Starting phenix.real_space_refine on Thu Aug 6 01:35:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vg0_43196/08_2026/8vg0_43196.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vg0_43196/08_2026/8vg0_43196.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vg0_43196/08_2026/8vg0_43196.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vg0_43196/08_2026/8vg0_43196.map" model { file = "/net/cci-nas-00/data/ceres_data/8vg0_43196/08_2026/8vg0_43196.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vg0_43196/08_2026/8vg0_43196.cif" } resolution = 3.07 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= 0.108 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 318 5.49 5 S 20 5.16 5 C 7214 2.51 5 N 2436 2.21 5 O 3053 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13042 Number of models: 1 Model: "" Number of chains: 12 Chain: "I" Number of atoms: 3258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 3258 Classifications: {'DNA': 159} Link IDs: {'rna3p': 158} Chain: "J" Number of atoms: 3261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 3261 Classifications: {'DNA': 159} Link IDs: {'rna3p': 158} Chain: "A" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, '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: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} 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: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 856 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "T" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 414 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 3, 'TRANS': 49} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12647 SG CYS T 271 13.598 101.162 82.539 1.00310.47 S ATOM 12666 SG CYS T 274 13.084 100.826 78.752 1.00313.28 S ATOM 12809 SG CYS T 292 16.436 99.804 80.350 1.00287.96 S ATOM 12828 SG CYS T 295 15.448 103.401 80.082 1.00302.98 S Time building chain proxies: 3.44, per 1000 atoms: 0.26 Number of scatterers: 13042 At special positions: 0 Unit cell: (81.312, 121.44, 147.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 20 16.00 P 318 15.00 O 3053 8.00 N 2436 7.00 C 7214 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 390.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN T 501 " pdb="ZN ZN T 501 " - pdb=" SG CYS T 295 " pdb="ZN ZN T 501 " - pdb=" SG CYS T 292 " pdb="ZN ZN T 501 " - pdb=" SG CYS T 274 " pdb="ZN ZN T 501 " - pdb=" SG CYS T 271 " Number of angles added : 6 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1534 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 11 sheets defined 69.5% alpha, 2.7% beta 159 base pairs and 284 stacking pairs defined. Time for finding SS restraints: 2.00 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.821A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.534A 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: 3.700A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.621A 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: 4.316A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 124 removed outlier: 3.600A pdb=" N ALA D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.930A 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 132 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.699A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.640A 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: 4.306A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 Processing helix chain 'T' and resid 292 through 303 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.831A 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: 7.264A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.636A 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: 7.218A 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: 7.472A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'T' and resid 283 through 284 423 hydrogen bonds defined for protein. 1239 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 387 hydrogen bonds 774 hydrogen bond angles 0 basepair planarities 159 basepair parallelities 284 stacking parallelities Total time for adding SS restraints: 2.63 Time building geometry restraints manager: 1.