Starting phenix.real_space_refine on Wed Aug 5 23:01:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f0o_50114/08_2026/9f0o_50114.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f0o_50114/08_2026/9f0o_50114.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9f0o_50114/08_2026/9f0o_50114.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f0o_50114/08_2026/9f0o_50114.map" model { file = "/net/cci-nas-00/data/ceres_data/9f0o_50114/08_2026/9f0o_50114.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f0o_50114/08_2026/9f0o_50114.cif" } resolution = 2.3 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= 0.001 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 294 5.49 5 S 10 5.16 5 C 6818 2.51 5 N 2324 2.21 5 O 2877 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 93 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: 12323 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 851 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "D" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 767 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "E" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 851 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "H" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 767 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3028 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 71 Classifications: {'peptide': 8} Modifications used: {'COO': 1} Link IDs: {'TRANS': 7} Chain: "L" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 71 Classifications: {'peptide': 8} Modifications used: {'COO': 1} Link IDs: {'TRANS': 7} Time building chain proxies: 2.37, per 1000 atoms: 0.19 Number of scatterers: 12323 At special positions: 0 Unit cell: (82.55, 117.65, 115.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 294 15.00 O 2877 8.00 N 2324 7.00 C 6818 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 266.6 milliseconds 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1484 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 71.3% alpha, 2.5% beta 146 base pairs and 269 stacking pairs defined. Time for finding SS restraints: 1.86 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 4.072A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.523A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.761A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.571A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) 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: 4.433A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.503A 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 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 122 removed outlier: 3.538A pdb=" N ALA D 104 " --> pdb=" O PRO D 100 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 4.117A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.522A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.548A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.502A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (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: 4.441A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.520A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 122 removed outlier: 3.731A pdb=" N ALA H 104 " --> pdb=" O PRO H 100 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS H 122 " --> pdb=" O TYR H 118 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.778A 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: 6.949A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (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: 6.719A 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: 6.775A 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: 6.969A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (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 78 410 hydrogen bonds defined for protein. 1206 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 373 hydrogen bonds 746 hydrogen bond angles 0 basepair planarities 146 basepair parallelities 269 stacking parallelities Total time for adding SS restraints: 2.28 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2873 1.34 - 1.46: 3811 1.46 - 1.58: 5845 1.58 - 1.70: 586 1.70 - 1.82: 20 Bond restraints: 13135 Sorted by residual: bond pdb=" C5' DG I -70 " pdb=" C4' DG I -70 " ideal model delta sigma weight residual 1.512 1.545 -0.033 7.00e-03 2.04e+04 2.26e+01 bond pdb=" C2 DG J -37 " pdb=" N2 DG J -37 " ideal model delta sigma weight residual 1.341 1.295 0.046 1.00e-02 1.00e+04 2.16e+01 bond pdb=" C2 DG J 20 " pdb=" N2 DG J 20 " ideal model delta sigma weight residual 1.341 1.295 0.046 1.00e-02 1.00e+04 2.15e+01 bond pdb=" C2 DG J 29 " pdb=" N2 DG J 29 " ideal model delta sigma weight residual 1.341 1.295 0.046 1.00e-02 1.00e+04 2.12e+01 bond pdb=" C2 DG I -30 " pdb=" N2 DG I -30 " ideal model delta sigma weight residual 1.341 1.295 0.046 1.00e-02 