (ttp80) cc_final: 0.5671 (tmm160) REVERT: A 769 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7882 (ttpt) REVERT: A 889 ILE cc_start: 0.8724 (pp) cc_final: 0.8428 (mt) REVERT: B 121 GLU cc_start: 0.5113 (mm-30) cc_final: 0.4870 (mm-30) REVERT: B 186 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7326 (mp0) REVERT: B 188 ARG cc_start: 0.7269 (mmm-85) cc_final: 0.6951 (mmm-85) REVERT: B 461 ARG cc_start: 0.5674 (ttp80) cc_final: 0.5404 (tmm160) REVERT: B 573 GLU cc_start: 0.7348 (mm-30) cc_final: 0.6961 (mm-30) REVERT: B 574 LYS cc_start: 0.8156 (tptp) cc_final: 0.7646 (tppt) REVERT: B 577 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7567 (mp0) REVERT: B 683 ARG cc_start: 0.7138 (tpt170) cc_final: 0.6354 (tmm-80) REVERT: B 889 ILE cc_start: 0.8824 (pp) cc_final: 0.8502 (mp) REVERT: B 904 MET cc_start: 0.7316 (mmp) cc_final: 0.6982 (mmp) outliers start: 27 outliers final: 7 residues processed: 175 average time/residue: 0.6398 time to fit residues: 120.1506 Evaluate side-chains 162 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 151 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 577 GLU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 773 ILE Chi-restraints excluded: chain B residue 821 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 59 optimal weight: 0.3980 chunk 114 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 130 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 709 GLN A 730 ASN B 199 GLN B 591 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.142637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.100500 restraints weight = 17580.867| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.23 r_work: 0.3092 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12206 Z= 0.182 Angle : 0.571 9.751 16522 Z= 0.299 Chirality : 0.041 0.136 1802 Planarity : 0.004 0.042 2060 Dihedral : 4.111 21.744 1612 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.95 % Allowed : 9.33 % Favored : 87.71 % 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: 1.23 (0.22), residues: 1418 helix: 2.28 (0.16), residues: 904 sheet: -1.17 (0.66), residues: 48 loop : -2.07 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 125 TYR 0.012 0.001 TYR B 687 PHE 0.027 0.002 PHE B 691 TRP 0.014 0.001 TRP B 427 HIS 0.009 0.001 HIS A 898 Details of bonding type rmsd covalent geometry : bond 0.00424 (12198) covalent geometry : angle 0.56977 (16506) SS BOND : bond 0.00214 ( 8) SS BOND : angle 1.29658 ( 16) hydrogen bonds : bond 0.05137 ( 732) hydrogen bonds : angle 4.66492 ( 2154) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 152 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7300 (mp0) REVERT: A 206 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7880 (mp10) REVERT: A 457 GLU cc_start: 0.6496 (mt-10) cc_final: 0.6269 (mt-10) REVERT: A 461 ARG cc_start: 0.6041 (ttp80) cc_final: 0.5793 (ttp80) REVERT: A 507 ILE cc_start: 0.7288 (OUTLIER) cc_final: 0.7041 (mp) REVERT: A 574 LYS cc_start: 0.8121 (tptp) cc_final: 0.7536 (tppt) REVERT: A 769 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7957 (ttpt) REVERT: A 878 MET cc_start: 0.8891 (mtt) cc_final: 0.8677 (mtt) REVERT: A 892 ASP cc_start: 0.7716 (p0) cc_final: 0.7473 (p0) REVERT: B 121 GLU cc_start: 0.5141 (mm-30) cc_final: 0.4862 (mm-30) REVERT: B 124 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8358 (mppt) REVERT: B 186 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7500 (mp0) REVERT: B 461 ARG cc_start: 0.5731 (ttp80) cc_final: 0.5298 (tmm160) REVERT: B 494 LEU cc_start: 0.7908 (tp) cc_final: 0.7601 (OUTLIER) REVERT: B 507 ILE cc_start: 0.7313 (OUTLIER) cc_final: 0.7094 (mp) REVERT: B 573 GLU cc_start: 0.7382 (mm-30) cc_final: 0.7130 (mm-30) REVERT: B 574 LYS cc_start: 0.8202 (tptp) cc_final: 0.7615 (tppt) REVERT: B 577 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7587 (mp0) REVERT: B 683 ARG cc_start: 0.7154 (tpt170) cc_final: 0.6424 (tmm-80) REVERT: B 904 MET cc_start: 0.7441 (mmp) cc_final: 0.7088 (mmp) outliers start: 38 outliers final: 15 residues processed: 174 average time/residue: 0.6522 time to fit residues: 121.7846 Evaluate side-chains 167 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 145 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 577 GLU Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 665 ARG Chi-restraints excluded: chain B residue 773 ILE Chi-restraints excluded: chain B residue 797 GLN Chi-restraints excluded: chain B residue 821 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 3 optimal weight: 3.9990 chunk 52 optimal weight: 0.0060 chunk 2 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 136 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 114 optimal weight: 0.9990 chunk 28 optimal weight: 0.3980 chunk 87 optimal weight: 0.3980 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 898 HIS B 591 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.143838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.101857 restraints weight = 17423.776| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.25 r_work: 0.3115 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12206 Z= 0.138 Angle : 0.546 9.560 16522 Z= 0.283 Chirality : 0.039 0.131 1802 Planarity : 0.004 0.066 2060 Dihedral : 4.118 22.364 1612 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.80 % Allowed : 10.89 % Favored : 86.31 % 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: 1.30 (0.22), residues: 1418 helix: 2.37 (0.16), residues: 898 sheet: -1.22 (0.64), residues: 48 loop : -2.07 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 753 TYR 0.011 0.001 TYR B 687 PHE 0.031 0.001 PHE B 126 TRP 0.016 0.001 TRP B 427 HIS 0.009 0.001 HIS A 898 Details of bonding type rmsd covalent geometry : bond 0.00304 (12198) covalent geometry : angle 0.54455 (16506) SS BOND : bond 0.00202 ( 8) SS BOND : angle 1.23921 ( 16) hydrogen bonds : bond 0.04786 ( 732) hydrogen bonds : angle 4.56276 ( 2154) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 146 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.8103 (mppt) REVERT: A 186 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7326 (mp0) REVERT: A 206 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.7962 (mp10) REVERT: A 457 GLU cc_start: 0.6457 (mt-10) cc_final: 0.6254 (mt-10) REVERT: A 461 ARG cc_start: 0.6180 (ttp80) cc_final: 0.5942 (ttp80) REVERT: A 574 LYS cc_start: 0.8147 (tptp) cc_final: 0.7566 (tppt) REVERT: A 769 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7959 (ttpt) REVERT: A 878 MET cc_start: 0.8886 (mtt) cc_final: 0.8665 (mtt) REVERT: A 892 ASP cc_start: 0.7728 (p0) cc_final: 0.7475 (p0) REVERT: B 186 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7483 (mp0) REVERT: B 461 ARG cc_start: 0.5704 (ttp80) cc_final: 0.5346 (tmm160) REVERT: B 507 ILE cc_start: 0.7226 (OUTLIER) cc_final: 0.6969 (mp) REVERT: B 573 GLU cc_start: 0.7363 (mm-30) cc_final: 0.7104 (mm-30) REVERT: B 574 LYS cc_start: 0.8223 (tptp) cc_final: 0.7640 (tppt) REVERT: B 577 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7577 (mp0) REVERT: B 683 ARG cc_start: 0.7134 (tpt170) cc_final: 0.6463 (tmm-80) REVERT: B 904 MET cc_start: 0.7426 (mmp) cc_final: 0.7043 (mmp) outliers start: 36 outliers final: 17 residues processed: 168 average time/residue: 0.6404 time to fit residues: 115.7296 Evaluate side-chains 168 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 171 PHE Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 797 GLN Chi-restraints excluded: chain A residue 909 MET Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 577 GLU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 665 ARG Chi-restraints excluded: chain B residue 773 ILE Chi-restraints excluded: chain B residue 797 GLN Chi-restraints excluded: chain B residue 821 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 