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2921 1.34 - 1.45: 4077 1.45 - 1.57: 6256 1.57 - 1.69: 634 1.69 - 1.81: 32 Bond restraints: 13920 Sorted by residual: bond pdb=" C1' DT J 55 " pdb=" N1 DT J 55 " ideal model delta sigma weight residual 1.468 1.544 -0.076 1.40e-02 5.10e+03 2.98e+01 bond pdb=" C1' DT J 54 " pdb=" N1 DT J 54 " ideal model delta sigma weight residual 1.468 1.540 -0.072 1.40e-02 5.10e+03 2.66e+01 bond pdb=" C1' DT I 29 " pdb=" N1 DT I 29 " ideal model delta sigma weight residual 1.468 1.538 -0.070 1.40e-02 5.10e+03 2.49e+01 bond pdb=" C1' DC I 110 " pdb=" N1 DC I 110 " ideal model delta sigma weight residual 1.468 1.532 -0.064 1.40e-02 5.10e+03 2.10e+01 bond pdb=" C1' DC I 111 " pdb=" N1 DC I 111 " ideal model delta sigma weight residual 1.468 1.532 -0.064 1.40e-02 5.10e+03 2.08e+01 ... (remaining 13915 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 19197 2.15 - 4.30: 930 4.30 - 6.45: 27 6.45 - 8.60: 1 8.60 - 10.75: 1 Bond angle restraints: 20156 Sorted by residual: angle pdb=" N3 DT I 90 " pdb=" C4 DT I 90 " pdb=" O4 DT I 90 " ideal model delta sigma weight residual 119.90 122.63 -2.73 6.00e-01 2.78e+00 2.07e+01 angle pdb=" N3 DT I 70 " pdb=" C4 DT I 70 " pdb=" O4 DT I 70 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.93e+01 angle pdb=" N3 DT I 71 " pdb=" C4 DT I 71 " pdb=" O4 DT I 71 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.93e+01 angle pdb=" N3 DT J 43 " pdb=" C4 DT J 43 " pdb=" O4 DT J 43 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" N3 DT I 54 " pdb=" C4 DT I 54 " pdb=" O4 DT I 54 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 ... (remaining 20151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.38: 6117 33.38 - 66.76: 1488 66.76 - 100.14: 40 100.14 - 133.53: 0 133.53 - 166.91: 2 Dihedral angle restraints: 7647 sinusoidal: 5268 harmonic: 2379 Sorted by residual: dihedral pdb=" C4' DG J 127 " pdb=" C3' DG J 127 " pdb=" O3' DG J 127 " pdb=" P DG J 128 " ideal model delta sinusoidal sigma weight residual 220.00 53.09 166.91 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' DC J 93 " pdb=" C3' DC J 93 " pdb=" O3' DC J 93 " pdb=" P DC J 94 " ideal model delta sinusoidal sigma weight residual 220.00 65.81 154.19 1 3.50e+01 8.16e-04 1.49e+01 dihedral pdb=" CG ARG A 131 " pdb=" CD ARG A 131 " pdb=" NE ARG A 131 " pdb=" CZ ARG A 131 " ideal model delta sinusoidal sigma weight residual 180.00 135.09 44.91 2 1.50e+01 4.44e-03 1.06e+01 ... (remaining 7644 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1485 0.035 - 0.070: 400 0.070 - 0.106: 121 0.106 - 0.141: 157 0.141 - 0.176: 127 Chirality restraints: 2290 Sorted by residual: chirality pdb=" C3' DA J 101 " pdb=" C4' DA J 101 " pdb=" O3' DA J 101 " pdb=" C2' DA J 101 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 7.74e-01 chirality pdb=" C3' DT I 121 " pdb=" C4' DT I 121 " pdb=" O3' DT I 121 " pdb=" C2' DT I 121 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.64e-01 chirality pdb=" C3' DG I 122 " pdb=" C4' DG I 122 " pdb=" O3' DG I 122 " pdb=" C2' DG I 122 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.63e-01 ... (remaining 2287 not shown) Planarity restraints: 1448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 83 " 0.001 2.00e-02 2.50e+03 1.50e-02 4.49e+00 pdb=" CG TYR D 83 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR D 83 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR D 83 " 0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR D 83 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR D 83 " -0.012 2.00e-02 2.50e+03 pdb=" CZ TYR D 83 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR D 83 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 131 " 0.026 2.00e-02 2.50e+03 1.13e-02 3.84e+00 pdb=" N9 DG I 131 " -0.025 2.00e-02 2.50e+03 pdb=" C8 DG I 131 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DG I 131 " -0.007 2.00e-02 2.50e+03 pdb=" C5 DG I 131 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DG I 131 " 0.006 2.00e-02 2.50e+03 pdb=" O6 DG I 131 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DG I 131 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 131 " 0.000 2.00e-02 2.50e+03 pdb=" N2 DG I 131 " -0.007 2.00e-02 2.50e+03 pdb=" N3 DG I 131 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 131 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 161 " 0.022 2.00e-02 2.50e+03 1.15e-02 3.31e+00 pdb=" N1 DT I 161 " -0.026 2.00e-02 2.50e+03 pdb=" C2 DT I 161 " -0.003 2.00e-02 2.50e+03 pdb=" O2 DT I 161 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DT I 161 