Starting phenix.real_space_refine on Thu Mar 5 13:06:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7scy_25042/03_2026/7scy_25042.cif Found real_map, /net/cci-nas-00/data/ceres_data/7scy_25042/03_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_25042/03_2026/7scy_25042.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7scy_25042/03_2026/7scy_25042.map" model { file = "/net/cci-nas-00/data/ceres_data/7scy_25042/03_2026/7scy_25042.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7scy_25042/03_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.87, per 1000 atoms: 0.17 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: 2.17 Conformation dependent library (CDL) restraints added in 617.3 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: 4.97 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: 5.83 Time building geometry restraints manager: 3.05 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: 43372 6.92 - 13.84: 209 13.84 - 20.76: 1 20.76 - 27.68: 1 27.68 - 34.60: 2 Bond angle restraints: 43585 Sorted by residual: 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=" C ARG F 17 " pdb=" CA ARG F 17 " pdb=" HA ARG F 17 " ideal model delta sigma weight residual 109.00 74.40 34.60 3.00e+00 1.11e-01 1.33e+02 angle pdb=" N ARG F 17 " pdb=" CA ARG F 17 " pdb=" HA ARG F 17 " ideal model delta sigma weight residual 110.00 77.76 32.24 3.00e+00 1.11e-01 1.15e+02 angle pdb=" CB ARG F 17 " pdb=" CA ARG F 17 " pdb=" HA ARG F 17 " ideal model delta sigma weight residual 109.00 84.22 24.78 3.00e+00 1.11e-01 6.83e+01 angle pdb=" O3' DT J -47 " pdb=" C3' DT J -47 " pdb=" C2' DT J -47 " ideal model delta sigma weight residual 111.50 121.91 -10.41 1.50e+00 4.44e-01 4.82e+01 ... (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: 2053 0.148 - 0.296: 165 0.296 - 0.444: 13 0.444 - 0.592: 0 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=" C4' DT I -67 " pdb=" C5' DT I -67 " pdb=" O4' DT I -67 " pdb=" C3' DT I -67 " both_signs ideal model delta sigma weight residual False -2.53 -2.08 -0.44 2.00e-01 2.50e+01 4.89e+00 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 -2.66 -2.26 -0.40 2.00e-01 2.50e+01 4.00e+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: 1.660 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: 0.140 Extract box with map and model: 0.360 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 26.400 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 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= 0.749 Angle : 1.934 14.578 19596 Z= 1.278 Chirality : 0.088 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 covalent geometry : bond 0.01355 (13590) covalent geometry : angle 1.93431 (19596) hydrogen bonds : bond 0.11316 ( 815) hydrogen bonds : angle 6.37425 ( 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 : 0.476 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: symmetry clash revert: symmetry clash REVERT: A 51 ILE cc_start: 0.7354 (mt) cc_final: 0.6662 (mt) REVERT: A 60 LEU cc_start: 0.8464 (mt) cc_final: 0.6795 (mp) REVERT: A 117 VAL cc_start: 0.7217 (m) cc_final: 0.6959 (p) REVERT: D 99 ARG cc_start: 0.7331 (mtt180) cc_final: 0.7104 (tpp80) REVERT: E 60 LEU cc_start: 0.8481 (mt) cc_final: 0.8231 (mp) REVERT: F 98 TYR cc_start: 0.4467 (m-10) cc_final: 0.4255 (m-10) outliers start: 4 outliers final: 4 residues processed: 397 average time/residue: 0.2823 time to fit residues: 149.0859 Evaluate side-chains 317 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 313 time to evaluate : 0.370 ------------------------------------------------------------------------------- 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: 1.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2517 r_free = 0.2517 target = 0.027628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2249 r_free = 0.2249 target = 0.020557 restraints weight = 247218.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2312 r_free = 0.2312 target = 0.022194 restraints weight = 73625.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2352 r_free = 0.2352 target = 0.023210 restraints weight = 34244.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2377 r_free = 0.2377 target = 0.023884 restraints weight = 20134.