Starting phenix.real_space_refine on Wed Feb 4 17:48:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f0o_50114/02_2026/9f0o_50114.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f0o_50114/02_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_50114/02_2026/9f0o_50114.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f0o_50114/02_2026/9f0o_50114.map" model { file = "/net/cci-nas-00/data/ceres_data/9f0o_50114/02_2026/9f0o_50114.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f0o_50114/02_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-2.0-5952/lib/python3.9/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: 2.76, 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: 0.91 Conformation dependent library (CDL) restraints added in 388.9 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: 2.60 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: 2.58 Time building geometry restraints manager: 1.27 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=" CZ ARG K 582 " pdb=" NH2 ARG K 582 " ideal model delta sigma weight residual 1.330 1.290 0.040 1.30e-02 5.92e+03 9.25e+00 bond pdb=" CZ ARG L 582 " pdb=" NH2 ARG L 582 " ideal model delta sigma weight residual 1.330 1.291 0.039 1.30e-02 5.92e+03 9.17e+00 bond pdb=" CZ ARG G 32 " pdb=" NH2 ARG G 32 " ideal model delta sigma weight residual 1.330 1.291 0.039 1.30e-02 5.92e+03 9.05e+00 bond pdb=" CZ ARG H 76 " pdb=" NH2 ARG H 76 " ideal model delta sigma weight residual 1.330 1.291 0.039 1.30e-02 5.92e+03 8.80e+00 bond pdb=" CZ ARG G 17 " pdb=" NH2 ARG G 17 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.71e+00 ... (remaining 13130 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 12459 1.70 - 3.41: 5291 3.41 - 5.11: 1143 5.11 - 6.81: 86 6.81 - 8.52: 12 Bond angle restraints: 18991 Sorted by residual: angle pdb=" CA PRO A 38 " pdb=" N PRO A 38 " pdb=" CD PRO A 38 " ideal model delta sigma weight residual 112.00 103.48 8.52 1.40e+00 5.10e-01 3.70e+01 angle pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 110.00 117.82 -7.82 1.50e+00 4.44e-01 2.72e+01 angle pdb=" OE1 GLN C 104 " pdb=" CD GLN C 104 " pdb=" NE2 GLN C 104 " ideal model delta sigma weight residual 122.60 117.44 5.16 1.00e+00 1.00e+00 2.67e+01 angle pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " ideal model delta sigma weight residual 110.00 117.64 -7.64 1.50e+00 4.44e-01 2.59e+01 angle pdb=" CA PRO E 38 " pdb=" N PRO E 38 " pdb=" CD PRO E 38 " ideal model delta sigma weight residual 112.00 105.05 6.95 1.40e+00 5.10e-01 2.47e+01 ... (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 - 0.092: 1767 0.092 - 0.184: 342 0.184 - 0.276: 39 0.276 - 0.367: 10 0.367 - 0.459: 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 -2.66 -2.20 -0.46 2.00e-01 2.50e+01 5.27e+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 -2.66 -2.22 -0.44 2.00e-01 2.50e+01 4.81e+00 chirality pdb=" P DT I -74 " pdb=" OP1 DT I -74 " pdb=" OP2 DT I -74 " pdb=" O5' DT I -74 " both_signs ideal model delta sigma weight residual True 2.35 -2.67 -0.33 2.00e-01 2.50e+01 2.67e+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: 2.980 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: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.660 Find NCS groups from input model: 0.120 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:8.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 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= 0.729 Angle : 1.840 8.516 18991 Z= 1.230 Chirality : 0.075 0.459 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 covalent geometry : bond 0.01298 (13135) covalent geometry : angle 1.83980 (18991) hydrogen bonds : bond 0.11414 ( 783) hydrogen bonds : angle 5.41058 ( 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 : 0.341 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: 1.0059 time to fit residues: 175.4708 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 : 0.303 ------------------------------------------------------------------------------- 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: 0.6980 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: 0.9980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 25 ASN C 84 GLN C 89 ASN C 104 GLN E 68 GLN F 27 GLN G 84 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.178505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.146890 restraints weight = 10365.151| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 0.87 r_work: 0.3514 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 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 : 0.004 0.049 13135 Z= 0.170 Angle : 0.600 5.368 18991 Z= 0.369 Chirality : 0.037 0.138 2160 Planarity : 0.004 0.029 1388 Dihedral : 30.505 167.063 4111 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 1.83 % Allowed : 8.37 % Favored : 89.80 % 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: 2.65 (0.29), residues: 770 helix: 2.34 (0.22), residues: 548 sheet: None (None), residues: 0 loop : 0.35 (0.36), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 92 TYR 0.014 0.002 TYR F 51 PHE 0.008 0.002 PHE E 67 HIS 0.004 0.001 HIS H 46 Details of bonding type rmsd covalent geometry : bond 0.00359 (13135) covalent geometry : angle 0.59978 (18991) hydrogen bonds : bond 0.03999 ( 783) hydrogen bonds : angle 2.83380 ( 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 164 