Starting phenix.real_space_refine on Tue Feb 11 17:48:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w6k_32328/02_2025/7w6k_32328.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w6k_32328/02_2025/7w6k_32328.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7w6k_32328/02_2025/7w6k_32328.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w6k_32328/02_2025/7w6k_32328.map" model { file = "/net/cci-nas-00/data/ceres_data/7w6k_32328/02_2025/7w6k_32328.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w6k_32328/02_2025/7w6k_32328.cif" } resolution = 3.5 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= 0.002 sd= 0.041 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: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 4202 2.51 5 N 1094 2.21 5 O 1142 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6468 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3234 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 14, 'TRANS': 395} Chain breaks: 1 Restraints were copied for chains: B Time building chain proxies: 4.79, per 1000 atoms: 0.74 Number of scatterers: 6468 At special positions: 0 Unit cell: (74.88, 92.56, 107.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 1142 8.00 N 1094 7.00 C 4202 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 995.0 milliseconds 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1544 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 0 sheets defined 82.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 37 through 54 removed outlier: 4.668A pdb=" N ASN A 41 " --> pdb=" O MET A 37 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TRP A 44 " --> pdb=" O PRO A 40 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLN A 45 " --> pdb=" O ASN A 41 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 50 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 73 Processing helix chain 'A' and resid 73 through 78 removed outlier: 3.578A pdb=" N LEU A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 73 through 78' Processing helix chain 'A' and resid 80 through 86 removed outlier: 4.036A pdb=" N ILE A 84 " --> pdb=" O PHE A 81 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N GLY A 85 " --> pdb=" O LYS A 82 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N GLN A 86 " --> pdb=" O GLY A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 99 removed outlier: 4.137A pdb=" N ALA A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 131 removed outlier: 4.097A pdb=" N GLY A 110 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 160 Processing helix chain 'A' and resid 160 through 165 removed outlier: 4.614A pdb=" N LYS A 165 " --> pdb=" O PRO A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 188 removed outlier: 3.632A pdb=" N PHE A 174 " --> pdb=" O GLY A 170 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ARG A 187 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 188 " --> pdb=" O SER A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 215 removed outlier: 3.864A pdb=" N LYS A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N TYR A 200 " --> pdb=" O HIS A 196 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N THR A 201 " --> pdb=" O ASP A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 249 Processing helix chain 'A' and resid 259 through 262 Processing helix chain 'A' and resid 263 through 288 removed outlier: 4.775A pdb=" N ALA A 271 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL A 272 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N LYS A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N SER A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ILE A 278 " --> pdb=" O ASP A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 325 Processing helix chain 'A' and resid 332 through 338 removed outlier: 3.911A pdb=" N MET A 338 " --> pdb=" O SER A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 363 removed outlier: 3.776A pdb=" N ILE A 344 " --> pdb=" O LYS A 340 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG A 345 " --> pdb=" O ASP A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 389 Processing helix chain 'A' and resid 459 through 468 removed outlier: 3.812A pdb=" N ILE A 463 " --> pdb=" O GLN A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 504 removed outlier: 4.012A pdb=" N ASP A 491 " --> pdb=" O VAL A 487 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU A 492 " --> pdb=" O ALA A 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 54 removed outlier: 4.668A pdb=" N ASN B 41 " --> pdb=" O MET B 37 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TRP B 44 " --> pdb=" O PRO B 40 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLN B 45 " --> pdb=" O ASN B 41 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL B 50 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 73 Processing helix chain 'B' and resid 73 through 78 removed outlier: 3.578A pdb=" N LEU B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 