Starting phenix.real_space_refine on Fri Jul 3 04:55:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f0o_50114/07_2026/9f0o_50114.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f0o_50114/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9f0o_50114/07_2026/9f0o_50114.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f0o_50114/07_2026/9f0o_50114.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9f0o_50114/07_2026/9f0o_50114.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f0o_50114/07_2026/9f0o_50114.map" } 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-dev-6108/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: 2.69, per 1000 atoms: 0.22 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: 1.00 Conformation dependent library (CDL) restraints added in 384.8 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: 1.89 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: 2.53 Time building geometry restraints manager: 1.35 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: 13136 1.80 - 3.60: 4897 3.60 - 5.41: 839 5.41 - 7.21: 103 7.21 - 9.01: 16 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: 2.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.940 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:6.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.100 ------------------------------------------------------------------------------- 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 : 1.848 9.012 18991 Z= 1.893 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 1.84844 / 1.89 (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 : 0.347 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: 1.1024 time to fit residues: 192.5114 Evaluate side-chains 149 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 148 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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: 1.9990 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 B 25 ASN C 84 GLN E 68 GLN F 27 GLN G 84 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.177125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.145199 restraints weight = 10301.370| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 0.87 r_work: 0.3491 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1782 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= 0.176 Angle : 0.795 7.843 18991 Z= 0.465 Chirality : 0.058 0.310 2160 Planarity : 0.005 0.037 1388 Dihedral : 30.559 171.365 4111 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.73 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: 2.32 (0.29), residues: 770 helix: 2.09 (0.22), residues: 548 sheet: None (None), residues: 0 loop : 0.21 (0.35), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 92 TYR 0.014 0.002 TYR B 51 PHE 0.013 0.002 PHE A 67 HIS 0.002 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.18 (13135) covalent geometry : angle 0.79493 / 0.46 (18991) hydrogen bonds : bond 0.05140 / 3.41 ( 783) hydrogen bonds : angle 3.01463 / 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 : 0.358 Fit side-chains REVERT: C 20 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.7450 (mtm-85) REVERT: D 31 LYS cc_start: 0.7972 (tptm) cc_final: 0.7706 (tptm) REVERT: F 52 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7902 (mp0) REVERT: G 15 LYS cc_start: 0.7527 (OUTLIER) cc_final: 0.7290 (pttm) REVERT: G 41 GLU cc_start: 0.8269 (tt0) cc_final: 0.8017 (tt0) REVERT: H 68 GLU cc_start: 0.7995 (mp0) cc_final: 0.7777 (mp0) REVERT: H 117 LYS cc_start: 0.7951 (ttmt) cc_final: 0.7446 (tttm) outliers start: 14 outliers final: 3 residues processed: 155 average time/residue: 1.1099 time to fit residues: 179.9372 Evaluate side-chains 151 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 146 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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: 0.9990 chunk 49 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 83 optimal weight: 20.0000 chunk 99 optimal weight: 20.0000 chunk 12 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 76 GLN C 73 ASN C 104 GLN E 68 GLN F 27 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.176189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.143881 restraints weight = 10395.547| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 0.88 r_work: 0.3472 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 13135 Z= 0.154 Angle : 0.692 7.025 18991 Z= 0.405 Chirality : 0.051 0.334 2160 Planarity : 0.005 0.035 1388 Dihedral : 31.094 170.582 4108 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 1.98 % Allowed : 11.26 % Favored : 86.76 % 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: 2.59 (0.29), residues: 770 helix: 2.35 (0.22), residues: 548 sheet: None (None), residues: 0 loop : 0.15 (0.35), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 92 TYR 0.015 0.002 TYR B 51 PHE 0.013 0.002 PHE A 67 