Starting phenix.real_space_refine on Wed Mar 4 01:27:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vby_31885/03_2026/7vby_31885_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vby_31885/03_2026/7vby_31885.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vby_31885/03_2026/7vby_31885_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vby_31885/03_2026/7vby_31885_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vby_31885/03_2026/7vby_31885.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vby_31885/03_2026/7vby_31885.map" } resolution = 2.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.033 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 11 5.49 5 S 34 5.16 5 C 5431 2.51 5 N 1306 2.21 5 O 1425 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8207 Number of models: 1 Model: "" Number of chains: 19 Chain: "B" Number of atoms: 2189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2189 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 13, 'TRANS': 272} Chain: "A" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 354 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Chain: "D" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 304 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "F" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 354 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Chain: "G" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 433 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "E" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 304 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "I" Number of atoms: 2189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2189 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 13, 'TRANS': 272} Chain: "H" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 458 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "C" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 463 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "J" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 433 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "B" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 184 Unusual residues: {'PC1': 3, 'UND': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 65 Unusual residues: {'PC1': 1, 'UND': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'UND': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'UND': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 195 Unusual residues: {'PC1': 3, 'UND': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "H" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 65 Unusual residues: {'PC1': 1, 'UND': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 119 Unusual residues: {'PC1': 2, 'UND': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'UND': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.68, per 1000 atoms: 0.20 Number of scatterers: 8207 At special positions: 0 Unit cell: (132.398, 110.472, 96.1362, 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 34 16.00 P 11 15.00 O 1425 8.00 N 1306 7.00 C 5431 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: 0.80 Conformation dependent library (CDL) restraints added in 222.4 milliseconds 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1734 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 3 sheets defined 36.7% alpha, 37.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'B' and resid 87 through 92 Processing helix chain 'B' and resid 308 through 310 No H-bonds generated for 'chain 'B' and resid 308 through 310' Processing helix chain 'A' and resid 26 through 37 removed outlier: 3.580A pdb=" N GLY A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 61 Processing helix chain 'D' and resid 14 through 48 Proline residue: D 42 - end of helix Processing helix chain 'F' and resid 26 through 37 Processing helix chain 'F' and resid 40 through 61 Processing helix chain 'G' and resid 5 through 39 removed outlier: 3.633A pdb=" N GLN G 10 " --> pdb=" O LYS G 6 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG G 11 " --> pdb=" O GLU G 7 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ILE G 28 " --> pdb=" O ARG G 24 " (cutoff:3.500A) Proline residue: G 29 - end of helix Processing helix chain 'G' and resid 48 through 53 Processing helix chain 'E' and resid 15 through 48 Proline residue: E 42 - end of helix Processing helix chain 'I' and resid 87 through 92 Processing helix chain 'I' and resid 308 through 310 No H-bonds generated for 'chain 'I' and resid 308 through 310' Processing helix chain 'H' and resid 64 through 96 removed outlier: 3.934A pdb=" N ASP H 68 " --> pdb=" O GLY H 64 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU H 69 " --> pdb=" O ALA H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 118 Processing helix chain 'C' and resid 63 through 96 Processing helix chain 'C' and resid 96 through 118 Processing helix chain 'J' and resid 6 through 25 removed outlier: 4.247A pdb=" N GLN J 10 " --> pdb=" O LYS J 6 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG J 11 " --> pdb=" O GLU J 7 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 39 Processing helix chain 'J' and resid 48 through 53 Processing sheet with id=AA1, first strand: chain 'B' and resid 193 through 194 removed outlier: 6.729A pdb=" N SER B 214 " --> pdb=" O PRO B 208 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU B 337 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N PHE B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU B 160 " --> pdb=" O THR B 180 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LYS B 175 " --> pdb=" O VAL B 190 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N VAL B 190 " --> pdb=" O LYS B 175 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ALA B 177 " --> pdb=" O TRP B 188 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N TRP B 188 " --> pdb=" O ALA B 177 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLN B 179 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 14.290A pdb=" N VAL B 186 " --> pdb=" O ASP B 209 " (cutoff:3.500A) removed outlier: 10.768A pdb=" N ASP B 209 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TRP B 188 " --> pdb=" O ASN B 207 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 140 through 142 removed outlier: 3.642A pdb=" N GLU B 145 " --> pdb=" O SER B 142 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 100 through 110 removed outlier: 6.182A pdb=" N PHE I 113 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU I 160 " --> pdb=" O THR I 180 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N GLN I 181 " --> pdb=" O PHE I 185 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N PHE I 185 " --> pdb=" O GLN I 181 " (cutoff:3.500A) removed outlier: 14.187A pdb=" N VAL I 186 " --> pdb=" O ASP I 209 " (cutoff:3.500A) removed outlier: 11.047A pdb=" N ASP I 209 " --> pdb=" O VAL I 186 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N TRP I 188 " --> pdb=" O ASN I 207 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N SER I 214 " --> pdb=" O PRO I 208 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU I 229 " --> pdb=" O ILE I 225 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA I 251 " --> pdb=" O GLY I 232 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY I 269 " --> pdb=" O GLY I 266 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE I 323 " --> pdb=" O ASP I 319 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LEU I 337 " --> pdb=" O LEU I 332 " (cutoff:3.500A) 556 hydrogen bonds defined for protein. 