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DT I 161 " 0.004 2.00e-02 2.50e+03 pdb=" O4 DT I 161 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DT I 161 " 0.002 2.00e-02 2.50e+03 pdb=" C7 DT I 161 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DT I 161 " 0.001 2.00e-02 2.50e+03 ... (remaining 1445 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 149 2.65 - 3.21: 10629 3.21 - 3.77: 24270 3.77 - 4.34: 31659 4.34 - 4.90: 44714 Nonbonded interactions: 111421 Sorted by model distance: nonbonded pdb=" OP1 DG J 103 " pdb=" OG SER D 32 " model vdw 2.082 3.040 nonbonded pdb=" OG SER G 18 " pdb=" O PHE G 25 " model vdw 2.110 3.040 nonbonded pdb=" OP1 DA I 144 " pdb=" OG SER H 32 " model vdw 2.141 3.040 nonbonded pdb=" OP1 DC I 53 " pdb=" NH1 ARG T 284 " model vdw 2.228 3.120 nonbonded pdb=" N GLU B 52 " pdb=" OE1 GLU B 52 " model vdw 2.230 3.120 ... (remaining 111416 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' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 10 through 118) } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.250 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 16.200 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: 0.010 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 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 : 0.007 0.076 13924 Z= 0.597 Angle : 0.863 10.746 20162 Z= 0.746 Chirality : 0.059 0.176 2290 Planarity : 0.004 0.037 1448 Dihedral : 27.185 166.908 6113 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 1.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % 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: 2.77 (0.29), residues: 805 helix: 2.64 (0.22), residues: 550 sheet: None (None), residues: 0 loop : 0.05 (0.36), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 79 TYR 0.028 0.002 TYR D 83 PHE 0.005 0.001 PHE A 67 TRP 0.001 0.000 TRP T 282 HIS 0.003 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00716 / 0.60 (13920) covalent geometry : angle 0.86277 / 0.75 (20156) hydrogen bonds : bond 0.10245 / 11.21 ( 810) hydrogen bonds : angle 3.48845 / 4.14 ( 2013) metal coordination : bond 0.00312 / 0.14 ( 4) metal coordination : angle 1.82904 / 3.27 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7893 (pm20) cc_final: 0.7370 (pm20) REVERT: A 76 GLN cc_start: 0.8480 (tp40) cc_final: 0.8238 (tp40) REVERT: A 115 LYS cc_start: 0.8984 (mtmm) cc_final: 0.8773 (mtmm) REVERT: B 88 TYR cc_start: 0.7682 (m-10) cc_final: 0.7441 (m-10) REVERT: D 59 MET cc_start: 0.8795 (tpp) cc_final: 0.8586 (mmm) REVERT: D 83 TYR cc_start: 0.8038 (m-80) cc_final: 0.7518 (m-80) REVERT: H 86 ARG cc_start: 0.8390 (mmt-90) cc_final: 0.7162 (mmm160) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.1754 time to fit residues: 32.5419 Evaluate side-chains 123 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN B 27 GLN F 75 HIS T 293 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.121844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.071842 restraints weight = 22219.198| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.30 r_work: 0.2740 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.0792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13924 Z= 0.183 Angle : 0.675 8.176 20162 Z= 0.402 Chirality : 0.047 0.390 2290 Planarity : 0.004 0.036 1448 Dihedral : 30.134 176.339 4473 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.61 % Allowed : 9.49 % Favored : 88.91 % 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: 2.77 (0.29), residues: 805 helix: 2.60 (0.21), residues: 560 sheet: None (None), residues: 0 loop : 0.02 (0.36), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 11 TYR 0.042 0.002 TYR D 83 PHE 0.009 0.001 PHE A 67 TRP 0.001 0.000 TRP T 282 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.18 (13920) covalent geometry : angle 0.67380 / 0.40 (20156) hydrogen bonds : bond 0.05319 / 6.02 ( 810) hydrogen bonds : angle 3.07037 / 3.65 ( 2013) metal coordination : bond 0.00320 / 0.26 ( 4) metal coordination : angle 2.41207 / 5.40 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8574 (tp40) cc_final: 0.8361 (tp40) REVERT: H 86 ARG cc_start: 0.8398 (mmt-90) cc_final: 0.7160 (mtm180) REVERT: T 299 MET cc_start: 0.6447 (tmm) cc_final: 0.5645 (pmm) outliers start: 11 outliers final: 7 residues processed: 130 average time/residue: 0.1494 time to fit residues: 25.6342 Evaluate side-chains 122 