Starting phenix.real_space_refine on Mon Jul 28 00:07:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vby_31885/07_2025/7vby_31885_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vby_31885/07_2025/7vby_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7vby_31885/07_2025/7vby_31885.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vby_31885/07_2025/7vby_31885.map" model { file = "/net/cci-nas-00/data/ceres_data/7vby_31885/07_2025/7vby_31885_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vby_31885/07_2025/7vby_31885_trim.cif" } resolution = 2.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.62, per 1000 atoms: 0.68 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: 2.20 Conformation dependent library (CDL) restraints added in 812.9 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: 0.80 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: 2.28 Time building geometry restraints manager: 2.57 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 361 or resid 901 through 905)) } ncs_group { reference = (chain 'C' and (resid 63 through 118 or resid 201)) selection = (chain 'H' and (resid 63 through 118 or resid 201)) } ncs_group { reference = (chain 'D' and resid 13 through 48) selection = chain 'E' } ncs_group { reference = (chain 'G' and (resid 2 through 55 or resid 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: 2.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 21.750 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.040 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.008 0.001 TRP C 86 HIS 0.006 0.001 HIS I 271 PHE 0.035 0.001 PHE I 147 TYR 0.007 0.001 TYR D 34 ARG 0.016 0.001 ARG A 33 Details of bonding type rmsd hydrogen bonds : bond 0.08707 ( 556) hydrogen bonds : angle 5.24707 ( 1602) covalent geometry : bond 0.00716 ( 8346) covalent geometry : angle 0.84625 (11112) *********************** 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 : 0.900 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: 1.4691 time to fit residues: 363.0132 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 : 0.796 ------------------------------------------------------------------------------- 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 75 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 42 optimal weight: 0.1980 chunk 52 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 G 20 GLN I 106 ASN I 271 HIS H 115 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.087307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.061414 restraints weight = 16211.209| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 2.58 r_work: 0.2703 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8346 Z= 0.164 Angle : 0.703 12.608 11112 Z= 0.352 Chirality : 0.047 0.474 1166 Planarity : 0.005 0.053 1337 Dihedral : 16.212 94.560 1643 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.73 % Allowed : 13.81 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.29), residues: 931 helix: 3.56 (0.28), residues: 319 sheet: 0.52 (0.26), residues: 386 loop : -1.04 (0.44), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 27 HIS 0.006 0.001 HIS I 271 PHE 0.048 0.002 PHE B 147 TYR 0.010 0.001 TYR C 78 ARG 0.014 0.001 ARG I 240 Details of bonding type rmsd hydrogen bonds : bond 0.03405 ( 556) hydrogen bonds : angle 4.38656 ( 1602) covalent geometry : bond 0.00374 ( 8346) covalent geometry : angle 0.70330 (11112) *********************** 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 255 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 225 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 141 LEU cc_start: 0.9086 (pp) cc_final: 0.8839 (pp) REVERT: B 176 MET cc_start: 0.8794 (mtm) cc_final: 0.8528 (mtm) REVERT: B 293 ARG cc_start: 0.9273 (mtp-110) cc_final: 0.9040 (ttm110) REVERT: B 319 ASP cc_start: 0.8895 (t0) cc_final: 0.8613 (t0) REVERT: B 329 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8598 (mt-10) REVERT: A 33 ARG cc_start: 0.8624 (mpt180) cc_final: 0.8416 (ptp-170) REVERT: A 37 ASP cc_start: 0.9161 (t0) cc_final: 0.8770 (t0) REVERT: D 19 LYS cc_start: 0.9206 (tppp) cc_final: 0.8717 (tppp) REVERT: D 23 ASP cc_start: 0.8938 (m-30) cc_final: 0.8592 (m-30) REVERT: D 34 TYR cc_start: 0.9231 (t80) cc_final: 0.8963 (t80) REVERT: D 38 LEU cc_start: 0.8986 (mp) cc_final: 0.8531 (mp) REVERT: F 40 ASP cc_start: 0.8405 (t70) cc_final: 0.8098 (t0) REVERT: G 44 MET cc_start: 0.8483 (mpp) cc_final: 0.8220 (mpp) REVERT: G 46 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.6073 (tp30) REVERT: E 15 GLU cc_start: 0.8403 (tp30) cc_final: 0.8063 (tp30) REVERT: E 19 LYS cc_start: 0.9321 (tppp) cc_final: 0.8957 (tppp) REVERT: E 22 GLU cc_start: 0.8517 (pp20) cc_final: 0.8078 (pp20) REVERT: E 23 ASP cc_start: 0.9080 (m-30) cc_final: 0.8685 (m-30) REVERT: E 38 LEU cc_start: 0.9002 (mp) cc_final: 0.8561 (mp) REVERT: I 176 MET cc_start: 0.8719 (mtm) cc_final: 0.8490 (mtm) REVERT: I 239 ARG cc_start: 0.8472 (tpt-90) cc_final: 0.8158 (tpp80) REVERT: I 293 ARG cc_start: 0.9341 (mtp-110) cc_final: 0.9053 (ttm110) REVERT: H 67 PHE cc_start: 0.8759 (t80) cc_final: 0.8401 (t80) REVERT: H 75 GLN cc_start: 0.8661 (tm-30) cc_final: 0.8240 (tm-30) REVERT: H 76 LYS cc_start: 0.8695 (mmmm) cc_final: 0.8372 (mmmt) REVERT: H 107 GLN cc_start: 0.8393 (tm-30) cc_final: 0.8016 (tm-30) REVERT: H 110 GLN cc_start: 0.8565 (pp30) cc_final: 0.8346 (pp30) REVERT: H 111 GLN cc_start: 0.8860 (tm-30) cc_final: 0.8587 (pp30) REVERT: C 75 GLN cc_start: 0.8121 (mm-40) cc_final: 0.7435 (tm-30) REVERT: C 76 LYS cc_start: 0.8694 (mmmm) cc_final: 0.8336 (mmmt) REVERT: C 104 GLU cc_start: 0.9002 (tp30) cc_final: 0.8800 (mm-30) REVERT: C 107 GLN cc_start: 0.8347 (tm-30) cc_final: 0.7977 (tm-30) REVERT: J 44 MET cc_start: 0.8401 (mpp) cc_final: 0.8095 (mpp) REVERT: J 46 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6387 (tp30) outliers start: 30 outliers final: 12 residues processed: 234 average time/residue: 1.2897 time to fit residues: 319.2592 Evaluate side-chains 226 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 211 time to evaluate : 0.861 ------------------------------------------------------------------------------- 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 E residue 28 ILE 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 72 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 267 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.087480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.061238 restraints weight = 16392.245| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 2.64 r_work: 0.2707 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 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 0.029 8346 Z= 0.147 Angle : 0.655 11.164 11112 Z= 0.327 Chirality : 0.044 0.375 1166 Planarity : 0.004 0.046 1337 Dihedral : 15.491 75.591 1639 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.29), residues: 931 helix: 3.56 (0.27), residues: 319 sheet: 0.66 (0.26), residues: 386 loop : -1.04 (0.43), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 27 HIS 0.003 0.001 HIS I 271 PHE 0.025 0.001 PHE I 147 TYR 0.009 0.001 TYR C 78 ARG 0.013 0.001 ARG B 240 Details of bonding type rmsd hydrogen bonds : bond 0.03143 ( 556) hydrogen bonds : angle 4.22157 ( 1602) covalent geometry : bond 0.00335 ( 8346) covalent geometry : angle 0.65463 (11112) *********************** 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 253 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 219 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 147 PHE cc_start: 0.7282 (OUTLIER) cc_final: 0.6949 (m-80) REVERT: B 176 MET cc_start: 0.8747 (mtm) cc_final: 0.8483 (mtm) REVERT: B 195 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.8688 (mtm-85) REVERT: B 293 ARG cc_start: 0.9315 (mtp-110) cc_final: 0.9067 (mtp-110) REVERT: B 294 MET cc_start: 0.9347 (mmm) cc_final: 0.8981 (mpm) REVERT: B 309 LYS cc_start: 0.9442 (OUTLIER) cc_final: 0.8961 (mppt) REVERT: B 319 ASP cc_start: 0.8934 (t0) cc_final: 0.8480 (t0) REVERT: B 329 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8615 (mt-10) REVERT: A 33 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.8259 (ptt-90) REVERT: A 37 ASP cc_start: 0.9188 (t0) cc_final: 0.8748 (t0) REVERT: D 15 GLU cc_start: 0.8911 (pm20) cc_final: 0.8274 (pm20) REVERT: D 16 MET cc_start: 0.9219 (mmm) cc_final: 0.8965 (mpt) REVERT: D 19 LYS cc_start: 0.9233 (tppp) cc_final: 0.8704 (tppp) REVERT: D 21 ARG cc_start: 0.8566 (tpp80) cc_final: 0.8326 (tpp80) REVERT: D 23 ASP cc_start: 0.8897 (m-30) cc_final: 0.8553 (m-30) REVERT: D 29 ARG cc_start: 0.8996 (ttp-110) cc_final: 0.8777 (ttp80) REVERT: F 33 ARG cc_start: 0.8504 (ptt-90) cc_final: 0.8235 (ptt-90) REVERT: F 40 ASP cc_start: 0.8369 (t70) cc_final: 0.8105 (t0) REVERT: G 10 GLN cc_start: 0.9140 (mp10) cc_final: 0.8740 (pm20) REVERT: G 13 GLN cc_start: 0.8368 (mt0) cc_final: 0.8028 (mp10) REVERT: G 14 GLN cc_start: 0.9031 (mt0) cc_final: 0.8374 (mm-40) REVERT: G 44 MET cc_start: 0.8485 (mpp) cc_final: 0.8164 (mpp) REVERT: G 46 GLU cc_start: 0.6928 (OUTLIER) cc_final: 0.6089 (tp30) REVERT: E 19 LYS cc_start: 0.9270 (tppp) cc_final: 0.8602 (tppp) REVERT: E 22 GLU cc_start: 0.8588 (pp20) cc_final: 0.7998 (pp20) REVERT: E 23 ASP cc_start: 0.9058 (m-30) cc_final: 0.8636 (m-30) REVERT: I 96 ILE cc_start: 0.9435 (OUTLIER) cc_final: 0.9164 (pp) REVERT: I 147 PHE cc_start: 0.7311 (OUTLIER) cc_final: 0.6710 (t80) REVERT: I 173 ARG cc_start: 0.8719 (ttm170) cc_final: 0.8107 (ttm170) REVERT: I 176 MET cc_start: 0.8714 (mtm) cc_final: 0.8494 (mtm) REVERT: I 239 ARG cc_start: 0.8501 (tpt-90) cc_final: 0.8260 (tpp80) REVERT: I 294 MET cc_start: 0.9401 (mpp) cc_final: 0.9152 (mpm) REVERT: H 67 PHE cc_start: 0.8746 (t80) cc_final: 0.8370 (t80) REVERT: H 75 GLN cc_start: 0.8719 (tm-30) cc_final: 0.8230 (tm-30) REVERT: H 76 LYS cc_start: 0.8731 (mmmm) cc_final: 0.8344 (mmmt) REVERT: H 104 GLU cc_start: 0.8762 (mm-30) cc_final: 0.8276 (tp30) REVERT: H 107 GLN cc_start: 0.8489 (tm-30) cc_final: 0.8073 (tm-30) REVERT: H 111 GLN cc_start: 0.8854 (tm-30) cc_final: 0.8545 (tm-30) REVERT: C 75 GLN cc_start: 0.8106 (mm-40) cc_final: 0.7561 (tm-30) REVERT: C 76 LYS cc_start: 0.8702 (mmmm) cc_final: 0.8303 (mmmt) REVERT: C 107 GLN cc_start: 0.8358 (tm-30) cc_final: 0.7919 (tm-30) REVERT: C 110 GLN cc_start: 0.8364 (pp30) cc_final: 0.8155 (pp30) REVERT: J 14 GLN cc_start: 0.9032 (mt0) cc_final: 0.8626 (mt0) REVERT: J 44 MET cc_start: 0.8471 (mpp) cc_final: 0.8176 (mpp) outliers start: 34 outliers final: 15 residues processed: 231 average time/residue: 1.3774 time to fit residues: 335.9305 Evaluate side-chains 230 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 207 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 309 LYS 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 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 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 H residue 112 GLN 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 11 optimal weight: 0.7980 chunk 56 optimal weight: 0.0570 chunk 0 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 overall best weight: 0.7100 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.088593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.062071 restraints weight = 