1602 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.01 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1231 1.32 - 1.44: 2069 1.44 - 1.56: 4966 1.56 - 1.68: 22 1.68 - 1.81: 58 Bond restraints: 8346 Sorted by residual: bond pdb=" C PRO I 148 " pdb=" O PRO I 148 " ideal model delta sigma weight residual 1.235 1.197 0.038 1.30e-02 5.92e+03 8.68e+00 bond pdb=" C PRO B 148 " pdb=" O PRO B 148 " ideal model delta sigma weight residual 1.235 1.197 0.038 1.30e-02 5.92e+03 8.62e+00 bond pdb=" CA SER I 142 " pdb=" CB SER I 142 " ideal model delta sigma weight residual 1.536 1.502 0.034 1.25e-02 6.40e+03 7.36e+00 bond pdb=" N GLY I 245 " pdb=" CA GLY I 245 " ideal model delta sigma weight residual 1.446 1.471 -0.025 9.50e-03 1.11e+04 7.06e+00 bond pdb=" N SER I 142 " pdb=" CA SER I 142 " ideal model delta sigma weight residual 1.452 1.480 -0.028 1.11e-02 8.12e+03 6.39e+00 ... (remaining 8341 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 10863 2.52 - 5.05: 219 5.05 - 7.57: 20 7.57 - 10.10: 8 10.10 - 12.62: 2 Bond angle restraints: 11112 Sorted by residual: angle pdb=" CA PHE I 147 " pdb=" CB PHE I 147 " pdb=" CG PHE I 147 " ideal model delta sigma weight residual 113.80 107.66 6.14 1.00e+00 1.00e+00 3.77e+01 angle pdb=" CA PHE I 147 " pdb=" C PHE I 147 " pdb=" O PHE I 147 " ideal model delta sigma weight residual 120.16 112.22 7.94 1.37e+00 5.33e-01 3.36e+01 angle pdb=" N PHE I 147 " pdb=" CA PHE I 147 " pdb=" C PHE I 147 " ideal model delta sigma weight residual 109.81 122.43 -12.62 2.21e+00 2.05e-01 3.26e+01 angle pdb=" N PHE B 147 " pdb=" CA PHE B 147 " pdb=" C PHE B 147 " ideal model delta sigma weight residual 109.81 122.39 -12.58 2.21e+00 2.05e-01 3.24e+01 angle pdb=" CA PHE B 147 " pdb=" C PHE B 147 " pdb=" O PHE B 147 " ideal model delta sigma weight residual 120.16 112.54 7.62 1.37e+00 5.33e-01 3.09e+01 ... (remaining 11107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 4419 17.74 - 35.47: 532 35.47 - 53.21: 141 53.21 - 70.95: 41 70.95 - 88.68: 16 Dihedral angle restraints: 5149 sinusoidal: 2448 harmonic: 2701 Sorted by residual: dihedral pdb=" C PHE I 147 " pdb=" N PHE I 147 " pdb=" CA PHE I 147 " pdb=" CB PHE I 147 " ideal model delta harmonic sigma weight residual -122.60 -162.75 40.15 0 2.50e+00 1.60e-01 2.58e+02 dihedral pdb=" N PHE I 147 " pdb=" C PHE I 147 " pdb=" CA PHE I 147 " pdb=" CB PHE I 147 " ideal model delta harmonic sigma weight residual 122.80 161.93 -39.13 0 2.50e+00 1.60e-01 2.45e+02 dihedral pdb=" C PHE B 147 " pdb=" N PHE B 147 " pdb=" CA PHE B 147 " pdb=" CB PHE B 147 " ideal model delta harmonic sigma weight residual -122.60 -159.55 36.95 0 2.50e+00 1.60e-01 2.18e+02 ... (remaining 5146 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.347: 1164 0.347 - 0.695: 0 0.695 - 1.042: 0 1.042 - 1.389: 0 1.389 - 1.736: 2 Chirality restraints: 1166 Sorted by residual: chirality pdb=" CA PHE I 147 " pdb=" N PHE I 147 " pdb=" C PHE I 147 " pdb=" CB PHE I 147 " both_signs ideal model delta sigma weight residual False 2.51 0.77 1.74 2.00e-01 2.50e+01 7.54e+01 chirality pdb=" CA PHE B 147 " pdb=" N PHE B 147 " pdb=" C PHE B 147 " pdb=" CB PHE B 147 " both_signs ideal model delta sigma weight residual False 2.51 0.92 1.59 2.00e-01 2.50e+01 6.35e+01 chirality pdb=" CA LEU I 141 " pdb=" N LEU I 141 " pdb=" C LEU I 141 " pdb=" CB LEU I 141 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 1163 not shown) Planarity restraints: 1337 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE I 147 " -0.025 2.00e-02 2.50e+03 1.71e-02 5.09e+00 pdb=" CG PHE I 147 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE I 147 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE I 147 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE I 147 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE I 147 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE I 147 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE I 147 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.61e+00 pdb=" C PHE I 147 " -0.037 2.00e-02 2.50e+03 pdb=" O PHE I 147 " 0.013 2.00e-02 2.50e+03 pdb=" N PRO I 148 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 147 " -0.010 2.00e-02 2.50e+03 2.05e-02 4.22e+00 pdb=" C PHE B 147 " 0.036 2.00e-02 2.50e+03 pdb=" O PHE B 147 " -0.012 2.00e-02 2.50e+03 pdb=" N PRO B 148 " -0.013 2.00e-02 2.50e+03 ... (remaining 1334 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 138 2.68 - 3.23: 7380 3.23 - 3.79: 11973 3.79 - 4.34: 16268 4.34 - 4.90: 28475 Nonbonded interactions: 64234 Sorted by model distance: nonbonded pdb=" O GLN B 182 " pdb=" OG SER B 183 " model vdw 2.120 3.040 nonbonded pdb=" OE1 GLN B 167 " pdb=" NE ARG B 173 " model vdw 2.196 3.120 nonbonded pdb=" NE2 GLN B 223 " pdb=" O LEU E 38 " model vdw 2.250 3.120 nonbonded pdb=" O SER J 5 " pdb=" NZ LYS J 9 " model vdw 2.254 3.120 nonbonded pdb=" O GLN H 112 " pdb=" OE1 GLN H 116 " model vdw 2.278 3.040 ... (remaining 64229 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 25 through 67) selection = (chain 'F' and resid 25 through 67) } ncs_group { reference = chain 'B' selection = (chain 'I' and resid 76 through 905) } ncs_group { reference = (chain 'C' and resid 63 through 201) selection = (chain 'H' and resid 63 through 201) } ncs_group { reference = (chain 'D' and resid 13 through 48) selection = chain 'E' } ncs_group { reference = (chain 'G' and resid 2 through 101) selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.130 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.220 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 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 0.051 8346 Z= 0.361 Angle : 0.846 12.624 11112 Z= 0.449 Chirality : 0.081 1.736 1166 Planarity : 0.004 0.049 1337 Dihedral : 16.966 88.683 3415 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.26 % Favored : 97.53 % Rotamer: Outliers : 0.75 % Allowed : 0.87 % Favored : 98.38 % Cbeta Deviations : 0.23 % 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: 1.56 (0.29), residues: 931 helix: 3.40 (0.29), residues: 325 sheet: 0.27 (0.26), residues: 382 loop : -1.18 (0.44), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 33 TYR 0.007 0.001 TYR D 34 PHE 0.035 0.001 PHE I 147 TRP 0.008 0.001 TRP C 86 HIS 0.006 0.001 HIS I 271 Details of bonding type rmsd covalent geometry : bond 0.00716 ( 8346) covalent geometry : angle 0.84625 (11112) hydrogen bonds : bond 0.08707 ( 556) hydrogen bonds : angle 5.24707 ( 1602) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 230 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: B 88 ARG cc_start: 0.8680 (ttm170) cc_final: 0.8398 (ttm170) REVERT: B 176 MET cc_start: 0.8072 (mtm) cc_final: 0.7786 (mtm) REVERT: A 37 ASP cc_start: 0.9009 (t0) cc_final: 0.8723 (t0) REVERT: D 13 PRO cc_start: 0.9451 (Cg_exo) cc_final: 0.9156 (Cg_endo) REVERT: D 19 LYS cc_start: 0.9259 (tppp) cc_final: 0.8744 (tppp) REVERT: D 23 ASP cc_start: 0.8711 (m-30) cc_final: 0.8417 (m-30) REVERT: F 40 ASP cc_start: 0.8529 (t70) cc_final: 0.8230 (t0) REVERT: G 10 GLN cc_start: 0.8735 (mp10) cc_final: 0.8219 (pm20) REVERT: E 19 LYS cc_start: 0.9340 (tppp) cc_final: 0.8374 (tppp) REVERT: E 23 ASP cc_start: 0.8830 (m-30) cc_final: 0.7984 (m-30) REVERT: I 176 MET cc_start: 