Starting phenix.real_space_refine on Sun Dec 29 04:52:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vby_31885/12_2024/7vby_31885_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vby_31885/12_2024/7vby_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_31885/12_2024/7vby_31885.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vby_31885/12_2024/7vby_31885.map" model { file = "/net/cci-nas-00/data/ceres_data/7vby_31885/12_2024/7vby_31885_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vby_31885/12_2024/7vby_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-5532/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: 3.36, per 1000 atoms: 0.41 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: 2.48 Conformation dependent library (CDL) restraints added in 922.8 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: 0.86 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: 2.35 Time building geometry restraints manager: 2.65 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: 0.010 Normalize map: mean=0, sd=1: 8.470 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 20.570 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.930 ------------------------------------------------------------------------------- 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= 0.447 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 *********************** 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 : 1.345 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: 1.5062 time to fit residues: 372.0904 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 : 0.952 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8346 Z= 0.241 Angle : 0.703 12.609 11112 Z= 0.352 Chirality : 0.047 0.469 1166 Planarity : 0.005 0.053 1337 Dihedral : 16.199 94.155 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 0.045 0.002 PHE B 147 TYR 0.010 0.001 TYR C 78 ARG 0.013 0.001 ARG I 240 *********************** 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 : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 141 LEU cc_start: 0.9090 (pp) cc_final: 0.8876 (pp) REVERT: B 176 MET cc_start: 0.8064 (mtm) cc_final: 0.7798 (mtm) REVERT: B 309 LYS cc_start: 0.9258 (OUTLIER) cc_final: 0.8974 (mppt) REVERT: B 319 ASP cc_start: 0.8557 (t0) cc_final: 0.8298 (t0) REVERT: B 329 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8045 (mt-10) REVERT: A 33 ARG cc_start: 0.8447 (mpt180) cc_final: 0.8232 (ptp-170) REVERT: A 37 ASP cc_start: 0.9262 (t0) cc_final: 0.8904 (t0) REVERT: D 18 ARG cc_start: 0.8398 (ttp80) cc_final: 0.7974 (ttp80) REVERT: D 19 LYS cc_start: 0.9213 (tppp) cc_final: 0.8648 (tppp) REVERT: D 22 GLU cc_start: 0.8460 (pm20) cc_final: 0.7811 (pm20) REVERT: D 23 ASP cc_start: 0.8808 (m-30) cc_final: 0.8411 (m-30) REVERT: D 34 TYR cc_start: 0.9214 (t80) cc_final: 0.8984 (t80) REVERT: D 38 LEU cc_start: 0.8993 (mp) cc_final: 0.8557 (mp) REVERT: F 40 ASP cc_start: 0.8408 (t70) cc_final: 0.8128 (t0) REVERT: G 46 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.6097 (tp30) REVERT: E 19 LYS cc_start: 0.9337 (tppp) cc_final: 0.8922 (tppp) REVERT: E 22 GLU cc_start: 0.8279 (pp20) cc_final: 0.7802 (pp20) REVERT: E 23 ASP cc_start: 0.8958 (m-30) cc_final: 0.8445 (m-30) REVERT: E 38 LEU cc_start: 0.9018 (mp) cc_final: 0.8608 (mp) REVERT: I 176 MET cc_start: 0.8010 (mtm) cc_final: 0.7780 (mtm) REVERT: I 239 ARG cc_start: 0.8522 (tpt-90) cc_final: 0.8192 (tpp80) REVERT: I 293 ARG cc_start: 0.8834 (mtp-110) cc_final: 0.8626 (ttm110) REVERT: H 67 PHE cc_start: 0.8806 (t80) cc_final: 0.8412 (t80) REVERT: H 75 GLN cc_start: 0.8742 (tm-30) cc_final: 0.8319 (tm-30) REVERT: H 76 LYS cc_start: 0.8895 (mmmm) cc_final: 0.8516 (mmmt) REVERT: H 104 GLU cc_start: 0.8702 (tp30) cc_final: 0.8475 (mm-30) REVERT: H 107 GLN cc_start: 0.8379 (tm-30) cc_final: 0.7996 (tm-30) REVERT: H 110 GLN cc_start: 0.8654 (pp30) cc_final: 0.8424 (pp30) REVERT: H 111 GLN cc_start: 0.8844 (tm-30) cc_final: 0.8539 (pp30) REVERT: C 75 GLN cc_start: 0.8189 (mm-40) cc_final: 0.7580 (tm-30) REVERT: C 76 LYS cc_start: 0.8855 (mmmm) cc_final: 0.8467 (mmmt) REVERT: C 104 GLU cc_start: 0.8698 (tp30) cc_final: 0.8470 (mm-30) REVERT: C 107 GLN cc_start: 0.8324 (tm-30) cc_final: 0.7945 (tm-30) REVERT: J 46 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6365 (tp30) outliers start: 30 outliers final: 10 residues processed: 234 average time/residue: 1.3147 time to fit residues: 325.7963 Evaluate side-chains 224 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 210 time to evaluate : 0.928 ------------------------------------------------------------------------------- 