73 through 78' Processing helix chain 'B' and resid 80 through 86 removed outlier: 4.037A pdb=" N ILE B 84 " --> pdb=" O PHE B 81 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N GLY B 85 " --> pdb=" O LYS B 82 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N GLN B 86 " --> pdb=" O GLY B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 99 removed outlier: 4.137A pdb=" N ALA B 91 " --> pdb=" O SER B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 131 removed outlier: 4.096A pdb=" N GLY B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 160 Processing helix chain 'B' and resid 160 through 165 removed outlier: 4.614A pdb=" N LYS B 165 " --> pdb=" O PRO B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 188 removed outlier: 3.632A pdb=" N PHE B 174 " --> pdb=" O GLY B 170 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER B 184 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ARG B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU B 188 " --> pdb=" O SER B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 215 removed outlier: 3.864A pdb=" N LYS B 193 " --> pdb=" O GLU B 189 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N TYR B 200 " --> pdb=" O HIS B 196 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N THR B 201 " --> pdb=" O ASP B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 249 Processing helix chain 'B' and resid 259 through 262 Processing helix chain 'B' and resid 263 through 288 removed outlier: 4.775A pdb=" N ALA B 271 " --> pdb=" O LYS B 267 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL B 272 " --> pdb=" O GLY B 268 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N LYS B 276 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N SER B 277 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ILE B 278 " --> pdb=" O ASP B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 325 Processing helix chain 'B' and resid 332 through 338 removed outlier: 3.910A pdb=" N MET B 338 " --> pdb=" O SER B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 363 removed outlier: 3.776A pdb=" N ILE B 344 " --> pdb=" O LYS B 340 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG B 345 " --> pdb=" O ASP B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 389 Processing helix chain 'B' and resid 459 through 468 removed outlier: 3.812A pdb=" N ILE B 463 " --> pdb=" O GLN B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 504 removed outlier: 4.012A pdb=" N ASP B 491 " --> pdb=" O VAL B 487 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU B 492 " --> pdb=" O ALA B 488 " (cutoff:3.500A) 466 hydrogen bonds defined for protein. 1386 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.74 Time building geometry restraints manager: 1.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1300 1.33 - 1.45: 1511 1.45 - 1.57: 3755 1.57 - 1.69: 0 1.69 - 1.82: 42 Bond restraints: 6608 Sorted by residual: bond pdb=" CA SER B 358 " pdb=" CB SER B 358 " ideal model delta sigma weight residual 1.528 1.466 0.063 1.56e-02 4.11e+03 1.62e+01 bond pdb=" CA SER A 358 " pdb=" CB SER A 358 " ideal model delta sigma weight residual 1.528 1.466 0.063 1.56e-02 4.11e+03 1.61e+01 bond pdb=" CA SER B 360 " pdb=" CB SER B 360 " ideal model delta sigma weight residual 1.529 1.470 0.059 1.58e-02 4.01e+03 1.40e+01 bond pdb=" N PRO A 369 " pdb=" CD PRO A 369 " ideal model delta sigma weight residual 1.473 1.525 -0.052 1.40e-02 5.10e+03 1.39e+01 bond pdb=" N PRO B 369 " pdb=" CD PRO B 369 " ideal model delta sigma weight residual 1.473 1.525 -0.052 1.40e-02 5.10e+03 1.39e+01 ... (remaining 6603 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 8196 1.85 - 3.70: 581 3.70 - 5.54: 143 5.54 - 7.39: 32 7.39 - 9.24: 10 Bond angle restraints: 8962 Sorted by residual: angle pdb=" N ILE B 252 " pdb=" CA ILE B 252 " pdb=" C ILE B 252 " ideal model delta sigma weight residual 108.35 99.46 8.89 1.32e+00 5.74e-01 4.54e+01 angle pdb=" N ILE A 252 " pdb=" CA ILE A 252 " pdb=" C ILE A 252 " ideal model delta sigma weight residual 108.35 99.46 8.89 1.32e+00 5.74e-01 4.53e+01 angle pdb=" N PHE B 470 " pdb=" CA PHE B 470 " pdb=" C PHE B 470 " ideal model delta sigma weight residual 110.23 100.99 9.24 1.45e+00 4.76e-01 4.06e+01 angle pdb=" N PHE A 470 " pdb=" CA PHE A 470 " pdb=" C PHE A 470 " ideal model delta sigma weight residual 110.23 100.99 9.24 1.45e+00 4.76e-01 4.06e+01 angle pdb=" N GLY A 114 " pdb=" CA GLY A 114 " pdb=" C GLY A 114 " ideal model delta sigma weight residual 112.50 119.17 -6.67 1.16e+00 7.43e-01 3.30e+01 ... (remaining 8957 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 3484 17.73 - 35.45: 374 35.45 - 53.18: 68 53.18 - 70.90: 6 70.90 - 88.63: 4 Dihedral angle restraints: 3936 sinusoidal: 1542 harmonic: 2394 Sorted by residual: dihedral pdb=" C PHE B 248 " pdb=" N PHE B 248 " pdb=" CA PHE B 248 " pdb=" CB PHE B 248 " ideal model delta harmonic sigma weight residual -122.60 -134.88 