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 0.261 Fit side-chains REVERT: C 20 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.7518 (mtm-85) REVERT: C 41 GLU cc_start: 0.8217 (tt0) cc_final: 0.8014 (tt0) REVERT: D 31 LYS cc_start: 0.7943 (tptm) cc_final: 0.7696 (tptm) REVERT: E 53 ARG cc_start: 0.8243 (ttp-110) cc_final: 0.7923 (tmt90) REVERT: F 52 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7787 (mp0) REVERT: G 15 LYS cc_start: 0.7562 (pttp) cc_final: 0.7265 (pttm) REVERT: H 117 LYS cc_start: 0.7928 (ttmt) cc_final: 0.7385 (tttm) outliers start: 12 outliers final: 4 residues processed: 156 average time/residue: 0.9824 time to fit residues: 160.3121 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 : 0.355 ------------------------------------------------------------------------------- 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 48 ASP 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: 8.9990 chunk 30 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 32 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 21 optimal weight: 0.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 76 GLN A 125 GLN C 73 ASN C 104 GLN D 46 HIS E 68 GLN F 25 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.176911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.144556 restraints weight = 10420.140| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 0.88 r_work: 0.3483 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13135 Z= 0.178 Angle : 0.584 5.313 18991 Z= 0.358 Chirality : 0.036 0.162 2160 Planarity : 0.004 0.035 1388 Dihedral : 30.607 171.464 4108 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 1.67 % Allowed : 11.11 % Favored : 87.21 % 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: 2.75 (0.29), residues: 770 helix: 2.47 (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 0.003 0.000 ARG G 71 TYR 0.014 0.002 TYR B 51 PHE 0.010 0.002 PHE E 67 HIS 0.004 0.001 HIS H 46 Details of bonding type rmsd covalent geometry : bond 0.00380 (13135) covalent geometry : angle 0.58384 (18991) hydrogen bonds : bond 0.04214 ( 783) hydrogen bonds : angle 2.80274 ( 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 158 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 147 time to evaluate : 0.329 Fit side-chains REVERT: C 20 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7546 (mtm-85) REVERT: D 31 LYS cc_start: 0.7940 (tptm) cc_final: 0.7699 (tptm) REVERT: E 53 ARG cc_start: 0.8259 (ttp-110) cc_final: 0.7970 (tmt90) REVERT: F 52 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7776 (mp0) REVERT: G 15 LYS cc_start: 0.7537 (pttp) cc_final: 0.7255 (pttm) REVERT: H 117 LYS cc_start: 0.7965 (ttmt) cc_final: 0.7394 (tttm) outliers start: 11 outliers final: 2 residues processed: 151 average time/residue: 1.0609 time to fit residues: 167.2011 Evaluate side-chains 147 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 144 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 114 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 70 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 67 optimal weight: 8.9990 chunk 2 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 64 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4039 r_free = 0.4039 target = 0.174060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.141608 restraints weight = 10241.909| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 0.87 r_work: 0.3453 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2487 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= 0.219 Angle : 0.611 5.224 18991 Z= 0.371 Chirality : 0.038 0.175 2160 Planarity : 0.005 0.040 1388 Dihedral : 30.937 173.634 4108 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 2.44 % Allowed : 12.02 % Favored : 85.54 % 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: 2.27 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.02 (0.34), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 92 TYR 0.015 0.002 TYR B 51 PHE 0.011 0.002 PHE A 67 HIS 0.005 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00477 (13135) covalent geometry : angle 0.61087 (18991) hydrogen bonds : bond 0.04973 ( 783) hydrogen bonds : angle 2.93351 ( 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 162 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 0.344 Fit side-chains REVERT: C 20 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.7577 (mtm-85) REVERT: C 91 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7342 (mt-10) REVERT: D 31 LYS cc_start: 0.7992 (tptm) cc_final: 0.7749 (tptm) REVERT: E 53 ARG cc_start: 0.8275 (ttp-110) cc_final: 0.7967 (tmt90) REVERT: F 52 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7854 (mp0) REVERT: F 77 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8433 (mttm) REVERT: G 15 LYS cc_start: 0.7566 (pttp) cc_final: 0.7313 (pttm) REVERT: G 91 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7316 (mt-10) REVERT: H 117 LYS cc_start: 0.7988 (ttmt) cc_final: 0.7444 (tttm) outliers start: 16 outliers final: 5 residues processed: 149 average time/residue: 1.1277 time to fit residues: 175.5304 Evaluate side-chains 154 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 145 time to evaluate : 0.206 ------------------------------------------------------------------------------- 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 74 LYS Chi-restraints