0.8018 (mtm) cc_final: 0.7771 (mtm) REVERT: H 67 PHE cc_start: 0.8797 (t80) cc_final: 0.8449 (t80) REVERT: H 75 GLN cc_start: 0.8662 (tm-30) cc_final: 0.8298 (tm-30) REVERT: H 76 LYS cc_start: 0.8878 (mmmm) cc_final: 0.8526 (mmmt) REVERT: H 104 GLU cc_start: 0.8746 (tp30) cc_final: 0.8524 (mm-30) REVERT: H 111 GLN cc_start: 0.9171 (tm-30) cc_final: 0.8583 (tm-30) REVERT: C 75 GLN cc_start: 0.8277 (mm-40) cc_final: 0.7602 (tm-30) REVERT: C 104 GLU cc_start: 0.8722 (tp30) cc_final: 0.8506 (mm-30) REVERT: J 14 GLN cc_start: 0.8975 (mt0) cc_final: 0.8570 (mt0) REVERT: J 15 LEU cc_start: 0.9331 (tp) cc_final: 0.9064 (tt) REVERT: J 41 ASP cc_start: 0.8707 (m-30) cc_final: 0.8470 (m-30) outliers start: 6 outliers final: 3 residues processed: 235 average time/residue: 0.6468 time to fit residues: 159.3123 Evaluate side-chains 209 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 206 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain E residue 28 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 HIS A 48 ASN F 39 ASN I 106 ASN I 271 HIS C 115 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.086262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.060199 restraints weight = 16486.343| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 2.60 r_work: 0.2678 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8346 Z= 0.212 Angle : 0.713 12.592 11112 Z= 0.358 Chirality : 0.048 0.493 1166 Planarity : 0.005 0.053 1337 Dihedral : 16.329 95.719 1643 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.86 % Allowed : 14.05 % Favored : 82.09 % 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: 1.79 (0.29), residues: 931 helix: 3.56 (0.28), residues: 319 sheet: 0.47 (0.26), residues: 386 loop : -1.06 (0.44), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 240 TYR 0.009 0.001 TYR C 78 PHE 0.049 0.002 PHE B 147 TRP 0.007 0.001 TRP A 27 HIS 0.006 0.001 HIS I 271 Details of bonding type rmsd covalent geometry : bond 0.00490 ( 8346) covalent geometry : angle 0.71295 (11112) hydrogen bonds : bond 0.03629 ( 556) hydrogen bonds : angle 4.44421 ( 1602) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 220 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 141 LEU cc_start: 0.9090 (pp) cc_final: 0.8835 (pp) REVERT: B 176 MET cc_start: 0.8808 (mtm) cc_final: 0.8522 (mtm) REVERT: B 293 ARG cc_start: 0.9279 (mtp-110) cc_final: 0.9048 (ttm110) REVERT: B 319 ASP cc_start: 0.8924 (t0) cc_final: 0.8676 (t0) REVERT: B 329 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8608 (mt-10) REVERT: A 33 ARG cc_start: 0.8619 (mpt180) cc_final: 0.8405 (ptp-110) REVERT: A 37 ASP cc_start: 0.9134 (t0) cc_final: 0.8739 (t0) REVERT: D 18 ARG cc_start: 0.8515 (ttp80) cc_final: 0.8103 (ttp80) REVERT: D 19 LYS cc_start: 0.9202 (tppp) cc_final: 0.8712 (tppp) REVERT: D 22 GLU cc_start: 0.8613 (pm20) cc_final: 0.8018 (pm20) REVERT: D 23 ASP cc_start: 0.8937 (m-30) cc_final: 0.8577 (m-30) REVERT: D 38 LEU cc_start: 0.9002 (mp) cc_final: 0.8593 (mp) REVERT: F 40 ASP cc_start: 0.8441 (t70) cc_final: 0.8125 (t0) REVERT: G 44 MET cc_start: 0.8471 (mpp) cc_final: 0.8199 (mpp) REVERT: G 46 GLU cc_start: 0.6935 (OUTLIER) cc_final: 0.6090 (tp30) REVERT: E 15 GLU cc_start: 0.8313 (tp30) cc_final: 0.7968 (tp30) REVERT: E 19 LYS cc_start: 0.9301 (tppp) cc_final: 0.8903 (tppp) REVERT: E 22 GLU cc_start: 0.8457 (pp20) cc_final: 0.7957 (pp20) REVERT: E 23 ASP cc_start: 0.9054 (m-30) cc_final: 0.8656 (m-30) REVERT: E 38 LEU cc_start: 0.9021 (mp) cc_final: 0.8588 (mp) REVERT: I 176 MET cc_start: 0.8736 (mtm) cc_final: 0.8491 (mtm) REVERT: I 293 ARG cc_start: 0.9352 (mtp-110) cc_final: 0.9070 (ttm110) REVERT: H 67 PHE cc_start: 0.8759 (t80) cc_final: 0.8404 (t80) REVERT: H 75 GLN cc_start: 0.8654 (tm-30) cc_final: 0.8235 (tm-30) REVERT: H 76 LYS cc_start: 0.8713 (mmmm) cc_final: 0.8375 (mmmt) REVERT: H 107 GLN cc_start: 0.8410 (tm-30) cc_final: 0.8069 (tm-30) REVERT: H 110 GLN cc_start: 0.8554 (pp30) cc_final: 0.8333 (pp30) REVERT: H 111 GLN cc_start: 0.8857 (tm-30) cc_final: 0.8575 (pp30) REVERT: C 75 GLN cc_start: 0.8134 (mm-40) cc_final: 0.7452 (tm-30) REVERT: C 76 LYS cc_start: 0.8704 (mmmm) cc_final: 0.8344 (mmmt) REVERT: C 104 GLU cc_start: 0.9009 (tp30) cc_final: 0.8808 (mm-30) REVERT: C 107 GLN cc_start: 0.8351 (tm-30) cc_final: 0.7953 (tm-30) REVERT: C 111 GLN cc_start: 0.9102 (pp30) cc_final: 0.8798 (pp30) REVERT: J 14 GLN cc_start: 0.9052 (mt0) cc_final: 0.8653 (mt0) REVERT: J 44 MET cc_start: 0.8419 (mpp) cc_final: 0.8103 (mpp) REVERT: J 46 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6325 (tp30) outliers start: 31 outliers final: 11 residues processed: 229 average time/residue: 0.5879 time to fit residues: 142.0270 Evaluate side-chains 219 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 205 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 309 LYS Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain I residue 139 LYS Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 50 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 30 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 45 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 ASN C 115 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.087133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.061111 restraints weight = 16293.042| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 2.63 r_work: 0.2703 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8346 Z= 0.148 Angle : 0.658 10.885 11112 Z= 0.328 Chirality : 0.044 0.378 1166 Planarity : 0.004 0.046 1337 Dihedral : 15.546 75.796 1637 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 4.23 % Allowed : 16.04 % Favored : 79.73 % 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: 1.86 (0.29), residues: 931 helix: 3.37 (0.28), residues: 325 sheet: 0.65 (0.26), residues: 386 loop : -1.03 (0.44), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 240 TYR 0.009 0.001 TYR C 78 PHE 0.025 0.001 PHE B 147 TRP 0.005 0.001 TRP F 27 HIS 0.003 0.001 HIS I 271 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 8346) covalent geometry : angle 0.65763 (11112) hydrogen bonds : bond 0.03167 ( 556) hydrogen bonds : angle 4.24149 ( 1602) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 218 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 ILE cc_start: 0.9391 (OUTLIER) cc_final: 0.9120 (pp) REVERT: B 141 LEU cc_start: 0.9076 (pp) cc_final: 0.8859 (pp) REVERT: B 147 PHE cc_start: 0.7254 (OUTLIER) cc_final: 0.6602 (m-80) REVERT: B 173 ARG cc_start: 0.8555 (tpp80) cc_final: 0.8256 (tpp-160) REVERT: B 176 MET cc_start: 0.8726 (mtm) cc_final: 0.8448 (mtm) REVERT: B 195 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.8686 (mtm-85) REVERT: B 293 ARG cc_start: 0.9323 (mtp-110) cc_final: 0.9069 (mtp-110) REVERT: B 294 MET cc_start: 0.9350 (mmm) cc_final: 0.8978 (mpm) REVERT: B 319 ASP cc_start: 0.8903 (t0) cc_final: 0.8457 (t0) REVERT: B 329 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8598 (mt-10) REVERT: A 33 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.8266 (ptt-90) REVERT: A 37 ASP cc_start: 0.9179 (t0) cc_final: 0.8736 (t0) REVERT: D 16 MET cc_start: 0.9228 (mmm) cc_final: 0.8686 (tpt) REVERT: D 18 ARG cc_start: 0.8659 (ttp80) cc_final: 0.8041 (ttp80) REVERT: D 19 LYS cc_start: 0.9177 (tppp) cc_final: 0.8683 (tppp) REVERT: D 21 ARG cc_start: 0.8551 (tpp80) cc_final: 0.8332 (tpp80) REVERT: D 22 