Starting phenix.real_space_refine on Thu Aug 6 00:36:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8pc5_17594/08_2026/8pc5_17594.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pc5_17594/08_2026/8pc5_17594.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pc5_17594/08_2026/8pc5_17594.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pc5_17594/08_2026/8pc5_17594.map" model { file = "/net/cci-nas-00/data/ceres_data/8pc5_17594/08_2026/8pc5_17594.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pc5_17594/08_2026/8pc5_17594.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8pc5_17594/08_2026/8pc5_17594.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8pc5_17594/08_2026/8pc5_17594.cif" } resolution = 3.02 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= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 294 5.49 5 S 13 5.16 5 C 7172 2.51 5 N 2399 2.21 5 O 2958 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 12836 Number of models: 1 Model: "" Number of chains: 11 Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "A" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 829 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ML3:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 694 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "G" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "K" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 710 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 11, 'TRANS': 74} Chain breaks: 1 Chain: "J" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Time building chain proxies: 2.06, per 1000 atoms: 0.16 Number of scatterers: 12836 At special positions: 0 Unit cell: (102.533, 125.04, 123.373, 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 13 16.00 P 294 15.00 O 2958 8.00 N 2399 7.00 C 7172 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: 0.70 Conformation dependent library (CDL) restraints added in 283.3 milliseconds 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1598 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 11 sheets defined 64.4% alpha, 5.0% beta 146 base pairs and 271 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.595A pdb=" N ALA A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.605A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.817A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.702A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.528A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.599A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) 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 Processing helix chain 'D' and resid 101 through 121 removed outlier: 3.523A pdb=" N HIS D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.783A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.548A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.520A 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 37 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.399A 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 92 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 removed outlier: 4.113A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.607A 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 removed outlier: 6.578A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.345A 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: 7.577A 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: 7.363A 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 Processing sheet with id=AB2, first strand: chain 'K' and resid 49 through 53 removed outlier: 3.850A pdb=" N GLU K 49 " --> pdb=" O PHE K 44 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA K 51 " --> pdb=" O ILE K 42 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE K 42 " --> pdb=" O ALA K 51 " (cutoff:3.500A) 407 hydrogen bonds defined for protein. 1203 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 374 hydrogen bonds 748 hydrogen bond angles 0 basepair planarities 146 basepair parallelities 271 stacking parallelities Total time for adding SS restraints: 1.73 Time building geometry restraints manager: 1.05 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: 2069 1.33 - 1.45: 4662 1.45 - 1.57: 6333 1.57 - 1.69: 586 1.69 - 1.81: 26 Bond restraints: 13676 Sorted by residual: bond pdb=" C3' DC J -71 " pdb=" C2' DC J -71 " ideal model delta sigma weight residual 1.516 1.552 -0.036 8.00e-03 1.56e+04 1.99e+01 bond pdb=" C1' DT J -59 " pdb=" N1 DT J -59 " ideal model delta sigma weight residual 1.468 1.518 -0.050 1.40e-02 5.10e+03 1.29e+01 bond pdb=" C5' DC I 56 " pdb=" C4' DC I 56 " ideal model delta sigma weight residual 1.512 1.537 -0.025 7.00e-03 2.04e+04 1.27e+01 bond pdb=" C3' DG I -53 " pdb=" C2' DG I -53 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.25e+01 bond pdb=" C3' DT J -59 " pdb=" C2' DT J -59 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.21e+01 ... (remaining 13671 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 18021 1.67 - 3.33: 1551 3.33 - 