excluded: chain C residue 91 GLU 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 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: 10.0000 chunk 43 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 chunk 8 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN E 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.174198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.141755 restraints weight = 10320.314| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 0.87 r_work: 0.3454 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2553 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= 0.214 Angle : 0.602 5.838 18991 Z= 0.366 Chirality : 0.037 0.178 2160 Planarity : 0.005 0.039 1388 Dihedral : 30.880 173.312 4108 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 1.98 % Allowed : 12.79 % 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: 2.35 (0.29), residues: 770 helix: 2.24 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.16 (0.33), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 92 TYR 0.015 0.002 TYR B 51 PHE 0.012 0.002 PHE A 67 HIS 0.005 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00466 (13135) covalent geometry : angle 0.60204 (18991) hydrogen bonds : bond 0.04869 ( 783) hydrogen bonds : angle 2.90261 ( 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 159 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 0.363 Fit side-chains REVERT: C 20 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.7562 (mtm-85) REVERT: D 31 LYS cc_start: 0.7992 (tptm) cc_final: 0.7757 (tptm) REVERT: D 68 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7727 (tp30) REVERT: E 53 ARG cc_start: 0.8287 (ttp-110) cc_final: 0.7980 (tmt90) REVERT: F 52 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7842 (mp0) REVERT: F 92 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7686 (ttp80) REVERT: G 15 LYS cc_start: 0.7558 (pttp) cc_final: 0.7323 (pttm) REVERT: H 68 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7733 (tp30) REVERT: H 117 LYS cc_start: 0.8002 (ttmt) cc_final: 0.7389 (tttm) outliers start: 13 outliers final: 4 residues processed: 149 average time/residue: 1.0323 time to fit residues: 160.7285 Evaluate side-chains 151 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 143 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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 114 VAL Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 92 ARG 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: 0.8980 chunk 61 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 46 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN E 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.173210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.140843 restraints weight = 10223.841| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 0.87 r_work: 0.3441 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2585 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= 0.237 Angle : 0.624 6.373 18991 Z= 0.377 Chirality : 0.038 0.188 2160 Planarity : 0.005 0.041 1388 Dihedral : 30.996 173.243 4108 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 1.98 % Allowed : 13.39 % 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: 2.21 (0.29), residues: 770 helix: 2.16 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.29 (0.33), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 71 TYR 0.015 0.002 TYR B 51 PHE 0.012 0.002 PHE A 67 HIS 0.006 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00519 (13135) covalent geometry : angle 0.62359 (18991) hydrogen bonds : bond 0.05392 ( 783) hydrogen bonds : angle 2.95399 ( 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 160 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 147 time to evaluate : 0.324 Fit side-chains REVERT: A 83 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.8493 (mtt-85) REVERT: C 20 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.7580 (mtm-85) REVERT: D 31 LYS cc_start: 0.8016 (tptm) cc_final: 0.7783 (tptm) REVERT: D 68 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7680 (tp30) REVERT: F 52 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7854 (mp0) REVERT: F 92 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7655 (ttp80) REVERT: G 15 LYS cc_start: 0.7542 (pttp) cc_final: 0.7308 (pttm) REVERT: H 68 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7681 (tp30) REVERT: H 117 LYS cc_start: 0.8008 (ttmt) cc_final: 0.7401 (tttm) outliers start: 13 outliers final: 5 residues processed: 152 average time/residue: 1.0252 time to fit residues: 163.0751 Evaluate side-chains 156 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 146 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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 114 VAL Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 92 ARG 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: 7.9990 chunk 36 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 88 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN E 68 GLN G 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.174154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.141899 restraints weight = 10185.274| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 0.86 r_work: 0.3456 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13135 Z= 0.190 Angle : 0.602 5.883 18991 Z= 0.366 