Starting phenix.real_space_refine on Wed Feb 4 00:25:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qjt_53210/02_2026/9qjt_53210.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qjt_53210/02_2026/9qjt_53210.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qjt_53210/02_2026/9qjt_53210.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qjt_53210/02_2026/9qjt_53210.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qjt_53210/02_2026/9qjt_53210.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qjt_53210/02_2026/9qjt_53210.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 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 32 5.16 5 C 5274 2.51 5 N 1185 2.21 5 O 1358 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7849 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 4207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 4207 Classifications: {'peptide': 512} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 25, 'TRANS': 486} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 3642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3642 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 20, 'TRANS': 418} Chain breaks: 10 Time building chain proxies: 1.39, per 1000 atoms: 0.18 Number of scatterers: 7849 At special positions: 0 Unit cell: (93.744, 85.932, 123.69, 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 32 16.00 O 1358 8.00 N 1185 7.00 C 5274 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.54 Conformation dependent library (CDL) restraints added in 175.6 milliseconds 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1864 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 2 sheets defined 80.3% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'B' and resid 4 through 9 Processing helix chain 'B' and resid 20 through 23 Processing helix chain 'B' and resid 24 through 33 Processing helix chain 'B' and resid 56 through 58 No H-bonds generated for 'chain 'B' and resid 56 through 58' Processing helix chain 'B' and resid 59 through 71 removed outlier: 4.005A pdb=" N LEU B 63 " --> pdb=" O ASN B 59 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 97 Processing helix chain 'B' and resid 104 through 116 removed outlier: 3.716A pdb=" N LEU B 108 " --> pdb=" O LYS B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 147 Proline residue: B 136 - end of helix Processing helix chain 'B' and resid 155 through 176 Processing helix chain 'B' and resid 177 through 189 removed outlier: 3.739A pdb=" N TYR B 188 " --> pdb=" O ARG B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 246 Proline residue: B 220 - end of helix removed outlier: 4.378A pdb=" N GLY B 226 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ILE B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LEU B 229 " --> pdb=" O PHE B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 256 removed outlier: 3.575A pdb=" N SER B 256 " --> pdb=" O ILE B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 278 Proline residue: B 268 - end of helix Processing helix chain 'B' and resid 278 through 287 Processing helix chain 'B' and resid 290 through 325 removed outlier: 3.949A pdb=" N VAL B 304 " --> pdb=" O ALA B 300 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ILE B 305 " --> pdb=" O LYS B 301 " (cutoff:3.500A) Proline residue: B 313 - end of helix removed outlier: 4.930A pdb=" N LEU B 322 " --> pdb=" O LEU B 318 " (cutoff:3.500A) Proline residue: B 323 - end of helix Processing helix chain 'B' and resid 358 through 369 removed outlier: 3.722A pdb=" N TYR B 366 " --> pdb=" O ASP B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 379 removed outlier: 3.758A pdb=" N LEU B 373 " --> pdb=" O VAL B 369 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU B 379 " --> pdb=" O GLN B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 395 removed outlier: 3.648A pdb=" N GLN B 391 " --> pdb=" O SER B 387 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS B 392 " --> pdb=" O ILE B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 411 removed outlier: 4.014A pdb=" N GLU B 404 " --> pdb=" O PHE B 400 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ILE B 407 " --> pdb=" O ALA B 403 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N GLY B 408 " --> pdb=" O GLU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 429 Processing helix chain 'B' and resid 430 through 433 removed outlier: 3.536A pdb=" N ALA B 433 " --> pdb=" O PRO B 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 430 through 433' Processing helix chain 'B' and resid 436 through 455 Processing helix chain 'B' and resid 460 through 483 Processing helix chain 'B' and resid 509 through 534 Processing helix chain 'B' and resid 562 through 590 Processing helix chain 'A' and resid 27 through 33 Processing helix chain 'A' and resid 61 through 71 removed outlier: 3.895A pdb=" N ASN A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ASP A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 97 removed outlier: 3.793A pdb=" N SER A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 removed outlier: 4.169A pdb=" N LEU A 108 " --> pdb=" O LYS A 104 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR A 109 " --> pdb=" O GLN A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 147 Proline residue: A 136 - end of helix Processing helix chain 'A' and resid 155 through 176 Processing helix chain 'A' and resid 177 through 186 removed outlier: 3.534A pdb=" N ASP A 183 " --> pdb=" O PRO A 179 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG A 184 " --> pdb=" O PHE A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 218 through 246 Processing helix chain 'A' and resid 262 through 277 Proline residue: A 268 - end of helix removed outlier: 