Starting phenix.real_space_refine on Wed Aug 5 17:14:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9be6_44471/08_2026/9be6_44471.cif Found real_map, /net/cci-nas-00/data/ceres_data/9be6_44471/08_2026/9be6_44471.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9be6_44471/08_2026/9be6_44471.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9be6_44471/08_2026/9be6_44471.map" model { file = "/net/cci-nas-00/data/ceres_data/9be6_44471/08_2026/9be6_44471.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9be6_44471/08_2026/9be6_44471.cif" } resolution = 3.0 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= -0.000 sd= 0.177 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 253 5.49 5 S 12 5.16 5 C 6227 2.51 5 N 2094 2.21 5 O 2577 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 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: 11163 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} 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: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 2587 Classifications: {'DNA': 127} Link IDs: {'rna3p': 126} Chain: "J" Number of atoms: 2617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 2617 Classifications: {'DNA': 127} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 126} Time building chain proxies: 2.66, per 1000 atoms: 0.24 Number of scatterers: 11163 At special positions: 0 Unit cell: (77.469, 121.618, 117.453, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 253 15.00 O 2577 8.00 N 2094 7.00 C 6227 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: 1.05 Conformation dependent library (CDL) restraints added in 190.2 milliseconds 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1406 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 10 sheets defined 72.8% alpha, 3.2% beta 123 base pairs and 219 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.523A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.667A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.556A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.604A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.989A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.661A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 22 removed outlier: 3.699A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.502A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 121 Processing helix chain 'E' and resid 44 through 55 removed outlier: 3.595A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.635A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.955A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.796A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 removed outlier: 3.509A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.722A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.534A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.521A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 121 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.637A 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 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.351A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.027A 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: 7.327A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 395 hydrogen bonds defined for protein. 1167 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 314 hydrogen bonds 628 hydrogen bond angles 0 basepair planarities 123 basepair parallelities 219 stacking parallelities Total time for adding SS restraints: 2.19 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1994 1.33 - 1.45: 3834 1.45 - 1.57: 5520 1.57 - 1.69: 505 1.69 - 1.81: 22 Bond restraints: 11875 Sorted by residual: bond pdb=" C3' DC J 34 " pdb=" C2' DC J 34 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.40e+01 bond pdb=" C3' DA J -38 " pdb=" C2' DA J -38 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.33e+01 bond pdb=" C3' DC J -58 " pdb=" C2' DC J -58 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.24e+01 bond pdb=" C3' DC I 4 " pdb=" C2' DC I 4 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" C3' DG J 23 " pdb=" C2' DG J 23 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.71e+00 ... (remaining 11870 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 15453 1.27 - 2.53: 1485 2.53 - 3.80: 167 3.80 - 5.06: 16 5.06 - 6.33: 5 Bond angle restraints: 17126 Sorted by residual: angle pdb=" N VAL E 117 " pdb=" CA VAL E 117 " pdb=" C VAL E 117 " ideal model delta sigma weight residual 113.53 108.43 5.10 9.80e-01 1.04e+00 2.71e+01 angle pdb=" N3 DT J -50 " pdb=" C4 DT J -50 " pdb=" O4 DT J -50 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 angle pdb=" N3 DT I 38 " pdb=" C4 DT I 38 " pdb=" O4 DT I 38 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" N3 DT J -24 " pdb=" C4 DT J -24 " pdb=" O4 DT J -24 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" N3 DT J -57 " pdb=" C4 DT J -57 " pdb=" O4 DT J -57 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.87e+01 ... (remaining 17121 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.26: 5196 33.26 - 66.53: 1288 66.53 - 99.79: 22 99.79 - 133.06: 2 133.06 - 166.32: 1 Dihedral angle restraints: 6509 sinusoidal: 4330 harmonic: 2179 Sorted by residual: dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 53.68 166.32 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" CA PRO H 100 " pdb=" C PRO H 100 " pdb=" N GLY H 101 " pdb=" CA GLY H 101 " ideal model delta harmonic sigma weight