Starting phenix.real_space_refine on Fri Jul 3 06:21:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8pc5_17594/07_2026/8pc5_17594.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pc5_17594/07_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_17594/07_2026/8pc5_17594.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pc5_17594/07_2026/8pc5_17594.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8pc5_17594/07_2026/8pc5_17594.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8pc5_17594/07_2026/8pc5_17594.cif" model { file = "/net/cci-nas-00/data/ceres_data/8pc5_17594/07_2026/8pc5_17594.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pc5_17594/07_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-dev-6108/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: 3.05, per 1000 atoms: 0.24 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: 1.11 Conformation dependent library (CDL) restraints added in 420.0 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: 2.15 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: 2.70 Time building geometry restraints manager: 1.50 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: 18087 1.67 - 3.33: 1486 3.33 - 5.00: 127 5.00 - 6.66: 19 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=" O3' DC I 49 " pdb=" P DA I 50 " pdb=" O5' DA I 50 " ideal model delta sigma weight residual 104.00 95.83 8.17 1.50e+00 4.44e-01 2.97e+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 ... (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: 7.870 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: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.420 Find NCS groups from input model: 0.150 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: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.200 ------------------------------------------------------------------------------- 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 : 0.908 8.330 19730 Z= 0.755 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 0.90772 / 0.75 (19730) hydrogen bonds : bond 0.12744 / 14.15 ( 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 : 0.355 Fit side-chains revert: symmetry clash REVERT: H 84 SER cc_start: 0.8922 (m) cc_final: 0.8721 (t) outliers start: 3 outliers final: 2 residues processed: 153 average time/residue: 0.1747 time to fit residues: 34.8079 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 : 0.226 ------------------------------------------------------------------------------- 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: 9.9990 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: 9.9990 chunk 106 optimal weight: 8.9990 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 = 0.3640 r_free = 0.3640 target = 0.083459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.054967 restraints weight = 37615.427| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 1.73 r_work: 0.2774 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9117 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13676 Z= 0.201 Angle : 0.719 10.453 19730 Z= 0.405 Chirality : 0.052 0.320 2229 Planarity : 0.005 0.040 1479 Dihedral : 32.078 163.172 4168 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.44 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: 1.32 (0.29), residues: 831 helix: 1.92 (0.22), residues: 559 sheet: -3.64 (0.70), residues: 17 loop : -1.18 (0.34), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 129 TYR 0.013 0.001 TYR B 51 PHE 0.014 0.002 PHE K 12 TRP 0.004 0.001 TRP K 82 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.20 (13676) covalent geometry : angle 0.71867 / 0.41 (19730) hydrogen bonds : bond 0.05618 / 6.09 ( 781) hydrogen bonds : angle 3.21393 / 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 114 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: K 1 MET cc_start: 0.4240 (ttm) cc_final: 0.3098 (tmm) REVERT: K 52 PHE cc_start: 0.7912 (m-80) cc_final: 0.7638 (m-80) outliers start: 11 outliers final: 6 residues processed: 109 average time/residue: 0.1474 time to fit residues: 21.7911 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 : 0.350 ------------------------------------------------------------------------------- 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: 3.9990 chunk 78 optimal weight: 0.5980 chunk 105 optimal weight: 10.0000 chunk 108 optimal weight: 20.0000 chunk 53 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 chunk 104 optimal weight: 9.9990 chunk 54 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 100 optimal weight: 9.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN E 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.082439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.053987 restraints weight = 37639.390| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 1.69 r_work: 0.2755 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9146 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13676 Z= 0.209 Angle : 0.664 11.126 19730 Z= 0.382 Chirality : 0.048 0.289 2229 Planarity : 0.005 0.041 1479 Dihedral : 31.633 164.692 4167 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.40 % Allowed : 13.18 % Favored : 85.41 % 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: 1.58 (0.29), residues: 831 helix: 2.09 (0.22), residues: 562 sheet: -2.40 (0.82), residues: 24 loop : -1.10 (0.35), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 24 TYR 0.009 0.001 TYR D 37 PHE 0.010 0.002 PHE E 104 TRP 0.004 0.001 TRP K 82 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.21 (13676) covalent geometry : angle 0.66427 / 0.38 (19730) hydrogen bonds : bond 0.05341 / 5.83 ( 781) hydrogen bonds : angle 2.97978 / 3.85 ( 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: 10 poor density : 101 time to evaluate : 0.354 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 108 average time/residue: 0.1459 time to fit residues: 21.4351 Evaluate side-chains 101 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 90 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 chunk 89 optimal weight: 7.9990 chunk 71 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 107 optimal weight: 20.0000 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 = 0.3602 r_free = 0.3602 target = 0.081977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.052596 restraints weight = 38381.446| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 1.80 r_work: 0.2683 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2564 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9152 moved from start: 0.2180 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= 0.194 Angle : 0.658 10.533 19730 Z= 0.374 Chirality : 0.048 0.309 2229 Planarity : 0.004 0.044 1479 Dihedral : 31.511 165.298 4167 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.68 % Allowed : 13.74 % Favored : 84.57 % 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: 1.75 (0.29), residues: 831 helix: 2.23 (0.22), residues: 559 sheet: -2.37 (0.87), residues: 23 loop : -1.03 (0.34), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 129 TYR 0.009 0.001 TYR B 51 PHE 0.013 0.002 PHE K 12 TRP 0.020 0.003 TRP K 82 HIS 0.004 0.001 HIS F 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.19 (13676) covalent geometry : angle 0.65762 / 0.37 (19730) hydrogen bonds : bond 0.04938 / 5.37 ( 781) hydrogen bonds : angle 2.95300 / 3.81 ( 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 114 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: H 90 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8262 (mp0) outliers start: 12 outliers final: 6 residues processed: 107 average time/residue: 0.1540 time to fit residues: 22.1334 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 : 0.344 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 5 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 chunk 76 optimal weight: 0.7980 chunk 87 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 108 ASN C 73 ASN F 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.082737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.053511 restraints weight = 38088.507| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 1.82 r_work: 0.2708 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2588 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9124 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13676 Z= 0.143 Angle : 0.613 9.794 19730 Z= 0.357 Chirality : 0.045 0.299 2229 Planarity : 0.004 0.041 1479 Dihedral : 31.346 165.827 4167 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.54 % Allowed : 14.87 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.29), residues: 831 helix: 2.46 (0.22), residues: 559 sheet: -2.13 (0.89), residues: 23 loop : -0.88 (0.35), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 96 TYR 0.008 0.001 TYR B 51 PHE 0.011 0.001 PHE K 12 TRP 0.011 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 0.61271 / 0.36 (19730) hydrogen bonds : bond 0.04435 / 4.76 ( 781) hydrogen bonds : angle 2.83280 / 3.63 ( 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 112 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: E 79 LYS cc_start: 0.9068 (tttt) cc_final: 0.8854 (tttt) REVERT: H 84 SER cc_start: 0.9260 (m) cc_final: 0.8716 (t) REVERT: H 90 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8229 (mp0) outliers start: 11 outliers final: 4 residues processed: 107 average time/residue: 0.1492 time to fit residues: 21.5943 Evaluate side-chains 104 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 99 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 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 62 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 107 optimal weight: 10.0000 chunk 1 optimal weight: 20.0000 chunk 45 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 78 optimal weight: 0.2980 chunk 63 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 72 optimal weight: 0.6980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN C 73 ASN F 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.081458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.052093 restraints weight = 37779.044| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 1.79 r_work: 0.2670 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2551 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9165 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13676 Z= 0.215 Angle : 0.665 9.854 19730 Z= 0.375 Chirality : 0.047 0.295 2229 Planarity : 0.005 0.043 1479 Dihedral : 31.413 168.659 4165 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.54 % Allowed : 15.01 % Favored : 83.45 % 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: 1.92 (0.29), residues: 831 helix: 2.34 (0.22), residues: 559 sheet: -1.86 (0.93), residues: 23 loop : -0.95 (0.35), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 129 TYR 0.017 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 0.00457 / 0.21 (13676) covalent geometry : angle 0.66485 / 0.38 (19730) hydrogen bonds : bond 0.05119 / 5.61 ( 781) hydrogen bonds : angle 2.93905 / 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 107 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.381 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 102 average time/residue: 0.1483 time to fit residues: 20.4451 Evaluate side-chains 103 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 87 VAL 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: 0.9980 chunk 15 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 7 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN C 73 ASN F 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.082520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.053318 restraints weight = 37929.176| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 1.81 r_work: 0.2702 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2582 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9131 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13676 Z= 0.137 Angle : 0.613 9.769 19730 Z= 0.355 Chirality : 0.045 0.289 2229 Planarity : 0.004 0.041 1479 Dihedral : 31.293 169.095 4165 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.68 % Allowed : 15.01 % 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: 2.19 (0.29), residues: 831 helix: 2.53 (0.22), residues: 559 sheet: -1.71 (0.96), residues: 23 loop : -0.81 (0.36), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 96 TYR 0.019 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 0.00245 / 0.14 (13676) covalent geometry : angle 0.61290 / 0.36 (19730) hydrogen bonds : bond 0.04434 / 4.76 ( 781) hydrogen bonds : angle 2.81643 / 3.59 ( 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 109 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: D 110 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8258 (mm-30) REVERT: H 84 SER cc_start: 0.9349 (m) cc_final: 0.8621 (t) REVERT: H 90 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8248 (mp0) outliers start: 12 outliers final: 6 residues processed: 103 average time/residue: 0.1207 time to fit residues: 16.8403 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 : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 0 optimal weight: 20.0000 chunk 57 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 91 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 105 optimal weight: 9.9990 chunk 77 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3606 r_free = 0.3606 target = 0.082113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.052846 restraints weight = 37872.929| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 