Starting phenix.real_space_refine on Wed Aug 5 23:52:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c4d_45182/08_2026/9c4d_45182.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c4d_45182/08_2026/9c4d_45182.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c4d_45182/08_2026/9c4d_45182.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c4d_45182/08_2026/9c4d_45182.map" model { file = "/net/cci-nas-00/data/ceres_data/9c4d_45182/08_2026/9c4d_45182.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c4d_45182/08_2026/9c4d_45182.cif" } resolution = 4.17 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= 0.012 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 Mn 16 7.51 5 P 154 5.49 5 S 24 5.16 5 C 7426 2.51 5 N 2149 2.21 5 O 2724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12493 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1563 Classifications: {'DNA': 77} Link IDs: {'rna3p': 76} Chain: "B" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1594 Classifications: {'DNA': 77} Link IDs: {'rna3p': 76} Chain: "C" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1165 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 137} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: D, E, F, G, H, I, J Time building chain proxies: 1.62, per 1000 atoms: 0.13 Number of scatterers: 12493 At special positions: 0 Unit cell: (94.8537, 91.5255, 269.584, 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) Mn 16 24.99 S 24 16.00 P 154 15.00 O 2724 8.00 N 2149 7.00 C 7426 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 488.1 milliseconds 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2128 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 8 sheets defined 84.4% alpha, 2.9% beta 74 base pairs and 133 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'C' and resid 3 through 21 removed outlier: 3.662A pdb=" N GLU C 7 " --> pdb=" O THR C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 33 Processing helix chain 'C' and resid 35 through 49 Processing helix chain 'C' and resid 63 through 88 removed outlier: 3.567A pdb=" N ILE C 87 " --> pdb=" O PHE C 83 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY C 88 " --> pdb=" O LEU C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 102 removed outlier: 4.172A pdb=" N TYR C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ASN C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 122 Processing helix chain 'C' and resid 124 through 139 Processing helix chain 'C' and resid 140 through 142 No H-bonds generated for 'chain 'C' and resid 140 through 142' Processing helix chain 'D' and resid 4 through 21 Processing helix chain 'D' and resid 24 through 33 Processing helix chain 'D' and resid 35 through 49 Processing helix chain 'D' and resid 63 through 88 removed outlier: 3.567A pdb=" N ILE D 87 " --> pdb=" O PHE D 83 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY D 88 " --> pdb=" O LEU D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 4.172A pdb=" N TYR D 95 " --> pdb=" O GLU D 91 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ASN D 96 " --> pdb=" O GLU D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 122 Processing helix chain 'D' and resid 124 through 139 Processing helix chain 'D' and resid 140 through 142 No H-bonds generated for 'chain 'D' and resid 140 through 142' Processing helix chain 'E' and resid 4 through 21 Processing helix chain 'E' and resid 24 through 33 Processing helix chain 'E' and resid 35 through 49 Processing helix chain 'E' and resid 63 through 88 removed outlier: 3.567A pdb=" N ILE E 87 " --> pdb=" O PHE E 83 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY E 88 " --> pdb=" O LEU E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 102 removed outlier: 4.171A pdb=" N TYR E 95 " --> pdb=" O GLU E 91 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ASN E 96 " --> pdb=" O GLU E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 122 Processing helix chain 'E' and resid 124 through 139 Processing helix chain 'E' and resid 140 through 142 No H-bonds generated for 'chain 'E' and resid 140 through 142' Processing helix chain 'F' and resid 4 through 21 Processing helix chain 'F' and resid 24 through 33 Processing helix chain 'F' and resid 35 through 49 Processing helix chain 'F' and resid 63 through 88 removed outlier: 3.567A pdb=" N ILE F 87 " --> pdb=" O PHE F 83 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY F 88 " --> pdb=" O LEU F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 102 removed outlier: 4.173A pdb=" N TYR F 95 " --> pdb=" O GLU F 91 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ASN F 96 " --> pdb=" O GLU F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 122 Processing helix chain 'F' and resid 124 through 139 Processing helix chain 'F' and resid 140 through 142 No H-bonds generated for 'chain 'F' and resid 140 through 142' Processing helix chain 'G' and resid 4 through 21 Processing helix chain 'G' and resid 24 through 33 Processing helix chain 'G' and resid 35 through 49 Processing helix chain 'G' and resid 63 through 88 removed outlier: 3.567A pdb=" N ILE G 87 " --> pdb=" O PHE G 83 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY G 88 " --> pdb=" O LEU G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 102 removed outlier: 4.172A pdb=" N TYR G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ASN G 96 " --> pdb=" O GLU G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 122 Processing helix chain 'G' and resid 124 through 139 Processing helix chain 'G' and resid 140 through 142 No H-bonds generated for 'chain 'G' and resid 140 through 142' Processing helix chain 'H' and resid 4 through 21 Processing helix chain 'H' and resid 24 through 33 Processing helix chain 'H' and resid 35 through 49 Processing helix chain 'H' and resid 63 through 88 removed outlier: 3.567A pdb=" N ILE H 87 " --> pdb=" O PHE H 83 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY H 88 " --> pdb=" O LEU H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 4.172A pdb=" N TYR H 95 " --> pdb=" O GLU H 91 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ASN H 96 " --> pdb=" O GLU H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 122 Processing helix chain 'H' and resid 124 through 139 Processing helix chain 'H' and resid 140 through 142 No H-bonds generated for 'chain 'H' and resid 140 through 142' Processing helix chain 'I' and resid 4 through 21 Processing helix chain 'I' and resid 24 through 33 Processing helix chain 'I' and resid 35 through 49 Processing helix chain 'I' and resid 63 through 88 removed outlier: 3.568A pdb=" N ILE I 87 " --> pdb=" O PHE I 83 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY I 88 " --> pdb=" O LEU I 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 102 removed outlier: 4.172A pdb=" N TYR I 95 " --> pdb=" O GLU I 91 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ASN I 96 " --> pdb=" O GLU I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 122 Processing helix chain 'I' and resid 124 through 139 Processing helix chain 'I' and resid 140 through 142 No H-bonds generated for 'chain 'I' and resid 140 through 142' Processing helix chain 'J' and resid 4 through 21 Processing helix chain 'J' and resid 24 through 33 Processing helix chain 'J' and resid 35 through 49 Processing helix chain 'J' and resid 63 through 88 removed outlier: 3.566A pdb=" N ILE J 87 " --> pdb=" O PHE J 83 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY J 88 " --> pdb=" O LEU J 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 90 through 102 removed outlier: 4.172A pdb=" N TYR J 95 " --> pdb=" O GLU J 91 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ASN J 96 " --> pdb=" O GLU J 92 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 122 Processing helix chain 'J' and resid 124 through 139 Processing helix chain 'J' and resid 140 through 142 No H-bonds generated for 'chain 'J' and resid 140 through 142' Processing sheet with id=AA1, first strand: chain 'C' and resid 52 through 54 Processing sheet with id=AA2, first strand: chain 'D' and resid 52 through 54 Processing sheet with id=AA3, first strand: chain 'E' and resid 52 through 54 Processing sheet with id=AA4, first strand: chain 'F' and resid 52 through 54 Processing sheet with id=AA5, first strand: chain 'G' and resid 52 through 54 Processing sheet with id=AA6, first strand: chain 'H' and resid 52 through 54 Processing sheet with id=AA7, first strand: chain 'I' and resid 52 through 54 Processing sheet with id=AA8, first strand: chain 'J' and resid 52 through 54 680 hydrogen bonds defined for protein. 2040 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 172 hydrogen bonds 344 hydrogen bond angles 0 basepair planarities 74 basepair parallelities 133 stacking parallelities Total time for adding SS restraints: 1.87 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2516 1.33 - 1.45: 3529 1.45 - 1.57: 6621 1.57 - 1.69: 306 1.69 - 1.80: 48 Bond restraints: 13020 Sorted by residual: bond pdb=" C3' DT B -43 " pdb=" C2' DT B -43 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" C3' DC B -63 " pdb=" C2' DC B -63 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 bond pdb=" C3' DC A 74 " pdb=" C2' DC A 74 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DA B -25 " pdb=" C2' DA B -25 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.00e+01 bond pdb=" C3' DG B -62 " pdb=" C2' DG B -62 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.36e+00 ... (remaining 13015 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 17155 1.30 - 2.59: 902 2.59 - 3.89: 112 3.89 - 5.18: 10 5.18 - 6.48: 8 Bond angle restraints: 18187 Sorted by residual: angle pdb=" N3 DT B -57 " pdb=" C4 DT B -57 " pdb=" O4 DT B -57 " ideal model delta sigma weight residual 119.90 122.64 -2.74 6.00e-01 2.78e+00 2.08e+01 angle pdb=" N3 DT A 26 " pdb=" C4 DT A 26 " pdb=" O4 DT A 26 " ideal model delta sigma weight residual 119.90 122.62 -2.72 6.00e-01 2.78e+00 2.05e+01 angle pdb=" N3 DT B -11 " pdb=" C4 DT B -11 " pdb=" O4 DT B -11 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.03e+01 angle pdb=" N3 DT A 40 " pdb=" C4 DT A 40 " pdb=" O4 DT A 40 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.02e+01 angle pdb=" N3 DT A 16 " pdb=" C4 DT A 16 " pdb=" O4 DT A 16 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.01e+01 ... (remaining 18182 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 6882 