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 115 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain F residue 50 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 87 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 94 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 96 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN H 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.124574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.075052 restraints weight = 22302.128| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.90 r_work: 0.2838 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13924 Z= 0.172 Angle : 0.644 7.649 20162 Z= 0.380 Chirality : 0.045 0.369 2290 Planarity : 0.004 0.035 1448 Dihedral : 30.579 171.633 4473 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.46 % Allowed : 10.95 % Favored : 87.59 % 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: 2.90 (0.29), residues: 805 helix: 2.70 (0.21), residues: 560 sheet: None (None), residues: 0 loop : 0.05 (0.37), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG T 318 TYR 0.015 0.002 TYR B 88 PHE 0.010 0.001 PHE A 67 TRP 0.001 0.000 TRP T 282 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.17 (13920) covalent geometry : angle 0.64209 / 0.38 (20156) hydrogen bonds : bond 0.04832 / 5.51 ( 810) hydrogen bonds : angle 2.86203 / 3.45 ( 2013) metal coordination : bond 0.00458 / 0.35 ( 4) metal coordination : angle 2.58017 / 5.50 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8785 (tp40) cc_final: 0.8567 (tp40) REVERT: F 95 ARG cc_start: 0.8470 (mtp85) cc_final: 0.8155 (mtt90) REVERT: H 86 ARG cc_start: 0.8634 (mmt-90) cc_final: 0.7522 (mtm180) REVERT: T 299 MET cc_start: 0.6543 (tmm) cc_final: 0.5815 (pmm) outliers start: 10 outliers final: 5 residues processed: 124 average time/residue: 0.1532 time to fit residues: 24.8607 Evaluate side-chains 118 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 113 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain F residue 50 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 43 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 11 optimal weight: 10.0000 chunk 42 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 3 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS A 125 GLN F 93 GLN H 47 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.124979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.075430 restraints weight = 22052.634| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.91 r_work: 0.2843 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13924 Z= 0.145 Angle : 0.627 7.631 20162 Z= 0.371 Chirality : 0.044 0.376 2290 Planarity : 0.004 0.034 1448 Dihedral : 30.573 170.854 4473 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.46 % Allowed : 11.39 % Favored : 87.15 % 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: 2.97 (0.29), residues: 805 helix: 2.75 (0.21), residues: 560 sheet: None (None), residues: 0 loop : 0.08 (0.37), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 129 TYR 0.022 0.002 TYR D 83 PHE 0.010 0.001 PHE A 67 TRP 0.001 0.000 TRP T 282 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.15 (13920) covalent geometry : angle 0.62583 / 0.37 (20156) hydrogen bonds : bond 0.04546 / 5.21 ( 810) hydrogen bonds : angle 2.79065 / 3.37 ( 2013) metal coordination : bond 0.00363 / 0.27 ( 4) metal coordination : angle 2.30795 / 4.98 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8809 (tp40) cc_final: 0.8594 (tp40) REVERT: D 35 GLU cc_start: 0.8546 (pt0) cc_final: 0.8259 (pt0) REVERT: D 93 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.7904 (mp0) REVERT: F 95 ARG cc_start: 0.8442 (mtp85) cc_final: 0.8125 (mtt90) REVERT: H 86 ARG cc_start: 0.8644 (mmt-90) cc_final: 0.7534 (mtm180) outliers start: 10 outliers final: 7 residues processed: 123 average time/residue: 0.1389 time to fit residues: 22.7262 Evaluate side-chains 121 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 47 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 66 optimal weight: 4.9990 chunk 54 optimal weight: 0.4980 chunk 42 optimal weight: 0.7980 chunk 103 optimal weight: 30.0000 chunk 94 optimal weight: 5.9990 chunk 48 optimal weight: 0.5980 chunk 12 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN H 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.125621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.075870 