3.609A pdb=" N THR A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL A 272 " --> pdb=" O PRO A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 287 Processing helix chain 'A' and resid 294 through 325 removed outlier: 4.419A pdb=" N VAL A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ILE A 305 " --> pdb=" O LYS A 301 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE A 306 " --> pdb=" O ASN A 302 " (cutoff:3.500A) Proline residue: A 313 - end of helix removed outlier: 4.247A pdb=" N LEU A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Proline residue: A 323 - end of helix Processing helix chain 'A' and resid 358 through 369 removed outlier: 3.714A pdb=" N ASP A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 377 removed outlier: 3.510A pdb=" N LEU A 373 " --> pdb=" O VAL A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 428 Processing helix chain 'A' and resid 429 through 433 Processing helix chain 'A' and resid 436 through 455 removed outlier: 3.511A pdb=" N ASN A 440 " --> pdb=" O ASP A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 458 No H-bonds generated for 'chain 'A' and resid 456 through 458' Processing helix chain 'A' and resid 460 through 483 Processing helix chain 'A' and resid 509 through 533 removed outlier: 3.625A pdb=" N SER A 513 " --> pdb=" O GLY A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 591 removed outlier: 3.792A pdb=" N SER A 591 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 38 through 42 removed outlier: 3.558A pdb=" N SER B 49 " --> pdb=" O PHE B 16 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE B 16 " --> pdb=" O SER B 49 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS B 12 " --> pdb=" O ILE B 53 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ASN B 17 " --> pdb=" O ILE B 73 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ILE B 73 " --> pdb=" O ASN B 17 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 42 removed outlier: 3.577A pdb=" N PHE A 16 " --> pdb=" O SER A 49 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL A 13 " --> pdb=" O ILE A 76 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ILE A 76 " --> pdb=" O VAL A 13 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N VAL A 15 " --> pdb=" O GLU A 74 " (cutoff:3.500A) 540 hydrogen bonds defined for protein. 1605 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: 1.10 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2234 1.34 - 1.46: 1627 1.46 - 1.58: 4170 1.58 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 8079 Sorted by residual: bond pdb=" N LEU A 63 " pdb=" CA LEU A 63 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.17e-02 7.31e+03 6.92e+00 bond pdb=" C LYS A 61 " pdb=" N PRO A 62 " ideal model delta sigma weight residual 1.334 1.362 -0.028 2.34e-02 1.83e+03 1.42e+00 bond pdb=" CA LEU A 63 " pdb=" C LEU A 63 " ideal model delta sigma weight residual 1.524 1.539 -0.014 1.24e-02 6.50e+03 1.37e+00 bond pdb=" C LEU A 63 " pdb=" O LEU A 63 " ideal model delta sigma weight residual 1.236 1.248 -0.012 1.15e-02 7.56e+03 1.06e+00 bond pdb=" N ASP B 71 " pdb=" CA ASP B 71 " ideal model delta sigma weight residual 1.457 1.471 -0.013 1.29e-02 6.01e+03 1.04e+00 ... (remaining 8074 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 10666 1.64 - 3.29: 235 3.29 - 4.93: 42 4.93 - 6.57: 26 6.57 - 8.21: 3 Bond angle restraints: 10972 Sorted by residual: angle pdb=" N LEU A 63 " pdb=" CA LEU A 63 " pdb=" CB LEU A 63 " ideal model delta sigma weight residual 109.91 116.29 -6.38 1.46e+00 4.69e-01 1.91e+01 angle pdb=" C ILE B 135 " pdb=" CA ILE B 135 " pdb=" CB ILE B 135 " ideal model delta sigma weight residual 113.70 110.69 3.01 9.50e-01 1.11e+00 1.00e+01 angle pdb=" C LEU B 70 " pdb=" N ASP B 71 " pdb=" CA ASP B 71 " ideal model delta sigma weight residual 121.54 126.92 -5.38 1.91e+00 2.74e-01 7.95e+00 angle pdb=" N LEU A 63 " pdb=" CA LEU A 63 " pdb=" C LEU A 63 " ideal model delta sigma weight residual 110.97 108.10 2.87 1.09e+00 8.42e-01 6.93e+00 angle pdb=" CA LEU B 46 " pdb=" CB LEU B 46 " pdb=" CG LEU B 46 " ideal model delta sigma weight residual 116.30 124.51 -8.21 3.50e+00 8.16e-02 5.51e+00 ... (remaining 10967 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 3963 17.77 - 35.54: 554 35.54 - 53.31: 166 53.31 - 71.08: 23 71.08 - 88.85: 6 Dihedral angle restraints: 4712 sinusoidal: 1859 harmonic: 2853 Sorted by residual: dihedral pdb=" CA ASP A 9 " pdb=" CB ASP A 9 " pdb=" CG ASP A 9 " pdb=" OD1 ASP A 9 " ideal model delta sinusoidal sigma weight residual -30.00 -89.25 59.25 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CB GLU B 240 " pdb=" CG GLU B 240 " pdb=" CD GLU B 240 " pdb=" OE1 GLU B 240 " ideal model delta sinusoidal sigma weight residual 0.00 -87.56 87.56 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CA LEU B 174 " pdb=" C LEU B 174 " pdb=" N TYR B 175 " pdb=" CA TYR B 175 " ideal model delta harmonic sigma weight residual 180.00 -164.27 -15.73 0 5.00e+00 4.00e-02 9.90e+00 ... (remaining 4709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 885 0.043 - 0.087: 285 0.087 - 0.130: 66 0.130 - 0.174: 7 0.174 - 0.217: 2 Chirality restraints: 1245 Sorted by residual: chirality pdb=" CB ILE B 36 " pdb=" CA ILE B 36 " pdb=" CG1 ILE B 36 " pdb=" CG2 ILE B 36 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA ASP B 71 " pdb=" N ASP B 71 " pdb=" C ASP B 71 " pdb=" CB ASP B 71 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.06e-01 chirality pdb=" CA ASP B 87 " pdb=" N ASP B 87 " pdb=" C ASP B 87 " pdb=" CB ASP B 87 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.28e-01 ... (remaining 1242 not shown) Planarity restraints: 1324 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP B 71 " -0.010 2.00e-02 2.50e+03 