35.90 - 71.80: 669 71.80 - 107.70: 0 107.70 - 143.60: 1 143.60 - 179.50: 10 Dihedral angle restraints: 7562 sinusoidal: 4250 harmonic: 3312 Sorted by residual: dihedral pdb=" CA GLU H 55 " pdb=" C GLU H 55 " pdb=" N LYS H 56 " pdb=" CA LYS H 56 " ideal model delta harmonic sigma weight residual -180.00 -158.40 -21.60 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA GLU I 55 " pdb=" C GLU I 55 " pdb=" N LYS I 56 " pdb=" CA LYS I 56 " ideal model delta harmonic sigma weight residual -180.00 -158.41 -21.59 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA GLU F 55 " pdb=" C GLU F 55 " pdb=" N LYS F 56 " pdb=" CA LYS F 56 " ideal model delta harmonic sigma weight residual -180.00 -158.41 -21.59 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 7559 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1331 0.034 - 0.067: 476 0.067 - 0.101: 130 0.101 - 0.134: 47 0.134 - 0.168: 8 Chirality restraints: 1992 Sorted by residual: chirality pdb=" C3' DA A 60 " pdb=" C4' DA A 60 " pdb=" O3' DA A 60 " pdb=" C2' DA A 60 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.06e-01 chirality pdb=" C3' DC B -66 " pdb=" C4' DC B -66 " pdb=" O3' DC B -66 " pdb=" C2' DC B -66 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.65e-01 chirality pdb=" C3' DA B -24 " pdb=" C4' DA B -24 " pdb=" O3' DA B -24 " pdb=" C2' DA B -24 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.96e-01 ... (remaining 1989 not shown) Planarity restraints: 1778 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT A 24 " 0.023 2.00e-02 2.50e+03 1.13e-02 3.17e+00 pdb=" N1 DT A 24 " -0.024 2.00e-02 2.50e+03 pdb=" C2 DT A 24 " -0.004 2.00e-02 2.50e+03 pdb=" O2 DT A 24 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DT A 24 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DT A 24 " 0.005 2.00e-02 2.50e+03 pdb=" O4 DT A 24 " 0.007 2.00e-02 2.50e+03 pdb=" C5 DT A 24 " 0.001 2.00e-02 2.50e+03 pdb=" C7 DT A 24 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DT A 24 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 55 " 0.006 2.00e-02 2.50e+03 1.13e-02 1.27e+00 pdb=" C GLU C 55 " -0.019 2.00e-02 2.50e+03 pdb=" O GLU C 55 " 0.007 2.00e-02 2.50e+03 pdb=" N LYS C 56 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU I 55 " 0.005 2.00e-02 2.50e+03 1.12e-02 1.25e+00 pdb=" C GLU I 55 " -0.019 2.00e-02 2.50e+03 pdb=" O GLU I 55 " 0.007 2.00e-02 2.50e+03 pdb=" N LYS I 56 " 0.006 2.00e-02 2.50e+03 ... (remaining 1775 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 248 2.65 - 3.21: 11050 3.21 - 3.77: 22212 3.77 - 4.34: 27150 4.34 - 4.90: 41222 Nonbonded interactions: 101882 Sorted by model distance: nonbonded pdb=" OP1 DT B -20 " pdb=" OH TYR D 54 " model vdw 2.085 3.040 nonbonded pdb=" OP1 DT A 27 " pdb=" NZ LYS E 56 " model vdw 2.114 3.120 nonbonded pdb=" OE1 GLU H 102 " pdb="MN MN H 201 " model vdw 2.123 2.320 nonbonded pdb=" OE1 GLU E 102 " pdb="MN MN E 201 " model vdw 2.124 2.320 nonbonded pdb=" OE1 GLU J 102 " pdb="MN MN J 201 " model vdw 2.124 2.320 ... (remaining 101877 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 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 10.540 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: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.530 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13020 Z= 0.367 Angle : 0.610 6.477 18187 Z= 0.532 Chirality : 0.040 0.168 1992 Planarity : 0.002 0.014 1778 Dihedral : 22.140 179.502 5434 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.34 % Allowed : 3.91 % Favored : 93.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 4.02 (0.26), residues: 1104 helix: 3.09 (0.18), residues: 880 sheet: None (None), residues: 0 loop : 0.86 (0.45), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 126 TYR 0.005 0.001 TYR D 75 PHE 0.003 0.001 PHE I 120 TRP 0.004 0.001 TRP F 107 HIS 0.002 0.001 HIS J 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.37 (13020) covalent geometry : angle 0.60993 / 0.53 (18187) hydrogen bonds : bond 0.10482 / 12.29 ( 852) hydrogen bonds : angle 4.13775 / 5.15 ( 2384) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 0.416 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: D 42 MET cc_start: 0.8849 (tpp) cc_final: 0.7901 (tpp) REVERT: E 112 ARG cc_start: 0.8147 (mmp80) cc_final: 0.7903 (mmp80) REVERT: F 14 TYR cc_start: 0.7095 (t80) cc_final: 0.6876 (t80) REVERT: F 51 TYR cc_start: 0.8041 (m-80) cc_final: 0.7620 (m-80) REVERT: F 80 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8414 (tp) REVERT: F 83 PHE cc_start: 0.8905 (t80) cc_final: 0.8607 (t80) REVERT: H 15 MET cc_start: 0.9108 (ttp) cc_final: 0.8852 (ttm) REVERT: H 42 MET cc_start: 0.8371 (tpp) cc_final: 0.8047 (tpp) REVERT: I 51 TYR cc_start: 0.7619 (m-80) cc_final: 0.7231 (m-10) REVERT: I 107 TRP cc_start: 0.5520 (m100) cc_final: 0.5280 (m100) REVERT: J 107 TRP cc_start: 0.6915 (m100) cc_final: 0.6476 (t-100) outliers start: 24 outliers final: 8 residues processed: 179 average time/residue: 0.1125 time to fit residues: 28.5027 Evaluate side-chains 85 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 123 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 HIS E 139 HIS ** F 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 12 GLN I 139 HIS ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.089855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.069749 restraints weight = 82480.