15927.525| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.65 r_work: 0.2719 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8346 Z= 0.124 Angle : 0.642 10.452 11112 Z= 0.320 Chirality : 0.043 0.323 1166 Planarity : 0.004 0.043 1337 Dihedral : 15.104 77.865 1637 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.10 % Allowed : 17.91 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.29), residues: 931 helix: 3.55 (0.28), residues: 319 sheet: 0.85 (0.26), residues: 384 loop : -0.87 (0.43), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 188 HIS 0.002 0.001 HIS I 271 PHE 0.023 0.001 PHE B 147 TYR 0.009 0.001 TYR C 78 ARG 0.010 0.001 ARG I 240 Details of bonding type rmsd hydrogen bonds : bond 0.02925 ( 556) hydrogen bonds : angle 4.10778 ( 1602) covalent geometry : bond 0.00281 ( 8346) covalent geometry : angle 0.64212 (11112) *********************** 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 256 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 223 time to evaluate : 1.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 176 MET cc_start: 0.8649 (mtm) cc_final: 0.8389 (mtm) REVERT: B 195 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.8684 (mtm-85) REVERT: B 293 ARG cc_start: 0.9327 (mtp-110) cc_final: 0.9050 (mtp-110) REVERT: B 294 MET cc_start: 0.9326 (mmm) cc_final: 0.8915 (mpm) REVERT: B 309 LYS cc_start: 0.9423 (OUTLIER) cc_final: 0.8912 (mppt) REVERT: B 319 ASP cc_start: 0.8862 (t0) cc_final: 0.8305 (t0) REVERT: A 37 ASP cc_start: 0.9162 (t0) cc_final: 0.8712 (t0) REVERT: D 15 GLU cc_start: 0.8933 (pm20) cc_final: 0.8374 (pm20) REVERT: D 16 MET cc_start: 0.9234 (mmm) cc_final: 0.8974 (mpt) REVERT: D 18 ARG cc_start: 0.8522 (ttp80) cc_final: 0.8034 (ttp80) REVERT: D 19 LYS cc_start: 0.9215 (tppp) cc_final: 0.8599 (tppp) REVERT: D 21 ARG cc_start: 0.8499 (tpp80) cc_final: 0.8233 (tpp80) REVERT: D 22 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8101 (pm20) REVERT: D 23 ASP cc_start: 0.8871 (m-30) cc_final: 0.8542 (m-30) REVERT: D 29 ARG cc_start: 0.8947 (ttp-110) cc_final: 0.8731 (ttp80) REVERT: F 40 ASP cc_start: 0.8275 (t70) cc_final: 0.8014 (t0) REVERT: G 10 GLN cc_start: 0.9105 (mp10) cc_final: 0.8884 (pm20) REVERT: G 13 GLN cc_start: 0.8289 (mt0) cc_final: 0.8059 (mt0) REVERT: G 14 GLN cc_start: 0.8975 (mt0) cc_final: 0.8360 (mm110) REVERT: G 44 MET cc_start: 0.8504 (mpp) cc_final: 0.8129 (mpp) REVERT: E 15 GLU cc_start: 0.8650 (tp30) cc_final: 0.8269 (tp30) REVERT: E 19 LYS cc_start: 0.9244 (tppp) cc_final: 0.8581 (tppp) REVERT: E 22 GLU cc_start: 0.8589 (pp20) cc_final: 0.8099 (pp20) REVERT: E 23 ASP cc_start: 0.9050 (m-30) cc_final: 0.8605 (m-30) REVERT: I 96 ILE cc_start: 0.9382 (OUTLIER) cc_final: 0.9108 (pp) REVERT: I 147 PHE cc_start: 0.7068 (OUTLIER) cc_final: 0.6361 (t80) REVERT: I 173 ARG cc_start: 0.8637 (ttm170) cc_final: 0.8069 (ttm170) REVERT: I 176 MET cc_start: 0.8632 (mtm) cc_final: 0.8429 (mtm) REVERT: I 239 ARG cc_start: 0.8417 (tpt-90) cc_final: 0.8166 (tpp80) REVERT: I 294 MET cc_start: 0.9391 (mpp) cc_final: 0.8987 (mpm) REVERT: H 67 PHE cc_start: 0.8743 (t80) cc_final: 0.8382 (t80) REVERT: H 75 GLN cc_start: 0.8682 (tm-30) cc_final: 0.8189 (tm-30) REVERT: H 76 LYS cc_start: 0.8658 (mmmm) cc_final: 0.8260 (mmmt) REVERT: H 104 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8259 (tp30) REVERT: H 107 GLN cc_start: 0.8422 (tm-30) cc_final: 0.8004 (tm-30) REVERT: H 111 GLN cc_start: 0.8881 (tm-30) cc_final: 0.8538 (tm-30) REVERT: H 115 GLN cc_start: 0.8908 (mm-40) cc_final: 0.8593 (mm-40) REVERT: C 75 GLN cc_start: 0.8026 (mm-40) cc_final: 0.7467 (tm-30) REVERT: C 76 LYS cc_start: 0.8628 (mmmm) cc_final: 0.8226 (mmmt) REVERT: C 104 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8306 (tp30) REVERT: C 107 GLN cc_start: 0.8309 (tm-30) cc_final: 0.7930 (tm-30) REVERT: J 14 GLN cc_start: 0.9039 (mt0) cc_final: 0.8658 (mt0) REVERT: J 44 MET cc_start: 0.8550 (mpp) cc_final: 0.8231 (mpp) REVERT: J 46 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.6264 (tp30) outliers start: 33 outliers final: 16 residues processed: 234 average time/residue: 1.3892 time to fit residues: 343.4233 Evaluate side-chains 236 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 214 time to evaluate : 0.821 ------------------------------------------------------------------------------- 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 D residue 45 LEU 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 96 ILE 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 46 GLU 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 35 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 60 optimal weight: 0.2980 chunk 30 optimal weight: 5.9990 chunk 57 optimal weight: 0.0980 chunk 77 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 ASN I 111 ASN H 115 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.087971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.061431 restraints weight = 15936.679| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 2.64 r_work: 0.2705 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2298 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= 0.155 Angle : 0.657 9.899 11112 Z= 0.326 Chirality : 0.043 0.293 1166 Planarity : 0.004 0.043 1337 Dihedral : 14.870 79.430 1637 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.98 % Allowed : 18.