Starting phenix.real_space_refine on Sat Jul 4 18:14:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7scy_25042/07_2026/7scy_25042.cif Found real_map, /net/cci-nas-00/data/ceres_data/7scy_25042/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/7scy_25042/07_2026/7scy_25042.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7scy_25042/07_2026/7scy_25042.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7scy_25042/07_2026/7scy_25042.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7scy_25042/07_2026/7scy_25042.map" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 294 5.49 5 S 19 5.16 5 C 7110 2.51 5 N 2388 2.21 5 O 2959 1.98 5 H 10436 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23206 Number of models: 1 Model: "" Number of chains: 11 Chain: "I" Number of atoms: 4682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 4682 Classifications: {'DNA': 147} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 4646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 4646 Classifications: {'DNA': 147} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 146} Chain: "A" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1616 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1271 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "C" Number of atoms: 1733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1733 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 1461 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 1684 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 1459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 1459 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "G" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 1667 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "H" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 1450 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "K" Number of atoms: 1537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1537 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Time building chain proxies: 3.26, per 1000 atoms: 0.14 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: 1.63 Conformation dependent library (CDL) restraints added in 325.6 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: 4.55 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: 5.54 Time building geometry restraints manager: 2.39 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: 43339 6.92 - 13.84: 242 13.84 - 20.76: 1 20.76 - 27.68: 1 27.68 - 34.60: 2 Bond angle restraints: 43585 Sorted by residual: angle pdb=" O5' DC I 70 " pdb=" C5' DC I 70 " pdb=" C4' DC I 70 " ideal model delta sigma weight residual 109.40 119.97 -10.57 8.00e-01 1.56e+00 1.75e+02 angle pdb=" O5' DT I 25 " pdb=" C5' DT I 25 " pdb=" C4' DT I 25 " ideal model delta sigma weight residual 109.40 119.24 -9.84 8.00e-01 1.56e+00 1.51e+02 angle pdb=" O5' DC I -58 " pdb=" C5' DC I -58 " pdb=" C4' DC I -58 " ideal model delta sigma weight residual 109.40 119.14 -9.74 8.00e-01 1.56e+00 1.48e+02 angle pdb=" N ARG F 17 " pdb=" CA ARG F 17 " pdb=" C ARG F 17 " ideal model delta sigma weight residual 110.61 125.19 -14.58 1.25e+00 6.40e-01 1.36e+02 angle pdb=" O5' DG J -58 " pdb=" C5' DG J -58 " pdb=" C4' DG J -58 " ideal model delta sigma weight residual 109.40 118.68 -9.28 8.00e-01 1.56e+00 1.35e+02 ... (remaining 43580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.20: 8346 35.20 - 70.39: 1622 70.39 - 105.59: 54 105.59 - 140.78: 0 140.78 - 175.98: 3 Dihedral angle restraints: 10025 sinusoidal: 7285 harmonic: 2740 Sorted by residual: dihedral pdb=" C ARG F 17 " pdb=" N ARG F 17 " pdb=" CA ARG F 17 " pdb=" CB ARG F 17 " ideal model delta harmonic sigma weight residual -122.60 -139.87 17.27 0 2.50e+00 1.60e-01 4.77e+01 dihedral pdb=" N ARG F 17 " pdb=" C ARG F 17 " pdb=" CA ARG F 17 " pdb=" CB ARG F 17 " ideal model delta harmonic sigma weight residual 122.80 138.75 -15.95 0 2.50e+00 1.60e-01 4.07e+01 dihedral pdb=" CA TYR H 37 " pdb=" C TYR H 37 " pdb=" N SER H 38 " pdb=" CA SER H 38 " ideal model delta harmonic sigma weight residual 180.00 -152.25 -27.75 0 5.00e+00 4.00e-02 3.08e+01 ... (remaining 10022 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.148: 2023 0.148 - 0.296: 193 0.296 - 0.444: 12 0.444 - 0.592: 3 0.592 - 0.739: 1 Chirality restraints: 2232 Sorted by residual: chirality pdb=" CA ARG F 17 " pdb=" N ARG F 17 " pdb=" C ARG F 17 " pdb=" CB ARG F 17 " both_signs ideal model delta sigma weight residual False 2.51 1.77 0.74 2.00e-01 2.50e+01 1.37e+01 chirality pdb=" C3' DG I -44 " pdb=" C4' DG I -44 " pdb=" O3' DG I -44 " pdb=" C2' DG I -44 " both_signs ideal model delta sigma weight residual False -2.73 -2.26 -0.47 2.00e-01 2.50e+01 5.53e+00 chirality pdb=" C3' DG I 20 " pdb=" C4' DG I 20 " pdb=" O3' DG I 20 " pdb=" C2' DG I 20 " both_signs ideal model delta sigma weight residual False -2.73 -2.27 -0.46 2.00e-01 2.50e+01 5.20e+00 ... (remaining 2229 not shown) Planarity restraints: 2501 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT J -39 " -0.444 2.00e-02 2.50e+03 1.92e-01 1.11e+03 pdb=" N1 DT J -39 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DT J -39 " 0.131 2.00e-02 2.50e+03 pdb=" O2 DT J -39 " 0.277 2.00e-02 2.50e+03 pdb=" N3 DT J -39 " 0.076 2.00e-02 2.50e+03 pdb=" C4 DT J -39 " -0.070 2.00e-02 2.50e+03 pdb=" O4 DT J -39 " -0.315 2.00e-02 2.50e+03 pdb=" C5 DT J -39 " 0.053 2.00e-02 2.50e+03 pdb=" C7 DT J -39 " 0.162 2.00e-02 2.50e+03 pdb=" C6 DT J -39 " 0.068 2.00e-02 2.50e+03 pdb=" H3 DT J -39 " -0.025 2.00e-02 2.50e+03 pdb=" H6 DT J -39 " 0.091 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT J -72 " 0.422 2.00e-02 2.50e+03 1.66e-01 8.27e+02 pdb=" N1 DT J -72 " -0.041 2.00e-02 2.50e+03 pdb=" C2 DT J -72 " -0.114 2.00e-02 2.50e+03 pdb=" O2 DT J -72 " -0.214 2.00e-02 2.50e+03 pdb=" N3 DT J -72 " -0.046 2.00e-02 2.50e+03 pdb=" C4 DT J -72 " 0.063 2.00e-02 2.50e+03 pdb=" O4 DT J -72 " 0.238 2.00e-02 2.50e+03 pdb=" C5 DT J -72 " -0.049 2.00e-02 2.50e+03 pdb=" C7 DT J -72 " -0.068 2.00e-02 2.50e+03 pdb=" C6 DT J -72 " -0.096 2.00e-02 2.50e+03 pdb=" H3 DT J -72 " 0.015 2.00e-02 2.50e+03 pdb=" H6 DT J -72 " -0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT J -47 " -0.306 2.00e-02 2.50e+03 1.59e-01 7.61e+02 pdb=" N1 DT J -47 " -0.067 2.00e-02 2.50e+03 pdb=" C2 DT J -47 " 0.081 2.00e-02 2.50e+03 pdb=" O2 DT J -47 " 0.347 2.00e-02 2.50e+03 pdb=" N3 DT J -47 " -0.064 2.00e-02 2.50e+03 pdb=" C4 DT J -47 " -0.086 2.00e-02 2.50e+03 pdb=" O4 DT J -47 " -0.167 2.00e-02 2.50e+03 pdb=" C5 DT J -47 " 0.021 2.00e-02 2.50e+03 pdb=" C7 DT J -47 " 0.181 2.00e-02 2.50e+03 pdb=" C6 DT J -47 " 0.024 2.00e-02 2.50e+03 pdb=" H3 DT J -47 " -0.035 2.00e-02 2.50e+03 pdb=" H6 DT J -47 " 0.070 2.00e-02 2.50e+03 ... (remaining 2498 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.16: 1099 2.16 - 2.77: 36051 2.77 - 3.38: 65221 3.38 - 3.99: 91349 3.99 - 4.60: 130381 Nonbonded interactions: 324101 Sorted by model distance: nonbonded pdb=" HG1 THR D 90 " pdb=" OE1 GLU D 93 " model vdw 1.556 2.450 nonbonded pdb=" HG1 THR H 90 " pdb=" OE1 GLU H 93 " model vdw 1.568 2.450 nonbonded pdb=" OP1 DA I 28 " pdb=" HG1 THR B 80 " model vdw 1.569 2.450 nonbonded pdb=" OP1 DG J 28 " pdb=" HG1 THR F 80 " model vdw 1.585 2.450 nonbonded pdb=" HG SER K 455 " pdb=" OD1 ASP K 457 " model vdw 1.592 2.450 ... (remaining 324096 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 38 through 133) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 25 through 101) } ncs_group { reference = (chain 'C' and resid 15 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 33 through 123) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 23.860 Find NCS groups from input model: 0.180 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.054 13590 Z= 1.342 Angle : 1.940 14.578 19596 Z= 1.955 Chirality : 0.092 0.739 2232 Planarity : 0.038 0.207 1456 Dihedral : 27.616 175.980 5861 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 0.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.56 % Allowed : 2.09 % Favored : 97.35 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.25), residues: 832 helix: -0.37 (0.18), residues: 582 sheet: None (None), residues: 0 loop : -0.57 (0.35), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 134 TYR 0.171 0.024 TYR A 41 PHE 0.063 0.017 PHE D 65 TRP 0.087 0.043 TRP K 481 HIS 0.018 0.004 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.01369 / 1.34 (13590) covalent geometry : angle 1.93998 / 1.96 (19596) hydrogen bonds : bond 0.11316 / 11.97 ( 815) hydrogen bonds : angle 6.37425 / 8.05 ( 2040) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 393 time to evaluate : 0.398 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: 0.2568 time to fit residues: 138.4029 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 : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 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: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.028127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2265 r_free = 0.2265 target = 0.021226 restraints weight = 245966.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2328 r_free = 0.2328 target = 0.022909 restraints weight = 73504.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2367 r_free = 0.2367 target = 0.023918 restraints weight = 33806.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2392 r_free = 0.2392 target = 0.024621 restraints weight = 19653.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2408 r_free = 0.2408 target = 0.025053 restraints weight = 13152.143| |-----------------------------------------------------------------------------| r_work (final): 0.2394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 13590 Z= 0.306 Angle : 0.926 9.154 19596 Z= 0.553 Chirality : 0.052 0.369 2232 Planarity : 0.007 0.085 1456 Dihedral : 31.961 173.392 4153 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % 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: -0.27 (0.26), residues: 832 helix: 0.32 (0.19), residues: 583 sheet: None (None), residues: 0 loop : -1.19 (0.33), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 128 TYR 0.019 0.002 TYR H 40 PHE 0.017 0.003 PHE H 65 TRP 0.008 0.003 TRP K 481 HIS 0.007 0.002 HIS K 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.31 (13590) covalent geometry : angle 0.92593 / 0.55 (19596) hydrogen bonds : bond 0.08369 / 9.46 ( 815) hydrogen bonds : angle 4.63248 / 5.89 ( 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 355 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 355 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9364 (mp0) cc_final: 0.9014 (mp0) REVERT: A 76 GLN cc_start: 0.9293 (tm-30) cc_final: 0.8984 (tp-100) REVERT: A 81 ASP cc_start: 0.9182 (m-30) cc_final: 0.8918 (m-30) REVERT: A 90 MET cc_start: 0.9459 (mmt) cc_final: 