2.00e-02 4.00e+00 pdb=" CG ASP B 71 " 0.035 2.00e-02 2.50e+03 pdb=" OD1 ASP B 71 " -0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP B 71 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 449 " 0.009 2.00e-02 2.50e+03 1.86e-02 3.47e+00 pdb=" C GLY A 449 " -0.032 2.00e-02 2.50e+03 pdb=" O GLY A 449 " 0.012 2.00e-02 2.50e+03 pdb=" N TYR A 450 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 61 " -0.028 5.00e-02 4.00e+02 4.19e-02 2.80e+00 pdb=" N PRO A 62 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 62 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 62 " -0.023 5.00e-02 4.00e+02 ... (remaining 1321 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 3611 2.93 - 3.43: 9174 3.43 - 3.92: 13429 3.92 - 4.41: 15305 4.41 - 4.90: 24016 Nonbonded interactions: 65535 Sorted by model distance: nonbonded pdb=" O LEU B 70 " pdb=" OD1 ASP B 71 " model vdw 2.442 3.040 nonbonded pdb=" O LEU B 84 " pdb=" OD1 ASP B 87 " model vdw 2.483 3.040 nonbonded pdb=" N THR B 19 " pdb=" OG1 THR B 19 " model vdw 2.532 2.496 nonbonded pdb=" C THR A 4 " pdb=" OG1 THR A 4 " model vdw 2.535 2.616 nonbonded pdb=" O TYR B 366 " pdb=" N ASN B 371 " model vdw 2.561 3.120 ... (remaining 65530 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 187 or resid 208 through 591)) selection = (chain 'B' and (resid 3 through 17 or resid 26 through 54 or resid 57 through 14 \ 7 or resid 152 through 187 or resid 189 through 190 or resid 210 through 247 or \ resid 261 through 288 or resid 293 through 325 or resid 356 through 377 or resid \ 413 through 492 or resid 508 through 591)) } 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: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.660 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 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:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6659 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 : 0.003 0.040 8079 Z= 0.159 Angle : 0.664 8.215 10972 Z= 0.353 Chirality : 0.044 0.217 1245 Planarity : 0.004 0.042 1324 Dihedral : 17.848 88.847 2848 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 6.29 % Allowed : 26.97 % Favored : 66.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.28), residues: 919 helix: 1.20 (0.20), residues: 667 sheet: -1.43 (0.84), residues: 38 loop : -1.35 (0.43), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 478 TYR 0.013 0.001 TYR B 426 PHE 0.020 0.001 PHE B 266 TRP 0.010 0.001 TRP A 165 HIS 0.006 0.001 HIS A 288 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 8079) covalent geometry : angle 0.66430 (10972) hydrogen bonds : bond 0.13029 ( 540) hydrogen bonds : angle 6.58026 ( 1605) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 233 time to evaluate : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 ASP cc_start: 0.7672 (t0) cc_final: 0.6868 (t0) REVERT: B 11 ASN cc_start: 0.7018 (m-40) cc_final: 0.6333 (m110) REVERT: B 35 ASN cc_start: 0.7413 (OUTLIER) cc_final: 0.6570 (p0) REVERT: B 41 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7207 (mm-30) REVERT: B 54 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.6891 (tmt-80) REVERT: B 84 LEU cc_start: 0.8144 (mm) cc_final: 0.7418 (mt) REVERT: B 85 SER cc_start: 0.8024 (t) cc_final: 0.7652 (p) REVERT: B 132 LYS cc_start: 0.7456 (ttpt) cc_final: 0.7193 (mtpp) REVERT: B 133 TRP cc_start: 0.7624 (m100) cc_final: 0.6674 (m-10) REVERT: B 177 TYR cc_start: 0.6788 (m-80) cc_final: 0.6534 (m-80) REVERT: B 223 LEU cc_start: 0.7184 (OUTLIER) cc_final: 0.6932 (mm) REVERT: B 229 LEU cc_start: 0.8589 (tt) cc_final: 0.7832 (tp) REVERT: B 233 GLN cc_start: 0.7998 (mm-40) cc_final: 0.7581 (mm-40) REVERT: B 239 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.8023 (mm) REVERT: B 288 HIS cc_start: 0.6867 (m90) cc_final: 0.6519 (m90) REVERT: B 293 ASN cc_start: 0.7820 (m-40) cc_final: 0.7391 (m-40) REVERT: B 296 LYS cc_start: 0.8455 (ptmt) cc_final: 0.7916 (ptmt) REVERT: B 297 SER cc_start: 0.8355 (p) cc_final: 0.7857 (p) REVERT: B 358 LYS cc_start: 0.8104 (mmtt) cc_final: 0.7750 (tptt) REVERT: B 417 MET cc_start: 0.7352 (mtp) cc_final: 0.7142 (mtp) REVERT: B 427 GLN cc_start: 0.8729 (mm-40) cc_final: 0.8461 (mm-40) REVERT: B 436 ASP cc_start: 0.7624 (t0) cc_final: 0.7068 (t0) REVERT: B 491 PHE cc_start: 0.7825 (p90) cc_final: 0.7601 (p90) REVERT: B 513 SER cc_start: 0.7620 (t) cc_final: 0.7374 (p) REVERT: B 572 PHE cc_start: 0.7393 (t80) cc_final: 0.6978 (t80) REVERT: B 574 GLU cc_start: 0.7563 (tm-30) cc_final: 0.7278 (tm-30) REVERT: A 37 HIS cc_start: 0.6465 (p-80) cc_final: 0.6166 (p-80) REVERT: A 53 ILE cc_start: 0.7246 (mp) cc_final: 0.7005 (tp) REVERT: A 85 SER cc_start: 0.7047 (OUTLIER) cc_final: 0.6766 (p) REVERT: A 89 HIS cc_start: 0.7034 (m-70) cc_final: 0.6763 (m-70) REVERT: A 97 SER cc_start: 0.7759 (OUTLIER) cc_final: 0.7302 (m) REVERT: A 133 TRP cc_start: 0.6993 (m100) cc_final: 0.6423 (m100) REVERT: A 161 PHE cc_start: 0.7353 (t80) cc_final: 0.6602 (t80) REVERT: A 165 TRP cc_start: 0.6006 (t60) cc_final: 0.5790 (t60) REVERT: A 178 GLU cc_start: 0.7033 (tm-30) cc_final: 0.6796 (tm-30) REVERT: A 274 TYR cc_start: 0.7143 (t80) cc_final: 0.6883 (t80) REVERT: A 287 ASN cc_start: 0.8310 (t0) cc_final: 0.7994 (t0) REVERT: A 299 GLU cc_start: 0.7987 (tp30) cc_final: 0.7736 (tp30) REVERT: A 358 LYS cc_start: 0.8267 (pptt) cc_final: 0.7930 (ttpp) REVERT: A 363 GLN cc_start: 0.8076 (tm-30) cc_final: 0.7570 (tm-30) REVERT: A 367 PHE cc_start: 0.6068 (m-80) cc_final: 0.5798 (m-80) REVERT: A 441 PHE cc_start: 0.8450 (OUTLIER) cc_final: 0.7752 (m-80) REVERT: A 453 MET cc_start: 0.7427 (mtt) cc_final: 0.7085 (mtp) REVERT: A 584 PHE cc_start: 0.7783 (m-80) cc_final: 0.7203 (m-80) outliers start: 56 outliers final: 40 residues processed: 268 average time/residue: 0.0674 time to fit residues: 25.1422 Evaluate side-chains 281 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 234 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 359 ARG Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 560 ASN Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 589 LYS Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 44 HIS Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 472 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.0970 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.0770 chunk 74 optimal weight: 1.9990 overall best weight: 0.5336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 HIS B 128 GLN B 512 ASN A 57 GLN A 565 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.156519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.137532 restraints weight = 15989.