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 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 45 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8346 Z= 0.290 Angle : 0.683 11.281 11112 Z= 0.340 Chirality : 0.045 0.414 1166 Planarity : 0.005 0.048 1337 Dihedral : 15.677 75.968 1639 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 4.23 % Allowed : 16.04 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.34 (0.28), residues: 325 sheet: 0.64 (0.26), residues: 386 loop : -1.05 (0.44), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 27 HIS 0.004 0.001 HIS I 271 PHE 0.028 0.001 PHE I 147 TYR 0.009 0.001 TYR C 78 ARG 0.012 0.001 ARG B 240 *********************** 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 250 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 216 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 147 PHE cc_start: 0.7227 (OUTLIER) cc_final: 0.6901 (m-80) REVERT: B 176 MET cc_start: 0.8067 (mtm) cc_final: 0.7794 (mtm) REVERT: B 195 ARG cc_start: 0.8985 (OUTLIER) cc_final: 0.8617 (mtm-85) REVERT: B 293 ARG cc_start: 0.8634 (ttm110) cc_final: 0.8250 (mtp-110) REVERT: B 319 ASP cc_start: 0.8626 (t0) cc_final: 0.8224 (t0) REVERT: B 329 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8056 (mt-10) REVERT: A 33 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.8056 (ptt-90) REVERT: A 37 ASP cc_start: 0.9302 (t0) cc_final: 0.8886 (t0) REVERT: D 15 GLU cc_start: 0.8773 (pm20) cc_final: 0.7935 (pm20) REVERT: D 18 ARG cc_start: 0.8486 (ttp80) cc_final: 0.7929 (ttp80) REVERT: D 19 LYS cc_start: 0.9213 (tppp) cc_final: 0.8541 (tppp) REVERT: D 21 ARG cc_start: 0.8787 (tpp80) cc_final: 0.8530 (tpp80) REVERT: D 22 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7960 (pm20) REVERT: D 23 ASP cc_start: 0.8766 (m-30) cc_final: 0.8383 (m-30) REVERT: D 29 ARG cc_start: 0.8905 (ttp-110) cc_final: 0.8647 (ttp80) REVERT: F 33 ARG cc_start: 0.8301 (ptt-90) cc_final: 0.8062 (ptt-90) REVERT: F 40 ASP cc_start: 0.8419 (t70) cc_final: 0.8174 (t0) REVERT: G 10 GLN cc_start: 0.8903 (mp10) cc_final: 0.8463 (pm20) REVERT: G 14 GLN cc_start: 0.8908 (mt0) cc_final: 0.8323 (mm-40) REVERT: G 46 GLU cc_start: 0.7008 (OUTLIER) cc_final: 0.6147 (tp30) REVERT: E 19 LYS cc_start: 0.9273 (tppp) cc_final: 0.8776 (tppp) REVERT: E 22 GLU cc_start: 0.8332 (pp20) cc_final: 0.7796 (pp20) REVERT: E 23 ASP cc_start: 0.8920 (m-30) cc_final: 0.8326 (m-30) REVERT: I 96 ILE cc_start: 0.9464 (OUTLIER) cc_final: 0.9193 (pp) REVERT: I 147 PHE cc_start: 0.7230 (OUTLIER) cc_final: 0.6373 (m-80) REVERT: I 173 ARG cc_start: 0.8488 (ttm170) cc_final: 0.8123 (ttm170) REVERT: I 176 MET cc_start: 0.8021 (mtm) cc_final: 0.7781 (mtm) REVERT: I 239 ARG cc_start: 0.8583 (tpt-90) cc_final: 0.8328 (tpp80) REVERT: H 67 PHE cc_start: 0.8824 (t80) cc_final: 0.8400 (t80) REVERT: H 75 GLN cc_start: 0.8779 (tm-30) cc_final: 0.8315 (tm-30) REVERT: H 76 LYS cc_start: 0.8921 (mmmm) cc_final: 0.8503 (mmmt) REVERT: H 104 GLU cc_start: 0.8696 (tp30) cc_final: 0.8482 (mm-30) REVERT: H 107 GLN cc_start: 0.8496 (tm-30) cc_final: 0.8086 (tm-30) REVERT: H 111 GLN cc_start: 0.8830 (tm-30) cc_final: 0.8472 (tm-30) REVERT: C 75 GLN cc_start: 0.8153 (mm-40) cc_final: 0.7709 (tm-30) REVERT: C 76 LYS cc_start: 0.8858 (mmmm) cc_final: 0.8425 (mmmt) REVERT: C 104 GLU cc_start: 0.8693 (tp30) cc_final: 0.8477 (mm-30) REVERT: C 107 GLN cc_start: 0.8376 (tm-30) cc_final: 0.7933 (tm-30) REVERT: C 110 GLN cc_start: 0.8475 (pp30) cc_final: 0.8260 (pp30) REVERT: J 14 GLN cc_start: 0.8928 (mt0) cc_final: 0.8533 (mt0) REVERT: J 46 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6438 (tp30) outliers start: 34 outliers final: 16 residues processed: 228 average time/residue: 1.2958 time to fit residues: 312.4311 Evaluate side-chains 232 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 207 time to evaluate : 0.912 ------------------------------------------------------------------------------- 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 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 28 ILE Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain I residue 76 CYS Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 139 LYS Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain I residue 147 PHE Chi-restraints excluded: chain I residue 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 C 111 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8346 Z= 0.281 Angle : 0.683 11.065 11112 Z= 0.338 Chirality : 0.045 0.371 1166 Planarity : 0.004 0.044 1337 Dihedral : 15.449 78.553 1639 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.60 % Allowed : 17.66 % Favored : 77.74 % 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: 2.01 (0.29), residues: 931 helix: 3.52 (0.28), residues: 319 sheet: 0.77 (0.26), residues: 384 loop : -0.92 (0.44), residues: 228 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 0.027 0.001 PHE B 147 TYR 0.008 0.001 TYR C 78 ARG 0.010 0.001 ARG I 240 *********************** 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 252 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 215 time to evaluate : 1.010 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: 0.9464 (OUTLIER) cc_final: 0.9188 (pp) REVERT: B 176 MET cc_start: 0.8065 (mtm) cc_final: 0.7780 (mtm) REVERT: B 195 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.8624 (mtm-85) REVERT: B 319 ASP cc_start: 0.8662 (t0) cc_final: 0.8184 (t0) REVERT: A 33 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.8096 (ptt-90) REVERT: A 37 ASP cc_start: 0.9304 (t0) cc_final: 0.8895 (t0) REVERT: D 19 LYS cc_start: 0.9179 (tppp) cc_final: 0.8567 (tppp) REVERT: D 21 ARG cc_start: 0.8784 (tpp80) cc_final: 0.8466 (tpp80) REVERT: D 23 ASP cc_start: 0.8744 (m-30) cc_final: 0.8382 (m-30) REVERT: D 29 ARG cc_start: 0.8899 (ttp-110) cc_final: 0.8644 (ttp80) REVERT: F 40 ASP cc_start: 0.8404 (t70) cc_final: 0.8149 (t0) REVERT: G 14 GLN cc_start: 0.8901 (mt0) cc_final: 0.8376 (mm110) REVERT: G 46 GLU cc_start: 0.6979 (OUTLIER) cc_final: 0.6125 (tp30) REVERT: E 19 LYS cc_start: 0.9296 (tppp) cc_final: 0.8839 (tppp) REVERT: E 22 GLU cc_start: 0.8390 (pp20) cc_final: 0.7875 (pp20) REVERT: E 23 ASP cc_start: 0.8933 (m-30) cc_final: 0.8336 (m-30) REVERT: I 96 ILE cc_start: 0.9469 (OUTLIER) cc_final: 0.9199 (pp) REVERT: I 147 PHE cc_start: 0.7097 (OUTLIER) cc_final: 0.6336 (m-80) REVERT: I 176 MET cc_start: 0.8024 (mtm) cc_final: 0.7776 (mtm) REVERT: I 239 ARG cc_start: 0.8598 (tpt-90) cc_final: 0.8324 (tpp80) REVERT: H 67 PHE cc_start: 0.8823 (t80) cc_final: 0.8422 (t80) REVERT: H 75 GLN cc_start: 0.8797 (tm-30) cc_final: 0.8326 (tm-30) REVERT: H 76 LYS cc_start: 0.8930 (mmmm) cc_final: 0.8488 (mmmt) REVERT: H 104 GLU cc_start: 0.8706 (tp30) cc_final: 0.8222 (tp30) REVERT: H 107 GLN cc_start: 0.8529 (tm-30) cc_final: 0.8079 (tm-30) REVERT: H 111 GLN cc_start: 0.8875 (tm-30) cc_final: 0.8493 (tm-30) REVERT: H 115 GLN cc_start: 0.8840 (mm-40) cc_final: 0.8519 (mm-40) REVERT: C 75 GLN cc_start: 0.8165 (mm-40) cc_final: 0.7722 (tm-30) REVERT: C 76 LYS cc_start: 0.8849 (mmmm) cc_final: 0.8391 (mmmt) REVERT: C 104 GLU cc_start: 0.8681 (tp30) cc_final: 0.8232 (tp30) REVERT: C 107 GLN cc_start: 0.8424 (tm-30) cc_final: 0.7951 (tm-30) REVERT: C 110 GLN cc_start: 0.8463 (pp30) cc_final: 0.8251 (pp30) REVERT: J 14 GLN cc_start: 0.8941 (mt0) cc_final: 0.8529 (mt0) REVERT: J 46 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6371 (tp30) outliers start: 37 outliers final: 16 residues processed: 225 average time/residue: 1.2987 time to fit residues: 308.3362 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 : 0.891 ------------------------------------------------------------------------------- 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 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 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 1 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 60 optimal weight: 0.1980 chunk 0 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 ASN C 111 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8346 Z= 0.210 Angle : 0.680 9.874 11112 Z= 0.335 Chirality : 0.043 0.315 1166 Planarity : 0.004 0.042 1337 Dihedral : 15.092 78.369 1637 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.73 % Allowed : 18.91 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 3.49 (0.28), residues: 319 sheet: 0.85 (0.26), residues: 384 loop : -0.79 (0.45), 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 0.029 0.001 PHE I 147 TYR 0.008 0.001 TYR C 78 ARG 0.010 0.001 ARG I 240 *********************** 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 248 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 218 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 176 MET cc_start: 0.8039 (mtm) cc_final: 0.7754 (mtm) REVERT: B 195 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.8621 (mtm-85) REVERT: B 293 ARG cc_start: 0.8666 (ptm-80) cc_final: 0.8303 (ptm-80) REVERT: B 294 MET cc_start: 0.8811 (mmm) cc_final: 0.8475 (mpm) REVERT: B 319 ASP cc_start: 0.8644 (t0) cc_final: 0.8169 (t0) REVERT: A 33 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.8069 (ptt-90) REVERT: A 37 ASP cc_start: 0.9298 (t0) cc_final: 0.8925 (t0) REVERT: D 15 GLU cc_start: 0.8782 (pm20) cc_final: 0.7984 (pm20) REVERT: D 19 LYS cc_start: 0.9213 (tppp) cc_final: 0.8547 (tppp) REVERT: D 20 MET cc_start: 0.8606 (mtp) cc_final: 0.8336 (mtm) REVERT: D 21 ARG cc_start: 0.8785 (tpp80) cc_final: 0.8452 (tpp80) REVERT: D 23 ASP cc_start: 0.8743 (m-30) cc_final: 0.8221 (m-30) REVERT: D 29 ARG cc_start: 0.8888 (ttp-110) cc_final: 0.8643 (ttp80) REVERT: F 33 ARG cc_start: 0.8266 (ptt-90) cc_final: 0.7994 (ptt-90) REVERT: F 40 ASP cc_start: 0.8328 (t70) cc_final: 0.8091 (t0) REVERT: G 9 LYS cc_start: 0.8916 (tmmt) cc_final: 0.8665 (tppp) REVERT: G 10 GLN cc_start: 0.8916 (pm20) cc_final: 0.8682 (pm20) REVERT: G 14 GLN cc_start: 0.8880 (mt0) cc_final: 0.8335 (mm110) REVERT: E 19 LYS cc_start: 0.9263 (tppp) cc_final: 0.8654 (tppp) REVERT: E 22 GLU cc_start: 0.8310 (pp20) cc_final: 0.7820 (pp20) REVERT: E 23 ASP cc_start: 0.8930 (m-30) cc_final: 0.8304 (m-30) REVERT: E 29 ARG cc_start: 0.8850 (ttp-110) cc_final: 0.8613 (ttp80) REVERT: I 176 MET cc_start: 0.8018 (mtm) cc_final: 0.7785 (mtm) REVERT: I 239 ARG cc_start: 0.8544 (tpt-90) cc_final: 0.8282 (tpp80) REVERT: H 67 PHE cc_start: 0.8810 (t80) cc_final: 0.8386 (t80) REVERT: H 72 PHE cc_start: 0.8985 (t80) cc_final: 0.8766 (t80) REVERT: H 75 GLN cc_start: 0.8835 (tm-30) cc_final: 0.8405 (tm-30) REVERT: H 76 LYS cc_start: 0.8938 (mmmm) cc_final: 0.8462 (mmmt) REVERT: H 104 GLU cc_start: 0.8702 (tp30) cc_final: 0.8240 (tp30) REVERT: H 107 GLN cc_start: 0.8504 (tm-30) cc_final: 0.8037 (tm-30) REVERT: H 111 GLN cc_start: 0.8901 (tm-30) cc_final: 0.8539 (tm-30) REVERT: C 75 GLN cc_start: 0.8149 (mm-40) cc_final: 0.7683 (tm-30) REVERT: C 76 LYS cc_start: 0.8840 (mmmm) cc_final: 0.8378 (mmmt) REVERT: C 104 GLU cc_start: 0.8648 (tp30) cc_final: 0.8193 (tp30) REVERT: C 107 GLN cc_start: 0.8416 (tm-30) cc_final: 0.7985 (tm-30) REVERT: C 110 GLN cc_start: 0.8419 (pp30) cc_final: 0.8146 (pp30) REVERT: J 14 GLN cc_start: 0.8941 (mt0) cc_final: 0.8568 (mt0) outliers start: 30 outliers final: 16 residues processed: 227 average time/residue: 1.2980 time to fit residues: 311.3237 Evaluate side-chains 228 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 210 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 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 142 SER Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 280 ASP Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain J residue 50 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 83 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8346 Z= 0.225 Angle : 0.683 9.790 11112 Z= 0.340 Chirality : 0.043 0.296 1166 Planarity : 0.005 0.063 1337 Dihedral : 14.937 79.513 1637 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.48 % Allowed : 19.40 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.13 (0.29), residues: 931 helix: 3.46 (0.28), residues: 319 sheet: 0.90 (0.26), residues: 384 loop : -0.74 (0.45), 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 0.013 0.001 ARG E 18 *********************** 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 242 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 214 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 96 ILE cc_start: 0.9474 (OUTLIER) cc_final: 0.9199 (pp) REVERT: B 176 MET cc_start: 0.8047 (mtm) cc_final: 0.7764 (mtm) REVERT: B 195 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.8624 (mtm-85) REVERT: B 293 ARG cc_start: 0.8681 (ptm-80) cc_final: 0.8416 (ttp80) REVERT: B 319 ASP cc_start: 0.8657 (t0) cc_final: 0.8145 (t0) REVERT: A 37 ASP cc_start: 0.9282 (t0) cc_final: 0.8945 (t0) REVERT: D 19 LYS cc_start: 0.9183 (tppp) cc_final: 0.8509 (tppp) REVERT: D 20 MET cc_start: 0.8652 (mtp) cc_final: 0.8392 (mtm) REVERT: D 21 ARG cc_start: 0.8777 (tpp80) cc_final: 0.8437 (tpp80) REVERT: D 23 ASP cc_start: 0.8738 (m-30) cc_final: 0.8168 (m-30) REVERT: D 29 ARG cc_start: 0.8889 (ttp-110) cc_final: 0.8648 (ttp80) REVERT: F 33 ARG cc_start: 0.8286 (ptt-90) cc_final: 0.7971 (ptt-90) REVERT: F 40 ASP cc_start: 0.8340 (t70) cc_final: 0.8085 (t0) REVERT: G 13 GLN cc_start: 0.8130 (mp10) cc_final: 0.7882 (mp10) REVERT: G 14 GLN cc_start: 0.8879 (mt0) cc_final: 0.8351 (mm110) REVERT: G 46 GLU cc_start: 0.6866 (OUTLIER) cc_final: 0.6006 (tp30) REVERT: E 19 LYS cc_start: 0.9258 (tppp) cc_final: 0.8533 (tppp) REVERT: E 22 GLU cc_start: 0.8377 (pp20) cc_final: 0.7893 (pp20) REVERT: E 23 ASP cc_start: 0.8937 (m-30) cc_final: 0.8299 (m-30) REVERT: E 29 ARG cc_start: 0.8843 (ttp-110) cc_final: 0.8606 (ttp80) REVERT: I 176 MET cc_start: 0.8016 (mtm) cc_final: 0.7777 (mtm) REVERT: I 239 ARG cc_start: 0.8547 (tpt-90) cc_final: 0.8279 (tpp80) REVERT: H 67 PHE