Starting phenix.real_space_refine on Fri Jul 3 04:09:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zk3_14753/07_2026/7zk3_14753_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zk3_14753/07_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_14753/07_2026/7zk3_14753.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zk3_14753/07_2026/7zk3_14753.map" model { file = "/net/cci-nas-00/data/ceres_data/7zk3_14753/07_2026/7zk3_14753_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zk3_14753/07_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-6108/lib/python3.11/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, 20 Ad-hoc single atom residues: {' CA': 3} Unusual residues: {'JRF': 1} Classifications: {'undetermined': 1} Chain breaks: 3 Restraints were copied for chains: B Time building chain proxies: 4.38, per 1000 atoms: 0.37 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: 0.65 Conformation dependent library (CDL) restraints added in 397.3 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: 0.19 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: 1.73 Time building geometry restraints manager: 0.94 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: 4.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.560 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 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/Z covalent geometry : bond 0.00323 / 0.16 (12198) covalent geometry : angle 0.58482 / 0.29 (16506) SS BOND : bond 0.00099 / 0.06 ( 8) SS BOND : angle 0.27933 / 0.15 ( 16) hydrogen bonds : bond 0.13333 / 9.63 ( 732) hydrogen bonds : angle 6.08122 / 4.33 ( 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 : 0.307 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 1 residues processed: 212 average time/residue: 0.5856 time to fit residues: 133.7451 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 : 0.362 ------------------------------------------------------------------------------- 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: 0.0670 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: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 B 709 GLN B 730 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.144266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.102421 restraints weight = 17300.038| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.22 r_work: 0.3117 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1939 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= 0.175 Angle : 0.594 9.486 16522 Z= 0.310 Chirality : 0.041 0.134 1802 Planarity : 0.004 0.033 2060 Dihedral : 4.075 21.396 1612 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.94 % Allowed : 8.86 % Favored : 89.19 % 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: 1.42 (0.22), residues: 1418 helix: 2.40 (0.16), residues: 906 sheet: -1.12 (0.63), residues: 58 loop : -1.96 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 127 TYR 0.019 0.001 TYR A 514 PHE 0.015 0.001 PHE B 585 TRP 0.014 0.001 TRP A 427 HIS 0.006 0.001 HIS A 898 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (12198) covalent geometry : angle 0.59282 / 0.31 (16506) SS BOND : bond 0.00225 / 0.12 ( 8) SS BOND : angle 1.24234 / 0.90 ( 16) hydrogen bonds : bond 0.05213 / 3.46 ( 732) hydrogen bonds : angle 4.88387 / 3.45 ( 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 186 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 0.521 Fit side-chains revert: symmetry clash REVERT: A 188 ARG cc_start: 0.7327 (mmm-85) cc_final: 0.7021 (mmm-85) REVERT: A 457 GLU cc_start: 0.6421 (mt-10) cc_final: 0.5779 (mp0) REVERT: A 461 ARG cc_start: 0.5941 (ttp80) cc_final: 0.5717 (tmm160) REVERT: A 769 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7900 (ttpt) REVERT: A 889 ILE cc_start: 0.8733 (pp) cc_final: 0.8453 (mt) REVERT: B 121 GLU cc_start: 0.5103 (mm-30) cc_final: 0.4866 (mm-30) REVERT: B 186 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7339 (mp0) REVERT: B 188 ARG cc_start: 0.7287 (mmm-85) cc_final: 0.6949 (mmm-85) REVERT: B 461 ARG cc_start: 0.5648 (ttp80) cc_final: 0.5374 (tmm160) REVERT: B 574 LYS cc_start: 0.8162 (tptp) cc_final: 0.7593 (tppt) REVERT: B 889 ILE cc_start: 0.8837 (pp) cc_final: 0.8513 (mp) REVERT: B 904 MET cc_start: 0.7304 (mmp) cc_final: 0.6967 (mmp) outliers start: 25 outliers final: 8 residues processed: 173 average time/residue: 0.5621 time to fit residues: 104.9064 Evaluate