0 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 92 optimal weight: 0.0570 chunk 112 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 39 optimal weight: 0.0470 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 591 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.143495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.101568 restraints weight = 17382.004| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.23 r_work: 0.3113 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12206 Z= 0.146 Angle : 0.566 12.821 16522 Z= 0.288 Chirality : 0.040 0.307 1802 Planarity : 0.004 0.067 2060 Dihedral : 4.124 22.831 1612 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.11 % Allowed : 10.58 % Favored : 86.31 % 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: 1.33 (0.22), residues: 1418 helix: 2.40 (0.16), residues: 898 sheet: -1.29 (0.63), residues: 48 loop : -2.05 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 753 TYR 0.011 0.001 TYR B 687 PHE 0.039 0.001 PHE B 126 TRP 0.015 0.001 TRP B 427 HIS 0.008 0.001 HIS A 898 Details of bonding type rmsd covalent geometry : bond 0.00331 (12198) covalent geometry : angle 0.56531 (16506) SS BOND : bond 0.00207 ( 8) SS BOND : angle 1.19030 ( 16) hydrogen bonds : bond 0.04782 ( 732) hydrogen bonds : angle 4.52951 ( 2154) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 152 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.8080 (mppt) REVERT: A 186 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7416 (mp0) REVERT: A 206 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7960 (mp10) REVERT: A 457 GLU cc_start: 0.6453 (mt-10) cc_final: 0.6247 (mt-10) REVERT: A 461 ARG cc_start: 0.6217 (ttp80) cc_final: 0.5965 (ttp80) REVERT: A 500 MET cc_start: 0.6363 (mtt) cc_final: 0.5693 (mtt) REVERT: A 507 ILE cc_start: 0.7379 (OUTLIER) cc_final: 0.7121 (mp) REVERT: A 574 LYS cc_start: 0.8174 (tptp) cc_final: 0.7603 (tppt) REVERT: A 683 ARG cc_start: 0.7144 (tpt170) cc_final: 0.6274 (tmm-80) REVERT: A 769 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7907 (ttpt) REVERT: A 878 MET cc_start: 0.8880 (mtt) cc_final: 0.8660 (mtt) REVERT: A 892 ASP cc_start: 0.7787 (p0) cc_final: 0.7510 (p0) REVERT: B 186 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7562 (mp0) REVERT: B 226 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.6720 (tmm160) REVERT: B 256 ARG cc_start: 0.6920 (OUTLIER) cc_final: 0.5184 (ptp90) REVERT: B 461 ARG cc_start: 0.5772 (ttp80) cc_final: 0.5402 (tmm160) REVERT: B 507 ILE cc_start: 0.7192 (OUTLIER) cc_final: 0.6936 (mp) REVERT: B 573 GLU cc_start: 0.7398 (mm-30) cc_final: 0.7126 (mm-30) REVERT: B 574 LYS cc_start: 0.8209 (tptp) cc_final: 0.7638 (tppt) REVERT: B 577 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7550 (mp0) REVERT: B 683 ARG cc_start: 0.7113 (tpt170) cc_final: 0.6513 (tmm-80) REVERT: B 904 MET cc_start: 0.7412 (mmp) cc_final: 0.7018 (mmp) outliers start: 40 outliers final: 16 residues processed: 178 average time/residue: 0.6344 time to fit residues: 121.3224 Evaluate side-chains 171 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 171 PHE Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 909 MET Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 226 ARG Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 577 GLU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 665 ARG Chi-restraints excluded: chain B residue 773 ILE Chi-restraints excluded: chain B residue 821 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 13 optimal weight: 0.6980 chunk 130 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 121 optimal weight: 0.6980 chunk 138 optimal weight: 0.5980 chunk 134 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 493 ASN B 591 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.142638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.100695 restraints weight = 