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.141857 restraints weight = 8865.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.144852 restraints weight = 5636.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.146753 restraints weight = 3937.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.148276 restraints weight = 3011.475| |-----------------------------------------------------------------------------| r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 moved from start: 0.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 8079 Z= 0.161 Angle : 0.651 12.364 10972 Z= 0.323 Chirality : 0.044 0.210 1245 Planarity : 0.004 0.045 1324 Dihedral : 9.025 53.524 1091 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 5.84 % Allowed : 26.63 % Favored : 67.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.28), residues: 919 helix: 1.30 (0.20), residues: 685 sheet: -1.32 (0.82), residues: 38 loop : -1.21 (0.45), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 33 TYR 0.022 0.001 TYR B 321 PHE 0.018 0.001 PHE A 232 TRP 0.009 0.001 TRP A 165 HIS 0.003 0.001 HIS A 288 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 8079) covalent geometry : angle 0.65084 (10972) hydrogen bonds : bond 0.04771 ( 540) hydrogen bonds : angle 5.49710 ( 1605) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 240 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 ASP cc_start: 0.7680 (t0) cc_final: 0.7096 (t0) REVERT: B 54 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7533 (tpt170) REVERT: B 84 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.8003 (mt) REVERT: B 85 SER cc_start: 0.7984 (t) cc_final: 0.7649 (p) REVERT: B 90 LYS cc_start: 0.8348 (ptpt) cc_final: 0.7845 (ptpt) REVERT: B 91 LEU cc_start: 0.8019 (tt) cc_final: 0.7607 (tp) REVERT: B 119 LYS cc_start: 0.8007 (mttt) cc_final: 0.7283 (mmmm) REVERT: B 132 LYS cc_start: 0.7452 (ttpt) cc_final: 0.7197 (mtpp) REVERT: B 133 TRP cc_start: 0.7740 (m100) cc_final: 0.6824 (m-10) REVERT: B 177 TYR cc_start: 0.6698 (m-80) cc_final: 0.6433 (m-80) REVERT: B 229 LEU cc_start: 0.8707 (tt) cc_final: 0.7960 (tp) REVERT: B 233 GLN cc_start: 0.8051 (mm-40) cc_final: 0.7632 (mm-40) REVERT: B 239 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7925 (mm) REVERT: B 240 GLU cc_start: 0.7446 (tp30) cc_final: 0.7106 (tp30) REVERT: B 293 ASN cc_start: 0.7780 (m-40) cc_final: 0.7318 (m-40) REVERT: B 296 LYS cc_start: 0.8455 (ptmt) cc_final: 0.7911 (ptmt) REVERT: B 297 SER cc_start: 0.8383 (p) cc_final: 0.7855 (p) REVERT: B 299 GLU cc_start: 0.7826 (tp30) cc_final: 0.7342 (tp30) REVERT: B 302 ASN cc_start: 0.7163 (t0) cc_final: 0.6906 (t0) REVERT: B 358 LYS cc_start: 0.8005 (mmtt) cc_final: 0.7625 (tptt) REVERT: B 417 MET cc_start: 0.7337 (mtp) cc_final: 0.7077 (mtp) REVERT: B 438 ASP cc_start: 0.6789 (OUTLIER) cc_final: 0.6565 (t0) REVERT: B 491 PHE cc_start: 0.7849 (p90) cc_final: 0.7615 (p90) REVERT: B 513 SER cc_start: 0.7557 (t) cc_final: 0.7294 (p) REVERT: B 569 TYR cc_start: 0.7067 (t80) cc_final: 0.6799 (t80) REVERT: B 572 PHE cc_start: 0.7428 (t80) cc_final: 0.7153 (t80) REVERT: B 574 GLU cc_start: 0.7536 (tm-30) cc_final: 0.7255 (tm-30) REVERT: A 37 HIS cc_start: 0.6404 (p-80) cc_final: 0.6114 (p-80) REVERT: A 40 ILE cc_start: 0.8140 (mm) cc_final: 0.7831 (tp) REVERT: A 89 HIS cc_start: 0.6981 (m-70) cc_final: 0.6725 (m-70) REVERT: A 133 TRP cc_start: 0.7048 (m100) cc_final: 0.6455 (m100) REVERT: A 165 TRP cc_start: 0.5971 (t60) cc_final: 0.5762 (t60) REVERT: A 178 GLU cc_start: 0.7025 (tm-30) cc_final: 0.6783 (tm-30) REVERT: A 282 MET cc_start: 0.6878 (mtt) cc_final: 0.6559 (mtm) REVERT: A 298 LYS cc_start: 0.8176 (mtmt) cc_final: 0.7968 (mtmt) REVERT: A 363 GLN cc_start: 0.7983 (tm-30) cc_final: 0.7477 (tm-30) REVERT: A 367 PHE cc_start: 0.6295 (m-80) cc_final: 0.5967 (m-80) REVERT: A 441 PHE cc_start: 0.8392 (OUTLIER) cc_final: 0.7681 (m-80) REVERT: A 453 MET cc_start: 0.7320 (mtt) cc_final: 0.6969 (mtp) outliers start: 52 outliers final: 37 residues processed: 270 average time/residue: 0.0629 time to fit residues: 23.7026 Evaluate side-chains 283 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 241 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 68 GLN Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 431 TRP Chi-restraints excluded: chain B residue 438 ASP Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 560 ASN Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 582 PHE Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 44 HIS Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 296 LYS Chi-restraints excluded: chain A residue 441 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 13 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 GLN B 363 GLN B 427 GLN ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.155257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.136325 restraints weight = 15905.