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.15 (13135) covalent geometry : angle 0.69219 / 0.40 (18991) hydrogen bonds : bond 0.04744 / 3.19 ( 783) hydrogen bonds : angle 2.89088 / 2.13 ( 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 160 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 147 time to evaluate : 0.393 Fit side-chains REVERT: C 20 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7551 (mtm-85) REVERT: D 31 LYS cc_start: 0.7953 (tptm) cc_final: 0.7701 (tptm) REVERT: E 53 ARG cc_start: 0.8284 (ttp-110) cc_final: 0.7938 (tmt90) REVERT: E 115 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8235 (mptp) REVERT: F 52 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7790 (mp0) REVERT: F 77 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8396 (mttm) REVERT: G 15 LYS cc_start: 0.7585 (pttp) cc_final: 0.7300 (pttm) REVERT: G 41 GLU cc_start: 0.8292 (tt0) cc_final: 0.8056 (tt0) REVERT: G 74 LYS cc_start: 0.7751 (mppt) cc_final: 0.7450 (mmtm) REVERT: H 117 LYS cc_start: 0.7943 (ttmt) cc_final: 0.7405 (tttm) outliers start: 13 outliers final: 3 residues processed: 152 average time/residue: 1.1057 time to fit residues: 176.0034 Evaluate side-chains 151 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 145 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 115 LYS Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 19 SER 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: 0.7980 chunk 22 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 = 0.4025 r_free = 0.4025 target = 0.172846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.140062 restraints weight = 10204.139| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 0.89 r_work: 0.3428 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13135 Z= 0.201 Angle : 0.748 8.252 18991 Z= 0.421 Chirality : 0.053 0.334 2160 Planarity : 0.005 0.047 1388 Dihedral : 31.453 173.795 4108 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 3.04 % Allowed : 11.11 % Favored : 85.84 % 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: 2.17 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.17 (0.33), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 27 TYR 0.018 0.002 TYR B 51 PHE 0.013 0.002 PHE A 67 HIS 0.007 0.002 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.20 (13135) covalent geometry : angle 0.74793 / 0.42 (18991) hydrogen bonds : bond 0.06263 / 4.23 ( 783) hydrogen bonds : angle 3.05220 / 2.25 ( 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 163 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 0.371 Fit side-chains REVERT: A 83 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.8495 (mtt-85) REVERT: C 20 ARG cc_start: 0.7818 (OUTLIER) cc_final: 0.7604 (mtm-85) REVERT: C 64 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7952 (tt0) REVERT: C 91 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7333 (mt-10) REVERT: D 31 LYS cc_start: 0.7997 (tptm) cc_final: 0.7773 (tptm) REVERT: D 68 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7712 (tp30) REVERT: D 105 LYS cc_start: 0.8406 (mttt) cc_final: 0.8167 (mttm) REVERT: E 53 ARG cc_start: 0.8291 (ttp-110) cc_final: 0.7990 (tmt90) REVERT: F 52 GLU cc_start: 0.8323 (mm-30) cc_final: 0.7875 (mp0) REVERT: F 77 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8419 (mttm) REVERT: F 92 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7648 (ttp80) REVERT: G 15 LYS cc_start: 0.7579 (pttp) cc_final: 0.7281 (pttm) REVERT: G 91 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7334 (mt-10) REVERT: H 117 LYS cc_start: 0.7993 (ttmt) cc_final: 0.7453 (tttm) outliers start: 20 outliers final: 7 residues processed: 150 average time/residue: 1.1359 time to fit residues: 178.1579 Evaluate side-chains 156 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain C residue 20 ARG Chi-restraints excluded: chain C residue 64 GLU 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 48 ASP Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 92 ARG 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: 0.9980 chunk 59 optimal weight: 0.9990 chunk 89 optimal weight: 30.0000 chunk 64 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 79 optimal weight: 20.0000 chunk 32 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 = 0.4045 r_free = 0.4045 target = 0.174698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.142295 restraints weight = 10329.922| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 0.87 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: 0.8445 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13135 Z= 0.152 Angle : 0.697 8.125 18991 Z= 0.398 Chirality : 0.050 0.335 2160 Planarity : 0.004 0.033 1388 Dihedral : 31.478 173.717 4108 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 2.44 % Allowed : 12.18 % 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: 2.31 (0.29), residues: 770 helix: 2.20 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.16 (0.34), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 42 TYR 0.013 0.002 TYR G 57 PHE 0.011 0.002 PHE E 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.15 (13135) covalent geometry : angle 0.69703 / 0.40 (18991) hydrogen bonds : bond 0.04835 / 3.25 ( 783) hydrogen bonds : angle 3.00400 / 2.21 ( 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 157 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.209 Fit side-chains REVERT: C 15 LYS cc_start: 0.7141 (tttt) cc_final: 0.6326 (ptpp) REVERT: C 20 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7550 (mtm-85) REVERT: C 91 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7311 (mt-10) REVERT: D 31 LYS cc_start: 0.7990 (tptm) cc_final: 0.7768 (tptm) REVERT: D 68 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7672 (tp30) REVERT: D 105 LYS cc_start: 0.8325 (mttt) cc_final: 0.8090 (mttm) REVERT: E 115 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8325 (mptp) REVERT: F 52 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7847 (mp0) REVERT: F 77 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8428 (mttm) REVERT: G 15 LYS cc_start: 0.7624 (pttp) cc_final: 0.7317 (pttm) REVERT: G 74 LYS cc_start: 0.7694 (mppt) cc_final: 0.7393 (mmtm) REVERT: G 91 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7288 (mt-10) REVERT: H 68 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7672 (tp30) REVERT: H 117 LYS cc_start: 0.7988 (ttmt) cc_final: 0.7384 (tttm) outliers start: 16 outliers final: 6 residues processed: 146 average time/residue: 1.0007 time to fit residues: 152.8425 Evaluate side-chains 153 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 140 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 65 LEU Chi-restraints excluded: chain E residue 115 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: 0.0970 chunk 61 optimal weight: 0.7980 chunk 81 optimal weight: 10.0000 chunk 9 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 7 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4057 r_free = 0.4057 target = 0.175999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.143766 restraints weight = 10285.387| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 0.87 r_work: 0.3476 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 13135 Z= 0.144 Angle : 0.678 10.560 18991 Z= 0.389 Chirality : 0.049 0.335 2160 Planarity : 0.004 0.034 1388 Dihedral : 31.429 174.483 4108 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 1.98 % Allowed : 13.09 % Favored : 84.93 % 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: 2.44 (0.29), residues: 770 helix: 2.28 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.09 (0.34), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 42 TYR 0.012 0.001 TYR F 51 PHE 0.012 0.001 PHE A 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.14 (13135) covalent geometry : angle 0.67838 / 0.39 (18991) hydrogen bonds : bond 0.04362 / 2.92 ( 783) hydrogen bonds : angle 2.93249 / 2.16 ( 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 154 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 0.358 Fit side-chains REVERT: C 15 LYS cc_start: 0.7118 (tttt) cc_final: 0.6318 (ptpp) REVERT: C 20 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.7563 (mtm-85) REVERT: C 91 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7322 (mt-10) REVERT: D 31 LYS cc_start: 0.7997 (tptm) cc_final: 0.7765 (tptm) REVERT: D 68 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7680 (tp30) REVERT: D 105 LYS cc_start: 0.8277 (mttt) cc_final: 0.8037 (mttm) REVERT: E 53 ARG cc_start: 0.8279 (ttp-110) cc_final: 0.7967 (tmt90) REVERT: F 52 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7834 (mp0) REVERT: F 77 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8418 (mttm) REVERT: G 15 LYS cc_start: 0.7613 (pttp) cc_final: 0.7312 (pttm) REVERT: G 74 LYS cc_start: 0.7695 (mppt) cc_final: 0.7394 (mmtm) REVERT: G 91 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7295 (mt-10) REVERT: H 68 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7658 (tp30) REVERT: H 117 LYS cc_start: 0.7979 (ttmt) cc_final: 0.7379 (tttm) outliers start: 13 outliers final: 4 residues processed: 146 average time/residue: 0.9893 time to fit residues: 151.2946 Evaluate side-chains 151 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 141 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.5980 chunk 57 optimal weight: 4.9990 chunk 77 optimal weight: 20.0000 chunk 36 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 88 optimal weight: 40.0000 chunk 30 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 65 optimal weight: 7.9990 chunk 53 optimal weight: 0.4980 chunk 95 optimal weight: 9.