Starting phenix.real_space_refine on Sun Sep 13 10:08:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7scy_25042/09_2026/7scy_25042.cif Found real_map, /net/cci-nas-00/data/ceres_data/7scy_25042/09_2026/7scy_25042.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7scy_25042/09_2026/7scy_25042.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7scy_25042/09_2026/7scy_25042.map" model { file = "/net/cci-nas-00/data/ceres_data/7scy_25042/09_2026/7scy_25042.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7scy_25042/09_2026/7scy_25042.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 294 5.49 5 S 19 5.16 5 C 7110 2.51 5 N 2388 2.21 5 O 2959 1.98 5 H 10436 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23206 Number of models: 1 Model: "" Number of chains: 11 Chain: "I" Number of atoms: 4682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 4682 Classifications: {'DNA': 147} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 4646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 4646 Classifications: {'DNA': 147} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 146} Chain: "A" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1616 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1271 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "C" Number of atoms: 1733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1733 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 1461 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 1684 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 1459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 1459 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "G" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 1667 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "H" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 1450 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "K" Number of atoms: 1537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1537 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Time building chain proxies: 3.08, per 1000 atoms: 0.13 Number of scatterers: 23206 At special positions: 0 Unit cell: (123.54, 117.15, 109.695, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 19 16.00 P 294 15.00 O 2959 8.00 N 2388 7.00 C 7110 6.00 H 10436 1.00 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: 2.14 Conformation dependent library (CDL) restraints added in 416.2 milliseconds 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1588 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 11 sheets defined 72.1% alpha, 3.2% beta 145 base pairs and 234 stacking pairs defined. Time for finding SS restraints: 3.67 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.825A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.810A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 3.991A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 removed outlier: 3.598A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.738A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.841A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.711A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL F 65 " --> pdb=" O PHE F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.305A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 123 Processing helix chain 'K' and resid 404 through 415 Processing helix chain 'K' and resid 422 through 426 Processing helix chain 'K' and resid 432 through 439 removed outlier: 4.195A pdb=" N VAL K 436 " --> pdb=" O THR K 432 " (cutoff:3.500A) Processing helix chain 'K' and resid 440 through 449 Processing helix chain 'K' and resid 456 through 463 removed outlier: 3.697A pdb=" N GLN K 460 " --> pdb=" O GLU K 456 " (cutoff:3.500A) Processing helix chain 'K' and resid 468 through 476 removed outlier: 3.906A pdb=" N LEU K 474 " --> pdb=" O GLN K 470 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.924A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.729A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.669A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.639A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.649A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 419 through 420 removed outlier: 5.710A pdb=" N ILE K 395 " --> pdb=" O THR K 420 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU K 396 " --> pdb=" O ILE K 430 " (cutoff:3.500A) 443 hydrogen bonds defined for protein. 1296 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 372 hydrogen bonds 744 hydrogen bond angles 0 basepair planarities 145 basepair parallelities 234 stacking parallelities Total time for adding SS restraints: 4.82 Time building geometry restraints manager: 2.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 2339 1.02 - 1.22: 8147 1.22 - 1.42: 6386 1.42 - 1.62: 7121 1.62 - 1.82: 33 Bond restraints: 24026 Sorted by residual: bond pdb=" C8 DG I 10 " pdb=" H8 DG I 10 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" C8 DA J -5 " pdb=" H8 DA J -5 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" C6 DT I -29 " pdb=" H6 DT I -29 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.62e+01 bond pdb=" N ALA E 91 " pdb=" H ALA E 91 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.61e+01 bond pdb=" C6 DT I 33 " pdb=" H6 DT I 33 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.61e+01 ... (remaining 24021 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.92: 43338 6.92 - 13.84: 243 13.84 - 20.76: 1 20.76 - 27.68: 1 27.68 - 34.60: 2 Bond angle restraints: 43585 Sorted by residual: angle pdb=" O5' DC I 70 " pdb=" C5' DC I 70 " pdb=" C4' DC I 70 " ideal model delta sigma weight residual 109.40 119.97 -10.57 8.00e-01 1.56e+00 1.75e+02 angle pdb=" O5' DT I 25 " pdb=" C5' DT I 25 " pdb=" C4' DT I 25 " ideal model delta sigma weight residual 109.40 119.24 -9.84 8.00e-01 1.56e+00 1.51e+02 angle pdb=" O5' DC I -58 " pdb=" C5' DC I -58 " pdb=" C4' DC I -58 " ideal model delta sigma weight residual 109.40 119.14 -9.74 8.00e-01 1.56e+00 1.48e+02 angle pdb=" N ARG F 17 " pdb=" CA ARG F 17 " pdb=" C ARG F 17 " ideal model delta sigma weight residual 110.61 125.19 -14.58 1.25e+00 6.40e-01 1.36e+02 angle pdb=" O5' DG J -58 " pdb=" C5' DG J -58 " pdb=" C4' DG J -58 " ideal model delta sigma weight residual 109.40 118.68 -9.28 8.00e-01 1.56e+00 1.35e+02 ... (remaining 43580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.20: 8346 35.20 - 70.39: 1622 70.39 - 105.59: 54 105.59 - 140.78: 0 140.78 - 175.98: 3 Dihedral angle restraints: 10025 sinusoidal: 7285 harmonic: 2740 Sorted by residual: dihedral pdb=" C ARG F 17 " pdb=" N ARG F 17 " pdb=" CA ARG F 17 " pdb=" CB ARG F 17 " ideal model delta harmonic sigma weight residual -122.60 -139.87 17.27 0 2.50e+00 1.60e-01 4.77e+01 dihedral pdb=" N ARG F 17 " pdb=" C ARG F 17 " pdb=" CA ARG F 17 " pdb=" CB ARG F 17 " ideal model delta harmonic sigma weight residual 122.80 138.75 -15.95 0 2.50e+00 1.60e-01 4.07e+01 dihedral pdb=" CA TYR H 37 " pdb=" C TYR H 37 " pdb=" N SER H 38 " pdb=" CA SER H 38 " ideal model delta harmonic sigma weight residual 180.00 -152.25 -27.75 0 5.00e+00 4.00e-02 3.08e+01 ... (remaining 10022 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.148: 2023 0.148 - 0.296: 193 0.296 - 0.444: 12 0.444 - 0.592: 3 0.592 - 0.739: 1 Chirality restraints: 2232 Sorted by residual: chirality pdb=" CA ARG F 17 " pdb=" N ARG F 17 " pdb=" C ARG F 17 " pdb=" CB ARG F 17 " both_signs ideal model delta sigma weight residual False 2.51 1.77 0.74 2.00e-01 2.50e+01 1.37e+01 chirality pdb=" C3' DG I -44 " pdb=" C4' DG I -44 " pdb=" O3' DG I -44 " pdb=" C2' DG I -44 " both_signs ideal model delta sigma weight residual False -2.73 -2.26 -0.47 2.00e-01 2.50e+01 5.53e+00 chirality pdb=" C3' DG I 20 " pdb=" C4' DG I 20 " pdb=" O3' DG I 20 " pdb=" C2' DG I 20 " both_signs ideal model delta sigma weight residual False -2.73 -2.27 -0.46 2.00e-01 2.50e+01 5.20e+00 ... (remaining 2229 not shown) Planarity restraints: 2501 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT J -39 " -0.444 2.00e-02 2.50e+03 1.92e-01 1.11e+03 pdb=" N1 DT J -39 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DT J -39 " 0.131 2.00e-02 2.50e+03 pdb=" O2 DT J -39 " 0.277 2.00e-02 2.50e+03 pdb=" N3 DT J -39 " 0.076 2.00e-02 2.50e+03 pdb=" C4 DT J -39 " -0.070 2.00e-02 2.50e+03 pdb=" O4 DT J -39 " -0.315 2.00e-02 2.50e+03 pdb=" C5 DT J -39 " 0.053 2.00e-02 2.50e+03 pdb=" C7 DT J -39 " 0.162 2.00e-02 2.50e+03 pdb=" C6 DT J -39 " 0.068 2.00e-02 2.50e+03 pdb=" H3 DT J -39 " -0.025 2.00e-02 2.50e+03 pdb=" H6 DT J -39 " 0.091 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT J -72 " 0.422 2.00e-02 2.50e+03 1.66e-01 8.27e+02 pdb=" N1 DT J -72 " -0.041 2.00e-02 2.50e+03 pdb=" C2 DT J -72 " -0.114 2.00e-02 2.50e+03 pdb=" O2 DT J -72 " -0.214 2.00e-02 2.50e+03 pdb=" N3 DT J -72 " -0.046 2.00e-02 2.50e+03 pdb=" C4 DT J -72 " 0.063 2.00e-02 2.50e+03 pdb=" O4 DT J -72 " 0.238 2.00e-02 2.50e+03 pdb=" C5 DT J -72 " -0.049 2.00e-02 2.50e+03 pdb=" C7 DT J -72 " -0.068 2.00e-02 2.50e+03 pdb=" C6 DT J -72 " -0.096 2.00e-02 2.50e+03 pdb=" H3 DT J -72 " 0.015 2.00e-02 2.50e+03 pdb=" H6 DT J -72 " -0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT J -47 " -0.306 2.00e-02 2.50e+03 1.59e-01 7.61e+02 pdb=" N1 DT J -47 " -0.067 2.00e-02 2.50e+03 pdb=" C2 DT J -47 " 0.081 2.00e-02 2.50e+03 pdb=" O2 DT J -47 " 0.347 2.00e-02 2.50e+03 pdb=" N3 DT J -47 " -0.064 2.00e-02 2.50e+03 pdb=" C4 DT J -47 " -0.086 2.00e-02 2.50e+03 pdb=" O4 DT J -47 " -0.167 2.00e-02 2.50e+03 pdb=" C5 DT J -47 " 0.021 2.00e-02 2.50e+03 pdb=" C7 DT J -47 " 0.181 2.00e-02 2.50e+03 pdb=" C6 DT J -47 " 0.024 2.00e-02 2.50e+03 pdb=" H3 DT J -47 " -0.035 2.00e-02 2.50e+03 pdb=" H6 DT J -47 " 0.070 2.00e-02 2.50e+03 ... (remaining 2498 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.16: 1099 2.16 - 2.77: 36051 2.77 - 3.38: 65221 3.38 - 3.99: 91349 3.99 - 4.60: 130381 Nonbonded interactions: 324101 Sorted by model distance: nonbonded pdb=" HG1 THR D 90 " pdb=" OE1 GLU D 93 " model vdw 1.556 2.450 nonbonded pdb=" HG1 THR H 90 " pdb=" OE1 GLU H 93 " model vdw 1.568 2.450 nonbonded pdb=" OP1 DA I 28 " pdb=" HG1 THR B 80 " model vdw 1.569 2.450 nonbonded pdb=" OP1 DG J 28 " pdb=" HG1 THR F 80 " model vdw 1.585 2.450 nonbonded pdb=" HG SER K 455 " pdb=" OD1 ASP K 457 " model vdw 1.592 2.450 ... (remaining 324096 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 'E' and resid 38 through 133) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 25 through 101) } ncs_group { reference = (chain 'C' and resid 15 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 33 through 123) 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: 1.060 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: 0.110 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 22.790 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 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 : 0.014 0.054 13590 Z= 1.342 Angle : 1.949 14.578 19596 Z= 1.965 Chirality : 0.092 0.739 2232 Planarity : 0.038 0.207 1456 Dihedral : 27.616 175.980 5861 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 0.