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.068788 restraints weight = 57815.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.068990 restraints weight = 48915.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.069064 restraints weight = 38239.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.069225 restraints weight = 36246.305| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 13020 Z= 0.233 Angle : 0.689 11.245 18187 Z= 0.387 Chirality : 0.045 0.276 1992 Planarity : 0.005 0.079 1778 Dihedral : 27.914 178.607 2986 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.20 % Allowed : 2.05 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.68 (0.25), residues: 1104 helix: 2.29 (0.17), residues: 888 sheet: None (None), residues: 0 loop : -0.40 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG I 76 TYR 0.022 0.002 TYR E 9 PHE 0.012 0.002 PHE H 120 TRP 0.015 0.003 TRP G 107 HIS 0.007 0.001 HIS F 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.23 (13020) covalent geometry : angle 0.68910 / 0.39 (18187) hydrogen bonds : bond 0.06125 / 6.95 ( 852) hydrogen bonds : angle 4.06920 / 5.05 ( 2384) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 83 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 15 MET cc_start: 0.8434 (ppp) cc_final: 0.8183 (ppp) REVERT: D 42 MET cc_start: 0.8703 (tpp) cc_final: 0.8117 (tpp) REVERT: F 42 MET cc_start: 0.8214 (tpt) cc_final: 0.7660 (tpp) REVERT: F 78 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8343 (pp20) REVERT: F 112 ARG cc_start: 0.8882 (mmp80) cc_final: 0.8518 (mmp80) REVERT: F 134 GLN cc_start: 0.8586 (pt0) cc_final: 0.8365 (pt0) REVERT: G 6 MET cc_start: 0.8639 (mtp) cc_final: 0.8116 (tmm) REVERT: G 82 GLN cc_start: 0.8761 (tm-30) cc_final: 0.8225 (tm-30) REVERT: G 117 VAL cc_start: 0.8732 (t) cc_final: 0.8402 (t) REVERT: G 142 GLN cc_start: 0.6959 (mt0) cc_final: 0.6585 (mp10) REVERT: H 42 MET cc_start: 0.8378 (tpp) cc_final: 0.8068 (tpp) REVERT: I 6 MET cc_start: 0.7288 (mmm) cc_final: 0.6900 (mmm) REVERT: I 51 TYR cc_start: 0.7813 (m-80) cc_final: 0.7503 (m-10) REVERT: J 107 TRP cc_start: 0.7456 (m100) cc_final: 0.6502 (t-100) outliers start: 2 outliers final: 0 residues processed: 85 average time/residue: 0.1225 time to fit residues: 14.7620 Evaluate side-chains 61 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 21 optimal weight: 0.8980 chunk 10 optimal weight: 8.9990 chunk 12 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 118 GLN ** H 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 139 HIS ** 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 = 0.3997 r_free = 0.3997 target = 0.090168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.069727 restraints weight = 82688.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.069167 restraints weight = 60108.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.069380 restraints weight = 47745.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.069406 restraints weight = 37334.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.069654 restraints weight = 35323.499| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13020 Z= 0.161 Angle : 0.580 7.158 18187 Z= 0.334 Chirality : 0.041 0.291 1992 Planarity : 0.003 0.039 1778 Dihedral : 27.996 179.420 2986 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 0.29 % Allowed : 3.32 % Favored : 96.39 % 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: 2.81 (0.26), residues: 1104 helix: 2.38 (0.17), residues: 888 sheet: None (None), residues: 0 loop : -0.41 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 112 TYR 0.016 0.001 TYR J 9 PHE 0.008 0.001 PHE J 120 TRP 0.006 0.001 TRP E 107 HIS 0.005 0.001 HIS F 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.16 (13020) covalent geometry : angle 0.58030 / 0.33 (18187) hydrogen bonds : bond 0.04612 / 5.09 ( 852) hydrogen bonds : angle 3.88038 / 4.80 ( 2384) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 81 time to evaluate : 0.335 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: C 15 MET cc_start: 0.8358 (ppp) cc_final: 0.8137 (ppp) REVERT: C 42 MET cc_start: 0.8664 (mmp) cc_final: 0.8216 (tpp) REVERT: D 42 MET cc_start: 0.8661 (tpp) cc_final: 0.8227 (tpp) REVERT: E 6 MET cc_start: 0.8030 (tmm) cc_final: 0.7805 (tmm) REVERT: E 118 GLN cc_start: 0.8637 (tm-30) cc_final: 0.7988 (tp-100) REVERT: E 121 GLU cc_start: 0.8488 (pt0) cc_final: 0.8036 (pp20) REVERT: F 42 MET cc_start: 0.8184 (tpt) cc_final: 0.7683 (tpp) REVERT: F 51 TYR cc_start: 0.8251 (m-80) cc_final: 0.7696 (m-80) REVERT: F 112 ARG cc_start: 0.8992 (mmp80) cc_final: 0.8744 (mmp80) REVERT: G 142 GLN cc_start: 0.7083 (mt0) cc_final: 0.6760 (mp10) REVERT: H 42 MET cc_start: 0.8489 (tpp) cc_final: 0.8175 (tpp) REVERT: I 51 TYR cc_start: 0.7707 (m-80) cc_final: 0.7313 (m-10) REVERT: J 107 TRP cc_start: 0.7418 (m100) cc_final: 0.6551 (t-100) outliers start: 3 outliers final: 1 residues processed: 83 average time/residue: 0.0932 time to fit residues: 11.7139 Evaluate side-chains 62 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 98 optimal weight: 2.9990 chunk 44 optimal weight: 0.0670 chunk 111 optimal weight: 8.9990 chunk 63 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 124 optimal weight: 9.9990 chunk 43 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 118 GLN ** H 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 134 GLN ** J 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.090209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.069278 restraints weight = 79946.