restraints weight = 22347.752| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.97 r_work: 0.2840 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13924 Z= 0.137 Angle : 0.618 9.054 20162 Z= 0.367 Chirality : 0.044 0.379 2290 Planarity : 0.003 0.033 1448 Dihedral : 30.580 170.144 4473 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.61 % Allowed : 12.12 % Favored : 86.28 % 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: 3.08 (0.29), residues: 805 helix: 2.82 (0.21), residues: 560 sheet: None (None), residues: 0 loop : 0.17 (0.38), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 53 TYR 0.021 0.001 TYR D 83 PHE 0.010 0.001 PHE A 67 TRP 0.000 0.000 TRP T 282 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.14 (13920) covalent geometry : angle 0.61698 / 0.37 (20156) hydrogen bonds : bond 0.04376 / 5.03 ( 810) hydrogen bonds : angle 2.71477 / 3.28 ( 2013) metal coordination : bond 0.00319 / 0.23 ( 4) metal coordination : angle 2.10453 / 4.59 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: B 95 ARG cc_start: 0.8644 (mtp85) cc_final: 0.8173 (mmt90) REVERT: D 35 GLU cc_start: 0.8501 (pt0) cc_final: 0.8188 (pt0) REVERT: D 93 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.7904 (mp0) REVERT: F 95 ARG cc_start: 0.8382 (mtp85) cc_final: 0.8033 (mtt90) REVERT: H 86 ARG cc_start: 0.8581 (mmt-90) cc_final: 0.7446 (mtm180) outliers start: 11 outliers final: 7 residues processed: 125 average time/residue: 0.1802 time to fit residues: 29.1861 Evaluate side-chains 123 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 114 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 64 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 5 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 15 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 55 optimal weight: 0.4980 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN H 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.123513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.073799 restraints weight = 22049.893| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 1.90 r_work: 0.2813 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13924 Z= 0.190 Angle : 0.660 7.890 20162 Z= 0.377 Chirality : 0.045 0.364 2290 Planarity : 0.004 0.034 1448 Dihedral : 30.833 167.790 4473 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.75 % Allowed : 12.26 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.91 (0.29), residues: 805 helix: 2.70 (0.21), residues: 560 sheet: None (None), residues: 0 loop : 0.08 (0.38), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 92 TYR 0.020 0.002 TYR D 83 PHE 0.009 0.001 PHE A 67 TRP 0.001 0.000 TRP T 282 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.19 (13920) covalent geometry : angle 0.65876 / 0.38 (20156) hydrogen bonds : bond 0.04762 / 5.41 ( 810) hydrogen bonds : angle 2.82390 / 3.43 ( 2013) metal coordination : bond 0.00380 / 0.31 ( 4) metal coordination : angle 2.31537 / 5.00 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8436 (m-10) cc_final: 0.7907 (m-10) REVERT: D 35 GLU cc_start: 0.8514 (pt0) cc_final: 0.8203 (pt0) REVERT: D 93 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.7929 (mp0) REVERT: H 68 ASP cc_start: 0.9032 (t0) cc_final: 0.8716 (t0) outliers start: 12 outliers final: 9 residues processed: 130 average time/residue: 0.1759 time to fit residues: 29.8653 Evaluate side-chains 127 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 47 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 4 optimal weight: 9.9990 chunk 74 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN H 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.124832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.075371 restraints weight = 22187.005| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.90 r_work: 0.2836 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13924 Z= 0.141 Angle : 0.628 8.023 20162 Z= 0.367 Chirality : 0.044 0.368 2290 Planarity : 0.003 0.034 1448 Dihedral : 30.775 166.929 4473 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.46 % Allowed : 12.70 % 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: 3.02 (0.29), residues: 805 helix: 2.78 (0.21), residues: 560 sheet: None (None), residues: 0 loop : 0.13 (0.38), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 79 TYR 0.029 0.002 TYR D 83 PHE 0.010 0.001 PHE A 67 TRP 0.000 