1.00e+04 2.10e+01 ... (remaining 13130 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 13110 1.80 - 3.60: 4860 3.60 - 5.41: 902 5.41 - 7.21: 101 7.21 - 9.01: 18 Bond angle restraints: 18991 Sorted by residual: angle pdb=" O5' DC J 37 " pdb=" C5' DC J 37 " pdb=" C4' DC J 37 " ideal model delta sigma weight residual 109.40 118.15 -8.75 8.00e-01 1.56e+00 1.20e+02 angle pdb=" O5' DG I 2 " pdb=" C5' DG I 2 " pdb=" C4' DG I 2 " ideal model delta sigma weight residual 109.40 117.88 -8.48 8.00e-01 1.56e+00 1.12e+02 angle pdb=" O5' DG I -70 " pdb=" C5' DG I -70 " pdb=" C4' DG I -70 " ideal model delta sigma weight residual 109.40 117.79 -8.39 8.00e-01 1.56e+00 1.10e+02 angle pdb=" O5' DG I -37 " pdb=" C5' DG I -37 " pdb=" C4' DG I -37 " ideal model delta sigma weight residual 109.40 117.62 -8.22 8.00e-01 1.56e+00 1.06e+02 angle pdb=" O5' DC I 35 " pdb=" C5' DC I 35 " pdb=" C4' DC I 35 " ideal model delta sigma weight residual 109.40 117.47 -8.07 8.00e-01 1.56e+00 1.02e+02 ... (remaining 18986 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.46: 5821 32.46 - 64.93: 1314 64.93 - 97.39: 34 97.39 - 129.86: 0 129.86 - 162.32: 3 Dihedral angle restraints: 7172 sinusoidal: 4876 harmonic: 2296 Sorted by residual: dihedral pdb=" CA PHE E 78 " pdb=" C PHE E 78 " pdb=" N LYS E 79 " pdb=" CA LYS E 79 " ideal model delta harmonic sigma weight residual 180.00 152.32 27.68 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA PRO D 100 " pdb=" C PRO D 100 " pdb=" N GLY D 101 " pdb=" CA GLY D 101 " ideal model delta harmonic sigma weight residual 180.00 158.87 21.13 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA ARG A 40 " pdb=" C ARG A 40 " pdb=" N TYR A 41 " pdb=" CA TYR A 41 " ideal model delta harmonic sigma weight residual 180.00 159.01 20.99 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 7169 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 1779 0.106 - 0.212: 354 0.212 - 0.318: 22 0.318 - 0.424: 3 0.424 - 0.530: 2 Chirality restraints: 2160 Sorted by residual: chirality pdb=" C3' DG J 20 " pdb=" C4' DG J 20 " pdb=" O3' DG J 20 " pdb=" C2' DG J 20 " both_signs ideal model delta sigma weight residual False -2.73 -2.20 -0.53 2.00e-01 2.50e+01 7.01e+00 chirality pdb=" C3' DT J -17 " pdb=" C4' DT J -17 " pdb=" O3' DT J -17 " pdb=" C2' DT J -17 " both_signs ideal model delta sigma weight residual False -2.73 -2.22 -0.51 2.00e-01 2.50e+01 6.48e+00 chirality pdb=" C3' DT J -72 " pdb=" C4' DT J -72 " pdb=" O3' DT J -72 " pdb=" C2' DT J -72 " both_signs ideal model delta sigma weight residual False -2.73 -2.36 -0.37 2.00e-01 2.50e+01 3.42e+00 ... (remaining 2157 not shown) Planarity restraints: 1388 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT I 30 " -0.274 2.00e-02 2.50e+03 1.25e-01 3.92e+02 pdb=" N1 DT I 30 " 0.060 2.00e-02 2.50e+03 pdb=" C2 DT I 30 " 0.084 2.00e-02 2.50e+03 pdb=" O2 DT I 30 " 0.118 2.00e-02 2.50e+03 pdb=" N3 DT I 30 " 0.019 2.00e-02 2.50e+03 pdb=" C4 DT I 30 " -0.036 2.00e-02 2.50e+03 pdb=" O4 DT I 30 " -0.195 2.00e-02 2.50e+03 pdb=" C5 DT I 30 " 0.056 2.00e-02 2.50e+03 pdb=" C7 DT I 30 " 0.069 2.00e-02 2.50e+03 pdb=" C6 DT I 30 " 0.099 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I -37 " -0.245 2.00e-02 2.50e+03 1.09e-01 3.57e+02 pdb=" N9 DG I -37 " 0.018 2.00e-02 2.50e+03 pdb=" C8 DG I -37 " 0.143 2.00e-02 2.50e+03 pdb=" N7 DG I -37 " 0.116 2.00e-02 2.50e+03 pdb=" C5 DG I -37 " 0.040 2.00e-02 2.50e+03 pdb=" C6 DG I -37 " -0.049 2.00e-02 2.50e+03 pdb=" O6 DG I -37 " -0.170 2.00e-02 2.50e+03 pdb=" N1 DG I -37 " -0.037 2.00e-02 2.50e+03 pdb=" C2 DG I -37 " 0.016 2.00e-02 2.50e+03 pdb=" N2 DG I -37 " 0.111 2.00e-02 2.50e+03 pdb=" N3 DG I -37 " 0.020 2.00e-02 2.50e+03 pdb=" C4 DG I -37 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT J 5 " -0.180 2.00e-02 2.50e+03 1.06e-01 2.78e+02 pdb=" N1 DT J 5 " -0.029 2.00e-02 2.50e+03 pdb=" C2 DT J 5 " 0.031 2.00e-02 2.50e+03 pdb=" O2 DT J 5 " 0.170 2.00e-02 2.50e+03 pdb=" N3 DT J 5 " 0.009 2.00e-02 2.50e+03 pdb=" C4 DT J 5 " -0.037 2.00e-02 2.50e+03 pdb=" O4 DT J 5 " -0.169 2.00e-02 2.50e+03 pdb=" C5 DT J 5 " 0.046 2.00e-02 2.50e+03 pdb=" C7 DT J 5 " 0.120 2.00e-02 2.50e+03 pdb=" C6 DT J 5 " 0.039 2.00e-02 2.50e+03 ... (remaining 1385 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 5356 3.02 - 3.49: 12442 3.49 - 3.96: 25449 3.96 - 4.43: 27627 4.43 - 4.90: 36745 Nonbonded interactions: 107619 Sorted by model distance: nonbonded pdb=" OG SER A 57 " pdb=" OE1 GLU A 59 " model vdw 2.549 3.040 nonbonded pdb=" OH TYR G 39 " pdb=" OE1 GLU H 68 " model vdw 2.573 3.040 nonbonded pdb=" OG SER E 57 " pdb=" OE2 GLU E 59 " model vdw 2.582 3.040 nonbonded pdb=" OE2 GLU G 56 " pdb=" OH TYR K 579 " model vdw 2.583 3.040 nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.586 3.040 ... (remaining 107614 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' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'K' selection = chain 'L' } 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 individual isotropic 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: 2.120 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: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.290 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 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 : 0.013 0.046 13135 Z= 1.271 Angle : 1.861 9.012 18991 Z= 1.907 Chirality : 0.081 0.530 2160 Planarity : 0.028 0.135 1388 Dihedral : 26.432 162.320 5688 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 0.