side-chains 159 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 149 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 346 SER 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 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: 0.9980 chunk 59 optimal weight: 0.2980 chunk 114 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 29 optimal weight: 0.2980 chunk 1 optimal weight: 4.9990 chunk 130 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 650 ASN A 709 GLN A 730 ASN ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 ASN B 650 ASN B 709 GLN B 730 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.144323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.102297 restraints weight = 17570.086| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.24 r_work: 0.3124 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2144 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= 0.151 Angle : 0.547 9.164 16522 Z= 0.286 Chirality : 0.040 0.136 1802 Planarity : 0.004 0.036 2060 Dihedral : 4.034 21.533 1612 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.33 % Allowed : 10.03 % Favored : 87.64 % 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: 1.38 (0.22), residues: 1418 helix: 2.40 (0.16), residues: 900 sheet: -1.30 (0.59), residues: 58 loop : -1.97 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 226 TYR 0.012 0.001 TYR B 687 PHE 0.022 0.001 PHE B 691 TRP 0.014 0.001 TRP B 427 HIS 0.009 0.001 HIS A 898 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (12198) covalent geometry : angle 0.54544 / 0.29 (16506) SS BOND : bond 0.00210 / 0.11 ( 8) SS BOND : angle 1.28480 / 0.93 ( 16) hydrogen bonds : bond 0.04931 / 3.27 ( 732) hydrogen bonds : angle 4.67736 / 3.31 ( 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 182 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7224 (mp0) REVERT: A 206 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.7945 (mp10) REVERT: A 457 GLU cc_start: 0.6469 (mt-10) cc_final: 0.6244 (mt-10) REVERT: A 461 ARG cc_start: 0.6052 (ttp80) cc_final: 0.5823 (ttp80) REVERT: A 574 LYS cc_start: 0.8091 (tptp) cc_final: 0.7510 (tppt) REVERT: A 769 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7943 (ttpt) REVERT: A 892 ASP cc_start: 0.7693 (p0) cc_final: 0.7434 (p0) REVERT: B 121 GLU cc_start: 0.5124 (mm-30) cc_final: 0.4919 (mm-30) REVERT: B 186 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7463 (mp0) REVERT: B 188 ARG cc_start: 0.7101 (mmm-85) cc_final: 0.6793 (mmm-85) REVERT: B 461 ARG cc_start: 0.5778 (ttp80) cc_final: 0.5416 (tmm160) REVERT: B 494 LEU cc_start: 0.7865 (tp) cc_final: 0.7650 (OUTLIER) REVERT: B 507 ILE cc_start: 0.7263 (OUTLIER) cc_final: 0.7006 (mp) REVERT: B 574 LYS cc_start: 0.8184 (tptp) cc_final: 0.7646 (tppt) REVERT: B 683 ARG cc_start: 0.7113 (tpt170) cc_final: 0.6323 (tmm-80) REVERT: B 889 ILE cc_start: 0.8835 (pp) cc_final: 0.8607 (mt) REVERT: B 904 MET cc_start: 0.7333 (mmp) cc_final: 0.7108 (mmp) outliers start: 30 outliers final: 13 residues processed: 168 average time/residue: 0.6129 time to fit residues: 111.1461 Evaluate side-chains 163 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 A residue 843 GLU Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 507 ILE 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 821 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 3 optimal weight: 2.9990 chunk 52 optimal weight: 0.3980 chunk 2 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 136 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 114 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 199 GLN B 591 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.142297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.100155 restraints weight = 17474.462| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.24 r_work: 0.3092 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2434 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= 0.184 Angle : 0.571 9.212 16522 Z= 0.298 Chirality : 0.041 0.131 1802 Planarity : 0.004 0.059 2060 Dihedral : 4.200 22.967 1612 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.42 % Allowed : 9.80 % Favored : 86.78 % 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: 1.25 (0.22), residues: 1418 helix: 2.31 (0.16), residues: 904 sheet: -1.37 (0.64), residues: 48 loop : -2.08 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 373 TYR 0.011 0.001 TYR B 687 PHE 0.032 0.002 PHE