residual -180.00 -160.84 -19.16 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" C4' DC I 4 " pdb=" C3' DC I 4 " pdb=" O3' DC I 4 " pdb=" P DC I 5 " ideal model delta sinusoidal sigma weight residual 220.00 104.68 115.32 1 3.50e+01 8.16e-04 1.12e+01 ... (remaining 6506 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1230 0.038 - 0.076: 539 0.076 - 0.114: 166 0.114 - 0.152: 16 0.152 - 0.190: 3 Chirality restraints: 1954 Sorted by residual: chirality pdb=" C3' DT J -17 " pdb=" C4' DT J -17 " pdb=" O3' DT J -17 " pdb=" C2' DT J -17 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 8.99e-01 chirality pdb=" CA GLU E 50 " pdb=" N GLU E 50 " pdb=" C GLU E 50 " pdb=" CB GLU E 50 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.03e-01 chirality pdb=" CG LEU A 61 " pdb=" CB LEU A 61 " pdb=" CD1 LEU A 61 " pdb=" CD2 LEU A 61 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.48e-01 ... (remaining 1951 not shown) Planarity restraints: 1289 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 26 " 0.022 2.00e-02 2.50e+03 9.27e-03 2.58e+00 pdb=" N9 DG I 26 " -0.021 2.00e-02 2.50e+03 pdb=" C8 DG I 26 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DG I 26 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DG I 26 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 26 " 0.004 2.00e-02 2.50e+03 pdb=" O6 DG I 26 " 0.006 2.00e-02 2.50e+03 pdb=" N1 DG I 26 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 26 " -0.000 2.00e-02 2.50e+03 pdb=" N2 DG I 26 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DG I 26 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DG I 26 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -35 " 0.022 2.00e-02 2.50e+03 9.40e-03 2.43e+00 pdb=" N9 DA I -35 " -0.020 2.00e-02 2.50e+03 pdb=" C8 DA I -35 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DA I -35 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DA I -35 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA I -35 " 0.003 2.00e-02 2.50e+03 pdb=" N6 DA I -35 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DA I -35 " 0.000 2.00e-02 2.50e+03 pdb=" C2 DA I -35 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DA I -35 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DA I -35 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " -0.026 5.00e-02 4.00e+02 3.88e-02 2.41e+00 pdb=" N PRO C 80 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " -0.022 5.00e-02 4.00e+02 ... (remaining 1286 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2266 2.81 - 3.33: 9267 3.33 - 3.85: 20158 3.85 - 4.38: 24761 4.38 - 4.90: 35512 Nonbonded interactions: 91964 Sorted by model distance: nonbonded pdb=" OG1 THR D 87 " pdb=" OE1 GLU D 90 " model vdw 2.285 3.040 nonbonded pdb=" OG1 THR F 73 " pdb=" OD2 ASP F 85 " model vdw 2.299 3.040 nonbonded pdb=" OH TYR D 39 " pdb=" OP2 DG I -52 " model vdw 2.326 3.040 nonbonded pdb=" OG1 THR D 29 " pdb=" OP1 DT I 30 " model vdw 2.326 3.040 nonbonded pdb=" O VAL E 46 " pdb=" OE1 GLU E 50 " model vdw 2.356 3.040 ... (remaining 91959 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' and resid 39 through 134) selection = (chain 'E' and resid 39 through 134) } ncs_group { reference = (chain 'B' and resid 25 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 118) } ncs_group { reference = (chain 'D' and resid 29 through 121) 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: 3.320 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 12.970 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 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 : 0.006 0.038 11875 Z= 0.536 Angle : 0.757 6.325 17126 Z= 0.664 Chirality : 0.045 0.190 1954 Planarity : 0.004 0.039 1289 Dihedral : 26.773 166.321 5103 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.16 % Allowed : 0.00 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.30), residues: 735 helix: 2.32 (0.22), residues: 529 sheet: None (None), residues: 0 loop : -1.21 (0.36), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 45 TYR 0.016 0.002 TYR C 50 PHE 0.015 0.002 PHE A 78 HIS 0.005 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00605 / 0.54 (11875) covalent geometry : angle 0.75708 / 0.66 (17126) hydrogen bonds : bond 0.12698 / 8.94 ( 709) hydrogen bonds : angle 4.24327 / 2.93 ( 1795) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 117 time to evaluate : 0.311 Fit side-chains REVERT: D 43 LYS cc_start: 0.8299 (mmtt) cc_final: 0.8099 (mmtp) REVERT: D 116 THR cc_start: 0.8461 (t) cc_final: 0.8236 (m) REVERT: F 44 LYS cc_start: 0.8298 (tttm) cc_final: 0.8097 (mtpp) REVERT: G 110 ASN cc_start: 0.8429 (p0) cc_final: 0.8107 (p0) outliers start: 1 outliers final: 0 residues processed: 118 average time/residue: 0.8914 time to fit residues: 110.8670 Evaluate side-chains 103 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.4980 chunk 74 optimal weight: 9.