12.28 0 2.50e+00 1.60e-01 2.41e+01 dihedral pdb=" C PHE A 248 " pdb=" N PHE A 248 " pdb=" CA PHE A 248 " pdb=" CB PHE A 248 " ideal model delta harmonic sigma weight residual -122.60 -134.86 12.26 0 2.50e+00 1.60e-01 2.40e+01 dihedral pdb=" C TYR A 257 " pdb=" N TYR A 257 " pdb=" CA TYR A 257 " pdb=" CB TYR A 257 " ideal model delta harmonic sigma weight residual -122.60 -134.00 11.40 0 2.50e+00 1.60e-01 2.08e+01 ... (remaining 3933 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 924 0.086 - 0.172: 78 0.172 - 0.259: 30 0.259 - 0.345: 8 0.345 - 0.431: 4 Chirality restraints: 1044 Sorted by residual: chirality pdb=" CA PHE B 248 " pdb=" N PHE B 248 " pdb=" C PHE B 248 " pdb=" CB PHE B 248 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" CA PHE A 248 " pdb=" N PHE A 248 " pdb=" C PHE A 248 " pdb=" CB PHE A 248 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" CA TYR A 257 " pdb=" N TYR A 257 " pdb=" C TYR A 257 " pdb=" CB TYR A 257 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.04e+00 ... (remaining 1041 not shown) Planarity restraints: 1112 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 161 " 0.020 2.00e-02 2.50e+03 4.07e-02 1.65e+01 pdb=" C PRO A 161 " -0.070 2.00e-02 2.50e+03 pdb=" O PRO A 161 " 0.026 2.00e-02 2.50e+03 pdb=" N TYR A 162 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 161 " 0.020 2.00e-02 2.50e+03 4.06e-02 1.65e+01 pdb=" C PRO B 161 " -0.070 2.00e-02 2.50e+03 pdb=" O PRO B 161 " 0.026 2.00e-02 2.50e+03 pdb=" N TYR B 162 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 163 " -0.018 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C ILE B 163 " 0.063 2.00e-02 2.50e+03 pdb=" O ILE B 163 " -0.023 2.00e-02 2.50e+03 pdb=" N LYS B 164 " -0.022 2.00e-02 2.50e+03 ... (remaining 1109 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 2519 2.85 - 3.36: 7355 3.36 - 3.87: 10787 3.87 - 4.39: 12544 4.39 - 4.90: 19461 Nonbonded interactions: 52666 Sorted by model distance: nonbonded pdb=" N SER A 221 " pdb=" OE2 GLU A 289 " model vdw 2.337 3.120 nonbonded pdb=" N SER B 221 " pdb=" OE2 GLU B 289 " model vdw 2.338 3.120 nonbonded pdb=" OD1 ASP A 135 " pdb=" OG SER A 138 " model vdw 2.360 3.040 nonbonded pdb=" OD1 ASP B 135 " pdb=" OG SER B 138 " model vdw 2.360 3.040 nonbonded pdb=" NZ LYS B 232 " pdb=" OD1 ASP B 279 " model vdw 2.366 3.120 ... (remaining 52661 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.370 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 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 0.063 6608 Z= 0.479 Angle : 1.134 9.238 8962 Z= 0.794 Chirality : 0.069 0.431 1044 Planarity : 0.006 0.041 1112 Dihedral : 14.610 88.630 2392 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 47.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 2.01 % Allowed : 10.06 % Favored : 87.93 % Cbeta Deviations : 0.52 % 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: -3.58 (0.24), residues: 812 helix: -1.77 (0.18), residues: 610 sheet: None (None), residues: 0 loop : -3.84 (0.34), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 44 HIS 0.010 0.002 HIS A 226 PHE 0.040 0.003 PHE A 248 TYR 0.020 0.002 TYR A 247 ARG 0.005 0.001 ARG A 365 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 175 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 PHE cc_start: 0.8116 (t80) cc_final: 0.7916 (t80) REVERT: B 77 LEU cc_start: 0.8760 (pp) cc_final: 0.8544 (tt) outliers start: 14 outliers final: 0 residues processed: 187 average time/residue: 0.2029 time to fit residues: 49.0808 Evaluate side-chains 110 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 41 optimal weight: 20.0000 chunk 33 optimal weight: 8.9990 chunk 64 optimal weight: 0.9990 chunk 24 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 74 optimal weight: 0.4980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 132 ASN A 179 ASN A 219 ASN A 330 GLN A 377 HIS A 384 ASN A 390 GLN B 86 GLN B 132 ASN B 219 ASN B 330 GLN B 377 HIS B 390 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.095353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.071946 restraints weight = 19454.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.075081 restraints weight = 10502.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.077230 restraints weight = 7060.082| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 6608 Z= 0.288 Angle : 0.818 8.484 8962 Z= 0.414 Chirality : 0.045 0.218 1044 Planarity : 0.005 0.055 1112 Dihedral : 5.390 21.634 896 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 4.17 % Allowed : 19.54 % Favored : 76.29 % 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: -1.58 (0.27), residues: 812 helix: -0.51 (0.19), residues: 628 sheet: None (None), residues: 0 loop : -2.54 (0.46), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 44 HIS 0.013 0.002 HIS A 322 PHE 0.026 0.002 PHE A 476 TYR 0.025 0.002 TYR A 269 ARG 0.005 0.001 ARG A 502 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 PHE