Starting phenix.real_space_refine on Tue Feb 3 17:21:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wzi_66403/02_2026/9wzi_66403.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wzi_66403/02_2026/9wzi_66403.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wzi_66403/02_2026/9wzi_66403.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wzi_66403/02_2026/9wzi_66403.map" model { file = "/net/cci-nas-00/data/ceres_data/9wzi_66403/02_2026/9wzi_66403.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wzi_66403/02_2026/9wzi_66403.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.015 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: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 3464 2.51 5 N 952 2.21 5 O 1072 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5544 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 693 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "B" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 693 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "C" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 693 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "D" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 693 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "E" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 693 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "F" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 693 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "G" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 693 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "H" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 693 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Time building chain proxies: 1.47, per 1000 atoms: 0.27 Number of scatterers: 5544 At special positions: 0 Unit cell: (86.7, 85, 77.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 1072 8.00 N 952 7.00 C 3464 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.49 Conformation dependent library (CDL) restraints added in 349.6 milliseconds 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1328 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 0 sheets defined 91.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 1 through 8 Processing helix chain 'A' and resid 9 through 17 Processing helix chain 'A' and resid 18 through 32 Processing helix chain 'A' and resid 36 through 46 removed outlier: 3.576A pdb=" N MET A 40 " --> pdb=" O ASN A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 62 Processing helix chain 'A' and resid 65 through 80 removed outlier: 3.792A pdb=" N CYS A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 88 Processing helix chain 'B' and resid 2 through 8 Processing helix chain 'B' and resid 9 through 17 Processing helix chain 'B' and resid 18 through 32 Processing helix chain 'B' and resid 36 through 46 removed outlier: 3.532A pdb=" N MET B 40 " --> pdb=" O ASN B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 62 Processing helix chain 'B' and resid 65 through 80 removed outlier: 3.716A pdb=" N CYS B 69 " --> pdb=" O GLY B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 87 Processing helix chain 'C' and resid 2 through 9 Processing helix chain 'C' and resid 9 through 17 removed outlier: 3.558A pdb=" N MET C 17 " --> pdb=" O PHE C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 32 Processing helix chain 'C' and resid 36 through 46 Processing helix chain 'C' and resid 49 through 62 Processing helix chain 'C' and resid 65 through 80 removed outlier: 3.682A pdb=" N CYS C 69 " --> pdb=" O GLY C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 88 Processing helix chain 'D' and resid 2 through 9 Processing helix chain 'D' and resid 9 through 17 Processing helix chain 'D' and resid 18 through 32 Processing helix chain 'D' and resid 36 through 46 Processing helix chain 'D' and resid 49 through 62 Processing helix chain 'D' and resid 65 through 80 removed outlier: 3.619A pdb=" N CYS D 69 " --> pdb=" O GLY D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 88 Processing helix chain 'E' and resid 2 through 9 Processing helix chain 'E' and resid 9 through 17 Processing helix chain 'E' and resid 18 through 32 Processing helix chain 'E' and resid 36 through 47 removed outlier: 3.984A pdb=" N ASN E 47 " --> pdb=" O VAL E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 62 Processing helix chain 'E' and resid 65 through 80 Processing helix chain 'E' and resid 80 through 88 Processing helix chain 'F' and resid 2 through 9 removed outlier: 3.583A pdb=" N LYS F 9 " --> pdb=" O VAL F 5 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 17 Processing helix chain 'F' and resid 18 through 32 Processing helix chain 'F' and resid 36 through 46 Processing helix chain 'F' and resid 50 through 62 Processing helix chain 'F' and resid 65 through 80 removed outlier: 3.577A pdb=" N CYS F 72 " --> pdb=" O ALA F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 88 Processing helix chain 'G' and resid 2 through 9 Processing helix chain 'G' and resid 9 through 17 Processing helix chain 'G' and resid 18 through 32 Processing helix chain 'G' and resid 36 through 47 removed outlier: 3.992A pdb=" N ASN G 47 " --> pdb=" O VAL G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 62 Processing helix chain 'G' and resid 65 through 80 Processing helix chain 'G' and resid 80 through 87 Processing helix chain 'H' and resid 2 through 9 Processing helix chain 'H' and resid 9 through 17 removed outlier: 3.518A pdb=" N MET H 17 " --> pdb=" O PHE H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 32 Processing helix chain 'H' and resid 36 through 46 Processing helix chain 'H' and resid 49 through 62 Processing helix chain 'H' and resid 65 through 80 Processing helix chain 'H' and resid 80 through 88 418 hydrogen bonds defined for protein. 1254 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: 0.91 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1856 1.34 - 1.46: 942 1.46 - 1.58: 2682 1.58 - 1.70: 0 1.70 - 1.82: 88 Bond restraints: 5568 Sorted by residual: bond pdb=" CG LEU H 29 " pdb=" CD2 LEU H 29 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.24e+00 bond pdb=" CA GLU A 8 " pdb=" CB GLU A 8 " ideal model delta sigma weight residual 1.529 1.545 -0.016 1.46e-02 4.69e+03 1.17e+00 bond pdb=" CA GLY C 18 " pdb=" C GLY C 18 " ideal model delta sigma weight residual 1.516 1.527 -0.011 1.01e-02 9.80e+03 1.11e+00 bond pdb=" CG GLU A 79 " pdb=" CD GLU A 79 " ideal model delta sigma weight residual 1.516 1.490 0.026 2.50e-02 1.60e+03 1.09e+00 bond pdb=" CA ARG A 33 " pdb=" CB ARG A 33 " ideal model delta sigma weight residual 1.530 1.547 -0.017 1.69e-02 3.50e+03 9.77e-01 ... (remaining 5563 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 6998 1.69 - 3.38: 353 3.38 - 5.07: 70 5.07 - 6.76: 11 6.76 - 8.45: 8 Bond angle restraints: 7440 Sorted by residual: angle pdb=" C LYS B 7 " pdb=" N GLU B 8 " pdb=" CA GLU B 8 " ideal model delta sigma weight residual 122.38 114.26 8.12 1.81e+00 3.05e-01 2.01e+01 angle pdb=" C GLU A 78 " pdb=" N GLU A 79 " pdb=" CA GLU A 79 " ideal model delta sigma weight residual 122.24 115.75 6.49 1.57e+00 4.06e-01 1.71e+01 angle pdb=" C LYS A 7 " pdb=" N GLU A 8 " pdb=" CA GLU A 8 " ideal model delta sigma weight residual 122.73 117.11 5.62 1.61e+00 3.86e-01 1.22e+01 angle pdb=" N GLU B 8 " pdb=" CA GLU B 8 " pdb=" CB GLU B 8 " ideal model delta sigma weight residual 110.44 114.96 -4.52 1.53e+00 4.27e-01 8.72e+00 angle pdb=" CA ARG A 33 " pdb=" CB ARG A 33 " pdb=" CG ARG A 33 " ideal model delta sigma weight residual 114.10 119.93 -5.83 2.00e+00 2.50e-01 8.51e+00 ... (remaining 7435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 3149 17.90 - 35.81: 328 35.81 - 53.71: 38 53.71 - 71.61: 12 71.61 - 89.52: 17 Dihedral angle restraints: 3544 sinusoidal: 1496 harmonic: 2048 Sorted by residual: dihedral pdb=" CA GLU A 78 " pdb=" C GLU A 78 " pdb=" N GLU A 79 " pdb=" CA GLU A 79 " ideal model delta harmonic sigma weight residual 180.00 158.68 21.32 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA CYS A 77 " pdb=" C CYS A 77 " pdb=" N GLU A 78 " pdb=" CA GLU A 78 " ideal model delta harmonic sigma weight residual -180.00 -161.83 -18.17 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CG ARG F 55 " pdb=" CD ARG F 55 " pdb=" NE ARG F 55 " pdb=" CZ ARG F 55 " ideal model delta sinusoidal sigma weight residual 90.00 133.16 -43.16 2 1.50e+01 4.44e-03 9.98e+00 ... (remaining 3541 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 509 0.031 - 0.062: 278 0.062 - 0.093: 81 0.093 - 0.124: 21 0.124 - 0.155: 7 Chirality restraints: 896 Sorted by residual: chirality pdb=" CA LYS A 7 " pdb=" N LYS A 7 " pdb=" C LYS A 7 " pdb=" CB LYS A 7 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.99e-01 chirality pdb=" CA GLU A 8 " pdb=" N GLU A 8 " pdb=" C GLU A 8 " pdb=" CB GLU A 8 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.12e-01 chirality pdb=" CA GLU D 79 " pdb=" N GLU D 79 " pdb=" C GLU D 79 " pdb=" CB GLU D 79 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.06e-01 ... (remaining 893 not shown) Planarity restraints: 936 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 75 " 0.019 2.00e-02 2.50e+03 1.68e-02 5.65e+00 pdb=" CG TYR A 75 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR A 75 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR A 75 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 75 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 75 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR A 75 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 