5.00: 126 5.00 - 6.66: 21 6.66 - 8.33: 11 Bond angle restraints: 19730 Sorted by residual: angle pdb=" O5' DG J 23 " pdb=" C5' DG J 23 " pdb=" C4' DG J 23 " ideal model delta sigma weight residual 109.40 114.17 -4.77 8.00e-01 1.56e+00 3.56e+01 angle pdb=" O5' DA J -62 " pdb=" C5' DA J -62 " pdb=" C4' DA J -62 " ideal model delta sigma weight residual 109.40 114.03 -4.63 8.00e-01 1.56e+00 3.34e+01 angle pdb=" O5' DA I 72 " pdb=" C5' DA I 72 " pdb=" C4' DA I 72 " ideal model delta sigma weight residual 109.40 113.94 -4.54 8.00e-01 1.56e+00 3.22e+01 angle pdb=" O5' DA I 67 " pdb=" C5' DA I 67 " pdb=" C4' DA I 67 " ideal model delta sigma weight residual 109.40 113.51 -4.11 8.00e-01 1.56e+00 2.64e+01 angle pdb=" O4' DA I -45 " pdb=" C4' DA I -45 " pdb=" C3' DA I -45 " ideal model delta sigma weight residual 106.00 103.10 2.90 6.00e-01 2.78e+00 2.33e+01 ... (remaining 19725 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 5857 35.94 - 71.87: 1586 71.87 - 107.81: 28 107.81 - 143.75: 3 143.75 - 179.69: 3 Dihedral angle restraints: 7477 sinusoidal: 5003 harmonic: 2474 Sorted by residual: dihedral pdb=" C4' DT J 69 " pdb=" C3' DT J 69 " pdb=" O3' DT J 69 " pdb=" P DC J 70 " ideal model delta sinusoidal sigma weight residual -140.00 39.69 -179.69 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC J 68 " pdb=" C3' DC J 68 " pdb=" O3' DC J 68 " pdb=" P DT J 69 " ideal model delta sinusoidal sigma weight residual -140.00 25.29 -165.29 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' DA J -73 " pdb=" C3' DA J -73 " pdb=" O3' DA J -73 " pdb=" P DT J -72 " ideal model delta sinusoidal sigma weight residual -140.00 18.69 -158.69 1 3.50e+01 8.16e-04 1.51e+01 ... (remaining 7474 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 2169 0.115 - 0.230: 49 0.230 - 0.346: 1 0.346 - 0.461: 1 0.461 - 0.576: 9 Chirality restraints: 2229 Sorted by residual: chirality pdb=" P DA J 65 " pdb=" OP1 DA J 65 " pdb=" OP2 DA J 65 " pdb=" O5' DA J 65 " both_signs ideal model delta sigma weight residual True 2.34 -2.91 -0.58 2.00e-01 2.50e+01 8.30e+00 chirality pdb=" P DT J 69 " pdb=" OP1 DT J 69 " pdb=" OP2 DT J 69 " pdb=" O5' DT J 69 " both_signs ideal model delta sigma weight residual True 2.34 -2.90 -0.57 2.00e-01 2.50e+01 8.06e+00 chirality pdb=" P DG J 64 " pdb=" OP1 DG J 64 " pdb=" OP2 DG J 64 " pdb=" O5' DG J 64 " both_signs ideal model delta sigma weight residual True 2.34 -2.90 -0.56 2.00e-01 2.50e+01 7.84e+00 ... (remaining 2226 not shown) Planarity restraints: 1479 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ML3 A 36 " 0.014 2.00e-02 2.50e+03 2.86e-02 8.17e+00 pdb=" C ML3 A 36 " -0.049 2.00e-02 2.50e+03 pdb=" O ML3 A 36 " 0.019 2.00e-02 2.50e+03 pdb=" N LYS A 37 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 49 " -0.029 2.00e-02 2.50e+03 1.85e-02 7.74e+00 pdb=" N1 DC I 49 " 0.043 2.00e-02 2.50e+03 pdb=" C2 DC I 49 " -0.017 2.00e-02 2.50e+03 pdb=" O2 DC I 49 " 0.009 2.00e-02 2.50e+03 pdb=" N3 DC I 49 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DC I 49 " -0.002 2.00e-02 2.50e+03 pdb=" N4 DC I 49 " -0.007 2.00e-02 2.50e+03 pdb=" C5 DC I 49 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DC I 49 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 47 " -0.032 2.00e-02 2.50e+03 1.56e-02 7.29e+00 pdb=" N9 DG I 47 " 0.042 2.00e-02 2.50e+03 pdb=" C8 DG I 47 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DG I 47 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DG I 47 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 47 " -0.005 2.00e-02 2.50e+03 pdb=" O6 DG I 47 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DG I 47 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DG I 47 " 0.000 2.00e-02 2.50e+03 pdb=" N2 DG I 47 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DG I 47 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DG I 47 " 0.003 2.00e-02 2.50e+03 ... (remaining 1476 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1385 2.74 - 3.28: 10741 3.28 - 3.82: 25026 3.82 - 4.36: 30240 4.36 - 4.90: 43301 Nonbonded interactions: 110693 Sorted by model distance: nonbonded pdb=" O HIS B 75 " pdb=" NH2 ARG D 89 " model vdw 2.205 3.120 nonbonded pdb=" OG1 THR B 73 " pdb=" OD2 ASP B 85 " model vdw 2.218 3.040 nonbonded pdb=" NH2 ARG B 35 " pdb=" OH TYR B 51 " model vdw 2.259 3.120 nonbonded pdb=" NE2 GLN C 104 " pdb=" OE2 GLU E 94 " model vdw 2.263 3.120 nonbonded pdb=" O PRO K 60 " pdb=" ND2 ASN K 64 " model vdw 2.277 3.120 ... (remaining 110688 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 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 20 through 101) } ncs_group { reference = chain 'C' selection = chain 'G' } 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=0.00 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: 5.570 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: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 10.370 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 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 0.057 13676 Z= 