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.068951 restraints weight = 60490.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.069269 restraints weight = 46448.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.069274 restraints weight = 41320.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.069511 restraints weight = 35534.657| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13020 Z= 0.143 Angle : 0.579 9.694 18187 Z= 0.329 Chirality : 0.041 0.292 1992 Planarity : 0.003 0.071 1778 Dihedral : 28.056 179.920 2986 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.10 % Allowed : 1.86 % Favored : 98.05 % 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: 2.87 (0.26), residues: 1104 helix: 2.43 (0.17), residues: 888 sheet: None (None), residues: 0 loop : -0.41 (0.44), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 76 TYR 0.027 0.001 TYR J 9 PHE 0.010 0.001 PHE C 83 TRP 0.006 0.001 TRP F 107 HIS 0.006 0.001 HIS C 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.14 (13020) covalent geometry : angle 0.57864 / 0.33 (18187) hydrogen bonds : bond 0.04438 / 4.93 ( 852) hydrogen bonds : angle 3.86085 / 4.83 ( 2384) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.313 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: C 42 MET cc_start: 0.8539 (mmp) cc_final: 0.8165 (tpp) REVERT: D 6 MET cc_start: 0.8172 (mmp) cc_final: 0.7663 (mmt) REVERT: D 42 MET cc_start: 0.8584 (tpp) cc_final: 0.8188 (tpp) REVERT: E 6 MET cc_start: 0.7975 (tmm) cc_final: 0.7707 (tmm) REVERT: E 118 GLN cc_start: 0.8589 (tm-30) cc_final: 0.7934 (tp-100) REVERT: E 121 GLU cc_start: 0.8408 (pt0) cc_final: 0.7994 (pp20) REVERT: F 42 MET cc_start: 0.8137 (tpt) cc_final: 0.7702 (tpp) REVERT: F 51 TYR cc_start: 0.8145 (m-80) cc_final: 0.7656 (m-80) REVERT: F 112 ARG cc_start: 0.9048 (mmp80) cc_final: 0.8825 (mmp80) REVERT: F 134 GLN cc_start: 0.8616 (pt0) cc_final: 0.8175 (pt0) REVERT: G 142 GLN cc_start: 0.6933 (mt0) cc_final: 0.6616 (mp10) REVERT: H 42 MET cc_start: 0.8572 (tpp) cc_final: 0.8216 (tpp) REVERT: I 51 TYR cc_start: 0.7538 (m-80) cc_final: 0.7143 (m-10) REVERT: J 107 TRP cc_start: 0.7397 (m100) cc_final: 0.6496 (t-100) outliers start: 1 outliers final: 0 residues processed: 84 average time/residue: 0.0913 time to fit residues: 11.8718 Evaluate side-chains 60 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 122 optimal weight: 4.9990 chunk 112 optimal weight: 10.0000 chunk 56 optimal weight: 0.5980 chunk 2 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 35 HIS D 134 GLN E 77 HIS ** F 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 GLN ** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 118 GLN ** H 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.089919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.069242 restraints weight = 81559.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.068482 restraints weight = 61706.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.068991 restraints weight = 47174.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.069013 restraints weight = 37803.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.069229 restraints weight = 35059.553| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13020 Z= 0.148 Angle : 0.579 7.409 18187 Z= 0.329 Chirality : 0.041 0.293 1992 Planarity : 0.003 0.031 1778 Dihedral : 28.093 179.126 2986 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.10 % Allowed : 2.25 % Favored : 97.66 % 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: 2.95 (0.26), residues: 1104 helix: 2.51 (0.17), residues: 888 sheet: None (None), residues: 0 loop : -0.47 (0.44), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 76 TYR 0.025 0.002 TYR C 51 PHE 0.007 0.001 PHE H 120 TRP 0.007 0.001 TRP F 107 HIS 0.005 0.001 HIS F 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.15 (13020) covalent geometry : angle 0.57870 / 0.33 (18187) hydrogen bonds : bond 0.04355 / 4.84 ( 852) hydrogen bonds : angle 3.84650 / 4.81 ( 2384) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.402 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: C 42 MET cc_start: 0.8718 (mmp) cc_final: 0.8314 (tpp) REVERT: D 42 MET cc_start: 0.8627 (tpp) cc_final: 0.8118 (tpp) REVERT: E 6 MET cc_start: 0.8034 (tmm) cc_final: 0.7746 (tmm) REVERT: E 121 GLU cc_start: 0.8346 (pt0) cc_final: 0.8108 (pp20) REVERT: F 42 MET cc_start: 0.8237 (tpt) cc_final: 0.7778 (tpp) REVERT: F 51 TYR cc_start: 0.8213 (m-80) cc_final: 0.7778 (m-80) REVERT: F 112 ARG cc_start: 0.9163 (mmp80) cc_final: 0.8848 (mmp80) REVERT: F 134 GLN cc_start: 0.8703 (pt0) cc_final: 0.8317 (pt0) REVERT: G 142 GLN cc_start: 0.7093 (mt0) cc_final: 0.6749 (mp10) REVERT: H 42 MET cc_start: 0.8649 (tpp) cc_final: 0.8200 (tpp) REVERT: I 51 TYR cc_start: 0.7485 (m-80) cc_final: 0.7165 (m-10) REVERT: J 107 TRP cc_start: 0.7458 (m100) cc_final: 0.6616 (t-100) outliers start: 1 outliers final: 0 residues processed: 81 average time/residue: 0.0949 time to fit residues: 11.5678 Evaluate side-chains 61 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 51 optimal weight: 0.7980 chunk 5 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 121 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 118 GLN ** H 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 134 GLN ** J 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.089260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.068176 restraints weight = 80999.