cc_start: 0.9412 (OUTLIER) cc_final: 0.9178 (t80) REVERT: A 169 TYR cc_start: 0.7669 (m-80) cc_final: 0.7366 (m-10) REVERT: A 280 GLU cc_start: 0.9533 (tp30) cc_final: 0.9224 (mt-10) REVERT: A 375 HIS cc_start: 0.9518 (m90) cc_final: 0.9023 (m90) REVERT: A 470 PHE cc_start: 0.8546 (m-10) cc_final: 0.8316 (m-80) REVERT: B 125 PHE cc_start: 0.9517 (OUTLIER) cc_final: 0.9229 (t80) REVERT: B 279 ASP cc_start: 0.8832 (m-30) cc_final: 0.8381 (t70) REVERT: B 280 GLU cc_start: 0.9497 (tp30) cc_final: 0.9177 (mt-10) REVERT: B 375 HIS cc_start: 0.9447 (m90) cc_final: 0.9013 (m90) REVERT: B 485 GLU cc_start: 0.8833 (tp30) cc_final: 0.8574 (tm-30) outliers start: 29 outliers final: 17 residues processed: 157 average time/residue: 0.1374 time to fit residues: 30.5773 Evaluate side-chains 119 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 505 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 39 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 5 optimal weight: 0.4980 chunk 10 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 GLN B 330 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.093602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.070440 restraints weight = 19226.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.073463 restraints weight = 10042.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.075568 restraints weight = 6621.727| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6608 Z= 0.233 Angle : 0.693 9.495 8962 Z= 0.349 Chirality : 0.042 0.188 1044 Planarity : 0.004 0.035 1112 Dihedral : 5.068 21.401 896 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.89 % Allowed : 21.12 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.28), residues: 812 helix: 0.31 (0.19), residues: 638 sheet: None (None), residues: 0 loop : -2.24 (0.48), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 44 HIS 0.014 0.002 HIS A 322 PHE 0.030 0.002 PHE B 248 TYR 0.024 0.002 TYR B 269 ARG 0.003 0.000 ARG B 298 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 119 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.7339 (mpp) cc_final: 0.7136 (pmm) REVERT: A 125 PHE cc_start: 0.9456 (OUTLIER) cc_final: 0.9217 (t80) REVERT: A 279 ASP cc_start: 0.8838 (m-30) cc_final: 0.8475 (t70) REVERT: A 280 GLU cc_start: 0.9492 (tp30) cc_final: 0.9217 (mt-10) REVERT: A 303 GLN cc_start: 0.8293 (tp40) cc_final: 0.7886 (mm110) REVERT: A 375 HIS cc_start: 0.9528 (m90) cc_final: 0.9035 (m90) REVERT: B 45 GLN cc_start: 0.9341 (mm110) cc_final: 0.9110 (mp10) REVERT: B 77 LEU cc_start: 0.9466 (mm) cc_final: 0.9124 (pp) REVERT: B 239 SER cc_start: 0.9703 (m) cc_final: 0.9414 (p) REVERT: B 247 TYR cc_start: 0.8879 (t80) cc_final: 0.7859 (t80) REVERT: B 248 PHE cc_start: 0.7738 (m-10) cc_final: 0.7227 (m-10) REVERT: B 258 MET cc_start: 0.7891 (ptt) cc_final: 0.7511 (ttp) REVERT: B 303 GLN cc_start: 0.8201 (tp40) cc_final: 0.7727 (mm110) REVERT: B 375 HIS cc_start: 0.9459 (m90) cc_final: 0.8987 (m90) REVERT: B 470 PHE cc_start: 0.8115 (m-80) cc_final: 0.7707 (m-80) REVERT: B 486 THR cc_start: 0.8918 (OUTLIER) cc_final: 0.8672 (m) outliers start: 34 outliers final: 18 residues processed: 140 average time/residue: 0.1429 time to fit residues: 28.5098 Evaluate side-chains 114 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 494 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 67 optimal weight: 0.1980 chunk 25 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 46 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.092513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.069629 restraints weight = 18976.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.072513 restraints weight = 10024.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.074577 restraints weight = 6684.272| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.4899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6608 Z= 0.227 Angle : 0.664 7.538 8962 Z= 0.337 Chirality : 0.041 0.142 1044 Planarity : 0.004 0.035 1112 Dihedral : 4.836 19.998 896 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 5.32 % Allowed : 22.56 % Favored : 72.13 % 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: 0.11 (0.29), residues: 812 helix: 0.64 (0.20), residues: 634 sheet: None (None), residues: 0 loop : -1.79 (0.49), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 44 HIS 0.010 0.002 HIS B 322 PHE 0.036 0.002 PHE A 248 TYR 0.025 0.002 TYR B 75 ARG 0.005 0.000 ARG B 298 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 113 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 THR cc_start: 0.8615 (OUTLIER) cc_final: 0.8355 (t) REVERT: A 125 PHE cc_start: 0.9467 (OUTLIER) cc_final: 0.9203 (t80) REVERT: A 230 VAL cc_start: 0.8165 (OUTLIER) cc_final: 0.7940 (t) REVERT: A 243 CYS cc_start: 0.9470 (t) cc_final: 0.9027 (t) REVERT: A 279 ASP cc_start: 0.8909 (m-30) cc_final: 0.8644 (t70) REVERT: A 280 GLU cc_start: 0.9496 (tp30) cc_final: 0.9187 (mt-10) REVERT: A 303 GLN cc_start: 0.8371 (tp40) cc_final: 0.7989 (mm110) REVERT: A 375 HIS cc_start: 0.9513 (m90) cc_final: 0.9013 (m90) REVERT: A 459 GLN cc_start: 0.8771 (mt0) cc_final: 0.8400 (pt0) REVERT: A 470 PHE cc_start: 0.8428 (m-80) cc_final: 0.7948 (m-80) REVERT: B 45 GLN cc_start: 0.9336 (mm110) cc_final: 0.9058 (mp10) REVERT: B 106 THR cc_start: 0.9284 (OUTLIER) cc_final: 0.9044 (m) REVERT: B 230 VAL cc_start: 0.8163 (OUTLIER) cc_final: 0.7866 (t) REVERT: B 247 TYR cc_start: 0.9044 (t80) cc_final: 0.7967 (t80) REVERT: B 248 PHE cc_start: 0.8066 (m-80) cc_final: 0.7360 (m-10) REVERT: B 279 ASP cc_start: 0.9097 (m-30) cc_final: 0.8556 (t70) REVERT: B 303 GLN cc_start: 0.8331 (tp40) cc_final: 0.7905 (mm110) REVERT: B 375 HIS cc_start: 0.9489 (m90) cc_final: 0.9036 (m90) REVERT: B 382 ASP cc_start: 0.9182 (t70) cc_final: 0.8954 (p0) REVERT: B 470 PHE cc_start: 0.8417 (m-80) cc_final: 0.8057 (m-80) outliers start: 37 outliers final: 27 residues processed: 136 average time/residue: 0.1400 time to fit residues: 27.3561 Evaluate side-chains 126 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 94 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 494 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 7 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 41 optimal weight: 20.0000 chunk 27 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 58 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 GLN B 359 ASN B 384 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.091686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.067887 restraints weight = 19062.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.070737 restraints weight = 10323.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.072793 restraints weight = 7007.952| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.5271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6608 Z= 0.238 Angle : 0.666 10.664 8962 Z= 0.337 Chirality : 0.043 0.348 1044 Planarity : 0.004 0.034 1112 Dihedral : 4.739 18.603 896 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 5.60 % Allowed : 23.71 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.43 (0.30), residues: 812 helix: 0.82 (0.20), residues: 644 sheet: None (None), residues: 0 loop : -1.59 (0.51), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 44 HIS 0.008 0.001 HIS B 322 PHE 0.026 0.002 PHE B 248 TYR 0.025 0.002 TYR B 75 ARG 0.004 0.000 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 99 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 THR cc_start: 0.8602 (OUTLIER) cc_final: 0.8296 (t) REVERT: A 125 PHE cc_start: 0.9408 (OUTLIER) cc_final: 0.9171 (t80) REVERT: A 223 GLU cc_start: 0.8282 (tt0) cc_final: 0.7060 (tm-30) REVERT: A 230 VAL cc_start: 0.8174 (OUTLIER) cc_final: 0.7921 (t) REVERT: A 243 CYS cc_start: 0.9501 (t) cc_final: 0.9055 (t) REVERT: A 279 ASP cc_start: 0.8885 (m-30) cc_final: 0.8427 (t70) REVERT: A 280 GLU cc_start: 0.9481 (tp30) cc_final: 0.9131 (mt-10) REVERT: A 303 GLN cc_start: 0.8452 (tp40) cc_final: 0.7759 (tp40) REVERT: A 375 HIS cc_start: 0.9516 (m90) cc_final: 0.9049 (m90) REVERT: A 382 ASP cc_start: 0.9244 (t70) cc_final: 0.9038 (p0) REVERT: A 470 PHE cc_start: 0.8337 (m-80) cc_final: 0.7817 (m-80) REVERT: A 496 GLU cc_start: 0.9258 (tp30) cc_final: 0.8683 (tp30) REVERT: B 102 THR cc_start: 0.8548 (OUTLIER) cc_final: 0.8285 (t) REVERT: B 106 THR cc_start: 0.9277 (OUTLIER) cc_final: 0.9055 (m) REVERT: B 258 MET cc_start: 0.7955 (ptt) cc_final: 0.7682 (tmm) REVERT: B 279 ASP cc_start: 0.9086 (m-30) cc_final: 0.8869 (t70) REVERT: B 303 GLN cc_start: 0.8446 (tp40) cc_final: 0.7454 (tp-100) REVERT: B 375 HIS cc_start: 0.9484 (m90) cc_final: 0.9031 (m90) REVERT: B 496 GLU cc_start: 0.9268 (tp30) cc_final: 0.8643 (tp30) outliers start: 39 outliers final: 28 residues processed: 125 average time/residue: 0.1322 time to fit residues: 24.1479 Evaluate side-chains 122 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 89 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 505 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 1 optimal weight: 8.9990 chunk 35 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 36 optimal weight: 0.0050 chunk 61 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 33 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.090442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.067189 restraints weight = 19210.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.070033 restraints weight = 10309.