Starting phenix.real_space_refine on Wed Jul 30 04:59:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zk3_14753/07_2025/7zk3_14753_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zk3_14753/07_2025/7zk3_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_2025/7zk3_14753.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zk3_14753/07_2025/7zk3_14753.map" model { file = "/net/cci-nas-00/data/ceres_data/7zk3_14753/07_2025/7zk3_14753_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zk3_14753/07_2025/7zk3_14753_trim.cif" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11898 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5926 Classifications: {'peptide': 721} Link IDs: {'PTRANS': 31, 'TRANS': 689} Chain breaks: 5 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 23 Unusual residues: {' CA': 3, 'JRF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Restraints were copied for chains: B Time building chain proxies: 13.24, per 1000 atoms: 1.11 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: 3.02 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.15 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: 3.48 Time building geometry restraints manager: 3.49 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: 0.06 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: 4.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 35.010 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 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:13.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 12206 Z= 0.162 Angle : 0.585 14.826 16522 Z= 0.286 Chirality : 0.036 0.135 1802 Planarity : 0.003 0.037 2060 Dihedral : 13.318 75.641 4492 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 14.60 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.017 0.001 TRP A 427 HIS 0.004 0.001 HIS B 402 PHE 0.008 0.001 PHE A 585 TYR 0.034 0.001 TYR A 314 ARG 0.006 0.000 ARG B 562 Details of bonding type rmsd hydrogen bonds : bond 0.13333 ( 732) hydrogen bonds : angle 6.08122 ( 2154) SS BOND : bond 0.00099 ( 8) SS BOND : angle 0.27933 ( 16) covalent geometry : bond 0.00323 (12198) covalent geometry : angle 0.58482 (16506) *********************** 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 : 1.348 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 1 residues processed: 212 average time/residue: 1.3300 time to fit residues: 303.6627 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 : 1.231 ------------------------------------------------------------------------------- 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 121 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 73 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 84 optimal weight: 0.3980 chunk 130 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3817 r_free = 0.3817 target = 0.143673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.101640 restraints weight = 17295.780| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.22 r_work: 0.3110 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12206 Z= 0.184 Angle : 0.605 9.580 16522 Z= 0.315 Chirality : 0.042 0.136 1802 Planarity : 0.004 0.034 2060 Dihedral : 4.084 19.937 1612 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.18 % Allowed : 8.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.22), residues: 1418 helix: 2.34 (0.16), residues: 906 sheet: -1.12 (0.62), residues: 58 loop : -1.94 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 427 HIS 0.006 0.001 HIS A 898 PHE 0.016 0.001 PHE B 585 TYR 0.019 0.001 TYR A 514 ARG 0.004 0.000 ARG B 461 Details of bonding type rmsd hydrogen bonds : bond 0.05307 ( 732) hydrogen bonds : angle 4.88010 ( 2154) SS BOND : bond 0.00218 ( 8) SS BOND : angle 1.29287 ( 16) covalent geometry : bond 0.00429 (12198) covalent geometry : angle 0.60356 (16506) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 1.236 Fit side-chains revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7123 (mp0) REVERT: A 457 GLU cc_start: 0.6400 (mt-10) cc_final: 0.5787 (mp0) REVERT: A 461 ARG cc_start: 0.5958 (ttp80) cc_final: 0.5729 (tmm160) REVERT: A 769 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7911 (ttpt) REVERT: A 889 ILE cc_start: 0.8733 (pp) cc_final: 0.8461 (mt) REVERT: B 121 GLU cc_start: 0.5116 (mm-30) cc_final: 0.4857 (mm-30) REVERT: B 186 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7359 (mp0) REVERT: B 188 ARG cc_start: 0.7275 (mmm-85) cc_final: 