17492.958| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.23 r_work: 0.3095 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12206 Z= 0.167 Angle : 0.575 10.564 16522 Z= 0.294 Chirality : 0.041 0.300 1802 Planarity : 0.004 0.066 2060 Dihedral : 4.196 23.099 1612 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.11 % Allowed : 12.05 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.22), residues: 1418 helix: 2.38 (0.16), residues: 898 sheet: -1.35 (0.62), residues: 48 loop : -2.03 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 753 TYR 0.011 0.001 TYR B 687 PHE 0.046 0.002 PHE B 126 TRP 0.015 0.001 TRP B 427 HIS 0.009 0.001 HIS A 898 Details of bonding type rmsd covalent geometry : bond 0.00389 (12198) covalent geometry : angle 0.57461 (16506) SS BOND : bond 0.00198 ( 8) SS BOND : angle 1.15700 ( 16) hydrogen bonds : bond 0.04935 ( 732) hydrogen bonds : angle 4.52327 ( 2154) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 156 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.8080 (mppt) REVERT: A 186 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7461 (mp0) REVERT: A 206 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.7947 (mp10) REVERT: A 359 THR cc_start: 0.8817 (m) cc_final: 0.8592 (m) REVERT: A 461 ARG cc_start: 0.6104 (ttp80) cc_final: 0.5861 (ttp80) REVERT: A 500 MET cc_start: 0.6644 (mtt) cc_final: 0.6104 (mtt) REVERT: A 507 ILE cc_start: 0.7389 (OUTLIER) cc_final: 0.7118 (mp) REVERT: A 574 LYS cc_start: 0.8228 (tptp) cc_final: 0.7641 (tppt) REVERT: A 683 ARG cc_start: 0.7176 (tpt170) cc_final: 0.6329 (tmm-80) REVERT: A 769 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7891 (ttpt) REVERT: A 878 MET cc_start: 0.8901 (mtt) cc_final: 0.8688 (mtt) REVERT: A 892 ASP cc_start: 0.7809 (p0) cc_final: 0.7551 (p0) REVERT: B 186 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7539 (mp0) REVERT: B 188 ARG cc_start: 0.7020 (mmm-85) cc_final: 0.6771 (mmm-85) REVERT: B 226 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.6647 (tmm160) REVERT: B 256 ARG cc_start: 0.6895 (OUTLIER) cc_final: 0.5317 (ptp90) REVERT: B 461 ARG cc_start: 0.5775 (ttp80) cc_final: 0.5400 (tmm160) REVERT: B 507 ILE cc_start: 0.7206 (OUTLIER) cc_final: 0.6948 (mp) REVERT: B 573 GLU cc_start: 0.7431 (mm-30) cc_final: 0.7152 (mm-30) REVERT: B 574 LYS cc_start: 0.8214 (tptp) cc_final: 0.7654 (tppt) REVERT: B 577 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7561 (mp0) REVERT: B 683 ARG cc_start: 0.7147 (tpt170) cc_final: 0.6544 (tmm-80) REVERT: B 904 MET cc_start: 0.7379 (mmp) cc_final: 0.7047 (mmp) outliers start: 40 outliers final: 19 residues processed: 178 average time/residue: 0.6250 time to fit residues: 119.6942 Evaluate side-chains 180 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 151 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 171 PHE Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 909 MET Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 226 ARG Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 577 GLU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 665 ARG Chi-restraints excluded: chain B residue 773 ILE Chi-restraints excluded: chain B residue 821 THR Chi-restraints excluded: chain B residue 909 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 112 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 84 optimal weight: 0.4980 chunk 115 optimal weight: 0.2980 chunk 4 optimal weight: 0.2980 chunk 85 optimal weight: 0.4980 chunk 135 optimal weight: 0.4980 chunk 65 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 493 ASN B 591 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.143713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.102206 restraints weight = 17401.670| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.22 r_work: 0.3119 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12206 Z= 0.136 Angle : 0.571 10.853 16522 Z= 0.289 Chirality : 0.040 0.187 1802 Planarity : 0.004 0.056 2060 Dihedral : 4.128 23.238 1612 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.72 % Allowed : 12.99 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.22), residues: 1418 helix: 2.44 (0.16), residues: 898 sheet: -1.41 (0.62), residues: 48 loop : -1.97 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 373 TYR 0.010 0.001 TYR B 687 PHE 0.015 0.001 PHE A 126 TRP 0.016 0.001 TRP A 427 HIS 0.009 0.001 HIS A 898 Details of bonding type rmsd covalent geometry : bond 0.00299 (12198) covalent geometry : angle 0.56994 (16506) SS BOND : bond 0.00213 ( 8) SS BOND : angle 1.15541 ( 16) hydrogen bonds : bond 0.04691 ( 732) hydrogen bonds : angle 4.48708 ( 2154) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 155 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.8044 (mppt) REVERT: A 186 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7458 (mp0) REVERT: A 206 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.7910 (mp10) REVERT: A 287 ASP cc_start: 0.8685 (m-30) cc_final: 0.8433 (m-30) REVERT: A 461 ARG cc_start: 0.6124 (ttp80) cc_final: 0.5892 (ttp80) REVERT: A 497 ILE cc_start: 0.6826 (OUTLIER) cc_final: 0.6605 (mt) REVERT: A 500 MET cc_start: 0.6679 (mtt) cc_final: 0.6201 (mtt) REVERT: A 507 ILE cc_start: 0.7342 (OUTLIER) cc_final: 0.7083 (mp) REVERT: A 574 LYS cc_start: 0.8176 (tptp) cc_final: 0.7597 (tppt) REVERT: A 578 GLU cc_start: 0.6847 (OUTLIER) cc_final: 0.6527 (tt0) REVERT: A 683 ARG cc_start: 0.7234 (tpt170) cc_final: 0.6431 (tmm-80) REVERT: A 769 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7864 (ttpt) REVERT: A 878 MET cc_start: 0.8891 (mtt) cc_final: 0.8670 (mtt) REVERT: A 892 ASP cc_start: 0.7761 (p0) cc_final: 0.7489 (p0) REVERT: B 186 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7500 (mp0) REVERT: B 226 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.6668 (tmm160) REVERT: B 256 ARG cc_start: 0.6924 (OUTLIER) cc_final: 0.5505 (ptp90) REVERT: B 507 ILE cc_start: 0.7174 (OUTLIER) cc_final: 0.6916 (mp) REVERT: B 573 GLU cc_start: 0.7415 (mm-30) cc_final: 0.7171 (mm-30) REVERT: B 574 LYS cc_start: 0.8217 (tptp) cc_final: 0.7661 (tppt) REVERT: B 577 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7560 (mp0) REVERT: B 683 ARG cc_start: 0.7164 (tpt170) cc_final: 0.6633 (tmm-80) REVERT: B 904 MET cc_start: 0.7337 (mmp) cc_final: 0.6813 (mmp) outliers start: 35 outliers final: 14 residues processed: 176 average time/residue: 0.6210 time to fit residues: 117.6707 Evaluate side-chains 173 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 909 MET Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 226 ARG Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 577 GLU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 665 ARG Chi-restraints excluded: chain B residue 773 ILE Chi-restraints excluded: chain B residue 821 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 4 optimal weight: 0.2980 chunk 39 optimal weight: 2.9990 chunk 107 optimal weight: 0.0040 chunk 21 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 84 optimal weight: 0.3980 chunk 33 optimal weight: 0.6980 chunk 117 optimal weight: 0.3980 chunk 96 optimal weight: 1.9990 overall best weight: 0.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 493 ASN B 591 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.144083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.102570 restraints weight = 17350.087| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.23 r_work: 0.3125 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12206 Z= 0.130 Angle : 0.580 13.984 16522 Z= 0.291 Chirality : 0.039 0.135 1802 Planarity : 0.004 0.052 2060 Dihedral : 4.106 24.903 1612 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.64 % Allowed : 13.37 % Favored : 83.98 % 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: 1.50 (0.22), residues: 1418 helix: 2.55 (0.16), residues: 890 sheet: -1.45 (0.61), residues: 