0.602 Angle : 0.918 8.330 19730 Z= 0.766 Chirality : 0.061 0.576 2229 Planarity : 0.006 0.048 1479 Dihedral : 29.262 179.686 5879 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.42 % Allowed : 11.08 % Favored : 88.50 % 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: 1.05 (0.29), residues: 831 helix: 1.76 (0.22), residues: 541 sheet: -3.81 (0.82), residues: 12 loop : -1.27 (0.32), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 52 TYR 0.010 0.002 TYR H 34 PHE 0.014 0.002 PHE A 78 TRP 0.004 0.001 TRP K 21 HIS 0.006 0.002 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00708 / 0.60 (13676) covalent geometry : angle 0.91845 / 0.77 (19730) hydrogen bonds : bond 0.12744 / 14.19 ( 781) hydrogen bonds : angle 4.25811 / 5.30 ( 1951) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 151 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: H 84 SER cc_start: 0.8922 (m) cc_final: 0.8717 (t) outliers start: 3 outliers final: 2 residues processed: 153 average time/residue: 0.1307 time to fit residues: 26.1788 Evaluate side-chains 103 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 101 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain K residue 58 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 20.0000 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 0.0050 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 106 optimal weight: 20.0000 overall best weight: 1.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 46 HIS E 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.083435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.054994 restraints weight = 37606.879| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 1.72 r_work: 0.2777 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9119 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13676 Z= 0.198 Angle : 0.735 10.965 19730 Z= 0.410 Chirality : 0.051 0.360 2229 Planarity : 0.005 0.041 1479 Dihedral : 31.955 163.729 4168 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.54 % Allowed : 12.76 % Favored : 85.69 % 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: 1.33 (0.29), residues: 831 helix: 1.93 (0.22), residues: 559 sheet: -3.62 (0.69), residues: 17 loop : -1.20 (0.34), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 96 TYR 0.013 0.001 TYR B 51 PHE 0.014 0.002 PHE K 12 TRP 0.003 0.001 TRP K 82 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.20 (13676) covalent geometry : angle 0.73514 / 0.41 (19730) hydrogen bonds : bond 0.05557 / 6.03 ( 781) hydrogen bonds : angle 3.19833 / 4.16 ( 1951) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.288 Fit side-chains REVERT: K 1 MET cc_start: 0.4344 (ttm) cc_final: 0.3194 (tmm) REVERT: K 52 PHE cc_start: 0.7905 (m-80) cc_final: 0.7634 (m-80) outliers start: 11 outliers final: 6 residues processed: 110 average time/residue: 0.1216 time to fit residues: 18.3205 Evaluate side-chains 102 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 62 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 47 optimal weight: 0.3980 chunk 78 optimal weight: 0.9980 chunk 105 optimal weight: 9.9990 chunk 108 optimal weight: 20.0000 chunk 53 optimal weight: 0.2980 chunk 67 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 54 optimal weight: 0.9980 chunk 33 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 70.872 > 50:) chunk 100 optimal weight: 20.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN C 73 ASN E 108 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.083893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.055755 restraints weight = 37704.732| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 1.69 r_work: 0.2800 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9101 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13676 Z= 0.155 Angle : 0.628 10.739 19730 Z= 0.367 Chirality : 0.046 0.317 2229 Planarity : 0.004 0.039 1479 Dihedral : 31.431 160.678 4167 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.12 % Allowed : 13.32 % 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: 1.84 (0.29), residues: 831 helix: 2.28 (0.22), residues: 561 sheet: -2.21 (0.85), residues: 24 loop : -0.96 (0.35), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 96 TYR 0.008 0.001 TYR D 39 PHE 0.008 0.001 PHE A 67 TRP 0.005 0.001 TRP K 82 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.16 (13676) covalent geometry : angle 0.62792 / 0.37 (19730) hydrogen bonds : bond 0.04702 / 5.09 ( 781) hydrogen bonds : angle 2.87233 / 3.71 ( 1951) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 84 SER cc_start: 0.9308 (m) cc_final: 0.8746 (t) REVERT: K 52 PHE cc_start: 0.7853 (m-80) cc_final: 0.7550 (m-80) outliers start: 8 outliers final: 3 residues processed: 108 average time/residue: 0.1238 time to fit residues: 18.4579 Evaluate side-chains 101 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 98 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain K residue 90 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 89 optimal weight: 