0.9115 (mmm) REVERT: A 117 VAL cc_start: 0.8986 (m) cc_final: 0.8633 (p) REVERT: A 120 MET cc_start: 0.8035 (mtp) cc_final: 0.7738 (mtt) REVERT: B 80 THR cc_start: 0.9249 (m) cc_final: 0.9026 (m) REVERT: C 75 LYS cc_start: 0.8485 (mmtp) cc_final: 0.8269 (mmtp) REVERT: C 115 LEU cc_start: 0.9344 (mt) cc_final: 0.9134 (mt) REVERT: D 47 GLN cc_start: 0.9516 (tm-30) cc_final: 0.9298 (tm-30) REVERT: D 62 MET cc_start: 0.9851 (mmp) cc_final: 0.9531 (mmm) REVERT: D 67 ASN cc_start: 0.9628 (m-40) cc_final: 0.9343 (m110) REVERT: D 68 ASP cc_start: 0.9456 (t70) cc_final: 0.9253 (t0) REVERT: D 73 ILE cc_start: 0.9866 (mt) cc_final: 0.9592 (tp) REVERT: D 99 ARG cc_start: 0.9272 (mtt180) cc_final: 0.9054 (tpp80) REVERT: E 120 MET cc_start: 0.8446 (mtt) cc_final: 0.8171 (mtp) REVERT: F 53 GLU cc_start: 0.9615 (tp30) cc_final: 0.9251 (tp30) REVERT: F 68 ASP cc_start: 0.9322 (m-30) cc_final: 0.8958 (m-30) REVERT: F 72 TYR cc_start: 0.9376 (m-10) cc_final: 0.9106 (m-10) REVERT: G 107 VAL cc_start: 0.8275 (m) cc_final: 0.7961 (m) REVERT: G 110 ASN cc_start: 0.9223 (t0) cc_final: 0.8932 (t0) REVERT: H 39 ILE cc_start: 0.9552 (tp) cc_final: 0.9229 (pt) REVERT: H 45 LEU cc_start: 0.9497 (tp) cc_final: 0.9274 (tp) REVERT: H 52 THR cc_start: 0.8671 (m) cc_final: 0.8112 (m) REVERT: H 62 MET cc_start: 0.9826 (mmm) cc_final: 0.9562 (mmm) REVERT: H 101 LEU cc_start: 0.9012 (mm) cc_final: 0.8743 (mm) REVERT: K 443 MET cc_start: 0.9342 (ppp) cc_final: 0.9116 (ppp) outliers start: 0 outliers final: 0 residues processed: 355 average time/residue: 0.2577 time to fit residues: 127.2675 Evaluate side-chains 314 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 314 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 106 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 96 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 1 optimal weight: 20.0000 chunk 48 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 chunk 81 optimal weight: 0.9980 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 67 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2544 r_free = 0.2544 target = 0.027758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2289 r_free = 0.2289 target = 0.020990 restraints weight = 244919.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2351 r_free = 0.2351 target = 0.022589 restraints weight = 72608.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2390 r_free = 0.2390 target = 0.023598 restraints weight = 33266.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2416 r_free = 0.2416 target = 0.024288 restraints weight = 19123.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2432 r_free = 0.2432 target = 0.024715 restraints weight = 12822.858| |-----------------------------------------------------------------------------| r_work (final): 0.2414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 13590 Z= 0.241 Angle : 0.767 9.334 19596 Z= 0.484 Chirality : 0.047 0.348 2232 Planarity : 0.006 0.059 1456 Dihedral : 31.769 174.454 4153 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % 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: 0.32 (0.27), residues: 832 helix: 0.81 (0.20), residues: 584 sheet: -3.75 (1.36), residues: 10 loop : -0.93 (0.35), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG G 29 TYR 0.015 0.002 TYR H 40 PHE 0.033 0.003 PHE C 25 TRP 0.004 0.001 TRP K 481 HIS 0.009 0.001 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.24 (13590) covalent geometry : angle 0.76686 / 0.48 (19596) hydrogen bonds : bond 0.06510 / 7.29 ( 815) hydrogen bonds : angle 4.31479 / 5.60 ( 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 345 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 345 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.9643 (t80) cc_final: 0.9430 (t80) REVERT: A 81 ASP cc_start: 0.9200 (m-30) cc_final: 0.8968 (m-30) REVERT: A 90 MET cc_start: 0.9430 (mmt) cc_final: 0.9154 (mmt) REVERT: C 75 LYS cc_start: 0.8462 (mmtp) cc_final: 0.8234 (mmtp) REVERT: D 35 GLU cc_start: 0.8215 (pp20) cc_final: 0.7983 (pp20) REVERT: D 47 GLN cc_start: 0.9507 (tm-30) cc_final: 0.9300 (tm-30) REVERT: D 62 MET cc_start: 0.9850 (mmp) cc_final: 0.9567 (mmm) REVERT: D 67 ASN cc_start: 0.9710 (m-40) cc_final: 0.9352 (m110) REVERT: D 73 ILE cc_start: 0.9806 (mt) cc_final: 0.9580 (tp) REVERT: D 101 LEU cc_start: 0.8361 (mm) cc_final: 0.8080 (mm) REVERT: E 55 GLN cc_start: 0.9185 (mt0) cc_final: 0.8784 (mt0) REVERT: E 120 MET cc_start: 0.8347 (mtt) cc_final: 0.8104 (mtp) REVERT: F 53 GLU cc_start: 0.9616 (tp30) cc_final: 0.9243 (tp30) REVERT: G 110 ASN cc_start: 0.9088 (t0) cc_final: 0.8584 (m-40) REVERT: G 115 LEU cc_start: 0.9297 (mt) cc_final: 0.9071 (mt) REVERT: H 39 ILE cc_start: 0.9493 (tp) cc_final: 0.9178 (pt) REVERT: H 45 LEU cc_start: 0.9432 (tp) cc_final: 0.9228 (tp) REVERT: H 62 MET cc_start: 0.9844 (mmm) cc_final: 0.9543 (mmm) REVERT: H 71 GLU cc_start: 0.9486 (mp0) cc_final: 0.9270 (mp0) REVERT: H 101 LEU cc_start: 0.8986 (mm) cc_final: 0.8613 (mm) outliers start: 0 outliers final: 0 residues processed: 345 average time/residue: 0.2617 time to fit residues: 125.0056 Evaluate side-chains 314 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 314 time to evaluate : 0.464 ------------------------------------------------------------------------------- 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: 5.9990 chunk 3 optimal weight: 20.0000 chunk 81 optimal weight: 1.9990 chunk 69 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.028240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2289 r_free = 0.2289 target = 0.021155 restraints weight = 242476.