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.140497 restraints weight = 8792.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.143404 restraints weight = 5595.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.145166 restraints weight = 3935.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.146699 restraints weight = 3040.910| |-----------------------------------------------------------------------------| r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8079 Z= 0.181 Angle : 0.666 11.287 10972 Z= 0.337 Chirality : 0.045 0.200 1245 Planarity : 0.004 0.046 1324 Dihedral : 7.790 57.636 1045 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 6.52 % Allowed : 26.97 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.28), residues: 919 helix: 1.31 (0.20), residues: 683 sheet: -1.49 (0.76), residues: 38 loop : -1.25 (0.45), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 54 TYR 0.016 0.001 TYR A 569 PHE 0.026 0.002 PHE A 232 TRP 0.010 0.001 TRP B 181 HIS 0.006 0.001 HIS B 56 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 8079) covalent geometry : angle 0.66612 (10972) hydrogen bonds : bond 0.04667 ( 540) hydrogen bonds : angle 5.40249 ( 1605) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 239 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 ASP cc_start: 0.7761 (t0) cc_final: 0.7225 (t0) REVERT: B 41 GLU cc_start: 0.7232 (mm-30) cc_final: 0.6932 (mm-30) REVERT: B 47 GLN cc_start: 0.7437 (pm20) cc_final: 0.7089 (pm20) REVERT: B 54 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7669 (tpt170) REVERT: B 85 SER cc_start: 0.7965 (t) cc_final: 0.7653 (p) REVERT: B 119 LYS cc_start: 0.8033 (mttt) cc_final: 0.7259 (mmmm) REVERT: B 132 LYS cc_start: 0.7511 (ttpt) cc_final: 0.7228 (mtpp) REVERT: B 133 TRP cc_start: 0.7757 (m100) cc_final: 0.6847 (m-10) REVERT: B 177 TYR cc_start: 0.6735 (m-80) cc_final: 0.6513 (m-80) REVERT: B 212 MET cc_start: 0.6734 (mmm) cc_final: 0.6268 (tmm) REVERT: B 229 LEU cc_start: 0.8729 (tt) cc_final: 0.8044 (tp) REVERT: B 233 GLN cc_start: 0.8067 (mm-40) cc_final: 0.7656 (mm-40) REVERT: B 239 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7935 (mm) REVERT: B 293 ASN cc_start: 0.7812 (m-40) cc_final: 0.7330 (m-40) REVERT: B 296 LYS cc_start: 0.8451 (ptmt) cc_final: 0.7922 (ptmt) REVERT: B 297 SER cc_start: 0.8381 (p) cc_final: 0.7886 (p) REVERT: B 299 GLU cc_start: 0.7749 (tp30) cc_final: 0.7541 (tp30) REVERT: B 358 LYS cc_start: 0.7941 (mmtt) cc_final: 0.7644 (tppt) REVERT: B 417 MET cc_start: 0.7468 (mtp) cc_final: 0.7200 (mtp) REVERT: B 491 PHE cc_start: 0.7897 (p90) cc_final: 0.7693 (p90) REVERT: B 513 SER cc_start: 0.7626 (t) cc_final: 0.7384 (p) REVERT: B 572 PHE cc_start: 0.7595 (t80) cc_final: 0.7334 (t80) REVERT: B 574 GLU cc_start: 0.7531 (tm-30) cc_final: 0.7271 (tm-30) REVERT: A 37 HIS cc_start: 0.6580 (p-80) cc_final: 0.6252 (p-80) REVERT: A 59 ASN cc_start: 0.8014 (t0) cc_final: 0.7812 (t0) REVERT: A 89 HIS cc_start: 0.7029 (m-70) cc_final: 0.6699 (m-70) REVERT: A 133 TRP cc_start: 0.7091 (m100) cc_final: 0.6427 (m100) REVERT: A 161 PHE cc_start: 0.7421 (t80) cc_final: 0.6685 (t80) REVERT: A 165 TRP cc_start: 0.5927 (t60) cc_final: 0.5677 (t60) REVERT: A 178 GLU cc_start: 0.7050 (tm-30) cc_final: 0.6825 (tm-30) REVERT: A 280 GLU cc_start: 0.6992 (OUTLIER) cc_final: 0.6715 (pm20) REVERT: A 282 MET cc_start: 0.6873 (mtt) cc_final: 0.6631 (mtt) REVERT: A 287 ASN cc_start: 0.8239 (t0) cc_final: 0.8038 (t0) REVERT: A 358 LYS cc_start: 0.8333 (pptt) cc_final: 0.7798 (ptmm) REVERT: A 367 PHE cc_start: 0.6340 (m-80) cc_final: 0.6059 (m-80) REVERT: A 441 PHE cc_start: 0.8425 (OUTLIER) cc_final: 0.7658 (m-80) REVERT: A 453 MET cc_start: 0.7357 (mtt) cc_final: 0.6978 (mtp) outliers start: 58 outliers final: 40 residues processed: 270 average time/residue: 0.0622 time to fit residues: 23.5667 Evaluate side-chains 279 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 235 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 68 GLN Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 431 TRP Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 560 ASN Chi-restraints excluded: chain B residue 582 PHE Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 44 HIS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 295 LYS Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 472 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 82 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 33 optimal weight: 0.1980 chunk 15 optimal weight: 0.9980 chunk 5 optimal weight: 0.0770 chunk 92 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 93 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.157232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.138419 restraints weight = 16052.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.142683 restraints weight = 8778.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.145592 restraints weight = 5514.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.147504 restraints weight = 3851.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.149033 restraints weight = 2923.172| |-----------------------------------------------------------------------------| r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6594 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8079 Z= 0.151 Angle : 0.659 11.561 10972 Z= 0.328 Chirality : 0.044 0.174 1245 Planarity : 0.004 0.047 1324 Dihedral : 7.309 56.776 1039 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 6.07 % Allowed : 29.44 % Favored : 64.