8.9990 chunk 71 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN F 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.081026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.051567 restraints weight = 38341.051| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 1.78 r_work: 0.2655 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2536 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9175 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 13676 Z= 0.277 Angle : 0.734 10.912 19730 Z= 0.403 Chirality : 0.052 0.341 2229 Planarity : 0.005 0.043 1479 Dihedral : 31.523 162.451 4165 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.40 % Allowed : 14.87 % Favored : 83.73 % 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: 1.52 (0.29), residues: 831 helix: 2.04 (0.22), residues: 560 sheet: -2.30 (0.89), residues: 23 loop : -1.09 (0.34), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 129 TYR 0.012 0.002 TYR G 57 PHE 0.013 0.002 PHE E 104 TRP 0.013 0.003 TRP K 82 HIS 0.006 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00611 / 0.28 (13676) covalent geometry : angle 0.73359 / 0.40 (19730) hydrogen bonds : bond 0.05799 / 6.43 ( 781) hydrogen bonds : angle 3.07857 / 3.97 ( 1951) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.349 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 105 average time/residue: 0.1372 time to fit residues: 19.6677 Evaluate side-chains 100 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 94 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 62 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 5 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 chunk 76 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN F 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.082566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.053334 restraints weight = 38135.898| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 1.79 r_work: 0.2703 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2583 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9137 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13676 Z= 0.141 Angle : 0.641 9.382 19730 Z= 0.366 Chirality : 0.047 0.337 2229 Planarity : 0.004 0.042 1479 Dihedral : 31.335 161.836 4165 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.54 % Allowed : 15.15 % Favored : 83.31 % 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: 1.98 (0.29), residues: 831 helix: 2.39 (0.22), residues: 559 sheet: -2.15 (0.93), residues: 23 loop : -0.91 (0.35), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 96 TYR 0.010 0.001 TYR B 51 PHE 0.011 0.001 PHE K 12 TRP 0.014 0.002 TRP K 82 HIS 0.006 0.001 HIS F 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.14 (13676) covalent geometry : angle 0.64057 / 0.37 (19730) hydrogen bonds : bond 0.04575 / 4.94 ( 781) hydrogen bonds : angle 2.87270 / 3.70 ( 1951) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: H 84 SER cc_start: 0.9381 (m) cc_final: 0.8723 (t) REVERT: H 90 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8226 (mp0) REVERT: K 1 MET cc_start: 0.4082 (ttm) cc_final: 0.3149 (tmm) outliers start: 11 outliers final: 6 residues processed: 106 average time/residue: 0.1261 time to fit residues: 18.2862 Evaluate side-chains 103 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain K residue 15 MET Chi-restraints excluded: chain K residue 58 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 107 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 45 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 4 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 chunk 10 optimal weight: 10.9990 chunk 7 optimal weight: 9.9990 chunk 72 optimal weight: 0.6980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.081287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.051926 restraints weight = 37722.532| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 1.77 r_work: 0.2666 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2546 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9169 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 13676 Z= 0.219 Angle : 0.685 9.992 19730 Z= 0.383 Chirality : 0.049 0.343 2229 Planarity : 0.005 0.043 1479 Dihedral : 31.355 163.147 4165 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.68 % Allowed : 15.43 % Favored : 82.89 % 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: 1.87 (0.29), residues: 831 helix: 2.29 (0.22), residues: 560 sheet: -1.90 (0.93), residues: 23 loop : -0.96 (0.35), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 129 TYR 0.018 0.001 TYR K 68 PHE 0.009 0.002 PHE E 104 TRP 0.012 0.002 TRP K 82 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.22 (13676) covalent geometry : angle 0.68483 / 0.38 (19730) hydrogen bonds : bond 0.05254 / 5.79 ( 781) hydrogen bonds : angle 2.95376 / 3.76 ( 1951) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: H 90 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8269 (mp0) outliers start: 12 outliers final: 7 residues