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2393 r_free = 0.2393 target = 0.024301 restraints weight = 13743.825| |-----------------------------------------------------------------------------| r_work (final): 0.2384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 13590 Z= 0.296 Angle : 0.744 5.200 19596 Z= 0.461 Chirality : 0.047 0.358 2232 Planarity : 0.005 0.039 1456 Dihedral : 31.461 171.770 4153 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.14 % Allowed : 1.82 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.26), residues: 832 helix: 0.77 (0.20), residues: 585 sheet: -3.02 (1.47), residues: 10 loop : -0.92 (0.35), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 128 TYR 0.019 0.002 TYR G 57 PHE 0.015 0.002 PHE H 65 TRP 0.005 0.002 TRP K 481 HIS 0.005 0.001 HIS G 82 Details of bonding type rmsd covalent geometry : bond 0.00584 (13590) covalent geometry : angle 0.74406 (19596) hydrogen bonds : bond 0.06592 ( 815) hydrogen bonds : angle 4.20112 ( 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 362 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 361 time to evaluate : 0.456 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: A 59 GLU cc_start: 0.9456 (mp0) cc_final: 0.9087 (mp0) REVERT: A 67 PHE cc_start: 0.9621 (t80) cc_final: 0.9397 (t80) REVERT: A 81 ASP cc_start: 0.9261 (m-30) cc_final: 0.9035 (m-30) REVERT: A 84 PHE cc_start: 0.9454 (m-80) cc_final: 0.9215 (m-80) REVERT: A 117 VAL cc_start: 0.8943 (m) cc_final: 0.8600 (p) REVERT: B 80 THR cc_start: 0.9282 (m) cc_final: 0.9079 (m) REVERT: C 25 PHE cc_start: 0.9002 (m-10) cc_final: 0.8784 (m-10) REVERT: C 61 GLU cc_start: 0.9209 (tp30) cc_final: 0.8942 (tp30) REVERT: C 115 LEU cc_start: 0.9354 (mt) cc_final: 0.9149 (mt) REVERT: D 37 TYR cc_start: 0.9211 (m-10) cc_final: 0.8819 (m-10) REVERT: D 47 GLN cc_start: 0.9512 (tm-30) cc_final: 0.9305 (tm-30) REVERT: D 62 MET cc_start: 0.9857 (mmp) cc_final: 0.9588 (mmm) REVERT: D 73 ILE cc_start: 0.9873 (mt) cc_final: 0.9641 (tp) REVERT: D 99 ARG cc_start: 0.9261 (mtt180) cc_final: 0.9051 (tpp80) REVERT: E 82 LEU cc_start: 0.9253 (mt) cc_final: 0.9025 (mt) REVERT: E 96 CYS cc_start: 0.9718 (m) cc_final: 0.9158 (p) REVERT: E 120 MET cc_start: 0.8473 (mtt) cc_final: 0.8077 (mtt) REVERT: E 129 ARG cc_start: 0.9504 (ttt180) cc_final: 0.9263 (mmm160) REVERT: F 43 VAL cc_start: 0.9346 (t) cc_final: 0.8924 (m) REVERT: F 53 GLU cc_start: 0.9644 (tp30) cc_final: 0.9234 (tp30) REVERT: F 68 ASP cc_start: 0.9323 (m-30) cc_final: 0.9102 (m-30) REVERT: G 102 ILE cc_start: 0.9224 (mp) cc_final: 0.8891 (tp) REVERT: G 110 ASN cc_start: 0.9277 (t0) cc_final: 0.9046 (t0) REVERT: H 39 ILE cc_start: 0.9565 (tp) cc_final: 0.9240 (pt) REVERT: H 45 LEU cc_start: 0.9461 (tp) cc_final: 0.9252 (tp) REVERT: H 52 THR cc_start: 0.8661 (m) cc_final: 0.8094 (m) REVERT: H 59 MET cc_start: 0.9019 (tpp) cc_final: 0.8773 (tpp) REVERT: H 62 MET cc_start: 0.9832 (mmm) cc_final: 0.9571 (mmm) outliers start: 1 outliers final: 1 residues processed: 361 average time/residue: 0.2662 time to fit residues: 129.9799 Evaluate side-chains 326 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 325 time to evaluate : 0.473 ------------------------------------------------------------------------------- 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: 8.9990 chunk 90 optimal weight: 7.9990 chunk 96 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 85 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 109 HIS H 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2464 r_free = 0.2464 target = 0.026389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2195 r_free = 0.2195 target = 0.019523 restraints weight = 257596.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2257 r_free = 0.2257 target = 0.021076 restraints weight = 76536.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2294 r_free = 0.2294 target = 0.022028 restraints weight = 35827.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2318 r_free = 0.2318 target = 0.022661 restraints weight = 21362.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2334 r_free = 0.2334 target = 0.023039 restraints weight = 14913.721| |-----------------------------------------------------------------------------| r_work (final): 0.2330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.4836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.096 13590 Z= 0.374 Angle : 0.744 5.197 19596 Z= 0.467 Chirality : 0.049 0.356 2232 Planarity : 0.006 0.063 1456 Dihedral : 31.157 171.589 4153 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.28 (0.26), residues: 832 helix: 0.39 (0.20), residues: 578 sheet: -3.87 (1.11), residues: 10 loop : -1.22 (0.35), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 45 TYR 0.021 0.002 TYR F 88 PHE 0.032 0.003 PHE C 25 TRP 0.010 0.003 TRP K 481 HIS 0.010 0.002 HIS G 82 Details of bonding type rmsd covalent geometry : bond 0.00739 (13590) covalent