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.29), residues: 931 helix: 3.59 (0.28), residues: 319 sheet: 0.91 (0.26), residues: 384 loop : -0.82 (0.44), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 188 HIS 0.002 0.001 HIS I 271 PHE 0.025 0.001 PHE B 147 TYR 0.008 0.001 TYR C 78 ARG 0.012 0.001 ARG I 240 Details of bonding type rmsd hydrogen bonds : bond 0.02958 ( 556) hydrogen bonds : angle 4.07392 ( 1602) covalent geometry : bond 0.00361 ( 8346) covalent geometry : angle 0.65670 (11112) *********************** 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 249 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 217 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 ILE cc_start: 0.9356 (OUTLIER) cc_final: 0.9086 (pp) REVERT: B 173 ARG cc_start: 0.8314 (tpp80) cc_final: 0.8058 (tpp80) REVERT: B 176 MET cc_start: 0.8662 (mtm) cc_final: 0.8402 (mtm) REVERT: B 195 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.8700 (mtm-85) REVERT: B 293 ARG cc_start: 0.9341 (mtp-110) cc_final: 0.9030 (mtp-110) REVERT: B 294 MET cc_start: 0.9316 (mmm) cc_final: 0.8885 (mpm) REVERT: B 319 ASP cc_start: 0.8917 (t0) cc_final: 0.8383 (t0) REVERT: A 37 ASP cc_start: 0.9161 (t0) cc_final: 0.8740 (t0) REVERT: D 15 GLU cc_start: 0.8936 (pm20) cc_final: 0.8328 (pm20) REVERT: D 16 MET cc_start: 0.9262 (mmm) cc_final: 0.8991 (mpt) REVERT: D 18 ARG cc_start: 0.8560 (ttp80) cc_final: 0.8320 (ttp80) REVERT: D 19 LYS cc_start: 0.9216 (tppp) cc_final: 0.8693 (tppp) REVERT: D 21 ARG cc_start: 0.8518 (tpp80) cc_final: 0.8209 (tpp80) REVERT: D 23 ASP cc_start: 0.8903 (m-30) cc_final: 0.8552 (m-30) REVERT: D 29 ARG cc_start: 0.8944 (ttp-110) cc_final: 0.8733 (ttp80) REVERT: F 33 ARG cc_start: 0.8463 (ptt-90) cc_final: 0.8203 (ptt-90) REVERT: F 40 ASP cc_start: 0.8238 (t70) cc_final: 0.7977 (t0) REVERT: G 10 GLN cc_start: 0.9117 (mp10) cc_final: 0.8901 (pm20) REVERT: G 13 GLN cc_start: 0.8325 (mt0) cc_final: 0.8065 (mt0) REVERT: G 14 GLN cc_start: 0.9008 (mt0) cc_final: 0.8380 (mm110) REVERT: G 44 MET cc_start: 0.8556 (mpp) cc_final: 0.8166 (mpp) REVERT: G 46 GLU cc_start: 0.6754 (OUTLIER) cc_final: 0.5946 (tp30) REVERT: E 19 LYS cc_start: 0.9306 (tppp) cc_final: 0.8824 (tppp) REVERT: E 22 GLU cc_start: 0.8626 (pp20) cc_final: 0.8155 (pp20) REVERT: E 23 ASP cc_start: 0.9042 (m-30) cc_final: 0.8653 (m-30) REVERT: I 96 ILE cc_start: 0.9388 (OUTLIER) cc_final: 0.9116 (pp) REVERT: I 147 PHE cc_start: 0.6846 (OUTLIER) cc_final: 0.6412 (t80) REVERT: I 173 ARG cc_start: 0.8602 (ttm170) cc_final: 0.8135 (ttm170) REVERT: I 176 MET cc_start: 0.8643 (mtm) cc_final: 0.8424 (mtm) REVERT: I 239 ARG cc_start: 0.8405 (tpt-90) cc_final: 0.8169 (tpp80) REVERT: I 294 MET cc_start: 0.9394 (mpp) cc_final: 0.8999 (mpm) REVERT: H 67 PHE cc_start: 0.8737 (t80) cc_final: 0.8367 (t80) REVERT: H 75 GLN cc_start: 0.8707 (tm-30) cc_final: 0.8278 (tm-30) REVERT: H 76 LYS cc_start: 0.8677 (mmmm) cc_final: 0.8276 (mmmt) REVERT: H 104 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8300 (tp30) REVERT: H 107 GLN cc_start: 0.8432 (tm-30) cc_final: 0.7951 (tm-30) REVERT: H 111 GLN cc_start: 0.8901 (tm-30) cc_final: 0.8596 (tm-30) REVERT: H 115 GLN cc_start: 0.9061 (mm110) cc_final: 0.8825 (mm-40) REVERT: C 75 GLN cc_start: 0.7965 (mm-40) cc_final: 0.7319 (tm-30) REVERT: C 76 LYS cc_start: 0.8632 (mmmm) cc_final: 0.8220 (mmmt) REVERT: C 104 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8336 (tp30) REVERT: C 107 GLN cc_start: 0.8372 (tm-30) cc_final: 0.7852 (tm-30) REVERT: J 10 GLN cc_start: 0.8958 (pm20) cc_final: 0.8753 (pm20) REVERT: J 14 GLN cc_start: 0.9059 (mt0) cc_final: 0.8672 (mt0) REVERT: J 44 MET cc_start: 0.8565 (mpp) cc_final: 0.8218 (mpp) REVERT: J 46 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6276 (tp30) outliers start: 32 outliers final: 15 residues processed: 226 average time/residue: 1.3018 time to fit residues: 310.4223 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 : 0.940 ------------------------------------------------------------------------------- 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 172 LEU Chi-restraints excluded: chain B residue 195 ARG 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 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 18 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 13 optimal weight: 0.2980 chunk 71 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.088861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.062401 restraints weight = 15955.087| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 2.66 r_work: 0.2728 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8346 Z= 0.125 Angle : 0.656 9.337 11112 Z= 0.325 Chirality : 0.042 0.245 1166 Planarity : 0.005 0.045 1337 Dihedral : 14.582 80.420 1637 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.23 % Allowed : 20.15 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.29), residues: 931 helix: 3.57 (0.28), residues: 319 sheet: 1.01 (0.26), residues: 382 loop : -0.78 (0.44), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 188 HIS 0.002 0.001 HIS I 271 PHE 0.024 0.001 PHE C 67 TYR 0.008 0.001 TYR C 78 ARG 0.011 0.001 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.02758 ( 556) hydrogen bonds : angle 3.99257 ( 1602) covalent geometry : bond 0.00288 ( 8346) covalent geometry : angle 0.65636 (11112) *********************** 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 243 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 217 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 176 MET cc_start: 0.8662 (mtm) cc_final: 0.8408 (mtm) REVERT: B 195 ARG cc_start: 0.8965 (OUTLIER) cc_final: 0.8703 (mtm-85) REVERT: B 293 ARG cc_start: 0.9354 (mtp-110) cc_final: 0.9047 (mtp-110) REVERT: B 294 MET cc_start: 0.9325 (mmm) cc_final: 0.8890 (mpm) REVERT: B 319 ASP cc_start: 0.8927 (t0) cc_final: 0.8398 (t0) REVERT: A 37 ASP cc_start: 0.9170 (t0) cc_final: 0.8865 (t0) REVERT: D 15 GLU cc_start: 0.8953 (pm20) cc_final: 