0.6942 (mmm-85) REVERT: B 461 ARG cc_start: 0.5669 (ttp80) cc_final: 0.5381 (tmm160) REVERT: B 573 GLU cc_start: 0.7349 (mm-30) cc_final: 0.6965 (mm-30) REVERT: B 574 LYS cc_start: 0.8150 (tptp) cc_final: 0.7580 (tppt) REVERT: B 577 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7584 (mp0) REVERT: B 683 ARG cc_start: 0.7117 (tpt170) cc_final: 0.6324 (tmm-80) REVERT: B 889 ILE cc_start: 0.8814 (pp) cc_final: 0.8496 (mp) REVERT: B 904 MET cc_start: 0.7307 (mmp) cc_final: 0.6962 (mmp) outliers start: 28 outliers final: 8 residues processed: 175 average time/residue: 1.3415 time to fit residues: 253.0987 Evaluate side-chains 161 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 577 GLU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 773 ILE Chi-restraints excluded: chain B residue 821 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 105 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 60 optimal weight: 0.0050 chunk 7 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 121 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 709 GLN A 730 ASN ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 ASN B 709 GLN B 730 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.142896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.100756 restraints weight = 17508.144| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.23 r_work: 0.3094 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2294 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= 0.178 Angle : 0.566 9.547 16522 Z= 0.297 Chirality : 0.041 0.134 1802 Planarity : 0.004 0.038 2060 Dihedral : 4.112 21.203 1612 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.41 % Allowed : 9.64 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.22), residues: 1418 helix: 2.24 (0.16), residues: 906 sheet: -1.07 (0.68), residues: 48 loop : -2.05 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 427 HIS 0.009 0.001 HIS A 898 PHE 0.026 0.001 PHE B 691 TYR 0.011 0.001 TYR B 687 ARG 0.003 0.000 ARG A 373 Details of bonding type rmsd hydrogen bonds : bond 0.05147 ( 732) hydrogen bonds : angle 4.69150 ( 2154) SS BOND : bond 0.00202 ( 8) SS BOND : angle 1.26530 ( 16) covalent geometry : bond 0.00415 (12198) covalent geometry : angle 0.56518 (16506) *********************** 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 184 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 153 time to evaluate : 1.325 Fit side-chains revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7159 (mp0) REVERT: A 188 ARG cc_start: 0.7228 (mmm-85) cc_final: 0.6824 (mmm-85) REVERT: A 206 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.7890 (mp10) REVERT: A 457 GLU cc_start: 0.6510 (mt-10) cc_final: 0.6284 (mt-10) REVERT: A 461 ARG cc_start: 0.6060 (ttp80) cc_final: 0.5820 (ttp80) REVERT: A 507 ILE cc_start: 0.7281 (OUTLIER) cc_final: 0.7009 (mp) REVERT: A 574 LYS cc_start: 0.8099 (tptp) cc_final: 0.7525 (tppt) REVERT: A 769 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7960 (ttpt) REVERT: A 878 MET cc_start: 0.8908 (mtt) cc_final: 0.8688 (mtt) REVERT: B 121 GLU cc_start: 0.5198 (mm-30) cc_final: 0.4953 (mm-30) REVERT: B 124 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8359 (mppt) REVERT: B 186 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7500 (mp0) REVERT: B 188 ARG cc_start: 0.7094 (mmm-85) cc_final: 0.6794 (mmm-85) REVERT: B 461 ARG cc_start: 0.5716 (ttp80) cc_final: 0.5358 (tmm160) REVERT: B 494 LEU cc_start: 0.7729 (tp) cc_final: 0.7456 (mp) REVERT: B 507 ILE cc_start: 0.7287 (OUTLIER) cc_final: 0.7048 (mp) REVERT: B 573 GLU cc_start: 0.7373 (mm-30) cc_final: 0.7119 (mm-30) REVERT: B 574 LYS cc_start: 0.8196 (tptp) cc_final: 0.7648 (tppt) REVERT: B 577 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7552 (mp0) REVERT: B 683 ARG cc_start: 0.7140 (tpt170) cc_final: 0.6369 (tmm-80) REVERT: B 904 MET cc_start: 0.7435 (mmp) cc_final: 0.7218 (mmp) outliers start: 31 outliers final: 10 residues processed: 169 average time/residue: 1.4114 time to fit residues: 256.5941 Evaluate side-chains 162 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 1.285 ------------------------------------------------------------------------------- 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 507 ILE Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 577 GLU Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 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 