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2351 r_free = 0.2351 target = 0.022753 restraints weight = 73127.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2387 r_free = 0.2387 target = 0.023757 restraints weight = 34272.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2411 r_free = 0.2411 target = 0.024380 restraints weight = 20250.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2425 r_free = 0.2425 target = 0.024812 restraints weight = 14336.541| |-----------------------------------------------------------------------------| r_work (final): 0.2406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.4408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13590 Z= 0.200 Angle : 0.705 7.764 19596 Z= 0.446 Chirality : 0.044 0.351 2232 Planarity : 0.005 0.041 1456 Dihedral : 31.745 173.799 4153 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % 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: 0.84 (0.28), residues: 832 helix: 1.25 (0.21), residues: 587 sheet: -3.92 (1.18), residues: 10 loop : -0.90 (0.36), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 131 TYR 0.012 0.001 TYR H 37 PHE 0.021 0.002 PHE D 65 TRP 0.003 0.001 TRP K 481 HIS 0.007 0.001 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.20 (13590) covalent geometry : angle 0.70500 / 0.45 (19596) hydrogen bonds : bond 0.05669 / 6.29 ( 815) hydrogen bonds : angle 3.98952 / 5.19 ( 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 347 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 347 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.9627 (t80) cc_final: 0.9394 (t80) REVERT: A 81 ASP cc_start: 0.9231 (m-30) cc_final: 0.9020 (m-30) REVERT: A 94 GLU cc_start: 0.9292 (mm-30) cc_final: 0.9071 (mm-30) REVERT: C 25 PHE cc_start: 0.8592 (m-10) cc_final: 0.8197 (m-10) REVERT: C 56 GLU cc_start: 0.8822 (tt0) cc_final: 0.8495 (tt0) REVERT: D 47 GLN cc_start: 0.9512 (tm-30) cc_final: 0.9302 (tm-30) REVERT: D 62 MET cc_start: 0.9854 (mmp) cc_final: 0.9555 (mmm) REVERT: D 73 ILE cc_start: 0.9816 (mt) cc_final: 0.9581 (tp) REVERT: E 55 GLN cc_start: 0.9354 (mt0) cc_final: 0.8939 (mt0) REVERT: E 82 LEU cc_start: 0.9378 (mt) cc_final: 0.9178 (mt) REVERT: E 120 MET cc_start: 0.8355 (mtt) cc_final: 0.8081 (mtp) REVERT: E 129 ARG cc_start: 0.9519 (ttt180) cc_final: 0.9267 (mmm160) REVERT: F 53 GLU cc_start: 0.9632 (tp30) cc_final: 0.9246 (tp30) REVERT: F 68 ASP cc_start: 0.9218 (m-30) cc_final: 0.8962 (m-30) REVERT: F 74 GLU cc_start: 0.9421 (mm-30) cc_final: 0.9101 (mm-30) REVERT: H 39 ILE cc_start: 0.9492 (tp) cc_final: 0.9163 (pt) REVERT: H 45 LEU cc_start: 0.9427 (tp) cc_final: 0.9225 (tp) REVERT: H 62 MET cc_start: 0.9839 (mmm) cc_final: 0.9600 (mmm) REVERT: K 443 MET cc_start: 0.9110 (ppp) cc_final: 0.8873 (ppp) outliers start: 0 outliers final: 0 residues processed: 347 average time/residue: 0.2605 time to fit residues: 126.1091 Evaluate side-chains 308 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 61 optimal weight: 0.1980 chunk 8 optimal weight: 20.0000 chunk 69 optimal weight: 10.0000 chunk 96 optimal weight: 0.5980 chunk 20 optimal weight: 9.9990 chunk 98 optimal weight: 8.9990 chunk 53 optimal weight: 0.0870 chunk 71 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 overall best weight: 1.3560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2559 r_free = 0.2559 target = 0.028771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2303 r_free = 0.2303 target = 0.021621 restraints weight = 238012.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2364 r_free = 0.2364 target = 0.023269 restraints weight = 71871.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2401 r_free = 0.2401 target = 0.024293 restraints weight = 33410.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2424 r_free = 0.2424 target = 0.024950 restraints weight = 19729.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2439 r_free = 0.2439 target = 0.025384 restraints weight = 13748.044| |-----------------------------------------------------------------------------| r_work (final): 0.2433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.4693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13590 Z= 0.166 Angle : 0.676 7.959 19596 Z= 0.429 Chirality : 0.045 0.348 2232 Planarity : 0.004 0.038 1456 Dihedral : 31.690 173.080 4153 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.28), residues: 832 helix: 1.67 (0.21), residues: 587 sheet: -3.49 (1.55), residues: 10 loop : -0.80 (0.36), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 403 TYR 0.034 0.002 TYR E 99 PHE 0.018 0.002 PHE H 65 TRP 0.002 0.001 TRP K 481 HIS 0.006 0.001 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.17 (13590) covalent geometry : angle 0.67558 / 0.43 (19596) hydrogen bonds : bond 0.04932 / 5.42 ( 815) hydrogen bonds : angle 3.69686 / 4.81 ( 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 347 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 347 time to evaluate : 0.481 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: A 67 PHE cc_start: 0.9605 (t80) cc_final: 0.9389 (t80) REVERT: A 81 ASP cc_start: 0.9205 (m-30) cc_final: 0.8983 (m-30) REVERT: A 94 GLU cc_start: 0.9300 (mm-30) cc_final: 0.9093 (mm-30) REVERT: C 56 