75 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 80 " 0.010 2.00e-02 2.50e+03 1.98e-02 3.93e+00 pdb=" C ASP A 80 " -0.034 2.00e-02 2.50e+03 pdb=" O ASP A 80 " 0.013 2.00e-02 2.50e+03 pdb=" N SER A 81 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU F 38 " 0.009 2.00e-02 2.50e+03 1.85e-02 3.42e+00 pdb=" CD GLU F 38 " -0.032 2.00e-02 2.50e+03 pdb=" OE1 GLU F 38 " 0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU F 38 " 0.012 2.00e-02 2.50e+03 ... (remaining 933 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 78 2.64 - 3.20: 5719 3.20 - 3.77: 8672 3.77 - 4.33: 10721 4.33 - 4.90: 17364 Nonbonded interactions: 42554 Sorted by model distance: nonbonded pdb=" OE1 GLU A 38 " pdb=" NZ LYS A 42 " model vdw 2.074 3.120 nonbonded pdb=" N GLU G 39 " pdb=" OE1 GLU G 39 " model vdw 2.210 3.120 nonbonded pdb=" O GLY A 18 " pdb=" OG1 THR A 21 " model vdw 2.229 3.040 nonbonded pdb=" OD2 ASP B 27 " pdb=" NH2 ARG E 55 " model vdw 2.246 3.120 nonbonded pdb=" N ASN H 36 " pdb=" OE2 GLU H 39 " model vdw 2.256 3.120 ... (remaining 42549 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.710 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.230 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 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 : 0.004 0.037 5568 Z= 0.173 Angle : 0.889 8.451 7440 Z= 0.467 Chirality : 0.042 0.155 896 Planarity : 0.005 0.057 936 Dihedral : 15.142 89.517 2216 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.32), residues: 696 helix: 1.10 (0.22), residues: 592 sheet: None (None), residues: 0 loop : -1.50 (0.50), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG F 33 TYR 0.040 0.002 TYR A 75 PHE 0.011 0.002 PHE E 13 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 5568) covalent geometry : angle 0.88893 ( 7440) hydrogen bonds : bond 0.16928 ( 418) hydrogen bonds : angle 5.84386 ( 1254) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 469 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 GLU cc_start: 0.8618 (pp20) cc_final: 0.7976 (pp20) REVERT: A 27 ASP cc_start: 0.9545 (m-30) cc_final: 0.9324 (m-30) REVERT: A 47 ASN cc_start: 0.8675 (m-40) cc_final: 0.8475 (t0) REVERT: A 53 LYS cc_start: 0.9274 (mtmm) cc_final: 0.8905 (mttp) REVERT: B 3 ASP cc_start: 0.9345 (p0) cc_final: 0.9008 (p0) REVERT: B 5 VAL cc_start: 0.9650 (t) cc_final: 0.9362 (t) REVERT: B 16 SER cc_start: 0.9594 (m) cc_final: 0.9347 (p) REVERT: B 19 GLU cc_start: 0.9224 (pm20) cc_final: 0.8962 (tm-30) REVERT: B 52 ASP cc_start: 0.9333 (m-30) cc_final: 0.8938 (m-30) REVERT: B 53 LYS cc_start: 0.9259 (mtmm) cc_final: 0.8886 (mttm) REVERT: B 78 GLU cc_start: 0.9040 (tm-30) cc_final: 0.8652 (tm-30) REVERT: B 80 ASP cc_start: 0.8823 (t0) cc_final: 0.8586 (t0) REVERT: C 3 ASP cc_start: 0.9483 (p0) cc_final: 0.8970 (p0) REVERT: C 4 LYS cc_start: 0.9721 (mptt) cc_final: 0.9496 (mppt) REVERT: C 7 LYS cc_start: 0.9268 (pttp) cc_final: 0.8990 (ptpp) REVERT: C 17 MET cc_start: 0.8653 (tpt) cc_final: 0.8172 (tpt) REVERT: C 27 ASP cc_start: 0.9488 (m-30) cc_final: 0.9232 (m-30) REVERT: C 37 LYS cc_start: 0.9137 (mmmm) cc_final: 0.8897 (tppp) REVERT: C 38 GLU cc_start: 0.8167 (tt0) cc_final: 0.7723 (tt0) REVERT: C 39 GLU cc_start: 0.9045 (pm20) cc_final: 0.8829 (mp0) REVERT: C 78 GLU cc_start: 0.9034 (tm-30) cc_final: 0.8827 (tm-30) REVERT: C 80 ASP cc_start: 0.8522 (t0) cc_final: 0.8211 (t70) REVERT: D 27 ASP cc_start: 0.9487 (m-30) cc_final: 0.9154 (m-30) REVERT: D 39 GLU cc_start: 0.8183 (mp0) cc_final: 0.7558 (mp0) REVERT: D 41 GLU cc_start: 0.9188 (tp30) cc_final: 0.8699 (tp30) REVERT: D 45 ARG cc_start: 0.9305 (tpp80) cc_final: 0.8880 (tpp80) REVERT: D 80 ASP cc_start: 0.8845 (t0) cc_final: 0.8408 (t0) REVERT: E 8 GLU cc_start: 0.9573 (tp30) cc_final: 0.9091 (tm-30) REVERT: E 19 GLU cc_start: 0.8616 (pp20) cc_final: 0.8251 (pp20) REVERT: E 27 ASP cc_start: 0.9484 (m-30) cc_final: 0.9156 (m-30) REVERT: E 52 ASP cc_start: 0.9148 (m-30) cc_final: 0.8637 (m-30) REVERT: E 69 CYS cc_start: 0.9568 (m) cc_final: 0.9317 (m) REVERT: E 78 GLU cc_start: 0.9083 (tm-30) cc_final: 0.8825 (tm-30) REVERT: E 79 GLU cc_start: 0.9116 (mm-30) cc_final: 0.8730 (mm-30) REVERT: E 80 ASP cc_start: 0.9043 (t0) cc_final: 0.8657 (t0) REVERT: F 8 GLU cc_start: 0.9545 (tp30) cc_final: 0.9026 (tm-30) REVERT: F 19 GLU cc_start: 0.8571 (pp20) cc_final: 0.8297 (pp20) REVERT: F 27 ASP cc_start: 0.9035 (m-30) cc_final: 0.8618 (m-30) REVERT: F 54 THR cc_start: 0.9517 (p) cc_final: 0.9274 (p) REVERT: F 80 ASP cc_start: 0.9162 (t0) cc_final: 0.8781 (t0) REVERT: G 8 GLU cc_start: 0.9499 (tp30) cc_final: 0.9179 (tp30) REVERT: G 27 ASP cc_start: 0.9135 (m-30) cc_final: 0.8820 (m-30) REVERT: G 42 LYS cc_start: 0.9746 (ttmt) cc_final: 0.9402 (ttmm) REVERT: G 80 ASP cc_start: 0.8921 (t0) cc_final: 0.8575 (t0) REVERT: H 7 LYS cc_start: 0.9693 (ttpp) cc_final: 0.9452 (tppp) REVERT: H 19 GLU cc_start: 0.8580 (pp20) cc_final: 0.8226 (pp20) REVERT: H 27 ASP cc_start: 0.8896 (m-30) cc_final: 0.8652 (m-30) REVERT: H 28 GLU cc_start: 0.9098 (tm-30) cc_final: 0.8845 (tm-30) REVERT: H 49 THR cc_start: 0.9109 (p) cc_final: 0.8502 (p) REVERT: H 80 ASP cc_start: 0.8998 (t0) cc_final: 0.8509 (t0) outliers start: 0 outliers final: 0 residues processed: 469 average time/residue: 0.1112 time to fit residues: 62.8089 Evaluate side-chains 428 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 428 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 62 optimal weight: 0.1980 chunk 51 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN B 23 ASN ** B 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 ASN E 67 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.058995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.049210 restraints weight = 21602.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.051355 restraints weight = 11749.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.052858 restraints weight = 7554.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.053941 restraints weight = 5289.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.054747 restraints weight = 3915.399| |-----------------------------------------------------------------------------| r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5568 Z= 0.174 Angle : 0.905 10.818 7440 Z= 0.452 Chirality : 0.049 0.212 896 Planarity : 0.005 0.033 936 Dihedral : 5.084 15.382 760 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 5.84 % Allowed : 24.19 % Favored : 69.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.31), residues: 696 helix: 0.68 (0.21), residues: 616 sheet: None (None), residues: 0 loop : -0.78 (0.60), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 33 TYR 0.025 0.002 TYR A 75 PHE 0.012 0.002 PHE E 13 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 5568) covalent geometry : angle 0.90525 ( 7440) hydrogen bonds : bond 0.04908 ( 418) hydrogen bonds : angle 4.78903 ( 1254) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 455 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ASP cc_start: 0.9418 (p0) cc_final: 0.9120 (p0) REVERT: A 5 VAL cc_start: 0.9800 (t) cc_final: 0.9577 (p) REVERT: A 17 MET cc_start: 0.8593 (tpp) cc_final: 0.8208 (tpt) REVERT: A 21 THR cc_start: 0.9392 (p) cc_final: 0.9053 (p) REVERT: A 23 ASN cc_start: 0.9701 (m-40) cc_final: 0.9091 (t0) REVERT: A 27 ASP cc_start: 0.9520 (m-30) cc_final: 0.9248 (m-30) REVERT: A 37 LYS cc_start: 0.9533 (ttmm) cc_final: 0.9272 (tppp) REVERT: A 42 LYS cc_start: 0.9325 (OUTLIER) cc_final: 0.9037 (pttt) REVERT: A 47 ASN cc_start: 0.8735 (m-40) cc_final: 0.8378 (t0) REVERT: A 53 LYS cc_start: 0.9338 (mtmm) cc_final: 0.8929 (mttm) REVERT: A 80 ASP cc_start: 0.8697 (t0) cc_final: 0.8225 (t0) REVERT: B 3 ASP cc_start: 0.9446 (p0) cc_final: 0.9136 (p0) REVERT: B 23 ASN cc_start: 0.9609 (m110) cc_final: 0.9389 (m-40) REVERT: B 51 MET cc_start: 0.8434 (ppp) cc_final: 0.6932 (ppp) REVERT: B 52 ASP cc_start: 0.9409 (m-30) cc_final: 0.8772 (m-30) REVERT: B 78 GLU cc_start: 0.9002 (tm-30) cc_final: 0.8639 (tm-30) REVERT: B 80 ASP cc_start: 0.8740 (t0) cc_final: 0.8453 (t0) REVERT: C 3 ASP cc_start: 0.9569 (p0) cc_final: 0.8699 (p0) REVERT: C 4 LYS cc_start: 0.9752 (mptt) cc_final: 0.9469 (mppt) REVERT: C 7 LYS cc_start: 0.9388 (pttp) cc_final: 0.9087 (ptpp) REVERT: C 17 MET cc_start: 0.8764 (tpt) cc_final: 0.8337 (tpt) REVERT: C 27 ASP cc_start: 0.9486 (m-30) cc_final: 0.9257 (m-30) REVERT: C 37 LYS cc_start: 0.9013 (mmmm) cc_final: 0.8736 (tppp) REVERT: C 40 MET cc_start: 0.9641 (ppp) cc_final: 0.9400 (tmm) REVERT: C 52 ASP cc_start: 0.9468 (m-30) cc_final: 0.9013 (p0) REVERT: C 53 LYS cc_start: 0.9433 (mmmt) cc_final: 0.9004 (mtpt) REVERT: C 80 ASP cc_start: 0.8647 (t0) cc_final: 0.8368 (t0) REVERT: D 27 ASP cc_start: 0.9479 (m-30) cc_final: 0.9105 (m-30) REVERT: D 28 GLU cc_start: 0.9340 (tp30) cc_final: 0.8819 (tp30) REVERT: D 32 THR cc_start: 0.9405 (t) cc_final: 0.9059 (t) REVERT: D 33 ARG cc_start: 0.9456 (mtm110) cc_final: 0.9211 (ttp-110) REVERT: D 39 GLU cc_start: 0.7665 (mp0) cc_final: 0.7372 (mp0) REVERT: D 41 GLU cc_start: 0.9194 (tp30) cc_final: 0.8766 (tp30) REVERT: D 53 LYS cc_start: 0.9357 (mttm) cc_final: 0.9082 (mmmt) REVERT: D 80 ASP cc_start: 0.8781 (t0) cc_final: 0.8306 (t0) REVERT: E 8 GLU cc_start: 0.9466 (tp30) cc_final: 0.9028 (tm-30) REVERT: E 19 GLU cc_start: 0.8500 (pp20) cc_final: 0.8034 (pp20) REVERT: E 27 ASP cc_start: 0.9448 (m-30) cc_final: 0.9158 (m-30) REVERT: E 28 GLU cc_start: 0.9432 (tp30) cc_final: 0.9046 (tp30) REVERT: E 32 THR cc_start: 0.9296 (t) cc_final: 0.9042 (t) REVERT: E 41 GLU cc_start: 0.8988 (tp30) cc_final: 