48 loop : -1.93 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 373 TYR 0.010 0.001 TYR A 687 PHE 0.025 0.001 PHE A 295 TRP 0.016 0.001 TRP A 427 HIS 0.010 0.001 HIS A 898 Details of bonding type rmsd covalent geometry : bond 0.00281 (12198) covalent geometry : angle 0.57882 (16506) SS BOND : bond 0.00211 ( 8) SS BOND : angle 1.13476 ( 16) hydrogen bonds : bond 0.04601 ( 732) hydrogen bonds : angle 4.45169 ( 2154) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 151 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.8025 (mppt) REVERT: A 186 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7487 (mp0) REVERT: A 206 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.7947 (mp10) REVERT: A 287 ASP cc_start: 0.8648 (m-30) cc_final: 0.8385 (m-30) REVERT: A 461 ARG cc_start: 0.6102 (ttp80) cc_final: 0.5867 (ttp80) REVERT: A 497 ILE cc_start: 0.6830 (OUTLIER) cc_final: 0.6628 (mt) REVERT: A 500 MET cc_start: 0.6674 (mtt) cc_final: 0.6226 (mtt) REVERT: A 507 ILE cc_start: 0.7321 (OUTLIER) cc_final: 0.7061 (mp) REVERT: A 574 LYS cc_start: 0.8185 (tptp) cc_final: 0.7588 (tppt) REVERT: A 683 ARG cc_start: 0.7228 (tpt170) cc_final: 0.6466 (tmm-80) REVERT: A 769 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7879 (ttpt) REVERT: A 878 MET cc_start: 0.8890 (mtt) cc_final: 0.8666 (mtt) REVERT: A 892 ASP cc_start: 0.7750 (p0) cc_final: 0.7490 (p0) REVERT: B 186 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7461 (mp0) REVERT: B 188 ARG cc_start: 0.6953 (mmm-85) cc_final: 0.6692 (mmm-85) REVERT: B 226 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.6720 (tmm160) REVERT: B 256 ARG cc_start: 0.6916 (OUTLIER) cc_final: 0.5444 (ptp90) REVERT: B 507 ILE cc_start: 0.7140 (OUTLIER) cc_final: 0.6881 (mp) REVERT: B 573 GLU cc_start: 0.7398 (mm-30) cc_final: 0.7128 (mm-30) REVERT: B 574 LYS cc_start: 0.8212 (tptp) cc_final: 0.7653 (tppt) REVERT: B 577 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7547 (mp0) REVERT: B 683 ARG cc_start: 0.7219 (tpt170) cc_final: 0.6688 (tmm-80) REVERT: B 904 MET cc_start: 0.7338 (mmp) cc_final: 0.6963 (mmm) outliers start: 34 outliers final: 15 residues processed: 171 average time/residue: 0.6426 time to fit residues: 118.3429 Evaluate side-chains 176 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 909 MET Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 226 ARG Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 577 GLU Chi-restraints excluded: chain B residue 665 ARG Chi-restraints excluded: chain B residue 773 ILE Chi-restraints excluded: chain B residue 821 THR Chi-restraints excluded: chain B residue 909 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 137 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 133 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 12 optimal weight: 0.4980 chunk 59 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 109 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 898 HIS B 493 ASN B 591 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.142375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.100610 restraints weight = 17492.806| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.23 r_work: 0.3099 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12206 Z= 0.177 Angle : 0.614 11.538 16522 Z= 0.310 Chirality : 0.040 0.177 1802 Planarity : 0.004 0.056 2060 Dihedral : 4.136 23.517 1610 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.64 % Allowed : 13.69 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.41 (0.22), residues: 1418 helix: 2.47 (0.16), residues: 890 sheet: -1.52 (0.61), residues: 48 loop : -1.92 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 461 TYR 0.010 0.001 TYR A 687 PHE 0.018 0.001 PHE B 126 TRP 0.013 0.001 TRP A 427 HIS 0.010 0.001 HIS A 898 Details of bonding type rmsd covalent geometry : bond 0.00416 (12198) covalent geometry : angle 0.61361 (16506) SS BOND : bond 0.00199 ( 8) SS