GLU cc_start: 0.8817 (tt0) cc_final: 0.8521 (tt0) REVERT: D 47 GLN cc_start: 0.9501 (tm-30) cc_final: 0.9282 (tm-30) REVERT: D 62 MET cc_start: 0.9850 (mmp) cc_final: 0.9544 (mmm) REVERT: D 73 ILE cc_start: 0.9838 (mt) cc_final: 0.9544 (tp) REVERT: D 113 GLU cc_start: 0.9301 (mt-10) cc_final: 0.8969 (mt-10) REVERT: E 55 GLN cc_start: 0.9364 (mt0) cc_final: 0.8870 (mt0) REVERT: E 120 MET cc_start: 0.8379 (mtt) cc_final: 0.8084 (mtp) REVERT: E 129 ARG cc_start: 0.9519 (ttt180) cc_final: 0.9252 (mmm160) REVERT: F 43 VAL cc_start: 0.9308 (t) cc_final: 0.8990 (m) REVERT: F 53 GLU cc_start: 0.9639 (tp30) cc_final: 0.9237 (tp30) REVERT: F 68 ASP cc_start: 0.9155 (m-30) cc_final: 0.8851 (m-30) REVERT: F 72 TYR cc_start: 0.9036 (m-80) cc_final: 0.8486 (m-10) REVERT: F 74 GLU cc_start: 0.9455 (mm-30) cc_final: 0.9159 (mm-30) REVERT: G 110 ASN cc_start: 0.9338 (t0) cc_final: 0.9124 (t0) REVERT: H 39 ILE cc_start: 0.9417 (tp) cc_final: 0.9020 (pt) REVERT: H 45 LEU cc_start: 0.9463 (tp) cc_final: 0.9052 (tp) REVERT: H 52 THR cc_start: 0.8566 (m) cc_final: 0.7522 (p) REVERT: H 62 MET cc_start: 0.9849 (mmm) cc_final: 0.9605 (mmm) REVERT: H 71 GLU cc_start: 0.9502 (mp0) cc_final: 0.9294 (mp0) REVERT: H 101 LEU cc_start: 0.9021 (mm) cc_final: 0.8520 (mm) outliers start: 0 outliers final: 0 residues processed: 347 average time/residue: 0.2538 time to fit residues: 122.7088 Evaluate side-chains 308 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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: 0.7980 chunk 79 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 25 optimal weight: 10.9990 chunk 84 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 chunk 24 optimal weight: 20.0000 chunk 82 optimal weight: 6.9990 chunk 1 optimal weight: 20.0000 chunk 76 optimal weight: 6.9990 overall best weight: 3.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2541 r_free = 0.2541 target = 0.028135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2284 r_free = 0.2284 target = 0.021054 restraints weight = 241592.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2344 r_free = 0.2344 target = 0.022669 restraints weight = 73131.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2381 r_free = 0.2381 target = 0.023673 restraints weight = 34264.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2404 r_free = 0.2404 target = 0.024311 restraints weight = 20313.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2420 r_free = 0.2420 target = 0.024744 restraints weight = 14234.943| |-----------------------------------------------------------------------------| r_work (final): 0.2422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.4939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 13590 Z= 0.208 Angle : 0.694 12.697 19596 Z= 0.437 Chirality : 0.043 0.352 2232 Planarity : 0.004 0.041 1456 Dihedral : 31.605 173.008 4153 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.28), residues: 832 helix: 1.51 (0.21), residues: 588 sheet: -3.80 (1.38), residues: 10 loop : -0.91 (0.36), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 33 TYR 0.041 0.002 TYR H 42 PHE 0.016 0.002 PHE D 65 TRP 0.003 0.001 TRP K 481 HIS 0.005 0.001 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.21 (13590) covalent geometry : angle 0.69354 / 0.44 (19596) hydrogen bonds : bond 0.05327 / 5.89 ( 815) hydrogen bonds : angle 3.91706 / 5.14 ( 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 342 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 0.517 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: A 81 ASP cc_start: 0.9227 (m-30) cc_final: 0.9026 (m-30) REVERT: B 74 GLU cc_start: 0.9336 (mm-30) cc_final: 0.8907 (mm-30) REVERT: D 62 MET cc_start: 0.9855 (mmp) cc_final: 0.9552 (mmm) REVERT: D 67 ASN cc_start: 0.9746 (t0) cc_final: 0.9134 (t0) REVERT: D 73 ILE cc_start: 0.9851 (mt) cc_final: 0.9567 (tp) REVERT: D 113 GLU cc_start: 0.9334 (mt-10) cc_final: 0.9052 (mt-10) REVERT: E 55 GLN cc_start: 0.9371 (mt0) cc_final: 0.8910 (mt0) REVERT: E 65 LEU cc_start: 0.9713 (mm) cc_final: 0.9475 (mm) REVERT: E 90 MET cc_start: 0.9270 (mmt) cc_final: 0.9037 (mmt) REVERT: E 120 MET cc_start: 0.8487 (mtt) cc_final: 0.8020 (mtt) REVERT: E 129 ARG cc_start: 0.9519 (ttt180) cc_final: 0.9253 (mmm160) REVERT: F 43 VAL cc_start: 0.9366 (t) cc_final: 0.9052 (m) REVERT: F 53 GLU cc_start: 0.9655 (tp30) cc_final: 0.9270 (tp30) REVERT: F 68 ASP cc_start: 0.9193 (m-30) cc_final: 0.8862 (m-30) REVERT: F 72 TYR cc_start: 0.9066 (m-80) cc_final: 0.8401 (m-10) REVERT: F 74 GLU cc_start: 0.9494 (mm-30) cc_final: 0.9191 (mm-30) REVERT: H 39 ILE cc_start: 0.9426 (tp) cc_final: 0.9042 (pt) REVERT: H 45 LEU cc_start: 0.9496 (tp) cc_final: 0.9275 (tp) REVERT: H 62 MET cc_start: 0.9875 (mmm) cc_final: 0.9624 (mmm) REVERT: H 101 LEU cc_start: 0.9042 (mm) cc_final: 0.8636 (mm) REVERT: H 105 GLU cc_start: 0.9687 (mp0) cc_final: 0.9484 (mp0) REVERT: K 403 ARG cc_start: 0.4015 (ptp-170) cc_final: 0.3492 (ptp-170) REVERT: K 411 MET cc_start: 0.7582 (ttp) cc_final: 0.6993 (ttp) outliers start: 0 outliers final: 0 residues processed: 342 average time/residue: 0.2579 time to fit residues: 122.6880 Evaluate side-chains 299 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 27 optimal weight: 20.0000 chunk 67 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 88 optimal weight: 0.0270 chunk 24 optimal weight: 10.0000 chunk 49 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 26 optimal weight: 20.0000 chunk 106 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 22 optimal weight: 20.0000 overall best weight: 3.