0.000 TRP T 282 HIS 0.004 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.14 (13920) covalent geometry : angle 0.62679 / 0.37 (20156) hydrogen bonds : bond 0.04383 / 5.03 ( 810) hydrogen bonds : angle 2.71350 / 3.29 ( 2013) metal coordination : bond 0.00299 / 0.23 ( 4) metal coordination : angle 2.01100 / 4.37 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: D 35 GLU cc_start: 0.8450 (pt0) cc_final: 0.8128 (pt0) REVERT: D 93 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8002 (mp0) REVERT: E 120 MET cc_start: 0.8383 (mtt) cc_final: 0.8057 (mtt) REVERT: H 86 ARG cc_start: 0.8598 (mmt-90) cc_final: 0.7564 (mtm180) outliers start: 10 outliers final: 9 residues processed: 125 average time/residue: 0.1741 time to fit residues: 28.5330 Evaluate side-chains 126 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 47 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 15 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 96 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.125129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.075232 restraints weight = 22018.283| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 1.97 r_work: 0.2833 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13924 Z= 0.144 Angle : 0.622 8.080 20162 Z= 0.364 Chirality : 0.043 0.367 2290 Planarity : 0.003 0.035 1448 Dihedral : 30.749 166.185 4473 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.61 % Allowed : 13.43 % Favored : 84.96 % 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: 3.02 (0.29), residues: 805 helix: 2.78 (0.21), residues: 560 sheet: None (None), residues: 0 loop : 0.13 (0.38), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 129 TYR 0.025 0.002 TYR D 83 PHE 0.010 0.001 PHE A 67 TRP 0.000 0.000 TRP T 282 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.14 (13920) covalent geometry : angle 0.62158 / 0.36 (20156) hydrogen bonds : bond 0.04337 / 4.98 ( 810) hydrogen bonds : angle 2.70116 / 3.27 ( 2013) metal coordination : bond 0.00286 / 0.22 ( 4) metal coordination : angle 1.87187 / 4.06 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 35 GLU cc_start: 0.8459 (pt0) cc_final: 0.8127 (pt0) REVERT: D 93 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.7948 (mp0) REVERT: E 120 MET cc_start: 0.8305 (mtt) cc_final: 0.7970 (mtt) REVERT: T 299 MET cc_start: 0.7102 (tmm) cc_final: 0.5977 (pmm) outliers start: 11 outliers final: 9 residues processed: 125 average time/residue: 0.1825 time to fit residues: 29.8132 Evaluate side-chains 127 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 47 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 77 optimal weight: 0.0470 chunk 5 optimal weight: 9.9990 chunk 65 optimal weight: 0.6980 chunk 59 optimal weight: 0.0030 chunk 76 optimal weight: 0.6980 chunk 48 optimal weight: 0.0070 chunk 50 optimal weight: 0.6980 chunk 0 optimal weight: 50.0000 chunk 11 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 83 optimal weight: 7.9990 overall best weight: 0.2906 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 47 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.126767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.077673 restraints weight = 22379.370| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.85 r_work: 0.2884 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 13924 Z= 0.126 Angle : 0.599 8.240 20162 Z= 0.358 Chirality : 0.042 0.370 2290 Planarity : 0.003 0.035 1448 Dihedral : 30.607 166.029 4473 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.02 % Allowed : 14.31 % Favored : 84.67 % 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: 3.16 (0.29), residues: 805 helix: 2.88 (0.21), residues: 560 sheet: None (None), residues: 0 loop : 0.22 (0.39), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 79 TYR 0.018 0.002 TYR D 83 PHE 0.011 0.001 PHE A 67 TRP 0.000 0.000 TRP T 282 HIS 0.002 0.000 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00192 / 0.13 (13920) covalent geometry : angle 0.59795 / 0.36 (20156) hydrogen bonds : bond 0.04089 / 4.70 ( 810) hydrogen bonds : angle 2.61274 / 3.19 ( 2013) metal coordination : bond 0.00226 / 0.17 ( 4) metal coordination : angle 1.60375 / 3.56 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 123 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: D 35 GLU cc_start: 0.8460 (pt0) cc_final: 0.8145 (pt0) REVERT: D 59 MET cc_start: 0.8914 (tpp) cc_final: 0.8627 (mmm) REVERT: D 93 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8027 (mp0) REVERT: E 60 LEU cc_start: 0.8895 (mt) cc_final: 0.8638 (mt) REVERT: H 86 ARG cc_start: 0.8560 (mmt-90) cc_final: 0.7508 (mtm180) REVERT: T 299 MET cc_start: 0.7093 (tmm) cc_final: 0.5964 (pmm) outliers start: 7 outliers final: 4 residues processed: 128 average time/residue: 0.1847 time to fit residues: 30.6303 Evaluate side-chains 122 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 117 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain H residue 47 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 85 optimal weight: 0.6980 chunk 41 optimal weight: 0.0570 chunk 100 optimal weight: 0.6980 chunk 84 optimal weight: 0.0050 chunk 50 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 8 optimal weight: 9.9990 chunk 75 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 77 optimal weight: 0.9980 overall best weight: 0.4712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.126795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.077725 restraints weight = 22423.611| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.86 r_work: 0.2885 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 13924 Z= 0.130 Angle : 0.609 9.049 20162 Z= 0.361 Chirality : 0.042 0.368 2290 Planarity : 0.003 0.035 1448 Dihedral : 30.607 166.658 4473 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.88 % Allowed : 14.60 % Favored : 84.53 % 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: 3.11 (0.29), residues: 805 helix: 2.84 (0.21), residues: 560 sheet: None (None), residues: 0 loop : 0.19 (0.39), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 79 TYR 0.069 0.002 TYR B 88 PHE 0.010 0.001 PHE A 67 TRP 0.000 0.000 TRP T 282 HIS 0.004 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.13 (13920) covalent geometry : angle 0.60881 / 0.36 (20156) hydrogen bonds : bond 0.04090 / 4.69 ( 810) hydrogen bonds : angle 2.63011 / 3.21 ( 2013) metal coordination : bond 0.00245 / 0.19 ( 4) metal coordination : angle 1.64377 / 3.61 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 119 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: C 74 LYS cc_start: 0.8945 (mtpp) cc_final: 0.8652 (mtpp) REVERT: D 35 GLU cc_start: 0.8460 (pt0) cc_final: 0.8142 (pt0) REVERT: D 59 MET cc_start: 0.8952 (tpp) cc_final: 0.8643 (mmm) REVERT: D 93 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8067 (mp0) REVERT: E 60 LEU cc_start: 0.8922 (mt) cc_final: 0.8687 (mt) REVERT: H 86 ARG cc_start: 0.8563 (mmt-90) cc_final: 0.7509 (mtm180) REVERT: T 299 MET cc_start: 0.7071 (tmm) cc_final: 0.5932 (pmm) outliers start: 6 outliers final: 3 residues processed: 122 average time/residue: 0.1765 time to fit residues: 28.1813 Evaluate side-chains 122 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 118 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 93 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 1.9990 chunk 15 optimal weight: 20.0000 chunk 90 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 1 optimal weight: 20.0000 chunk 106 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 104 GLN H 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.122095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.072555 restraints weight = 22171.594| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.89 r_work: 0.2781 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 13924 Z= 0.255 Angle : 0.723 8.505 20162 Z= 0.400 Chirality : 0.047 0.338 2290 Planarity : 0.005 0.040 1448 Dihedral : 31.075 166.089 4473 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.88 % Allowed : 14.60 % Favored : 84.53 % 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: 2.54 (0.29), residues: 805 helix: 2.42 (0.21), residues: 560 sheet: None (None), residues: 0 loop : -0.03 (0.39), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 35 TYR 0.092 0.003 TYR B 88 PHE 0.011 0.002 PHE C 25 TRP 0.004 0.001 TRP T 282 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.26 (13920) covalent geometry : angle 0.72173 / 0.40 (20156) hydrogen bonds : bond 0.05247 / 5.89 ( 810) hydrogen bonds : angle 3.01258 / 3.68 ( 2013) metal coordination : bond 0.00453 / 0.37 ( 4) metal coordination : angle 2.25311 / 4.50 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2867.19 seconds wall clock time: 49 minutes 44.09 seconds (2984.09 seconds total)