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.072012 restraints weight = 6955.788| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.5487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6608 Z= 0.272 Angle : 0.672 8.642 8962 Z= 0.341 Chirality : 0.041 0.157 1044 Planarity : 0.004 0.033 1112 Dihedral : 4.613 18.970 896 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 5.89 % Allowed : 24.86 % Favored : 69.25 % 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: 0.64 (0.30), residues: 812 helix: 0.98 (0.20), residues: 644 sheet: None (None), residues: 0 loop : -1.59 (0.51), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 44 HIS 0.008 0.001 HIS B 322 PHE 0.040 0.002 PHE A 248 TYR 0.026 0.002 TYR B 75 ARG 0.004 0.000 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 99 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 PHE cc_start: 0.9445 (OUTLIER) cc_final: 0.9180 (t80) REVERT: A 196 HIS cc_start: 0.3135 (OUTLIER) cc_final: 0.2928 (t-90) REVERT: A 223 GLU cc_start: 0.8281 (tt0) cc_final: 0.7094 (tm-30) REVERT: A 230 VAL cc_start: 0.8226 (OUTLIER) cc_final: 0.8006 (t) REVERT: A 243 CYS cc_start: 0.9486 (t) cc_final: 0.9026 (t) REVERT: A 248 PHE cc_start: 0.8753 (m-10) cc_final: 0.8543 (m-10) REVERT: A 279 ASP cc_start: 0.8902 (m-30) cc_final: 0.8484 (t70) REVERT: A 280 GLU cc_start: 0.9473 (tp30) cc_final: 0.9152 (mt-10) REVERT: A 303 GLN cc_start: 0.8444 (tp40) cc_final: 0.7424 (tp-100) REVERT: A 375 HIS cc_start: 0.9521 (m90) cc_final: 0.9039 (m90) REVERT: A 470 PHE cc_start: 0.8337 (m-80) cc_final: 0.7803 (m-80) REVERT: A 496 GLU cc_start: 0.9268 (tp30) cc_final: 0.8711 (tp30) REVERT: B 230 VAL cc_start: 0.8261 (OUTLIER) cc_final: 0.8013 (t) REVERT: B 243 CYS cc_start: 0.9403 (t) cc_final: 0.9070 (t) REVERT: B 258 MET cc_start: 0.8327 (ptt) cc_final: 0.7710 (ttp) REVERT: B 279 ASP cc_start: 0.9114 (m-30) cc_final: 0.8774 (t70) REVERT: B 303 GLN cc_start: 0.8529 (tp40) cc_final: 0.8178 (mm-40) REVERT: B 375 HIS cc_start: 0.9494 (m90) cc_final: 0.9033 (m90) REVERT: B 470 PHE cc_start: 0.8471 (m-80) cc_final: 0.7871 (m-80) REVERT: B 496 GLU cc_start: 0.9291 (tp30) cc_final: 0.8780 (tp30) outliers start: 41 outliers final: 32 residues processed: 125 average time/residue: 0.1238 time to fit residues: 22.8544 Evaluate side-chains 126 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 90 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 196 HIS Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 459 GLN Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 494 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 48 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 53 optimal weight: 0.6980 chunk 3 optimal weight: 10.0000 chunk 76 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 44 optimal weight: 9.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.091660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.068475 restraints weight = 18914.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.071395 restraints weight = 10221.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.073343 restraints weight = 6866.096| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.5768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6608 Z= 0.214 Angle : 0.632 8.941 8962 Z= 0.321 Chirality : 0.040 0.165 1044 Planarity : 0.004 0.033 1112 Dihedral : 4.532 20.381 896 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 5.60 % Allowed : 24.43 % Favored : 69.97 % 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: 0.72 (0.30), residues: 812 helix: 1.07 (0.20), residues: 648 sheet: None (None), residues: 0 loop : -1.80 (0.51), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 44 HIS 0.007 0.001 HIS B 322 PHE 0.026 0.002 PHE B 148 TYR 0.026 0.001 TYR B 75 ARG 0.004 0.000 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 97 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 THR cc_start: 0.8602 (OUTLIER) cc_final: 0.8390 (t) REVERT: A 223 GLU cc_start: 0.8229 (tt0) cc_final: 0.7008 (tm-30) REVERT: A 230 VAL cc_start: 0.8115 (OUTLIER) cc_final: 0.7870 (t) REVERT: A 243 CYS cc_start: 0.9466 (t) cc_final: 0.9018 (t) REVERT: A 279 ASP cc_start: 0.8903 (m-30) cc_final: 0.8587 (t70) REVERT: A 303 GLN cc_start: 0.8346 (tp40) cc_final: 0.7372 (tp-100) REVERT: A 375 HIS cc_start: 0.9513 (m90) cc_final: 0.9035 (m90) REVERT: A 470 PHE cc_start: 0.8266 (m-80) cc_final: 0.7745 (m-80) REVERT: A 496 GLU cc_start: 0.9271 (tp30) cc_final: 0.8661 (tp30) REVERT: B 106 THR cc_start: 0.9315 (OUTLIER) cc_final: 0.9112 (m) REVERT: B 223 GLU cc_start: 0.8252 (tt0) cc_final: 0.7203 (tm-30) REVERT: B 230 VAL cc_start: 0.8212 (OUTLIER) cc_final: 0.7953 (t) REVERT: B 243 CYS cc_start: 0.9368 (t) cc_final: 0.8997 (t) REVERT: B 258 MET cc_start: 0.8421 (ptt) cc_final: 0.8008 (ttp) REVERT: B 303 GLN cc_start: 0.8491 (tp40) cc_final: 0.8078 (mm110) REVERT: B 375 HIS cc_start: 0.9475 (m90) cc_final: 0.9015 (m90) REVERT: B 470 PHE cc_start: 0.8413 (m-80) cc_final: 0.7800 (m-80) REVERT: B 496 GLU cc_start: 0.9272 (tp30) cc_final: 0.8676 (tp30) outliers start: 39 outliers final: 28 residues processed: 121 average time/residue: 0.1413 time to fit residues: 24.7955 Evaluate side-chains 121 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 89 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 505 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 45 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 7 optimal weight: 7.9990 chunk 48 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 41 optimal weight: 20.0000 chunk 69 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 13 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.095606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.072232 restraints weight = 17968.