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.28), residues: 919 helix: 1.44 (0.20), residues: 677 sheet: -1.34 (0.77), residues: 38 loop : -1.29 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 478 TYR 0.017 0.001 TYR A 569 PHE 0.027 0.001 PHE A 232 TRP 0.010 0.001 TRP A 165 HIS 0.004 0.001 HIS B 56 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 8079) covalent geometry : angle 0.65859 (10972) hydrogen bonds : bond 0.04393 ( 540) hydrogen bonds : angle 5.21861 ( 1605) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 250 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 ASP cc_start: 0.7723 (t0) cc_final: 0.7095 (t0) REVERT: B 54 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7516 (tpt170) REVERT: B 85 SER cc_start: 0.7965 (t) cc_final: 0.7640 (p) REVERT: B 119 LYS cc_start: 0.8041 (mttt) cc_final: 0.7217 (mmmm) REVERT: B 132 LYS cc_start: 0.7512 (ttpt) cc_final: 0.7235 (mtpp) REVERT: B 133 TRP cc_start: 0.7761 (m100) cc_final: 0.6868 (m-10) REVERT: B 177 TYR cc_start: 0.6743 (m-80) cc_final: 0.6505 (m-80) REVERT: B 212 MET cc_start: 0.6715 (mmm) cc_final: 0.6152 (tmm) REVERT: B 229 LEU cc_start: 0.8672 (tt) cc_final: 0.7945 (tp) REVERT: B 233 GLN cc_start: 0.8050 (mm-40) cc_final: 0.7501 (mm-40) REVERT: B 239 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7924 (mm) REVERT: B 293 ASN cc_start: 0.7798 (m-40) cc_final: 0.7336 (m-40) REVERT: B 296 LYS cc_start: 0.8390 (ptmt) cc_final: 0.7863 (ptmt) REVERT: B 297 SER cc_start: 0.8345 (p) cc_final: 0.7880 (p) REVERT: B 298 LYS cc_start: 0.7798 (mtpt) cc_final: 0.7540 (mtpt) REVERT: B 362 ASP cc_start: 0.7089 (m-30) cc_final: 0.6704 (t0) REVERT: B 363 GLN cc_start: 0.7148 (mt0) cc_final: 0.6933 (mt0) REVERT: B 400 PHE cc_start: 0.6223 (m-80) cc_final: 0.5990 (m-80) REVERT: B 417 MET cc_start: 0.7479 (mtp) cc_final: 0.7207 (mtp) REVERT: B 491 PHE cc_start: 0.7916 (p90) cc_final: 0.7706 (p90) REVERT: B 513 SER cc_start: 0.7588 (t) cc_final: 0.7347 (p) REVERT: B 566 ILE cc_start: 0.6979 (OUTLIER) cc_final: 0.6689 (mm) REVERT: B 572 PHE cc_start: 0.7514 (t80) cc_final: 0.7270 (t80) REVERT: B 574 GLU cc_start: 0.7526 (tm-30) cc_final: 0.7255 (tm-30) REVERT: A 59 ASN cc_start: 0.7967 (t0) cc_final: 0.7700 (t0) REVERT: A 89 HIS cc_start: 0.7058 (m-70) cc_final: 0.6714 (m-70) REVERT: A 105 GLN cc_start: 0.6652 (mp10) cc_final: 0.6372 (mp10) REVERT: A 133 TRP cc_start: 0.7074 (m100) cc_final: 0.6377 (m100) REVERT: A 165 TRP cc_start: 0.5903 (t60) cc_final: 0.5663 (t60) REVERT: A 178 GLU cc_start: 0.6976 (tm-30) cc_final: 0.6747 (tm-30) REVERT: A 282 MET cc_start: 0.6832 (mtt) cc_final: 0.6570 (mtt) REVERT: A 287 ASN cc_start: 0.8231 (t0) cc_final: 0.8003 (t0) REVERT: A 358 LYS cc_start: 0.8374 (pptt) cc_final: 0.7822 (ptmm) REVERT: A 367 PHE cc_start: 0.6213 (m-80) cc_final: 0.5969 (m-80) REVERT: A 441 PHE cc_start: 0.8391 (OUTLIER) cc_final: 0.7661 (m-80) REVERT: A 453 MET cc_start: 0.7310 (mtt) cc_final: 0.6955 (mtp) REVERT: A 517 MET cc_start: 0.7916 (tmm) cc_final: 0.7650 (tmm) outliers start: 54 outliers final: 39 residues processed: 281 average time/residue: 0.0685 time to fit residues: 26.7001 Evaluate side-chains 282 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 239 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 68 GLN Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 431 TRP Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 560 ASN Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 44 HIS Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 472 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 41 optimal weight: 0.9980 chunk 44 optimal weight: 0.1980 chunk 9 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 77 optimal weight: 0.0020 chunk 72 optimal weight: 4.9990 chunk 60 optimal weight: 0.0970 chunk 43 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 overall best weight: 0.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 GLN ** 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 = 0.4140 r_free = 0.4140 target = 0.157401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.139198 restraints weight = 15892.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.143261 restraints weight = 8793.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.146089 restraints weight = 5594.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.147920 restraints weight = 3921.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.149352 restraints weight = 2981.588| |-----------------------------------------------------------------------------| r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6574 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8079 Z= 0.141 Angle : 0.671 11.561 10972 Z= 0.331 Chirality : 0.044 0.180 1245 Planarity : 0.004 0.048 1324 Dihedral : 7.213 56.537 1039 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 5.73 % Allowed : 30.22 % Favored : 64.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.28), residues: 919 helix: 1.45 (0.20), residues: 678 sheet: -1.30 (0.76), residues: 38 loop : -1.31 (0.45), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 33 TYR 0.028 0.002 TYR B 488 PHE 0.025 0.001 PHE A 232 TRP 0.011 0.001 TRP B 285 HIS 0.004 0.001 HIS B 56 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 8079) covalent geometry : angle 0.67112 (10972) hydrogen bonds : bond 0.04250 ( 540) hydrogen bonds : angle 5.10529 ( 1605) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 243 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 ASP cc_start: 0.7665 (t0) cc_final: 0.7134 (t70) REVERT: B 54 ARG cc_start: 0.8166 (tmt-80) cc_final: 0.7515 (tpt170) REVERT: B 120 GLN cc_start: 0.8101 (mt0) cc_final: 0.7896 (mt0) REVERT: B 132 LYS cc_start: 0.7510 (ttpt) cc_final: 0.7256 (mtpp) REVERT: B 133 TRP cc_start: 0.7752 (m100) cc_final: 0.6802 (m-10) REVERT: B 177 TYR cc_start: 0.6713 (m-80) cc_final: 0.6465 (m-80) REVERT: B 212 MET cc_start: 0.6667 (mmm) cc_final: 0.6190 (tmm) REVERT: B 229 LEU cc_start: 0.8756 (tt) cc_final: 0.8331 (tp) REVERT: B 233 GLN cc_start: 0.8104 (mm-40) cc_final: 0.7868 (mm-40) REVERT: B 242 PHE cc_start: 0.6809 (t80) cc_final: 0.6599 (t80) REVERT: B 243 ILE cc_start: 0.8180 (mm) cc_final: 0.7965 (mm) REVERT: B 288 HIS cc_start: 0.6709 (m90) cc_final: 0.6430 (m-70) REVERT: B 293 ASN cc_start: 0.7776 (m-40) cc_final: 0.7292 (m-40) REVERT: B 296 LYS cc_start: 0.8376 (ptmt) cc_final: 0.7848 (ptmt) REVERT: B 297 SER cc_start: 0.8326 (p) cc_final: 0.7789 (p) REVERT: B 299 GLU cc_start: 0.7726 (tp30) cc_final: 0.7378 (tp30) REVERT: B 375 GLN cc_start: 0.7548 (tp40) cc_final: 0.7272 (tp40) REVERT: B 400 PHE cc_start: 0.6416 (m-80) cc_final: 0.6037 (m-80) REVERT: B 513 SER cc_start: 0.7559 (t) cc_final: 0.7308 (p) REVERT: B 566 ILE cc_start: 0.6959 (OUTLIER) cc_final: 0.6658 (mm) REVERT: B 574 GLU cc_start: 0.7518 (tm-30) cc_final: 0.7241 (tm-30) REVERT: A 59 ASN cc_start: 0.8252 (t0) cc_final: 0.7972 (t0) REVERT: A 89 HIS cc_start: 0.7003 (m-70) cc_final: 0.6658 (m-70) REVERT: A 133 TRP cc_start: 0.7039 (m100) cc_final: 0.6268 (m100) REVERT: A 144 ILE cc_start: 0.6605 (pt) cc_final: 0.6253 (tp) REVERT: A 165 TRP cc_start: 0.5881 (t60) cc_final: 0.5677 (t60) REVERT: A 178 GLU cc_start: 0.6933 (tm-30) cc_final: 0.6716 (tm-30) REVERT: A 282 MET cc_start: 0.6815 (mtt) cc_final: 0.6564 (mtt) REVERT: A 287 ASN cc_start: 0.8189 (t0) cc_final: 0.7881 (t0) REVERT: A 363 GLN cc_start: 0.8057 (tp40) cc_final: 0.7496 (tm-30) REVERT: A 367 PHE cc_start: 0.6184 (m-80) cc_final: 0.5911 (m-80) REVERT: A 441 PHE cc_start: 0.8379 (OUTLIER) cc_final: 0.7668 (m-80) REVERT: A 453 MET cc_start: 0.7374 (mtt) cc_final: 0.7046 (mtp) REVERT: A 476 ASP cc_start: 0.6069 (m-30) cc_final: 0.5842 (m-30) REVERT: A 517 MET cc_start: 0.7927 (tmm) cc_final: 0.7646 (tmm) outliers start: 51 outliers final: 35 residues processed: 277 average time/residue: 0.0642 time to fit residues: 25.3119 Evaluate side-chains 276 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 239 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 431 TRP Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 44 HIS Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 472 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 23 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 60 optimal weight: 0.0470 chunk 20 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.156569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.137612 restraints weight = 15838.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.141820 restraints weight = 8685.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.144592 restraints weight = 5499.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.146646 restraints weight = 3908.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.148056 restraints weight = 2955.485| |-----------------------------------------------------------------------------| r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6608 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8079 Z= 0.166 Angle : 0.701 11.304 10972 Z= 0.348 Chirality : 0.046 0.332 1245 Planarity : 0.004 0.047 1324 Dihedral : 6.596 56.679 1024 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.92 % Favored : 95.97 % Rotamer: Outliers : 5.62 % Allowed : 30.79 % Favored : 63.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.28), residues: 919 helix: 1.35 (0.20), residues: 678 sheet: -1.35 (0.72), residues: 38 loop : -1.27 (0.46), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 33 TYR 0.017 0.002 TYR A 426 PHE 0.025 0.001 PHE A 232 TRP 0.010 0.001 TRP B 181 HIS 0.004 0.001 HIS B 56 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 8079) covalent geometry : angle 0.70132 (10972) hydrogen bonds : bond 0.04358 ( 540) hydrogen bonds : angle 5.18798 ( 1605) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 240 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 ASP cc_start: 0.7656 (t0) cc_final: 0.7066 (t70) REVERT: B 41 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7106 (mm-30) REVERT: B 54 ARG cc_start: 0.8204 (tmt-80) cc_final: 0.7654 (tpt170) REVERT: B 117 ASN cc_start: 0.7952 (t0) cc_final: 0.7568 (t0) REVERT: B 120 GLN cc_start: 0.8139 (mt0) cc_final: 0.7825 (mt0) REVERT: B 132 LYS cc_start: 0.7503 (ttpt) cc_final: 0.7251 (mtpp) REVERT: B 133 TRP cc_start: 0.7749 (m100) cc_final: 0.6798 (m-10) REVERT: B 177 TYR cc_start: 0.6753 (m-80) cc_final: 0.6495 (m-80) REVERT: B 212 MET cc_start: 0.6659 (mmm) cc_final: 0.6176 (tmm) REVERT: B 229 LEU cc_start: 0.8794 (tt) cc_final: 0.8511 (tp) REVERT: B 233 GLN cc_start: 0.8244 (mm-40) cc_final: 0.8031 (mm-40) REVERT: B 240 GLU cc_start: 0.7440 (tp30) cc_final: 0.7223 (tp30) REVERT: B 242 PHE cc_start: 0.6972 (t80) cc_final: 0.6767 (t80) REVERT: B 243 ILE cc_start: 0.8209 (mm) cc_final: 0.7922 (mm) REVERT: B 293 ASN cc_start: 0.7808 (m-40) cc_final: 0.7397 (m-40) REVERT: B 297 SER cc_start: 0.8333 (p) cc_final: 0.7872 (p) REVERT: B 299 GLU cc_start: 0.7721 (tp30) cc_final: 0.7456 (tp30) REVERT: B 375 GLN cc_start: 0.7576 (tp40) cc_final: 0.7274 (tp40) REVERT: B 513 SER cc_start: 0.7587 (t) cc_final: 0.7334 (p) REVERT: B 566 ILE cc_start: 0.6970 (OUTLIER) cc_final: 0.6673 (mm) REVERT: B 574 GLU cc_start: 0.7538 (tm-30) cc_final: 0.7248 (tm-30) REVERT: A 59 ASN cc_start: 0.8219 (t0) cc_final: 0.7934 (t0) REVERT: A 89 HIS cc_start: 0.7057 (m-70) cc_final: 0.6715 (m-70) REVERT: A 133 TRP cc_start: 0.7076 (m100) cc_final: 0.6288 (m100) REVERT: A 144 ILE cc_start: 0.6729 (pt) cc_final: 0.6387 (tp) REVERT: A 161 PHE cc_start: 0.7338 (t80) cc_final: 0.6667 (t80) REVERT: A 165 TRP cc_start: 0.5935 (t60) cc_final: 0.5702 (t60) REVERT: A 178 GLU cc_start: 0.6984 (tm-30) cc_final: 0.6765 (tm-30) REVERT: A 282 MET cc_start: 0.6807 (mtt) cc_final: 0.6543 (mtt) REVERT: A 286 