B 126 TRP 0.015 0.001 TRP A 427 HIS 0.009 0.001 HIS A 898 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.18 (12198) covalent geometry : angle 0.57030 / 0.30 (16506) SS BOND : bond 0.00198 / 0.11 ( 8) SS BOND : angle 1.21282 / 0.88 ( 16) hydrogen bonds : bond 0.05110 / 3.38 ( 732) hydrogen bonds : angle 4.62696 / 3.27 ( 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 191 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 147 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.8165 (mppt) REVERT: A 186 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7368 (mp0) REVERT: A 206 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.7970 (mp10) REVERT: A 457 GLU cc_start: 0.6457 (mt-10) cc_final: 0.6251 (mt-10) REVERT: A 461 ARG cc_start: 0.6062 (ttp80) cc_final: 0.5799 (ttp80) REVERT: A 507 ILE cc_start: 0.7351 (OUTLIER) cc_final: 0.7080 (mp) REVERT: A 574 LYS cc_start: 0.8148 (tptp) cc_final: 0.7553 (tppt) REVERT: A 769 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7969 (ttpt) REVERT: A 878 MET cc_start: 0.8911 (mtt) cc_final: 0.8695 (mtt) REVERT: A 892 ASP cc_start: 0.7808 (p0) cc_final: 0.7521 (p0) REVERT: B 121 GLU cc_start: 0.5091 (mm-30) cc_final: 0.4837 (mm-30) REVERT: B 126 PHE cc_start: 0.6790 (t80) cc_final: 0.6564 (t80) REVERT: B 186 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7496 (mp0) REVERT: B 252 GLU cc_start: 0.7655 (tp30) cc_final: 0.6960 (tp30) REVERT: B 256 ARG cc_start: 0.6812 (OUTLIER) cc_final: 0.5458 (ptp90) REVERT: B 461 ARG cc_start: 0.5634 (ttp80) cc_final: 0.5287 (tmm160) REVERT: B 494 LEU cc_start: 0.7817 (tp) cc_final: 0.7557 (OUTLIER) REVERT: B 507 ILE cc_start: 0.7238 (OUTLIER) cc_final: 0.6973 (mp) REVERT: B 573 GLU cc_start: 0.7429 (mm-30) cc_final: 0.7123 (mm-30) REVERT: B 574 LYS cc_start: 0.8232 (tptp) cc_final: 0.7642 (tppt) REVERT: B 577 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7579 (mp0) REVERT: B 683 ARG cc_start: 0.7185 (tpt170) cc_final: 0.6437 (tmm-80) REVERT: B 702 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7591 (mm-30) REVERT: B 753 ARG cc_start: 0.7754 (tmm160) cc_final: 0.7422 (tmt170) REVERT: B 797 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7591 (pt0) REVERT: B 904 MET cc_start: 0.7457 (mmp) cc_final: 0.6978 (mmp) outliers start: 44 outliers final: 19 residues processed: 172 average time/residue: 0.6209 time to fit residues: 115.2391 Evaluate side-chains 175 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LYS 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 797 GLN Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 231 LEU 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 702 GLU Chi-restraints excluded: chain B residue 773 ILE Chi-restraints excluded: chain B residue 797 GLN Chi-restraints excluded: chain B residue 821 THR Chi-restraints excluded: chain B residue 909 MET 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: 2.9990 chunk 114 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 92 optimal weight: 0.2980 chunk 112 optimal weight: 1.9990 chunk 115 optimal weight: 0.0270 chunk 90 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 591 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.142887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.100993 restraints weight = 17431.908| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.23 r_work: 0.3104 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12206 Z= 0.154 Angle : 0.548 8.783 16522 Z= 0.287 Chirality : 0.040 0.135 1802 Planarity : 0.004 0.041 2060 Dihedral : 4.142 22.477 1612 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.34 % Allowed : 10.65 % Favored : 86.00 % 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: 1.29 (0.22), residues: 1418 helix: 2.38 (0.16), residues: 898 sheet: -1.40 (0.63), residues: 48 loop : -2.08 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 373 TYR 0.011 0.001 TYR B 687 PHE 0.024 0.001 PHE B 126 TRP 0.016 0.001 TRP B 427 HIS 0.008 0.001 HIS A 898 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (12198) covalent geometry : angle 0.54663 / 0.29 (16506) SS BOND : bond 0.00199 / 0.10 ( 8) SS BOND : angle 1.16815 / 0.85 ( 16) hydrogen bonds : bond 0.04888 / 3.24 ( 732) hydrogen bonds : angle 4.57211 / 3.24 ( 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 194 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 151 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.8056 (mppt) REVERT: A 186 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7276 (mp0) REVERT: A 206 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.7948 (mp10) REVERT: A 359 THR cc_start: 0.8795 (m) cc_final: 0.8572 (m) REVERT: A 457 GLU cc_start: 0.6458 (mt-10) cc_final: 0.6249 (mt-10) REVERT: A 461 ARG cc_start: 0.6172 (ttp80) cc_final: 0.5927 (ttp80) REVERT: A 507 ILE cc_start: 0.7399 (OUTLIER) cc_final: 0.7132 (mp) REVERT: A 574 LYS cc_start: 0.8150 (tptp) cc_final: 0.7544 (tppt) REVERT: A 683 ARG cc_start: 0.7157 (tpt170) cc_final: 0.6258 (tmm-80) REVERT: A 702 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7640 (mm-30) REVERT: A 769 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7969 (ttpt) REVERT: A 878 MET cc_start: 0.8899 (mtt) cc_final: 0.8674 (mtt) REVERT: A 892 ASP cc_start: 0.7789 (p0) cc_final: 0.7486 (p0) REVERT: B 126 PHE cc_start: 0.6827 (t80) cc_final: 0.6483 (t80) REVERT: B 186 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7553 (mp0) REVERT: B 226 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.6655 (tmm160) REVERT: B 256 ARG cc_start: 0.6834 (OUTLIER) cc_final: 0.5477 (ptp90) REVERT: B 461 ARG cc_start: 0.5765 (ttp80) cc_final: 0.5395 (tmm160) REVERT: B 507 ILE cc_start: 0.7200 (OUTLIER) cc_final: 0.6943 (mp) REVERT: B 573 GLU cc_start: 0.7405 (mm-30) cc_final: 0.7102 (mm-30) REVERT: B 574 LYS cc_start: 0.8215 (tptp) cc_final: 0.7638 (tppt) REVERT: B 577 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7561 (mp0) REVERT: B 683 ARG cc_start: 0.7152 (tpt170) cc_final: 0.6485 (tmm-80) REVERT: B 702 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7613 (mm-30) REVERT: B 904 MET cc_start: 0.7420 (mmp) cc_final: 0.7025 (mmp) outliers start: 43 outliers final: 19 residues processed: 179 average time/residue: 0.5802 time to fit residues: 112.1592 Evaluate side-chains 176 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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 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 702 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 231 LEU Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 507 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 702 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 13 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 121 optimal weight: 0.6980 chunk 138 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 591 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.141241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.099229 restraints weight = 17445.394| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.22 r_work: 0.3072 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 12206 Z= 0.200 Angle : 0.596 9.788 16522 Z= 0.308 Chirality : 0.041 0.139 1802 Planarity : 0.004 0.086 2060 Dihedral : 4.242 23.170 1612 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.42 % Allowed : 11.20 % Favored : 85.38 % 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: 1.21 (0.22), residues: 1418 helix: 2.30 (0.16), residues: 898 sheet: -1.57 (0.62), residues: 48 loop : -2.06 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 753 TYR 0.011 0.001 TYR A 687 PHE 0.022 0.002 PHE B 126 TRP 0.015 0.001 TRP A 427 HIS 0.008 0.001 HIS A 898 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.20 (12198) covalent geometry : angle 0.59484 / 0.31 (16506) SS BOND : bond 0.00187 / 0.10 ( 8) SS BOND : angle 1.13563 / 0.83 ( 16) hydrogen bonds : bond 0.05180 / 3.43 ( 732) hydrogen bonds : angle 4.59639 / 3.25 ( 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: 44 poor density : 152 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7298 (mp0) REVERT: A 206 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7931 (mp10) REVERT: A 461 ARG cc_start: 0.6074 (ttp80) cc_final: 0.5788 (ttp80) REVERT: A 497 ILE cc_start: 0.6869 (OUTLIER) cc_final: 0.6629 (mt) REVERT: A 500 MET cc_start: 0.6586 (mtt) cc_final: 0.5974 (mtt) REVERT: A 507 ILE cc_start: 0.7420 (OUTLIER) cc_final: 0.7151 (mp) REVERT: A 574 LYS cc_start: 0.8238 (tptp) cc_final: 0.7652 (tppt) REVERT: A 578 GLU cc_start: 0.6896 (OUTLIER) cc_final: 0.6568 (tt0) REVERT: A 683 ARG cc_start: 0.7126 (tpt170) cc_final: 0.6295 (tmm-80) REVERT: A 702 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7727 (mm-30) REVERT: A 769 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7942 (ttpt) REVERT: A 878 MET cc_start: 0.8922 (mtt) cc_final: 0.8707 (mtt) REVERT: A 892 