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 55 GLN G 38 ASN G 94 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.181383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.142386 restraints weight = 11301.125| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 0.81 r_work: 0.3373 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.0804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 11875 Z= 0.153 Angle : 0.634 7.880 17126 Z= 0.373 Chirality : 0.046 0.328 1954 Planarity : 0.004 0.034 1289 Dihedral : 29.940 167.542 3623 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.44 % Allowed : 8.32 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.48 (0.31), residues: 735 helix: 2.62 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -1.15 (0.37), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 96 TYR 0.009 0.001 TYR F 51 PHE 0.012 0.002 PHE A 78 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.15 (11875) covalent geometry : angle 0.63447 / 0.37 (17126) hydrogen bonds : bond 0.06378 / 4.23 ( 709) hydrogen bonds : angle 2.92459 / 2.07 ( 1795) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 0.404 Fit side-chains REVERT: A 105 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7683 (mt-10) REVERT: D 43 LYS cc_start: 0.7938 (mmtt) cc_final: 0.7666 (mmtp) REVERT: D 116 THR cc_start: 0.8034 (t) cc_final: 0.7822 (m) REVERT: G 110 ASN cc_start: 0.8640 (p0) cc_final: 0.8299 (p0) outliers start: 9 outliers final: 4 residues processed: 109 average time/residue: 0.8309 time to fit residues: 95.5471 Evaluate side-chains 112 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 108 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 28 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 52 optimal weight: 0.0270 chunk 6 optimal weight: 0.9980 chunk 80 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 27 GLN G 38 ASN G 94 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.179139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.144144 restraints weight = 11276.848| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 0.77 r_work: 0.3306 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11875 Z= 0.160 Angle : 0.611 7.631 17126 Z= 0.363 Chirality : 0.045 0.335 1954 Planarity : 0.004 0.033 1289 Dihedral : 30.026 166.434 3623 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.60 % Allowed : 11.04 % Favored : 87.36 % 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: 2.57 (0.31), residues: 735 helix: 2.68 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -1.12 (0.37), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 96 TYR 0.011 0.001 TYR G 50 PHE 0.014 0.002 PHE A 78 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.16 (11875) covalent geometry : angle 0.61149 / 0.36 (17126) hydrogen bonds : bond 0.06652 / 4.39 ( 709) hydrogen bonds : angle 2.82957 / 1.99 ( 1795) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.310 Fit side-chains REVERT: D 116 THR cc_start: 0.8311 (t) cc_final: 0.8086 (m) REVERT: G 110 ASN cc_start: 0.8724 (p0) cc_final: 0.8473 (p0) REVERT: H 32 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7108 (mt-10) outliers start: 10 outliers final: 6 residues processed: 110 average time/residue: 0.9023 time to fit residues: 104.3562 Evaluate side-chains 114 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 69 optimal weight: 0.4980 chunk 25 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 27 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN G 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.178174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.143428 restraints weight = 11230.872| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 0.73 r_work: 0.3175 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11875 Z= 0.173 Angle : 0.634 8.152 17126 Z= 0.368 Chirality : 0.046 0.332 1954 Planarity : 0.004 0.033 1289 Dihedral : 30.101 167.090 3623 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.76 % Allowed : 11.84 % Favored : 86.40 % 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: 2.45 (0.31), residues: 735 helix: 2.59 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.18 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 96 TYR 0.010 0.002 TYR F 51 PHE 0.016 0.002 PHE A 78 HIS 0.005 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.17 (11875) covalent geometry : angle 0.63448 / 0.37 (17126) hydrogen bonds : bond 0.06846 / 4.52 ( 709) hydrogen bonds : angle 2.83227 / 1.99 ( 1795) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.314 Fit side-chains REVERT: D 83 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.6454 (mtt180) REVERT: D 116 THR cc_start: 0.8424 (t) cc_final: 0.8202 (m) REVERT: H 32 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7968 (mt-10) outliers start: 11 outliers final: 6 residues processed: 106 average time/residue: 0.8500 time to fit residues: 94.8489 Evaluate side-chains 110 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 83 ARG Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 5 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 85 optimal weight: 20.0000 chunk 56 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.178798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.143219 restraints weight = 11145.261| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 0.76 r_work: 0.3173 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11875 Z= 0.153 Angle : 0.614 7.933 17126 Z= 0.359 Chirality : 0.045 0.326 1954 Planarity : 0.004 0.032 1289 Dihedral : 30.098 167.325 3623 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.60 % Allowed : 12.80 % Favored : 85.60 % 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: 2.55 (0.31), residues: 735 helix: 2.67 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.18 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 96 TYR 0.009 0.001 TYR F 51 PHE 0.010 0.002 PHE A 78 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.15 (11875) covalent geometry : angle 0.61355 / 0.36 (17126) hydrogen bonds : bond 0.06517 / 4.31 ( 709) hydrogen bonds : angle 2.83995 / 2.00 ( 1795) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.185 