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.075305 restraints weight = 8790.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.077199 restraints weight = 5597.658| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.5938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6608 Z= 0.258 Angle : 0.647 8.478 8962 Z= 0.330 Chirality : 0.040 0.134 1044 Planarity : 0.004 0.032 1112 Dihedral : 4.472 21.269 896 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 5.03 % Allowed : 26.01 % Favored : 68.97 % 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: 0.91 (0.30), residues: 812 helix: 1.21 (0.20), residues: 648 sheet: None (None), residues: 0 loop : -1.76 (0.52), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 301 HIS 0.007 0.001 HIS A 322 PHE 0.029 0.002 PHE B 248 TYR 0.027 0.001 TYR B 75 ARG 0.004 0.000 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 91 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 THR cc_start: 0.8522 (OUTLIER) cc_final: 0.8314 (t) REVERT: A 223 GLU cc_start: 0.8246 (tt0) cc_final: 0.7052 (tm-30) REVERT: A 230 VAL cc_start: 0.8218 (OUTLIER) cc_final: 0.8013 (t) REVERT: A 243 CYS cc_start: 0.9485 (t) cc_final: 0.9060 (t) REVERT: A 303 GLN cc_start: 0.8420 (tp40) cc_final: 0.7437 (tp-100) REVERT: A 375 HIS cc_start: 0.9501 (m90) cc_final: 0.9016 (m90) REVERT: A 470 PHE cc_start: 0.8233 (m-80) cc_final: 0.7736 (m-80) REVERT: A 496 GLU cc_start: 0.9238 (tp30) cc_final: 0.8621 (tp30) REVERT: B 106 THR cc_start: 0.9331 (OUTLIER) cc_final: 0.9120 (m) REVERT: B 223 GLU cc_start: 0.8245 (tt0) cc_final: 0.7042 (tm-30) REVERT: B 230 VAL cc_start: 0.8200 (OUTLIER) cc_final: 0.7967 (t) REVERT: B 243 CYS cc_start: 0.9372 (t) cc_final: 0.9053 (t) REVERT: B 258 MET cc_start: 0.8429 (ptt) cc_final: 0.7885 (ttp) REVERT: B 303 GLN cc_start: 0.8498 (tp40) cc_final: 0.8101 (mm110) REVERT: B 375 HIS cc_start: 0.9466 (m90) cc_final: 0.9009 (m90) REVERT: B 470 PHE cc_start: 0.8329 (m-80) cc_final: 0.7759 (m-80) REVERT: B 496 GLU cc_start: 0.9240 (tp30) cc_final: 0.8673 (tp30) outliers start: 35 outliers final: 28 residues processed: 112 average time/residue: 0.1418 time to fit residues: 23.1172 Evaluate side-chains 119 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 87 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 459 GLN Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 494 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 0.9980 chunk 6 optimal weight: 0.4980 chunk 36 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 ASN B 390 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.092164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.068762 restraints weight = 19535.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.071679 restraints weight = 10683.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.073518 restraints weight = 7261.498| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.6133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6608 Z= 0.198 Angle : 0.649 8.855 8962 Z= 0.328 Chirality : 0.040 0.186 1044 Planarity : 0.004 0.032 1112 Dihedral : 4.451 21.836 896 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 5.32 % Allowed : 25.57 % Favored : 69.11 % 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: 1.05 (0.30), residues: 812 helix: 1.32 (0.20), residues: 648 sheet: None (None), residues: 0 loop : -1.77 (0.52), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 44 HIS 0.006 0.001 HIS B 322 PHE 0.025 0.002 PHE B 148 TYR 0.029 0.001 TYR B 75 ARG 0.003 0.000 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 93 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 THR cc_start: 0.8725 (OUTLIER) cc_final: 0.8517 (t) REVERT: A 223 GLU cc_start: 0.8245 (tt0) cc_final: 0.7122 (tm-30) REVERT: A 230 VAL cc_start: 0.8207 (OUTLIER) cc_final: 0.7979 (t) REVERT: A 243 CYS cc_start: 0.9478 (t) cc_final: 0.9014 (t) REVERT: A 258 MET cc_start: 0.7958 (tmm) cc_final: 0.7740 (tmm) REVERT: A 303 GLN cc_start: 0.8362 (tp40) cc_final: 0.7408 (tp-100) REVERT: A 375 HIS cc_start: 0.9502 (m90) cc_final: 0.9014 (m90) REVERT: A 381 GLN cc_start: 0.9462 (mm-40) cc_final: 0.8995 (mm-40) REVERT: A 470 PHE cc_start: 0.8191 (m-80) cc_final: 0.7713 (m-80) REVERT: A 496 GLU cc_start: 0.9249 (tp30) cc_final: 0.8573 (tp30) REVERT: B 106 THR cc_start: 0.9285 (OUTLIER) cc_final: 0.9074 (m) REVERT: B 223 GLU cc_start: 0.8239 (tt0) cc_final: 0.7026 (tm-30) REVERT: B 230 VAL cc_start: 0.8236 (OUTLIER) cc_final: 0.7989 (t) REVERT: B 243 CYS cc_start: 0.9365 (t) cc_final: 0.9097 (t) REVERT: B 258 MET cc_start: 0.8430 (ptt) cc_final: 0.8142 (ttp) REVERT: B 303 GLN cc_start: 0.8480 (tp40) cc_final: 0.8083 (mm110) REVERT: B 