0.8693 (tp30) REVERT: E 52 ASP cc_start: 0.9288 (m-30) cc_final: 0.8903 (m-30) REVERT: E 69 CYS cc_start: 0.9631 (m) cc_final: 0.8738 (m) REVERT: E 78 GLU cc_start: 0.9008 (tm-30) cc_final: 0.8807 (tm-30) REVERT: E 79 GLU cc_start: 0.9055 (mm-30) cc_final: 0.8575 (mm-30) REVERT: E 80 ASP cc_start: 0.8885 (t0) cc_final: 0.8377 (t0) REVERT: F 8 GLU cc_start: 0.9489 (tp30) cc_final: 0.8911 (tm-30) REVERT: F 27 ASP cc_start: 0.9029 (m-30) cc_final: 0.8600 (m-30) REVERT: F 28 GLU cc_start: 0.9217 (tm-30) cc_final: 0.8660 (tm-30) REVERT: F 38 GLU cc_start: 0.9414 (tp30) cc_final: 0.9158 (tp30) REVERT: F 40 MET cc_start: 0.9445 (ppp) cc_final: 0.9137 (tmm) REVERT: F 41 GLU cc_start: 0.9123 (tp30) cc_final: 0.8841 (tp30) REVERT: F 52 ASP cc_start: 0.8033 (p0) cc_final: 0.7760 (p0) REVERT: F 80 ASP cc_start: 0.8936 (t0) cc_final: 0.8485 (t0) REVERT: G 13 PHE cc_start: 0.9587 (m-80) cc_final: 0.9304 (t80) REVERT: G 17 MET cc_start: 0.8524 (ttp) cc_final: 0.8187 (ttt) REVERT: G 27 ASP cc_start: 0.9118 (m-30) cc_final: 0.8814 (m-30) REVERT: G 28 GLU cc_start: 0.9310 (tm-30) cc_final: 0.8653 (tm-30) REVERT: G 79 GLU cc_start: 0.9307 (mm-30) cc_final: 0.9081 (mm-30) REVERT: G 80 ASP cc_start: 0.8825 (t0) cc_final: 0.8379 (t0) REVERT: H 7 LYS cc_start: 0.9661 (ttpp) cc_final: 0.9452 (tppp) REVERT: H 13 PHE cc_start: 0.9557 (OUTLIER) cc_final: 0.8975 (t80) REVERT: H 19 GLU cc_start: 0.8522 (pp20) cc_final: 0.8108 (pp20) REVERT: H 27 ASP cc_start: 0.8981 (m-30) cc_final: 0.8576 (m-30) REVERT: H 28 GLU cc_start: 0.9179 (tm-30) cc_final: 0.8704 (tm-30) REVERT: H 41 GLU cc_start: 0.9018 (tp30) cc_final: 0.8600 (tp30) REVERT: H 80 ASP cc_start: 0.8775 (t0) cc_final: 0.8250 (t0) outliers start: 36 outliers final: 22 residues processed: 456 average time/residue: 0.1111 time to fit residues: 60.8742 Evaluate side-chains 447 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 423 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain E residue 22 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 71 ILE Chi-restraints excluded: chain H residue 13 PHE Chi-restraints excluded: chain H residue 17 MET Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 71 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 40 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 6 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 16 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 12 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 ASN C 47 ASN D 23 ASN D 47 ASN D 70 GLN E 23 ASN ** G 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.058911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.048915 restraints weight = 21305.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.051039 restraints weight = 11637.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.052525 restraints weight = 7555.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.053630 restraints weight = 5360.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.054451 restraints weight = 3992.321| |-----------------------------------------------------------------------------| r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5568 Z= 0.168 Angle : 0.878 10.684 7440 Z= 0.441 Chirality : 0.046 0.171 896 Planarity : 0.004 0.030 936 Dihedral : 5.092 16.233 760 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 7.31 % Allowed : 29.06 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.31), residues: 696 helix: 0.55 (0.21), residues: 616 sheet: None (None), residues: 0 loop : -0.60 (0.65), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 33 TYR 0.024 0.002 TYR A 75 PHE 0.009 0.001 PHE B 13 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 5568) covalent geometry : angle 0.87773 ( 7440) hydrogen bonds : bond 0.04445 ( 418) hydrogen bonds : angle 4.73011 ( 1254) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 457 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 GLU cc_start: 0.8506 (pp20) cc_final: 0.8294 (pp20) REVERT: A 21 THR cc_start: 0.9389 (p) cc_final: 0.8978 (p) REVERT: A 27 ASP cc_start: 0.9495 (m-30) cc_final: 0.9284 (m-30) REVERT: A 37 LYS cc_start: 0.9450 (ttmm) cc_final: 0.9203 (tppp) REVERT: A 42 LYS cc_start: 0.9304 (OUTLIER) cc_final: 0.8668 (pttt) REVERT: A 53 LYS cc_start: 0.9362 (mtmm) cc_final: 0.8829 (mttm) REVERT: A 78 GLU cc_start: 0.8950 (pp20) cc_final: 0.8711 (pp20) REVERT: A 80 ASP cc_start: 0.8665 (t0) cc_final: 0.8279 (t0) REVERT: B 3 ASP cc_start: 0.9453 (p0) cc_final: 0.8757 (p0) REVERT: B 4 LYS cc_start: 0.9556 (mmmm) cc_final: 0.9269 (mmmm) REVERT: B 7 LYS cc_start: 0.9115 (ptpp) cc_final: 0.8262 (ptpp) REVERT: B 51 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.7606 (ppp) REVERT: B 52 ASP cc_start: 0.9461 (m-30) cc_final: 0.8849 (m-30) REVERT: B 53 LYS cc_start: 0.9495 (mtpt) cc_final: 0.9281 (mtpt) REVERT: B 80 ASP cc_start: 0.8765 (t0) cc_final: 0.8353 (t0) REVERT: C 3 ASP cc_start: 0.9565 (p0) cc_final: 0.9050 (p0) REVERT: C 27 ASP cc_start: 0.9509 (m-30) cc_final: 0.9127 (m-30) REVERT: C 38 GLU cc_start: 0.9079 (tp30) cc_final: 0.8698 (tt0) REVERT: C 40 MET cc_start: 0.9687 (ppp) cc_final: 0.9479 (tmm) REVERT: C 52 ASP cc_start: 0.9477 (m-30) cc_final: 0.9047 (p0) REVERT: C 53 LYS cc_start: 0.9444 (mmmt) cc_final: 0.9004 (mtpt) REVERT: C 80 ASP cc_start: 0.8670 (t0) cc_final: 0.8401 (t0) REVERT: D 17 MET cc_start: 0.8278 (tpt) cc_final: 0.7359 (tpt) REVERT: D 22 ILE cc_start: 0.9639 (OUTLIER) cc_final: 0.9346 (mm) REVERT: D 27 ASP cc_start: 0.9473 (m-30) cc_final: 0.9094 (m-30) REVERT: D 28 GLU cc_start: 0.9319 (tp30) cc_final: 0.8801 (tp30) REVERT: D 33 ARG cc_start: 0.9463 (mtm110) cc_final: 0.9206 (ttp-110) REVERT: D 39 GLU cc_start: 0.7548 (mp0) cc_final: 0.7213 (mp0) REVERT: D 41 GLU cc_start: 0.9186 (tp30) cc_final: 0.8692 (tp30) REVERT: D 80 ASP cc_start: 0.8813 (t0) cc_final: 0.8431 (t0) REVERT: E 8 GLU cc_start: 0.9447 (tp30) cc_final: 0.9055 (tm-30) REVERT: E 19 GLU cc_start: 0.8578 (pp20) cc_final: 0.8133 (pp20) REVERT: E 27 ASP cc_start: 0.9432 (m-30) cc_final: 0.9128 (m-30) REVERT: E 28 GLU cc_start: 0.9392 (tp30) cc_final: 0.8982 (tp30) REVERT: E 32 THR cc_start: 0.9146 (t) cc_final: 0.8888 (t) REVERT: E 41 GLU cc_start: 0.9033 (tp30) cc_final: 0.8605 (tp30) REVERT: E 52 ASP cc_start: 0.9295 (m-30) cc_final: 0.8938 (m-30) REVERT: E 64 LYS cc_start: 0.9366 (mmmm) cc_final: 0.9137 (mmmm) REVERT: E 80 ASP cc_start: 0.8864 (t0) cc_final: 0.8433 (t0) REVERT: F 8 GLU cc_start: 0.9476 (tp30) cc_final: 0.8887 (tm-30) REVERT: F 13 PHE cc_start: 0.9340 (m-80) cc_final: 0.9136 (t80) REVERT: F 27 ASP cc_start: 0.9018 (m-30) cc_final: 0.8598 (m-30) REVERT: F 28 GLU cc_start: 0.9207 (tm-30) cc_final: 0.8644 (tm-30) REVERT: F 38 GLU cc_start: 0.9446 (tp30) cc_final: 0.9190 (tp30) REVERT: F 40 MET cc_start: 0.9489 (ppp) cc_final: 0.9127 (tmm) REVERT: F 41 GLU cc_start: 0.9117 (tp30) cc_final: 0.8816 (tp30) REVERT: F 80 ASP cc_start: 0.8947 (t0) cc_final: 0.8497 (t0) REVERT: G 27 ASP cc_start: 0.9103 (m-30) cc_final: 0.8791 (m-30) REVERT: G 28 GLU cc_start: 0.9190 (tm-30) cc_final: 0.8623 (tm-30) REVERT: G 29 LEU cc_start: 0.9736 (OUTLIER) cc_final: 0.9514 (tp) REVERT: G 52 ASP cc_start: 0.9417 (m-30) cc_final: 0.8961 (p0) REVERT: G 79 GLU cc_start: 0.9313 (mm-30) cc_final: 0.9086 (mm-30) REVERT: G 80 ASP cc_start: 0.8707 (t0) cc_final: 0.8270 (t0) REVERT: H 4 LYS cc_start: 0.9406 (mppt) cc_final: 0.9093 (mppt) REVERT: H 7 LYS cc_start: 0.9685 (ttpp) cc_final: 0.9435 (tppp) REVERT: H 13 PHE cc_start: 0.9559 (OUTLIER) cc_final: 0.9205 (t80) REVERT: H 19 GLU cc_start: 0.8511 (pp20) cc_final: 0.8111 (pp20) REVERT: H 27 ASP cc_start: 0.8943 (m-30) cc_final: 0.8550 (m-30) REVERT: H 28 GLU cc_start: 0.9192 (tm-30) cc_final: 0.8682 (tm-30) REVERT: H 39 GLU cc_start: 0.8941 (pm20) cc_final: 0.8702 (pm20) REVERT: H 41 GLU cc_start: 0.8997 (tp30) cc_final: 0.8593 (tp30) REVERT: H 80 ASP cc_start: 0.8762 (t0) cc_final: 0.8229 (t0) REVERT: H 83 LEU cc_start: 0.9734 (tt) cc_final: 0.9519 (tp) outliers start: 45 outliers final: 23 residues processed: 458 average time/residue: 0.1151 time to fit residues: 63.1822 Evaluate side-chains 467 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 439 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain E residue 22 ILE Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 72 CYS Chi-restraints excluded: chain H residue 13 PHE Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 17 MET Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 62 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 12 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 49 optimal weight: 7.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN B 23 ASN D 47 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.058621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.048430 restraints weight = 21653.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.050549 restraints weight = 11921.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.052042 restraints weight = 7766.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.053163 restraints weight = 5523.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.054010 restraints weight = 4138.021| |-----------------------------------------------------------------------------| r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5568 Z= 0.174 Angle : 0.890 11.554 7440 Z= 0.441 Chirality : 0.048 0.185 896 Planarity : 0.004 0.026 936 Dihedral : 5.160 15.412 760 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 6.82 % Allowed : 34.90 % Favored : 58.