geometry : angle 0.74437 (19596) hydrogen bonds : bond 0.07291 ( 815) hydrogen bonds : angle 4.62444 ( 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 333 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 333 time to evaluate : 0.448 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: A 60 LEU cc_start: 0.8132 (mt) cc_final: 0.7910 (mt) REVERT: A 67 PHE cc_start: 0.9693 (t80) cc_final: 0.9407 (t80) REVERT: A 84 PHE cc_start: 0.9426 (m-80) cc_final: 0.9205 (m-80) REVERT: A 90 MET cc_start: 0.9446 (mmt) cc_final: 0.9211 (mmt) REVERT: B 29 ILE cc_start: 0.9520 (mm) cc_final: 0.9270 (tp) REVERT: C 25 PHE cc_start: 0.9129 (m-10) cc_final: 0.8802 (m-10) REVERT: C 110 ASN cc_start: 0.9281 (t0) cc_final: 0.9009 (m110) REVERT: D 62 MET cc_start: 0.9845 (mmp) cc_final: 0.9567 (mmm) REVERT: D 73 ILE cc_start: 0.9908 (mt) cc_final: 0.9682 (tp) REVERT: F 43 VAL cc_start: 0.9487 (t) cc_final: 0.9272 (p) REVERT: F 53 GLU cc_start: 0.9741 (tp30) cc_final: 0.9364 (tp30) REVERT: F 68 ASP cc_start: 0.9434 (m-30) cc_final: 0.9200 (m-30) REVERT: F 84 MET cc_start: 0.9446 (tpt) cc_final: 0.9128 (tpp) REVERT: H 39 ILE cc_start: 0.9562 (tp) cc_final: 0.9269 (pt) REVERT: H 62 MET cc_start: 0.9821 (mmm) cc_final: 0.9560 (mmm) REVERT: H 98 VAL cc_start: 0.9667 (t) cc_final: 0.9466 (p) outliers start: 0 outliers final: 0 residues processed: 333 average time/residue: 0.2637 time to fit residues: 118.8885 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 : 0.435 ------------------------------------------------------------------------------- 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: 3.9990 chunk 3 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 69 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.2526 r_free = 0.2526 target = 0.027932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2267 r_free = 0.2267 target = 0.021048 restraints weight = 244221.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2329 r_free = 0.2329 target = 0.022701 restraints weight = 71905.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2369 r_free = 0.2369 target = 0.023722 restraints weight = 33014.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2395 r_free = 0.2395 target = 0.024399 restraints weight = 19243.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2410 r_free = 0.2410 target = 0.024811 restraints weight = 13159.984| |-----------------------------------------------------------------------------| r_work (final): 0.2407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.5134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13590 Z= 0.209 Angle : 0.651 5.077 19596 Z= 0.407 Chirality : 0.041 0.351 2232 Planarity : 0.004 0.038 1456 Dihedral : 31.005 171.696 4153 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % 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: 0.77 (0.28), residues: 832 helix: 1.25 (0.20), residues: 583 sheet: -3.82 (1.16), residues: 10 loop : -1.05 (0.36), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 95 TYR 0.023 0.002 TYR E 99 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 covalent geometry : bond 0.00420 (13590) covalent geometry : angle 0.65054 (19596) hydrogen bonds : bond 0.04647 ( 815) hydrogen bonds : angle 3.93040 ( 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 339 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 339 time to evaluate : 0.453 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: A 67 PHE cc_start: 0.9682 (t80) cc_final: 0.9431 (t80) REVERT: A 84 PHE cc_start: 0.9408 (m-80) cc_final: 0.9171 (m-80) REVERT: A 94 GLU cc_start: 0.9324 (mm-30) cc_final: 0.9084 (mm-30) REVERT: B 29 ILE cc_start: 0.9571 (mm) cc_final: 0.9317 (tp) REVERT: B 70 VAL cc_start: 0.9911 (p) cc_final: 0.9585 (p) REVERT: B 74 GLU cc_start: 0.9543 (tp30) cc_final: 0.9254 (mm-30) REVERT: C 115 LEU cc_start: 0.9381 (mt) cc_final: 0.9176 (mt) REVERT: D 47 GLN cc_start: 0.9562 (tm-30) cc_final: 0.9347 (tm-30) REVERT: D 62 MET cc_start: 0.9855 (mmp) cc_final: 0.9589 (mmm) REVERT: D 73 ILE cc_start: 0.9887 (mt) cc_final: 0.9621 (tp) REVERT: E 82 LEU cc_start: 0.9237 (mt) cc_final: 0.8929 (mt) REVERT: E 84 PHE cc_start: 0.9317 (m-80) cc_final: 0.9099 (m-10) REVERT: F 53 GLU cc_start: 0.9702 (tp30) cc_final: 0.9326 (tp30) REVERT: F 68 ASP cc_start: 0.9326 (m-30) cc_final: 0.9124 (m-30) REVERT: F 84 MET cc_start: 0.9349 (tpt) cc_final: 0.8951 (tpp) REVERT: H 39 ILE cc_start: 0.9541 (tp) cc_final: 0.9207 (pt) REVERT: H 45 LEU cc_start: 0.9430 (tp) cc_final: 0.9105 (tp) REVERT: H 62 MET cc_start: 0.9790 (mmm) cc_final: 0.9585 (mmm) REVERT: H 