50 optimal weight: 0.7980 chunk 20 optimal weight: 0.0470 chunk 51 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 107 optimal weight: 0.0980 chunk 93 optimal weight: 0.7980 chunk 122 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 709 GLN A 730 ASN A 898 HIS B 199 GLN B 591 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 = 0.3823 r_free = 0.3823 target = 0.144042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.102213 restraints weight = 17243.005| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.22 r_work: 0.3119 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12206 Z= 0.137 Angle : 0.547 9.529 16522 Z= 0.282 Chirality : 0.039 0.129 1802 Planarity : 0.004 0.058 2060 Dihedral : 4.086 22.390 1612 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.88 % Allowed : 10.50 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.22), residues: 1418 helix: 2.37 (0.16), residues: 898 sheet: -1.21 (0.65), residues: 48 loop : -2.04 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 427 HIS 0.009 0.001 HIS A 898 PHE 0.032 0.001 PHE B 126 TYR 0.011 0.001 TYR A 687 ARG 0.007 0.000 ARG B 753 Details of bonding type rmsd hydrogen bonds : bond 0.04766 ( 732) hydrogen bonds : angle 4.57164 ( 2154) SS BOND : bond 0.00205 ( 8) SS BOND : angle 1.24072 ( 16) covalent geometry : bond 0.00303 (12198) covalent geometry : angle 0.54550 (16506) *********************** 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 183 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 146 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7416 (mp0) REVERT: A 206 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7934 (mp10) REVERT: A 457 GLU cc_start: 0.6457 (mt-10) cc_final: 0.6253 (mt-10) REVERT: A 461 ARG cc_start: 0.6086 (ttp80) cc_final: 0.5819 (ttp80) REVERT: A 507 ILE cc_start: 0.7285 (OUTLIER) cc_final: 0.7010 (mp) REVERT: A 574 LYS cc_start: 0.8116 (tptp) cc_final: 0.7571 (tppt) REVERT: A 769 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7962 (ttpt) REVERT: A 878 MET cc_start: 0.8883 (mtt) cc_final: 0.8662 (mtt) REVERT: B 186 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7572 (mp0) REVERT: B 256 ARG cc_start: 0.6781 (OUTLIER) cc_final: 0.5447 (ptp90) REVERT: B 461 ARG cc_start: 0.5691 (ttp80) cc_final: 0.5328 (tmm160) REVERT: B 494 LEU cc_start: 0.7761 (tp) cc_final: 0.7558 (OUTLIER) REVERT: B 507 ILE cc_start: 0.7228 (OUTLIER) cc_final: 0.6980 (mp) REVERT: B 573 GLU cc_start: 0.7362 (mm-30) cc_final: 0.7101 (mm-30) REVERT: B 574 LYS cc_start: 0.8222 (tptp) cc_final: 0.7639 (tppt) REVERT: B 577 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7573 (mp0) REVERT: B 683 ARG cc_start: 0.7130 (tpt170) cc_final: 0.6472 (tmm-80) REVERT: B 904 MET cc_start: 0.7426 (mmp) cc_final: 0.7047 (mmp) outliers start: 37 outliers final: 17 residues processed: 169 average time/residue: 1.3942 time to fit residues: 254.2037 Evaluate side-chains 167 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 1.392 ------------------------------------------------------------------------------- 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 507 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 773 ILE Chi-restraints excluded: chain B residue 797 GLN Chi-restraints excluded: chain B residue 821 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 108 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 59 optimal weight: 0.0980 chunk 91 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 134 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 709 GLN A 730 ASN A 898 HIS B 591 ASN B 709 GLN B 730 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.143152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.101258 restraints weight = 17247.246| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.22 r_work: 0.3107 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2539 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= 0.155 Angle : 0.563 13.500 16522 Z= 0.289 Chirality : 0.041 0.368 1802 Planarity : 0.004 0.072 2060 Dihedral : 4.128 22.749 1612 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.34 % Allowed : 10.81 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.22), residues: 1418 helix: 2.38 (0.16), residues: 898 sheet: -1.25 (0.64), residues: 48 loop : -2.05 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 427 HIS 0.008 0.001 HIS A 898 PHE 0.040 0.001 PHE B 126 TYR 0.011 0.001 TYR B 687 ARG 0.005 0.000 ARG A 