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.31), residues: 696 helix: 0.44 (0.21), residues: 616 sheet: None (None), residues: 0 loop : -0.84 (0.65), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 33 TYR 0.017 0.002 TYR A 75 PHE 0.006 0.001 PHE F 13 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 5568) covalent geometry : angle 0.89004 ( 7440) hydrogen bonds : bond 0.04349 ( 418) hydrogen bonds : angle 4.79524 ( 1254) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 445 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ASP cc_start: 0.9378 (p0) cc_final: 0.9069 (p0) REVERT: A 17 MET cc_start: 0.8391 (tpt) cc_final: 0.8032 (tpt) REVERT: A 21 THR cc_start: 0.9418 (p) cc_final: 0.9156 (p) REVERT: A 37 LYS cc_start: 0.9483 (ttmm) cc_final: 0.9240 (tppp) REVERT: A 42 LYS cc_start: 0.9287 (OUTLIER) cc_final: 0.8981 (pttt) REVERT: A 47 ASN cc_start: 0.8193 (OUTLIER) cc_final: 0.7598 (t0) REVERT: A 53 LYS cc_start: 0.9376 (mtmm) cc_final: 0.8948 (mttp) REVERT: A 80 ASP cc_start: 0.8793 (t0) cc_final: 0.8389 (t0) REVERT: B 3 ASP cc_start: 0.9447 (p0) cc_final: 0.8777 (p0) REVERT: B 5 VAL cc_start: 0.9676 (p) cc_final: 0.9461 (m) REVERT: B 7 LYS cc_start: 0.9065 (ptpp) cc_final: 0.8443 (ptpp) REVERT: B 51 MET cc_start: 0.8412 (ppp) cc_final: 0.7587 (ppp) REVERT: B 52 ASP cc_start: 0.9446 (m-30) cc_final: 0.8833 (m-30) REVERT: B 80 ASP cc_start: 0.8775 (t0) cc_final: 0.8463 (t0) REVERT: C 3 ASP cc_start: 0.9561 (p0) cc_final: 0.9122 (p0) REVERT: C 7 LYS cc_start: 0.9426 (ptpp) cc_final: 0.9016 (ptpp) REVERT: C 38 GLU cc_start: 0.9060 (tp30) cc_final: 0.8663 (tt0) REVERT: C 40 MET cc_start: 0.9730 (ppp) cc_final: 0.9478 (tmm) REVERT: C 52 ASP cc_start: 0.9468 (m-30) cc_final: 0.9258 (m-30) REVERT: C 80 ASP cc_start: 0.8858 (t0) cc_final: 0.8497 (t0) REVERT: D 7 LYS cc_start: 0.9840 (ttmm) cc_final: 0.9633 (ttpp) REVERT: D 19 GLU cc_start: 0.8292 (pp20) cc_final: 0.7657 (pp20) REVERT: D 27 ASP cc_start: 0.9469 (m-30) cc_final: 0.9126 (m-30) REVERT: D 28 GLU cc_start: 0.9293 (tp30) cc_final: 0.8782 (tp30) REVERT: D 33 ARG cc_start: 0.9464 (mtm110) cc_final: 0.9211 (ttm110) REVERT: D 39 GLU cc_start: 0.7578 (mp0) cc_final: 0.7168 (mp0) REVERT: D 41 GLU cc_start: 0.9200 (tp30) cc_final: 0.8686 (tp30) REVERT: D 47 ASN cc_start: 0.9156 (OUTLIER) cc_final: 0.8353 (t0) REVERT: D 80 ASP cc_start: 0.8851 (t0) cc_final: 0.8353 (t0) REVERT: E 8 GLU cc_start: 0.9434 (tp30) cc_final: 0.9050 (tm-30) REVERT: E 19 GLU cc_start: 0.8598 (pp20) cc_final: 0.8139 (pp20) REVERT: E 27 ASP cc_start: 0.9434 (m-30) cc_final: 0.9129 (m-30) REVERT: E 28 GLU cc_start: 0.9410 (tp30) cc_final: 0.8976 (tp30) REVERT: E 32 THR cc_start: 0.9087 (t) cc_final: 0.8770 (t) REVERT: E 41 GLU cc_start: 0.9102 (tp30) cc_final: 0.8635 (tp30) REVERT: E 45 ARG cc_start: 0.9076 (tpp80) cc_final: 0.8848 (tpp80) REVERT: E 52 ASP cc_start: 0.9292 (m-30) cc_final: 0.8905 (m-30) REVERT: E 80 ASP cc_start: 0.8927 (t0) cc_final: 0.8496 (t0) REVERT: F 8 GLU cc_start: 0.9460 (tp30) cc_final: 0.8947 (tm-30) REVERT: F 11 LYS cc_start: 0.9447 (mtpp) cc_final: 0.9021 (ttmm) REVERT: F 27 ASP cc_start: 0.9032 (m-30) cc_final: 0.8606 (m-30) REVERT: F 28 GLU cc_start: 0.9223 (tm-30) cc_final: 0.8648 (tm-30) REVERT: F 38 GLU cc_start: 0.9455 (tp30) cc_final: 0.9217 (tp30) REVERT: F 40 MET cc_start: 0.9472 (ppp) cc_final: 0.9066 (tmm) REVERT: F 41 GLU cc_start: 0.9105 (tp30) cc_final: 0.8778 (tp30) REVERT: F 64 LYS cc_start: 0.9444 (mmmm) cc_final: 0.9218 (mmmm) REVERT: F 80 ASP cc_start: 0.8958 (t0) cc_final: 0.8499 (t0) REVERT: G 27 ASP cc_start: 0.9124 (m-30) cc_final: 0.8801 (m-30) REVERT: G 28 GLU cc_start: 0.9311 (tm-30) cc_final: 0.9011 (tm-30) REVERT: G 41 GLU cc_start: 0.9089 (tp30) cc_final: 0.8874 (tp30) REVERT: G 45 ARG cc_start: 0.9225 (tpp80) cc_final: 0.9020 (tpp80) REVERT: G 79 GLU cc_start: 0.9333 (mm-30) cc_final: 0.9089 (mm-30) REVERT: G 80 ASP cc_start: 0.8663 (t0) cc_final: 0.8279 (t0) REVERT: G 89 LEU cc_start: 0.7606 (pt) cc_final: 0.7324 (pt) REVERT: H 13 PHE cc_start: 0.9602 (OUTLIER) cc_final: 0.9115 (t80) REVERT: H 19 GLU cc_start: 0.8565 (pp20) cc_final: 0.8166 (pp20) REVERT: H 27 ASP cc_start: 0.8972 (m-30) cc_final: 0.8583 (m-30) REVERT: H 28 GLU cc_start: 0.9241 (tm-30) cc_final: 0.8706 (tm-30) REVERT: H 31 GLN cc_start: 0.9210 (tp-100) cc_final: 0.8975 (tp40) REVERT: H 41 GLU cc_start: 0.9021 (tp30) cc_final: 0.8363 (tp30) REVERT: H 80 ASP cc_start: 0.8765 (t0) cc_final: 0.8173 (t0) outliers start: 42 outliers final: 29 residues processed: 447 average time/residue: 0.1117 time to fit residues: 59.9090 Evaluate side-chains 463 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 430 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 47 ASN Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain E residue 22 ILE Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 72 CYS Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 13 PHE Chi-restraints excluded: chain H residue 17 MET Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 62 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 51 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 54 optimal weight: 0.0070 chunk 35 optimal weight: 0.9980 chunk 28 optimal weight: 0.1980 chunk 38 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 overall best weight: 1.4402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN C 47 ASN ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 47 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.058951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 20)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.048764 restraints weight = 21995.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 16)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.050968 restraints weight = 12126.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.052498 restraints weight = 7864.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.053618 restraints weight = 5576.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.054456 restraints weight = 4154.416| |-----------------------------------------------------------------------------| r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5568 Z= 0.170 Angle : 0.938 10.804 7440 Z= 0.458 Chirality : 0.048 0.267 896 Planarity : 0.004 0.025 936 Dihedral : 5.207 14.933 760 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 6.66 % Allowed : 36.20 % Favored : 57.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.31), residues: 696 helix: 0.41 (0.21), residues: 616 sheet: None (None), residues: 0 loop : -0.91 (0.67), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 33 TYR 0.013 0.001 TYR A 75 PHE 0.009 0.001 PHE D 13 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 5568) covalent geometry : angle 0.93771 ( 7440) hydrogen bonds : bond 0.04225 ( 418) hydrogen bonds : angle 4.72730 ( 1254) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 449 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.9292 (ptpp) cc_final: 0.8969 (pttt) REVERT: A 17 MET cc_start: 0.8398 (tpt) cc_final: 0.8012 (tpt) REVERT: A 21 THR cc_start: 0.9421 (p) cc_final: 0.9056 (p) REVERT: A 37 LYS cc_start: 0.9487 (ttmm) cc_final: 0.9249 (tppp) REVERT: A 42 LYS cc_start: 0.9283 (OUTLIER) cc_final: 0.9027 (pttt) REVERT: A 47 ASN cc_start: 0.8389 (OUTLIER) cc_final: 0.7690 (t0) REVERT: A 53 LYS cc_start: 0.9407 (mtmm) cc_final: 0.8821 (mttm) REVERT: A 80 ASP cc_start: 0.8762 (t0) cc_final: 0.8410 (t0) REVERT: B 3 ASP cc_start: 0.9454 (p0) cc_final: 0.9237 (p0) REVERT: B 7 LYS cc_start: 0.9246 (ptpp) cc_final: 0.8908 (ptpp) REVERT: B 23 ASN cc_start: 0.9585 (m-40) cc_final: 0.9304 (t0) REVERT: B 35 LEU cc_start: 0.8579 (tp) cc_final: 0.8278 (tp) REVERT: B 39 GLU cc_start: 0.7582 (mp0) cc_final: 0.7317 (mp0) REVERT: B 47 ASN cc_start: 0.8809 (m-40) cc_final: 0.8597 (m-40) REVERT: B 51 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.7599 (ppp) REVERT: B 52 ASP cc_start: 0.9444 (m-30) cc_final: 0.8812 (m-30) REVERT: B 53 LYS cc_start: 0.9412 (mtpt) cc_final: 0.8972 (mttm) REVERT: B 80 ASP cc_start: 0.8765 (t0) cc_final: 0.8487 (t0) REVERT: C 3 ASP cc_start: 0.9543 (p0) cc_final: 0.9104 (p0) REVERT: C 28 GLU cc_start: 0.9569 (tp30) cc_final: 0.9318 (tp30) REVERT: C 38 GLU cc_start: 0.8918 (tp30) cc_final: 0.8578 (tt0) REVERT: C 40 MET cc_start: 0.9737 (ppp) cc_final: 0.9471 (tmm) REVERT: C 47 ASN cc_start: 0.9068 (OUTLIER) cc_final: 0.7974 (m-40) REVERT: C 52 ASP cc_start: 0.9462 (m-30) cc_final: 0.9180 (p0) REVERT: C 53 LYS cc_start: 0.9471 (mtpt) cc_final: 0.9240 (mttm) REVERT: C 80 ASP cc_start: 0.8876 (t0) cc_final: 0.8533 (t0) REVERT: D 19 GLU cc_start: 0.8487 (pp20) cc_final: 0.7861 (pp20) REVERT: D 27 ASP cc_start: 0.9453 (m-30) cc_final: 0.9140 (m-30) REVERT: D 28 GLU cc_start: 0.9324 (tp30) cc_final: 0.8774 (tp30) REVERT: D 33 ARG cc_start: 0.9467 (mtm110) cc_final: 0.9204 (ttm110) REVERT: D 39 GLU cc_start: 0.7614 (mp0) cc_final: 0.7165 (mp0) REVERT: D 41 GLU cc_start: 0.9233 (tp30) cc_final: 0.8686 (tp30) REVERT: D 47 ASN cc_start: 0.9404 (m-40) cc_final: 0.7833 (t0) REVERT: D 52 ASP cc_start: 0.9380 (m-30) cc_final: 0.8869 (p0) REVERT: D 80 ASP cc_start: 0.8801 (t0) cc_final: 0.8353 (t0) REVERT: E 8 GLU cc_start: 0.9392 (tp30) cc_final: 0.9025 (tm-30) REVERT: E 19 GLU cc_start: 0.8629 (pp20) cc_final: 0.8170 (pp20) REVERT: E 27 ASP cc_start: 0.9429 (m-30) cc_final: 0.9076 (m-30) REVERT: E 28 GLU cc_start: 0.9405 (tp30) cc_final: 0.8962 (tp30) REVERT: E 32 THR cc_start: 0.9037 (t) cc_final: 0.8700 (t) REVERT: E 40 MET cc_start: 0.9407 (tmm) cc_final: 0.9011 (tmm) REVERT: E 41 GLU cc_start: 0.9094 (tp30) cc_final: 0.8881 (tp30) REVERT: E 45 ARG cc_start: 0.9085 (tpp80) cc_final: 