cc_start: 0.8816 (t80) cc_final: 0.8393 (t80) REVERT: H 72 PHE cc_start: 0.8972 (t80) cc_final: 0.8741 (t80) REVERT: H 75 GLN cc_start: 0.8826 (tm-30) cc_final: 0.8399 (tm-30) REVERT: H 76 LYS cc_start: 0.8946 (mmmm) cc_final: 0.8442 (mmmt) REVERT: H 104 GLU cc_start: 0.8698 (tp30) cc_final: 0.8246 (tp30) REVERT: H 107 GLN cc_start: 0.8500 (tm-30) cc_final: 0.8015 (tm-30) REVERT: H 111 GLN cc_start: 0.8912 (tm-30) cc_final: 0.8679 (tm-30) REVERT: C 75 GLN cc_start: 0.8103 (mm-40) cc_final: 0.7524 (tm-30) REVERT: C 76 LYS cc_start: 0.8841 (mmmm) cc_final: 0.8385 (mmmt) REVERT: C 104 GLU cc_start: 0.8646 (tp30) cc_final: 0.8223 (tp30) REVERT: C 107 GLN cc_start: 0.8485 (tm-30) cc_final: 0.7924 (tm-30) REVERT: C 110 GLN cc_start: 0.8385 (pp30) cc_final: 0.8151 (pp30) REVERT: J 9 LYS cc_start: 0.8763 (mptt) cc_final: 0.8231 (mptt) REVERT: J 13 GLN cc_start: 0.8567 (mt0) cc_final: 0.8065 (mt0) REVERT: J 14 GLN cc_start: 0.8952 (mt0) cc_final: 0.8582 (mt0) REVERT: J 46 GLU cc_start: 0.7069 (OUTLIER) cc_final: 0.6192 (tp30) outliers start: 28 outliers final: 18 residues processed: 223 average time/residue: 1.3171 time to fit residues: 309.9665 Evaluate side-chains 229 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 207 time to evaluate : 0.963 ------------------------------------------------------------------------------- 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 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 F residue 66 ASP Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2420 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= 0.251 Angle : 0.708 9.473 11112 Z= 0.349 Chirality : 0.043 0.277 1166 Planarity : 0.005 0.056 1337 Dihedral : 14.855 81.885 1637 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.86 % Allowed : 20.27 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 2.14 (0.29), residues: 931 helix: 3.42 (0.28), residues: 319 sheet: 0.94 (0.26), residues: 384 loop : -0.73 (0.45), 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 0.032 0.001 PHE I 147 TYR 0.008 0.001 TYR E 34 ARG 0.012 0.001 ARG E 18 *********************** 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 242 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 211 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 176 MET cc_start: 0.8060 (mtm) cc_final: 0.7776 (mtm) REVERT: B 195 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.8644 (mtm-85) REVERT: B 293 ARG cc_start: 0.8639 (ptm-80) cc_final: 0.8169 (ppp80) REVERT: B 319 ASP cc_start: 0.8696 (t0) cc_final: 0.8184 (t0) REVERT: A 33 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.8075 (ptt-90) REVERT: A 37 ASP cc_start: 0.9290 (t0) cc_final: 0.8955 (t0) REVERT: D 19 LYS cc_start: 0.9176 (tppp) cc_final: 0.8391 (tppp) REVERT: D 20 MET cc_start: 0.8622 (mtp) cc_final: 0.8362 (mtm) REVERT: D 22 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8215 (pm20) REVERT: D 23 ASP cc_start: 0.8766 (m-30) cc_final: 0.8255 (m-30) REVERT: D 29 ARG cc_start: 0.8887 (ttp-110) cc_final: 0.8647 (ttp80) REVERT: F 33 ARG cc_start: 0.8273 (ptt-90) cc_final: 0.7961 (ptt-90) REVERT: F 40 ASP cc_start: 0.8342 (t70) cc_final: 0.8094 (t0) REVERT: G 9 LYS cc_start: 0.8904 (tmmt) cc_final: 0.8632 (tppp) REVERT: G 10 GLN cc_start: 0.8838 (pm20) cc_final: 0.8590 (pm20) REVERT: G 14 GLN cc_start: 0.8862 (mt0) cc_final: 0.8312 (mm110) REVERT: G 46 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6098 (tp30) REVERT: E 15 GLU cc_start: 0.7669 (tp30) cc_final: 0.7323 (tp30) REVERT: E 19 LYS cc_start: 0.9259 (tppp) cc_final: 0.8513 (tppp) REVERT: E 22 GLU cc_start: 0.8401 (pp20) cc_final: 0.7917 (pp20) REVERT: E 23 ASP cc_start: 0.8966 (m-30) cc_final: 0.8342 (m-30) REVERT: E 38 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8905 (mp) REVERT: I 96 ILE cc_start: 0.9487 (OUTLIER) cc_final: 0.9217 (pp) REVERT: I 176 MET cc_start: 0.8033 (mtm) cc_final: 0.7786 (mtm) REVERT: I 239 ARG cc_start: 0.8577 (tpt-90) cc_final: 0.8312 (tpp80) REVERT: H 67 PHE cc_start: 0.8841 (t80) cc_final: 0.8431 (t80) REVERT: H 72 PHE cc_start: 0.8974 (t80) cc_final: 0.8724 (t80) REVERT: H 75 GLN cc_start: 0.8823 (tm-30) cc_final: 0.8343 (tm-30) REVERT: H 76 LYS cc_start: 0.8950 (mmmm) cc_final: 0.8436 (mmmt) REVERT: H 104 GLU cc_start: 0.8705 (tp30) cc_final: 0.8257 (tp30) REVERT: H 107 GLN cc_start: 0.8509 (tm-30) cc_final: 0.8027 (tm-30) REVERT: H 111 GLN cc_start: 0.8927 (tm-30) cc_final: 0.8708 (tm-30) REVERT: C 75 GLN cc_start: 0.8121 (mm-40) cc_final: 0.7704 (tm-30) REVERT: C 76 LYS cc_start: 0.8851 (mmmm) cc_final: 0.8375 (mmmt) REVERT: C 104 GLU cc_start: 0.8656 (tp30) cc_final: 0.8237 (tp30) REVERT: C 107 GLN cc_start: 0.8450 (tm-30) cc_final: 0.8000 (tm-30) REVERT: C 110 GLN cc_start: 0.8392 (pp30) cc_final: 0.8147 (pp30) REVERT: C 115 GLN cc_start: 0.9365 (tm-30) cc_final: 0.9134 (pp30) REVERT: J 9 LYS cc_start: 0.8797 (mptt) cc_final: 0.8576 (mptt) REVERT: J 13 GLN cc_start: 0.8562 (mt0) cc_final: 0.8280 (mt0) REVERT: J 14 GLN cc_start: 0.8960 (mt0) cc_final: 0.8593 (mt0) REVERT: J 46 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6235 (tp30) outliers start: 31 outliers final: 16 residues processed: 222 average time/residue: 1.3771 time to fit residues: 322.7789 Evaluate side-chains 228 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 205 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain F residue 66 ASP Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain I residue 76 CYS Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain I residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 8 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 75 optimal weight: 20.0000 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 ASN I 267 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8346 Z= 0.246 Angle : 0.731 9.521 11112 Z= 0.361 Chirality : 0.043 0.266 1166 Planarity : 0.005 0.044 1337 Dihedral : 14.757 81.023 1637 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.48 % Allowed : 21.64 % Favored : 74.88 % 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: 2.13 (0.29), residues: 931 helix: 3.35 (0.28), residues: 319 sheet: 0.97 (0.26), residues: 384 loop : -0.70 (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 0.027 0.001 PHE I 147 TYR 0.008 0.001 TYR E 34 ARG 0.015 0.001 ARG I 240 *********************** 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 243 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 215 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 GLU cc_start: 0.8094 (pp20) cc_final: 0.7886 (pp20) REVERT: B 176 MET cc_start: 0.8064 (mtm) cc_final: 0.7783 (mtm) REVERT: B 195 ARG cc_start: 0.8981 (OUTLIER) cc_final: 0.8644 (mtm-85) REVERT: B 293 ARG cc_start: 0.8639 (ptm-80) cc_final: 0.8169 (ppp80) REVERT: B 319 ASP cc_start: 0.8667 (t0) cc_final: 0.8180 (t0) REVERT: A 33 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.8099 (ptt-90) REVERT: A 37 ASP cc_start: 0.9285 (t0) cc_final: 0.8976 (t0) REVERT: D 19 LYS cc_start: 0.9175 (tppp) cc_final: 0.8447 (tppp) REVERT: D 20 MET cc_start: 0.8606 (mtp) cc_final: 0.8394 (mtm) REVERT: D 23 ASP cc_start: 0.8759 (m-30) cc_final: 0.8228 (m-30) REVERT: D 29 ARG cc_start: 0.8882 (ttp-110) cc_final: 0.8646 (ttp80) REVERT: F 33 ARG cc_start: 0.8273 (ptt-90) cc_final: 0.7955 (ptt-90) REVERT: F 40 ASP cc_start: 0.8377 (t70) cc_final: 0.8125 (t0) REVERT: G 14 GLN cc_start: 0.8869 (mt0) cc_final: 0.8378 (mm110) REVERT: G 46 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6085 (tp30) REVERT: E 19 LYS cc_start: 0.9314 (tppp) cc_final: 0.8641 (tppp) REVERT: E 22 GLU cc_start: 0.8410 (pp20) cc_final: 0.7894 (pp20) REVERT: E 23 ASP cc_start: 0.8960 (m-30) cc_final: 0.8347 (m-30) REVERT: E 38 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8916 (mp) REVERT: I 173 ARG cc_start: 0.8305 (ttm170) cc_final: 0.7362 (ttm170) REVERT: I 176 MET cc_start: 0.8036 (mtm) cc_final: 0.7799 (mtm) REVERT: I 239 ARG cc_start: 0.8544 (tpt-90) cc_final: 0.8278 (tpp80) REVERT: H 67 PHE cc_start: 0.8846 (t80) cc_final: 0.8437 (t80) REVERT: H 72 PHE cc_start: 0.8970 (t80) cc_final: 0.8741 (t80) REVERT: H 75 GLN cc_start: 0.8826 (tm-30) cc_final: 0.8360 (tm-30) REVERT: H 76 LYS cc_start: 0.8951 (mmmm) cc_final: 0.8461 (mmmt) REVERT: H 104 GLU cc_start: 0.8702 (tp30) cc_final: 0.8258 (tp30) REVERT: H 107 GLN cc_start: 0.8519 (tm-30) cc_final: 0.8068 (tm-30) REVERT: H 111 GLN cc_start: 0.8922 (tm-30) cc_final: 0.8556 (tm-30) REVERT: H 115 GLN cc_start: 0.8800 (mm-40) cc_final: 0.8401 (mm-40) REVERT: C 75 GLN cc_start: 0.8088 (mm-40) cc_final: 0.7573 (tm-30) REVERT: C 76 LYS cc_start: 0.8846 (mmmm) cc_final: 0.8383 (mmmt) REVERT: C 104 GLU cc_start: 0.8651 (tp30) cc_final: 0.8052 (tp30) REVERT: C 107 GLN cc_start: 0.8516 (tm-30) cc_final: 0.8011 (tm-30) REVERT: C 110 GLN cc_start: 0.8392 (pp30) cc_final: 0.8155 (pp30) REVERT: C 115 GLN cc_start: 0.9346 (tm-30) cc_final: 0.9137 (pp30) REVERT: J 9 LYS cc_start: 0.8786 (mptt) cc_final: 0.8171 (mptt) REVERT: J 10 GLN cc_start: 0.8852 (pm20) cc_final: 0.8535 (pm20) REVERT: J 13 GLN cc_start: 0.8558 (mt0) cc_final: 0.8006 (mt0) REVERT: J 14 GLN cc_start: 0.8963 (mt0) cc_final: 0.8580 (mt0) REVERT: J 46 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6224 (tp30) outliers start: 28 outliers final: 16 