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.4070 r_free = 0.4070 target = 0.177296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.145276 restraints weight = 10278.526| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 0.87 r_work: 0.3492 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13135 Z= 0.138 Angle : 0.645 7.366 18991 Z= 0.375 Chirality : 0.047 0.336 2160 Planarity : 0.004 0.036 1388 Dihedral : 31.317 175.272 4108 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 1.52 % Allowed : 13.55 % Favored : 84.93 % 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: 2.57 (0.29), residues: 770 helix: 2.40 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.07 (0.35), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 42 TYR 0.011 0.001 TYR G 57 PHE 0.011 0.001 PHE E 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.14 (13135) covalent geometry : angle 0.64524 / 0.38 (18991) hydrogen bonds : bond 0.04171 / 2.80 ( 783) hydrogen bonds : angle 2.85470 / 2.11 ( 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: 10 poor density : 141 time to evaluate : 0.329 Fit side-chains REVERT: C 20 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.7556 (mtm-85) REVERT: D 31 LYS cc_start: 0.7986 (tptm) cc_final: 0.7753 (tptm) REVERT: D 68 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7681 (tp30) REVERT: E 53 ARG cc_start: 0.8273 (ttp-110) cc_final: 0.7968 (tmt90) REVERT: F 52 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7772 (mp0) REVERT: G 15 LYS cc_start: 0.7600 (pttp) cc_final: 0.7321 (pttm) REVERT: G 74 LYS cc_start: 0.7716 (mppt) cc_final: 0.7433 (mmtm) REVERT: H 68 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7670 (tp30) REVERT: H 117 LYS cc_start: 0.7975 (ttmt) cc_final: 0.7377 (tttm) outliers start: 10 outliers final: 3 residues processed: 146 average time/residue: 0.9248 time to fit residues: 141.4820 Evaluate side-chains 145 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 139 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 81 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 69 optimal weight: 0.9990 chunk 94 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 54 optimal weight: 10.0000 chunk 99 optimal weight: 20.0000 chunk 33 optimal weight: 5.9990 chunk 25 optimal weight: 0.5980 chunk 93 optimal weight: 20.0000 chunk 38 optimal weight: 4.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 125 GLN C 104 GLN E 68 GLN F 27 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.171859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.139074 restraints weight = 10135.487| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 0.89 r_work: 0.3419 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13135 Z= 0.245 Angle : 0.774 8.609 18991 Z= 0.429 Chirality : 0.055 0.338 2160 Planarity : 0.006 0.053 1388 Dihedral : 31.557 175.124 4108 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.52 % Allowed : 13.55 % Favored : 84.93 % 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: 2.15 (0.29), residues: 770 helix: 2.11 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.32 (0.33), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 67 TYR 0.017 0.003 TYR E 54 PHE 0.012 0.003 PHE G 25 HIS 0.007 0.002 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.25 (13135) covalent geometry : angle 0.77358 / 0.43 (18991) hydrogen bonds : bond 0.06907 / 4.67 ( 783) hydrogen bonds : angle 3.09102 / 2.28 ( 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 155 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 145 time to evaluate : 0.231 Fit side-chains REVERT: C 20 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7615 (mtm-85) REVERT: D 31 LYS cc_start: 0.8002 (tptm) cc_final: 0.7787 (tptm) REVERT: D 68 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7713 (tp30) REVERT: F 52 GLU cc_start: 0.8320 (mm-30) cc_final: 0.7883 (mp0) REVERT: G 15 LYS cc_start: 0.7579 (pttp) cc_final: 0.7310 (pttm) REVERT: G 74 LYS cc_start: 0.7724 (mppt) cc_final: 0.7516 (tppp) REVERT: H 68 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7719 (tp30) REVERT: H 117 LYS cc_start: 0.8008 (ttmt) cc_final: 0.7411 (tttm) outliers start: 10 outliers final: 3 residues processed: 148 average time/residue: 0.9549 time to fit residues: 147.8447 Evaluate side-chains 147 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 141 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 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: 1.9990 chunk 43 optimal weight: 0.8980 chunk 96 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 53 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 71 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.174500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.142195 restraints weight = 10186.438| |-----------------------------------------------------------------------------| r_work (start): 0.3656 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: 3.15 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13135 Z= 0.143 Angle : 0.707 9.618 18991 Z= 0.400 Chirality : 0.050 0.336 2160 Planarity : 0.005 0.035 1388 Dihedral : 31.580 174.243 4108 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 1.07 % Allowed : 14.61 % Favored : 84.32 % 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: 2.20 (0.29), residues: 770 helix: 2.15 (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 G 32 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 0.00229 / 0.14 (13135) covalent geometry : angle 0.70741 / 0.40 (18991) hydrogen bonds : bond 0.05033 / 3.39 ( 783) hydrogen bonds : angle 3.05465 / 2.26 ( 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 151 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 144 time to evaluate : 0.313 Fit side-chains REVERT: C 20 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.7522 (mtm-85) REVERT: D 31 LYS cc_start: 0.7995 (tptm) cc_final: 0.7779 (tptm) REVERT: D 68 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7678 (tp30) REVERT: F 52 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7837 (mp0) REVERT: G 15 LYS cc_start: 0.7573 (pttp) cc_final: 0.7306 (pttm) REVERT: G 74 LYS cc_start: 0.7742 (mppt) cc_final: 0.7461 (mmtm) REVERT: H 68 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7682 (tp30) REVERT: H 117 LYS cc_start: 0.7990 (ttmt) cc_final: 0.7393 (tttm) outliers start: 7 outliers final: 3 residues processed: 147 average time/residue: 1.0765 time to fit residues: 165.5720 Evaluate side-chains 146 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 140 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 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 26 optimal weight: 0.0000 chunk 50 optimal weight: 0.8980 chunk 46 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 93 optimal weight: 20.0000 chunk 48 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 79 optimal weight: 20.0000 chunk 33 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 = 0.173885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.141143 restraints weight = 10235.391| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 0.88 r_work: 0.3448 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13135 Z= 0.173 Angle : 0.698 10.267 18991 Z= 0.395 Chirality : 0.050 0.335 2160 Planarity : 0.005 0.040 1388 Dihedral : 31.476 175.810 4108 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.91 % Allowed : 14.61 % 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: 2.22 (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 0.003 0.000 ARG E 42 TYR 0.014 0.002 TYR B 51 PHE 0.011 0.002 PHE E 67 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.17 (13135) covalent geometry : angle 0.69758 / 0.40 (18991) hydrogen bonds : bond 0.05167 / 3.48 ( 783) hydrogen bonds : angle 2.97267 / 2.20 ( 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: 6 poor density : 142 time to evaluate : 0.352 Fit side-chains REVERT: C 20 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7564 (mtm-85) REVERT: D 31 LYS cc_start: 0.7999 (tptm) cc_final: 0.7765 (tptm) REVERT: D 68 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7704 (tp30) REVERT: E 53 ARG cc_start: 0.8285 (ttp-110) cc_final: 0.7956 (tmt90) REVERT: F 52 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7836 (mp0) REVERT: G 15 LYS cc_start: 0.7566 (pttp) cc_final: 0.7315 (pttm) REVERT: G 74 LYS cc_start: 0.7751 (mppt) cc_final: 0.7463 (mmtm) REVERT: H 68 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7696 (tp30) REVERT: H 117 LYS cc_start: 0.7996 (ttmt) cc_final: 0.7403 (tttm) outliers start: 6 outliers final: 3 residues processed: 144 average time/residue: 1.0957 time to fit residues: 165.1444 Evaluate side-chains 146 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 140 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 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: 0.6980 chunk 82 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 85 optimal weight: 20.0000 chunk 12 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 90 optimal weight: 20.0000 chunk 69 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.4041 r_free = 0.4041 target = 0.174084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.141410 restraints weight = 10102.672| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 0.87 r_work: 0.3452 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13135 Z= 0.157 Angle : 0.692 9.608 18991 Z= 0.393 Chirality : 0.049 0.336 2160 Planarity : 0.005 0.039 1388 Dihedral : 31.478 175.830 4108 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.91 % Allowed : 14.46 % 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: 2.29 (0.29), residues: 770 helix: 2.22 (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 0.003 0.000 ARG A 42 TYR 0.013 0.002 TYR F 51 PHE 0.012 0.002 PHE E 67 HIS 0.005 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.16 (13135) covalent geometry : angle 0.69245 / 0.39 (18991) hydrogen bonds : bond 0.05104 / 3.44 ( 783) hydrogen bonds : angle 2.96981 / 2.20 ( 1952) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5474.80 seconds wall clock time: 93 minutes 37.25 seconds (5617.25 seconds total)