Chirality : 0.036 0.204 2160 Planarity : 0.004 0.035 1388 Dihedral : 31.004 172.988 4108 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 2.13 % Allowed : 13.24 % 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: 2.25 (0.29), residues: 770 helix: 2.19 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.27 (0.34), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 27 TYR 0.013 0.002 TYR B 51 PHE 0.012 0.002 PHE E 67 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00408 (13135) covalent geometry : angle 0.60163 (18991) hydrogen bonds : bond 0.04980 ( 783) hydrogen bonds : angle 2.92947 ( 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 161 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 0.368 Fit side-chains REVERT: C 20 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7559 (mtm-85) REVERT: C 91 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7339 (mt-10) REVERT: D 68 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7669 (tp30) REVERT: F 52 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7837 (mp0) REVERT: F 77 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8407 (mttm) REVERT: F 92 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7638 (ttp80) REVERT: G 15 LYS cc_start: 0.7537 (pttp) cc_final: 0.7292 (pttm) REVERT: G 91 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7314 (mt-10) REVERT: H 68 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7668 (tp30) REVERT: H 117 LYS cc_start: 0.7982 (ttmt) cc_final: 0.7392 (tttm) outliers start: 14 outliers final: 4 residues processed: 151 average time/residue: 1.0827 time to fit residues: 171.2708 Evaluate side-chains 155 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 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 F residue 77 LYS Chi-restraints excluded: chain F residue 92 ARG 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: 5.9990 chunk 28 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 99 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 93 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN E 68 GLN G 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.172554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.140146 restraints weight = 10162.327| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 0.88 r_work: 0.3434 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 13135 Z= 0.258 Angle : 0.640 6.138 18991 Z= 0.385 Chirality : 0.040 0.203 2160 Planarity : 0.005 0.041 1388 Dihedral : 31.149 172.812 4108 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 2.28 % Allowed : 13.24 % 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: 2.10 (0.29), residues: 770 helix: 2.09 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.38 (0.34), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 71 TYR 0.015 0.002 TYR B 51 PHE 0.012 0.002 PHE E 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00565 (13135) covalent geometry : angle 0.63975 (18991) hydrogen bonds : bond 0.05703 ( 783) hydrogen bonds : angle 2.99654 ( 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 162 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 147 time to evaluate : 0.328 Fit side-chains REVERT: C 20 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.7572 (mtm-85) REVERT: C 91 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7352 (mt-10) REVERT: E 53 ARG cc_start: 0.8265 (ttp-110) cc_final: 0.7995 (tmt90) REVERT: F 52 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7867 (mp0) REVERT: F 77 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8422 (mttm) REVERT: F 92 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7662 (ttp80) REVERT: G 15 LYS cc_start: 0.7574 (pttp) cc_final: 0.7326 (pttm) REVERT: G 91 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7354 (mt-10) REVERT: H 117 LYS cc_start: 0.8019 (ttmt) cc_final: 0.7417 (tttm) outliers start: 15 outliers final: 6 residues processed: 150 average time/residue: 1.1080 time to fit residues: 173.7266 Evaluate side-chains 155 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 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 91 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 56 LYS 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 91 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 31 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 47 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 43 optimal weight: 0.5980 chunk 96 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN E 68 GLN G 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.173882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.141612 restraints weight = 10155.623| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 0.86 r_work: 0.3452 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13135 Z= 0.189 Angle : 0.606 5.816 18991 Z= 0.369 Chirality : 0.036 0.209 2160 Planarity : 0.004 0.034 1388 Dihedral : 31.151 172.522 4108 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 2.44 % Allowed : 13.24 % 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: 2.18 (0.29), residues: 770 helix: 2.15 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.35 (0.34), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 71 TYR 0.013 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 covalent geometry : bond 0.00404 (13135) covalent geometry : angle 0.60605 (18991) hydrogen bonds : bond 0.05015 ( 783) hydrogen bonds : angle 2.95995 ( 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 161 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 0.349 Fit side-chains REVERT: C 20 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7548 (mtm-85) REVERT: C 74 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7278 (mtmm) REVERT: C 91 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7337 (mt-10) REVERT: D 68 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7692 (tp30) REVERT: E 53 ARG cc_start: 0.8247 (ttp-110) cc_final: 0.7970 (tmt90) REVERT: F 52 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7844 (mp0) REVERT: F 77 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8415 (mttm) REVERT: F 92 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7657 (ttp80) REVERT: G 15 LYS cc_start: 0.7569 (pttp) cc_final: 0.7312 (pttm) REVERT: G 91 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7320 (mt-10) REVERT: G 104 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7829 (mm110) REVERT: H 68 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7696 (tp30) REVERT: H 117 LYS cc_start: 0.7992 (ttmt) cc_final: 0.7411 (tttm) outliers start: 16 outliers final: 5 residues processed: 148 average time/residue: 1.1425 time to fit residues: 176.7453 Evaluate side-chains 157 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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 74 LYS 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 F residue 59 LYS Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 104 GLN 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: 0.3980 chunk 50 optimal weight: 1.9990 chunk 46 optimal weight: 0.1980 chunk 37 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN E 68 GLN G 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.174117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.141834 restraints weight = 10243.864| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 0.86 r_work: 0.3455 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.133 13135 Z= 0.201 Angle : 0.814 59.110 18991 Z= 0.496 Chirality : 0.036 0.198 2160 Planarity : 0.005 0.053 1388 Dihedral : 31.142 172.595 4108 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 2.59 % Allowed : 13.39 % Favored : 84.02 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.29), residues: 770 helix: 2.15 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.34 (0.34), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 42 TYR 0.013 0.002 TYR B 51 PHE 0.012 0.002 PHE E 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00410 (13135) covalent geometry : angle 0.81369 (18991) hydrogen bonds : bond 0.05000 ( 783) hydrogen bonds : angle 2.95683 ( 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 160 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 0.346 Fit side-chains REVERT: C 20 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.7547 (mtm-85) REVERT: C 74 LYS cc_start: 0.7679 (OUTLIER) cc_final: 0.7275 (mtmm) REVERT: C 91 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7326 (mt-10) REVERT: D 68 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7687 (tp30) REVERT: E 53 ARG cc_start: 0.8244 (ttp-110) cc_final: 0.7923 (tmt90) REVERT: F 52 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7844 (mp0) REVERT: F 77 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8412 (mttm) REVERT: F 92 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7650 (ttp80) REVERT: G 15 LYS cc_start: 0.7565 (pttp) cc_final: 0.7296 (pttm) REVERT: G 91 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7316 (mt-10) REVERT: H 68 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7691 (tp30) REVERT: H 117 LYS cc_start: 0.7983 (ttmt) cc_final: 0.7401 (tttm) outliers start: 17 outliers final: 8 residues processed: 146 average time/residue: 1.0289 time to fit residues: 157.4233 Evaluate side-chains 158 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 20 ARG Chi-restraints excluded: chain C residue 74 LYS 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 F residue 59 LYS Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 91 GLU 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 93 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 104 GLN E 68 GLN ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.174097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.141865 restraints weight = 10119.777| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 0.86 r_work: 0.3455 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.133 13135 Z= 0.201 Angle : 0.814 59.109 18991 Z= 0.496 Chirality : 0.036 0.198 2160 Planarity : 0.005 0.053 1388 Dihedral : 31.142 172.595 4108 Min Nonbonded Distance : 1.443 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 2.44 % Allowed : 13.39 % Favored : 84.17 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.29), residues: 770 helix: 2.15 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.34 (0.34), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 42 TYR 0.013 0.002 TYR B 51 PHE 0.012 0.002 PHE E 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00410 (13135) covalent geometry : angle 0.81368 (18991) hydrogen bonds : bond 0.05000 ( 783) hydrogen bonds : angle 2.95683 ( 1952) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5540.09 seconds wall clock time: 94 minutes 31.97 seconds (5671.97 seconds total)