residues processed: 225 average time/residue: 1.3315 time to fit residues: 316.6689 Evaluate side-chains 227 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 206 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain F residue 66 ASP Chi-restraints excluded: chain G residue 12 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 E residue 38 LEU Chi-restraints excluded: chain I residue 76 CYS Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 286 VAL Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 50 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 8.9990 chunk 83 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 35 optimal weight: 0.0970 chunk 63 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 85 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 267 GLN F 39 ASN I 267 GLN ** H 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8346 Z= 0.204 Angle : 0.747 9.821 11112 Z= 0.367 Chirality : 0.043 0.271 1166 Planarity : 0.004 0.041 1337 Dihedral : 14.540 80.356 1637 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.61 % Allowed : 22.76 % 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: 2.14 (0.29), residues: 931 helix: 3.31 (0.28), residues: 319 sheet: 1.03 (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 130 PHE 0.023 0.001 PHE I 147 TYR 0.007 0.001 TYR C 78 ARG 0.014 0.001 ARG E 18 *********************** 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: 21 poor density : 210 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 176 MET cc_start: 0.8059 (mtm) cc_final: 0.7776 (mtm) REVERT: B 195 ARG cc_start: 0.8965 (OUTLIER) cc_final: 0.8631 (mtm-85) REVERT: B 293 ARG cc_start: 0.8640 (ptm-80) cc_final: 0.8175 (ppp80) REVERT: B 319 ASP cc_start: 0.8608 (t0) cc_final: 0.8202 (t0) REVERT: A 37 ASP cc_start: 0.9286 (t0) cc_final: 0.8994 (t0) REVERT: D 19 LYS cc_start: 0.9169 (tppp) cc_final: 0.8473 (tppp) REVERT: D 23 ASP cc_start: 0.8762 (m-30) cc_final: 0.8232 (m-30) REVERT: D 29 ARG cc_start: 0.8875 (ttp-110) cc_final: 0.8645 (ttp80) REVERT: F 40 ASP cc_start: 0.8303 (t70) cc_final: 0.8031 (t0) REVERT: G 9 LYS cc_start: 0.8894 (tppp) cc_final: 0.8608 (tmmt) REVERT: G 14 GLN cc_start: 0.8848 (mt0) cc_final: 0.8604 (mt0) REVERT: G 46 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6066 (tp30) REVERT: E 19 LYS cc_start: 0.9278 (tppp) cc_final: 0.8605 (tppp) REVERT: E 22 GLU cc_start: 0.8397 (pp20) cc_final: 0.7933 (pp20) REVERT: E 23 ASP cc_start: 0.8961 (m-30) cc_final: 0.8318 (m-30) REVERT: E 29 ARG cc_start: 0.8826 (ttp-110) cc_final: 0.8596 (ttp80) REVERT: E 38 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8917 (mp) REVERT: I 173 ARG cc_start: 0.8288 (ttm170) cc_final: 0.8032 (ttm170) REVERT: I 176 MET cc_start: 0.8018 (mtm) cc_final: 0.7779 (mtm) REVERT: I 239 ARG cc_start: 0.8539 (tpt-90) cc_final: 0.8272 (tpp80) REVERT: H 67 PHE cc_start: 0.8828 (t80) cc_final: 0.8421 (t80) REVERT: H 72 PHE cc_start: 0.8955 (t80) cc_final: 0.8748 (t80) REVERT: H 75 GLN cc_start: 0.8820 (tm-30) cc_final: 0.8346 (tm-30) REVERT: H 76 LYS cc_start: 0.8945 (mmmm) cc_final: 0.8458 (mmmt) REVERT: H 104 GLU cc_start: 0.8686 (tp30) cc_final: 0.8038 (tp30) REVERT: H 107 GLN cc_start: 0.8517 (tm-30) cc_final: 0.8049 (tm-30) REVERT: H 111 GLN cc_start: 0.8911 (tm-30) cc_final: 0.8650 (tm-30) REVERT: H 115 GLN cc_start: 0.8831 (mm-40) cc_final: 0.8604 (mm-40) REVERT: C 75 GLN cc_start: 0.8082 (mm-40) cc_final: 0.7547 (tm-30) REVERT: C 76 LYS cc_start: 0.8843 (mmmm) cc_final: 0.8386 (mmmt) REVERT: C 104 GLU cc_start: 0.8639 (tp30) cc_final: 0.8029 (tp30) REVERT: C 107 GLN cc_start: 0.8518 (tm-30) cc_final: 0.8014 (tm-30) REVERT: C 110 GLN cc_start: 0.8383 (pp30) cc_final: 0.8153 (pp30) REVERT: J 9 LYS cc_start: 0.8738 (mptt) cc_final: 0.8161 (mptt) REVERT: J 10 GLN cc_start: 0.8845 (pm20) cc_final: 0.8590 (pm20) REVERT: J 13 GLN cc_start: 0.8570 (mt0) cc_final: 0.8029 (mt0) REVERT: J 14 GLN cc_start: 0.8946 (mt0) cc_final: 0.8572 (mt0) REVERT: J 46 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6301 (tp30) outliers start: 21 outliers final: 15 residues processed: 219 average time/residue: 1.3227 time to fit residues: 305.9119 Evaluate side-chains 223 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 204 time to evaluate : 0.810 ------------------------------------------------------------------------------- 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 28 ILE Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain 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 204 THR Chi-restraints excluded: chain I residue 280 ASP Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 50 