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8111 (pm20) REVERT: D 23 ASP cc_start: 0.8906 (m-30) cc_final: 0.8568 (m-30) REVERT: D 29 ARG cc_start: 0.8984 (ttp-110) cc_final: 0.8764 (ttp80) REVERT: F 33 ARG cc_start: 0.8469 (ptt-90) cc_final: 0.8226 (ptt-90) REVERT: F 40 ASP cc_start: 0.8388 (t70) cc_final: 0.8104 (t0) REVERT: G 10 GLN cc_start: 0.9157 (mp10) cc_final: 0.8795 (pm20) REVERT: G 13 GLN cc_start: 0.8382 (mt0) cc_final: 0.8038 (mp10) REVERT: G 14 GLN cc_start: 0.9026 (mt0) cc_final: 0.8358 (mm-40) REVERT: G 44 MET cc_start: 0.8499 (mpp) cc_final: 0.8199 (mpp) REVERT: E 15 GLU cc_start: 0.8513 (tp30) cc_final: 0.8170 (tp30) REVERT: E 19 LYS cc_start: 0.9270 (tppp) cc_final: 0.8697 (tppp) REVERT: E 22 GLU cc_start: 0.8582 (pp20) cc_final: 0.7991 (pp20) REVERT: E 23 ASP cc_start: 0.9044 (m-30) cc_final: 0.8635 (m-30) REVERT: I 96 ILE cc_start: 0.9421 (OUTLIER) cc_final: 0.9151 (pp) REVERT: I 147 PHE cc_start: 0.7189 (OUTLIER) cc_final: 0.6533 (t80) REVERT: I 173 ARG cc_start: 0.8699 (ttm170) cc_final: 0.8021 (ttm170) REVERT: I 176 MET cc_start: 0.8702 (mtm) cc_final: 0.8479 (mtm) REVERT: I 239 ARG cc_start: 0.8490 (tpt-90) cc_final: 0.8253 (tpp80) REVERT: I 294 MET cc_start: 0.9416 (mpp) cc_final: 0.9159 (mpm) REVERT: H 67 PHE cc_start: 0.8752 (t80) cc_final: 0.8380 (t80) REVERT: H 75 GLN cc_start: 0.8713 (tm-30) cc_final: 0.8230 (tm-30) REVERT: H 76 LYS cc_start: 0.8705 (mmmm) cc_final: 0.8328 (mmmt) REVERT: H 104 GLU cc_start: 0.8762 (mm-30) cc_final: 0.8276 (tp30) REVERT: H 107 GLN cc_start: 0.8479 (tm-30) cc_final: 0.8061 (tm-30) REVERT: H 111 GLN cc_start: 0.8856 (tm-30) cc_final: 0.8528 (pp30) REVERT: C 75 GLN cc_start: 0.8057 (mm-40) cc_final: 0.7529 (tm-30) REVERT: C 76 LYS cc_start: 0.8666 (mmmm) cc_final: 0.8271 (mmmt) REVERT: C 107 GLN cc_start: 0.8352 (tm-30) cc_final: 0.7931 (tm-30) REVERT: C 110 GLN cc_start: 0.8402 (pp30) cc_final: 0.8182 (pp30) REVERT: J 7 GLU cc_start: 0.8828 (tm-30) cc_final: 0.7705 (tm-30) REVERT: J 44 MET cc_start: 0.8461 (mpp) cc_final: 0.8172 (mpp) outliers start: 34 outliers final: 13 residues processed: 230 average time/residue: 0.5938 time to fit residues: 143.8348 Evaluate side-chains 229 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 208 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain I residue 76 CYS Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 139 LYS Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain I residue 147 PHE Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 280 ASP Chi-restraints excluded: chain J residue 50 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 24 optimal weight: 0.0270 chunk 47 optimal weight: 0.0670 chunk 80 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 56 optimal weight: 0.3980 chunk 30 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 267 GLN F 39 ASN C 115 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.088853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.062349 restraints weight = 16266.464| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 2.67 r_work: 0.2726 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 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 8346 Z= 0.116 Angle : 0.632 9.765 11112 Z= 0.317 Chirality : 0.043 0.293 1166 Planarity : 0.004 0.044 1337 Dihedral : 14.971 78.223 1637 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.10 % Allowed : 17.79 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.29), residues: 931 helix: 3.55 (0.28), residues: 319 sheet: 0.80 (0.26), residues: 386 loop : -0.91 (0.43), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 240 TYR 0.009 0.001 TYR C 78 PHE 0.022 0.001 PHE H 72 TRP 0.004 0.001 TRP I 188 HIS 0.002 0.001 HIS I 271 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 8346) covalent geometry : angle 0.63227 (11112) hydrogen bonds : bond 0.02847 ( 556) hydrogen bonds : angle 4.08989 ( 1602) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 225 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 176 MET cc_start: 0.8644 (mtm) cc_final: 0.8386 (mtm) REVERT: B 195 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.8697 (mtm-85) REVERT: B 293 ARG cc_start: 0.9336 (mtp-110) cc_final: 0.9041 (mtp-110) REVERT: B 294 MET cc_start: 0.9324 (mmm) cc_final: 0.8906 (mpm) REVERT: B 309 LYS cc_start: 0.9403 (OUTLIER) cc_final: 0.8912 (mppt) REVERT: B 319 ASP cc_start: 0.8863 (t0) cc_final: 0.8350 (t0) REVERT: A 37 ASP cc_start: 0.9160 (t0) cc_final: 0.8731 (t0) REVERT: D 16 MET cc_start: 0.9136 (mmm) cc_final: 0.8740 (tpt) REVERT: D 19 LYS cc_start: 0.9188 (tppp) cc_final: 0.8587 (tppp) REVERT: D 21 ARG cc_start: 0.8505 (tpp80) cc_final: 0.8189 (tpp80) REVERT: D 22 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8167 (pp20) REVERT: D 23 ASP cc_start: 0.8875 (m-30) cc_final: 0.8478 (m-30) REVERT: D 29 ARG cc_start: 0.8945 (ttp-110) cc_final: 0.8733 (ttp80) REVERT: F 40 ASP cc_start: 0.8223 (t70) cc_final: 0.8003 (t0) REVERT: G 10 GLN cc_start: 0.9105 (mp10) cc_final: 0.8841 (pm20) REVERT: G 13 GLN cc_start: 0.8287 (mt0) cc_final: 0.7816 (mt0) REVERT: G 14 GLN cc_start: 0.8970 (mt0) cc_final: 0.8333 (mm110) REVERT: G 44 MET cc_start: 0.8517 (mpp) cc_final: 0.8162 (mpp) REVERT: G 46 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.6107 (tp30) REVERT: E 15 GLU cc_start: 0.8651 (tp30) cc_final: 0.8254 (tp30) REVERT: E 19 LYS cc_start: 0.9234 (tppp) cc_final: 0.8862 (tppp) REVERT: E 22 GLU cc_start: 0.8600 (pp20) cc_final: 0.8163 (pp20) REVERT: E 23 ASP cc_start: 0.9046 (m-30) cc_final: 0.8658 (m-30) REVERT: I 147 PHE cc_start: 0.6914 (OUTLIER) cc_final: 0.6419 (t80) REVERT: I 173 ARG cc_start: 0.8629 (ttm170) cc_final: 0.8128 (ttm170) REVERT: I 176 MET cc_start: 0.8595 (mtm) cc_final: 0.8384 (mtm) REVERT: I 239 ARG cc_start: 0.8395 (tpt-90) cc_final: 0.8162 (tpp80) REVERT: I 294 MET cc_start: 0.9416 (mpp) cc_final: 0.9008 (mpm) REVERT: H 67 PHE cc_start: 0.8743 (t80) cc_final: 0.8390 (t80) REVERT: H 75 GLN cc_start: 0.8687 (tm-30) cc_final: 0.8188 (tm-30) REVERT: H 76 LYS cc_start: 0.8659 (mmmm) cc_final: 0.8260 (mmmt) REVERT: H 104 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8258 (tp30) REVERT: H 107 GLN cc_start: 0.8442 (tm-30) cc_final: 0.8005 (tm-30) REVERT: H 111 GLN cc_start: 0.8881 (tm-30) cc_final: 0.8524 (tm-30) REVERT: H 115 GLN cc_start: 0.9013 (mm-40) cc_final: 0.8642 (mm-40) REVERT: C 75 GLN cc_start: 0.7982 (mm-40) cc_final: 0.7438 (tm-30) REVERT: C 76 LYS cc_start: 0.8627 (mmmm) cc_final: 0.8219 (mmmt) REVERT: C 104 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8343 (tp30) REVERT: C 107 GLN cc_start: 0.8326 (tm-30) cc_final: 0.7862 (tm-30) REVERT: C 110 GLN cc_start: 0.8311 (pp30) cc_final: 0.8089 (pp30) REVERT: J 9 LYS cc_start: 0.8732 (mptt) cc_final: 0.8406 (mptt) REVERT: J 10 GLN cc_start: 0.9041 (pm20) cc_final: 0.8825 (pm20) REVERT: J 13 GLN cc_start: 0.8675 (mt0) cc_final: 0.8231 (mt0) REVERT: J 14 GLN cc_start: 0.9053 (mt0) cc_final: 0.8664 (mt0) REVERT: J 44 MET cc_start: 0.8552 (mpp) cc_final: 0.8208 (mpp) outliers start: 33 outliers final: 16 residues processed: 236 average time/residue: 0.6004 time to fit residues: 149.0503 Evaluate side-chains 231 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 210 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 309 LYS Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain I residue 76 CYS Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain I residue 147 PHE Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 280 ASP Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain J residue 50 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 41 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 267 GLN F 39 ASN I 111 ASN H 115 GLN C 111 GLN C 115 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.087837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.061114 restraints weight = 16214.382| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 2.68 r_work: 0.2696 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8346 Z= 0.160 Angle : 0.656 9.566 11112 Z= 0.325 Chirality : 0.043 0.287 1166 Planarity : 0.004 0.043 1337 Dihedral : 14.848 79.731 1637 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.86 % Allowed : 18.66 % Favored : 77.49 % 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: 2.17 (0.29), residues: 931 helix: 3.58 (0.28), residues: 319 sheet: 0.92 (0.26), residues: 384 loop : -0.87 (0.43), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 240 TYR 0.008 0.001 TYR E 34 PHE 0.023 0.001 PHE B 147 TRP 0.006 0.001 TRP I 188 HIS 0.002 0.001 HIS I 271 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 8346) covalent geometry : angle 0.65642 (11112) hydrogen bonds : bond 0.02984 ( 556) hydrogen bonds : angle 4.05989 ( 1602) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 214 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 176 MET cc_start: 0.8671 (mtm) cc_final: 0.8411 (mtm) REVERT: B 195 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.8697 (mtm-85) REVERT: B 293 ARG cc_start: 0.9362 (mtp-110) cc_final: 0.9043 (mtp-110) REVERT: B 294 MET cc_start: 0.9324 (mmm) cc_final: 0.8890 (mpm) REVERT: B 319 ASP cc_start: 0.8974 (t0) cc_final: 0.8418 (t0) REVERT: A 37 ASP cc_start: 0.9159 (t0) cc_final: 0.8745 (t0) REVERT: D 16 MET cc_start: 0.9157 (mmm) cc_final: 0.8794 (tpt) REVERT: D 18 ARG cc_start: 0.8591 (ttp80) cc_final: 0.8149 (ttp80) REVERT: D 19 LYS cc_start: 0.9225 (tppp) cc_final: 0.8618 (tppp) REVERT: D 20 MET cc_start: 0.8372 (mtp) cc_final: 0.8021 (mtp) REVERT: D 21 ARG cc_start: 0.8506 (tpp80) cc_final: 0.8235 (tpp80) REVERT: D 22 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8133 (pm20) REVERT: D 23 ASP cc_start: 0.8912 (m-30) cc_final: 0.8537 (m-30) REVERT: D 29 ARG cc_start: 0.8947 (ttp-110) cc_final: 0.8736 (ttp80) REVERT: F 33 ARG cc_start: 0.8454 (ptt-90) cc_final: 0.8173 (ptt-90) REVERT: F 40 ASP cc_start: 0.8235 (t70) cc_final: 0.7994 (t0) REVERT: G 10 GLN cc_start: 0.9111 (mp10) cc_final: 0.8886 (pm20) REVERT: G 13 GLN cc_start: 0.8320 (mt0) cc_final: 0.7853 (mt0) REVERT: G 14 GLN cc_start: 0.9018 (mt0) cc_final: 0.8373 (mm110) REVERT: G 44 MET cc_start: 0.8555 (mpp) cc_final: 0.8157 (mpp) REVERT: G 46 GLU cc_start: 0.6769 (OUTLIER) cc_final: 0.5958 (tp30) REVERT: E 19 LYS cc_start: 0.9281 (tppp) cc_final: 0.8777 (tppp) REVERT: E 22 GLU cc_start: 0.8628 (pp20) cc_final: 0.8149 (pp20) REVERT: E 23 ASP cc_start: 0.9031 (m-30) cc_final: 0.8661 (m-30) REVERT: I 96 ILE cc_start: 0.9392 (OUTLIER) cc_final: 0.9124 (pp) REVERT: I 147 PHE cc_start: 0.6800 (OUTLIER) cc_final: 0.6407 (t80) REVERT: I 173 ARG cc_start: 0.8611 (ttm170) cc_final: 0.8099 (ttm170) REVERT: I 176 MET cc_start: 0.8654 (mtm) cc_final: 0.8440 (mtm) REVERT: I 239 ARG cc_start: 0.8416 (tpt-90) cc_final: 0.8179 (tpp80) REVERT: I 294 MET cc_start: 0.9409 (mpp) cc_final: 0.9021 (mpm) REVERT: H 67 PHE cc_start: 0.8745 (t80) cc_final: 0.8365 (t80) REVERT: H 75 GLN cc_start: 0.8715 (tm-30) cc_final: 0.8284 (tm-30) REVERT: H 76 LYS cc_start: 0.8679 (mmmm) cc_final: 0.8276 (mmmt) REVERT: H 104 GLU cc_start: 0.8757 (mm-30) cc_final: 0.8295 (tp30) REVERT: H 107 GLN cc_start: 0.8435 (tm-30) cc_final: 0.7985 (tm-30) REVERT: H 111 GLN cc_start: 0.8886 (tm-30) cc_final: 0.8613 (tm-30) REVERT: C 75 GLN cc_start: 0.7966 (mm-40) cc_final: 0.7303 (tm-30) REVERT: C 76 LYS cc_start: 0.8633 (mmmm) cc_final: 0.8223 (mmmt) REVERT: C 104 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8366 (tp30) REVERT: C 107 GLN cc_start: 0.8331 (tm-30) cc_final: 0.7931 (tm-30) REVERT: C 110 GLN cc_start: 0.8185 (pp30) cc_final: 0.7968 (pp30) REVERT: J 9 LYS cc_start: 0.8752 (mptt) cc_final: 0.8447 (mptt) REVERT: J 13 GLN cc_start: 0.8681 (mt0) cc_final: 0.8219 (mt0) REVERT: J 14 GLN cc_start: 0.9062 (mt0) cc_final: 0.8636 (mt0) REVERT: J 44 MET cc_start: 0.8572 (mpp) cc_final: 0.8215 (mpp) REVERT: J 46 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6276 (tp30) outliers start: 31 outliers final: 14 residues processed: 223 average time/residue: 0.5931 time to fit residues: 139.4663 Evaluate side-chains 228 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 208 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain I residue 76 CYS Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain I residue 147 PHE Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 280 ASP Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 50 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 10 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 15 optimal weight: 0.7980 chunk 80 optimal weight: 7.9990 chunk 88 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 ASN C 115 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.088663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.062069 restraints weight = 15965.722| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 2.67 r_work: 0.2720 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8346 Z= 0.130 Angle : 0.661 9.434 11112 Z= 0.327 Chirality : 0.042 0.255 1166 Planarity : 0.005 0.045 1337 Dihedral : 14.632 80.445 1637 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.61 % Allowed : 20.15 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.29), residues: 931 helix: 3.59 (0.28), residues: 319 sheet: 1.00 (0.26), residues: 382 loop : -0.79 (0.44), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 240 TYR 0.008 0.001 TYR C 78 PHE 0.022 0.001 PHE C 67 TRP 0.005 0.001 TRP I 188 HIS 0.002 0.001 HIS I 271 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 8346) covalent geometry : angle 0.66052 (11112) hydrogen bonds : bond 0.02787 ( 556) hydrogen bonds : angle 3.98402 ( 1602) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 216 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 176 MET cc_start: 0.8671 (mtm) cc_final: 0.8406 (mtm) REVERT: B 195 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.8706 (mtm-85) REVERT: B 293 ARG cc_start: 0.9368 (mtp-110) cc_final: 0.9054 (mtp-110) REVERT: B 294 MET cc_start: 0.9329 (mmm) cc_final: 0.8891 (mpm) REVERT: B 319 ASP cc_start: 0.8940 (t0) cc_final: 0.8372 (t0) REVERT: A 37 ASP cc_start: 0.9165 (t0) cc_final: 0.8863 (t0) REVERT: D 15 GLU cc_start: 0.8925 (pm20) cc_final: 0.8565 (pm20) REVERT: D 18 ARG cc_start: 0.8550 (ttp80) cc_final: 0.8020 (ttp80) REVERT: D 19 LYS cc_start: 0.9205 (tppp) cc_final: 0.8543 (tppp) REVERT: D 20 MET cc_start: 0.8378 (mtp) cc_final: 0.8081 (mtp) REVERT: D 21 ARG cc_start: 0.8505 (tpp80) cc_final: 0.8219 (tpp80) REVERT: D 22 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8082 (pm20) REVERT: D 23 ASP cc_start: 0.8892 (m-30) cc_final: 0.8465 (m-30) REVERT: D 29 ARG cc_start: 0.8932 (ttp-110) cc_final: 0.8726 (ttp80) REVERT: F 40 ASP cc_start: 0.8263 (t70) cc_final: 0.7987 (t0) REVERT: G 10 GLN cc_start: 0.9101 (mp10) cc_final: 0.8853 (pm20) REVERT: G 14 GLN cc_start: 0.8994 (mt0) cc_final: 0.8346 (mm110) REVERT: G 44 MET cc_start: 0.8559 (mpp) cc_final: 0.8137 (mpp) REVERT: G 46 GLU cc_start: 0.6777 (OUTLIER) cc_final: 0.5970 (tp30) REVERT: E 19 LYS cc_start: 0.9294 (tppp) cc_final: 0.8713 (tppp) REVERT: E 22 GLU cc_start: 0.8636 (pp20) cc_final: 0.8141 (pp20) REVERT: E 23 ASP cc_start: 0.9025 (m-30) cc_final: 0.8619 (m-30) REVERT: I 173 ARG cc_start: 0.8577 (ttm170) cc_final: 0.8200 (ttm170) REVERT: I 176 MET cc_start: 0.8640 (mtm) cc_final: 0.8430 (mtm) REVERT: I 239 ARG cc_start: 0.8404 (tpt-90) cc_final: 0.8161 (tpp80) REVERT: I 294 MET cc_start: 0.9406 (mpp) cc_final: 0.9016 (mpm) REVERT: H 67 PHE cc_start: 0.8749 (t80) cc_final: 0.8369 (t80) REVERT: H 75 GLN cc_start: 0.8709 (tm-30) cc_final: 0.8205 (tm-30) REVERT: H 76 LYS cc_start: 0.8684 (mmmm) cc_final: 0.8265 (mmmt) REVERT: H 104 GLU cc_start: 0.8762 (mm-30) cc_final: 0.8277 (tp30) REVERT: H 107 GLN cc_start: 0.8418 (tm-30) cc_final: 0.7967 (tm-30) REVERT: H 111 GLN cc_start: 0.8930 (tm-30) cc_final: 0.8706 (tm-30) REVERT: C 75 GLN cc_start: 0.7942 (mm-40) cc_final: 0.7450 (tm-30) REVERT: C 76 LYS cc_start: 0.8625 (mmmm) cc_final: 0.8200 (mmmt) REVERT: C 104 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8370 (tp30) REVERT: C 107 GLN cc_start: 0.8402 (tm-30) cc_final: 0.7856 (tm-30) REVERT: J 7 GLU cc_start: 0.8872 (tm-30) cc_final: 0.8622 (tm-30) REVERT: J 9 LYS cc_start: 0.8777 (mptt) cc_final: 0.8375 (mptt) REVERT: J 13 GLN cc_start: 0.8694 (mt0) cc_final: 0.8213 (mt0) REVERT: J 14 GLN cc_start: 0.9085 (mt0) cc_final: 0.8696 (mt0) REVERT: J 44 MET cc_start: 0.8617 (mpp) cc_final: 0.8244 (mpp) REVERT: J 46 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6238 (tp30) outliers start: 29 outliers final: 14 residues processed: 224 average time/residue: 0.5956 time to fit residues: 140.4889 Evaluate side-chains 226 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 208 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain I residue 76 CYS Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 280 ASP Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 50 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 10 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 75 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 ASN C 111 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.087740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.061225 restraints weight = 16326.063| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 2.67 r_work: 0.2696 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8346 Z= 0.176 Angle : 0.703 9.539 11112 Z= 0.346 Chirality : 0.043 0.300 1166 Planarity : 0.005 0.053 1337 Dihedral : 14.620 81.238 1637 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.86 % Allowed : 20.27 % Favored : 75.87 % 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: 931 helix: 3.55 (0.28), residues: 319 sheet: 1.02 (0.26), residues: 382 loop : -0.83 (0.44), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 18 TYR 0.008 0.001 TYR E 34 PHE 0.022 0.001 PHE H 72 TRP 0.006 0.001 TRP I 188 HIS 0.002 0.001 HIS B 220 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 8346) covalent geometry : angle 0.70315 (11112) hydrogen bonds : bond 0.02969 ( 556) hydrogen bonds : angle 4.02706 ( 1602) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 208 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 GLU cc_start: 0.8576 (pp20) cc_final: 0.8306 (pp20) REVERT: B 176 MET cc_start: 0.8699 (mtm) cc_final: 0.8424 (mtm) REVERT: B 195 ARG cc_start: 0.8991 (OUTLIER) cc_final: 0.8720 (mtm-85) REVERT: B 293 ARG cc_start: 0.9377 (mtp-110) cc_final: 0.9051 (mtp-110) REVERT: B 294 MET cc_start: 0.9335 (mmm) cc_final: 0.8889 (mpm) REVERT: B 319 ASP cc_start: 0.8977 (t0) cc_final: 0.8408 (t0) REVERT: A 37 ASP cc_start: 0.9166 (t0) cc_final: 0.8777 (t0) REVERT: D 16 MET cc_start: 0.8356 (mpt) cc_final: 0.8114 (mpt) REVERT: D 18 ARG cc_start: 0.8562 (ttp80) cc_final: 0.8325 (ttp80) REVERT: D 19 LYS cc_start: 0.9191 (tppp) cc_final: 0.8621 (tppp) REVERT: D 20 MET cc_start: 0.8367 (mtp) cc_final: 0.8060 (mtm) REVERT: D 23 ASP cc_start: 0.8907 (m-30) cc_final: 0.8506 (m-30) REVERT: D 29 ARG cc_start: 0.8943 (ttp-110) cc_final: 0.8737 (ttp80) REVERT: F 33 ARG cc_start: 0.8482 (ptt-90) cc_final: 0.8186 (ptt-90) REVERT: F 40 ASP cc_start: 0.8280 (t70) cc_final: 0.7973 (t0) REVERT: G 10 GLN cc_start: 0.9088 (mp10) cc_final: 0.8854 (pm20) REVERT: G 14 GLN cc_start: 0.8928 (mt0) cc_final: 0.8687 (mt0) REVERT: G 44 MET cc_start: 0.8542 (mpp) cc_final: 0.8086 (mpp) REVERT: G 46 GLU cc_start: 0.6810 (OUTLIER) cc_final: 0.5995 (tp30) REVERT: E 19 LYS cc_start: 0.9312 (tppp) cc_final: 0.8728 (tppp) REVERT: E 22 GLU cc_start: 0.8636 (pp20) cc_final: 0.8110 (pp20) REVERT: E 23 ASP cc_start: 0.9006 (m-30) cc_final: 0.8589 (m-30) REVERT: E 38 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8663 (mp) REVERT: I 96 ILE cc_start: 0.9395 (OUTLIER) cc_final: 0.9128 (pp) REVERT: I 173 ARG cc_start: 0.8595 (ttm170) cc_final: 0.8382 (ttm170) REVERT: I 176 MET cc_start: 0.8677 (mtm) cc_final: 0.8468 (mtm) REVERT: I 239 ARG cc_start: 0.8412 (tpt-90) cc_final: 0.8181 (tpp80) REVERT: I 294 MET cc_start: 0.9404 (mpp) cc_final: 0.9010 (mpm) REVERT: H 67 PHE cc_start: 0.8785 (t80) cc_final: 0.8421 (t80) REVERT: H 75 GLN cc_start: 0.8703 (tm-30) cc_final: 0.8246 (tm-30) REVERT: H 76 LYS cc_start: 0.8690 (mmmm) cc_final: 0.8255 (mmmt) REVERT: H 104 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8321 (tp30) REVERT: H 107 GLN cc_start: 0.8430 (tm-30) cc_final: 0.8005 (tm-30) REVERT: H 111 GLN cc_start: 0.8914 (tm-30) cc_final: 0.8712 (tm-30) REVERT: C 75 GLN cc_start: 0.7950 (mm-40) cc_final: 0.7453 (tm-30) REVERT: C 76 LYS cc_start: 0.8633 (mmmm) cc_final: 0.8207 (mmmt) REVERT: C 104 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8375 (tp30) REVERT: C 107 GLN cc_start: 0.8367 (tm-30) cc_final: 0.7963 (tm-30) REVERT: C 115 GLN cc_start: 0.9521 (tm-30) cc_final: 0.9264 (pp30) REVERT: J 7 GLU cc_start: 0.8714 (tm-30) cc_final: 0.8502 (tm-30) REVERT: J 10 GLN cc_start: 0.8957 (pm20) cc_final: 0.8688 (pm20) REVERT: J 14 GLN cc_start: 0.9092 (mt0) cc_final: 0.8703 (mt0) REVERT: J 44 MET cc_start: 0.8589 (mpp) cc_final: 0.8213 (mpp) REVERT: J 46 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6236 (tp30) outliers start: 31 outliers final: 16 residues processed: 221 average time/residue: 0.6199 time to fit residues: 144.1479 Evaluate side-chains 226 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 205 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain I residue 76 CYS Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 286 VAL Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 50 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 52 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.087232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.060551 restraints weight = 16211.061| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 2.68 r_work: 0.2681 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8346 Z= 0.212 Angle : 0.724 9.659 11112 Z= 0.357 Chirality : 0.044 0.320 1166 Planarity : 0.005 0.043 1337 Dihedral : 14.725 81.150 1637 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.11 % Allowed : 22.26 % Favored : 74.63 % 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: 931 helix: 3.55 (0.28), residues: 319 sheet: 1.02 (0.26), residues: 382 loop : -0.78 (0.43), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 240 TYR 0.009 0.001 TYR E 34 PHE 0.025 0.002 PHE B 147 TRP 0.006 0.001 TRP B 188 HIS 0.003 0.001 HIS I 271 Details of bonding type rmsd covalent geometry : bond 0.00500 ( 8346) covalent geometry : angle 0.72432 (11112) hydrogen bonds : bond 0.03091 ( 556) hydrogen bonds : angle 4.05658 ( 1602) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 208 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 176 MET cc_start: 0.8728 (mtm) cc_final: 0.8443 (mtm) REVERT: B 195 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.8746 (mtm-85) REVERT: B 293 ARG cc_start: 0.9364 (mtp-110) cc_final: 0.9030 (mtp-110) REVERT: B 294 MET cc_start: 0.9330 (mmm) cc_final: 0.8891 (mpm) REVERT: B 319 ASP cc_start: 0.8996 (t0) cc_final: 0.8733 (t0) REVERT: A 33 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8227 (ptt-90) REVERT: A 37 ASP cc_start: 0.9162 (t0) cc_final: 0.8754 (t0) REVERT: D 16 MET cc_start: 0.8435 (mpt) cc_final: 0.8229 (mpt) REVERT: D 18 ARG cc_start: 0.8562 (ttp80) cc_final: 0.8311 (ttp80) REVERT: D 19 LYS cc_start: 0.9199 (tppp) cc_final: 0.8622 (tppp) REVERT: D 20 MET cc_start: 0.8398 (mtp) cc_final: 0.8100 (mtm) REVERT: D 23 ASP cc_start: 0.8912 (m-30) cc_final: 0.8505 (m-30) REVERT: D 29 ARG cc_start: 0.8950 (ttp-110) cc_final: 0.8742 (ttp80) REVERT: F 33 ARG cc_start: 0.8453 (ptt-90) cc_final: 0.8153 (ptt-90) REVERT: F 40 ASP cc_start: 0.8305 (t70) cc_final: 0.7993 (t0) REVERT: G 10 GLN cc_start: 0.9084 (mp10) cc_final: 0.8850 (pm20) REVERT: G 14 GLN cc_start: 0.8914 (mt0) cc_final: 0.8670 (mt0) REVERT: G 44 MET cc_start: 0.8544 (mpp) cc_final: 0.8101 (mpp) REVERT: G 46 GLU cc_start: 0.6792 (OUTLIER) cc_final: 0.5973 (tp30) REVERT: E 15 GLU cc_start: 0.8649 (tp30) cc_final: 0.8196 (tp30) REVERT: E 19 LYS cc_start: 0.9317 (tppp) cc_final: 0.8809 (tppp) REVERT: E 22 GLU cc_start: 0.8650 (pp20) cc_final: 0.8105 (pp20) REVERT: E 23 ASP cc_start: 0.9008 (m-30) cc_final: 0.8591 (m-30) REVERT: E 38 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8756 (mp) REVERT: I 96 ILE cc_start: 0.9400 (OUTLIER) cc_final: 0.9130 (pp) REVERT: I 147 PHE cc_start: 0.6732 (OUTLIER) cc_final: 0.6305 (t80) REVERT: I 173 ARG cc_start: 0.8622 (ttm170) cc_final: 0.8075 (ttm170) REVERT: I 176 MET cc_start: 0.8690 (mtm) cc_final: 0.8460 (mtm) REVERT: I 239 ARG cc_start: 0.8455 (tpt-90) cc_final: 0.8212 (tpp80) REVERT: I 294 MET cc_start: 0.9400 (mpp) cc_final: 0.9001 (mpm) REVERT: H 67 PHE cc_start: 0.8781 (t80) cc_final: 0.8415 (t80) REVERT: H 75 GLN cc_start: 0.8711 (tm-30) cc_final: 0.8249 (tm-30) REVERT: H 76 LYS cc_start: 0.8703 (mmmm) cc_final: 0.8258 (mmmt) REVERT: H 104 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8368 (tp30) REVERT: H 107 GLN cc_start: 0.8451 (tm-30) cc_final: 0.8063 (tm-30) REVERT: H 111 GLN cc_start: 0.8928 (tm-30) cc_final: 0.8697 (tm-30) REVERT: C 75 GLN cc_start: 0.7964 (mm-40) cc_final: 0.7352 (tm-30) REVERT: C 76 LYS cc_start: 0.8657 (mmmm) cc_final: 0.8228 (mmmt) REVERT: C 104 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8386 (tp30) REVERT: C 107 GLN cc_start: 0.8413 (tm-30) cc_final: 0.7974 (tm-30) REVERT: C 115 GLN cc_start: 0.9508 (tm-30) cc_final: 0.9269 (pp30) REVERT: J 13 GLN cc_start: 0.8679 (mt0) cc_final: 0.8429 (mt0) REVERT: J 14 GLN cc_start: 0.9083 (mt0) cc_final: 0.8692 (mt0) REVERT: J 44 MET cc_start: 0.8569 (mpp) cc_final: 0.8214 (mpp) REVERT: J 46 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6238 (tp30) outliers start: 25 outliers final: 15 residues processed: 219 average time/residue: 0.6045 time to fit residues: 139.6214 Evaluate side-chains 227 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 205 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain F residue 66 ASP Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain I residue 76 CYS Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain I residue 147 PHE Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 286 VAL Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 50 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.087119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.060363 restraints weight = 16177.165| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 2.67 r_work: 0.2673 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8346 Z= 0.215 Angle : 0.749 9.692 11112 Z= 0.371 Chirality : 0.044 0.312 1166 Planarity : 0.005 0.048 1337 Dihedral : 14.798 81.382 1637 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.86 % Allowed : 23.13 % Favored : 74.00 % 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: 931 helix: 3.36 (0.28), residues: 325 sheet: 1.03 (0.26), residues: 382 loop : -0.77 (0.44), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG I 240 TYR 0.009 0.001 TYR E 34 PHE 0.023 0.001 PHE B 147 TRP 0.006 0.001 TRP B 188 HIS 0.003 0.001 HIS I 271 Details of bonding type rmsd covalent geometry : bond 0.00507 ( 8346) covalent geometry : angle 0.74921 (11112) hydrogen bonds : bond 0.03145 ( 556) hydrogen bonds : angle 4.07810 ( 1602) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 206 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 176 MET cc_start: 0.8735 (mtm) cc_final: 0.8444 (mtm) REVERT: B 195 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.8737 (mtm-85) REVERT: B 293 ARG cc_start: 0.9366 (mtp-110) cc_final: 0.9005 (mtp-110) REVERT: B 294 MET cc_start: 0.9328 (mmm) cc_final: 0.8877 (mpm) REVERT: B 319 ASP cc_start: 0.8988 (t0) cc_final: 0.8712 (t0) REVERT: A 33 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.8213 (ptt-90) REVERT: A 37 ASP cc_start: 0.9169 (t0) cc_final: 0.8752 (t0) REVERT: D 18 ARG cc_start: 0.8581 (ttp80) cc_final: 0.7950 (ttp80) REVERT: D 19 LYS cc_start: 0.9191 (tppp) cc_final: 0.8598 (tppp) REVERT: D 20 MET cc_start: 0.8345 (mtp) cc_final: 0.8076 (mtm) REVERT: D 22 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8072 (pm20) REVERT: D 23 ASP cc_start: 0.8913 (m-30) cc_final: 0.8530 (m-30) REVERT: F 40 ASP cc_start: 0.8328 (t70) cc_final: 0.8038 (t0) REVERT: G 10 GLN cc_start: 0.9096 (mp10) cc_final: 0.8812 (pm20) REVERT: G 14 GLN cc_start: 0.8917 (mt0) cc_final: 0.8668 (mt0) REVERT: G 44 MET cc_start: 0.8500 (mpp) cc_final: 0.8068 (mpp) REVERT: G 46 GLU cc_start: 0.6799 (OUTLIER) cc_final: 0.5971 (tp30) REVERT: E 15 GLU cc_start: 0.8648 (tp30) cc_final: 0.8161 (tp30) REVERT: E 19 LYS cc_start: 0.9324 (tppp) cc_final: 0.8453 (tppp) REVERT: E 22 GLU cc_start: 0.8643 (pp20) cc_final: 0.8043 (pp20) REVERT: E 23 ASP cc_start: 0.9005 (m-30) cc_final: 0.8538 (m-30) REVERT: E 38 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8746 (mp) REVERT: I 147 PHE cc_start: 0.6724 (OUTLIER) cc_final: 0.6382 (t80) REVERT: I 173 ARG cc_start: 0.8627 (ttm170) cc_final: 0.8081 (ttm170) REVERT: I 176 MET cc_start: 0.8704 (mtm) cc_final: 0.8475 (mtm) REVERT: I 239 ARG cc_start: 0.8415 (tpt-90) cc_final: 0.8186 (tpp80) REVERT: I 294 MET cc_start: 0.9396 (mpp) cc_final: 0.8990 (mpm) REVERT: H 67 PHE cc_start: 0.8764 (t80) cc_final: 0.8397 (t80) REVERT: H 75 GLN cc_start: 0.8712 (tm-30) cc_final: 0.8248 (tm-30) REVERT: H 76 LYS cc_start: 0.8694 (mmmm) cc_final: 0.8265 (mmmt) REVERT: H 104 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8383 (tp30) REVERT: H 107 GLN cc_start: 0.8455 (tm-30) cc_final: 0.8035 (tm-30) REVERT: C 75 GLN