processed: 104 average time/residue: 0.1241 time to fit residues: 17.5638 Evaluate side-chains 102 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain K residue 15 MET Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 62 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 20.0000 chunk 75 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 18 optimal weight: 0.1980 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 7 optimal weight: 10.0000 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN ** F 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.082194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.053069 restraints weight = 37971.639| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 1.78 r_work: 0.2699 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2581 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9141 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13676 Z= 0.144 Angle : 0.635 9.605 19730 Z= 0.363 Chirality : 0.046 0.342 2229 Planarity : 0.004 0.042 1479 Dihedral : 31.245 162.442 4165 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.54 % Allowed : 15.71 % Favored : 82.75 % 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: 2.11 (0.29), residues: 831 helix: 2.46 (0.22), residues: 561 sheet: -1.79 (0.95), residues: 23 loop : -0.85 (0.35), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 42 TYR 0.018 0.001 TYR K 68 PHE 0.008 0.001 PHE A 67 TRP 0.010 0.002 TRP K 82 HIS 0.004 0.001 HIS F 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.14 (13676) covalent geometry : angle 0.63550 / 0.36 (19730) hydrogen bonds : bond 0.04536 / 4.90 ( 781) hydrogen bonds : angle 2.84243 / 3.61 ( 1951) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: E 79 LYS cc_start: 0.9076 (tttt) cc_final: 0.8851 (tttt) REVERT: H 84 SER cc_start: 0.9390 (m) cc_final: 0.8766 (t) REVERT: H 90 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8265 (mp0) outliers start: 11 outliers final: 7 residues processed: 105 average time/residue: 0.1209 time to fit residues: 17.1837 Evaluate side-chains 104 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain K residue 15 MET Chi-restraints excluded: chain K residue 38 ASN Chi-restraints excluded: chain K residue 58 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 0 optimal weight: 20.0000 chunk 57 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 91 optimal weight: 9.9990 chunk 84 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 79 optimal weight: 0.0870 chunk 105 optimal weight: 9.9990 chunk 77 optimal weight: 0.0570 chunk 44 optimal weight: 1.9990 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** F 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.082660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.053584 restraints weight = 37978.991| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 1.78 r_work: 0.2713 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2594 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9132 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13676 Z= 0.142 Angle : 0.623 9.864 19730 Z= 0.359 Chirality : 0.045 0.344 2229 Planarity : 0.004 0.040 1479 Dihedral : 31.144 161.841 4165 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.54 % Allowed : 15.71 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.29), residues: 831 helix: 2.56 (0.22), residues: 560 sheet: -1.68 (0.98), residues: 24 loop : -0.75 (0.35), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 42 TYR 0.021 0.001 TYR K 68 PHE 0.009 0.001 PHE A 67 TRP 0.017 0.002 TRP K 82 HIS 0.004 0.001 HIS F 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.14 (13676) covalent geometry : angle 0.62309 / 0.36 (19730) hydrogen bonds : bond 0.04380 / 4.72 ( 781) hydrogen bonds : angle 2.80939 / 3.54 ( 1951) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: F 95 ARG cc_start: 0.9169 (OUTLIER) cc_final: 0.8941 (mtt-85) REVERT: H 84 SER cc_start: 0.9368 (m) cc_final: 0.8747 (t) REVERT: H 90 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8260 (mp0) outliers start: 11 outliers final: 8 residues processed: 105 average time/residue: 0.1319 time to fit residues: 18.8714 Evaluate side-chains 107 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain K residue 15 MET Chi-restraints excluded: chain K residue 38 ASN Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 62 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 10.0000 chunk 81 optimal weight: 0.6980 chunk 105 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 84 optimal weight: 0.6980 chunk 9 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.081563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.052284 restraints weight = 38055.150| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 1.77 r_work: 0.2677 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2559 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9158 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13676 Z= 0.204 Angle : 0.671 10.271 19730 Z= 0.375 Chirality : 0.047 0.348 