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 470 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.028186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2296 r_free = 0.2296 target = 0.021302 restraints weight = 242811.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2358 r_free = 0.2358 target = 0.022913 restraints weight = 72105.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2395 r_free = 0.2395 target = 0.023939 restraints weight = 33857.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2420 r_free = 0.2420 target = 0.024628 restraints weight = 19741.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2436 r_free = 0.2436 target = 0.025072 restraints weight = 13448.258| |-----------------------------------------------------------------------------| r_work (final): 0.2437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.5183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13590 Z= 0.204 Angle : 0.686 8.226 19596 Z= 0.434 Chirality : 0.044 0.350 2232 Planarity : 0.004 0.040 1456 Dihedral : 31.545 173.333 4153 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % 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: 0.96 (0.28), residues: 832 helix: 1.34 (0.21), residues: 589 sheet: -4.00 (1.25), residues: 10 loop : -0.90 (0.36), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 45 TYR 0.049 0.002 TYR F 51 PHE 0.010 0.002 PHE A 67 TRP 0.004 0.001 TRP K 481 HIS 0.006 0.001 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.20 (13590) covalent geometry : angle 0.68577 / 0.43 (19596) hydrogen bonds : bond 0.05425 / 6.00 ( 815) hydrogen bonds : angle 3.92566 / 5.13 ( 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 337 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 337 time to evaluate : 0.487 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 94 GLU cc_start: 0.9467 (mm-30) cc_final: 0.9173 (mm-30) REVERT: B 74 GLU cc_start: 0.9366 (mm-30) cc_final: 0.8954 (mm-30) REVERT: D 35 GLU cc_start: 0.9230 (pm20) cc_final: 0.8835 (pp20) REVERT: D 47 GLN cc_start: 0.9550 (tm-30) cc_final: 0.9309 (tm-30) REVERT: D 62 MET cc_start: 0.9868 (mmp) cc_final: 0.9561 (mmm) REVERT: D 67 ASN cc_start: 0.9518 (t0) cc_final: 0.9173 (t0) REVERT: D 71 GLU cc_start: 0.9593 (mm-30) cc_final: 0.9277 (mm-30) REVERT: D 73 ILE cc_start: 0.9865 (mt) cc_final: 0.9587 (tp) REVERT: D 113 GLU cc_start: 0.9354 (mt-10) cc_final: 0.9044 (mt-10) REVERT: E 82 LEU cc_start: 0.9408 (mt) cc_final: 0.9167 (mt) REVERT: E 120 MET cc_start: 0.8387 (mtt) cc_final: 0.7994 (mtt) REVERT: F 43 VAL cc_start: 0.9370 (t) cc_final: 0.9034 (m) REVERT: F 53 GLU cc_start: 0.9670 (tp30) cc_final: 0.9278 (tp30) REVERT: F 68 ASP cc_start: 0.9206 (m-30) cc_final: 0.9001 (m-30) REVERT: F 74 GLU cc_start: 0.9521 (mm-30) cc_final: 0.9190 (mm-30) REVERT: G 56 GLU cc_start: 0.8889 (tt0) cc_final: 0.8646 (tt0) REVERT: H 39 ILE cc_start: 0.9422 (tp) cc_final: 0.9027 (pt) REVERT: H 45 LEU cc_start: 0.9512 (tp) cc_final: 0.9311 (tp) REVERT: H 62 MET cc_start: 0.9879 (mmm) cc_final: 0.9627 (mmm) REVERT: H 101 LEU cc_start: 0.8995 (mm) cc_final: 0.8700 (mm) outliers start: 0 outliers final: 0 residues processed: 337 average time/residue: 0.2614 time to fit residues: 121.8487 Evaluate side-chains 302 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 2 optimal weight: 20.0000 chunk 81 optimal weight: 4.9990 chunk 15 optimal weight: 20.0000 chunk 7 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2529 r_free = 0.2529 target = 0.027643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2276 r_free = 0.2276 target = 0.020803 restraints weight = 251489.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2337 r_free = 0.2337 target = 0.022395 restraints weight = 76835.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2374 r_free = 0.2374 target = 0.023386 restraints weight = 36137.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2398 r_free = 0.2398 target = 0.024017 restraints weight = 21376.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2414 r_free = 0.2414 target = 0.024444 restraints weight = 14908.319| |-----------------------------------------------------------------------------| r_work (final): 0.2409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.5419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 13590 Z= 0.256 Angle : 0.705 8.417 19596 Z= 0.447 Chirality : 0.043 0.350 2232 Planarity : 0.004 0.042 1456 Dihedral : 31.458 173.777 4153 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.27), residues: 832 helix: 0.87 (0.20), residues: 582 sheet: -4.26 (1.11), residues: 10 loop : -0.96 (0.35), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 45 TYR 0.037 0.002 TYR F 51 PHE 0.016 0.002 PHE E 104 TRP 0.006 0.002 TRP K 481 HIS 0.006 0.001 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.26 (13590) covalent geometry : angle 0.70488 / 0.45 (19596) hydrogen bonds : bond 0.06460 / 7.13 ( 815) hydrogen bonds : angle 4.21706 / 5.49 ( 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 329 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 329 time to evaluate : 0.421 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: B 74 GLU cc_start: 0.9417 (mm-30) cc_final: 0.9002 (mm-30) REVERT: D 62 MET cc_start: 0.9883 (mmp) cc_final: 