cc_start: 0.8055 (mm-40) cc_final: 0.7430 (tm-30) REVERT: C 76 LYS cc_start: 0.8656 (mmmm) cc_final: 0.8227 (mmmt) REVERT: C 104 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8414 (tp30) REVERT: C 107 GLN cc_start: 0.8443 (tm-30) cc_final: 0.8014 (tm-30) REVERT: C 115 GLN cc_start: 0.9471 (tm-30) cc_final: 0.9232 (pp30) REVERT: J 13 GLN cc_start: 0.8670 (mt0) cc_final: 0.8407 (mt0) REVERT: J 14 GLN cc_start: 0.9083 (mt0) cc_final: 0.8692 (mt0) REVERT: J 44 MET cc_start: 0.8560 (mpp) cc_final: 0.8202 (mpp) REVERT: J 46 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6242 (tp30) outliers start: 23 outliers final: 14 residues processed: 216 average time/residue: 0.6056 time to fit residues: 137.8935 Evaluate side-chains 225 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 204 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain F residue 66 ASP Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain I residue 76 CYS Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain I residue 147 PHE Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 280 ASP Chi-restraints excluded: chain I residue 286 VAL Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 50 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 57 optimal weight: 0.8980 chunk 85 optimal weight: 20.0000 chunk 65 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 13 optimal weight: 0.0870 chunk 17 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 ASN G 10 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.087767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.061319 restraints weight = 16014.654| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 2.66 r_work: 0.2695 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8346 Z= 0.163 Angle : 0.751 9.734 11112 Z= 0.373 Chirality : 0.043 0.282 1166 Planarity : 0.005 0.050 1337 Dihedral : 14.585 80.251 1637 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.99 % Allowed : 23.76 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.29), residues: 931 helix: 3.46 (0.28), residues: 319 sheet: 1.05 (0.26), residues: 382 loop : -0.67 (0.44), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 18 TYR 0.008 0.001 TYR F 32 PHE 0.027 0.001 PHE C 67 TRP 0.006 0.001 TRP B 188 HIS 0.002 0.001 HIS I 271 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 8346) covalent geometry : angle 0.75136 (11112) hydrogen bonds : bond 0.02995 ( 556) hydrogen bonds : angle 4.04079 ( 1602) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 207 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 176 MET cc_start: 0.8727 (mtm) cc_final: 0.8442 (mtm) REVERT: B 195 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.8723 (mtm-85) REVERT: B 293 ARG cc_start: 0.9372 (mtp-110) cc_final: 0.8969 (mtp-110) REVERT: B 294 MET cc_start: 0.9328 (mmm) cc_final: 0.8824 (mpm) REVERT: B 319 ASP cc_start: 0.8971 (t0) cc_final: 0.8670 (t0) REVERT: A 33 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.8218 (ptt-90) REVERT: A 37 ASP cc_start: 0.9185 (t0) cc_final: 0.8774 (t0) REVERT: D 19 LYS cc_start: 0.9190 (tppp) cc_final: 0.8644 (tppp) REVERT: D 20 MET cc_start: 0.8379 (mtp) cc_final: 0.8137 (mtm) REVERT: D 23 ASP cc_start: 0.8909 (m-30) cc_final: 0.8517 (m-30) REVERT: F 40 ASP cc_start: 0.8260 (t70) cc_final: 0.7957 (t0) REVERT: G 10 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.8800 (pm20) REVERT: G 14 GLN cc_start: 0.8902 (mt0) cc_final: 0.8640 (mt0) REVERT: G 44 MET cc_start: 0.8484 (mpp) cc_final: 0.8031 (mpp) REVERT: G 46 GLU cc_start: 0.6785 (OUTLIER) cc_final: 0.5968 (tp30) REVERT: E 15 GLU cc_start: 0.8582 (tp30) cc_final: 0.8080 (tp30) REVERT: E 19 LYS cc_start: 0.9318 (tppp) cc_final: 0.8416 (tppp) REVERT: E 22 GLU cc_start: 0.8641 (pp20) cc_final: 0.8028 (pp20) REVERT: E 23 ASP cc_start: 0.9001 (m-30) cc_final: 0.8540 (m-30) REVERT: E 38 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8672 (mp) REVERT: I 147 PHE cc_start: 0.6597 (OUTLIER) cc_final: 0.6338 (t80) REVERT: I 173 ARG cc_start: 0.8620 (ttm170) cc_final: 0.8081 (ttm170) REVERT: I 176 MET cc_start: 0.8700 (mtm) cc_final: 0.8486 (mtm) REVERT: I 239 ARG cc_start: 0.8395 (tpt-90) cc_final: 0.8176 (tpp80) REVERT: I 240 ARG cc_start: 0.8355 (ttm110) cc_final: 0.8149 (mtm110) REVERT: I 294 MET cc_start: 0.9393 (mpp) cc_final: 0.8985 (mpm) REVERT: H 67 PHE cc_start: 0.8774 (t80) cc_final: 0.8394 (t80) REVERT: H 75 GLN cc_start: 0.8713 (tm-30) cc_final: 0.8244 (tm-30) REVERT: H 76 LYS cc_start: 0.8700 (mmmm) cc_final: 0.8267 (mmmt) REVERT: H 104 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8367 (tp30) REVERT: H 107 GLN cc_start: 0.8441 (tm-30) cc_final: 0.8079 (tm-30) REVERT: H 111 GLN cc_start: 0.8885 (tm-30) cc_final: 0.8607 (tm-30) REVERT: C 75 GLN cc_start: 0.7951 (mm-40) cc_final: 0.7361 (tm-30) REVERT: C 76 LYS cc_start: 0.8658 (mmmm) cc_final: 0.8234 (mmmt) REVERT: C 104 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8218 (tp30) REVERT: C 107 GLN cc_start: 0.8437 (tm-30) cc_final: 0.7979 (tm-30) REVERT: J 9 LYS cc_start: 0.8474 (mptt) cc_final: 0.8269 (mptt) REVERT: J 10 GLN cc_start: 0.9034 (pm20) cc_final: 0.8812 (pm20) REVERT: J 13 GLN cc_start: 0.8669 (mt0) cc_final: 0.8407 (mt0) REVERT: J 14 GLN cc_start: 0.9070 (mt0) cc_final: 0.8670 (mt0) REVERT: J 44 MET cc_start: 0.8555 (mpp) cc_final: 0.8208 (mpp) REVERT: J 46 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6238 (tp30) outliers start: 24 outliers final: 14 residues processed: 218 average time/residue: 0.5889 time to fit residues: 135.2927 Evaluate side-chains 226 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 205 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain F residue 66 ASP Chi-restraints excluded: chain G residue 10 GLN Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain I residue 76 CYS Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain I residue 147 PHE Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 280 ASP Chi-restraints excluded: chain I residue 286 VAL Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 50 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 8 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 89 optimal weight: 0.0170 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 ASN G 10 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.088428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.061894 restraints weight = 16042.640| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.67 r_work: 0.2712 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8346 Z= 0.140 Angle : 0.748 11.854 11112 Z= 0.371 Chirality : 0.043 0.249 1166 Planarity : 0.005 0.092 1337 Dihedral : 14.409 80.302 1637 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.86 % Allowed : 23.38 % Favored : 73.76 % 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: 2.28 (0.29), residues: 931 helix: 3.44 (0.28), residues: 319 sheet: 1.09 (0.26), residues: 382 loop : -0.59 (0.44), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG D 18 TYR 0.007 0.001 TYR C 78 PHE 0.023 0.001 PHE H 72 TRP 0.005 0.001 TRP I 188 HIS 0.002 0.001 HIS I 271 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 8346) covalent geometry : angle 0.74825 (11112) hydrogen bonds : bond 0.02872 ( 556) hydrogen bonds : angle 4.00660 ( 1602) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3626.94 seconds wall clock time: 62 minutes 14.97 seconds (3734.97 seconds total)