BOND : angle 1.10968 ( 16) hydrogen bonds : bond 0.04908 ( 732) hydrogen bonds : angle 4.49674 ( 2154) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 151 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.8045 (mppt) REVERT: A 186 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7487 (mp0) REVERT: A 206 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.7861 (mp10) REVERT: A 287 ASP cc_start: 0.8697 (m-30) cc_final: 0.8439 (m-30) REVERT: A 461 ARG cc_start: 0.6069 (ttp80) cc_final: 0.5832 (ttp80) REVERT: A 497 ILE cc_start: 0.6833 (OUTLIER) cc_final: 0.6630 (mt) REVERT: A 500 MET cc_start: 0.6875 (mtt) cc_final: 0.6416 (mtt) REVERT: A 507 ILE cc_start: 0.7340 (OUTLIER) cc_final: 0.7064 (mp) REVERT: A 574 LYS cc_start: 0.8220 (tptp) cc_final: 0.7631 (tppt) REVERT: A 577 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7567 (mp0) REVERT: A 683 ARG cc_start: 0.7250 (tpt170) cc_final: 0.6484 (tmm-80) REVERT: A 769 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7829 (ttpt) REVERT: A 878 MET cc_start: 0.8902 (mtt) cc_final: 0.8690 (mtt) REVERT: A 892 ASP cc_start: 0.7797 (p0) cc_final: 0.7537 (p0) REVERT: B 186 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7500 (mp0) REVERT: B 188 ARG cc_start: 0.7002 (mmm-85) cc_final: 0.6765 (mmm-85) REVERT: B 226 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.6696 (tmm160) REVERT: B 252 GLU cc_start: 0.7625 (tp30) cc_final: 0.7088 (tp30) REVERT: B 256 ARG cc_start: 0.6887 (OUTLIER) cc_final: 0.5343 (ptp90) REVERT: B 507 ILE cc_start: 0.7159 (OUTLIER) cc_final: 0.6892 (mp) REVERT: B 573 GLU cc_start: 0.7405 (mm-30) cc_final: 0.7069 (mm-30) REVERT: B 574 LYS cc_start: 0.8211 (tptp) cc_final: 0.7618 (tppt) REVERT: B 577 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7511 (mp0) REVERT: B 683 ARG cc_start: 0.7258 (tpt170) cc_final: 0.6700 (tmm-80) REVERT: B 904 MET cc_start: 0.7358 (mmp) cc_final: 0.6976 (mmm) outliers start: 34 outliers final: 15 residues processed: 169 average time/residue: 0.6509 time to fit residues: 118.2920 Evaluate side-chains 174 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 577 GLU Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 909 MET Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 226 ARG Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 327 LYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 577 GLU Chi-restraints excluded: chain B residue 665 ARG Chi-restraints excluded: chain B residue 773 ILE Chi-restraints excluded: chain B residue 821 THR Chi-restraints excluded: chain B residue 909 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 29 optimal weight: 0.0770 chunk 18 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 60 optimal weight: 0.5980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 898 HIS B 591 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.142935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.101144 restraints weight = 17449.827| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.22 r_work: 0.3107 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12206 Z= 0.158 Angle : 0.618 12.466 16522 Z= 0.310 Chirality : 0.040 0.150 1802 Planarity : 0.004 0.052 2060 Dihedral : 4.147 23.404 1610 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.57 % Allowed : 14.00 % Favored : 83.44 % 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: 1.51 (0.22), residues: 1418 helix: 2.52 (0.16), residues: 886 sheet: -1.37 (0.64), residues: 48 loop : -1.80 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 461 TYR 0.009 0.001 TYR B 687 PHE 0.023 0.001 PHE A 126 TRP 0.014 0.001 TRP A 427 HIS 0.010 0.001 HIS A 898 Details of bonding type rmsd covalent geometry : bond 0.00362 (12198) covalent geometry : angle 0.61690 (16506) SS BOND : bond 0.00204 ( 8) SS BOND : angle 1.12104 ( 16) hydrogen bonds : bond 0.04808 ( 732) hydrogen bonds : angle 4.50456 ( 2154) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 