0.8882 (tpp80) REVERT: E 52 ASP cc_start: 0.9288 (m-30) cc_final: 0.8874 (m-30) REVERT: E 80 ASP cc_start: 0.8911 (t0) cc_final: 0.8516 (t0) REVERT: F 8 GLU cc_start: 0.9434 (tp30) cc_final: 0.8940 (tm-30) REVERT: F 11 LYS cc_start: 0.9404 (mtpp) cc_final: 0.8918 (ttmm) REVERT: F 17 MET cc_start: 0.8221 (mmm) cc_final: 0.7811 (tpt) REVERT: F 27 ASP cc_start: 0.9018 (m-30) cc_final: 0.8588 (m-30) REVERT: F 28 GLU cc_start: 0.9221 (tm-30) cc_final: 0.8650 (tm-30) REVERT: F 38 GLU cc_start: 0.9464 (tp30) cc_final: 0.9203 (tp30) REVERT: F 40 MET cc_start: 0.9473 (ppp) cc_final: 0.9072 (tmm) REVERT: F 41 GLU cc_start: 0.9094 (tp30) cc_final: 0.8694 (tp30) REVERT: F 47 ASN cc_start: 0.8332 (m-40) cc_final: 0.7725 (m-40) REVERT: F 80 ASP cc_start: 0.8951 (t0) cc_final: 0.8516 (t0) REVERT: G 27 ASP cc_start: 0.9094 (m-30) cc_final: 0.8775 (m-30) REVERT: G 28 GLU cc_start: 0.9350 (tm-30) cc_final: 0.9020 (tm-30) REVERT: G 41 GLU cc_start: 0.9016 (tp30) cc_final: 0.8482 (tp30) REVERT: G 45 ARG cc_start: 0.9221 (tpp80) cc_final: 0.8854 (tpp80) REVERT: G 47 ASN cc_start: 0.9067 (OUTLIER) cc_final: 0.8094 (t0) REVERT: G 79 GLU cc_start: 0.9356 (mm-30) cc_final: 0.9095 (mm-30) REVERT: G 80 ASP cc_start: 0.8637 (t0) cc_final: 0.8225 (t0) REVERT: H 13 PHE cc_start: 0.9569 (OUTLIER) cc_final: 0.8949 (t80) REVERT: H 19 GLU cc_start: 0.8558 (pp20) cc_final: 0.8163 (pp20) REVERT: H 27 ASP cc_start: 0.8963 (m-30) cc_final: 0.8573 (m-30) REVERT: H 28 GLU cc_start: 0.9223 (tm-30) cc_final: 0.8658 (tm-30) REVERT: H 41 GLU cc_start: 0.9020 (tp30) cc_final: 0.8285 (tp30) REVERT: H 80 ASP cc_start: 0.8721 (t0) cc_final: 0.8150 (t0) outliers start: 41 outliers final: 29 residues processed: 454 average time/residue: 0.1146 time to fit residues: 62.4088 Evaluate side-chains 475 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 440 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 47 ASN Chi-restraints excluded: chain G residue 71 ILE Chi-restraints excluded: chain G residue 72 CYS Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 13 PHE Chi-restraints excluded: chain H residue 17 MET Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 49 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 4 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 44 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 12 optimal weight: 0.5980 chunk 57 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN C 47 ASN ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 47 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.058022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.048067 restraints weight = 22095.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.050173 restraints weight = 12268.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.051644 restraints weight = 7978.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.052751 restraints weight = 5678.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.053561 restraints weight = 4234.323| |-----------------------------------------------------------------------------| r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5568 Z= 0.197 Angle : 0.937 10.611 7440 Z= 0.460 Chirality : 0.049 0.355 896 Planarity : 0.004 0.024 936 Dihedral : 5.248 15.844 760 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 7.31 % Allowed : 37.82 % Favored : 54.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.32), residues: 696 helix: 0.47 (0.21), residues: 616 sheet: None (None), residues: 0 loop : -1.03 (0.66), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 45 TYR 0.011 0.002 TYR A 75 PHE 0.008 0.001 PHE D 13 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 5568) covalent geometry : angle 0.93658 ( 7440) hydrogen bonds : bond 0.04285 ( 418) hydrogen bonds : angle 4.71312 ( 1254) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 436 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.8567 (tpt) cc_final: 0.8214 (tpt) REVERT: A 21 THR cc_start: 0.9420 (p) cc_final: 0.9029 (p) REVERT: A 42 LYS cc_start: 0.9271 (OUTLIER) cc_final: 0.9020 (pttt) REVERT: A 47 ASN cc_start: 0.8724 (OUTLIER) cc_final: 0.7911 (t0) REVERT: A 53 LYS cc_start: 0.9411 (mtmm) cc_final: 0.9115 (mtmm) REVERT: A 80 ASP cc_start: 0.8841 (t0) cc_final: 0.8485 (t0) REVERT: B 3 ASP cc_start: 0.9461 (p0) cc_final: 0.9226 (p0) REVERT: B 23 ASN cc_start: 0.9579 (m-40) cc_final: 0.9016 (t0) REVERT: B 51 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.7573 (ppp) REVERT: B 52 ASP cc_start: 0.9458 (m-30) cc_final: 0.8826 (m-30) REVERT: B 53 LYS cc_start: 0.9415 (mtpt) cc_final: 0.8977 (mttm) REVERT: B 78 GLU cc_start: 0.9111 (tm-30) cc_final: 0.8791 (tm-30) REVERT: B 80 ASP cc_start: 0.8899 (t0) cc_final: 0.8626 (t0) REVERT: C 3 ASP cc_start: 0.9557 (p0) cc_final: 0.8745 (p0) REVERT: C 4 LYS cc_start: 0.9785 (mmmm) cc_final: 0.9422 (mppt) REVERT: C 8 GLU cc_start: 0.9421 (mm-30) cc_final: 0.9210 (mm-30) REVERT: C 17 MET cc_start: 0.8368 (tpp) cc_final: 0.8099 (tpp) REVERT: C 27 ASP cc_start: 0.9052 (p0) cc_final: 0.8688 (p0) REVERT: C 28 GLU cc_start: 0.9585 (tp30) cc_final: 0.9329 (tp30) REVERT: C 38 GLU cc_start: 0.8865 (tp30) cc_final: 0.8557 (tt0) REVERT: C 40 MET cc_start: 0.9739 (ppp) cc_final: 0.9481 (tmm) REVERT: C 47 ASN cc_start: 0.9334 (OUTLIER) cc_final: 0.8403 (m-40) REVERT: C 52 ASP cc_start: 0.9481 (m-30) cc_final: 0.9223 (p0) REVERT: C 53 LYS cc_start: 0.9467 (mtpt) cc_final: 0.9153 (mtpt) REVERT: C 80 ASP cc_start: 0.8975 (t0) cc_final: 0.8714 (t0) REVERT: D 19 GLU cc_start: 0.8662 (pp20) cc_final: 0.8106 (pp20) REVERT: D 27 ASP cc_start: 0.9429 (m-30) cc_final: 0.9156 (m-30) REVERT: D 28 GLU cc_start: 0.9383 (tp30) cc_final: 0.8862 (tp30) REVERT: D 33 ARG cc_start: 0.9495 (mtm110) cc_final: 0.9220 (ttm110) REVERT: D 39 GLU cc_start: 0.7399 (mp0) cc_final: 0.6919 (mp0) REVERT: D 41 GLU cc_start: 0.9242 (tp30) cc_final: 0.8720 (tp30) REVERT: D 47 ASN cc_start: 0.9366 (m-40) cc_final: 0.9102 (t0) REVERT: D 80 ASP cc_start: 0.8842 (t0) cc_final: 0.8368 (t0) REVERT: E 8 GLU cc_start: 0.9401 (tp30) cc_final: 0.9054 (tm-30) REVERT: E 19 GLU cc_start: 0.8737 (pp20) cc_final: 0.8289 (pp20) REVERT: E 27 ASP cc_start: 0.9441 (m-30) cc_final: 0.9102 (m-30) REVERT: E 28 GLU cc_start: 0.9430 (tp30) cc_final: 0.8996 (tp30) REVERT: E 32 THR cc_start: 0.9064 (t) cc_final: 0.8729 (t) REVERT: E 40 MET cc_start: 0.9443 (tmm) cc_final: 0.9052 (tmm) REVERT: E 41 GLU cc_start: 0.9135 (tp30) cc_final: 0.8597 (tp30) REVERT: E 45 ARG cc_start: 0.9111 (tpp80) cc_final: 0.8742 (tpp80) REVERT: E 52 ASP cc_start: 0.9300 (m-30) cc_final: 0.8865 (m-30) REVERT: E 80 ASP cc_start: 0.8996 (t0) cc_final: 0.8627 (t0) REVERT: F 8 GLU cc_start: 0.9468 (tp30) cc_final: 0.8976 (tm-30) REVERT: F 11 LYS cc_start: 0.9244 (mtpp) cc_final: 0.8709 (ttmm) REVERT: F 17 MET cc_start: 0.8387 (mmm) cc_final: 0.7916 (tpt) REVERT: F 19 GLU cc_start: 0.8668 (pp20) cc_final: 0.8335 (tm-30) REVERT: F 27 ASP cc_start: 0.9027 (m-30) cc_final: 0.8588 (m-30) REVERT: F 28 GLU cc_start: 0.9241 (tm-30) cc_final: 0.8663 (tm-30) REVERT: F 38 GLU cc_start: 0.9458 (tp30) cc_final: 0.9182 (tp30) REVERT: F 40 MET cc_start: 0.9506 (ppp) cc_final: 0.9090 (tmm) REVERT: F 41 GLU cc_start: 0.9152 (tp30) cc_final: 0.8807 (tp30) REVERT: F 47 ASN cc_start: 0.8487 (m-40) cc_final: 0.8002 (m-40) REVERT: F 80 ASP cc_start: 0.8975 (t0) cc_final: 0.8543 (t0) REVERT: G 27 ASP cc_start: 0.9122 (m-30) cc_final: 0.8810 (m-30) REVERT: G 28 GLU cc_start: 0.9362 (tm-30) cc_final: 0.9030 (tm-30) REVERT: G 41 GLU cc_start: 0.9061 (tp30) cc_final: 0.8555 (tp30) REVERT: G 47 ASN cc_start: 0.9263 (OUTLIER) cc_final: 0.8667 (t0) REVERT: G 79 GLU cc_start: 0.9402 (mm-30) cc_final: 0.9124 (mm-30) REVERT: G 80 ASP cc_start: 0.8772 (t0) cc_final: 0.8412 (t0) REVERT: G 89 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.7231 (pt) REVERT: H 13 PHE cc_start: 0.9556 (OUTLIER) cc_final: 0.9055 (t80) REVERT: H 19 GLU cc_start: 0.8643 (pp20) cc_final: 0.8128 (tm-30) REVERT: H 27 ASP cc_start: 0.8997 (m-30) cc_final: 0.8615 (m-30) REVERT: H 31 GLN cc_start: 0.9229 (tp-100) cc_final: 0.9021 (tp40) REVERT: H 38 GLU cc_start: 0.9298 (tp30) cc_final: 0.8983 (tp30) REVERT: H 41 GLU cc_start: 0.9023 (tp30) cc_final: 0.8282 (tp30) REVERT: H 80 ASP cc_start: 0.8775 (t0) cc_final: 0.8292 (t0) outliers start: 45 outliers final: 35 residues processed: 443 average time/residue: 0.1197 time to fit residues: 63.5031 Evaluate side-chains 471 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 429 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 47 ASN Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 71 ILE Chi-restraints excluded: chain G residue 72 CYS Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 13 PHE Chi-restraints excluded: chain H residue 17 MET Chi-restraints excluded: chain H residue 40 MET Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 62 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 1 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 0 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 47 ASN ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 GLN F 70 GLN G 47 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.058265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.048542 restraints weight = 21992.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.050621 restraints weight = 12189.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.052073 restraints weight = 7918.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.053148 restraints weight = 5597.