ASP cc_start: 0.7816 (p0) cc_final: 0.7502 (p0) REVERT: B 126 PHE cc_start: 0.6774 (t80) cc_final: 0.6221 (t80) REVERT: B 186 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7517 (mp0) REVERT: B 226 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.6599 (tmm160) REVERT: B 256 ARG cc_start: 0.6895 (OUTLIER) cc_final: 0.5519 (ptp90) REVERT: B 461 ARG cc_start: 0.5770 (ttp80) cc_final: 0.5377 (tmm160) REVERT: B 507 ILE cc_start: 0.7227 (OUTLIER) cc_final: 0.6972 (mp) REVERT: B 573 GLU cc_start: 0.7455 (mm-30) cc_final: 0.7139 (mm-30) REVERT: B 574 LYS cc_start: 0.8227 (tptp) cc_final: 0.7664 (tppt) REVERT: B 577 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7530 (mp0) REVERT: B 578 GLU cc_start: 0.6883 (OUTLIER) cc_final: 0.6543 (tt0) REVERT: B 683 ARG cc_start: 0.7167 (tpt170) cc_final: 0.6551 (tmm-80) REVERT: B 702 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7538 (mm-30) REVERT: B 753 ARG cc_start: 0.7760 (tmm160) cc_final: 0.7519 (tmt170) REVERT: B 904 MET cc_start: 0.7413 (mmp) cc_final: 0.6939 (mmp) outliers start: 44 outliers final: 18 residues processed: 176 average time/residue: 0.5579 time to fit residues: 106.3888 Evaluate side-chains 180 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 497 ILE Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain A residue 702 GLU 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 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 577 GLU Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 665 ARG Chi-restraints excluded: chain B residue 702 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 112 optimal weight: 0.5980 chunk 20 optimal weight: 0.3980 chunk 119 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 84 optimal weight: 0.0980 chunk 115 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 135 optimal weight: 0.0570 chunk 65 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 overall best weight: 0.3498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.143753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.102238 restraints weight = 17402.163| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.23 r_work: 0.3124 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12206 Z= 0.128 Angle : 0.557 10.724 16522 Z= 0.285 Chirality : 0.039 0.138 1802 Planarity : 0.004 0.047 2060 Dihedral : 4.138 23.221 1612 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.57 % Allowed : 12.67 % Favored : 84.76 % 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: 1.44 (0.22), residues: 1418 helix: 2.51 (0.16), residues: 892 sheet: -1.59 (0.61), residues: 48 loop : -1.95 (0.26), residues: 478 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 0.020 0.001 PHE B 126 TRP 0.018 0.001 TRP A 427 HIS 0.009 0.001 HIS A 898 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (12198) covalent geometry : angle 0.55641 / 0.28 (16506) SS BOND : bond 0.00212 / 0.11 ( 8) SS BOND : angle 1.15684 / 0.84 ( 16) hydrogen bonds : bond 0.04647 / 3.08 ( 732) hydrogen bonds : angle 4.46546 / 3.17 ( 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 186 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 153 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7289 (mp0) REVERT: A 206 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.7860 (mp10) REVERT: A 287 ASP cc_start: 0.8664 (m-30) cc_final: 0.8408 (m-30) REVERT: A 461 ARG cc_start: 0.6103 (ttp80) cc_final: 0.5877 (ttp80) REVERT: A 507 ILE cc_start: 0.7266 (OUTLIER) cc_final: 0.7006 (mp) REVERT: A 574 LYS cc_start: 0.8183 (tptp) cc_final: 0.7586 (tppt) REVERT: A 578 GLU cc_start: 0.6836 (OUTLIER) cc_final: 0.6519 (tt0) REVERT: A 683 ARG cc_start: 0.7198 (tpt170) cc_final: 0.6470 (tmm-80) REVERT: A 702 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7458 (mm-30) REVERT: A 769 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7869 (ttpt) REVERT: A 892 ASP cc_start: 0.7732 (p0) cc_final: 0.7442 (p0) REVERT: B 126 PHE cc_start: 0.6710 (t80) cc_final: 0.6155 (t80) REVERT: B 186 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7432 (mp0) REVERT: B 188 ARG cc_start: 0.7048 (mmm-85) cc_final: 0.6768 (mmm-85) REVERT: B 226 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.6615 (tmm160) REVERT: B 256 ARG cc_start: 0.6862 (OUTLIER) cc_final: 0.5528 (ptp90) REVERT: B 507 ILE cc_start: 0.7216 (OUTLIER) cc_final: 0.6969 (mp) REVERT: B 573 GLU cc_start: 0.7446 (mm-30) cc_final: 0.7162 (mm-30) REVERT: B 574 LYS