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.46 % Allowed : 1.83 % Favored : 97.72 % 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: 0.79 (0.27), residues: 770 helix: 0.77 (0.20), residues: 546 sheet: None (None), residues: 0 loop : 0.20 (0.35), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 35 TYR 0.130 0.021 TYR C 57 PHE 0.052 0.014 PHE H 67 HIS 0.010 0.003 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.01331 / 1.27 (13135) covalent geometry : angle 1.86088 / 1.91 (18991) hydrogen bonds : bond 0.11414 / 7.47 ( 783) hydrogen bonds : angle 5.41058 / 3.94 ( 1952) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 167 time to evaluate : 0.330 Fit side-chains REVERT: C 91 GLU cc_start: 0.7525 (pm20) cc_final: 0.7212 (pm20) REVERT: D 68 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7679 (mp0) REVERT: G 91 GLU cc_start: 0.7470 (pm20) cc_final: 0.7197 (pm20) outliers start: 3 outliers final: 0 residues processed: 167 average time/residue: 0.9455 time to fit residues: 165.4167 Evaluate side-chains 150 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 149 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN C 84 GLN E 68 GLN F 27 GLN G 84 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.176960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.145031 restraints weight = 10294.176| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 0.87 r_work: 0.3491 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13135 Z= 0.178 Angle : 0.810 7.641 18991 Z= 0.468 Chirality : 0.059 0.321 2160 Planarity : 0.004 0.031 1388 Dihedral : 30.414 169.444 4111 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 2.13 % Allowed : 8.52 % Favored : 89.35 % 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: 2.27 (0.29), residues: 770 helix: 2.07 (0.22), residues: 548 sheet: None (None), residues: 0 loop : 0.18 (0.35), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 89 TYR 0.014 0.002 TYR F 51 PHE 0.013 0.002 PHE A 67 HIS 0.003 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.18 (13135) covalent geometry : angle 0.80955 / 0.47 (18991) hydrogen bonds : bond 0.05005 / 3.31 ( 783) hydrogen bonds : angle 3.01623 / 2.23 ( 1952) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 151 time to evaluate : 0.322 Fit side-chains REVERT: C 20 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.7430 (ttp-170) REVERT: C 41 GLU cc_start: 0.8200 (tt0) cc_final: 0.7998 (tt0) REVERT: D 31 LYS cc_start: 0.7975 (tptm) cc_final: 0.7713 (tptm) REVERT: F 52 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7916 (mp0) REVERT: G 15 LYS cc_start: 0.7556 (OUTLIER) cc_final: 0.7263 (pttm) REVERT: G 41 GLU cc_start: 0.8270 (tt0) cc_final: 0.8017 (tt0) REVERT: H 68 GLU cc_start: 0.7998 (mp0) cc_final: 0.7778 (mp0) REVERT: H 117 LYS cc_start: 0.7941 (ttmt) cc_final: 0.7384 (tttm) outliers start: 14 outliers final: 3 residues processed: 155 average time/residue: 1.0757 time to fit residues: 174.6484 Evaluate side-chains 153 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 148 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 48 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 71 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 83 optimal weight: 20.0000 chunk 99 optimal weight: 20.0000 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 76 GLN B 25 ASN C 73 ASN C 104 GLN E 68 GLN F 27 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.175007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.142464 restraints weight = 10354.444| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 0.88 r_work: 0.3457 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13135 Z= 0.166 Angle : 0.724 7.482 18991 Z= 0.415 Chirality : 0.053 0.364 2160 Planarity : 0.005 0.039 1388 Dihedral : 31.081 169.666 4108 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 2.74 % Allowed : 10.65 % Favored : 86.61 % 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: 2.47 (0.29), residues: 770 helix: 2.27 (0.22), residues: 548 sheet: None (None), residues: 0 loop : 0.06 (0.34), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 42 TYR 0.016 0.002 TYR B 51 PHE 0.012 0.002 PHE E 67 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.17 (13135) covalent geometry : angle 0.72442 / 0.41 (18991) hydrogen bonds : bond 0.05098 / 3.43 ( 783) hydrogen bonds : angle 2.94191 / 2.17 ( 1952) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 time to evaluate : 0.367 Fit side-chains REVERT: C 20 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.7415 (ttp-170) REVERT: E 53 ARG cc_start: 0.8305 (ttp-110) cc_final: 0.7957 (tmt90) REVERT: F 52 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7829 (mp0) REVERT: F 77 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8400 (mttm) REVERT: G 15 LYS cc_start: 0.7616 (pttp) cc_final: 0.7310 (pttm) REVERT: H 117 LYS cc_start: 0.7957 (ttmt) cc_final: 0.7423 (tttm) outliers start: 18 outliers final: 3 residues processed: 152 average time/residue: 1.0891 time to fit residues: 173.3440 Evaluate side-chains 148 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 143 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 114 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 70 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 96 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN C 104 GLN D 46 HIS E 68 GLN F 25 ASN F 27 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.173290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.140681 restraints weight = 10208.063| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 0.86 r_work: 0.3438 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13135 Z= 0.190 Angle : 0.743 7.981 18991 Z= 0.417 Chirality : 0.053 0.365 2160 Planarity : 0.005 0.042 1388 Dihedral : 31.342 173.160 4108 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 2.44 % Allowed : 11.57 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.29), residues: 770 helix: 2.16 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.21 (0.33), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 42 TYR 0.016 0.002 TYR B 51 PHE 0.013 0.002 PHE A 67 HIS 0.006 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.19 (13135) covalent geometry : angle 0.74341 / 0.42 (18991) hydrogen bonds : bond 0.05796 / 3.91 ( 783) hydrogen bonds : angle 3.01882 / 2.23 ( 1952) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 0.338 Fit side-chains REVERT: C 20 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.7336 (ttp-170) REVERT: C 91 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7327 (mt-10) REVERT: D 31 LYS cc_start: 0.8000 (tptm) cc_final: 0.7780 (tptm) REVERT: D 68 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7734 (tp30) REVERT: E 53 ARG cc_start: 0.8303 (ttp-110) cc_final: 0.8007 (tmt90) REVERT: F 52 GLU cc_start: 0.8307 (mm-30) cc_final: 0.7865 (mp0) REVERT: F 77 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8421 (mttm) REVERT: G 15 LYS cc_start: 0.7594 (pttp) cc_final: 0.7298 (pttm) REVERT: G 91 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7312 (mt-10) REVERT: H 117 LYS cc_start: 0.8001 (ttmt) cc_final: 0.7467 (tttm) outliers start: 16 outliers final: 5 residues processed: 151 average time/residue: 1.0870 time to fit residues: 172.0326 Evaluate side-chains 154 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 144 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain C residue 20 ARG Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 114 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 48 optimal weight: 7.9990 chunk 88 optimal weight: 40.0000 chunk 43 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 89 optimal weight: 30.0000 chunk 64 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 79 optimal weight: 20.0000 chunk 32 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN C 104 GLN E 68 GLN F 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.174080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.141622 restraints weight = 10317.770| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 0.87 r_work: 0.3450 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13135 Z= 0.160 Angle : 0.720 7.667 18991 Z= 0.406 Chirality : 0.051 0.368 2160 Planarity : 0.005 0.038 1388 Dihedral : 31.356 173.209 4108 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 2.13 % Allowed : 12.79 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.29), residues: 770 helix: 2.18 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.21 (0.33), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 71 TYR 0.014 0.002 TYR F 51 PHE 0.012 0.002 PHE E 67 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.16 (13135) covalent geometry : angle 0.71980 / 0.41 (18991) hydrogen bonds : bond 0.05218 / 3.51 ( 783) hydrogen bonds : angle 3.00684 / 2.22 ( 1952) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 0.350 Fit side-chains REVERT: C 20 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.7324 (ttp-170) REVERT: C 91 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7323 (mt-10) REVERT: D 31 LYS cc_start: 0.7991 (tptm) cc_final: 0.7769 (tptm) REVERT: D 68 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7686 (tp30) REVERT: F 52 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7845 (mp0) REVERT: F 77 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8425 (mttm) REVERT: G 15 LYS cc_start: 0.7613 (pttp) cc_final: 0.7342 (pttm) REVERT: G 74 LYS cc_start: 0.7686 (mppt) cc_final: 0.7418 (mmtm) REVERT: G 91 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7302 (mt-10) REVERT: H 68 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7699 (tp30) REVERT: H 117 LYS cc_start: 0.7996 (ttmt) cc_final: 0.7393 (tttm) outliers start: 14 outliers final: 6 residues processed: 147 average time/residue: 1.0889 time to fit residues: 167.6731 Evaluate side-chains 153 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain C residue 20 ARG Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 68 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 9 optimal weight: 0.0980 chunk 63 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 46 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN C 104 GLN E 68 GLN F 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.174526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.142060 restraints weight = 10242.569| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 0.87 r_work: 0.3456 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13135 Z= 0.155 Angle : 0.711 8.315 18991 Z= 0.402 Chirality : 0.051 0.367 2160 Planarity : 0.004 0.038 1388 Dihedral : 31.343 173.497 4108 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 1.67 % Allowed : 13.09 % Favored : 85.24 % 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: 2.31 (0.29), residues: 770 helix: 2.21 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.18 (0.34), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 67 TYR 0.013 0.002 TYR F 51 PHE 0.012 0.002 PHE A 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.16 (13135) covalent geometry : angle 0.71104 / 0.40 (18991) hydrogen bonds : bond 0.04955 / 3.33 ( 783) hydrogen bonds : angle 2.98083 / 2.20 ( 1952) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 140 time to evaluate : 0.343 Fit side-chains REVERT: C 20 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7374 (ttp-170) REVERT: C 91 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7328 (mt-10) REVERT: D 31 LYS cc_start: 0.7998 (tptm) cc_final: 0.7776 (tptm) REVERT: D 68 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7696 (tp30) REVERT: E 53 ARG cc_start: 0.8283 (ttp-110) cc_final: 0.7969 (tmt90) REVERT: E 56 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8170 (ttmp) REVERT: F 52 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7835 (mp0) REVERT: G 15 LYS cc_start: 0.7618 (pttp) cc_final: 0.7337 (pttm) REVERT: G 74 LYS cc_start: 0.7696 (mppt) cc_final: 0.7423 (mmtm) REVERT: G 91 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7287 (mt-10) REVERT: H 68 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7682 (tp30) REVERT: H 117 LYS cc_start: 0.7996 (ttmt) cc_final: 0.7396 (tttm) outliers start: 11 outliers final: 5 residues processed: 144 average time/residue: 1.0948 time to fit residues: 165.0130 Evaluate side-chains 148 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 137 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain C residue 20 ARG Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 68 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 77 optimal weight: 20.0000 chunk 36 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 88 optimal weight: 40.0000 chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 65 optimal weight: 6.9990 chunk 53 optimal weight: 0.6980 chunk 95 optimal weight: 20.0000 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN C 104 GLN E 68 GLN F 27 GLN G 104 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.175060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.142743 restraints weight = 10217.617| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 0.87 r_work: 0.3463 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13135 Z= 0.158 Angle : 0.698 7.495 18991 Z= 0.395 Chirality : 0.050 0.367 2160 Planarity : 0.005 0.038 1388 Dihedral : 31.313 174.079 4108 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 1.67 % Allowed : 13.24 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.34 (0.29), residues: 770 helix: 2.23 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.19 (0.34), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 42 TYR 0.013 0.002 TYR B 51 PHE 0.012 0.002 PHE E 67 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.16 (13135) covalent geometry : angle 0.69827 / 0.40 (18991) hydrogen bonds : bond 0.04785 / 3.21 ( 783) hydrogen bonds : angle 2.94452 / 2.17 ( 1952) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 140 time to evaluate : 0.336 Fit side-chains REVERT: C 20 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.7426 (ttp-170) REVERT: C 91 