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.56 % Allowed : 2.09 % Favored : 97.35 % Cbeta Deviations : 0.13 % 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: -0.81 (0.25), residues: 832 helix: -0.37 (0.18), residues: 582 sheet: None (None), residues: 0 loop : -0.57 (0.35), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 134 TYR 0.171 0.024 TYR A 41 PHE 0.063 0.017 PHE D 65 TRP 0.087 0.043 TRP K 481 HIS 0.018 0.004 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.01369 / 1.34 (13590) covalent geometry : angle 1.94944 / 1.97 (19596) hydrogen bonds : bond 0.11316 / 12.08 ( 815) hydrogen bonds : angle 6.37425 / 8.05 ( 2040) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 393 time to evaluate : 0.343 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash REVERT: A 51 ILE cc_start: 0.7354 (mt) cc_final: 0.6704 (mt) REVERT: A 60 LEU cc_start: 0.8464 (mt) cc_final: 0.6801 (mp) REVERT: A 117 VAL cc_start: 0.7217 (m) cc_final: 0.6973 (p) REVERT: D 99 ARG cc_start: 0.7331 (mtt180) cc_final: 0.7117 (tpp80) REVERT: E 60 LEU cc_start: 0.8481 (mt) cc_final: 0.8131 (mp) REVERT: F 98 TYR cc_start: 0.4467 (m-10) cc_final: 0.4262 (m-10) outliers start: 4 outliers final: 4 residues processed: 397 average time/residue: 0.2662 time to fit residues: 144.2391 Evaluate side-chains 314 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 310 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2526 r_free = 0.2526 target = 0.028263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2267 r_free = 0.2267 target = 0.021306 restraints weight = 246173.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2331 r_free = 0.2331 target = 0.023008 restraints weight = 73132.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2369 r_free = 0.2369 target = 0.024011 restraints weight = 33492.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2394 r_free = 0.2394 target = 0.024695 restraints weight = 19559.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2410 r_free = 0.2410 target = 0.025167 restraints weight = 13319.000| |-----------------------------------------------------------------------------| r_work (final): 0.2406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13590 Z= 0.278 Angle : 0.922 8.974 19596 Z= 0.554 Chirality : 0.052 0.373 2232 Planarity : 0.007 0.095 1456 Dihedral : 31.894 174.166 4153 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Cbeta Deviations : 0.13 % 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: -0.09 (0.26), residues: 832 helix: 0.45 (0.20), residues: 586 sheet: None (None), residues: 0 loop : -1.11 (0.34), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 128 TYR 0.019 0.002 TYR H 40 PHE 0.015 0.003 PHE H 65 TRP 0.007 0.003 TRP K 481 HIS 0.006 0.002 HIS K 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.28 (13590) covalent geometry : angle 0.92178 / 0.55 (19596) hydrogen bonds : bond 0.08124 / 9.20 ( 815) hydrogen bonds : angle 4.52621 / 5.76 ( 2040) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 356 time to evaluate : 0.510 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9349 (mp0) cc_final: 0.8996 (mp0) REVERT: A 76 GLN cc_start: 0.9287 (tm-30) cc_final: 0.8971 (tp-100) REVERT: A 81 ASP cc_start: 0.9243 (m-30) cc_final: 0.9019 (m-30) REVERT: A 90 MET cc_start: 0.9513 (mmt) cc_final: 0.9070 (mmm) REVERT: A 94 GLU cc_start: 0.9281 (mm-30) cc_final: 0.8766 (mm-30) REVERT: A 117 VAL cc_start: 0.8969 (m) cc_final: 0.8607 (p) REVERT: A 120 MET cc_start: 0.8024 (mtp) cc_final: 0.7817 (mtp) REVERT: C 115 LEU cc_start: 0.9368 (mt) cc_final: 0.9167 (mt) REVERT: D 47 GLN cc_start: 0.9519 (tm-30) cc_final: 0.9310 (tm-30) REVERT: D 62 MET cc_start: 0.9851 (mmp) cc_final: 0.9535 (mmm) REVERT: D 67 ASN cc_start: 0.9627 (m-40) cc_final: 0.9378 (m-40) REVERT: D 68 ASP cc_start: 0.9449 (t70) cc_final: 0.9234 (t0) REVERT: D 73 ILE cc_start: 0.9867 (mt) cc_final: 0.9592 (tp) REVERT: D 99 ARG cc_start: 0.9272 (mtt180) cc_final: 0.9060 (tpp80) REVERT: E 82 LEU cc_start: 0.9263 (mt) cc_final: 0.9051 (mt) REVERT: E 90 MET cc_start: 0.9368 (mmp) cc_final: 0.9074 (mmm) REVERT: E 93 GLN cc_start: 0.9673 (tt0) cc_final: 0.9307 (tm-30) REVERT: E 118 THR cc_start: 0.9042 (m) cc_final: 0.8782 (m) REVERT: E 120 MET cc_start: 0.8416 (mtt) cc_final: 0.8148 (mtp) REVERT: F 43 VAL cc_start: 0.9235 (t) cc_final: 0.8750 (m) REVERT: F 53 GLU cc_start: 0.9618 (tp30) cc_final: 0.9247 (tp30) REVERT: F 68 ASP cc_start: 0.9321 (m-30) cc_final: 0.8950 (m-30) REVERT: F 72 TYR cc_start: 0.9368 (m-10) cc_final: 0.9095 (m-10) REVERT: G 107 VAL cc_start: 0.8281 (m) cc_final: 0.7970 (m) REVERT: G 110 ASN cc_start: 0.9215 (t0) cc_final: 0.8920 (t0) REVERT: H 45 LEU cc_start: 0.9506 (tp) cc_final: 0.9281 (tp) REVERT: H 52 THR cc_start: 0.8747 (m) cc_final: 0.8205 (m) REVERT: H 62 MET cc_start: 0.9829 (mmm) cc_final: 0.9572 (mmm) REVERT: H 101 LEU cc_start: 0.9011 (mm) cc_final: 0.8743 (mm) REVERT: K 443 MET cc_start: 0.9345 (ppp) cc_final: 0.9123 (ppp) outliers start: 0 outliers final: 0 residues processed: 356 average time/residue: 0.2443 time to fit residues: 120.9500 Evaluate side-chains 315 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 315 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 106 optimal weight: 7.9990 chunk 90 optimal weight: 8.9990 chunk 96 optimal weight: 7.9990 chunk 42 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.027638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2286 r_free = 0.2286 target = 0.020849 restraints weight = 248513.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2348 r_free = 0.2348 target = 0.022440 restraints weight = 73095.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2387 r_free = 0.2387 target = 0.023413 restraints weight = 33486.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2412 r_free = 0.2412 target = 0.024090 restraints weight = 19520.