0.9589 (mmm) REVERT: D 67 ASN cc_start: 0.9464 (t0) cc_final: 0.9128 (t0) REVERT: D 71 GLU cc_start: 0.9607 (mm-30) cc_final: 0.9275 (mm-30) REVERT: D 73 ILE cc_start: 0.9876 (mt) cc_final: 0.9606 (tp) REVERT: D 113 GLU cc_start: 0.9362 (mt-10) cc_final: 0.9051 (mt-10) REVERT: E 62 ILE cc_start: 0.9553 (mm) cc_final: 0.9257 (mm) REVERT: E 93 GLN cc_start: 0.9566 (tt0) cc_final: 0.9139 (tp40) REVERT: E 120 MET cc_start: 0.8331 (mtt) cc_final: 0.7957 (mtt) REVERT: F 43 VAL cc_start: 0.9438 (t) cc_final: 0.9103 (m) REVERT: F 53 GLU cc_start: 0.9685 (tp30) cc_final: 0.9300 (tp30) REVERT: F 68 ASP cc_start: 0.9347 (m-30) cc_final: 0.9142 (m-30) REVERT: F 74 GLU cc_start: 0.9563 (mm-30) cc_final: 0.9218 (mm-30) REVERT: G 110 ASN cc_start: 0.9299 (t0) cc_final: 0.8819 (m110) REVERT: G 111 ILE cc_start: 0.9455 (mp) cc_final: 0.9004 (mp) REVERT: H 39 ILE cc_start: 0.9447 (tp) cc_final: 0.9051 (pt) REVERT: H 45 LEU cc_start: 0.9517 (tp) cc_final: 0.9314 (tp) REVERT: H 59 MET cc_start: 0.9525 (tpt) cc_final: 0.9159 (tpp) REVERT: H 62 MET cc_start: 0.9867 (mmm) cc_final: 0.9627 (mmm) REVERT: H 65 PHE cc_start: 0.9693 (t80) cc_final: 0.9447 (t80) REVERT: H 105 GLU cc_start: 0.9705 (mp0) cc_final: 0.9497 (mp0) outliers start: 0 outliers final: 0 residues processed: 329 average time/residue: 0.2556 time to fit residues: 116.7435 Evaluate side-chains 292 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 292 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 7 optimal weight: 20.0000 chunk 59 optimal weight: 3.9990 chunk 11 optimal weight: 20.0000 chunk 87 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 6 optimal weight: 20.0000 chunk 36 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2540 r_free = 0.2540 target = 0.028088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2285 r_free = 0.2285 target = 0.021239 restraints weight = 248618.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2347 r_free = 0.2347 target = 0.022873 restraints weight = 75408.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2387 r_free = 0.2387 target = 0.023874 restraints weight = 35216.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2413 r_free = 0.2413 target = 0.024561 restraints weight = 20901.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2430 r_free = 0.2430 target = 0.025007 restraints weight = 14245.215| |-----------------------------------------------------------------------------| r_work (final): 0.2422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.5564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 13590 Z= 0.220 Angle : 0.680 8.473 19596 Z= 0.433 Chirality : 0.043 0.350 2232 Planarity : 0.004 0.041 1456 Dihedral : 31.475 174.168 4153 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % 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: 0.48 (0.27), residues: 832 helix: 0.98 (0.20), residues: 580 sheet: -4.08 (1.21), residues: 10 loop : -0.98 (0.35), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 45 TYR 0.020 0.002 TYR F 51 PHE 0.031 0.002 PHE C 25 TRP 0.005 0.001 TRP K 481 HIS 0.006 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.22 (13590) covalent geometry : angle 0.68049 / 0.43 (19596) hydrogen bonds : bond 0.05810 / 6.42 ( 815) hydrogen bonds : angle 4.16403 / 5.50 ( 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 324 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 324 time to evaluate : 0.505 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: A 67 PHE cc_start: 0.9630 (t80) cc_final: 0.9411 (t80) REVERT: B 29 ILE cc_start: 0.9536 (mm) cc_final: 0.9231 (tp) REVERT: B 74 GLU cc_start: 0.9411 (mm-30) cc_final: 0.9001 (mm-30) REVERT: C 25 PHE cc_start: 0.8414 (m-10) cc_final: 0.8180 (m-80) REVERT: C 56 GLU cc_start: 0.8998 (tt0) cc_final: 0.8623 (mt-10) REVERT: D 47 GLN cc_start: 0.9577 (tm-30) cc_final: 0.9374 (tm-30) REVERT: D 62 MET cc_start: 0.9869 (mmp) cc_final: 0.9567 (mmm) REVERT: D 67 ASN cc_start: 0.9507 (t0) cc_final: 0.9123 (t0) REVERT: D 71 GLU cc_start: 0.9613 (mm-30) cc_final: 0.9287 (mm-30) REVERT: D 73 ILE cc_start: 0.9873 (mt) cc_final: 0.9589 (tp) REVERT: D 113 GLU cc_start: 0.9323 (mt-10) cc_final: 0.8992 (mt-10) REVERT: E 61 LEU cc_start: 0.8858 (mm) cc_final: 0.8636 (mm) REVERT: E 62 ILE cc_start: 0.9551 (mm) cc_final: 0.9274 (mm) REVERT: E 93 GLN cc_start: 0.9577 (tt0) cc_final: 0.9123 (tp40) REVERT: F 53 GLU cc_start: 0.9688 (tp30) cc_final: 0.9306 (tp30) REVERT: F 68 ASP cc_start: 0.9247 (m-30) cc_final: 0.9002 (m-30) REVERT: F 74 GLU cc_start: 0.9556 (mm-30) cc_final: 0.9218 (mm-30) REVERT: G 110 ASN cc_start: 0.9295 (t0) cc_final: 0.8839 (m110) REVERT: G 111 ILE cc_start: 0.9446 (mp) cc_final: 0.9006 (mp) REVERT: H 39 ILE cc_start: 0.9468 (tp) cc_final: 0.9110 (pt) REVERT: H 45 LEU cc_start: 0.9520 (tp) cc_final: 0.9319 (tp) REVERT: H 62 MET cc_start: 0.9871 (mmm) cc_final: 0.9645 (mmm) REVERT: H 101 LEU cc_start: 0.8897 (mm) cc_final: 0.8654 (mm) REVERT: H 105 GLU cc_start: 0.9700 (mp0) cc_final: 0.9485 (mp0) REVERT: K 443 MET cc_start: 0.9146 (ppp) cc_final: 0.8941 (ppp) outliers start: 0 outliers final: 0 residues processed: 324 average time/residue: 0.2522 time to fit residues: 113.9150 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 : 0.431 ------------------------------------------------------------------------------- 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: 7.9990 chunk 104 optimal weight: 7.9990 chunk 101 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 76 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 16 optimal weight: 20.0000 chunk 75 optimal weight: 9.9990 chunk 34 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2513 r_free = 0.2513 target = 0.027277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2263 r_free = 0.2263 target = 0.020710 restraints weight = 257458.