cc_start: 0.8229 (tptp) cc_final: 0.7639 (tppt) REVERT: B 577 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7534 (mp0) REVERT: B 683 ARG cc_start: 0.7235 (tpt170) cc_final: 0.6681 (tmm-80) REVERT: B 702 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7482 (mm-30) REVERT: B 753 ARG cc_start: 0.7606 (tmm160) cc_final: 0.7368 (tmt170) REVERT: B 904 MET cc_start: 0.7372 (mmp) cc_final: 0.6853 (mmp) outliers start: 33 outliers final: 12 residues processed: 175 average time/residue: 0.5755 time to fit residues: 108.7531 Evaluate side-chains 171 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 385 THR Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 702 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 577 GLU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 702 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 4 optimal weight: 0.8980 chunk 39 optimal weight: 0.4980 chunk 107 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 59 optimal weight: 0.0040 chunk 65 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 117 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3813 r_free = 0.3813 target = 0.143070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.101485 restraints weight = 17355.923| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.22 r_work: 0.3107 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2836 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= 0.149 Angle : 0.580 11.099 16522 Z= 0.295 Chirality : 0.040 0.186 1802 Planarity : 0.004 0.067 2060 Dihedral : 4.140 24.876 1612 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.64 % Allowed : 13.61 % Favored : 83.75 % 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: 1.48 (0.22), residues: 1418 helix: 2.55 (0.16), residues: 890 sheet: -1.58 (0.61), residues: 48 loop : -1.94 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 373 TYR 0.010 0.001 TYR A 687 PHE 0.021 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/Z covalent geometry : bond 0.00339 / 0.15 (12198) covalent geometry : angle 0.57894 / 0.30 (16506) SS BOND : bond 0.00202 / 0.10 ( 8) SS BOND : angle 1.12099 / 0.81 ( 16) hydrogen bonds : bond 0.04768 / 3.16 ( 732) hydrogen bonds : angle 4.44705 / 3.16 ( 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 182 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 148 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7316 (mp0) REVERT: A 287 ASP cc_start: 0.8669 (m-30) cc_final: 0.8407 (m-30) REVERT: A 461 ARG cc_start: 0.6130 (ttp80) cc_final: 0.5896 (ttp80) REVERT: A 497 ILE cc_start: 0.6849 (OUTLIER) cc_final: 0.6616 (mt) REVERT: A 500 MET cc_start: 0.6385 (mtt) cc_final: 0.5709 (mtt) REVERT: A 507 ILE cc_start: 0.7344 (OUTLIER) cc_final: 0.7080 (mp) REVERT: A 574 LYS cc_start: 0.8233 (tptp) cc_final: 0.7653 (tppt) REVERT: A 578 GLU cc_start: 0.6839 (OUTLIER) cc_final: 0.6523 (tt0) REVERT: A 683 ARG cc_start: 0.7201 (tpt170) cc_final: 0.6492 (tmm-80) REVERT: A 702 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7602 (mm-30) REVERT: A 769 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7889 (ttpt) REVERT: A 892 ASP cc_start: 0.7751 (p0) cc_final: 0.7461 (p0) REVERT: B 126 PHE cc_start: 0.6460 (t80) cc_final: 0.5837 (t80) REVERT: B 186 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7355 (mp0) REVERT: B 188 ARG cc_start: 0.7089 (mmm-85) cc_final: 0.6812 (mmm-85) REVERT: B 226 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.6716 (tmm160) REVERT: B 256 ARG cc_start: 0.6876 (OUTLIER) cc_final: 0.5538 (ptp90) REVERT: B 507 ILE cc_start: 0.7180 (OUTLIER) cc_final: 0.6929 (mp) REVERT: B 573 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7081 (mm-30) REVERT: B 574 LYS cc_start: 0.8230 (tptp) cc_final: 0.7667 (tppt) REVERT: B 577 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7543 (mp0) REVERT: B 683 ARG cc_start: 0.7217 (tpt170) cc_final: 0.6711 (tmm-80) REVERT: B 702 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7565 (mm-30) REVERT: B 753 ARG cc_start: 0.7600 (tmm160) cc_final: 0.7344 (tmt170) REVERT: B 904 MET cc_start: 0.7375 (mmp) cc_final: 0.7007 (mmm) outliers start: 34 outliers final: 11 residues processed: 168 average time/residue: 0.5834 time to fit residues: 106.0562 Evaluate side-chains 169 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 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 702 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 577 GLU