Starting phenix.real_space_refine on Fri Dec 27 18:37:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w6k_32328/12_2024/7w6k_32328.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w6k_32328/12_2024/7w6k_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_32328/12_2024/7w6k_32328.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w6k_32328/12_2024/7w6k_32328.map" model { file = "/net/cci-nas-00/data/ceres_data/7w6k_32328/12_2024/7w6k_32328.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w6k_32328/12_2024/7w6k_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 5.37, per 1000 atoms: 0.83 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: 1.82 Conformation dependent library (CDL) restraints added in 907.5 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: 0.60 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: 1.76 Time building geometry restraints manager: 2.05 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: 0.00 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.480 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: 0.050 Set scattering table: 0.060 Process input model: 19.330 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.120 ------------------------------------------------------------------------------- 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 : 0.833 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: 0.2030 time to fit residues: 49.3610 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 : 0.791 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 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 : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 PHE cc_start: 0.8487 (OUTLIER) cc_final: 0.8236 (t80) REVERT: A 375 HIS cc_start: 0.8438 (m90) cc_final: 0.8158 (m90) REVERT: B 125 PHE cc_start: 0.8546 (OUTLIER) cc_final: 0.8284 (t80) REVERT: B 375 HIS cc_start: 0.8459 (m90) cc_final: 0.8223 (m90) outliers start: 29 outliers final: 17 residues processed: 157 average time/residue: 0.1389 time to fit residues: 30.9808 Evaluate side-chains 116 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.772 ------------------------------------------------------------------------------- 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 41 optimal weight: 30.0000 chunk 23 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 74 optimal weight: 0.0570 chunk 80 optimal weight: 0.5980 chunk 66 optimal weight: 0.0970 chunk 73 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 59 optimal weight: 6.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6608 Z= 0.247 Angle : 0.702 9.582 8962 Z= 0.355 Chirality : 0.042 0.205 1044 Planarity : 0.005 0.036 1112 Dihedral : 5.115 21.285 896 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 5.32 % Allowed : 21.41 % Favored : 73.28 % 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: -0.60 (0.28), residues: 812 helix: 0.20 (0.19), residues: 632 sheet: None (None), residues: 0 loop : -2.28 (0.47), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 44 HIS 0.012 0.002 HIS A 322 PHE 0.029 0.002 PHE B 248 TYR 0.024 0.002 TYR B 75 ARG 0.004 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 149 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 112 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.7358 (mpp) cc_final: 0.7123 (pmm) REVERT: A 125 PHE cc_start: 0.8496 (OUTLIER) cc_final: 0.8264 (t80) REVERT: A 375 HIS cc_start: 0.8418 (m90) cc_final: 0.8163 (m90) REVERT: B 37 MET cc_start: 0.7515 (mpp) cc_final: 0.7204 (pmm) REVERT: B 77 LEU cc_start: 0.8774 (mm) cc_final: 0.8545 (tt) REVERT: B 247 TYR cc_start: 0.8581 (t80) cc_final: 0.8213 (t80) REVERT: B 248 PHE cc_start: 0.6543 (m-10) cc_final: 0.6274 (m-10) REVERT: B 258 MET cc_start: 0.7667 (ptt) cc_final: 0.7087 (ttp) REVERT: B 375 HIS cc_start: 0.8424 (m90) cc_final: 0.8195 (m90) outliers start: 37 outliers final: 21 residues processed: 136 average time/residue: 0.1365 time to fit residues: 26.6349 Evaluate side-chains 112 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.762 ------------------------------------------------------------------------------- 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 201 THR 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 A residue 494 ILE 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 201 THR 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 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 73 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 35 optimal weight: 0.0770 chunk 50 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 GLN B 384 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.4825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6608 Z= 0.224 Angle : 0.658 7.815 8962 Z= 0.339 Chirality : 0.041 0.146 1044 Planarity : 0.004 0.035 1112 Dihedral : 4.908 19.900 896 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 5.46 % Allowed : 22.56 % Favored : 71.98 % 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: -0.03 (0.29), residues: 812 helix: 0.54 