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.053942 restraints weight = 4183.738| |-----------------------------------------------------------------------------| r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 5568 Z= 0.214 Angle : 0.973 10.848 7440 Z= 0.480 Chirality : 0.048 0.178 896 Planarity : 0.004 0.032 936 Dihedral : 5.361 15.929 760 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 8.12 % Allowed : 38.80 % Favored : 53.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.32), residues: 696 helix: 0.47 (0.21), residues: 616 sheet: None (None), residues: 0 loop : -1.10 (0.65), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 33 TYR 0.011 0.002 TYR D 82 PHE 0.008 0.001 PHE D 13 Details of bonding type rmsd covalent geometry : bond 0.00496 ( 5568) covalent geometry : angle 0.97331 ( 7440) hydrogen bonds : bond 0.04376 ( 418) hydrogen bonds : angle 4.66681 ( 1254) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 435 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.8658 (tpt) cc_final: 0.8280 (tpt) REVERT: A 21 THR cc_start: 0.9456 (p) cc_final: 0.9032 (p) REVERT: A 35 LEU cc_start: 0.9153 (mp) cc_final: 0.8888 (pp) REVERT: A 42 LYS cc_start: 0.9265 (OUTLIER) cc_final: 0.9004 (pttt) REVERT: A 52 ASP cc_start: 0.9544 (m-30) cc_final: 0.9174 (p0) REVERT: A 53 LYS cc_start: 0.9415 (mtmm) cc_final: 0.8935 (mtmm) REVERT: A 80 ASP cc_start: 0.8887 (t0) cc_final: 0.8647 (t0) REVERT: B 3 ASP cc_start: 0.9550 (p0) cc_final: 0.9182 (p0) REVERT: B 23 ASN cc_start: 0.9571 (m-40) cc_final: 0.9006 (t0) REVERT: B 51 MET cc_start: 0.8332 (ppp) cc_final: 0.7581 (ppp) REVERT: B 52 ASP cc_start: 0.9425 (m-30) cc_final: 0.8760 (m-30) REVERT: B 53 LYS cc_start: 0.9446 (mtpt) cc_final: 0.9147 (mtmm) REVERT: B 78 GLU cc_start: 0.9055 (tm-30) cc_final: 0.8756 (tm-30) REVERT: C 3 ASP cc_start: 0.9545 (p0) cc_final: 0.9076 (p0) REVERT: C 8 GLU cc_start: 0.9411 (mm-30) cc_final: 0.9172 (mm-30) REVERT: C 17 MET cc_start: 0.8387 (tpp) cc_final: 0.8116 (tpp) REVERT: C 27 ASP cc_start: 0.9046 (p0) cc_final: 0.8793 (p0) REVERT: C 28 GLU cc_start: 0.9590 (tp30) cc_final: 0.9175 (tp30) REVERT: C 38 GLU cc_start: 0.8824 (tp30) cc_final: 0.8539 (tt0) REVERT: C 40 MET cc_start: 0.9738 (ppp) cc_final: 0.9484 (tmm) REVERT: C 47 ASN cc_start: 0.9482 (OUTLIER) cc_final: 0.8746 (m-40) REVERT: C 52 ASP cc_start: 0.9439 (m-30) cc_final: 0.9220 (p0) REVERT: C 53 LYS cc_start: 0.9474 (mtpt) cc_final: 0.9173 (mtpt) REVERT: C 80 ASP cc_start: 0.8993 (t0) cc_final: 0.8781 (t0) REVERT: D 19 GLU cc_start: 0.8705 (pp20) cc_final: 0.8156 (pp20) REVERT: D 27 ASP cc_start: 0.9396 (m-30) cc_final: 0.9136 (m-30) REVERT: D 28 GLU cc_start: 0.9391 (tp30) cc_final: 0.8970 (tp30) REVERT: D 33 ARG cc_start: 0.9473 (mtm110) cc_final: 0.9201 (ttm110) REVERT: D 39 GLU cc_start: 0.7417 (mp0) cc_final: 0.6835 (mp0) REVERT: D 41 GLU cc_start: 0.9263 (tp30) cc_final: 0.8748 (tp30) REVERT: D 47 ASN cc_start: 0.9382 (m-40) cc_final: 0.9113 (t0) REVERT: D 80 ASP cc_start: 0.8811 (t0) cc_final: 0.8349 (t0) REVERT: E 8 GLU cc_start: 0.9373 (tp30) cc_final: 0.9040 (tm-30) REVERT: E 19 GLU cc_start: 0.8748 (pp20) cc_final: 0.8275 (tm-30) REVERT: E 27 ASP cc_start: 0.9410 (m-30) cc_final: 0.9082 (m-30) REVERT: E 28 GLU cc_start: 0.9444 (tp30) cc_final: 0.9020 (tp30) REVERT: E 32 THR cc_start: 0.9110 (t) cc_final: 0.8809 (t) REVERT: E 41 GLU cc_start: 0.9131 (tp30) cc_final: 0.8340 (tp30) REVERT: E 45 ARG cc_start: 0.9109 (tpp80) cc_final: 0.8697 (tpp80) REVERT: E 52 ASP cc_start: 0.9259 (m-30) cc_final: 0.8845 (m-30) REVERT: E 79 GLU cc_start: 0.9488 (tp30) cc_final: 0.9025 (mm-30) REVERT: E 80 ASP cc_start: 0.9031 (t0) cc_final: 0.8681 (t0) REVERT: F 8 GLU cc_start: 0.9442 (tp30) cc_final: 0.8959 (tm-30) REVERT: F 11 LYS cc_start: 0.9311 (mtpp) cc_final: 0.8757 (ttmm) REVERT: F 17 MET cc_start: 0.8564 (mmm) cc_final: 0.8108 (tpt) REVERT: F 19 GLU cc_start: 0.8643 (pp20) cc_final: 0.8314 (tm-30) REVERT: F 27 ASP cc_start: 0.9031 (m-30) cc_final: 0.8591 (m-30) REVERT: F 28 GLU cc_start: 0.9250 (tm-30) cc_final: 0.8682 (tm-30) REVERT: F 38 GLU cc_start: 0.9401 (OUTLIER) cc_final: 0.9094 (tp30) REVERT: F 40 MET cc_start: 0.9533 (ppp) cc_final: 0.9069 (tmm) REVERT: F 41 GLU cc_start: 0.9125 (tp30) cc_final: 0.8709 (tp30) REVERT: F 80 ASP cc_start: 0.8996 (t0) cc_final: 0.8580 (t0) REVERT: G 17 MET cc_start: 0.8109 (tpt) cc_final: 0.7678 (tpt) REVERT: G 21 THR cc_start: 0.9142 (p) cc_final: 0.8841 (p) REVERT: G 27 ASP cc_start: 0.9115 (m-30) cc_final: 0.8802 (m-30) REVERT: G 28 GLU cc_start: 0.9385 (tm-30) cc_final: 0.9078 (tm-30) REVERT: G 41 GLU cc_start: 0.9039 (tp30) cc_final: 0.8634 (tp30) REVERT: G 47 ASN cc_start: 0.9401 (OUTLIER) cc_final: 0.8888 (t0) REVERT: G 80 ASP cc_start: 0.8807 (t0) cc_final: 0.8492 (t0) REVERT: H 13 PHE cc_start: 0.9583 (OUTLIER) cc_final: 0.9083 (t80) REVERT: H 19 GLU cc_start: 0.8629 (pp20) cc_final: 0.8196 (tm-30) REVERT: H 27 ASP cc_start: 0.8987 (m-30) cc_final: 0.8614 (m-30) REVERT: H 28 GLU cc_start: 0.9296 (tm-30) cc_final: 0.8873 (tm-30) REVERT: H 38 GLU cc_start: 0.9169 (tp30) cc_final: 0.8760 (tp30) REVERT: H 39 GLU cc_start: 0.9265 (pm20) cc_final: 0.8898 (pm20) REVERT: H 41 GLU cc_start: 0.9003 (tp30) cc_final: 0.8470 (tp30) REVERT: H 80 ASP cc_start: 0.8845 (t0) cc_final: 0.8406 (t0) REVERT: H 83 LEU cc_start: 0.9700 (tp) cc_final: 0.9396 (tt) outliers start: 50 outliers final: 41 residues processed: 445 average time/residue: 0.1185 time to fit residues: 63.2153 Evaluate side-chains 472 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 426 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 47 ASN Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 71 ILE Chi-restraints excluded: chain G residue 72 CYS Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 13 PHE Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 17 MET Chi-restraints excluded: chain H residue 40 MET Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 62 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 52 optimal weight: 0.9990 chunk 36 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 41 optimal weight: 0.4980 chunk 61 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 24 optimal weight: 10.0000 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN C 47 ASN ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.059170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.049201 restraints weight = 21558.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.051334 restraints weight = 11979.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.052836 restraints weight = 7788.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.053937 restraints weight = 5492.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.054738 restraints weight = 4102.941| |-----------------------------------------------------------------------------| r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5568 Z= 0.187 Angle : 1.034 11.532 7440 Z= 0.496 Chirality : 0.048 0.224 896 Planarity : 0.004 0.025 936 Dihedral : 5.317 16.931 760 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 6.66 % Allowed : 41.07 % Favored : 52.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.32), residues: 696 helix: 0.42 (0.21), residues: 616 sheet: None (None), residues: 0 loop : -1.25 (0.65), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 33 TYR 0.013 0.002 TYR G 75 PHE 0.008 0.001 PHE D 13 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 5568) covalent geometry : angle 1.03422 ( 7440) hydrogen bonds : bond 0.04368 ( 418) hydrogen bonds : angle 4.68776 ( 1254) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 452 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.9231 (ptpp) cc_final: 0.8956 (ptpp) REVERT: A 17 MET cc_start: 0.8455 (tpt) cc_final: 0.8235 (tpt) REVERT: A 21 THR cc_start: 0.9358 (p) cc_final: 0.8886 (p) REVERT: A 38 GLU cc_start: 0.8056 (pp20) cc_final: 0.7804 (pp20) REVERT: A 42 LYS cc_start: 0.9214 (OUTLIER) cc_final: 0.8900 (pttt) REVERT: A 47 ASN cc_start: 0.8722 (OUTLIER) cc_final: 0.7499 (t0) REVERT: A 53 LYS cc_start: 0.9341 (mtmm) cc_final: 0.8881 (mttm) REVERT: A 80 ASP cc_start: 0.8856 (t0) cc_final: 0.8579 (t0) REVERT: B 3 ASP cc_start: 0.9509 (p0) cc_final: 0.9178 (p0) REVERT: B 17 MET cc_start: 0.8127 (tpp) cc_final: 0.7767 (tpp) REVERT: B 23 ASN cc_start: 0.9552 (m-40) cc_final: 0.9219 (t0) REVERT: B 27 ASP cc_start: 0.9275 (m-30) cc_final: 0.9037 (p0) REVERT: B 51 MET cc_start: 0.8279 (ppp) cc_final: 0.7583 (ppp) REVERT: B 52 ASP cc_start: 0.9444 (m-30) cc_final: 0.8821 (m-30) REVERT: B 53 LYS cc_start: 0.9384 (mtpt) cc_final: 0.9083 (mtmm) REVERT: C 3 ASP cc_start: 0.9532 (p0) cc_final: 0.8821 (p0) REVERT: C 4 LYS cc_start: 0.9772 (mmmm) cc_final: 0.9485 (mppt) REVERT: C 27 ASP cc_start: 0.9054 (p0) cc_final: 0.8750 (p0) REVERT: C 28 GLU cc_start: 0.9567 (tp30) cc_final: 0.9231 (tp30) REVERT: C 38 GLU cc_start: 0.8835 (tp30) cc_final: 0.8235 (tt0) REVERT: C 39 GLU cc_start: 0.9190 (pm20) cc_final: 0.8709 (mp0) REVERT: C 40 MET cc_start: 0.9751 (ppp) cc_final: 0.9427 (tmm) REVERT: C 47 ASN cc_start: 0.9514 (OUTLIER) cc_final: 0.8541 (t0) REVERT: C 52 ASP cc_start: 0.9475 (m-30) cc_final: 0.9200 (m-30) REVERT: C 53 LYS cc_start: 0.9427 (mtpt) cc_final: 0.9222 (mtpt) REVERT: C 80 ASP cc_start: 0.8926 (t0) cc_final: 0.8615 (t0) REVERT: D 19 GLU cc_start: 0.8628 (pp20) cc_final: 0.8031 (pp20) REVERT: D 27 ASP cc_start: 0.9421 (m-30) cc_final: 0.9170 (m-30) REVERT: D 28 GLU cc_start: 0.9414 (tp30) cc_final: 0.8986 (tp30) REVERT: D 32 THR cc_start: 0.9329 (t) cc_final: 0.9083 (t) REVERT: D 37 LYS cc_start: 0.9249 (ttmm) cc_final: 0.8848 (tppp) REVERT: D 41 GLU cc_start: 0.9279 (tp30) cc_final: 0.8603 (tp30) REVERT: D 45 ARG cc_start: 0.9277 (tpp80) cc_final: 0.8835 (tpp80) REVERT: D 47 ASN cc_start: 0.9313 (m-40) cc_final: 0.8903 (t0) REVERT: D 80 ASP cc_start: 0.8712 (t0) cc_final: 0.8231 (t0) REVERT: E 8 GLU cc_start: 0.9362 (tp30) cc_final: 0.9026 (tm-30) REVERT: E 19 GLU cc_start: 0.8697 (pp20) cc_final: 0.8247 (pp20) REVERT: E 27 ASP cc_start: 0.9439 (m-30) cc_final: 0.9093 (m-30) REVERT: E 28 GLU cc_start: 0.9427 (tp30) cc_final: 0.8986 (tp30) REVERT: E 32 THR cc_start: 0.9029 (t) cc_final: 0.8690 (t) REVERT: E 40 MET cc_start: 0.9417 (tmm) cc_final: 0.9105 (tmm) REVERT: E 41 GLU cc_start: 0.9095 (tp30) cc_final: 0.8490 (tp30) REVERT: E 45 ARG cc_start: 0.9101 (tpp80) cc_final: 0.8628 (tpp80) REVERT: E 52 ASP cc_start: 0.9304 (m-30) cc_final: 0.8878 (m-30) REVERT: E 78 GLU cc_start: 0.8755 (tm-30) cc_final: 0.8039 (tm-30) REVERT: E 79 GLU cc_start: 0.9525 (tp30) cc_final: 0.9014 (mm-30) REVERT: E 80 ASP cc_start: 0.8987 (t0) cc_final: 0.8612 (t0) REVERT: F 3 ASP cc_start: 0.9502 (p0) cc_final: 0.8702 (m-30) REVERT: F 8 GLU cc_start: 0.9471 (tp30) cc_final: 0.8994 (tm-30) REVERT: F 11 LYS cc_start: 0.9229 (mtpp) cc_final: 0.8595 (ttmm) REVERT: F 17 MET cc_start: 0.8407 (mmm) cc_final: 0.8008 (tpt) REVERT: F 27 ASP cc_start: 0.8993 (m-30) cc_final: 0.8539 (m-30) REVERT: F 28 GLU cc_start: 0.9262 (tm-30) cc_final: 0.8711 (tm-30) REVERT: F 38 GLU cc_start: 0.9443 (OUTLIER) cc_final: 0.9127 (tp30) REVERT: F 40 MET cc_start: 0.9549 (ppp) cc_final: 0.9079 (tmm) REVERT: F 41 GLU cc_start: 0.9133 (tp30) cc_final: 0.8762 (tp30) REVERT: F 47 ASN cc_start: 0.8546 (m-40) cc_final: 0.7944 (m-40) REVERT: F 80 ASP cc_start: 0.8948 (t0) cc_final: 0.8514 (t0) REVERT: G 17 MET cc_start: 0.8122 (tpt) cc_final: 0.7685 (tpt) REVERT: G 21 THR cc_start: 0.9080 (p) cc_final: 0.8739 (p) REVERT: G 27 ASP cc_start: 0.9034 (m-30) cc_final: 0.8727 (m-30) REVERT: G 28 GLU cc_start: 0.9380 (tm-30) cc_final: 0.9048 (tm-30) REVERT: G 40 MET cc_start: 0.9417 (tmm) cc_final: 0.9048 (tmm) REVERT: G 41 GLU cc_start: 0.9058 (tp30) cc_final: 0.8657 (tp30) REVERT: G 51 MET cc_start: 0.8644 (mpp) cc_final: 0.7706 (mtm) REVERT: G 80 ASP cc_start: 0.8681 (t0) cc_final: 0.8311 (t0) REVERT: H 13 PHE cc_start: 0.9567 (OUTLIER) cc_final: 0.9110 (t80) REVERT: H 19 GLU cc_start: 0.8632 (pp20) cc_final: 0.8218 (pp20) REVERT: H 27 ASP cc_start: 0.8963 (m-30) cc_final: 0.8576 (m-30) REVERT: H 39 GLU cc_start: 0.9276 (pm20) cc_final: 0.8991 (pm20) REVERT: H 41 GLU cc_start: 0.9016 (tp30) cc_final: 0.8210 (tp30) REVERT: H 45 ARG cc_start: 0.9376 (tpp80) cc_final: 0.8963 (tpp80) REVERT: H 80 ASP cc_start: 0.8727 (t0) cc_final: 0.8219 (t0) REVERT: H 83 LEU cc_start: 0.9676 (tp) cc_final: 0.9419 (tt) outliers start: 41 outliers final: 27 residues processed: 458 average time/residue: 0.1149 time to fit residues: 63.3101 Evaluate side-chains 466 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 434 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 72 CYS Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 13 PHE Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 17 MET Chi-restraints excluded: chain H residue 40 MET Chi-restraints excluded: chain H residue 49 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 36 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 16 optimal weight: 9.9990 chunk 49 optimal weight: 8.9990 chunk 28 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN ** B 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 GLN ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.058920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.048907 restraints weight = 21925.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.051047 restraints weight = 12108.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.052556 restraints weight = 7861.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.053661 restraints weight = 5539.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.054407 restraints weight = 4119.390| |-----------------------------------------------------------------------------| r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.4710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 5568 Z= 0.194 Angle : 1.097 13.264 7440 Z= 0.522 Chirality : 0.050 0.291 896 Planarity : 0.005 0.031 936 Dihedral : 5.416 17.357 760 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 6.98 % Allowed : 42.21 % Favored : 50.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.31), residues: 696 helix: 0.35 (0.21), residues: 616 sheet: None (None), residues: 0 loop : -1.45 (0.62), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 33 TYR 0.042 0.003 TYR A 75 PHE 0.025 0.001 PHE B 13 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 5568) covalent geometry : angle 1.09667 ( 7440) hydrogen bonds : bond 0.04443 ( 418) hydrogen bonds : angle 4.78453 ( 1254) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 445 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ASP cc_start: 0.9304 (p0) cc_final: 0.9043 (p0) REVERT: A 17 MET cc_start: 0.8439 (tpt) cc_final: 0.8210 (tpt) REVERT: A 21 THR cc_start: 0.9362 (p) cc_final: 0.8848 (p) REVERT: A 42 LYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8944 (pttt) REVERT: A 47 ASN cc_start: 0.8912 (OUTLIER) cc_final: 0.7801 (t0) REVERT: A 53 LYS cc_start: 0.9366 (mtmm) cc_final: 0.8975 (mttm) REVERT: A 80 ASP cc_start: 0.8848 (t0) cc_final: 0.8614 (t0) REVERT: B 3 ASP cc_start: 0.9528 (p0) cc_final: 0.9156 (p0) REVERT: B 7 LYS cc_start: 0.9347 (ptpp) cc_final: 0.8780 (ptpt) REVERT: B 17 MET cc_start: 0.8294 (tpp) cc_final: 0.8051 (tpp) REVERT: B 23 ASN cc_start: 0.9543 (m-40) cc_final: 0.9026 (t0) REVERT: B 51 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7850 (ppp) REVERT: B 53 LYS cc_start: 0.9408 (mtpt) cc_final: 0.9106 (mtmm) REVERT: B 87 LEU cc_start: 0.9540 (mm) cc_final: 0.9288 (mm) REVERT: C 3 ASP cc_start: 0.9535 (p0) cc_final: 0.8710 (p0) REVERT: C 4 LYS cc_start: 0.9756 (mmmm) cc_final: 0.9084 (mppt) REVERT: C 7 LYS cc_start: 0.9427 (ptpp) cc_final: 0.8684 (pttm) REVERT: C 8 GLU cc_start: 0.9323 (mm-30) cc_final: 0.8970 (mm-30) REVERT: C 27 ASP cc_start: 0.9040 (p0) cc_final: 0.8719 (p0) REVERT: C 28 GLU cc_start: 0.9566 (tp30) cc_final: 0.9227 (tp30) REVERT: C 38 GLU cc_start: 0.8817 (tp30) cc_final: 0.8254 (tt0) REVERT: C 39 GLU cc_start: 0.9197 (pm20) cc_final: 0.8734 (mp0) REVERT: C 40 MET cc_start: 0.9747 (ppp) cc_final: 0.9408 (tmm) REVERT: C 47 ASN cc_start: 0.9554 (m-40) cc_final: 0.8814 (t0) REVERT: C 52 ASP cc_start: 0.9453 (m-30) cc_final: 0.9208 (m-30) REVERT: C 80 ASP cc_start: 0.8935 (t0) cc_final: 0.8658 (t0) REVERT: D 19 GLU cc_start: 0.8644 (pp20) cc_final: 0.8080 (pp20) REVERT: D 27 ASP cc_start: 0.9393 (m-30) cc_final: 0.9139 (m-30) REVERT: D 28 GLU cc_start: 0.9437 (tp30) cc_final: 0.9029 (tp30) REVERT: D 32 THR cc_start: 0.9300 (t) cc_final: 0.9069 (t) REVERT: D 33 ARG cc_start: 0.9511 (mtm110) cc_final: 0.9262 (ttp-110) REVERT: D 37 LYS cc_start: 0.9231 (ttmm) cc_final: 0.8861 (tppp) REVERT: D 41 GLU cc_start: 0.9300 (tp30) cc_final: 0.8623 (tp30) REVERT: D 45 ARG cc_start: 0.9285 (tpp80) cc_final: 0.8835 (tpp80) REVERT: D 47 ASN cc_start: 0.9300 (m-40) cc_final: 0.9016 (t0) REVERT: D 80 ASP cc_start: 0.8692 (t0) cc_final: 0.8208 (t0) REVERT: E 8 GLU cc_start: 0.9365 (tp30) cc_final: 0.8954 (tm-30) REVERT: E 19 GLU cc_start: 0.8684 (pp20) cc_final: 0.8248 (pp20) REVERT: E 27 ASP cc_start: 0.9442 (m-30) cc_final: 0.9095 (m-30) REVERT: E 28 GLU cc_start: 0.9441 (tp30) cc_final: 0.8993 (tp30) REVERT: E 32 THR cc_start: 0.9023 (t) cc_final: 0.8673 (t) REVERT: E 40 MET cc_start: 0.9423 (tmm) cc_final: 0.9090 (tmm) REVERT: E 41 GLU cc_start: 0.9101 (tp30) cc_final: 0.8575 (tp30) REVERT: E 45 ARG cc_start: 0.9097 (tpp80) cc_final: 0.8809 (tpp80) REVERT: E 52 ASP cc_start: 0.9304 (m-30) cc_final: 0.8858 (m-30) REVERT: E 78 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8029 (tm-30) REVERT: E 79 GLU cc_start: 0.9518 (tp30) cc_final: 0.9030 (mm-30) REVERT: E 80 ASP cc_start: 0.9004 (t0) cc_final: 0.8631 (t0) REVERT: F 8 GLU cc_start: 0.9465 (tp30) cc_final: 0.8991 (tm-30) REVERT: F 11 LYS cc_start: 0.9249 (mtpp) cc_final: 0.8607 (ttmm) REVERT: F 17 MET cc_start: 0.8372 (mmm) cc_final: 0.8010 (tpt) REVERT: F 27 ASP cc_start: 0.8961 (m-30) cc_final: 0.8521 (m-30) REVERT: F 28 GLU cc_start: 0.9312 (tm-30) cc_final: 0.8774 (tm-30) REVERT: F 38 GLU cc_start: 0.9429 (OUTLIER) cc_final: 0.9088 (tp30) REVERT: F 40 MET cc_start: 0.9544 (ppp) cc_final: 0.9100 (tmm) REVERT: F 41 GLU cc_start: 0.9150 (tp30) cc_final: 0.8787 (tp30) REVERT: F 47 ASN cc_start: 0.8615 (m-40) cc_final: 0.8107 (m-40) REVERT: F 80 ASP cc_start: 0.8981 (t0) cc_final: 0.8559 (t0) REVERT: G 17 MET cc_start: 0.8202 (tpt) cc_final: 0.7804 (tpt) REVERT: G 21 THR cc_start: 0.9120 (p) cc_final: 0.8771 (p) REVERT: G 27 ASP cc_start: 0.9005 (m-30) cc_final: 0.8688 (m-30) REVERT: G 28 GLU cc_start: 0.9303 (tm-30) cc_final: 0.9059 (tm-30) REVERT: G 32 THR cc_start: 0.9017 (m) cc_final: 0.8656 (t) REVERT: G 40 MET cc_start: 0.9435 (tmm) cc_final: 0.9069 (tmm) REVERT: G 41 GLU cc_start: 0.9099 (tp30) cc_final: 0.8802 (tp30) REVERT: G 47 ASN cc_start: 0.9399 (m-40) cc_final: 0.8363 (t0) REVERT: G 80 ASP cc_start: 0.8677 (t0) cc_final: 0.8325 (t0) REVERT: H 13 PHE cc_start: 0.9574 (OUTLIER) cc_final: 0.9087 (t80) REVERT: H 19 GLU cc_start: 0.8634 (pp20) cc_final: 0.8109 (tm-30) REVERT: H 27 ASP cc_start: 0.8956 (m-30) cc_final: 0.8557 (m-30) REVERT: H 38 GLU cc_start: 0.9262 (tp30) cc_final: 0.8908 (tp30) REVERT: H 39 GLU cc_start: 0.9260 (pm20) cc_final: 0.8997 (pm20) REVERT: H 41 GLU cc_start: 0.9047 (tp30) cc_final: 0.8178 (tp30) REVERT: H 45 ARG cc_start: 0.9389 (tpp80) cc_final: 0.8970 (tpp80) REVERT: H 80 ASP cc_start: 0.8727 (t0) cc_final: 0.8222 (t0) REVERT: H 83 LEU cc_start: 0.9680 (tp) cc_final: 0.9415 (tt) outliers start: 43 outliers final: 33 residues processed: 450 average time/residue: 0.1126 time to fit residues: 60.9309 Evaluate side-chains 477 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 439 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain E residue 22 ILE Chi-restraints excluded: chain E residue 31 GLN Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 72 CYS Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 13 PHE Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 17 MET Chi-restraints excluded: chain H residue 40 MET Chi-restraints excluded: chain H residue 49 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 53 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN ** B 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 GLN ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 47 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.059579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.049815 restraints weight = 21809.