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2429 r_free = 0.2429 target = 0.024534 restraints weight = 13178.655| |-----------------------------------------------------------------------------| r_work (final): 0.2405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 13590 Z= 0.275 Angle : 0.790 7.776 19596 Z= 0.493 Chirality : 0.048 0.359 2232 Planarity : 0.006 0.049 1456 Dihedral : 31.703 173.780 4153 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % 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: 0.04 (0.27), residues: 832 helix: 0.61 (0.20), residues: 584 sheet: -3.85 (1.31), residues: 10 loop : -1.08 (0.35), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 92 TYR 0.014 0.002 TYR H 40 PHE 0.039 0.003 PHE C 25 TRP 0.004 0.001 TRP K 481 HIS 0.010 0.001 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.28 (13590) covalent geometry : angle 0.78960 / 0.49 (19596) hydrogen bonds : bond 0.07061 / 7.97 ( 815) hydrogen bonds : angle 4.45808 / 5.77 ( 2040) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 0.390 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.9633 (t80) cc_final: 0.9408 (t80) REVERT: A 81 ASP cc_start: 0.9331 (m-30) cc_final: 0.9098 (m-30) REVERT: A 90 MET cc_start: 0.9528 (mmt) cc_final: 0.9149 (mmp) REVERT: A 94 GLU cc_start: 0.9518 (mm-30) cc_final: 0.9195 (mm-30) REVERT: C 25 PHE cc_start: 0.8869 (m-10) cc_final: 0.8384 (m-10) REVERT: C 56 GLU cc_start: 0.9041 (tt0) cc_final: 0.8649 (tt0) REVERT: D 62 MET cc_start: 0.9855 (mmp) cc_final: 0.9560 (mmm) REVERT: D 67 ASN cc_start: 0.9719 (m-40) cc_final: 0.9366 (m110) REVERT: D 73 ILE cc_start: 0.9831 (mt) cc_final: 0.9615 (tp) REVERT: D 101 LEU cc_start: 0.8577 (mm) cc_final: 0.8265 (mm) REVERT: E 90 MET cc_start: 0.9393 (mmp) cc_final: 0.9090 (mmm) REVERT: E 120 MET cc_start: 0.8403 (mtt) cc_final: 0.8092 (mtt) REVERT: F 53 GLU cc_start: 0.9652 (tp30) cc_final: 0.9270 (tp30) REVERT: G 110 ASN cc_start: 0.9165 (t0) cc_final: 0.8939 (t0) REVERT: H 39 ILE cc_start: 0.9560 (tp) cc_final: 0.9247 (pt) REVERT: H 45 LEU cc_start: 0.9471 (tp) cc_final: 0.9267 (tp) REVERT: H 62 MET cc_start: 0.9833 (mmm) cc_final: 0.9571 (mmm) REVERT: H 101 LEU cc_start: 0.9064 (mm) cc_final: 0.8754 (mm) outliers start: 0 outliers final: 0 residues processed: 342 average time/residue: 0.2535 time to fit residues: 121.9076 Evaluate side-chains 304 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 67 optimal weight: 7.9990 chunk 3 optimal weight: 20.0000 chunk 81 optimal weight: 1.9990 chunk 69 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 86 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 27 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 chunk 52 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.028150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2288 r_free = 0.2288 target = 0.021293 restraints weight = 242230.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2351 r_free = 0.2351 target = 0.022941 restraints weight = 71962.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2389 r_free = 0.2389 target = 0.023960 restraints weight = 33106.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2414 r_free = 0.2414 target = 0.024624 restraints weight = 19193.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2430 r_free = 0.2430 target = 0.025084 restraints weight = 13145.158| |-----------------------------------------------------------------------------| r_work (final): 0.2427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13590 Z= 0.188 Angle : 0.709 8.235 19596 Z= 0.449 Chirality : 0.045 0.351 2232 Planarity : 0.004 0.040 1456 Dihedral : 31.684 174.019 4153 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % 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: 0.85 (0.28), residues: 832 helix: 1.25 (0.21), residues: 591 sheet: -4.03 (1.11), residues: 10 loop : -0.93 (0.37), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 69 TYR 0.012 0.002 TYR H 37 PHE 0.020 0.002 PHE D 65 TRP 0.003 0.001 TRP K 481 HIS 0.006 0.001 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.19 (13590) covalent geometry : angle 0.70943 / 0.45 (19596) hydrogen bonds : bond 0.05511 / 6.11 ( 815) hydrogen bonds : angle 3.95270 / 5.15 ( 2040) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 345 time to evaluate : 0.411 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: symmetry clash REVERT: A 67 PHE cc_start: 0.9602 (t80) cc_final: 0.9397 (t80) REVERT: A 90 MET cc_start: 0.9526 (mmt) cc_final: 0.9297 (mmt) REVERT: A 94 GLU cc_start: 0.9491 (mm-30) cc_final: 0.9254 (mm-30) REVERT: C 25 PHE cc_start: 0.8854 (m-10) cc_final: 0.8359 (m-10) REVERT: C 56 GLU cc_start: 0.8948 (tt0) cc_final: 0.8510 (mt-10) REVERT: D 47 GLN cc_start: 0.9526 (tm-30) cc_final: 0.9291 (tm-30) REVERT: D 62 MET cc_start: 0.9853 (mmp) cc_final: 0.9545 (mmm) REVERT: D 73 ILE cc_start: 0.9828 (mt) cc_final: 0.9594 (tp) REVERT: E 90 MET cc_start: 0.9349 (mmp) cc_final: 0.9117 (mmm) REVERT: E 120 MET cc_start: 0.8391 (mtt) cc_final: 0.8056 (mtt) REVERT: E 129 ARG cc_start: 0.9507 (ttt180) cc_final: 0.9243 (mmm160) REVERT: F 43 VAL cc_start: 0.9226 (t) cc_final: 0.8796 (m) REVERT: F 53 GLU cc_start: 0.9635 (tp30) cc_final: 0.9246 (tp30) REVERT: F 68 ASP cc_start: 0.9210 (m-30) cc_final: 0.8812 (m-30) REVERT: F 72 TYR cc_start: 0.9178 (m-10) cc_final: 0.8735 (m-10) REVERT: H 45 LEU cc_start: 0.9452 (tp) cc_final: 0.9160 (tp) REVERT: H 62 MET cc_start: 0.9825 (mmm) cc_final: 0.9588 (mmm) REVERT: K 443 MET cc_start: 0.9127 (ppp) cc_final: 0.8792 (ppp) outliers start: 0 outliers final: 0 residues processed: 345 average time/residue: 0.2384 time to fit residues: 116.1463 Evaluate side-chains 311 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 311 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 61 optimal weight: 0.1980 chunk 8 optimal weight: 20.0000 chunk 69 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.028517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2296 r_free = 0.2296 target = 0.021623 restraints weight = 241294.