0.8318 (pm20) REVERT: D 16 MET cc_start: 0.9250 (mmm) cc_final: 0.8990 (mpt) REVERT: D 18 ARG cc_start: 0.8566 (ttp80) cc_final: 0.8211 (ttp80) REVERT: D 19 LYS cc_start: 0.9200 (tppp) cc_final: 0.8609 (tppp) REVERT: D 21 ARG cc_start: 0.8514 (tpp80) cc_final: 0.8199 (tpp80) REVERT: D 23 ASP cc_start: 0.8906 (m-30) cc_final: 0.8525 (m-30) REVERT: D 29 ARG cc_start: 0.8934 (ttp-110) cc_final: 0.8727 (ttp80) REVERT: F 40 ASP cc_start: 0.8272 (t70) cc_final: 0.7996 (t0) REVERT: G 10 GLN cc_start: 0.9111 (mp10) cc_final: 0.8858 (pm20) REVERT: G 13 GLN cc_start: 0.8324 (mt0) cc_final: 0.7861 (mt0) REVERT: G 14 GLN cc_start: 0.8994 (mt0) cc_final: 0.8339 (mm110) REVERT: G 44 MET cc_start: 0.8556 (mpp) cc_final: 0.8148 (mpp) REVERT: E 19 LYS cc_start: 0.9305 (tppp) cc_final: 0.8753 (tppp) REVERT: E 22 GLU cc_start: 0.8624 (pp20) cc_final: 0.8136 (pp20) REVERT: E 23 ASP cc_start: 0.9030 (m-30) cc_final: 0.8632 (m-30) REVERT: I 173 ARG cc_start: 0.8568 (ttm170) cc_final: 0.8091 (ttm170) REVERT: I 176 MET cc_start: 0.8643 (mtm) cc_final: 0.8442 (mtm) REVERT: I 239 ARG cc_start: 0.8400 (tpt-90) cc_final: 0.8152 (tpp80) REVERT: I 294 MET cc_start: 0.9395 (mpp) cc_final: 0.8992 (mpm) REVERT: H 67 PHE cc_start: 0.8747 (t80) cc_final: 0.8363 (t80) REVERT: H 75 GLN cc_start: 0.8707 (tm-30) cc_final: 0.8207 (tm-30) REVERT: H 76 LYS cc_start: 0.8685 (mmmm) cc_final: 0.8268 (mmmt) REVERT: H 104 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8304 (tp30) REVERT: H 107 GLN cc_start: 0.8417 (tm-30) cc_final: 0.7957 (tm-30) REVERT: H 111 GLN cc_start: 0.8928 (tm-30) cc_final: 0.8643 (tm-30) REVERT: C 75 GLN cc_start: 0.7939 (mm-40) cc_final: 0.7449 (tm-30) REVERT: C 76 LYS cc_start: 0.8623 (mmmm) cc_final: 0.8207 (mmmt) REVERT: C 104 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8340 (tp30) REVERT: C 107 GLN cc_start: 0.8293 (tm-30) cc_final: 0.7897 (tm-30) REVERT: J 14 GLN cc_start: 0.9060 (mt0) cc_final: 0.8676 (mt0) REVERT: J 44 MET cc_start: 0.8611 (mpp) cc_final: 0.8229 (mpp) REVERT: J 46 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6243 (tp30) outliers start: 26 outliers final: 17 residues processed: 225 average time/residue: 1.4363 time to fit residues: 341.1785 Evaluate side-chains 226 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 207 time to evaluate : 1.080 ------------------------------------------------------------------------------- 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 50 LEU Chi-restraints excluded: chain E residue 45 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 6.9990 chunk 57 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 75 optimal weight: 20.0000 chunk 85 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 = 0.3456 r_free = 0.3456 target = 0.087878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.061211 restraints weight = 16077.015| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 2.67 r_work: 0.2699 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8346 Z= 0.174 Angle : 0.700 9.716 11112 Z= 0.345 Chirality : 0.043 0.285 1166 Planarity : 0.005 0.054 1337 Dihedral : 14.566 80.933 1637 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.36 % Allowed : 21.02 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.29), residues: 931 helix: 3.58 (0.28), residues: 319 sheet: 1.03 (0.26), residues: 382 loop : -0.79 (0.44), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 188 HIS 0.002 0.001 HIS I 271 PHE 0.022 0.001 PHE H 72 TYR 0.008 0.001 TYR E 34 ARG 0.013 0.001 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.02951 ( 556) hydrogen bonds : angle 4.01718 ( 1602) covalent geometry : bond 0.00409 ( 8346) covalent geometry : angle 0.69996 (11112) *********************** 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 235 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 208 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 GLU cc_start: 0.8569 (pp20) cc_final: 0.8310 (pp20) REVERT: B 176 MET cc_start: 0.8689 (mtm) cc_final: 0.8415 (mtm) REVERT: B 195 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.8717 (mtm-85) REVERT: B 293 ARG cc_start: 0.9365 (mtp-110) cc_final: 0.9043 (mtp-110) REVERT: B 294 MET cc_start: 0.9329 (mmm) cc_final: 0.8885 (mpm) REVERT: B 319 ASP cc_start: 0.8967 (t0) cc_final: 0.8390 (t0) REVERT: A 37 ASP cc_start: 0.9167 (t0) cc_final: 0.8764 (t0) REVERT: D 16 MET cc_start: 0.9255 (mmm) cc_final: 0.8814 (tpt) REVERT: D 18 ARG cc_start: 0.8586 (ttp80) cc_final: 0.7963 (ttp80) REVERT: D 19 LYS cc_start: 0.9208 (tppp) cc_final: 0.8574 (tppp) REVERT: D 20 MET cc_start: 0.8416 (mtp) cc_final: 0.8069 (mtp) REVERT: D 22 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8074 (pm20) REVERT: D 23 ASP cc_start: 0.8925 (m-30) cc_final: 0.8517 (m-30) REVERT: D 29 ARG cc_start: 0.8943 (ttp-110) cc_final: 0.8737 (ttp80) REVERT: F 33 ARG cc_start: 0.8485 (ptt-90) cc_final: 0.8187 (ptt-90) REVERT: F 40 ASP cc_start: 0.8269 (t70) cc_final: 0.7991 (t0) REVERT: G 44 MET cc_start: 0.8548 (mpp) cc_final: 0.8153 (mpp) REVERT: E 19 LYS cc_start: 0.9311 (tppp) cc_final: 0.8728 (tppp) REVERT: E 22 GLU cc_start: 0.8650 (pp20) cc_final: 0.8143 (pp20) REVERT: E 23 ASP cc_start: 0.9029 (m-30) cc_final: 0.8626 (m-30) REVERT: I 96 ILE cc_start: 0.9390 (OUTLIER) cc_final: 0.9123 (pp) REVERT: I 147 PHE cc_start: 0.6890 (OUTLIER) cc_final: 0.6114 (t80) REVERT: I 173 ARG cc_start: 0.8567 (ttm170) cc_final: 0.8059 (ttm170) REVERT: I 176 MET cc_start: 0.8668 (mtm) cc_final: 0.8456 (mtm) REVERT: I 239 ARG cc_start: 0.8397 (tpt-90) cc_final: 0.8157 (tpp80) REVERT: I 294 MET cc_start: 0.9382 (mpp) cc_final: 0.8981 (mpm) REVERT: H 67 PHE cc_start: 0.8772 (t80) cc_final: 0.8403 (t80) REVERT: H 75 GLN cc_start: 0.8716 (tm-30) cc_final: 0.8238 (tm-30) REVERT: H 76 LYS cc_start: 0.8689 (mmmm) cc_final: 0.8274 (mmmt) REVERT: H 104 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8322 (tp30) REVERT: H 107 GLN cc_start: 0.8424 (tm-30) cc_final: 0.7955 (tm-30) REVERT: H 111 GLN cc_start: 0.8904 (tm-30) cc_final: 0.8665 (tm-30) REVERT: H 115 GLN cc_start: 0.8939 (mm-40) cc_final: 0.8716 (mm-40) REVERT: C 75 GLN cc_start: 0.7946 (mm-40) cc_final: 0.7452 (tm-30) REVERT: C 76 LYS cc_start: 0.8625 (mmmm) cc_final: 0.8205 (mmmt) REVERT: C 104 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8352 (tp30) REVERT: C 107 GLN cc_start: 0.8367 (tm-30) cc_final: 0.7941 (tm-30) REVERT: C 115 GLN cc_start: 0.9530 (tm-30) cc_final: 0.9293 (pp30) REVERT: J 7 GLU cc_start: 0.8812 (tm-30) cc_final: 0.8584 (tm-30) REVERT: J 10 GLN cc_start: 0.8964 (pm20) cc_final: 0.8757 (pm20) REVERT: J 13 GLN cc_start: 0.8680 (mt0) cc_final: 0.8437 (mt0) REVERT: J 14 GLN cc_start: 0.9059 (mt0) cc_final: 0.8646 (mt0) REVERT: J 44 MET cc_start: 0.8625 (mpp) cc_final: 0.8275 (mpp) REVERT: J 46 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6269 (tp30) outliers start: 27 outliers final: 14 residues processed: 218 average time/residue: 1.3216 time to fit residues: 303.9284 Evaluate side-chains 224 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 205 time to evaluate : 0.855 ------------------------------------------------------------------------------- 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 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 50 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 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 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 73 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 63 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 ** H 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.087364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.060774 restraints weight = 16326.697| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 2.68 r_work: 0.2684 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2588 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= 0.197 Angle : 0.730 12.360 11112 Z= 0.359 Chirality : 0.044 0.306 1166 Planarity : 0.004 0.045 1337 Dihedral : 14.635 82.107 1637 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.99 % Allowed : 22.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.29), residues: 931 helix: 3.59 (0.28), residues: 319 sheet: 1.04 (0.26), residues: 382 loop : -0.78 (0.44), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 188 HIS 0.003 0.001 HIS I 271 PHE 0.026 0.001 PHE B 147 TYR 0.009 0.001 TYR E 34 ARG 0.012 0.001 ARG B 240 Details of bonding type rmsd hydrogen bonds : bond 0.03058 ( 556) hydrogen bonds : angle 4.05041 ( 1602) covalent geometry : bond 0.00465 ( 8346) covalent geometry : angle 0.73032 (11112) *********************** 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 231 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 207 time to evaluate : 0.908 Fit side-chains revert: symmetry clash REVERT: B 176 MET cc_start: 0.8718 (mtm) cc_final: 0.8438 (mtm) REVERT: B 195 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.8717 (mtm-85) REVERT: B 293 ARG cc_start: 0.9366 (mtp-110) cc_final: 0.9048 (mtp-110) REVERT: B 294 MET cc_start: 0.9335 (mmm) cc_final: 0.8898 (mpm) REVERT: B 319 ASP cc_start: 0.8988 (t0) cc_final: 0.8734 (t0) REVERT: A 33 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.8239 (ptt-90) REVERT: A 37 ASP cc_start: 0.9164 (t0) cc_final: 0.8769 (t0) REVERT: D 16 MET cc_start: 0.9161 (mmm) cc_final: 0.8769 (tpt) REVERT: D 18 ARG cc_start: 0.8595 (ttp80) cc_final: 0.7960 (ttp80) REVERT: D 19 LYS cc_start: 0.9215 (tppp) cc_final: 0.8577 (tppp) REVERT: D 20 MET cc_start: 0.8421 (mtp) cc_final: 0.8040 (mtm) REVERT: D 22 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8089 (pm20) REVERT: D 23 ASP cc_start: 0.8938 (m-30) cc_final: 0.8533 (m-30) REVERT: D 29 ARG cc_start: 0.8941 (ttp-110) cc_final: 0.8736 (ttp80) REVERT: F 33 ARG cc_start: 0.8458 (ptt-90) cc_final: 0.8158 (ptt-90) REVERT: F 40 ASP cc_start: 0.8288 (t70) cc_final: 0.7989 (t0) REVERT: G 44 MET cc_start: 0.8553 (mpp) cc_final: 0.8087 (mpp) REVERT: G 46 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6099 (tp30) REVERT: E 15 GLU cc_start: 0.8662 (tp30) cc_final: 0.8228 (tp30) REVERT: E 19 LYS cc_start: 0.9317 (tppp) cc_final: 0.8791 (tppp) REVERT: E 22 GLU cc_start: 0.8643 (pp20) cc_final: 0.8094 (pp20) REVERT: E 23 ASP cc_start: 0.9013 (m-30) cc_final: 0.8590 (m-30) REVERT: I 147 PHE cc_start: 0.6868 (OUTLIER) cc_final: 0.6053 (t80) REVERT: I 173 ARG cc_start: 0.8593 (ttm170) cc_final: 0.8061 (ttm170) REVERT: I 176 MET cc_start: 0.8687 (mtm) cc_final: 0.8462 (mtm) REVERT: I 239 ARG cc_start: 0.8443 (tpt-90) cc_final: 0.8193 (tpp80) REVERT: I 294 MET cc_start: 0.9383 (mpp) cc_final: 0.8971 (mpm) REVERT: H 67 PHE cc_start: 0.8780 (t80) cc_final: 0.8411 (t80) REVERT: H 75 GLN cc_start: 0.8720 (tm-30) cc_final: 0.8249 (tm-30) REVERT: H 76 LYS cc_start: 0.8697 (mmmm) cc_final: 0.8261 (mmmt) REVERT: H 104 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8345 (tp30) REVERT: H 107 GLN cc_start: 0.8449 (tm-30) cc_final: 0.8011 (tm-30) REVERT: H 111 GLN cc_start: 0.8904 (tm-30) cc_final: 0.8633 (tm-30) REVERT: H 115 GLN cc_start: 0.8946 (mm-40) cc_final: 0.8700 (mm-40) REVERT: C 75 GLN cc_start: 0.7958 (mm-40) cc_final: 0.7348 (tm-30) REVERT: C 76 LYS cc_start: 0.8648 (mmmm) cc_final: 0.8222 (mmmt) REVERT: C 104 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8367 (tp30) REVERT: C 107 GLN cc_start: 0.8406 (tm-30) cc_final: 0.7959 (tm-30) REVERT: C 115 GLN cc_start: 0.9511 (tm-30) cc_final: 0.9216 (pp30) REVERT: J 13 GLN cc_start: 0.8687 (mt0) cc_final: 0.8440 (mt0) REVERT: J 14 GLN cc_start: 0.9063 (mt0) cc_final: 0.8645 (mt0) REVERT: J 44 MET cc_start: 0.8614 (mpp) cc_final: 0.8244 (mpp) REVERT: J 46 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.6247 (tp30) outliers start: 24 outliers final: 15 residues processed: 215 average time/residue: 1.3037 time to fit residues: 295.8242 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 : 0.831 ------------------------------------------------------------------------------- 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 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 28 ILE 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 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 81 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 ASN ** H 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.088025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.061359 restraints weight = 16265.634| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 2.68 r_work: 0.2698 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8346 Z= 0.159 Angle : 0.736 9.646 11112 Z= 0.365 Chirality : 0.043 0.276 1166 Planarity : 0.005 0.047 1337 Dihedral : 14.515 81.165 1637 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.86 % Allowed : 22.89 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.29), residues: 931 helix: 3.57 (0.28), residues: 319 sheet: 1.07 (0.26), residues: 382 loop : -0.70 (0.44), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 188 HIS 0.002 0.001 HIS I 271 PHE 0.026 0.001 PHE C 67 TYR 0.007 0.001 TYR E 34 ARG 0.016 0.001 ARG I 240 Details of bonding type rmsd hydrogen bonds : bond 0.02940 ( 556) hydrogen bonds : angle 4.02331 ( 1602) covalent geometry : bond 0.00376 ( 8346) covalent geometry : angle 0.73572 (11112) *********************** 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 231 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 208 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 176 MET cc_start: 0.8721 (mtm) cc_final: 0.8439 (mtm) REVERT: B 195 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.8719 (mtm-85) REVERT: B 293 ARG cc_start: 0.9353 (mtp-110) cc_final: 0.8967 (mtp-110) REVERT: B 294 MET cc_start: 0.9335 (mmm) cc_final: 0.8837 (mpm) REVERT: B 319 ASP cc_start: 0.8976 (t0) cc_final: 0.8410 (t0) REVERT: A 37 ASP cc_start: 0.9168 (t0) cc_final: 0.8768 (t0) REVERT: D 16 MET cc_start: 0.9151 (mmm) cc_final: 0.8781 (tpt) REVERT: D 18 ARG cc_start: 0.8592 (ttp80) cc_final: 0.7972 (ttp80) REVERT: D 19 LYS cc_start: 0.9217 (tppp) cc_final: 0.8583 (tppp) REVERT: D 20 MET cc_start: 0.8424 (mtp) cc_final: 0.8036 (mtm) REVERT: D 22 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8101 (pm20) REVERT: D 23 ASP cc_start: 0.8936 (m-30) cc_final: 0.8531 (m-30) REVERT: D 29 ARG cc_start: 0.8943 (ttp-110) cc_final: 0.8741 (ttp80) REVERT: F 40 ASP cc_start: 0.8287 (t70) cc_final: 0.7999 (t0) REVERT: G 10 GLN cc_start: 0.9060 (pm20) cc_final: 0.8513 (pm20) REVERT: G 14 GLN cc_start: 0.8947 (mt0) cc_final: 0.8219 (mm-40) REVERT: G 44 MET cc_start: 0.8527 (mpp) cc_final: 0.8104 (mpp) REVERT: G 46 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6112 (tp30) REVERT: E 15 GLU cc_start: 0.8676 (tp30) cc_final: 0.8206 (tp30) REVERT: E 19 LYS cc_start: 0.9317 (tppp) cc_final: 0.8422 (tppp) REVERT: E 22 GLU cc_start: 0.8638 (pp20) cc_final: 0.8049 (pp20) REVERT: E 23 ASP cc_start: 0.9020 (m-30) cc_final: 0.8544 (m-30) REVERT: I 147 PHE cc_start: 0.6795 (OUTLIER) cc_final: 0.6026 (t80) REVERT: I 173 ARG cc_start: 0.8575 (ttm170) cc_final: 0.8064 (ttm170) REVERT: I 176 MET cc_start: 0.8684 (mtm) cc_final: 0.8472 (mtm) REVERT: I 239 ARG cc_start: 0.8404 (tpt-90) cc_final: 0.8170 (tpp80) REVERT: I 294 MET cc_start: 0.9392 (mpp) cc_final: 0.8975 (mpm) REVERT: H 67 PHE cc_start: 0.8786 (t80) cc_final: 0.8421 (t80) REVERT: H 75 GLN cc_start: 0.8715 (tm-30) cc_final: 0.8245 (tm-30) REVERT: H 76 LYS cc_start: 0.8695 (mmmm) cc_final: 0.8280 (mmmt) REVERT: H 104 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8365 (tp30) REVERT: H 107 GLN cc_start: 0.8431 (tm-30) cc_final: 0.8045 (tm-30) REVERT: H 111 GLN cc_start: 0.8921 (tm-30) cc_final: 0.8597 (tm-30) REVERT: C 75 GLN cc_start: 0.7943 (mm-40) cc_final: 0.7355 (tm-30) REVERT: C 76 LYS cc_start: 0.8647 (mmmm) cc_final: 0.8223 (mmmt) REVERT: C 104 GLU cc_start: 0.8831 (mm-30) cc_final: 0.8385 (tp30) REVERT: C 107 GLN cc_start: 0.8402 (tm-30) cc_final: 0.8024 (tm-30) REVERT: J 13 GLN cc_start: 0.8674 (mt0) cc_final: 0.8412 (mt0) REVERT: J 14 GLN cc_start: 0.9065 (mt0) cc_final: 0.8645 (mt0) REVERT: J 44 MET cc_start: 0.8616 (mpp) cc_final: 0.8267 (mpp) REVERT: J 46 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6249 (tp30) outliers start: 23 outliers final: 17 residues processed: 217 average time/residue: 1.3832 time to fit residues: 317.7177 Evaluate side-chains 226 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 204 time to evaluate : 0.832 ------------------------------------------------------------------------------- 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 26 SER Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 13 GLN 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 147 PHE Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain I residue 204 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 85 optimal weight: 20.0000 chunk 36 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3456 r_free = 0.3456 target = 