98 VAL cc_start: 0.9630 (t) cc_final: 0.9388 (p) REVERT: H 105 GLU cc_start: 0.9665 (mp0) cc_final: 0.9456 (mp0) outliers start: 0 outliers final: 0 residues processed: 339 average time/residue: 0.2681 time to fit residues: 123.8284 Evaluate side-chains 300 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 0.446 ------------------------------------------------------------------------------- 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: 4.9990 chunk 8 optimal weight: 7.9990 chunk 69 optimal weight: 7.9990 chunk 96 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 98 optimal weight: 8.9990 chunk 53 optimal weight: 8.9990 chunk 71 optimal weight: 0.8980 chunk 45 optimal weight: 9.9990 chunk 55 optimal weight: 7.9990 chunk 54 optimal weight: 0.8980 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.2532 r_free = 0.2532 target = 0.028070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2266 r_free = 0.2266 target = 0.020992 restraints weight = 240435.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2328 r_free = 0.2328 target = 0.022670 restraints weight = 71698.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2367 r_free = 0.2367 target = 0.023708 restraints weight = 33201.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2393 r_free = 0.2393 target = 0.024389 restraints weight = 19511.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2410 r_free = 0.2410 target = 0.024816 restraints weight = 13439.467| |-----------------------------------------------------------------------------| r_work (final): 0.2410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.5545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13590 Z= 0.201 Angle : 0.639 7.195 19596 Z= 0.398 Chirality : 0.041 0.350 2232 Planarity : 0.004 0.037 1456 Dihedral : 30.862 172.386 4153 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % 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: 1.14 (0.28), residues: 832 helix: 1.56 (0.21), residues: 586 sheet: -2.97 (1.45), residues: 10 loop : -1.08 (0.36), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 95 TYR 0.038 0.002 TYR E 99 PHE 0.010 0.001 PHE K 458 TRP 0.002 0.001 TRP K 481 HIS 0.004 0.001 HIS G 82 Details of bonding type rmsd covalent geometry : bond 0.00411 (13590) covalent geometry : angle 0.63913 (19596) hydrogen bonds : bond 0.04688 ( 815) hydrogen bonds : angle 3.74282 ( 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 333 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 333 time to evaluate : 0.498 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 84 PHE cc_start: 0.9436 (m-80) cc_final: 0.9213 (m-80) REVERT: A 94 GLU cc_start: 0.9358 (mm-30) cc_final: 0.9141 (mm-30) REVERT: A 106 ASP cc_start: 0.9296 (m-30) cc_final: 0.9089 (m-30) REVERT: A 110 CYS cc_start: 0.9678 (m) cc_final: 0.9040 (t) REVERT: B 29 ILE cc_start: 0.9563 (mm) cc_final: 0.9273 (tp) REVERT: B 70 VAL cc_start: 0.9903 (p) cc_final: 0.9563 (p) REVERT: B 74 GLU cc_start: 0.9535 (tp30) cc_final: 0.9201 (mm-30) REVERT: C 25 PHE cc_start: 0.8801 (m-10) cc_final: 0.8550 (m-10) REVERT: D 37 TYR cc_start: 0.9174 (m-80) cc_final: 0.8914 (m-80) REVERT: D 62 MET cc_start: 0.9861 (mmp) cc_final: 0.9603 (mmm) REVERT: D 65 PHE cc_start: 0.9711 (t80) cc_final: 0.9496 (t80) REVERT: D 73 ILE cc_start: 0.9884 (mt) cc_final: 0.9596 (tp) REVERT: E 60 LEU cc_start: 0.7486 (mm) cc_final: 0.7226 (mm) REVERT: E 82 LEU cc_start: 0.9222 (mt) cc_final: 0.8880 (mt) REVERT: E 84 PHE cc_start: 0.9332 (m-80) cc_final: 0.9130 (m-10) REVERT: E 106 ASP cc_start: 0.9299 (m-30) cc_final: 0.8946 (p0) REVERT: E 110 CYS cc_start: 0.9620 (m) cc_final: 0.8875 (t) REVERT: F 53 GLU cc_start: 0.9697 (tp30) cc_final: 0.9300 (tp30) REVERT: F 68 ASP cc_start: 0.9343 (m-30) cc_final: 0.9088 (m-30) REVERT: F 72 TYR cc_start: 0.9183 (m-10) cc_final: 0.8970 (m-10) REVERT: F 84 MET cc_start: 0.9295 (tpt) cc_final: 0.8923 (tpp) REVERT: H 39 ILE cc_start: 0.9507 (tp) cc_final: 0.9162 (pt) REVERT: H 45 LEU cc_start: 0.9497 (tp) cc_final: 0.9260 (tp) REVERT: H 65 PHE cc_start: 0.9696 (t80) cc_final: 0.9492 (t80) REVERT: H 105 GLU cc_start: 0.9652 (mp0) cc_final: 0.9435 (mp0) REVERT: K 403 ARG cc_start: 0.7073 (mtp-110) cc_final: 0.6813 (mtp180) outliers start: 0 outliers final: 0 residues processed: 333 average time/residue: 0.2602 time to fit residues: 118.5291 Evaluate side-chains 293 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 0.449 ------------------------------------------------------------------------------- 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: 0.9990 chunk 79 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 84 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 82 optimal weight: 8.9990 chunk 1 optimal weight: 7.9990 chunk 76 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN H 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2507 r_free = 0.2507 target = 0.027276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2240 r_free = 0.2240 target = 0.020366 restraints weight = 254706.