150 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.8022 (mppt) REVERT: A 186 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7451 (mp0) REVERT: A 206 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.7845 (mp10) REVERT: A 287 ASP cc_start: 0.8670 (m-30) cc_final: 0.8408 (m-30) REVERT: A 461 ARG cc_start: 0.6012 (ttp80) cc_final: 0.5777 (ttp80) REVERT: A 500 MET cc_start: 0.6764 (mtt) cc_final: 0.6336 (mtt) REVERT: A 507 ILE cc_start: 0.7308 (OUTLIER) cc_final: 0.7037 (mp) REVERT: A 574 LYS cc_start: 0.8198 (tptp) cc_final: 0.7610 (tppt) REVERT: A 577 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7563 (mp0) REVERT: A 683 ARG cc_start: 0.7221 (tpt170) cc_final: 0.6507 (tmm-80) REVERT: A 769 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7751 (ttpt) REVERT: A 878 MET cc_start: 0.8870 (mtt) cc_final: 0.8645 (mtt) REVERT: A 892 ASP cc_start: 0.7764 (p0) cc_final: 0.7498 (p0) REVERT: B 186 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7338 (mp0) REVERT: B 188 ARG cc_start: 0.6984 (mmm-85) cc_final: 0.6728 (mmm-85) REVERT: B 226 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.6659 (tmm160) REVERT: B 252 GLU cc_start: 0.7606 (tp30) cc_final: 0.7072 (tp30) REVERT: B 256 ARG cc_start: 0.6816 (OUTLIER) cc_final: 0.5294 (ptp90) REVERT: B 507 ILE cc_start: 0.7121 (OUTLIER) cc_final: 0.6850 (mp) REVERT: B 573 GLU cc_start: 0.7406 (mm-30) cc_final: 0.7127 (mm-30) REVERT: B 574 LYS cc_start: 0.8183 (tptp) cc_final: 0.7578 (tppt) REVERT: B 577 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7489 (mp0) REVERT: B 683 ARG cc_start: 0.7239 (tpt170) cc_final: 0.6692 (tmm-80) REVERT: B 904 MET cc_start: 0.7344 (mmp) cc_final: 0.6957 (mmm) outliers start: 33 outliers final: 13 residues processed: 168 average time/residue: 0.6364 time to fit residues: 114.8287 Evaluate side-chains 172 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 577 GLU Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 909 MET Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 226 ARG Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 577 GLU Chi-restraints excluded: chain B residue 665 ARG Chi-restraints excluded: chain B residue 773 ILE Chi-restraints excluded: chain B residue 821 THR Chi-restraints excluded: chain B residue 909 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 81 optimal weight: 0.0000 chunk 122 optimal weight: 0.1980 chunk 25 optimal weight: 0.5980 chunk 137 optimal weight: 0.4980 chunk 68 optimal weight: 0.6980 chunk 142 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 59 optimal weight: 0.4980 chunk 82 optimal weight: 0.7980 overall best weight: 0.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 591 ASN A 898 HIS B 591 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.143686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.102101 restraints weight = 17359.717| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.22 r_work: 0.3109 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12206 Z= 0.135 Angle : 0.602 11.616 16522 Z= 0.303 Chirality : 0.039 0.144 1802 Planarity : 0.004 0.038 2060 Dihedral : 4.149 23.412 1610 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.10 % Allowed : 14.70 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.22), residues: 1418 helix: 2.55 (0.16), residues: 886 sheet: -1.36 (0.65), residues: 48 loop : -1.78 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 461 TYR 0.009 0.001 TYR B 687 PHE 0.014 0.001 PHE B 126 TRP 0.016 0.001 TRP A 427 HIS 0.010 0.001 HIS A 898 Details of bonding type rmsd covalent geometry : bond 0.00297 (12198) covalent geometry : angle 0.60154 (16506) SS BOND : bond 0.00213 ( 8) SS BOND : angle 1.12776 ( 16) hydrogen bonds : bond 0.04682 ( 732) hydrogen bonds : angle 4.49643 ( 2154) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4456.55 seconds wall clock time: 76 minutes 28.41 seconds (4588.41 seconds total)