Chi-restraints excluded: chain B residue 702 GLU 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: 0.6980 chunk 87 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 12 optimal weight: 0.4980 chunk 59 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 109 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3808 r_free = 0.3808 target = 0.142730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.101133 restraints weight = 17478.327| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.22 r_work: 0.3104 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12206 Z= 0.161 Angle : 0.605 13.057 16522 Z= 0.305 Chirality : 0.040 0.162 1802 Planarity : 0.004 0.081 2060 Dihedral : 4.120 23.677 1610 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.64 % Allowed : 13.84 % Favored : 83.51 % 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: 2.54 (0.16), residues: 886 sheet: -1.60 (0.62), residues: 48 loop : -1.85 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 461 TYR 0.010 0.001 TYR A 687 PHE 0.019 0.001 PHE B 126 TRP 0.015 0.001 TRP A 427 HIS 0.010 0.001 HIS A 898 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (12198) covalent geometry : angle 0.60427 / 0.30 (16506) SS BOND : bond 0.00201 / 0.10 ( 8) SS BOND : angle 1.10956 / 0.80 ( 16) hydrogen bonds : bond 0.04834 / 3.19 ( 732) hydrogen bonds : angle 4.45089 / 3.16 ( 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 182 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 148 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7323 (mp0) REVERT: A 287 ASP cc_start: 0.8681 (m-30) cc_final: 0.8421 (m-30) REVERT: A 461 ARG cc_start: 0.6142 (ttp80) cc_final: 0.5905 (ttp80) REVERT: A 497 ILE cc_start: 0.6858 (OUTLIER) cc_final: 0.6623 (mt) REVERT: A 500 MET cc_start: 0.6399 (mtt) cc_final: 0.5750 (mtt) REVERT: A 507 ILE cc_start: 0.7362 (OUTLIER) cc_final: 0.7093 (mp) REVERT: A 574 LYS cc_start: 0.8244 (tptp) cc_final: 0.7666 (tppt) REVERT: A 578 GLU cc_start: 0.6852 (OUTLIER) cc_final: 0.6534 (tt0) REVERT: A 683 ARG cc_start: 0.7214 (tpt170) cc_final: 0.6521 (tmm-80) REVERT: A 702 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7612 (mm-30) REVERT: A 769 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7862 (ttpt) REVERT: A 892 ASP cc_start: 0.7762 (p0) cc_final: 0.7473 (p0) REVERT: B 126 PHE cc_start: 0.6545 (t80) cc_final: 0.5847 (t80) REVERT: B 186 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7373 (mp0) REVERT: B 188 ARG cc_start: 0.7061 (mmm-85) cc_final: 0.6761 (mmm-85) REVERT: B 226 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.6712 (tmm160) REVERT: B 256 ARG cc_start: 0.6914 (OUTLIER) cc_final: 0.5526 (ptp90) REVERT: B 507 ILE cc_start: 0.7184 (OUTLIER) cc_final: 0.6929 (mp) REVERT: B 573 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7156 (mm-30) REVERT: B 574 LYS cc_start: 0.8248 (tptp) cc_final: 0.7654 (tppt) REVERT: B 577 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7543 (mp0) REVERT: B 578 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.6552 (tt0) REVERT: B 683 ARG cc_start: 0.7216 (tpt170) cc_final: 0.6715 (tmm-80) REVERT: B 702 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7598 (mm-30) REVERT: B 753 ARG cc_start: 0.7559 (tmm160) cc_final: 0.7308 (tmt170) REVERT: B 904 MET cc_start: 0.7378 (mmp) cc_final: 0.7000 (mmm) outliers start: 34 outliers final: 14 residues processed: 170 average time/residue: 0.5434 time to fit residues: 99.8525 Evaluate side-chains 170 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 198 LEU 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 664 ILE Chi-restraints excluded: chain A residue 702 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 568 GLU Chi-restraints excluded: chain B residue 577 GLU Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 702 GLU 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: 0.9980 chunk 18 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 127 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 51 optimal weight: 0.4980 chunk 60 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3803 r_free = 0.3803 target = 0.142417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.100459 restraints weight = 17495.348| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.24 r_work: 0.3099 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12206 Z= 0.168 Angle : 0.632 14.863 16522 Z= 0.315 Chirality : 0.041 0.217 1802 Planarity : 