Starting phenix.real_space_refine on Fri Jul 3 07:16:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vg0_43196/07_2026/8vg0_43196.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vg0_43196/07_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_43196/07_2026/8vg0_43196.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vg0_43196/07_2026/8vg0_43196.map" model { file = "/net/cci-nas-00/data/ceres_data/8vg0_43196/07_2026/8vg0_43196.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vg0_43196/07_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-dev-6108/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: 2.74, per 1000 atoms: 0.21 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: 0.96 Conformation dependent library (CDL) restraints added in 473.0 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: 1.46 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: 2.42 Time building geometry restraints manager: 1.40 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: 19204 2.15 - 4.30: 924 4.30 - 6.45: 26 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: 2.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 14.150 Find NCS groups from input model: 0.090 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:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.230 ------------------------------------------------------------------------------- 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 : 0.857 10.746 20162 Z= 0.740 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 0.85629 / 0.74 (20156) hydrogen bonds : bond 0.10245 / 11.17 ( 810) hydrogen bonds : angle 3.48845 / 4.13 ( 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 : 0.220 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: 0.1591 time to fit residues: 29.2131 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 : 0.204 ------------------------------------------------------------------------------- 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 = 0.121805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.071815 restraints weight = 22228.317| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.30 r_work: 0.2738 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.0820 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= 0.187 Angle : 0.659 7.792 20162 Z= 0.397 Chirality : 0.046 0.364 2290 Planarity : 0.004 0.037 1448 Dihedral : 30.266 174.667 4473 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.75 % Allowed : 9.20 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.75 (0.29), residues: 805 helix: 2.58 (0.21), residues: 560 sheet: None (None), residues: 0 loop : 0.01 (0.36), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 11 TYR 0.044 0.002 TYR D 83 PHE 0.009 0.001 PHE A 67 TRP 0.001 0.000 TRP T 282 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.19 (13920) covalent geometry : angle 0.65794 / 0.40 (20156) hydrogen bonds : bond 0.05271 / 5.95 ( 810) hydrogen bonds : angle 3.05944 / 3.64 ( 2013) metal coordination : bond 0.00322 / 0.26 ( 4) metal coordination : angle 2.50986 / 5.61 ( 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 135 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8564 (tp40) cc_final: 0.8363 (tp40) REVERT: H 86 ARG cc_start: 0.8394 (mmt-90) cc_final: 0.7154 (mtm180) REVERT: T 299 MET cc_start: 0.6447 (tmm) cc_final: 0.5646 (pmm) outliers start: 12 outliers final: 7 residues processed: 131 average time/residue: 0.1397 time to fit residues: 23.9157 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 : 0.232 ------------------------------------------------------------------------------- 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: 0.7980 chunk 58 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 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: 9.9990 chunk 96 optimal weight: 0.4980 chunk 68 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3851 r_free = 0.3851 target = 0.125741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.076251 restraints weight = 22365.278| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.92 r_work: 0.2857 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1092 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= 0.149 Angle : 0.609 7.310 20162 Z= 0.371 Chirality : 0.044 0.343 2290 Planarity : 0.004 0.034 1448 Dihedral : 30.516 171.371 4473 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.17 % Allowed : 11.09 % Favored : 87.74 % 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: 3.01 (0.29), residues: 805 helix: 2.77 (0.21), residues: 560 sheet: None (None), residues: 0 loop : 0.15 (0.37), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG T 311 TYR 0.021 0.002 TYR D 83 PHE 0.010 0.001 PHE A 67 TRP 0.001 0.000 TRP T 282 HIS 0.002 0.000 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.15 (13920) covalent geometry : angle 0.60808 / 0.37 (20156) hydrogen bonds : bond 0.04672 / 5.33 ( 810) hydrogen bonds : angle 2.81069 / 3.38 ( 2013) metal coordination : bond 0.00418 / 0.30 ( 4) metal coordination : angle 2.36569 / 4.99 ( 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 129 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 121 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8813 (tp40) cc_final: 0.8606 (tp40) REVERT: C 74 LYS cc_start: 0.9019 (mtpp) cc_final: 0.8734 (mtpp) REVERT: D 35 GLU cc_start: 0.8488 (pt0) cc_final: 0.8216 (pt0) REVERT: H 86 ARG cc_start: 0.8657 (mmt-90) cc_final: 0.7539 (mtm180) REVERT: T 299 MET