375 HIS cc_start: 0.9470 (m90) cc_final: 0.9004 (m90) REVERT: B 470 PHE cc_start: 0.8206 (m-80) cc_final: 0.7565 (m-80) REVERT: B 496 GLU cc_start: 0.9234 (tp30) cc_final: 0.8613 (tp30) outliers start: 37 outliers final: 30 residues processed: 115 average time/residue: 0.1368 time to fit residues: 23.0395 Evaluate side-chains 122 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 88 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 459 GLN Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 494 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 80 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 56 optimal weight: 7.9990 chunk 69 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 59 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 76 optimal weight: 0.0370 overall best weight: 0.9862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 ASN A 390 GLN ** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.092355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.068700 restraints weight = 19620.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.071582 restraints weight = 10851.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.073511 restraints weight = 7435.446| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.6232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6608 Z= 0.194 Angle : 0.653 9.310 8962 Z= 0.330 Chirality : 0.040 0.186 1044 Planarity : 0.004 0.033 1112 Dihedral : 4.399 20.453 896 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 4.60 % Allowed : 26.72 % Favored : 68.68 % 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: 1.15 (0.30), residues: 812 helix: 1.40 (0.21), residues: 648 sheet: None (None), residues: 0 loop : -1.75 (0.51), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 301 HIS 0.005 0.001 HIS B 322 PHE 0.025 0.002 PHE B 148 TYR 0.028 0.001 TYR B 75 ARG 0.003 0.000 ARG B 294 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 92 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 THR cc_start: 0.8734 (OUTLIER) cc_final: 0.8532 (t) REVERT: A 223 GLU cc_start: 0.8237 (tt0) cc_final: 0.7102 (tm-30) REVERT: A 230 VAL cc_start: 0.8227 (OUTLIER) cc_final: 0.7999 (t) REVERT: A 243 CYS cc_start: 0.9474 (t) cc_final: 0.9026 (t) REVERT: A 258 MET cc_start: 0.8050 (tmm) cc_final: 0.7829 (tmm) REVERT: A 303 GLN cc_start: 0.8401 (tp40) cc_final: 0.7460 (tp-100) REVERT: A 375 HIS cc_start: 0.9504 (m90) cc_final: 0.8998 (m90) REVERT: A 381 GLN cc_start: 0.9469 (mm-40) cc_final: 0.9023 (mm-40) REVERT: A 470 PHE cc_start: 0.8202 (m-80) cc_final: 0.7708 (m-80) REVERT: A 496 GLU cc_start: 0.9284 (tp30) cc_final: 0.8599 (tp30) REVERT: B 106 THR cc_start: 0.9284 (OUTLIER) cc_final: 0.9070 (m) REVERT: B 223 GLU cc_start: 0.8159 (tt0) cc_final: 0.6978 (tm-30) REVERT: B 230 VAL cc_start: 0.8250 (OUTLIER) cc_final: 0.7998 (t) REVERT: B 243 CYS cc_start: 0.9375 (t) cc_final: 0.8944 (t) REVERT: B 258 MET cc_start: 0.8450 (ptt) cc_final: 0.8156 (ttp) REVERT: B 303 GLN cc_start: 0.8500 (tp40) cc_final: 0.8036 (mm110) REVERT: B 375 HIS cc_start: 0.9468 (m90) cc_final: 0.9003 (m90) REVERT: B 381 GLN cc_start: 0.9456 (mm-40) cc_final: 0.9059 (mm110) REVERT: B 470 PHE cc_start: 0.8294 (m-80) cc_final: 0.7633 (m-80) REVERT: B 496 GLU cc_start: 0.9265 (tp30) cc_final: 0.8664 (tp30) outliers start: 32 outliers final: 27 residues processed: 113 average time/residue: 0.1318 time to fit residues: 22.2366 Evaluate side-chains 120 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 89 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 459 GLN Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 494 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 18 optimal weight: 0.0040 chunk 70 optimal weight: 0.8980 chunk 77 optimal weight: 0.1980 chunk 54 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 ASN ** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.093165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.069638 restraints weight = 19684.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.072623 restraints weight = 10773.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.074676 restraints weight = 7298.232| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.6331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6608 Z= 0.182 Angle : 0.672 10.663 8962 Z= 0.333 Chirality : 0.041 0.293 1044 Planarity : 0.004 0.034 1112 Dihedral : 4.380 19.515 896 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 4.89 % Allowed : 26.58 % Favored : 68.53 % 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: 1.21 (0.30), residues: 812 helix: 1.45 (0.21), residues: 648 sheet: None (None), residues: 0 loop : -1.79 (0.51), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 44 HIS 0.005 0.001 HIS B 322 PHE 0.024 0.002 PHE B 148 TYR 0.030 0.001 TYR B 75 ARG 0.003 0.000 ARG B 294 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2055.87 seconds wall clock time: 37 minutes 57.84 seconds (2277.84 seconds total)