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2357 r_free = 0.2357 target = 0.023262 restraints weight = 72495.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2395 r_free = 0.2395 target = 0.024300 restraints weight = 33694.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2421 r_free = 0.2421 target = 0.024991 restraints weight = 19574.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2437 r_free = 0.2437 target = 0.025442 restraints weight = 13249.094| |-----------------------------------------------------------------------------| r_work (final): 0.2429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.4749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13590 Z= 0.185 Angle : 0.710 9.822 19596 Z= 0.443 Chirality : 0.044 0.350 2232 Planarity : 0.004 0.039 1456 Dihedral : 31.630 173.065 4153 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.28), residues: 832 helix: 1.40 (0.21), residues: 589 sheet: -4.05 (1.06), residues: 10 loop : -0.95 (0.37), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 29 TYR 0.026 0.002 TYR H 42 PHE 0.017 0.002 PHE H 65 TRP 0.002 0.001 TRP K 481 HIS 0.006 0.001 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.19 (13590) covalent geometry : angle 0.70956 / 0.44 (19596) hydrogen bonds : bond 0.05342 / 5.95 ( 815) hydrogen bonds : angle 3.87847 / 5.08 ( 2040) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 346 time to evaluate : 0.515 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.9612 (t80) cc_final: 0.9390 (t80) REVERT: A 90 MET cc_start: 0.9518 (mmt) cc_final: 0.9301 (mmt) REVERT: A 94 GLU cc_start: 0.9487 (mm-30) cc_final: 0.9284 (mm-30) REVERT: C 25 PHE cc_start: 0.8739 (m-10) cc_final: 0.8460 (m-10) REVERT: C 56 GLU cc_start: 0.8912 (tt0) cc_final: 0.8559 (tt0) REVERT: D 47 GLN cc_start: 0.9524 (tm-30) cc_final: 0.9293 (tm-30) REVERT: D 62 MET cc_start: 0.9851 (mmp) cc_final: 0.9554 (mmm) REVERT: D 67 ASN cc_start: 0.9755 (t0) cc_final: 0.9133 (t0) REVERT: D 70 PHE cc_start: 0.9755 (t80) cc_final: 0.9550 (t80) REVERT: D 73 ILE cc_start: 0.9845 (mt) cc_final: 0.9564 (tp) REVERT: D 113 GLU cc_start: 0.9277 (mt-10) cc_final: 0.8979 (mt-10) REVERT: E 90 MET cc_start: 0.9346 (mmp) cc_final: 0.9136 (mmm) REVERT: E 120 MET cc_start: 0.8403 (mtt) cc_final: 0.8062 (mtt) REVERT: E 129 ARG cc_start: 0.9516 (ttt180) cc_final: 0.9248 (mmm160) REVERT: F 43 VAL cc_start: 0.9244 (t) cc_final: 0.8900 (m) REVERT: F 53 GLU cc_start: 0.9647 (tp30) cc_final: 0.9264 (tp30) REVERT: F 68 ASP cc_start: 0.9184 (m-30) cc_final: 0.8798 (m-30) REVERT: F 72 TYR cc_start: 0.9168 (m-10) cc_final: 0.8735 (m-10) REVERT: F 74 GLU cc_start: 0.9420 (mm-30) cc_final: 0.9079 (mm-30) REVERT: G 110 ASN cc_start: 0.9245 (t0) cc_final: 0.9043 (t0) REVERT: H 39 ILE cc_start: 0.9464 (tp) cc_final: 0.9128 (pt) REVERT: H 45 LEU cc_start: 0.9489 (tp) cc_final: 0.9250 (tp) REVERT: H 62 MET cc_start: 0.9842 (mmm) cc_final: 0.9599 (mmm) REVERT: K 443 MET cc_start: 0.9147 (ppp) cc_final: 0.8921 (ppp) outliers start: 0 outliers final: 0 residues processed: 346 average time/residue: 0.2457 time to fit residues: 119.3416 Evaluate side-chains 307 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 107 optimal weight: 9.9990 chunk 79 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 84 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 chunk 1 optimal weight: 20.0000 chunk 76 optimal weight: 0.7980 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2517 r_free = 0.2517 target = 0.027370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2265 r_free = 0.2265 target = 0.020679 restraints weight = 252198.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2326 r_free = 0.2326 target = 0.022253 restraints weight = 75189.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2363 r_free = 0.2363 target = 0.023236 restraints weight = 34794.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2387 r_free = 0.2387 target = 0.023876 restraints weight = 20326.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2403 r_free = 0.2403 target = 0.024297 restraints weight = 14014.725| |-----------------------------------------------------------------------------| r_work (final): 0.2403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.5036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 13590 Z= 0.269 Angle : 0.728 8.808 19596 Z= 0.456 Chirality : 0.044 0.349 2232 Planarity : 0.004 0.042 1456 Dihedral : 31.523 173.699 4153 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % 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: 0.40 (0.27), residues: 832 helix: 0.94 (0.20), residues: 581 sheet: -3.49 (1.60), residues: 10 loop : -1.09 (0.35), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG G 29 TYR 0.012 0.002 TYR C 39 PHE 0.011 0.002 PHE F 61 TRP 0.005 0.002 TRP K 481 HIS 0.006 0.001 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.27 (13590) covalent geometry : angle 0.72831 / 0.46 (19596) hydrogen bonds : bond 0.06561 / 7.31 ( 815) hydrogen bonds : angle 4.31048 / 5.62 ( 2040) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 336 time to evaluate : 0.411 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.9590 (t80) cc_final: 0.9365 (t80) REVERT: A 90 MET cc_start: 0.9560 (mmt) cc_final: 0.9164 (mmp) REVERT: C 25 PHE cc_start: 0.8760 (m-10) cc_final: 0.8392 (m-10) REVERT: C 56 GLU cc_start: 0.9029 (tt0) cc_final: 0.8646 (tt0) REVERT: D 62 MET cc_start: 0.9873 (mmp) cc_final: 0.9581 (mmm) REVERT: D 67 ASN cc_start: 0.9538 (t0) cc_final: 0.9161 (t0) REVERT: D 71 GLU cc_start: 0.9607 (mm-30) cc_final: 0.9277 (mm-30) REVERT: D 73 ILE cc_start: 0.9869 (mt) cc_final: 0.9599 (tp) REVERT: D 113 GLU cc_start: 0.9378 (mt-10) cc_final: 0.9055 (mt-10) REVERT: E 82 LEU cc_start: 0.9467 (mt) cc_final: 0.9229 (mt) REVERT: E 90 MET cc_start: 0.9375 (mmp) cc_final: 0.9088 (mmm) REVERT: E 119 ILE cc_start: 0.9019 (pt) cc_final: 0.8715 (pt) REVERT: E 120 MET cc_start: 0.8448 (mtt) cc_final: 0.8094 (mtt) REVERT: F 53 GLU cc_start: 0.9687 (tp30) cc_final: 0.9293 (tp30) REVERT: F 84 MET cc_start: 0.9379 (tpt) cc_final: 0.8993 (tpp) REVERT: H 39 ILE cc_start: 0.9490 (tp) cc_final: 0.9153 (pt) REVERT: H 45 LEU cc_start: 0.9542 (tp) cc_final: 0.9339 (tp) REVERT: H 62 MET cc_start: 0.9865 (mmm) cc_final: 0.9613 (mmm) REVERT: H 101 LEU cc_start: 0.9078 (mm) cc_final: 0.8689 (mm) REVERT: K 411 MET cc_start: 0.7813 (ttp) cc_final: 0.7308 (ttp) REVERT: K 413 GLU cc_start: 0.9768 (tp30) cc_final: 0.9550 (pp20) outliers start: 0 outliers final: 0 residues processed: 336 average time/residue: 0.2371 time to fit residues: 112.1370 Evaluate side-chains 297 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 27 optimal weight: 20.0000 chunk 67 optimal weight: 9.9990 chunk 66 optimal weight: 0.7980 chunk 88 optimal weight: 10.0000 chunk 24 optimal weight: 20.0000 chunk 49 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 106 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 22 optimal weight: 20.0000 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2541 r_free = 0.2541 target = 0.027994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2289 r_free = 0.2289 target = 0.021166 restraints weight = 245491.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2351 r_free = 0.2351 target = 0.022791 restraints weight = 72475.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2389 r_free = 0.2389 target = 0.023809 restraints weight = 33513.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2414 r_free = 0.2414 target = 0.024462 restraints weight = 19471.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2429 r_free = 0.2429 target = 0.024902 restraints weight = 13373.740| |-----------------------------------------------------------------------------| r_work (final): 0.2429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.5259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13590 Z= 0.202 Angle : 0.693 8.921 19596 Z= 0.436 Chirality : 0.044 0.347 2232 Planarity : 0.004 0.041 1456 Dihedral : 31.516 173.594 4153 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.28), residues: 832 helix: 1.20 (0.21), residues: 586 sheet: -4.09 (1.24), residues: 10 loop : -1.06 (0.36), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 29 TYR 0.017 0.002 TYR H 42 PHE 0.016 0.002 PHE D 70 TRP 0.004 0.001 TRP K 481 HIS 0.006 0.001 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.20 (13590) covalent geometry : angle 0.69298 / 0.44 (19596) hydrogen bonds : bond 0.05550 / 6.15 ( 815) hydrogen bonds : angle 4.06274 / 5.33 ( 2040) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 334 time to evaluate : 0.320 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.9575 (t80) cc_final: 0.9335 (t80) REVERT: A 90 MET cc_start: 0.9543 (mmt) cc_final: 0.9148 (mmp) REVERT: B 29 ILE cc_start: 0.9529 (mm) cc_final: 0.9272 (tp) REVERT: D 47 GLN cc_start: 0.9560 (tm-30) cc_final: 0.9338 (tm-30) REVERT: D 62 MET cc_start: 0.9866 (mmp) cc_final: 0.9558 (mmm) REVERT: D 67 ASN cc_start: 0.9540 (t0) cc_final: 0.9181 (t0) REVERT: D 70 PHE cc_start: 0.9751 (t80) cc_final: 0.9543 (t80) REVERT: D 71 GLU cc_start: 0.9598 (mm-30) cc_final: 0.9303 (mm-30) REVERT: D 73 ILE cc_start: 0.9871 (mt) cc_final: 0.9584 (tp) REVERT: D 113 GLU cc_start: 0.9359 (mt-10) cc_final: 0.9037 (mt-10) REVERT: E 82 LEU cc_start: 0.9440 (mt) cc_final: 0.9193 (mt) REVERT: F 53 GLU cc_start: 0.9683 (tp30) cc_final: 0.9306 (tp30) REVERT: F 74 GLU cc_start: 0.9501 (mm-30) cc_final: 0.9165 (mm-30) REVERT: F 84 MET cc_start: 0.9345 (tpt) cc_final: 0.8957 (tpp) REVERT: H 39 ILE cc_start: 0.9468 (tp) cc_final: 0.9152 (pt) REVERT: H 45 LEU cc_start: 0.9539 (tp) cc_final: 0.9334 (tp) REVERT: H 62 MET cc_start: 0.9864 (mmm) cc_final: 0.9609 (mmm) REVERT: H 101 LEU cc_start: 0.9021 (mm) cc_final: 0.8800 (mm) REVERT: H 105 GLU cc_start: 0.9698 (mp0) cc_final: 0.9485 (mp0) REVERT: K 411 MET cc_start: 0.7926 (ttp) cc_final: 0.7397 (ttp) REVERT: K 413 GLU cc_start: 0.9752 (tp30) cc_final: 0.9524 (pp20) outliers start: 0 outliers final: 0 residues processed: 334 average time/residue: 0.2406 time to fit residues: 113.3269 Evaluate side-chains 301 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 15 optimal weight: 20.0000 chunk 7 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 109 HIS ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.027384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2271 r_free = 0.2271 target = 0.020765 restraints weight = 255055.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2332 r_free = 0.2332 target = 0.022362 restraints weight = 77153.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2371 r_free = 0.2371 target = 0.023370 restraints weight = 35838.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2396 r_free = 0.2396 target = 0.024017 restraints weight = 20835.