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.068061 restraints weight = 58957.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.068711 restraints weight = 43572.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.068182 restraints weight = 36479.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.068547 restraints weight = 35614.441| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13020 Z= 0.152 Angle : 0.585 7.517 18187 Z= 0.332 Chirality : 0.042 0.294 1992 Planarity : 0.003 0.027 1778 Dihedral : 28.096 178.120 2986 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.29 % Allowed : 1.66 % Favored : 98.05 % 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: 2.91 (0.26), residues: 1104 helix: 2.48 (0.17), residues: 888 sheet: None (None), residues: 0 loop : -0.52 (0.44), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 126 TYR 0.017 0.001 TYR F 14 PHE 0.014 0.001 PHE F 120 TRP 0.008 0.001 TRP E 107 HIS 0.005 0.001 HIS F 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.15 (13020) covalent geometry : angle 0.58517 / 0.33 (18187) hydrogen bonds : bond 0.04382 / 4.90 ( 852) hydrogen bonds : angle 3.85531 / 4.83 ( 2384) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 76 time to evaluate : 0.401 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: C 15 MET cc_start: 0.8483 (ppp) cc_final: 0.8279 (ppp) REVERT: C 42 MET cc_start: 0.8701 (mmp) cc_final: 0.8314 (tpp) REVERT: D 6 MET cc_start: 0.8174 (mmp) cc_final: 0.7857 (mmt) REVERT: D 42 MET cc_start: 0.8803 (tpp) cc_final: 0.8359 (tpp) REVERT: E 6 MET cc_start: 0.8027 (tmm) cc_final: 0.7707 (tmm) REVERT: E 121 GLU cc_start: 0.8387 (pt0) cc_final: 0.8126 (pp20) REVERT: F 42 MET cc_start: 0.8270 (tpt) cc_final: 0.7822 (tpp) REVERT: F 51 TYR cc_start: 0.8189 (m-80) cc_final: 0.7760 (m-80) REVERT: F 134 GLN cc_start: 0.8588 (pt0) cc_final: 0.8174 (pt0) REVERT: H 42 MET cc_start: 0.8643 (tpp) cc_final: 0.8170 (tpp) REVERT: I 51 TYR cc_start: 0.7437 (m-80) cc_final: 0.7134 (m-10) REVERT: J 107 TRP cc_start: 0.7463 (m100) cc_final: 0.6601 (t-100) REVERT: J 134 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7663 (mm-40) outliers start: 3 outliers final: 0 residues processed: 79 average time/residue: 0.0846 time to fit residues: 10.3992 Evaluate side-chains 58 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 86 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 60 optimal weight: 0.0770 chunk 82 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 88 optimal weight: 0.3980 chunk 12 optimal weight: 5.9990 chunk 108 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 11 optimal weight: 8.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 134 GLN ** F 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 139 HIS ** 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 = 0.3981 r_free = 0.3981 target = 0.089262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.067732 restraints weight = 81434.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.066870 restraints weight = 57476.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.067451 restraints weight = 45403.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.067423 restraints weight = 36763.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.067690 restraints weight = 34627.479| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13020 Z= 0.139 Angle : 0.568 7.108 18187 Z= 0.324 Chirality : 0.041 0.295 1992 Planarity : 0.003 0.027 1778 Dihedral : 28.091 178.179 2986 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.10 % Allowed : 1.07 % Favored : 98.83 % 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: 2.94 (0.26), residues: 1104 helix: 2.51 (0.18), residues: 888 sheet: None (None), residues: 0 loop : -0.56 (0.45), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 112 TYR 0.016 0.001 TYR F 14 PHE 0.010 0.001 PHE D 120 TRP 0.007 0.001 TRP F 107 HIS 0.004 0.001 HIS F 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.14 (13020) covalent geometry : angle 0.56842 / 0.32 (18187) hydrogen bonds : bond 0.04172 / 4.65 ( 852) hydrogen bonds : angle 3.84000 / 4.84 ( 2384) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.330 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: C 42 MET cc_start: 0.8718 (mmp) cc_final: 0.8293 (tpp) REVERT: D 42 MET cc_start: 0.8794 (tpp) cc_final: 0.8270 (tpp) REVERT: E 6 MET cc_start: 0.8040 (tmm) cc_final: 0.7704 (tmm) REVERT: E 49 ASP cc_start: 0.8865 (t70) cc_final: 0.8558 (p0) REVERT: E 121 GLU cc_start: 0.8381 (pt0) cc_final: 0.8151 (pp20) REVERT: F 42 MET