cc_start: 0.6535 (tmm) cc_final: 0.5807 (pmm) outliers start: 8 outliers final: 4 residues processed: 126 average time/residue: 0.1320 time to fit residues: 21.6711 Evaluate side-chains 120 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 116 time to evaluate : 0.280 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 71 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 3 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3845 r_free = 0.3845 target = 0.125379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.075690 restraints weight = 22063.656| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.96 r_work: 0.2841 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13924 Z= 0.150 Angle : 0.611 7.057 20162 Z= 0.368 Chirality : 0.043 0.347 2290 Planarity : 0.004 0.034 1448 Dihedral : 30.577 170.392 4473 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.17 % Allowed : 12.12 % Favored : 86.72 % 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: 3.04 (0.29), residues: 805 helix: 2.80 (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 0.050 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 0.00271 / 0.15 (13920) covalent geometry : angle 0.61018 / 0.37 (20156) hydrogen bonds : bond 0.04545 / 5.19 ( 810) hydrogen bonds : angle 2.79020 / 3.36 ( 2013) metal coordination : bond 0.00375 / 0.27 ( 4) metal coordination : angle 2.21813 / 4.77 ( 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 123 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8542 (pm20) cc_final: 0.8333 (pm20) REVERT: C 74 LYS cc_start: 0.8986 (mtpp) cc_final: 0.8695 (mtpp) REVERT: D 35 GLU cc_start: 0.8521 (pt0) cc_final: 0.8235 (pt0) REVERT: D 93 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.7850 (mp0) REVERT: F 95 ARG cc_start: 0.8394 (mtp85) cc_final: 0.8034 (mtt90) REVERT: H 86 ARG cc_start: 0.8580 (mmt-90) cc_final: 0.7444 (mtm180) outliers start: 8 outliers final: 6 residues processed: 122 average time/residue: 0.1349 time to fit residues: 21.7103 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 : 0.212 ------------------------------------------------------------------------------- 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 D residue 122 THR 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: 0.0870 chunk 42 optimal weight: 0.9990 chunk 103 optimal weight: 30.0000 chunk 94 optimal weight: 0.0470 chunk 48 optimal weight: 0.2980 chunk 12 optimal weight: 9.9990 chunk 60 optimal weight: 0.5980 chunk 75 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN F 93 GLN H 47 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.126466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.077050 restraints weight = 22340.274| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.92 r_work: 0.2870 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1309 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 : 0.594 9.158 20162 Z= 0.361 Chirality : 0.043 0.349 2290 Planarity : 0.003 0.033 1448 Dihedral : 30.573 169.773 4473 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.17 % Allowed : 12.41 % Favored : 86.42 % 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: 3.17 (0.29), residues: 805 helix: 2.88 (0.21), residues: 560 sheet: None (None), residues: 0 loop : 0.22 (0.38), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 129 TYR 0.036 0.002 TYR D 83 PHE 0.010 0.001 PHE A 67 TRP 0.000 0.000 TRP T 282 HIS 0.005 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.13 (13920) covalent geometry : angle 0.59337 / 0.36 (20156) hydrogen bonds : bond 0.04313 / 4.94 ( 810) hydrogen bonds : angle 2.68107 / 3.24 ( 2013) metal coordination : bond 0.00317 / 0.23 ( 4) metal coordination : angle 2.03333 / 4.42 ( 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 131 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 123 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8549 (pm20) cc_final: 0.8267 (pm20) REVERT: C 74 LYS cc_start: 0.8994 (mtpp) cc_final: 0.8702 (mtpp) REVERT: D 35 GLU cc_start: 0.8467 (pt0) cc_final: 0.8175 (pt0) REVERT: D 93 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8019 (mp0) REVERT: G 13 LYS cc_start: 0.8363 (tptt) cc_final: 0.8087 (tptp) REVERT: H 86 ARG cc_start: 0.8610 (mmt-90) cc_final: 0.7510 (mtm180) REVERT: T 299 MET cc_start: 0.7151 (tmm) cc_final: 0.6164 (pmm) outliers start: 8 outliers final: 3 residues processed: 128 average time/residue: 0.1691 time to fit residues: 28.0732 Evaluate side-chains 121 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 117 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 64 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 5 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 15 optimal weight: 9.9990 chunk 81 optimal weight: 0.8980 chunk 55 optimal weight: 0.0980 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 = 0.3844 r_free = 0.3844 target = 0.125148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.075570 restraints weight = 22123.474| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.90 r_work: 0.2842 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13924 Z= 0.168 Angle : 0.618 7.881 20162 Z= 0.365 Chirality : 0.043 0.339 2290 Planarity : 0.004 0.033 1448 Dihedral : 30.771 168.137 4473 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.02 % Allowed : 13.14 % 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: 3.07 (0.29), residues: 805 helix: 2.82 (0.21), residues: 560 sheet: None (None), residues: 0 loop : 0.16 (0.38), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 92 TYR 0.027 0.002 TYR D 83 PHE 0.009 0.001 PHE A 67 TRP 0.001 0.000 TRP T 282 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.17 (13920) covalent geometry : angle 0.61739 / 0.37 (20156) hydrogen bonds : bond 0.04531 / 5.14 ( 810) hydrogen bonds : angle 2.74385 / 3.33 ( 2013) metal coordination : bond 0.00338 / 0.27 ( 4) metal coordination : angle 2.18129 / 4.76 ( 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 124 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 117 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8604 (pm20) cc_final: 0.8373 (pm20) REVERT: D 35 GLU cc_start: 0.8470 (pt0) cc_final: 0.8174 (pt0) REVERT: D 93 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8019 (mp0) REVERT: H 86 ARG cc_start: 0.8663 (mmt-90) cc_final: 0.7544 (mtm180) outliers start: 7 outliers final: 6 residues processed: 123 average time/residue: 0.1465 time to fit residues: 23.4334 Evaluate side-chains 123 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 116 time to evaluate : 0.249 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 4 optimal weight: 9.9990 chunk 74 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 70 optimal weight: 0.2980 chunk 84 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3854 r_free = 0.3854 target = 0.125784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.076283 restraints weight = 22247.372| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.91 r_work: 0.2863 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13924 Z= 0.141 Angle : 0.600 7.379 20162 Z= 0.358 Chirality : 0.043 0.340 2290 Planarity : 0.003 0.033 1448 Dihedral : 30.773 167.156 4473 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.17 % Allowed : 13.28 % Favored : 85.55 % 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: 2.85 (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 0.001 0.000 ARG B 92 TYR 0.037 0.002 TYR B 88 PHE 0.009 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 0.00250 / 0.14 (13920) covalent geometry : angle 0.59956 / 0.36 (20156) hydrogen bonds : bond 0.04333 / 4.96 ( 810) hydrogen bonds : angle 2.68688 / 3.26 ( 2013) metal coordination : bond 0.00305 / 0.24 ( 4) metal coordination : angle 1.99898 / 4.34 ( 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 129 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 121 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8625 (pm20) cc_final: 0.8384 (pm20) REVERT: D 35 GLU cc_start: 0.8456 (pt0) cc_final: 0.8154 (pt0) REVERT: D 93 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8024 (mp0) REVERT: H 86 ARG cc_start: 0.8630 (mmt-90) cc_final: 0.7527 (mtm180) outliers start: 8 outliers final: 5 residues processed: 126 average time/residue: 0.1501 time to fit residues: 24.6098 Evaluate side-chains 126 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 120 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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 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: 9.9990 chunk 105 optimal weight: 40.0000 chunk 40 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 chunk 36 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.125662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.076289 restraints weight = 22049.148| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.87 r_work: 0.2868 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13924 Z= 0.146 Angle : 0.605 7.418 20162 Z= 0.360 Chirality : 0.042 0.337 2290 Planarity : 0.004 0.033 1448 Dihedral : 30.780 166.279 4473 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.46 % Allowed : 12.99 % Favored : 85.55 % 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: 3.10 (0.29), residues: 805 helix: 2.84 (0.21), residues: 560 sheet: None (None), residues: 0 loop : 0.18 (0.38), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 92 TYR 0.036 0.002 TYR B 88 PHE 0.009 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 0.00265 / 0.15 (13920) covalent geometry : angle 0.60378 / 0.36 (20156) hydrogen bonds : bond 0.04316 / 4.92 ( 810) hydrogen bonds : angle 2.68126 / 3.25 ( 2013) metal coordination : bond 0.00292 / 0.23 ( 4) metal coordination : angle 1.89053 / 4.08 ( 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 132 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8655 (pm20) cc_final: 0.8416 (pm20) REVERT: D 35 GLU cc_start: 0.8435 (pt0) cc_final: 0.8134 (pt0) REVERT: D 93 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8044 (mp0) REVERT: H 86 ARG cc_start: 0.8673 (mmt-90) cc_final: 0.7587 (mtm180) outliers start: 10 outliers final: 7 residues processed: 129 average time/residue: 0.1691 time to fit residues: 28.4133 Evaluate side-chains 130 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 77 optimal weight: 0.6980 chunk 5 optimal weight: 10.0000 chunk 65 optimal weight: 0.6980 chunk 59 optimal weight: 0.0980 chunk 76 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 50 optimal weight: 0.0270 chunk 0 optimal weight: 50.0000 chunk 11 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 overall best weight: 0.4238 ------------------------------------------------------------------------------- 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 = 0.3871 r_free = 0.3871 target = 0.126890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.077871 restraints weight = 22418.514| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.86 r_work: 0.2895 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 