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2412 r_free = 0.2412 target = 0.024456 restraints weight = 14212.765| |-----------------------------------------------------------------------------| r_work (final): 0.2404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.5508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 13590 Z= 0.281 Angle : 0.732 9.077 19596 Z= 0.459 Chirality : 0.044 0.350 2232 Planarity : 0.005 0.043 1456 Dihedral : 31.439 174.008 4153 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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: -0.10 (0.27), residues: 832 helix: 0.56 (0.20), residues: 582 sheet: -4.70 (1.00), residues: 10 loop : -1.22 (0.35), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 42 TYR 0.022 0.002 TYR F 72 PHE 0.013 0.002 PHE C 25 TRP 0.006 0.002 TRP K 481 HIS 0.006 0.001 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.28 (13590) covalent geometry : angle 0.73183 / 0.46 (19596) hydrogen bonds : bond 0.06878 / 7.62 ( 815) hydrogen bonds : angle 4.45004 / 5.80 ( 2040) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 324 time to evaluate : 0.408 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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 67 PHE cc_start: 0.9584 (t80) cc_final: 0.9334 (t80) REVERT: A 90 MET cc_start: 0.9488 (mmt) cc_final: 0.9123 (mmp) REVERT: B 29 ILE cc_start: 0.9474 (mm) cc_final: 0.9215 (tp) REVERT: B 74 GLU cc_start: 0.9577 (tp30) cc_final: 0.9296 (tp30) REVERT: C 25 PHE cc_start: 0.9172 (m-10) cc_final: 0.8498 (m-10) REVERT: D 62 MET cc_start: 0.9870 (mmp) cc_final: 0.9581 (mmm) REVERT: D 67 ASN cc_start: 0.9523 (t0) cc_final: 0.9202 (t0) REVERT: D 71 GLU cc_start: 0.9621 (mm-30) cc_final: 0.9325 (mm-30) REVERT: D 73 ILE cc_start: 0.9879 (mt) cc_final: 0.9599 (tp) REVERT: D 113 GLU cc_start: 0.9343 (mt-10) cc_final: 0.9010 (mt-10) REVERT: E 120 MET cc_start: 0.8468 (mtt) cc_final: 0.8133 (mtt) REVERT: F 43 VAL cc_start: 0.9382 (t) cc_final: 0.9082 (m) REVERT: F 53 GLU cc_start: 0.9717 (tp30) cc_final: 0.9374 (tp30) REVERT: F 74 GLU cc_start: 0.9531 (mm-30) cc_final: 0.9214 (mm-30) REVERT: F 84 MET cc_start: 0.9401 (tpt) cc_final: 0.8997 (tpp) REVERT: H 39 ILE cc_start: 0.9510 (tp) cc_final: 0.9188 (pt) REVERT: H 62 MET cc_start: 0.9863 (mmm) cc_final: 0.9652 (mmm) REVERT: K 403 ARG cc_start: 0.4353 (ptp-170) cc_final: 0.4081 (ptm160) REVERT: K 411 MET cc_start: 0.7826 (ttp) cc_final: 0.7313 (ttp) REVERT: K 413 GLU cc_start: 0.9748 (tp30) cc_final: 0.9533 (pp20) outliers start: 0 outliers final: 0 residues processed: 324 average time/residue: 0.2251 time to fit residues: 103.6123 Evaluate side-chains 289 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 7 optimal weight: 20.0000 chunk 59 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 chunk 86 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 chunk 6 optimal weight: 20.0000 chunk 36 optimal weight: 0.7980 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2535 r_free = 0.2535 target = 0.027766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2280 r_free = 0.2280 target = 0.020986 restraints weight = 250090.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2341 r_free = 0.2341 target = 0.022584 restraints weight = 74585.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2380 r_free = 0.2380 target = 0.023597 restraints weight = 34563.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2406 r_free = 0.2406 target = 0.024262 restraints weight = 20205.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2421 r_free = 0.2421 target = 0.024674 restraints weight = 13860.435| |-----------------------------------------------------------------------------| r_work (final): 0.2426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.5585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 13590 Z= 0.206 Angle : 0.681 9.095 19596 Z= 0.432 Chirality : 0.043 0.351 2232 Planarity : 0.004 0.041 1456 Dihedral : 31.450 174.230 4153 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.28), residues: 832 helix: 1.03 (0.21), residues: 586 sheet: -4.89 (0.92), residues: 10 loop : -1.19 (0.36), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 45 TYR 0.019 0.002 TYR F 72 PHE 0.010 0.002 PHE B 61 TRP 0.005 0.001 TRP K 481 HIS 0.006 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.21 (13590) covalent geometry : angle 0.68057 / 0.43 (19596) hydrogen bonds : bond 0.05669 / 6.27 ( 815) hydrogen bonds : angle 4.12917 / 5.41 ( 2040) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 328 time to evaluate : 0.381 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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 67 PHE cc_start: 0.9582 (t80) cc_final: 0.9359 (t80) REVERT: A 124 ILE cc_start: 0.9671 (mp) cc_final: 0.9348 (mp) REVERT: B 29 ILE cc_start: 0.9524 (mm) cc_final: 0.9276 (tp) REVERT: B 53 GLU cc_start: 0.9572 (tp30) cc_final: 0.8903 (tt0) REVERT: D 62 MET cc_start: 0.9860 (mmp) cc_final: 0.9570 (mmm) REVERT: D 65 PHE cc_start: 0.9687 (t80) cc_final: 0.9433 (t80) REVERT: D 71 GLU cc_start: 0.9622 (mm-30) cc_final: 0.9283 (mm-30) REVERT: D 73 ILE cc_start: 0.9873 (mt) cc_final: 0.9583 (tp) REVERT: D 113 GLU cc_start: 0.9328 (mt-10) cc_final: 0.8970 (mt-10) REVERT: E 82 LEU cc_start: 0.9226 (mt) cc_final: 0.8908 (mt) REVERT: E 90 MET cc_start: 0.9376 (mmp) cc_final: 0.9074 (mmm) REVERT: E 120 MET cc_start: 0.8500 (mtt) cc_final: 0.8123 (mtt) REVERT: F 43 VAL cc_start: 0.9433 (t) cc_final: 0.9094 (m) REVERT: F 53 GLU cc_start: 0.9717 (tp30) cc_final: 0.9359 (tp30) REVERT: F 74 GLU cc_start: 0.9549 (mm-30) cc_final: 0.9218 (mm-30) REVERT: F 84 MET cc_start: 0.9369 (tpt) cc_final: 0.8969 (tpp) REVERT: G 110 ASN cc_start: 0.9388 (t0) cc_final: 0.8913 (m110) REVERT: H 39 ILE cc_start: 0.9511 (tp) cc_final: 0.9176 (pt) REVERT: H 62 MET cc_start: 0.9840 (mmm) cc_final: 0.9626 (mmm) REVERT: H 105 GLU cc_start: 0.9696 (mp0) cc_final: 0.9428 (mp0) REVERT: K 411 MET cc_start: 0.7771 (ttp) cc_final: 0.7108 (ttt) REVERT: K 413 GLU cc_start: 0.9750 (tp30) cc_final: 0.9540 (pp20) outliers start: 0 outliers final: 0 residues processed: 328 average time/residue: 0.2337 time to fit residues: 107.4910 Evaluate side-chains 292 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 292 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 66 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 79 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 16 optimal weight: 20.0000 chunk 75 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.028194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2294 r_free = 0.2294 target = 0.021328 restraints weight = 246294.