373 Details of bonding type rmsd hydrogen bonds : bond 0.04856 ( 732) hydrogen bonds : angle 4.55983 ( 2154) SS BOND : bond 0.00202 ( 8) SS BOND : angle 1.16612 ( 16) covalent geometry : bond 0.00356 (12198) covalent geometry : angle 0.56168 (16506) *********************** 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 195 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 152 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7424 (mp0) REVERT: A 206 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.7947 (mp10) REVERT: A 457 GLU cc_start: 0.6458 (mt-10) cc_final: 0.6252 (mt-10) REVERT: A 461 ARG cc_start: 0.6208 (ttp80) cc_final: 0.5957 (ttp80) REVERT: A 497 ILE cc_start: 0.6878 (OUTLIER) cc_final: 0.6634 (mt) REVERT: A 500 MET cc_start: 0.6387 (mtt) cc_final: 0.5721 (mtt) REVERT: A 507 ILE cc_start: 0.7208 (OUTLIER) cc_final: 0.6932 (mp) REVERT: A 574 LYS cc_start: 0.8195 (tptp) cc_final: 0.7629 (tppt) REVERT: A 683 ARG cc_start: 0.7163 (tpt170) cc_final: 0.6261 (tmm-80) REVERT: A 769 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7959 (ttpt) REVERT: A 878 MET cc_start: 0.8888 (mtt) cc_final: 0.8672 (mtt) REVERT: B 186 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7575 (mp0) REVERT: B 226 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.6705 (tmm160) REVERT: B 252 GLU cc_start: 0.7606 (tp30) cc_final: 0.6911 (tp30) REVERT: B 256 ARG cc_start: 0.6829 (OUTLIER) cc_final: 0.5470 (ptp90) REVERT: B 461 ARG cc_start: 0.5765 (ttp80) cc_final: 0.5392 (tmm160) REVERT: B 507 ILE cc_start: 0.7220 (OUTLIER) cc_final: 0.6974 (mp) REVERT: B 573 GLU cc_start: 0.7381 (mm-30) cc_final: 0.7108 (mm-30) REVERT: B 574 LYS cc_start: 0.8213 (tptp) cc_final: 0.7643 (tppt) REVERT: B 577 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7545 (mp0) REVERT: B 683 ARG cc_start: 0.7121 (tpt170) cc_final: 0.6516 (tmm-80) REVERT: B 904 MET cc_start: 0.7417 (mmp) cc_final: 0.7017 (mmp) outliers start: 43 outliers final: 16 residues processed: 177 average time/residue: 1.2945 time to fit residues: 247.7009 Evaluate side-chains 170 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 1.373 ------------------------------------------------------------------------------- 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 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 664 ILE Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 909 MET Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 226 ARG Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 577 GLU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 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 129 optimal weight: 0.0970 chunk 134 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 137 optimal weight: 0.0060 chunk 114 optimal weight: 0.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 898 HIS B 591 ASN B 709 GLN B 730 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.143517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.101575 restraints weight = 17562.478| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.24 r_work: 0.3113 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2645 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= 0.145 Angle : 0.575 15.173 16522 Z= 0.290 Chirality : 0.040 0.324 1802 Planarity : 0.004 0.058 2060 Dihedral : 4.147 22.822 1612 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.72 % Allowed : 12.36 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.22), residues: 1418 helix: 2.42 (0.16), residues: 898 sheet: -1.30 (0.63), residues: 48 loop : -2.00 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 427 HIS 0.009 0.001 HIS A 898 PHE 0.039 0.001 PHE B 126 TYR 0.010 0.001 TYR A 687 ARG 0.006 0.000 ARG A 373 Details of bonding type rmsd hydrogen bonds : bond 0.04764 ( 732) hydrogen bonds : angle 4.52729 ( 2154) SS BOND : bond 0.00208 ( 8) SS BOND : angle 1.15433 ( 16) covalent geometry : bond 0.00325 (12198) covalent geometry : angle 0.57445 (16506) *********************** 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 186 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 151 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7400 (mp0) REVERT: A 206 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.7939 (mp10) REVERT: A 359 THR cc_start: 0.8726 (m) cc_final: 0.8504 (m) REVERT: A 461 ARG cc_start: 0.6082 (ttp80) cc_final: 0.5854 (ttp80) REVERT: A 497 ILE cc_start: 0.6809 (OUTLIER) cc_final: 0.6599 (mt) REVERT: A 500 MET cc_start: 0.6538 (mtt) cc_final: 0.5988 (mtt) REVERT: A 507 ILE cc_start: 0.7195 (OUTLIER) cc_final: 0.6922 (mp) REVERT: A 574 LYS cc_start: 0.8176 (tptp) cc_final: 0.7605 (tppt) REVERT: A 683 ARG cc_start: 0.7173 (tpt170) cc_final: 0.6292 (tmm-80) REVERT: A 769 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7805 (ttpt) REVERT: A 878 MET cc_start: 0.8868 (mtt) cc_final: 0.8644 (mtt) REVERT: B 186 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7341 (mp0) REVERT: B 188 ARG cc_start: 0.6986 (mmm-85) cc_final: 0.6617 (mmm-85) REVERT: B 226 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.6641 (tmm160) REVERT: B 256 ARG cc_start: 0.6765 (OUTLIER) cc_final: 0.5412 (ptp90) REVERT: B 461 ARG cc_start: 0.5758 (ttp80) cc_final: 0.5353 (tmm160) REVERT: B 507 ILE cc_start: 0.7153 (OUTLIER) cc_final: 0.6905 (mp) REVERT: B 573 GLU cc_start: 0.7423 (mm-30) cc_final: 0.7153 (mm-30) REVERT: B 574 LYS cc_start: 0.8157 (tptp) cc_final: 0.7599 (tppt) REVERT: B 577 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7546 (mp0) REVERT: B 683 ARG cc_start: 0.7187 (tpt170) cc_final: 0.6586 (tmm-80) REVERT: B 904 MET cc_start: 0.7359 (mmp) cc_final: 0.6959 (mmp) outliers start: 35 outliers final: 16 residues processed: 170 average time/residue: 1.3860 time to fit residues: 254.3747 Evaluate side-chains 171 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 171 PHE Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 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 665 ARG Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 909 MET Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 226 ARG Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 577 GLU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 773 ILE Chi-restraints excluded: chain B residue 821 THR Chi-restraints excluded: chain B residue 909 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 4 optimal weight: 0.0970 chunk 101 optimal weight: 0.4980 chunk 133 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 51 optimal weight: 0.7980 chunk 132 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 898 HIS B 591 ASN B 709 GLN B 730 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.143343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.101669 restraints weight = 17494.556| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.23 r_work: 0.3113 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2742 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= 0.148 Angle : 0.581 10.933 16522 Z= 0.294 Chirality : 0.040 0.222 1802 Planarity : 0.004 0.064 2060 Dihedral : 4.129 23.072 1612 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.64 % Allowed : 13.22 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.22), residues: 1418 helix: 2.43 (0.16), residues: 898 sheet: -1.43 (0.62), residues: 48 loop : -1.97 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 427 HIS 0.009 0.001 HIS A 898 PHE 0.014 0.001 PHE B 585 TYR 0.010 0.001 TYR B 687 ARG 0.007 0.000 ARG A 373 Details of bonding type rmsd hydrogen bonds : bond 0.04751 ( 732) hydrogen bonds : angle 4.51277 ( 2154) SS BOND : bond 0.00206 ( 8) SS BOND : angle 1.12065 ( 16) covalent geometry : bond 0.00334 (12198) covalent geometry : angle 0.58038 (16506) *********************** 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 182 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 148 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7445 (mp0) REVERT: A 206 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7865 (mp10) REVERT: A 287 ASP cc_start: 0.8673 (m-30) cc_final: 0.8407 (m-30) REVERT: A 461 ARG cc_start: 0.6139 (ttp80) cc_final: 0.5907 (ttp80) REVERT: A 497 ILE cc_start: 0.6852 (OUTLIER) cc_final: 0.6638 (mt) REVERT: A 500 MET cc_start: 0.6700 (mtt) cc_final: 0.6227 (mtt) REVERT: A 507 ILE cc_start: 0.7162 (OUTLIER) cc_final: 0.6895 (mp) REVERT: A 574 LYS cc_start: 0.8226 (tptp) cc_final: 0.7658 (tppt) REVERT: A 683 ARG cc_start: 0.7187 (tpt170) cc_final: 0.6358 (tmm-80) REVERT: A 769 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7867 (ttpt) REVERT: A 878 MET cc_start: 0.8898 (mtt) cc_final: 0.8683 (mtt) REVERT: B 186 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7479 (mp0) REVERT: B 188 ARG cc_start: 0.7055 (mmm-85) cc_final: 0.6789 (mmm-85) REVERT: B 226 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.6635 (tmm160) REVERT: B 256 ARG cc_start: 0.6848 (OUTLIER) cc_final: 