2229 Planarity : 0.004 0.042 1479 Dihedral : 31.195 162.864 4165 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.54 % Allowed : 15.43 % Favored : 83.03 % 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: 2.07 (0.29), residues: 831 helix: 2.43 (0.22), residues: 561 sheet: -1.33 (1.00), residues: 23 loop : -0.90 (0.35), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 129 TYR 0.020 0.001 TYR K 68 PHE 0.009 0.001 PHE H 62 TRP 0.012 0.002 TRP K 82 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.20 (13676) covalent geometry : angle 0.67053 / 0.37 (19730) hydrogen bonds : bond 0.04960 / 5.44 ( 781) hydrogen bonds : angle 2.89600 / 3.65 ( 1951) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: C 72 ASP cc_start: 0.8932 (t0) cc_final: 0.8692 (t0) REVERT: F 95 ARG cc_start: 0.9208 (OUTLIER) cc_final: 0.8940 (mtt-85) REVERT: H 84 SER cc_start: 0.9392 (m) cc_final: 0.8591 (t) REVERT: H 90 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8290 (mp0) REVERT: K 78 ASN cc_start: 0.6555 (p0) cc_final: 0.5939 (p0) outliers start: 11 outliers final: 9 residues processed: 104 average time/residue: 0.1312 time to fit residues: 18.2331 Evaluate side-chains 108 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain K residue 15 MET Chi-restraints excluded: chain K residue 38 ASN Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 62 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 100 optimal weight: 20.0000 chunk 28 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 108 optimal weight: 20.0000 chunk 34 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN C 73 ASN ** F 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.081188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.051914 restraints weight = 38145.769| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 1.78 r_work: 0.2669 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2550 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9166 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13676 Z= 0.200 Angle : 0.665 10.297 19730 Z= 0.374 Chirality : 0.047 0.350 2229 Planarity : 0.004 0.041 1479 Dihedral : 31.146 163.719 4165 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.68 % Allowed : 15.29 % Favored : 83.03 % 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: 1.99 (0.29), residues: 831 helix: 2.36 (0.22), residues: 561 sheet: -1.24 (1.02), residues: 23 loop : -0.94 (0.34), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 42 TYR 0.018 0.001 TYR K 68 PHE 0.009 0.001 PHE H 62 TRP 0.016 0.002 TRP K 82 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.20 (13676) covalent geometry : angle 0.66517 / 0.37 (19730) hydrogen bonds : bond 0.04983 / 5.45 ( 781) hydrogen bonds : angle 2.90413 / 3.66 ( 1951) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: C 72 ASP cc_start: 0.8985 (t0) cc_final: 0.8744 (t0) REVERT: F 95 ARG cc_start: 0.9206 (OUTLIER) cc_final: 0.8941 (mtt-85) REVERT: H 84 SER cc_start: 0.9319 (m) cc_final: 0.8807 (t) outliers start: 12 outliers final: 9 residues processed: 101 average time/residue: 0.1194 time to fit residues: 16.3878 Evaluate side-chains 103 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain K residue 15 MET Chi-restraints excluded: chain K residue 38 ASN Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 62 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 105 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 55 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 108 optimal weight: 20.0000 chunk 35 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 58 optimal weight: 0.2980 chunk 88 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 13 optimal weight: 10.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN ** F 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.081610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.052411 restraints weight = 37947.467| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 1.77 r_work: 0.2686 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2567 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9155 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13676 Z= 0.161 Angle : 0.652 10.292 19730 Z= 0.369 Chirality : 0.046 0.346 2229 Planarity : 0.004 0.042 1479 Dihedral : 31.098 163.611 4165 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.96 % Allowed : 15.29 % Favored : 82.75 % 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: 2.09 (0.29), residues: 831 helix: 2.42 (0.22), residues: 561 sheet: -1.37 (1.00), residues: 24 loop : -0.83 (0.35), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 129 TYR 0.017 0.001 TYR K 68 PHE 0.008 0.001 PHE H 62 TRP 0.013 0.002 TRP K 82 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.16 (13676) covalent geometry : angle 0.65202 / 0.37 (19730) hydrogen bonds : bond 0.04713 / 5.12 ( 781) hydrogen bonds : angle 2.86847 / 3.61 ( 1951) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3363.47 seconds wall clock time: 57 minutes 44.55 seconds (3464.55 seconds total)