0.087942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.061392 restraints weight = 15929.595| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 2.66 r_work: 0.2701 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8346 Z= 0.167 Angle : 0.760 10.542 11112 Z= 0.378 Chirality : 0.043 0.267 1166 Planarity : 0.005 0.046 1337 Dihedral : 14.454 81.011 1637 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.86 % Allowed : 23.63 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.29), residues: 931 helix: 3.44 (0.28), residues: 319 sheet: 1.09 (0.26), residues: 382 loop : -0.63 (0.44), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 188 HIS 0.002 0.001 HIS I 271 PHE 0.023 0.001 PHE H 72 TYR 0.008 0.001 TYR F 32 ARG 0.015 0.001 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.02960 ( 556) hydrogen bonds : angle 4.02165 ( 1602) covalent geometry : bond 0.00397 ( 8346) covalent geometry : angle 0.75986 (11112) ********************** 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 229 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 206 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 176 MET cc_start: 0.8719 (mtm) cc_final: 0.8439 (mtm) REVERT: B 195 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.8724 (mtm-85) REVERT: B 293 ARG cc_start: 0.9379 (mtp-110) cc_final: 0.8992 (mtp-110) REVERT: B 294 MET cc_start: 0.9344 (mmm) cc_final: 0.8849 (mpm) REVERT: B 319 ASP cc_start: 0.8953 (t0) cc_final: 0.8395 (t0) REVERT: A 37 ASP cc_start: 0.9168 (t0) cc_final: 0.8776 (t0) REVERT: D 16 MET cc_start: 0.9154 (mmm) cc_final: 0.8774 (tpt) REVERT: D 18 ARG cc_start: 0.8602 (ttp80) cc_final: 0.7981 (ttp80) REVERT: D 19 LYS cc_start: 0.9226 (tppp) cc_final: 0.8600 (tppp) REVERT: D 20 MET cc_start: 0.8433 (mtp) cc_final: 0.8051 (mtm) REVERT: D 22 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8097 (pm20) REVERT: D 23 ASP cc_start: 0.8936 (m-30) cc_final: 0.8535 (m-30) REVERT: D 29 ARG cc_start: 0.8935 (ttp-110) cc_final: 0.8734 (ttp80) REVERT: F 40 ASP cc_start: 0.8275 (t70) cc_final: 0.7960 (t0) REVERT: G 14 GLN cc_start: 0.8951 (mt0) cc_final: 0.8192 (mm-40) REVERT: G 44 MET cc_start: 0.8515 (mpp) cc_final: 0.8087 (mpp) REVERT: G 46 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6110 (tp30) REVERT: E 15 GLU cc_start: 0.8675 (tp30) cc_final: 0.8170 (tp30) REVERT: E 19 LYS cc_start: 0.9309 (tppp) cc_final: 0.8781 (tppp) REVERT: E 22 GLU cc_start: 0.8636 (pp20) cc_final: 0.8148 (pp20) REVERT: E 23 ASP cc_start: 0.9011 (m-30) cc_final: 0.8614 (m-30) REVERT: I 147 PHE cc_start: 0.6743 (OUTLIER) cc_final: 0.6027 (t80) REVERT: I 173 ARG cc_start: 0.8574 (ttm170) cc_final: 0.8072 (ttm170) REVERT: I 176 MET cc_start: 0.8695 (mtm) cc_final: 0.8485 (mtm) REVERT: I 239 ARG cc_start: 0.8426 (tpt-90) cc_final: 0.8177 (tpp80) REVERT: I 240 ARG cc_start: 0.8343 (ttm110) cc_final: 0.8141 (mtm110) REVERT: I 294 MET cc_start: 0.9389 (mpp) cc_final: 0.8977 (mpm) REVERT: H 67 PHE cc_start: 0.8772 (t80) cc_final: 0.8402 (t80) REVERT: H 75 GLN cc_start: 0.8700 (tm-30) cc_final: 0.8245 (tm-30) REVERT: H 76 LYS cc_start: 0.8698 (mmmm) cc_final: 0.8285 (mmmt) REVERT: H 104 GLU cc_start: 0.8820 (mm-30) cc_final: 0.8364 (tp30) REVERT: H 107 GLN cc_start: 0.8440 (tm-30) cc_final: 0.8036 (tm-30) REVERT: H 111 GLN cc_start: 0.8942 (tm-30) cc_final: 0.8546 (tm-30) REVERT: C 75 GLN cc_start: 0.7943 (mm-40) cc_final: 0.7345 (tm-30) REVERT: C 76 LYS cc_start: 0.8644 (mmmm) cc_final: 0.8215 (mmmt) REVERT: C 104 GLU cc_start: 0.8834 (mm-30) cc_final: 0.8392 (tp30) REVERT: C 107 GLN cc_start: 0.8429 (tm-30) cc_final: 0.7990 (tm-30) REVERT: J 13 GLN cc_start: 0.8673 (mt0) cc_final: 0.8177 (mt0) REVERT: J 14 GLN cc_start: 0.9069 (mt0) cc_final: 0.8680 (mt0) REVERT: J 44 MET cc_start: 0.8592 (mpp) cc_final: 0.8245 (mpp) REVERT: J 46 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6258 (tp30) outliers start: 23 outliers final: 17 residues processed: 216 average time/residue: 1.3475 time to fit residues: 307.6528 Evaluate side-chains 224 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 202 time to evaluate : 0.864 ------------------------------------------------------------------------------- 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 26 SER Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 45 LEU 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 23 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 83 optimal weight: 0.7980 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 = 0.3450 r_free = 0.3450 target = 0.087582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.060989 restraints weight = 16235.741| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 2.67 r_work: 0.2687 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2701 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= 0.194 Angle : 0.761 11.652 11112 Z= 0.379 Chirality : 0.044 0.291 1166 Planarity : 0.005 0.048 1337 Dihedral : 14.498 81.003 1637 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.86 % Allowed : 23.51 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.29), residues: 931 helix: 3.42 (0.28), residues: 319 sheet: 1.09 (0.26), residues: 382 loop : -0.65 (0.44), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 188 HIS 0.003 0.001 HIS I 271 PHE 0.028 0.002 PHE C 67 TYR 0.009 0.001 TYR D 34 ARG 0.015 0.001 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.03083 ( 556) hydrogen bonds : angle 4.06126 ( 1602) covalent geometry : bond 0.00458 ( 8346) covalent geometry : angle 0.76132 (11112) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9235.93 seconds wall clock time: 163 minutes 54.68 seconds (9834.68 seconds total)