0.5494 (ptp90) REVERT: B 507 ILE cc_start: 0.7181 (OUTLIER) cc_final: 0.6935 (mp) REVERT: B 573 GLU cc_start: 0.7421 (mm-30) cc_final: 0.7176 (mm-30) REVERT: B 574 LYS cc_start: 0.8210 (tptp) cc_final: 0.7651 (tppt) REVERT: B 577 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7565 (mp0) REVERT: B 683 ARG cc_start: 0.7190 (tpt170) cc_final: 0.6664 (tmm-80) REVERT: B 904 MET cc_start: 0.7336 (mmp) cc_final: 0.6819 (mmp) outliers start: 34 outliers final: 15 residues processed: 170 average time/residue: 1.5837 time to fit residues: 291.5333 Evaluate side-chains 169 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 PHE 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 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 665 ARG Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 909 MET Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 226 ARG Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 577 GLU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 773 ILE Chi-restraints excluded: chain B residue 821 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 135 optimal weight: 0.0970 chunk 119 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 898 HIS B 591 ASN B 709 GLN B 730 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.142464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.100750 restraints weight = 17510.087| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.24 r_work: 0.3097 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12206 Z= 0.173 Angle : 0.621 16.525 16522 Z= 0.309 Chirality : 0.040 0.170 1802 Planarity : 0.004 0.057 2060 Dihedral : 4.181 23.339 1612 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.88 % Allowed : 13.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.22), residues: 1418 helix: 2.45 (0.16), residues: 890 sheet: -1.45 (0.62), residues: 48 loop : -1.95 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 427 HIS 0.009 0.001 HIS A 898 PHE 0.020 0.001 PHE A 295 TYR 0.010 0.001 TYR A 687 ARG 0.008 0.000 ARG A 373 Details of bonding type rmsd hydrogen bonds : bond 0.04907 ( 732) hydrogen bonds : angle 4.54471 ( 2154) SS BOND : bond 0.00200 ( 8) SS BOND : angle 1.11046 ( 16) covalent geometry : bond 0.00405 (12198) covalent geometry : angle 0.62005 (16506) *********************** 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 191 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 154 time to evaluate : 1.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7446 (mp0) REVERT: A 206 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7845 (mp10) REVERT: A 287 ASP cc_start: 0.8695 (m-30) cc_final: 0.8424 (m-30) REVERT: A 461 ARG cc_start: 0.6074 (ttp80) cc_final: 0.5842 (ttp80) REVERT: A 497 ILE cc_start: 0.6812 (OUTLIER) cc_final: 0.6608 (mt) REVERT: A 500 MET cc_start: 0.6838 (mtt) cc_final: 0.6392 (mtt) REVERT: A 507 ILE cc_start: 0.7231 (OUTLIER) cc_final: 0.6956 (mp) REVERT: A 574 LYS cc_start: 0.8207 (tptp) cc_final: 0.7639 (tppt) REVERT: A 578 GLU cc_start: 0.6825 (OUTLIER) cc_final: 0.6504 (tt0) REVERT: A 683 ARG cc_start: 0.7254 (tpt170) cc_final: 0.6473 (tmm-80) REVERT: A 769 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7807 (ttpt) REVERT: A 878 MET cc_start: 0.8876 (mtt) cc_final: 0.8656 (mtt) REVERT: B 186 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7522 (mp0) REVERT: B 188 ARG cc_start: 0.7058 (mmm-85) cc_final: 0.6785 (mmm-85) REVERT: B 226 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.6705 (tmm160) REVERT: B 256 ARG cc_start: 0.6797 (OUTLIER) cc_final: 0.5435 (ptp90) REVERT: B 461 ARG cc_start: 0.5690 (ttp80) cc_final: 0.5435 (tmm160) REVERT: B 507 ILE cc_start: 0.7184 (OUTLIER) cc_final: 0.6929 (mp) REVERT: B 573 GLU cc_start: 0.7394 (mm-30) cc_final: 0.7145 (mm-30) REVERT: B 574 LYS cc_start: 0.8192 (tptp) cc_final: 0.7597 (tppt) REVERT: B 577 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7517 (mp0) REVERT: B 683 ARG cc_start: 0.7241 (tpt170) cc_final: 0.6676 (tmm-80) REVERT: B 904 MET cc_start: 0.7355 (mmp) cc_final: 0.6811 (mmp) outliers start: 37 outliers final: 18 residues processed: 173 average time/residue: 1.3234 time to fit residues: 248.5567 Evaluate side-chains 178 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 149 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 171 PHE 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 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 622 