0.004 0.077 2060 Dihedral : 4.144 23.622 1610 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.33 % Allowed : 14.39 % Favored : 83.28 % 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: 1.49 (0.22), residues: 1418 helix: 2.53 (0.16), residues: 886 sheet: -1.62 (0.62), residues: 48 loop : -1.83 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 461 TYR 0.010 0.001 TYR A 687 PHE 0.026 0.001 PHE A 295 TRP 0.015 0.001 TRP A 427 HIS 0.010 0.001 HIS A 898 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (12198) covalent geometry : angle 0.63124 / 0.31 (16506) SS BOND : bond 0.00201 / 0.10 ( 8) SS BOND : angle 1.10710 / 0.80 ( 16) hydrogen bonds : bond 0.04900 / 3.23 ( 732) hydrogen bonds : angle 4.45855 / 3.17 ( 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 173 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7333 (mp0) REVERT: A 287 ASP cc_start: 0.8689 (m-30) cc_final: 0.8428 (m-30) REVERT: A 461 ARG cc_start: 0.6085 (ttp80) cc_final: 0.5836 (ttp80) REVERT: A 507 ILE cc_start: 0.7353 (OUTLIER) cc_final: 0.7082 (mp) REVERT: A 574 LYS cc_start: 0.8248 (tptp) cc_final: 0.7685 (tppt) REVERT: A 578 GLU cc_start: 0.6852 (OUTLIER) cc_final: 0.6530 (tt0) REVERT: A 683 ARG cc_start: 0.7211 (tpt170) cc_final: 0.6520 (tmm-80) REVERT: A 702 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7640 (mm-30) REVERT: A 769 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7850 (ttpt) REVERT: A 892 ASP cc_start: 0.7783 (p0) cc_final: 0.7495 (p0) REVERT: B 186 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7402 (mp0) REVERT: B 226 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.6684 (tmm160) REVERT: B 256 ARG cc_start: 0.6886 (OUTLIER) cc_final: 0.5476 (ptp90) REVERT: B 507 ILE cc_start: 0.7192 (OUTLIER) cc_final: 0.6937 (mp) REVERT: B 573 GLU cc_start: 0.7456 (mm-30) cc_final: 0.7160 (mm-30) REVERT: B 574 LYS cc_start: 0.8240 (tptp) cc_final: 0.7643 (tppt) REVERT: B 577 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7555 (mp0) REVERT: B 578 GLU cc_start: 0.6885 (OUTLIER) cc_final: 0.6559 (tt0) REVERT: B 683 ARG cc_start: 0.7215 (tpt170) cc_final: 0.6719 (tmm-80) REVERT: B 702 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7610 (mm-30) REVERT: B 753 ARG cc_start: 0.7646 (tmm160) cc_final: 0.7392 (tmt170) REVERT: B 904 MET cc_start: 0.7373 (mmp) cc_final: 0.6993 (mmm) outliers start: 30 outliers final: 12 residues processed: 162 average time/residue: 0.6082 time to fit residues: 106.3414 Evaluate side-chains 166 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 198 LEU 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 578 GLU Chi-restraints excluded: chain A residue 702 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 577 GLU Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 702 GLU 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: 0.2980 chunk 122 optimal weight: 0.0470 chunk 25 optimal weight: 0.6980 chunk 137 optimal weight: 0.0870 chunk 68 optimal weight: 0.8980 chunk 142 optimal weight: 0.3980 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 chunk 59 optimal weight: 0.0980 chunk 82 optimal weight: 0.7980 overall best weight: 0.1856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3840 r_free = 0.3840 target = 0.145343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.104224 restraints weight = 17415.840| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.23 r_work: 0.3152 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12206 Z= 0.120 Angle : 0.583 12.878 16522 Z= 0.293 Chirality : 0.039 0.157 1802 Planarity : 0.004 0.054 2060 Dihedral : 4.092 23.535 1610 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.94 % Allowed : 14.54 % Favored : 83.51 % 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: 1.62 (0.22), residues: 1418 helix: 2.63 (0.16), residues: 886 sheet: -1.59 (0.62), residues: 48 loop : -1.77 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 461 TYR 0.010 0.001 TYR A 687 PHE 0.019 0.001 PHE B 126 TRP 0.019 0.001 TRP A 427 HIS 0.010 0.001 HIS A 898 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 (12198) covalent geometry : angle 0.58231 / 0.29 (16506) SS BOND : bond 0.00232 / 0.12 ( 8) SS BOND : angle 1.17623 / 0.83 ( 16) hydrogen bonds : bond 0.04414 / 2.91 ( 732) hydrogen bonds : angle 4.37588 / 3.11 ( 2154) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4136.45 seconds wall clock time: 71 minutes 8.27 seconds (4268.27 seconds total)