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -1.84 (0.49), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 44 HIS 0.011 0.001 HIS B 322 PHE 0.034 0.002 PHE A 248 TYR 0.027 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 148 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 110 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 PHE cc_start: 0.8524 (OUTLIER) cc_final: 0.8294 (t80) REVERT: A 375 HIS cc_start: 0.8390 (m90) cc_final: 0.8158 (m90) REVERT: B 248 PHE cc_start: 0.6941 (m-80) cc_final: 0.6738 (m-10) REVERT: B 375 HIS cc_start: 0.8432 (m90) cc_final: 0.8227 (m90) outliers start: 38 outliers final: 25 residues processed: 131 average time/residue: 0.1376 time to fit residues: 25.9850 Evaluate side-chains 116 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 0.752 ------------------------------------------------------------------------------- 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 106 THR Chi-restraints excluded: chain A residue 115 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 262 GLU 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 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 115 LEU Chi-restraints excluded: chain B residue 118 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 494 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 59 optimal weight: 0.0870 chunk 32 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 54 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 71 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 overall best weight: 1.3962 ------------------------------------------------------------------------------- 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 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.5247 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= 0.237 Angle : 0.674 9.324 8962 Z= 0.340 Chirality : 0.044 0.423 1044 Planarity : 0.004 0.035 1112 Dihedral : 4.750 18.527 896 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 5.17 % Allowed : 24.28 % Favored : 70.55 % 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: 0.36 (0.30), residues: 812 helix: 0.83 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -1.84 (0.51), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 301 HIS 0.013 0.001 HIS B 322 PHE 0.035 0.002 PHE A 248 TYR 0.028 0.002 TYR B 75 ARG 0.006 0.000 ARG B 298 *********************** 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 137 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 101 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 PHE cc_start: 0.8524 (OUTLIER) cc_final: 0.8294 (t80) REVERT: A 375 HIS cc_start: 0.8371 (m90) cc_final: 0.8136 (m90) REVERT: B 248 PHE cc_start: 0.7144 (m-80) cc_final: 0.6940 (m-10) REVERT: B 375 HIS cc_start: 0.8429 (m90) cc_final: 0.8199 (m90) outliers start: 36 outliers final: 29 residues processed: 121 average time/residue: 0.1354 time to fit residues: 23.7704 Evaluate side-chains 114 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 84 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU 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 106 THR Chi-restraints excluded: chain A residue 115 LEU 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 262 GLU 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 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 209 CYS Chi-restraints excluded: chain B residue 299 PHE 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 0.0570 chunk 71 optimal weight: 4.9990 chunk 15 optimal weight: 20.0000 chunk 46 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 36 optimal weight: 0.0980 chunk 6 optimal weight: 6.9990 chunk 41 optimal weight: 20.0000 chunk 76 optimal weight: 0.0270 overall best weight: 0.3756 ------------------------------------------------------------------------------- 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 303 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.5659 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= 0.190 Angle : 0.672 9.863 8962 Z= 0.336 Chirality : 0.041 0.193 1044 Planarity : 0.004 0.035 1112 Dihedral : 4.717 22.574 896 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.17 % Allowed : 26.58 % 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: 0.53 (0.30), residues: 812 helix: 0.95 (0.20), residues: 644 sheet: None (None), residues: 0 loop : -1.84 (0.51), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 90 HIS 0.010 0.001 HIS B 322 PHE 0.026 0.002 PHE B 148 TYR 0.029 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 133 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 104 time to evaluate : 0.762 Fit side-chains revert: symmetry clash REVERT: A 125 PHE cc_start: 0.8516 (OUTLIER) cc_final: 0.8276 (t80) REVERT: A 375 HIS cc_start: 0.8344 (m90) cc_final: 0.8121 (m90) REVERT: B 248 PHE cc_start: 0.7121 (m-80) cc_final: 0.6905 (m-10) REVERT: B 279 ASP cc_start: 0.7710 (t70) cc_final: 0.7503 (t70) REVERT: B 375 HIS cc_start: 0.8402 (m90) cc_final: 0.8153 (m90) outliers start: 29 outliers final: 24 residues processed: 120 