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 ASN ** G 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8346 Z= 0.237 Angle : 0.787 14.737 11112 Z= 0.390 Chirality : 0.043 0.258 1166 Planarity : 0.005 0.067 1337 Dihedral : 14.494 80.814 1637 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.49 % Allowed : 22.76 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.16 (0.29), residues: 931 helix: 3.27 (0.28), residues: 319 sheet: 1.06 (0.26), residues: 382 loop : -0.65 (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 E 34 ARG 0.016 0.001 ARG I 240 ********************** 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 226 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 206 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 176 MET cc_start: 0.8065 (mtm) cc_final: 0.7784 (mtm) REVERT: B 195 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.8637 (mtm-85) REVERT: B 293 ARG cc_start: 0.8646 (ptm-80) cc_final: 0.8176 (ppp80) REVERT: B 319 ASP cc_start: 0.8627 (t0) cc_final: 0.8221 (t0) REVERT: A 37 ASP cc_start: 0.9287 (t0) cc_final: 0.8997 (t0) REVERT: D 19 LYS cc_start: 0.9147 (tppp) cc_final: 0.8406 (tppp) REVERT: D 23 ASP cc_start: 0.8760 (m-30) cc_final: 0.8327 (m-30) REVERT: D 29 ARG cc_start: 0.8877 (ttp-110) cc_final: 0.8647 (ttp80) REVERT: F 40 ASP cc_start: 0.8334 (t70) cc_final: 0.8058 (t0) REVERT: G 14 GLN cc_start: 0.8851 (mt0) cc_final: 0.8592 (mt0) REVERT: G 46 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6097 (tp30) REVERT: E 19 LYS cc_start: 0.9292 (tppp) cc_final: 0.8453 (tppp) REVERT: E 22 GLU cc_start: 0.8414 (pp20) cc_final: 0.8104 (pp20) REVERT: E 23 ASP cc_start: 0.8965 (m-30) cc_final: 0.8311 (m-30) REVERT: E 29 ARG cc_start: 0.8836 (ttp-110) cc_final: 0.8606 (ttp80) REVERT: E 38 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8927 (mp) REVERT: I 173 ARG cc_start: 0.8288 (ttm170) cc_final: 0.7545 (ttm170) REVERT: I 176 MET cc_start: 0.8042 (mtm) cc_final: 0.7804 (mtm) REVERT: I 239 ARG cc_start: 0.8532 (tpt-90) cc_final: 0.8277 (tpp80) REVERT: I 240 ARG cc_start: 0.8061 (mtm110) cc_final: 0.7824 (mtm110) REVERT: H 67 PHE cc_start: 0.8841 (t80) cc_final: 0.8436 (t80) REVERT: H 72 PHE cc_start: 0.8973 (t80) cc_final: 0.8745 (t80) REVERT: H 75 GLN cc_start: 0.8815 (tm-30) cc_final: 0.8346 (tm-30) REVERT: H 76 LYS cc_start: 0.8946 (mmmm) cc_final: 0.8460 (mmmt) REVERT: H 104 GLU cc_start: 0.8679 (tp30) cc_final: 0.8050 (tp30) REVERT: H 107 GLN cc_start: 0.8498 (tm-30) cc_final: 0.8086 (tm-30) REVERT: H 111 GLN cc_start: 0.8916 (tm-30) cc_final: 0.8605 (tm-30) REVERT: C 75 GLN cc_start: 0.8076 (mm-40) cc_final: 0.7555 (tm-30) REVERT: C 76 LYS cc_start: 0.8847 (mmmm) cc_final: 0.8376 (mmmt) REVERT: C 104 GLU cc_start: 0.8641 (tp30) cc_final: 0.8041 (tp30) REVERT: C 107 GLN cc_start: 0.8523 (tm-30) cc_final: 0.8016 (tm-30) REVERT: C 110 GLN cc_start: 0.8387 (pp30) cc_final: 0.8167 (pp30) REVERT: C 112 GLN cc_start: 0.9220 (tt0) cc_final: 0.9009 (tm-30) REVERT: J 9 LYS cc_start: 0.8761 (mptt) cc_final: 0.8191 (mptt) REVERT: J 10 GLN cc_start: 0.8825 (pm20) cc_final: 0.8605 (pm20) REVERT: J 13 GLN cc_start: 0.8570 (mt0) cc_final: 0.8029 (mt0) REVERT: J 14 GLN cc_start: 0.8942 (mt0) cc_final: 0.8571 (mt0) REVERT: J 46 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6383 (tp30) outliers start: 20 outliers final: 16 residues processed: 214 average time/residue: 1.3180 time to fit residues: 297.8812 Evaluate side-chains 224 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 204 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain I residue 76 CYS Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain I residue 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3470 r_free = 0.3470 target = 0.088550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.061844 restraints weight = 15862.855| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 2.67 r_work: 0.2715 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8346 Z= 0.222 Angle : 0.772 11.435 11112 Z= 0.381 Chirality : 0.043 0.241 1166 Planarity : 0.004 0.047 1337 Dihedral : 14.371 81.126 1637 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.49 % Allowed : 22.26 % Favored : 75.25 % 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: 2.18 (0.29), residues: 931 helix: 3.26 (0.28), residues: 319 sheet: 1.07 (0.26), residues: 382 loop : -0.59 (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 276 PHE 0.021 0.001 PHE B 147 TYR 0.008 0.001 TYR E 34 ARG 0.016 0.001 ARG I 240 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4847.58 seconds wall clock time: 86 minutes 57.70 seconds (5217.70 seconds total)