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2302 r_free = 0.2302 target = 0.021999 restraints weight = 77718.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2341 r_free = 0.2341 target = 0.022980 restraints weight = 36423.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2366 r_free = 0.2366 target = 0.023644 restraints weight = 21695.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2384 r_free = 0.2384 target = 0.024105 restraints weight = 14905.094| |-----------------------------------------------------------------------------| r_work (final): 0.2383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.5822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 13590 Z= 0.274 Angle : 0.655 5.002 19596 Z= 0.411 Chirality : 0.044 0.348 2232 Planarity : 0.004 0.038 1456 Dihedral : 30.740 173.842 4153 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % 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: 0.70 (0.28), residues: 832 helix: 1.20 (0.21), residues: 590 sheet: -3.13 (1.35), residues: 10 loop : -1.21 (0.36), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 45 TYR 0.023 0.002 TYR E 99 PHE 0.014 0.002 PHE D 65 TRP 0.003 0.001 TRP K 481 HIS 0.005 0.001 HIS K 476 Details of bonding type rmsd covalent geometry : bond 0.00546 (13590) covalent geometry : angle 0.65528 (19596) hydrogen bonds : bond 0.05752 ( 815) hydrogen bonds : angle 4.08307 ( 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 331 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 331 time to evaluate : 0.493 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 84 PHE cc_start: 0.9461 (m-80) cc_final: 0.9253 (m-80) REVERT: A 110 CYS cc_start: 0.9696 (m) cc_final: 0.9162 (t) REVERT: B 29 ILE cc_start: 0.9537 (mm) cc_final: 0.9238 (tp) REVERT: B 70 VAL cc_start: 0.9910 (p) cc_final: 0.9548 (p) REVERT: B 74 GLU cc_start: 0.9548 (tp30) cc_final: 0.9223 (mm-30) REVERT: C 25 PHE cc_start: 0.8719 (m-10) cc_final: 0.8389 (m-10) REVERT: C 56 GLU cc_start: 0.8972 (tt0) cc_final: 0.8577 (mt-10) REVERT: D 37 TYR cc_start: 0.9195 (m-80) cc_final: 0.8938 (m-80) REVERT: D 62 MET cc_start: 0.9869 (mmp) cc_final: 0.9605 (mmm) REVERT: D 73 ILE cc_start: 0.9887 (mt) cc_final: 0.9605 (tp) REVERT: D 113 GLU cc_start: 0.9463 (mt-10) cc_final: 0.9140 (mt-10) REVERT: E 60 LEU cc_start: 0.7527 (mm) cc_final: 0.7230 (mm) REVERT: E 84 PHE cc_start: 0.9329 (m-80) cc_final: 0.9067 (m-80) REVERT: E 110 CYS cc_start: 0.9655 (m) cc_final: 0.9029 (t) REVERT: F 53 GLU cc_start: 0.9722 (tp30) cc_final: 0.9316 (tp30) REVERT: F 68 ASP cc_start: 0.9299 (m-30) cc_final: 0.9070 (m-30) REVERT: F 84 MET cc_start: 0.9333 (tpt) cc_final: 0.8945 (tpp) REVERT: F 91 LYS cc_start: 0.9688 (ttmm) cc_final: 0.9483 (mmmm) REVERT: H 39 ILE cc_start: 0.9582 (tp) cc_final: 0.9266 (pt) outliers start: 0 outliers final: 0 residues processed: 331 average time/residue: 0.2608 time to fit residues: 117.8251 Evaluate side-chains 294 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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: 7.9990 chunk 67 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 106 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.2519 r_free = 0.2519 target = 0.027576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2253 r_free = 0.2253 target = 0.020625 restraints weight = 251601.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2315 r_free = 0.2315 target = 0.022281 restraints weight = 76777.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2354 r_free = 0.2354 target = 0.023270 restraints weight = 35992.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2378 r_free = 0.2378 target = 0.023936 restraints weight = 21447.