13924 Z= 0.129 Angle : 0.587 7.610 20162 Z= 0.355 Chirality : 0.042 0.339 2290 Planarity : 0.003 0.033 1448 Dihedral : 30.695 167.447 4473 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.17 % Allowed : 13.43 % Favored : 85.40 % 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: 3.18 (0.29), residues: 805 helix: 2.88 (0.21), residues: 560 sheet: None (None), residues: 0 loop : 0.26 (0.39), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 79 TYR 0.049 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 D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.13 (13920) covalent geometry : angle 0.58680 / 0.35 (20156) hydrogen bonds : bond 0.04137 / 4.74 ( 810) hydrogen bonds : angle 2.63292 / 3.21 ( 2013) metal coordination : bond 0.00241 / 0.19 ( 4) metal coordination : angle 1.66713 / 3.64 ( 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 131 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 123 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: D 35 GLU cc_start: 0.8433 (pt0) cc_final: 0.8135 (pt0) REVERT: D 93 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8030 (mp0) REVERT: H 86 ARG cc_start: 0.8585 (mmt-90) cc_final: 0.7493 (mtm180) REVERT: T 299 MET cc_start: 0.7031 (tmm) cc_final: 0.5914 (pmm) outliers start: 8 outliers final: 5 residues processed: 130 average time/residue: 0.1683 time to fit residues: 28.2996 Evaluate side-chains 123 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 117 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain B residue 30 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 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: 0.9980 chunk 41 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 84 optimal weight: 0.0040 chunk 50 optimal weight: 0.9980 chunk 12 optimal weight: 9.9990 chunk 32 optimal weight: 0.7980 chunk 8 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 overall best weight: 0.9594 ------------------------------------------------------------------------------- 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 = 0.3864 r_free = 0.3864 target = 0.126351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.076774 restraints weight = 22439.645| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.92 r_work: 0.2875 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13924 Z= 0.153 Angle : 0.602 8.647 20162 Z= 0.359 Chirality : 0.042 0.334 2290 Planarity : 0.004 0.034 1448 Dihedral : 30.738 167.886 4473 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.88 % Allowed : 14.01 % Favored : 85.11 % 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: 3.06 (0.29), residues: 805 helix: 2.81 (0.21), residues: 560 sheet: None (None), residues: 0 loop : 0.17 (0.39), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 79 TYR 0.067 0.002 TYR B 88 PHE 0.009 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 0.00287 / 0.15 (13920) covalent geometry : angle 0.60160 / 0.36 (20156) hydrogen bonds : bond 0.04243 / 4.84 ( 810) hydrogen bonds : angle 2.67531 / 3.27 ( 2013) metal coordination : bond 0.00279 / 0.22 ( 4) metal coordination : angle 1.76743 / 3.83 ( 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 : 0.325 Fit side-chains revert: symmetry clash REVERT: D 35 GLU cc_start: 0.8462 (pt0) cc_final: 0.8162 (pt0) REVERT: D 93 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8090 (mp0) REVERT: E 60 LEU cc_start: 0.8925 (mt) cc_final: 0.8685 (mt) REVERT: H 86 ARG cc_start: 0.8629 (mmt-90) cc_final: 0.7524 (mtm180) REVERT: T 299 MET cc_start: 0.7031 (tmm) cc_final: 0.5920 (pmm) outliers start: 6 outliers final: 5 residues processed: 125 average time/residue: 0.1508 time to fit residues: 24.6086 Evaluate side-chains 124 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 118 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain B residue 30 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 H residue 47 GLN 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: 9.9990 chunk 90 optimal weight: 0.5980 chunk 18 optimal weight: 9.9990 chunk 1 optimal weight: 20.0000 chunk 106 optimal weight: 4.9990 chunk 107 optimal weight: 20.0000 chunk 49 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 24 optimal weight: 9.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 = 0.3847 r_free = 0.3847 target = 0.125119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.075852 restraints weight = 22229.795| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 1.86 r_work: 0.2858 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13924 Z= 0.186 Angle : 0.628 8.473 20162 Z= 0.368 Chirality : 0.043 0.325 2290 Planarity : 0.004 0.034 1448 Dihedral : 30.843 168.245 4473 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.46 % Allowed : 13.28 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.94 (0.29), residues: 805 helix: 2.73 (0.21), residues: 560 sheet: None (None), residues: 0 loop : 0.08 (0.39), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 35 TYR 0.079 0.002 TYR B 88 PHE 0.008 0.001 PHE A 67 TRP 0.001 0.000 TRP T 282 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.19 (13920) covalent geometry : angle 0.62749 / 0.37 (20156) hydrogen bonds : bond 0.04428 / 5.03 ( 810) hydrogen bonds : angle 2.75811 / 3.36 ( 2013) metal coordination : bond 0.00326 / 0.26 ( 4) metal coordination : angle 1.89621 / 4.01 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2799.30 seconds wall clock time: 48 minutes 29.98 seconds (2909.98 seconds total)