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2325 r_free = 0.2325 target = 0.022299 restraints weight = 78387.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2364 r_free = 0.2364 target = 0.023288 restraints weight = 36561.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2389 r_free = 0.2389 target = 0.023923 restraints weight = 21345.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2405 r_free = 0.2405 target = 0.024350 restraints weight = 14567.549| |-----------------------------------------------------------------------------| r_work (final): 0.2397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.5713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 13590 Z= 0.302 Angle : 0.725 8.550 19596 Z= 0.459 Chirality : 0.043 0.349 2232 Planarity : 0.005 0.045 1456 Dihedral : 31.435 174.960 4153 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % 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: -0.29 (0.27), residues: 832 helix: 0.38 (0.20), residues: 582 sheet: -4.77 (0.88), residues: 10 loop : -1.20 (0.35), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 42 TYR 0.020 0.002 TYR F 51 PHE 0.021 0.002 PHE D 65 TRP 0.008 0.002 TRP K 481 HIS 0.006 0.002 HIS K 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.30 (13590) covalent geometry : angle 0.72476 / 0.46 (19596) hydrogen bonds : bond 0.07191 / 7.95 ( 815) hydrogen bonds : angle 4.56844 / 6.01 ( 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 312 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 0.438 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: A 67 PHE cc_start: 0.9649 (t80) cc_final: 0.9446 (t80) REVERT: A 106 ASP cc_start: 0.9287 (m-30) cc_final: 0.9060 (m-30) REVERT: A 110 CYS cc_start: 0.9608 (m) cc_final: 0.9150 (t) REVERT: A 124 ILE cc_start: 0.9697 (mp) cc_final: 0.9348 (mp) REVERT: B 29 ILE cc_start: 0.9483 (mm) cc_final: 0.9161 (tp) REVERT: B 53 GLU cc_start: 0.9616 (tp30) cc_final: 0.8953 (tt0) REVERT: B 74 GLU cc_start: 0.9457 (mm-30) cc_final: 0.9041 (mm-30) REVERT: D 47 GLN cc_start: 0.9582 (tm-30) cc_final: 0.9380 (tm-30) REVERT: D 62 MET cc_start: 0.9873 (mmp) cc_final: 0.9595 (mmm) REVERT: D 71 GLU cc_start: 0.9624 (mm-30) cc_final: 0.9289 (mm-30) REVERT: D 73 ILE cc_start: 0.9887 (mt) cc_final: 0.9591 (tp) REVERT: D 113 GLU cc_start: 0.9392 (mt-10) cc_final: 0.9054 (mt-10) REVERT: E 62 ILE cc_start: 0.9547 (mm) cc_final: 0.9289 (mm) REVERT: E 93 GLN cc_start: 0.9596 (tt0) cc_final: 0.9164 (tp40) REVERT: F 53 GLU cc_start: 0.9717 (tp30) cc_final: 0.9344 (tp30) REVERT: F 68 ASP cc_start: 0.9342 (m-30) cc_final: 0.9130 (m-30) REVERT: F 74 GLU cc_start: 0.9573 (mm-30) cc_final: 0.9232 (mm-30) REVERT: H 39 ILE cc_start: 0.9510 (tp) cc_final: 0.9155 (pt) REVERT: H 59 MET cc_start: 0.9518 (tpt) cc_final: 0.9210 (tpp) REVERT: K 443 MET cc_start: 0.9205 (ppp) cc_final: 0.8997 (ppp) outliers start: 0 outliers final: 0 residues processed: 312 average time/residue: 0.2427 time to fit residues: 106.1037 Evaluate side-chains 277 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 5 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 14 optimal weight: 20.0000 chunk 40 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 24 optimal weight: 20.0000 chunk 51 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 4 optimal weight: 10.0000 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2539 r_free = 0.2539 target = 0.028058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2285 r_free = 0.2285 target = 0.021249 restraints weight = 249329.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2346 r_free = 0.2346 target = 0.022853 restraints weight = 75557.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2386 r_free = 0.2386 target = 0.023871 restraints weight = 35377.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2411 r_free = 0.2411 target = 0.024522 restraints weight = 20771.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2427 r_free = 0.2427 target = 0.024968 restraints weight = 14331.217| |-----------------------------------------------------------------------------| r_work (final): 0.2420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.5799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13590 Z= 0.199 Angle : 0.668 8.504 19596 Z= 0.426 Chirality : 0.043 0.350 2232 Planarity : 0.004 0.038 1456 Dihedral : 31.482 175.173 4153 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.28), residues: 832 helix: 0.90 (0.21), residues: 587 sheet: -4.69 (0.92), residues: 10 loop : -1.09 (0.36), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG K 403 TYR 0.018 0.002 TYR F 51 PHE 0.033 0.002 PHE C 25 TRP 0.005 0.001 TRP K 481 HIS 0.006 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.20 (13590) covalent geometry : angle 0.66837 / 0.43 (19596) hydrogen bonds : bond 0.05724 / 6.30 ( 815) hydrogen bonds : angle 4.16207 / 5.48 ( 2040) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4166.54 seconds wall clock time: 71 minutes 53.57 seconds (4313.57 seconds total)