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2393 r_free = 0.2393 target = 0.024314 restraints weight = 14748.542| |-----------------------------------------------------------------------------| r_work (final): 0.2393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.6049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13590 Z= 0.248 Angle : 0.645 4.962 19596 Z= 0.403 Chirality : 0.043 0.351 2232 Planarity : 0.004 0.038 1456 Dihedral : 30.728 173.156 4153 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % 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: 0.68 (0.28), residues: 832 helix: 1.20 (0.21), residues: 590 sheet: -2.96 (1.41), residues: 10 loop : -1.28 (0.36), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG K 403 TYR 0.023 0.002 TYR E 99 PHE 0.011 0.002 PHE K 458 TRP 0.002 0.001 TRP K 481 HIS 0.005 0.001 HIS K 476 Details of bonding type rmsd covalent geometry : bond 0.00496 (13590) covalent geometry : angle 0.64489 (19596) hydrogen bonds : bond 0.05222 ( 815) hydrogen bonds : angle 4.04275 ( 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 326 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 326 time to evaluate : 0.496 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 84 PHE cc_start: 0.9459 (m-80) cc_final: 0.9255 (m-80) REVERT: A 110 CYS cc_start: 0.9730 (m) cc_final: 0.9148 (t) REVERT: B 29 ILE cc_start: 0.9536 (mm) cc_final: 0.9173 (tp) REVERT: B 70 VAL cc_start: 0.9912 (p) cc_final: 0.9530 (p) REVERT: B 74 GLU cc_start: 0.9592 (tp30) cc_final: 0.9278 (mm-30) REVERT: C 25 PHE cc_start: 0.8906 (m-10) cc_final: 0.8685 (m-10) REVERT: C 36 LYS cc_start: 0.9728 (mmpt) cc_final: 0.9524 (mmmt) REVERT: D 62 MET cc_start: 0.9858 (mmp) cc_final: 0.9606 (mmm) REVERT: D 73 ILE cc_start: 0.9888 (mt) cc_final: 0.9606 (tp) REVERT: E 60 LEU cc_start: 0.7592 (mm) cc_final: 0.7295 (mm) REVERT: E 84 PHE cc_start: 0.9310 (m-80) cc_final: 0.8993 (m-80) REVERT: E 110 CYS cc_start: 0.9706 (m) cc_final: 0.9109 (t) REVERT: F 43 VAL cc_start: 0.9527 (t) cc_final: 0.9194 (m) REVERT: F 53 GLU cc_start: 0.9719 (tp30) cc_final: 0.9271 (tp30) REVERT: F 91 LYS cc_start: 0.9705 (ttmm) cc_final: 0.9503 (mmmm) REVERT: H 39 ILE cc_start: 0.9579 (tp) cc_final: 0.9264 (pt) REVERT: H 45 LEU cc_start: 0.9569 (tp) cc_final: 0.9363 (tp) REVERT: H 98 VAL cc_start: 0.9441 (p) cc_final: 0.9235 (p) outliers start: 0 outliers final: 0 residues processed: 326 average time/residue: 0.2492 time to fit residues: 110.8050 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 : 0.450 ------------------------------------------------------------------------------- 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: 0.8980 chunk 39 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 76 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** 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 = 0.2503 r_free = 0.2503 target = 0.027511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2233 r_free = 0.2233 target = 0.020505 restraints weight = 252089.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2296 r_free = 0.2296 target = 0.022176 restraints weight = 76580.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2336 r_free = 0.2336 target = 0.023206 restraints weight = 35873.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2363 r_free = 0.2363 target = 0.023891 restraints weight = 21020.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2380 r_free = 0.2380 target = 0.024329 restraints weight = 14406.266| |-----------------------------------------------------------------------------| r_work (final): 0.2384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.6251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13590 Z= 0.252 Angle : 0.646 5.299 19596 Z= 0.403 Chirality : 0.043 0.351 2232 Planarity : 0.004 0.040 1456 Dihedral : 30.735 173.539 4153 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: 0.61 (0.28), residues: 832 helix: 1.16 (0.21), residues: 589 sheet: -2.94 (1.52), residues: 10 loop : -1.33 (0.36), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 69 TYR 0.020 0.002 TYR E 99 PHE 0.022 0.002 PHE D 65 TRP 0.002 0.001 TRP K 481 HIS 0.006 0.001 HIS K 476 Details of bonding type rmsd covalent geometry : bond 0.00503 (13590) covalent geometry : angle 0.64607 (19596) hydrogen bonds : bond 0.05427 ( 815) hydrogen bonds : angle 4.02218 ( 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 322 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 0.327 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: A 110 CYS cc_start: 0.9729 (m) cc_final: 0.9184 (t) REVERT: B 29 ILE cc_start: 0.9507 (mm) cc_final: 0.9198 (tp) REVERT: B 70 VAL cc_start: 0.9908 (p) cc_final: 0.9512 (p) REVERT: B 74 GLU cc_start: 0.9596 (tp30) cc_final: 0.9279 (mm-30) REVERT: B 85 ASP cc_start: 0.9018 (m-30) cc_final: 0.8799 (m-30) REVERT: D 62 MET cc_start: 0.9871 (mmp) cc_final: 0.9625 (mmm) REVERT: D 73 ILE cc_start: 0.9883 (mt) cc_final: 0.9602 (tp) REVERT: E 110 CYS cc_start: 0.9718 (m) cc_final: 0.9178 (t) REVERT: F 43 VAL cc_start: 