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7335 (mt-10) REVERT: D 31 LYS cc_start: 0.7999 (tptm) cc_final: 0.7768 (tptm) REVERT: D 68 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7680 (tp30) REVERT: E 53 ARG cc_start: 0.8286 (ttp-110) cc_final: 0.7960 (tmt90) REVERT: F 52 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7802 (mp0) REVERT: G 15 LYS cc_start: 0.7579 (pttp) cc_final: 0.7296 (pttm) REVERT: G 74 LYS cc_start: 0.7718 (mppt) cc_final: 0.7441 (mmtm) REVERT: G 91 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7301 (mt-10) REVERT: H 68 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7676 (tp30) REVERT: H 117 LYS cc_start: 0.8001 (ttmt) cc_final: 0.7408 (tttm) outliers start: 11 outliers final: 5 residues processed: 144 average time/residue: 1.0786 time to fit residues: 162.8063 Evaluate side-chains 149 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 139 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain C residue 20 ARG Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 68 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 81 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 69 optimal weight: 0.8980 chunk 94 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 99 optimal weight: 20.0000 chunk 33 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 93 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN C 104 GLN E 68 GLN F 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.173017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.140441 restraints weight = 10178.092| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 0.87 r_work: 0.3435 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13135 Z= 0.194 Angle : 0.739 8.084 18991 Z= 0.412 Chirality : 0.053 0.367 2160 Planarity : 0.005 0.047 1388 Dihedral : 31.396 174.347 4108 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 1.52 % Allowed : 13.09 % Favored : 85.39 % 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: 2.18 (0.29), residues: 770 helix: 2.13 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.30 (0.33), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 67 TYR 0.015 0.002 TYR B 51 PHE 0.012 0.002 PHE E 67 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.19 (13135) covalent geometry : angle 0.73927 / 0.41 (18991) hydrogen bonds : bond 0.05851 / 3.94 ( 783) hydrogen bonds : angle 3.01046 / 2.22 ( 1952) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 144 time to evaluate : 0.333 Fit side-chains REVERT: C 20 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.7433 (ttp-170) REVERT: D 31 LYS cc_start: 0.8005 (tptm) cc_final: 0.7783 (tptm) REVERT: D 68 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7705 (tp30) REVERT: E 53 ARG cc_start: 0.8290 (ttp-110) cc_final: 0.7965 (tmt90) REVERT: F 52 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7857 (mp0) REVERT: G 15 LYS cc_start: 0.7576 (pttp) cc_final: 0.7295 (pttm) REVERT: G 74 LYS cc_start: 0.7734 (mppt) cc_final: 0.7449 (mmtm) REVERT: H 68 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7702 (tp30) REVERT: H 117 LYS cc_start: 0.8012 (ttmt) cc_final: 0.7421 (tttm) outliers start: 10 outliers final: 5 residues processed: 148 average time/residue: 1.0870 time to fit residues: 168.5812 Evaluate side-chains 149 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 141 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain C residue 20 ARG Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 68 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 47 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 96 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 53 optimal weight: 0.2980 chunk 56 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN E 68 GLN F 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.174415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.141821 restraints weight = 10142.981| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 0.87 r_work: 0.3457 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 13135 Z= 0.142 Angle : 0.706 7.535 18991 Z= 0.400 Chirality : 0.050 0.372 2160 Planarity : 0.005 0.043 1388 Dihedral : 31.394 174.064 4108 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 1.83 % Allowed : 13.55 % Favored : 84.63 % 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: 2.24 (0.29), residues: 770 helix: 2.17 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.28 (0.34), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 42 TYR 0.012 0.002 TYR B 51 PHE 0.013 0.002 PHE E 67 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.14 (13135) covalent geometry : angle 0.70554 / 0.40 (18991) hydrogen bonds : bond 0.05074 / 3.42 ( 783) hydrogen bonds : angle 2.99794 / 2.21 ( 1952) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 0.333 Fit side-chains REVERT: C 20 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7390 (ttp-170) REVERT: D 31 LYS cc_start: 0.7992 (tptm) cc_final: 0.7758 (tptm) REVERT: D 68 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7682 (tp30) REVERT: F 52 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7831 (mp0) REVERT: F 92 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7593 (ttp80) REVERT: G 15 LYS cc_start: 0.7557 (pttp) cc_final: 0.7296 (pttm) REVERT: G 74 LYS cc_start: 0.7737 (mppt) cc_final: 0.7450 (mmtm) REVERT: H 68 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7679 (tp30) REVERT: H 117 LYS cc_start: 0.7991 (ttmt) cc_final: 0.7400 (tttm) outliers start: 12 outliers final: 6 residues processed: 148 average time/residue: 0.9744 time to fit residues: 151.1292 Evaluate side-chains 150 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 140 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain C residue 20 ARG Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 68 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 26 optimal weight: 0.2980 chunk 50 optimal weight: 0.8980 chunk 46 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 93 optimal weight: 20.0000 chunk 48 optimal weight: 8.9990 chunk 56 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 79 optimal weight: 20.0000 chunk 33 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN C 104 GLN E 68 GLN F 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.174391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.141739 restraints weight = 10246.132| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 0.87 r_work: 0.3455 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13135 Z= 0.153 Angle : 0.705 8.538 18991 Z= 0.396 Chirality : 0.050 0.365 2160 Planarity : 0.004 0.037 1388 Dihedral : 31.378 174.510 4108 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 1.22 % Allowed : 14.31 % Favored : 84.47 % 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: 2.29 (0.29), residues: 770 helix: 2.21 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.25 (0.34), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 42 TYR 0.012 0.002 TYR B 51 PHE 0.012 0.002 PHE E 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.15 (13135) covalent geometry : angle 0.70522 / 0.40 (18991) hydrogen bonds : bond 0.04936 / 3.31 ( 783) hydrogen bonds : angle 2.96278 / 2.19 ( 1952) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 140 time to evaluate : 0.365 Fit side-chains REVERT: C 20 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.7435 (ttp-170) REVERT: D 31 LYS cc_start: 0.8002 (tptm) cc_final: 0.7764 (tptm) REVERT: D 68 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7686 (tp30) REVERT: E 53 ARG cc_start: 0.8267 (ttp-110) cc_final: 0.7945 (tmt90) REVERT: F 52 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7832 (mp0) REVERT: G 15 LYS cc_start: 0.7580 (pttp) cc_final: 0.7315 (pttm) REVERT: G 74 LYS cc_start: 0.7739 (mppt) cc_final: 0.7449 (mmtm) REVERT: H 68 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7691 (tp30) REVERT: H 117 LYS cc_start: 0.8001 (ttmt) cc_final: 0.7413 (tttm) outliers start: 8 outliers final: 5 residues processed: 144 average time/residue: 0.9600 time to fit residues: 144.8778 Evaluate side-chains 148 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 140 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain C residue 20 ARG Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 68 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 93 optimal weight: 20.0000 chunk 43 optimal weight: 0.9990 chunk 82 optimal weight: 9.9990 chunk 3 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 85 optimal weight: 20.0000 chunk 12 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 90 optimal weight: 20.0000 chunk 69 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN C 104 GLN E 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.174572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.142205 restraints weight = 10168.057| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 0.87 r_work: 0.3458 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13135 Z= 0.164 Angle : 0.703 8.948 18991 Z= 0.395 Chirality : 0.050 0.367 2160 Planarity : 0.005 0.039 1388 Dihedral : 31.340 175.184 4108 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 1.22 % Allowed : 14.16 % Favored : 84.63 % 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: 2.31 (0.29), residues: 770 helix: 2.22 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.24 (0.34), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 42 TYR 0.013 0.002 TYR F 51 PHE 0.012 0.002 PHE E 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.16 (13135) covalent geometry : angle 0.70258 / 0.39 (18991) hydrogen bonds : bond 0.04874 / 3.27 ( 783) hydrogen bonds : angle 2.94106 / 2.17 ( 1952) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5267.93 seconds wall clock time: 90 minutes 4.60 seconds (5404.60 seconds total)