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2356 r_free = 0.2356 target = 0.022950 restraints weight = 73636.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2396 r_free = 0.2396 target = 0.023985 restraints weight = 34016.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2421 r_free = 0.2421 target = 0.024640 restraints weight = 19869.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2437 r_free = 0.2437 target = 0.025076 restraints weight = 13744.276| |-----------------------------------------------------------------------------| r_work (final): 0.2440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.5684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 13590 Z= 0.185 Angle : 0.671 9.060 19596 Z= 0.424 Chirality : 0.043 0.348 2232 Planarity : 0.004 0.037 1456 Dihedral : 31.449 174.229 4153 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.28), residues: 832 helix: 1.35 (0.21), residues: 586 sheet: -4.79 (0.98), residues: 10 loop : -1.14 (0.36), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 79 TYR 0.018 0.002 TYR B 51 PHE 0.021 0.002 PHE E 104 TRP 0.003 0.001 TRP K 481 HIS 0.005 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.18 (13590) covalent geometry : angle 0.67119 / 0.42 (19596) hydrogen bonds : bond 0.05213 / 5.76 ( 815) hydrogen bonds : angle 3.95033 / 5.14 ( 2040) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 326 time to evaluate : 0.407 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.9572 (t80) cc_final: 0.9363 (t80) REVERT: A 124 ILE cc_start: 0.9668 (mp) cc_final: 0.9341 (mp) REVERT: B 29 ILE cc_start: 0.9540 (mm) cc_final: 0.9302 (tp) REVERT: B 53 GLU cc_start: 0.9558 (tp30) cc_final: 0.8900 (tt0) REVERT: B 74 GLU cc_start: 0.9568 (tp30) cc_final: 0.9273 (tp30) REVERT: C 25 PHE cc_start: 0.9073 (m-10) cc_final: 0.8588 (m-10) REVERT: D 62 MET cc_start: 0.9870 (mmp) cc_final: 0.9566 (mmm) REVERT: D 71 GLU cc_start: 0.9604 (mm-30) cc_final: 0.9247 (mm-30) REVERT: D 73 ILE cc_start: 0.9866 (mt) cc_final: 0.9565 (tp) REVERT: D 113 GLU cc_start: 0.9338 (mt-10) cc_final: 0.9006 (mt-10) REVERT: E 82 LEU cc_start: 0.9239 (mt) cc_final: 0.8879 (mt) REVERT: E 110 CYS cc_start: 0.9471 (m) cc_final: 0.8647 (t) REVERT: F 43 VAL cc_start: 0.9448 (t) cc_final: 0.9113 (m) REVERT: F 53 GLU cc_start: 0.9713 (tp30) cc_final: 0.9329 (tp30) REVERT: F 74 GLU cc_start: 0.9552 (mm-30) cc_final: 0.9212 (mm-30) REVERT: F 84 MET cc_start: 0.9352 (tpt) cc_final: 0.8973 (tpp) REVERT: H 39 ILE cc_start: 0.9513 (tp) cc_final: 0.9164 (pt) REVERT: H 105 GLU cc_start: 0.9682 (mp0) cc_final: 0.9471 (mp0) REVERT: K 411 MET cc_start: 0.7857 (ttp) cc_final: 0.7227 (ttt) REVERT: K 413 GLU cc_start: 0.9751 (tp30) cc_final: 0.9533 (pp20) outliers start: 0 outliers final: 0 residues processed: 326 average time/residue: 0.2289 time to fit residues: 105.5428 Evaluate side-chains 295 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 5 optimal weight: 20.0000 chunk 10 optimal weight: 20.0000 chunk 77 optimal weight: 0.7980 chunk 14 optimal weight: 20.0000 chunk 40 optimal weight: 7.9990 chunk 101 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 24 optimal weight: 20.0000 chunk 51 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.027758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2277 r_free = 0.2277 target = 0.021041 restraints weight = 252087.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2338 r_free = 0.2338 target = 0.022634 restraints weight = 76271.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2378 r_free = 0.2378 target = 0.023619 restraints weight = 35692.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2404 r_free = 0.2404 target = 0.024304 restraints weight = 21146.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2420 r_free = 0.2420 target = 0.024732 restraints weight = 14386.677| |-----------------------------------------------------------------------------| r_work (final): 0.2420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.5814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 13590 Z= 0.238 Angle : 0.687 9.083 19596 Z= 0.434 Chirality : 0.042 0.348 2232 Planarity : 0.004 0.042 1456 Dihedral : 31.404 175.002 4153 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.27), residues: 832 helix: 0.99 (0.20), residues: 584 sheet: -4.89 (0.97), residues: 10 loop : -1.19 (0.36), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 131 TYR 0.015 0.002 TYR C 39 PHE 0.014 0.002 PHE C 25 TRP 0.005 0.001 TRP K 481 HIS 0.006 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.24 (13590) covalent geometry : angle 0.68714 / 0.43 (19596) hydrogen bonds : bond 0.06050 / 6.71 ( 815) hydrogen bonds : angle 4.20480 / 5.44 ( 2040) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3878.55 seconds wall clock time: 67 minutes 13.09 seconds (4033.09 seconds total)