0.9577 (t) cc_final: 0.9260 (m) REVERT: F 53 GLU cc_start: 0.9673 (tp30) cc_final: 0.9208 (tp30) REVERT: F 70 VAL cc_start: 0.9811 (p) cc_final: 0.9565 (p) REVERT: F 74 GLU cc_start: 0.9607 (mm-30) cc_final: 0.9153 (mm-30) REVERT: H 39 ILE cc_start: 0.9575 (tp) cc_final: 0.9254 (pt) REVERT: K 413 GLU cc_start: 0.9762 (tp30) cc_final: 0.9551 (pp20) outliers start: 0 outliers final: 0 residues processed: 322 average time/residue: 0.2551 time to fit residues: 112.4773 Evaluate side-chains 291 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 0.486 ------------------------------------------------------------------------------- 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: 7.9990 chunk 59 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 48 optimal weight: 8.9990 chunk 86 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2531 r_free = 0.2531 target = 0.027886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2264 r_free = 0.2264 target = 0.020892 restraints weight = 246727.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2327 r_free = 0.2327 target = 0.022559 restraints weight = 74440.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2367 r_free = 0.2367 target = 0.023601 restraints weight = 34775.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2394 r_free = 0.2394 target = 0.024274 restraints weight = 20364.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2411 r_free = 0.2411 target = 0.024729 restraints weight = 13942.322| |-----------------------------------------------------------------------------| r_work (final): 0.2413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.6442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13590 Z= 0.222 Angle : 0.636 5.738 19596 Z= 0.395 Chirality : 0.042 0.351 2232 Planarity : 0.004 0.040 1456 Dihedral : 30.741 173.181 4153 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % 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: 0.80 (0.28), residues: 832 helix: 1.33 (0.21), residues: 589 sheet: -2.85 (1.56), residues: 10 loop : -1.34 (0.36), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 95 TYR 0.022 0.002 TYR G 50 PHE 0.016 0.002 PHE C 25 TRP 0.002 0.001 TRP K 481 HIS 0.004 0.001 HIS G 82 Details of bonding type rmsd covalent geometry : bond 0.00447 (13590) covalent geometry : angle 0.63583 (19596) hydrogen bonds : bond 0.04859 ( 815) hydrogen bonds : angle 3.90477 ( 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 : 0.425 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 59 GLU cc_start: 0.9404 (mp0) cc_final: 0.9186 (mp0) REVERT: A 110 CYS cc_start: 0.9735 (m) cc_final: 0.9166 (t) REVERT: B 29 ILE cc_start: 0.9523 (mm) cc_final: 0.9227 (tp) REVERT: B 45 ARG cc_start: 0.9023 (ttt-90) cc_final: 0.8795 (ttm-80) REVERT: B 70 VAL cc_start: 0.9903 (p) cc_final: 0.9509 (p) REVERT: B 74 GLU cc_start: 0.9590 (tp30) cc_final: 0.9279 (mm-30) REVERT: C 25 PHE cc_start: 0.9136 (m-10) cc_final: 0.8457 (m-10) REVERT: D 62 MET cc_start: 0.9848 (mmp) cc_final: 0.9598 (mmm) REVERT: D 73 ILE cc_start: 0.9881 (mt) cc_final: 0.9598 (tp) REVERT: E 82 LEU cc_start: 0.9169 (mt) cc_final: 0.8708 (mt) REVERT: E 84 PHE cc_start: 0.9292 (m-80) cc_final: 0.8869 (m-80) REVERT: E 110 CYS cc_start: 0.9741 (m) cc_final: 0.9191 (t) REVERT: F 43 VAL cc_start: 0.9567 (t) cc_final: 0.9270 (m) REVERT: F 53 GLU cc_start: 0.9677 (tp30) cc_final: 0.9310 (tp30) REVERT: F 70 VAL cc_start: 0.9832 (p) cc_final: 0.9518 (p) REVERT: F 74 GLU cc_start: 0.9583 (mm-30) cc_final: 0.9262 (mm-30) REVERT: H 39 ILE cc_start: 0.9575 (tp) cc_final: 0.9259 (pt) outliers start: 0 outliers final: 0 residues processed: 328 average time/residue: 0.2525 time to fit residues: 113.4670 Evaluate side-chains 287 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 0.494 ------------------------------------------------------------------------------- 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: 8.9990 chunk 104 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 62 optimal weight: 8.9990 chunk 98 optimal weight: 8.9990 chunk 16 optimal weight: 8.9990 chunk 75 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.028676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2284 r_free = 0.2284 target = 0.021610 restraints weight = 245743.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2347 r_free = 0.2347 target = 0.023311 restraints weight = 74956.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2387 r_free = 0.2387 target = 0.024367 restraints weight = 35169.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2412 r_free = 0.2412 target = 0.025021 restraints weight = 20613.