MET Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 909 MET Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 226 ARG Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 577 GLU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 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 24 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 106 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 124 optimal weight: 0.0050 chunk 47 optimal weight: 0.4980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 898 HIS B 591 ASN B 709 GLN B 730 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.143304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.101822 restraints weight = 17489.990| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.23 r_work: 0.3114 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 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 : 0.003 0.040 12206 Z= 0.144 Angle : 0.610 14.559 16522 Z= 0.304 Chirality : 0.040 0.136 1802 Planarity : 0.004 0.052 2060 Dihedral : 4.179 23.285 1612 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.49 % Allowed : 13.61 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.22), residues: 1418 helix: 2.51 (0.16), residues: 886 sheet: -1.45 (0.62), residues: 48 loop : -1.82 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 427 HIS 0.010 0.001 HIS A 898 PHE 0.015 0.001 PHE B 126 TYR 0.010 0.001 TYR A 687 ARG 0.009 0.000 ARG A 373 Details of bonding type rmsd hydrogen bonds : bond 0.04735 ( 732) hydrogen bonds : angle 4.50878 ( 2154) SS BOND : bond 0.00213 ( 8) SS BOND : angle 1.11945 ( 16) covalent geometry : bond 0.00323 (12198) covalent geometry : angle 0.60897 (16506) *********************** 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 181 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 149 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7468 (mp0) REVERT: A 206 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7894 (mp10) REVERT: A 287 ASP cc_start: 0.8676 (m-30) cc_final: 0.8404 (m-30) REVERT: A 461 ARG cc_start: 0.6111 (ttp80) cc_final: 0.5874 (ttp80) REVERT: A 497 ILE cc_start: 0.6847 (OUTLIER) cc_final: 0.6640 (mt) REVERT: A 500 MET cc_start: 0.6813 (mtt) cc_final: 0.6385 (mtt) REVERT: A 507 ILE cc_start: 0.7215 (OUTLIER) cc_final: 0.6951 (mp) REVERT: A 574 LYS cc_start: 0.8229 (tptp) cc_final: 0.7677 (tppt) REVERT: A 578 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.6561 (tt0) REVERT: A 683 ARG cc_start: 0.7229 (tpt170) cc_final: 0.6531 (tmm-80) REVERT: A 769 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7860 (ttpt) REVERT: A 878 MET cc_start: 0.8887 (mtt) cc_final: 0.8667 (mtt) REVERT: B 186 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7428 (mp0) REVERT: B 188 ARG cc_start: 0.7082 (mmm-85) cc_final: 0.6791 (mmm-85) REVERT: B 226 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.6690 (tmm160) REVERT: B 252 GLU cc_start: 0.7629 (tp30) cc_final: 0.7023 (tp30) REVERT: B 256 ARG cc_start: 0.6848 (OUTLIER) cc_final: 0.5488 (ptp90) REVERT: B 461 ARG cc_start: 0.5834 (ttp80) cc_final: 0.5548 (tmm160) REVERT: B 507 ILE cc_start: 0.7159 (OUTLIER) cc_final: 0.6913 (mp) REVERT: B 573 GLU cc_start: 0.7389 (mm-30) cc_final: 0.7127 (mm-30) REVERT: B 574 LYS cc_start: 0.8214 (tptp) cc_final: 0.7628 (tppt) REVERT: B 577 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7513 (mp0) REVERT: B 683 ARG cc_start: 0.7210 (tpt170) cc_final: 0.6690 (tmm-80) REVERT: B 904 MET cc_start: 0.7374 (mmp) cc_final: 0.6992 (mmm) outliers start: 32 outliers final: 16 residues processed: 167 average time/residue: 1.4652 time to fit residues: 264.1134 Evaluate side-chains 173 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 171 PHE 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 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 769 LYS Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 909 MET Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 226 ARG Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 577 GLU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 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 125 optimal weight: 0.1980 chunk 140 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 128 optimal weight: 0.5980 chunk 101 optimal weight: 0.0770 chunk 92 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 898 HIS B 591 ASN B 709 GLN B 730 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.143128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.101672 