average time/residue: 0.1340 time to fit residues: 24.0672 Evaluate side-chains 107 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 82 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 115 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 272 VAL 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 115 LEU Chi-restraints excluded: chain B residue 199 VAL 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 5.9990 chunk 45 optimal weight: 0.0370 chunk 57 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 48 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 overall best weight: 0.7458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 GLN B 179 ASN ** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.5907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6608 Z= 0.190 Angle : 0.648 8.358 8962 Z= 0.328 Chirality : 0.040 0.162 1044 Planarity : 0.004 0.033 1112 Dihedral : 4.565 20.100 896 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 4.31 % Allowed : 26.72 % 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: 0.74 (0.30), residues: 812 helix: 1.14 (0.20), residues: 644 sheet: None (None), residues: 0 loop : -1.94 (0.50), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 301 HIS 0.011 0.001 HIS A 322 PHE 0.022 0.002 PHE B 148 TYR 0.030 0.001 TYR B 75 ARG 0.003 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 116 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 86 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 PHE cc_start: 0.8514 (OUTLIER) cc_final: 0.8281 (t80) REVERT: A 375 HIS cc_start: 0.8345 (m90) cc_final: 0.8115 (m90) REVERT: B 179 ASN cc_start: 0.9320 (OUTLIER) cc_final: 0.8994 (m110) REVERT: B 375 HIS cc_start: 0.8380 (m90) cc_final: 0.8139 (m90) REVERT: B 382 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7344 (p0) outliers start: 30 outliers final: 23 residues processed: 102 average time/residue: 0.1294 time to fit residues: 19.6706 Evaluate side-chains 105 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 79 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 115 LEU 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 262 GLU 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 115 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 179 ASN Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 382 ASP Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 494 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 chunk 50 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 ASN ** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.6039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6608 Z= 0.211 Angle : 0.646 7.808 8962 Z= 0.334 Chirality : 0.041 0.168 1044 Planarity : 0.004 0.033 1112 Dihedral : 4.500 21.122 896 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 4.45 % Allowed : 26.44 % 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: 0.83 (0.30), residues: 812 helix: 1.21 (0.20), residues: 642 sheet: None (None), residues: 0 loop : -1.93 (0.50), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 301 HIS 0.006 0.001 HIS B 322 PHE 0.026 0.002 PHE B 148 TYR 0.029 0.001 TYR B 75 ARG 0.003 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 112 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 81 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 LEU cc_start: 0.9088 (tt) cc_final: 0.8885 (tt) REVERT: A 375 HIS cc_start: 0.8385 (m90) cc_final: 0.8148 (m90) REVERT: B 179 ASN cc_start: 0.9333 (OUTLIER) cc_final: 0.9035 (m110) REVERT: B 330 GLN cc_start: 0.8185 (tp-100) cc_final: 0.7463 (mm-40) REVERT: B 375 HIS cc_start: 0.8426 (m90) cc_final: 0.8192 (m90) REVERT: B 382 ASP cc_start: 0.7845 (OUTLIER) cc_final: 0.7379 (p0) outliers start: 31 outliers final: 24 residues processed: 98 average time/residue: 0.1304 time to fit residues: 19.1040 Evaluate side-chains 105 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 79 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 115 LEU 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 262 GLU Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 341 ASP 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 92 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 179 ASN Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 382 ASP 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 75 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 73 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 ASN ** A 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 ASN ** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.6200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6608 Z= 0.200 Angle : 0.654 8.395 8962 Z= 0.336 Chirality : 0.041 0.187 1044 Planarity : 0.004 0.032 1112 Dihedral : 4.485 21.511 896 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.45 % Allowed : 26.58 % 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: 1.28 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -1.92 (0.49), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 301 HIS 0.006 0.001 HIS B 322 