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2429 r_free = 0.2429 target = 0.025497 restraints weight = 14317.983| |-----------------------------------------------------------------------------| r_work (final): 0.2424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.6564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13590 Z= 0.209 Angle : 0.624 5.289 19596 Z= 0.389 Chirality : 0.042 0.350 2232 Planarity : 0.004 0.057 1456 Dihedral : 30.704 173.447 4153 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % 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: 0.95 (0.28), residues: 832 helix: 1.44 (0.21), residues: 589 sheet: -2.79 (1.62), residues: 10 loop : -1.26 (0.36), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 71 TYR 0.032 0.002 TYR G 50 PHE 0.035 0.002 PHE K 473 TRP 0.002 0.001 TRP K 481 HIS 0.006 0.001 HIS K 476 Details of bonding type rmsd covalent geometry : bond 0.00424 (13590) covalent geometry : angle 0.62441 (19596) hydrogen bonds : bond 0.04740 ( 815) hydrogen bonds : angle 3.83430 ( 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 323 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 323 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: A 110 CYS cc_start: 0.9730 (m) cc_final: 0.9174 (t) REVERT: B 29 ILE cc_start: 0.9529 (mm) cc_final: 0.9202 (tp) REVERT: B 45 ARG cc_start: 0.9019 (ttt-90) cc_final: 0.8792 (ttm-80) REVERT: B 70 VAL cc_start: 0.9897 (p) cc_final: 0.9504 (p) REVERT: B 74 GLU cc_start: 0.9582 (tp30) cc_final: 0.9241 (mm-30) REVERT: D 62 MET cc_start: 0.9859 (mmp) cc_final: 0.9594 (mmm) REVERT: D 73 ILE cc_start: 0.9872 (mt) cc_final: 0.9557 (tp) REVERT: D 101 LEU cc_start: 0.8669 (mt) cc_final: 0.8416 (mt) REVERT: E 82 LEU cc_start: 0.9174 (mt) cc_final: 0.8726 (mt) REVERT: E 84 PHE cc_start: 0.9300 (m-80) cc_final: 0.8855 (m-80) REVERT: E 105 GLU cc_start: 0.9327 (mt-10) cc_final: 0.8912 (mm-30) REVERT: E 110 CYS cc_start: 0.9730 (m) cc_final: 0.9257 (t) REVERT: F 43 VAL cc_start: 0.9533 (t) cc_final: 0.9175 (m) REVERT: F 53 GLU cc_start: 0.9666 (tp30) cc_final: 0.9289 (tp30) REVERT: F 70 VAL cc_start: 0.9832 (p) cc_final: 0.9599 (p) REVERT: F 74 GLU cc_start: 0.9552 (mm-30) cc_final: 0.9161 (mm-30) REVERT: H 39 ILE cc_start: 0.9574 (tp) cc_final: 0.9248 (pt) outliers start: 0 outliers final: 0 residues processed: 323 average time/residue: 0.2547 time to fit residues: 113.0183 Evaluate side-chains 285 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 0.450 ------------------------------------------------------------------------------- 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: 7.9990 chunk 10 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 14 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 24 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 52 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 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 = 0.2572 r_free = 0.2572 target = 0.028915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2300 r_free = 0.2300 target = 0.021732 restraints weight = 245943.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2363 r_free = 0.2363 target = 0.023453 restraints weight = 75083.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2404 r_free = 0.2404 target = 0.024507 restraints weight = 35133.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2431 r_free = 0.2431 target = 0.025213 restraints weight = 20739.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2449 r_free = 0.2449 target = 0.025694 restraints weight = 14286.710| |-----------------------------------------------------------------------------| r_work (final): 0.2448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.6629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13590 Z= 0.182 Angle : 0.617 6.506 19596 Z= 0.383 Chirality : 0.040 0.352 2232 Planarity : 0.004 0.046 1456 Dihedral : 30.683 173.255 4153 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.28), residues: 832 helix: 1.66 (0.21), residues: 591 sheet: None (None), residues: 0 loop : -1.32 (0.35), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 71 TYR 0.030 0.002 TYR G 50 PHE 0.009 0.001 PHE C 25 TRP 0.002 0.001 TRP K 481 HIS 0.004 0.001 HIS K 476 Details of bonding type rmsd covalent geometry : bond 0.00377 (13590) covalent geometry : angle 0.61665 (19596) hydrogen bonds : bond 0.04208 ( 815) hydrogen bonds : angle 3.65464 ( 2040) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4156.73 seconds wall clock time: 71 minutes 25.80 seconds (4285.80 seconds total)