restraints weight = 17412.304| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.21 r_work: 0.3115 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12206 Z= 0.151 Angle : 0.607 13.596 16522 Z= 0.303 Chirality : 0.040 0.136 1802 Planarity : 0.004 0.049 2060 Dihedral : 4.189 25.233 1612 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.33 % Allowed : 14.31 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.22), residues: 1418 helix: 2.52 (0.16), residues: 886 sheet: -1.49 (0.62), residues: 48 loop : -1.83 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 427 HIS 0.010 0.001 HIS A 898 PHE 0.026 0.001 PHE A 295 TYR 0.010 0.001 TYR A 687 ARG 0.009 0.000 ARG A 373 Details of bonding type rmsd hydrogen bonds : bond 0.04733 ( 732) hydrogen bonds : angle 4.50830 ( 2154) SS BOND : bond 0.00207 ( 8) SS BOND : angle 1.11102 ( 16) covalent geometry : bond 0.00344 (12198) covalent geometry : angle 0.60659 (16506) ********************** 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 177 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7479 (mp0) REVERT: A 194 ILE cc_start: 0.4127 (OUTLIER) cc_final: 0.3862 (mp) REVERT: A 206 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7862 (mp10) REVERT: A 287 ASP cc_start: 0.8673 (m-30) cc_final: 0.8398 (m-30) REVERT: A 461 ARG cc_start: 0.6114 (ttp80) cc_final: 0.5876 (ttp80) REVERT: A 500 MET cc_start: 0.6799 (mtt) cc_final: 0.6383 (mtt) REVERT: A 507 ILE cc_start: 0.7149 (OUTLIER) cc_final: 0.6880 (mp) REVERT: A 574 LYS cc_start: 0.8226 (tptp) cc_final: 0.7673 (tppt) REVERT: A 578 GLU cc_start: 0.6866 (OUTLIER) cc_final: 0.6552 (tt0) REVERT: A 683 ARG cc_start: 0.7210 (tpt170) cc_final: 0.6527 (tmm-80) REVERT: A 769 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7841 (ttpt) REVERT: A 878 MET cc_start: 0.8886 (mtt) cc_final: 0.8670 (mtt) REVERT: B 186 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7307 (mp0) REVERT: B 226 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.6671 (tmm160) REVERT: B 252 GLU cc_start: 0.7629 (tp30) cc_final: 0.7024 (tp30) REVERT: B 256 ARG cc_start: 0.6874 (OUTLIER) cc_final: 0.5531 (ptp90) REVERT: B 461 ARG cc_start: 0.5786 (ttp80) cc_final: 0.5482 (tmm160) REVERT: B 507 ILE cc_start: 0.7167 (OUTLIER) cc_final: 0.6921 (mp) REVERT: B 573 GLU cc_start: 0.7411 (mm-30) cc_final: 0.7168 (mm-30) REVERT: B 574 LYS cc_start: 0.8213 (tptp) cc_final: 0.7626 (tppt) REVERT: B 577 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7518 (mp0) REVERT: B 683 ARG cc_start: 0.7223 (tpt170) cc_final: 0.6708 (tmm-80) REVERT: B 904 MET cc_start: 0.7379 (mmp) cc_final: 0.6989 (mmm) outliers start: 30 outliers final: 14 residues processed: 164 average time/residue: 1.3734 time to fit residues: 245.8899 Evaluate side-chains 168 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 909 MET Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 226 ARG Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 577 GLU Chi-restraints excluded: chain B residue 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 121 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 12 optimal weight: 0.2980 chunk 44 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 898 HIS B 591 ASN B 709 GLN B 730 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.142637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.101062 restraints weight = 17450.448| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.22 r_work: 0.3109 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12206 Z= 0.173 Angle : 0.612 13.209 16522 Z= 0.307 Chirality : 0.040 0.134 1802 Planarity : 0.004 0.050 2060 Dihedral : 4.159 23.493 1610 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.41 % Allowed : 14.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.22), residues: 1418 helix: 2.49 (0.16), residues: 886 sheet: -1.50 (0.62), residues: 48 loop : -1.83 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 427 HIS 0.010 0.001 HIS A 898 PHE 0.016 0.001 PHE A 126 TYR 0.011 0.001 TYR A 761 ARG 0.010 0.000 ARG A 373 Details of bonding type rmsd hydrogen bonds : bond 0.04811 ( 732) hydrogen bonds : angle 4.53128 ( 2154) SS BOND : bond 0.00203 ( 8) SS BOND : angle 1.10264 ( 16) covalent geometry : bond 0.00409 (12198) covalent geometry : angle 0.61113 (16506) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10958.64 seconds wall clock time: 191 minutes 52.52 seconds (11512.52 seconds total)