1.80 r_work: 0.2692 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2572 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9137 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13676 Z= 0.165 Angle : 0.628 9.758 19730 Z= 0.360 Chirality : 0.045 0.279 2229 Planarity : 0.004 0.040 1479 Dihedral : 31.229 172.412 4165 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.68 % Allowed : 15.15 % Favored : 83.17 % 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: 2.23 (0.29), residues: 831 helix: 2.57 (0.22), residues: 559 sheet: -1.60 (0.97), residues: 24 loop : -0.82 (0.36), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 129 TYR 0.021 0.001 TYR K 68 PHE 0.009 0.001 PHE A 67 TRP 0.010 0.002 TRP K 82 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.17 (13676) covalent geometry : angle 0.62768 / 0.36 (19730) hydrogen bonds : bond 0.04654 / 5.07 ( 781) hydrogen bonds : angle 2.82251 / 3.58 ( 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 108 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: C 72 ASP cc_start: 0.8960 (t0) cc_final: 0.8652 (t0) REVERT: D 110 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8299 (mm-30) REVERT: H 90 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8269 (mp0) outliers start: 12 outliers final: 8 residues processed: 103 average time/residue: 0.1564 time to fit residues: 21.5041 Evaluate side-chains 101 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 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 47 THR 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: 9.9990 chunk 81 optimal weight: 0.8980 chunk 105 optimal weight: 9.9990 chunk 59 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.3594 r_free = 0.3594 target = 0.081468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.052193 restraints weight = 38066.810| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 1.78 r_work: 0.2674 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2556 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9160 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13676 Z= 0.194 Angle : 0.651 10.090 19730 Z= 0.369 Chirality : 0.046 0.279 2229 Planarity : 0.004 0.042 1479 Dihedral : 31.252 176.495 4165 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % 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: 2.11 (0.29), residues: 831 helix: 2.47 (0.22), residues: 558 sheet: -1.23 (1.00), residues: 23 loop : -0.90 (0.35), residues: 250 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 0.001 PHE H 62 TRP 0.010 0.002 TRP K 82 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.19 (13676) covalent geometry : angle 0.65076 / 0.37 (19730) hydrogen bonds : bond 0.04902 / 5.35 ( 781) hydrogen bonds : angle 2.90329 / 3.66 ( 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 102 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: C 72 ASP cc_start: 0.8983 (t0) cc_final: 0.8679 (t0) REVERT: D 110 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8344 (mm-30) REVERT: H 90 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8306 (mp0) outliers start: 11 outliers final: 8 residues processed: 98 average time/residue: 0.1338 time to fit residues: 17.9331 Evaluate side-chains 99 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain E residue 87 SER 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 47 THR 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: 9.9990 chunk 28 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 108 optimal weight: 20.0000 chunk 34 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 63 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 90 optimal weight: 0.7980 chunk 92 optimal weight: 7.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 = 0.3595 r_free = 0.3595 target = 0.081508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.052229 restraints weight = 38054.877| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 1.78 r_work: 0.2676 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2558 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9159 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13676 Z= 0.186 Angle : 0.642 10.402 19730 Z= 0.365 Chirality : 0.046 0.290 2229 Planarity : 0.004 0.040 1479 Dihedral : 31.195 178.575 4165 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.26 % Allowed : 15.43 % 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: 2.14 (0.29), residues: 831 helix: 2.48 (0.22), residues: 559 sheet: -1.10 (1.02), residues: 23 loop : -0.88 (0.34), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 129 TYR 0.019 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 G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.19 (13676) covalent geometry : angle 0.64166 / 0.37 (19730) hydrogen bonds : bond 0.04811 / 5.25 ( 781) hydrogen bonds : angle 2.88272 / 3.65 ( 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 99 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: C 72 ASP cc_start: 0.8985 (t0) cc_final: 0.8686 (t0) REVERT: D 110 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8326 (mm-30) outliers start: 9 outliers final: 8 residues processed: 96 average time/residue: 0.1424 time to fit residues: 18.4862 Evaluate side-chains 97 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain K residue 15 MET Chi-restraints excluded: chain K residue 47 THR 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: 0.5980 chunk 32 optimal weight: 5.9990 chunk 108 optimal weight: 20.0000 chunk 35 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 13 optimal weight: 10.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.081741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.052542 restraints weight = 37826.479| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 1.77 r_work: 0.2687 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2568 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9151 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13676 Z= 0.156 Angle : 0.634 10.400 19730 Z= 0.362 Chirality : 0.045 0.292 2229 Planarity : 0.004 0.041 1479 Dihedral : 31.181 178.611 4165 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.40 % Allowed : 15.29 % 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: 2.19 (0.29), residues: 831 helix: 2.52 (0.22), residues: 559 sheet: -1.26 (0.99), residues: 24 loop : -0.83 (0.35), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 129 TYR 0.016 0.001 TYR K 68 PHE 0.009 0.001 PHE A 67 TRP 0.009 0.001 TRP K 82 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.16 (13676) covalent geometry : angle 0.63361 / 0.36 (19730) hydrogen bonds : bond 0.04667 / 5.07 ( 781) hydrogen bonds : angle 2.85404 / 3.60 ( 1951) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3755.03 seconds wall clock time: 64 minutes 45.01 seconds (3885.01 seconds total)