Fit side-chains REVERT: D 83 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.6461 (mtt180) REVERT: D 116 THR cc_start: 0.8382 (t) cc_final: 0.8153 (m) REVERT: H 32 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7615 (mt-10) outliers start: 10 outliers final: 6 residues processed: 105 average time/residue: 0.7344 time to fit residues: 81.1254 Evaluate side-chains 110 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 83 ARG Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 32 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 71 optimal weight: 50.0000 chunk 68 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 94 optimal weight: 20.0000 chunk 72 optimal weight: 20.0000 chunk 76 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.179108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.143375 restraints weight = 11278.414| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 0.76 r_work: 0.3314 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11875 Z= 0.145 Angle : 0.604 7.832 17126 Z= 0.355 Chirality : 0.045 0.326 1954 Planarity : 0.004 0.031 1289 Dihedral : 30.093 167.647 3623 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.76 % Allowed : 12.64 % Favored : 85.60 % 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: 2.61 (0.31), residues: 735 helix: 2.72 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.17 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 131 TYR 0.009 0.001 TYR F 51 PHE 0.009 0.001 PHE B 61 HIS 0.002 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.15 (11875) covalent geometry : angle 0.60449 / 0.36 (17126) hydrogen bonds : bond 0.06311 / 4.17 ( 709) hydrogen bonds : angle 2.83229 / 1.99 ( 1795) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.205 Fit side-chains REVERT: D 83 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.6408 (mtt180) REVERT: D 116 THR cc_start: 0.8312 (t) cc_final: 0.8078 (m) REVERT: H 32 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7969 (mt-10) outliers start: 11 outliers final: 7 residues processed: 105 average time/residue: 0.7632 time to fit residues: 84.3480 Evaluate side-chains 111 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 83 ARG Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 32 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 3 optimal weight: 1.9990 chunk 71 optimal weight: 50.0000 chunk 8 optimal weight: 0.8980 chunk 26 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 78 optimal weight: 9.9990 chunk 94 optimal weight: 20.0000 chunk 30 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 82 optimal weight: 30.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.178792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.142883 restraints weight = 11194.297| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 0.70 r_work: 0.3296 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11875 Z= 0.157 Angle : 0.605 7.857 17126 Z= 0.355 Chirality : 0.045 0.338 1954 Planarity : 0.004 0.036 1289 Dihedral : 30.055 168.306 3623 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.08 % Allowed : 12.96 % 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: 2.57 (0.31), residues: 735 helix: 2.68 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.13 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 96 TYR 0.010 0.001 TYR F 51 PHE 0.014 0.002 PHE A 78 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.16 (11875) covalent geometry : angle 0.60522 / 0.36 (17126) hydrogen bonds : bond 0.06405 / 4.22 ( 709) hydrogen bonds : angle 2.76527 / 1.93 ( 1795) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.323 Fit side-chains REVERT: D 83 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.6501 (mtt180) REVERT: D 116 THR cc_start: 0.8380 (t) cc_final: 0.8145 (m) REVERT: F 40 ARG cc_start: 0.8891 (ttm170) cc_final: 0.8636 (ttm170) REVERT: H 32 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7692 (mt-10) outliers start: 13 outliers final: 7 residues processed: 110 average time/residue: 0.8627 time to fit residues: 99.9754 Evaluate side-chains 113 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 83 ARG Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 32 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 52 optimal weight: 0.4980 chunk 18 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 chunk 65 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 76 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3966 r_free = 0.3966 target = 0.179185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.144183 restraints weight = 11212.390| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 0.75 r_work: 0.3170 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11875 Z= 0.146 Angle : 0.597 7.811 17126 Z= 0.352 Chirality : 0.044 0.334 1954 Planarity : 0.004 0.031 1289 Dihedral : 30.053 168.598 3623 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.76 % Allowed : 12.96 % Favored : 85.28 % 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: 2.64 (0.31), residues: 735 helix: 2.73 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.11 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 96 TYR 0.010 0.001 TYR D 118 PHE 0.010 0.002 PHE A 78 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.15 (11875) covalent geometry : angle 0.59706 / 0.35 (17126) hydrogen bonds : bond 0.06225 / 4.11 ( 709) hydrogen bonds : angle 2.79516 / 1.95 ( 1795) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.364 Fit side-chains REVERT: D 83 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.6518 (mtt180) REVERT: D 116 THR cc_start: 0.8382 (t) cc_final: 0.8138 (m) REVERT: F 40 ARG cc_start: 0.8885 (ttm170) cc_final: 0.8636 (ttm170) REVERT: H 32 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7672 (mt-10) outliers start: 11 outliers final: 9 residues processed: 107 average time/residue: 0.9206 time to fit residues: 103.7331 Evaluate side-chains 114 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 83 ARG Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 36 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 34 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 24 optimal weight: 0.5980 chunk 77 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3964 r_free = 0.3964 target = 0.179022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.144189 restraints weight = 11144.124| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 0.72 r_work: 0.3322 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11875 Z= 0.152 Angle : 0.601 7.933 17126 Z= 0.353 Chirality : 0.044 0.336 1954 Planarity : 0.004 0.032 1289 Dihedral : 30.053 169.104 3623 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.40 % Allowed : 12.48 % Favored : 85.12 % 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: 2.64 (0.31), residues: 735 helix: 2.73 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.09 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 96 TYR 0.013 0.001 TYR D 118 PHE 0.011 0.002 PHE A 78 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.15 (11875) covalent geometry : angle 0.60101 / 0.35 (17126) hydrogen bonds : bond 0.06261 / 4.14 ( 709) hydrogen bonds : angle 2.76601 / 1.93 ( 1795) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.295 Fit side-chains REVERT: A 105 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7594 (mt-10) REVERT: D 83 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.6462 (mtt180) REVERT: D 116 THR cc_start: 0.8309 (t) cc_final: 0.8073 (m) REVERT: F 40 ARG cc_start: 0.8880 (ttm170) cc_final: 0.8643 (ttm170) REVERT: H 32 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7704 (mt-10) outliers start: 15 outliers final: 10 residues processed: 109 average time/residue: 0.9126 time to fit residues: 104.7683 Evaluate side-chains 116 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 83 ARG Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 39 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 74 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 89 optimal weight: 9.9990 chunk 94 optimal weight: 20.0000 chunk 42 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3964 r_free = 0.3964 target = 0.179089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.144162 restraints weight = 11193.473| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 0.72 r_work: 0.3207 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11875 Z= 0.151 Angle : 0.597 7.892 17126 Z= 0.351 Chirality : 0.044 0.337 1954 Planarity : 0.004 0.032 1289 Dihedral : 30.049 169.034 3623 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.92 % Allowed : 13.12 % 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: 2.65 (0.31), residues: 735 helix: 2.73 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.08 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 96 TYR 0.013 0.001 TYR D 118 PHE 0.010 0.002 PHE A 78 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.15 (11875) covalent geometry : angle 0.59729 / 0.35 (17126) hydrogen bonds : bond 0.06204 / 4.10 ( 709) hydrogen bonds : angle 2.79290 / 1.95 ( 1795) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.309 Fit side-chains REVERT: A 105 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7571 (mt-10) REVERT: D 83 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.6535 (mtt180) REVERT: D 116 THR cc_start: 0.8402 (t) cc_final: 0.8166 (m) REVERT: H 32 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7661 (mt-10) outliers start: 12 outliers final: 10 residues processed: 107 average time/residue: 0.9190 time to fit residues: 103.6454 Evaluate side-chains 116 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 83 ARG Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 91 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 94 optimal weight: 20.0000 chunk 77 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 75 optimal weight: 9.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3965 r_free = 0.3965 target = 0.179160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.143117 restraints weight = 11281.103| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 0.70 r_work: 0.3300 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11875 Z= 0.146 Angle : 0.596 7.878 17126 Z= 0.350 Chirality : 0.044 0.336 1954 Planarity : 0.004 0.032 1289 Dihedral : 30.049 169.059 3623 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.92 % Allowed : 13.28 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.66 (0.31), residues: 735 helix: 2.74 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.08 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 96 TYR 0.012 0.001 TYR D 118 PHE 0.009 0.001 PHE B 61 HIS 0.002 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.15 (11875) covalent geometry : angle 0.59560 / 0.35 (17126) hydrogen bonds : bond 0.06168 / 4.08 ( 709) hydrogen bonds : angle 2.79117 / 1.95 ( 1795) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3286.27 seconds wall clock time: 56 minutes 34.78 seconds (3394.78 seconds total)