cc_start: 0.8292 (tpt) cc_final: 0.7828 (tpp) REVERT: F 51 TYR cc_start: 0.8218 (m-80) cc_final: 0.7754 (m-80) REVERT: F 134 GLN cc_start: 0.8568 (pt0) cc_final: 0.8161 (pt0) REVERT: H 42 MET cc_start: 0.8723 (tpp) cc_final: 0.8169 (tpp) REVERT: I 51 TYR cc_start: 0.7682 (m-80) cc_final: 0.7353 (m-10) REVERT: J 107 TRP cc_start: 0.7467 (m100) cc_final: 0.6614 (t-100) outliers start: 1 outliers final: 0 residues processed: 84 average time/residue: 0.0920 time to fit residues: 11.5907 Evaluate side-chains 60 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 9.9990 chunk 104 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 89 optimal weight: 0.0980 chunk 27 optimal weight: 0.2980 chunk 40 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 124 optimal weight: 8.9990 chunk 80 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 139 HIS ** 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 = 0.3971 r_free = 0.3971 target = 0.088744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.067478 restraints weight = 81542.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.067018 restraints weight = 57930.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.067389 restraints weight = 45422.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.067442 restraints weight = 37170.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.067588 restraints weight = 35676.089| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13020 Z= 0.152 Angle : 0.590 8.066 18187 Z= 0.333 Chirality : 0.042 0.303 1992 Planarity : 0.003 0.031 1778 Dihedral : 28.079 178.359 2986 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % 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: 2.85 (0.26), residues: 1104 helix: 2.46 (0.18), residues: 888 sheet: None (None), residues: 0 loop : -0.63 (0.45), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 126 TYR 0.017 0.001 TYR F 14 PHE 0.015 0.001 PHE F 120 TRP 0.008 0.001 TRP F 107 HIS 0.005 0.001 HIS F 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.15 (13020) covalent geometry : angle 0.59027 / 0.33 (18187) hydrogen bonds : bond 0.04351 / 4.88 ( 852) hydrogen bonds : angle 3.88751 / 4.90 ( 2384) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.336 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: C 15 MET cc_start: 0.8605 (ppp) cc_final: 0.8385 (ppp) REVERT: C 42 MET cc_start: 0.8724 (mmp) cc_final: 0.8404 (tpp) REVERT: D 6 MET cc_start: 0.8091 (mmp) cc_final: 0.7740 (mmt) REVERT: D 42 MET cc_start: 0.8810 (tpp) cc_final: 0.8347 (tpp) REVERT: E 6 MET cc_start: 0.8063 (tmm) cc_final: 0.7746 (tmm) REVERT: E 121 GLU cc_start: 0.8336 (pt0) cc_final: 0.8101 (pp20) REVERT: F 42 MET cc_start: 0.8324 (tpt) cc_final: 0.7851 (tpp) REVERT: F 51 TYR cc_start: 0.8192 (m-80) cc_final: 0.7883 (m-80) REVERT: F 134 GLN cc_start: 0.8568 (pt0) cc_final: 0.8145 (pt0) REVERT: H 42 MET cc_start: 0.8734 (tpp) cc_final: 0.8172 (tpp) REVERT: I 51 TYR cc_start: 0.7614 (m-80) cc_final: 0.7273 (m-10) REVERT: J 106 SER cc_start: 0.6355 (t) cc_final: 0.6004 (t) REVERT: J 107 TRP cc_start: 0.7468 (m100) cc_final: 0.6608 (t-100) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.0891 time to fit residues: 10.1602 Evaluate side-chains 60 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 29 optimal weight: 0.2980 chunk 70 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 0.0970 chunk 98 optimal weight: 7.9990 chunk 92 optimal weight: 0.1980 chunk 124 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 134 GLN ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 GLN ** F 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.089309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.067181 restraints weight = 81151.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.066728 restraints weight = 57256.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.067161 restraints weight = 43094.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.067209 restraints weight = 36440.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.067196 restraints weight = 34471.148| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13020 Z= 0.124 Angle : 0.564 7.092 18187 Z= 0.318 Chirality : 0.041 0.305 1992 Planarity : 0.003 0.028 1778 Dihedral : 28.061 178.336 2986 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % 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: 2.96 (0.26), residues: 1104 helix: 2.54 (0.18), residues: 888 sheet: None (None), residues: 0 loop : -0.60 (0.45), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 76 TYR 0.015 0.001 TYR G 51 PHE 0.013 0.001 PHE F 120 TRP 0.009 0.001 TRP E 107 HIS 0.004 0.001 HIS F 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.12 (13020) covalent geometry : angle 0.56384 / 0.32 (18187) hydrogen bonds : bond 0.03881 / 4.30 ( 852) hydrogen bonds : angle 3.82352 / 4.83 ( 2384) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.285 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: C 15 MET cc_start: 0.8560 (ppp) cc_final: 0.8358 (ppp) REVERT: C 42 MET cc_start: 0.8767 (mmp) cc_final: 0.8396 (tpp) REVERT: D 42 MET cc_start: 0.8816 (tpp) cc_final: 0.8296 (tpp) REVERT: E 6 MET cc_start: 0.8084 (tmm) cc_final: 0.7720 (tmm) REVERT: E 42 MET cc_start: 0.8106 (tpp) cc_final: 0.7566 (tpt) REVERT: E 121 GLU cc_start: 0.8357 (pt0) cc_final: 0.8154 (pp20) REVERT: F 42 MET cc_start: 0.8275 (tpt) cc_final: 0.8031 (tpt) REVERT: F 51 TYR cc_start: 0.8176 (m-80) cc_final: 0.7694 (m-80) REVERT: F 134 GLN cc_start: 0.8549 (pt0) cc_final: 0.8143 (pt0) REVERT: H 42 MET cc_start: 0.8676 (tpp) cc_final: 0.8134 (tpp) REVERT: I 51 TYR cc_start: 0.7929 (m-80) cc_final: 0.7680 (m-10) REVERT: J 106 SER cc_start: 0.6374 (t) cc_final: 0.6002 (t) REVERT: J 107 TRP cc_start: 0.7448 (m100) cc_final: 0.6616 (t-100) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.0843 time to fit residues: 10.5043 Evaluate side-chains 62 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 44 optimal weight: 0.5980 chunk 66 optimal weight: 0.1980 chunk 76 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 109 optimal weight: 0.8980 chunk 28 optimal weight: 0.4980 chunk 119 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 5 optimal weight: 9.9990 chunk 3 optimal weight: 8.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 134 GLN ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 139 HIS ** 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 = 0.3980 r_free = 0.3980 target = 0.089228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.067724 restraints weight = 80618.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.066965 restraints weight = 60912.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.067600 restraints weight = 48137.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.067550 restraints weight = 38636.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.067815 restraints weight = 36399.709| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13020 Z= 0.133 Angle : 0.581 10.326 18187 Z= 0.325 Chirality : 0.041 0.308 1992 Planarity : 0.003 0.031 1778 Dihedral : 28.040 178.407 2986 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.93 (0.26), residues: 1104 helix: 2.53 (0.18), residues: 888 sheet: None (None), residues: 0 loop : -0.66 (0.45), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 126 TYR 0.013 0.001 TYR E 9 PHE 0.022 0.001 PHE F 120 TRP 0.007 0.001 TRP E 107 HIS 0.004 0.001 HIS F 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.13 (13020) covalent geometry : angle 0.58069 / 0.33 (18187) hydrogen bonds : bond 0.04010 / 4.48 ( 852) hydrogen bonds : angle 3.82472 / 4.82 ( 2384) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.395 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: C 6 MET cc_start: 0.7541 (ptt) cc_final: 0.7334 (ppp) REVERT: C 15 MET cc_start: 0.8559 (ppp) cc_final: 0.8316 (ppp) REVERT: C 42 MET cc_start: 0.8733 (mmp) cc_final: 0.8395 (tpp) REVERT: D 6 MET cc_start: 0.8043 (mmp) cc_final: 0.7660 (mmt) REVERT: D 42 MET cc_start: 0.8754 (tpp) cc_final: 0.8366 (tpp) REVERT: E 6 MET cc_start: 0.8161 (tmm) cc_final: 0.7835 (tmm) REVERT: E 42 MET cc_start: 0.8113 (tpp) cc_final: 0.7617 (tpt) REVERT: E 121 GLU cc_start: 0.8384 (pt0) cc_final: 0.8114 (pp20) REVERT: F 134 GLN cc_start: 0.8558 (pt0) cc_final: 0.8127 (pt0) REVERT: H 42 MET cc_start: 0.8662 (tpp) cc_final: 0.8119 (tpp) REVERT: I 51 TYR cc_start: 0.7772 (m-80) cc_final: 0.7495 (m-10) REVERT: J 106 SER cc_start: 0.6357 (t) cc_final: 0.6008 (t) REVERT: J 107 TRP cc_start: 0.7444 (m100) cc_final: 0.6597 (t-100) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.0783 time to fit residues: 9.7136 Evaluate side-chains 60 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 0 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 59 optimal weight: 0.0980 chunk 43 optimal weight: 0.1980 chunk 78 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 7 optimal weight: 30.0000 chunk 17 optimal weight: 0.0010 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 134 GLN ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 139 HIS ** 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 = 0.3982 r_free = 0.3982 target = 0.089218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.067736 restraints weight = 80473.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.067155 restraints weight = 57201.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.067821 restraints weight = 44933.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.067764 restraints weight = 36241.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.067843 restraints weight = 34067.002| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 13020 Z= 0.128 Angle : 0.583 10.970 18187 Z= 0.326 Chirality : 0.041 0.311 1992 Planarity : 0.003 0.029 1778 Dihedral : 28.027 178.334 2986 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: 2.89 (0.26), residues: 1104 helix: 2.50 (0.18), residues: 888 sheet: None (None), residues: 0 loop : -0.71 (0.45), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 126 TYR 0.015 0.001 TYR E 9 PHE 0.014 0.001 PHE F 120 TRP 0.006 0.001 TRP E 107 HIS 0.003 0.001 HIS F 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.13 (13020) covalent geometry : angle 0.58336 / 0.33 (18187) hydrogen bonds : bond 0.03963 / 4.35 ( 852) hydrogen bonds : angle 3.83603 / 4.79 ( 2384) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1902.83 seconds wall clock time: 33 minutes 42.37 seconds (2022.37 seconds total)