PHE 0.024 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 114 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 83 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 375 HIS cc_start: 0.8341 (m90) cc_final: 0.8105 (m90) REVERT: B 179 ASN cc_start: 0.9314 (OUTLIER) cc_final: 0.9103 (m110) REVERT: B 279 ASP cc_start: 0.7604 (t70) cc_final: 0.7349 (t70) REVERT: B 330 GLN cc_start: 0.8169 (tp-100) cc_final: 0.7580 (mm110) REVERT: B 375 HIS cc_start: 0.8421 (m90) cc_final: 0.8191 (m90) REVERT: B 382 ASP cc_start: 0.7829 (OUTLIER) cc_final: 0.7350 (p0) outliers start: 31 outliers final: 25 residues processed: 101 average time/residue: 0.1321 time to fit residues: 19.8368 Evaluate side-chains 105 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 78 time to evaluate : 0.740 ------------------------------------------------------------------------------- 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 102 THR Chi-restraints excluded: chain A residue 115 LEU 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 262 GLU Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 341 ASP 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 92 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 179 ASN Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 382 ASP 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 36 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 chunk 75 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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** ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 ASN ** A 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 ASN ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.6265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6608 Z= 0.298 Angle : 0.689 8.380 8962 Z= 0.360 Chirality : 0.042 0.227 1044 Planarity : 0.005 0.032 1112 Dihedral : 4.502 21.691 896 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.02 % Allowed : 26.58 % Favored : 69.40 % 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: 1.04 (0.30), residues: 812 helix: 1.37 (0.21), residues: 642 sheet: None (None), residues: 0 loop : -1.88 (0.51), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 301 HIS 0.005 0.001 HIS A 322 PHE 0.025 0.002 PHE B 178 TYR 0.026 0.002 TYR B 75 ARG 0.004 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 103 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 75 time to evaluate : 0.735 Fit side-chains revert: symmetry clash REVERT: A 375 HIS cc_start: 0.8389 (m90) cc_final: 0.8144 (m90) REVERT: B 179 ASN cc_start: 0.9307 (OUTLIER) cc_final: 0.9017 (m110) REVERT: B 279 ASP cc_start: 0.7677 (t70) cc_final: 0.7448 (t70) REVERT: B 330 GLN cc_start: 0.8215 (tp-100) cc_final: 0.7649 (mm110) REVERT: B 375 HIS cc_start: 0.8487 (m90) cc_final: 0.8227 (m90) REVERT: B 382 ASP cc_start: 0.7887 (OUTLIER) cc_final: 0.7409 (p0) outliers start: 28 outliers final: 23 residues processed: 90 average time/residue: 0.1391 time to fit residues: 18.9427 Evaluate side-chains 98 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 73 time to evaluate : 0.843 ------------------------------------------------------------------------------- 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 102 THR Chi-restraints excluded: chain A residue 115 LEU 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 324 CYS Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain B residue 75 TYR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 179 ASN Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 382 ASP 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: 6.9990 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 66 optimal weight: 0.0570 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.1102 ------------------------------------------------------------------------------- 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 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN B 179 ASN ** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.092475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.069192 restraints weight = 19134.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.072047 restraints weight = 10723.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.074077 restraints weight = 7354.121| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.6417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6608 Z= 0.203 Angle : 0.663 8.727 8962 Z= 0.341 Chirality : 0.040 0.220 1044 Planarity : 0.004 0.032 1112 Dihedral : 4.500 20.283 896 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 4.02 % Allowed : 27.59 % Favored : 68.39 % 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: 1.09 (0.30), residues: 812 helix: 1.41 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -1.99 (0.52), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 301 HIS 0.004 0.001 HIS B 322 PHE 0.031 0.002 PHE B 248 TYR 0.029 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: 1468.14 seconds wall clock time: 27 minutes 40.94 seconds (1660.94 seconds total)