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.051907 restraints weight = 11983.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.053377 restraints weight = 7735.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.054460 restraints weight = 5434.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.055273 restraints weight = 4029.237| |-----------------------------------------------------------------------------| r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.4836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 5568 Z= 0.203 Angle : 1.159 13.539 7440 Z= 0.550 Chirality : 0.051 0.310 896 Planarity : 0.005 0.035 936 Dihedral : 5.461 17.799 760 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 6.66 % Allowed : 43.83 % Favored : 49.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.31), residues: 696 helix: 0.35 (0.21), residues: 616 sheet: None (None), residues: 0 loop : -1.57 (0.62), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 33 TYR 0.042 0.003 TYR D 75 PHE 0.010 0.001 PHE B 13 Details of bonding type rmsd covalent geometry : bond 0.00487 ( 5568) covalent geometry : angle 1.15920 ( 7440) hydrogen bonds : bond 0.04591 ( 418) hydrogen bonds : angle 4.86680 ( 1254) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 440 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 THR cc_start: 0.9341 (p) cc_final: 0.8807 (p) REVERT: A 47 ASN cc_start: 0.9016 (OUTLIER) cc_final: 0.8169 (t0) REVERT: A 53 LYS cc_start: 0.9358 (mtmm) cc_final: 0.9155 (mttm) REVERT: B 3 ASP cc_start: 0.9539 (p0) cc_final: 0.9197 (p0) REVERT: B 17 MET cc_start: 0.8272 (tpp) cc_final: 0.8028 (tpp) REVERT: B 23 ASN cc_start: 0.9532 (m-40) cc_final: 0.9202 (t0) REVERT: B 28 GLU cc_start: 0.9428 (tp30) cc_final: 0.8992 (tp30) REVERT: B 51 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.7847 (ppp) REVERT: B 53 LYS cc_start: 0.9433 (mtpt) cc_final: 0.9122 (mtmm) REVERT: C 3 ASP cc_start: 0.9546 (p0) cc_final: 0.9071 (p0) REVERT: C 27 ASP cc_start: 0.9021 (p0) cc_final: 0.8711 (p0) REVERT: C 28 GLU cc_start: 0.9569 (tp30) cc_final: 0.9206 (tp30) REVERT: C 38 GLU cc_start: 0.8798 (tp30) cc_final: 0.8231 (tt0) REVERT: C 39 GLU cc_start: 0.9166 (pm20) cc_final: 0.8633 (mp0) REVERT: C 40 MET cc_start: 0.9760 (ppp) cc_final: 0.9432 (tmm) REVERT: C 47 ASN cc_start: 0.9508 (m-40) cc_final: 0.8664 (t0) REVERT: C 52 ASP cc_start: 0.9426 (m-30) cc_final: 0.9114 (m-30) REVERT: C 80 ASP cc_start: 0.8859 (t0) cc_final: 0.8642 (t0) REVERT: D 17 MET cc_start: 0.8121 (tpp) cc_final: 0.7792 (tpp) REVERT: D 19 GLU cc_start: 0.8674 (pp20) cc_final: 0.8102 (pp20) REVERT: D 28 GLU cc_start: 0.9455 (tp30) cc_final: 0.9128 (tp30) REVERT: D 32 THR cc_start: 0.9327 (t) cc_final: 0.9113 (t) REVERT: D 33 ARG cc_start: 0.9466 (mtm110) cc_final: 0.9205 (ttp-110) REVERT: D 37 LYS cc_start: 0.9272 (ttmm) cc_final: 0.8909 (tppp) REVERT: D 41 GLU cc_start: 0.9303 (tp30) cc_final: 0.8616 (tp30) REVERT: D 45 ARG cc_start: 0.9294 (tpp80) cc_final: 0.8842 (tpp80) REVERT: D 47 ASN cc_start: 0.9339 (m-40) cc_final: 0.9065 (t0) REVERT: D 78 GLU cc_start: 0.9214 (pp20) cc_final: 0.8077 (pp20) REVERT: D 80 ASP cc_start: 0.8703 (t0) cc_final: 0.8196 (t0) REVERT: E 8 GLU cc_start: 0.9256 (tp30) cc_final: 0.8901 (tm-30) REVERT: E 19 GLU cc_start: 0.8759 (pp20) cc_final: 0.8293 (tm-30) REVERT: E 27 ASP cc_start: 0.9405 (m-30) cc_final: 0.9065 (m-30) REVERT: E 28 GLU cc_start: 0.9449 (tp30) cc_final: 0.9001 (tp30) REVERT: E 32 THR cc_start: 0.9036 (t) cc_final: 0.8702 (t) REVERT: E 40 MET cc_start: 0.9397 (tmm) cc_final: 0.9089 (tmm) REVERT: E 41 GLU cc_start: 0.9091 (tp30) cc_final: 0.8554 (tp30) REVERT: E 45 ARG cc_start: 0.9080 (tpp80) cc_final: 0.8805 (tpp80) REVERT: E 52 ASP cc_start: 0.9270 (m-30) cc_final: 0.8837 (m-30) REVERT: E 64 LYS cc_start: 0.9430 (mmtp) cc_final: 0.8860 (mmmm) REVERT: E 78 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8079 (tm-30) REVERT: E 79 GLU cc_start: 0.9489 (tp30) cc_final: 0.9022 (mm-30) REVERT: E 80 ASP cc_start: 0.9005 (t0) cc_final: 0.8658 (t0) REVERT: F 3 ASP cc_start: 0.9433 (p0) cc_final: 0.8733 (m-30) REVERT: F 8 GLU cc_start: 0.9417 (tp30) cc_final: 0.9106 (tm-30) REVERT: F 11 LYS cc_start: 0.9267 (mtpp) cc_final: 0.8597 (ttmm) REVERT: F 17 MET cc_start: 0.8430 (mmm) cc_final: 0.8091 (tpt) REVERT: F 27 ASP cc_start: 0.8958 (m-30) cc_final: 0.8573 (m-30) REVERT: F 28 GLU cc_start: 0.9215 (tm-30) cc_final: 0.8743 (tm-30) REVERT: F 38 GLU cc_start: 0.9335 (OUTLIER) cc_final: 0.8982 (tp30) REVERT: F 40 MET cc_start: 0.9529 (ppp) cc_final: 0.9115 (tmm) REVERT: F 41 GLU cc_start: 0.9148 (tp30) cc_final: 0.8686 (tp30) REVERT: F 45 ARG cc_start: 0.9279 (tpp80) cc_final: 0.8912 (tpp80) REVERT: F 47 ASN cc_start: 0.8745 (m-40) cc_final: 0.8245 (m-40) REVERT: F 80 ASP cc_start: 0.8983 (t0) cc_final: 0.8609 (t0) REVERT: G 11 LYS cc_start: 0.9276 (ttmm) cc_final: 0.8903 (tppt) REVERT: G 17 MET cc_start: 0.8247 (tpt) cc_final: 0.7828 (tpt) REVERT: G 21 THR cc_start: 0.9167 (p) cc_final: 0.8799 (p) REVERT: G 27 ASP cc_start: 0.8987 (m-30) cc_final: 0.8660 (m-30) REVERT: G 28 GLU cc_start: 0.9274 (tm-30) cc_final: 0.9059 (tm-30) REVERT: G 32 THR cc_start: 0.8943 (m) cc_final: 0.8585 (t) REVERT: G 41 GLU cc_start: 0.9097 (tp30) cc_final: 0.8639 (tp30) REVERT: G 47 ASN cc_start: 0.9354 (OUTLIER) cc_final: 0.8882 (t0) REVERT: G 80 ASP cc_start: 0.8673 (t0) cc_final: 0.8339 (t0) REVERT: H 13 PHE cc_start: 0.9576 (OUTLIER) cc_final: 0.9094 (t80) REVERT: H 15 ARG cc_start: 0.9367 (ttm-80) cc_final: 0.9125 (ttm-80) REVERT: H 19 GLU cc_start: 0.8573 (pp20) cc_final: 0.8074 (tm-30) REVERT: H 27 ASP cc_start: 0.8942 (m-30) cc_final: 0.8560 (m-30) REVERT: H 38 GLU cc_start: 0.9253 (tp30) cc_final: 0.8908 (tp30) REVERT: H 39 GLU cc_start: 0.9220 (pm20) cc_final: 0.8969 (pm20) REVERT: H 41 GLU cc_start: 0.9028 (tp30) cc_final: 0.8433 (tp30) REVERT: H 80 ASP cc_start: 0.8730 (t0) cc_final: 0.8250 (t0) REVERT: H 83 LEU cc_start: 0.9696 (tp) cc_final: 0.9431 (tt) outliers start: 41 outliers final: 31 residues processed: 447 average time/residue: 0.1148 time to fit residues: 61.4595 Evaluate side-chains 470 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 434 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain E residue 22 ILE Chi-restraints excluded: chain E residue 31 GLN Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 47 ASN Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 72 CYS Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 13 PHE Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 17 MET Chi-restraints excluded: chain H residue 49 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 51 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 48 optimal weight: 9.9990 chunk 6 optimal weight: 0.9980 chunk 3 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN ** B 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.058518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.048502 restraints weight = 21953.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.050593 restraints weight = 12259.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.052074 restraints weight = 8002.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.053156 restraints weight = 5656.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.053957 restraints weight = 4238.095| |-----------------------------------------------------------------------------| r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.4899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 5568 Z= 0.218 Angle : 1.162 13.012 7440 Z= 0.557 Chirality : 0.052 0.310 896 Planarity : 0.005 0.033 936 Dihedral : 5.524 17.736 760 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 18.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 6.82 % Allowed : 44.16 % Favored : 49.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.31), residues: 696 helix: 0.34 (0.21), residues: 616 sheet: None (None), residues: 0 loop : -1.58 (0.63), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 33 TYR 0.037 0.003 TYR A 75 PHE 0.007 0.001 PHE D 13 Details of bonding type rmsd covalent geometry : bond 0.00519 ( 5568) covalent geometry : angle 1.16204 ( 7440) hydrogen bonds : bond 0.04577 ( 418) hydrogen bonds : angle 4.88984 ( 1254) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1380.16 seconds wall clock time: 24 minutes 46.18 seconds (1486.18 seconds total)