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8180 (mt-10) REVERT: A 287 ASN cc_start: 0.8213 (t0) cc_final: 0.7909 (t0) REVERT: A 295 LYS cc_start: 0.5789 (mtmm) cc_final: 0.5283 (ptpp) REVERT: A 358 LYS cc_start: 0.8493 (pptt) cc_final: 0.8103 (ttpp) REVERT: A 363 GLN cc_start: 0.8081 (tp40) cc_final: 0.7520 (tm-30) REVERT: A 367 PHE cc_start: 0.6358 (m-80) cc_final: 0.6059 (m-80) REVERT: A 441 PHE cc_start: 0.8404 (OUTLIER) cc_final: 0.7688 (m-80) REVERT: A 453 MET cc_start: 0.7411 (mtt) cc_final: 0.7048 (mtp) REVERT: A 476 ASP cc_start: 0.6175 (m-30) cc_final: 0.5957 (m-30) REVERT: A 485 LYS cc_start: 0.7854 (ttmt) cc_final: 0.7322 (ptpt) REVERT: A 584 PHE cc_start: 0.7785 (m-80) cc_final: 0.7204 (m-80) outliers start: 50 outliers final: 42 residues processed: 272 average time/residue: 0.0652 time to fit residues: 25.2903 Evaluate side-chains 284 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 240 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 431 TRP Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 560 ASN Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 44 HIS Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 214 LYS Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 472 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 63 optimal weight: 0.0980 chunk 84 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 73 optimal weight: 0.3980 chunk 72 optimal weight: 0.6980 chunk 61 optimal weight: 0.3980 chunk 12 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 68 optimal weight: 0.0970 chunk 60 optimal weight: 0.8980 overall best weight: 0.3178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 372 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.158522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.139413 restraints weight = 15919.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.143711 restraints weight = 8753.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.146670 restraints weight = 5578.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.148715 restraints weight = 3920.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.150202 restraints weight = 2962.897| |-----------------------------------------------------------------------------| r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6572 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8079 Z= 0.135 Angle : 0.688 11.941 10972 Z= 0.337 Chirality : 0.045 0.191 1245 Planarity : 0.004 0.048 1324 Dihedral : 6.397 57.052 1022 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 5.62 % Allowed : 31.46 % Favored : 62.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.28), residues: 919 helix: 1.43 (0.20), residues: 678 sheet: -1.20 (0.73), residues: 38 loop : -1.22 (0.46), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 359 TYR 0.037 0.002 TYR B 247 PHE 0.026 0.001 PHE B 307 TRP 0.010 0.001 TRP A 165 HIS 0.004 0.001 HIS B 56 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 8079) covalent geometry : angle 0.68785 (10972) hydrogen bonds : bond 0.04144 ( 540) hydrogen bonds : angle 5.05040 ( 1605) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 236 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 ASP cc_start: 0.7585 (t0) cc_final: 0.7039 (t70) REVERT: B 41 GLU cc_start: 0.7428 (mm-30) cc_final: 0.7044 (mm-30) REVERT: B 54 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7716 (tpt170) REVERT: B 117 ASN cc_start: 0.7928 (t0) cc_final: 0.7693 (t0) REVERT: B 132 LYS cc_start: 0.7489 (ttpt) cc_final: 0.7256 (mtpp) REVERT: B 133 TRP cc_start: 0.7728 (m100) cc_final: 0.6782 (m-10) REVERT: B 177 TYR cc_start: 0.6728 (m-80) cc_final: 0.6405 (m-80) REVERT: B 212 MET cc_start: 0.6711 (mmm) cc_final: 0.6184 (tmm) REVERT: B 229 LEU cc_start: 0.8721 (tt) cc_final: 0.8257 (tp) REVERT: B 233 GLN cc_start: 0.8293 (mm-40) cc_final: 0.8048 (mm-40) REVERT: B 240 GLU cc_start: 0.7437 (tp30) cc_final: 0.7228 (tp30) REVERT: B 293 ASN cc_start: 0.7787 (m-40) cc_final: 0.7389 (m-40) REVERT: B 296 LYS cc_start: 0.8444 (ptmt) cc_final: 0.7935 (ptmt) REVERT: B 297 SER cc_start: 0.8273 (p) cc_final: 0.7861 (p) REVERT: B 400 PHE cc_start: 0.6271 (m-80) cc_final: 0.5828 (m-80) REVERT: B 417 MET cc_start: 0.7453 (mtp) cc_final: 0.7220 (mtp) REVERT: B 513 SER cc_start: 0.7559 (t) cc_final: 0.7303 (p) REVERT: B 566 ILE cc_start: 0.6951 (OUTLIER) cc_final: 0.6656 (mm) REVERT: B 574 GLU cc_start: 0.7537 (tm-30) cc_final: 0.7251 (tm-30) REVERT: A 59 ASN cc_start: 0.8260 (t0) cc_final: 0.7994 (t0) REVERT: A 89 HIS cc_start: 0.7018 (m-70) cc_final: 0.6652 (m-70) REVERT: A 133 TRP cc_start: 0.7046 (m100) cc_final: 0.6245 (m100) REVERT: A 165 TRP cc_start: 0.5961 (t60) cc_final: 0.5734 (t60) REVERT: A 178 GLU cc_start: 0.6946 (tm-30) cc_final: 0.6718 (tm-30) REVERT: A 275 ASN cc_start: 0.7313 (m-40) cc_final: 0.6854 (t0) REVERT: A 282 MET cc_start: 0.6741 (mtt) cc_final: 0.6460 (mtt) REVERT: A 286 GLU cc_start: 0.8292 (mt-10) cc_final: 0.8045 (mt-10) REVERT: A 287 ASN cc_start: 0.8169 (t0) cc_final: 0.7858 (t0) REVERT: A 295 LYS cc_start: 0.6483 (mtmm) cc_final: 0.6115 (mptt) REVERT: A 363 GLN cc_start: 0.8056 (tp40) cc_final: 0.7482 (tm-30) REVERT: A 367 PHE cc_start: 0.6318 (m-80) cc_final: 0.6012 (m-80) REVERT: A 441 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.7711 (m-80) REVERT: A 453 MET cc_start: 0.7380 (mtt) cc_final: 0.6988 (mtp) REVERT: A 485 LYS cc_start: 0.7698 (ttmt) cc_final: 0.7154 (ptpt) REVERT: A 584 PHE cc_start: 0.7767 (m-80) cc_final: 0.7187 (m-80) outliers start: 50 outliers final: 35 residues processed: 264 average time/residue: 0.0671 time to fit residues: 25.1146 Evaluate side-chains 272 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 234 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 431 TRP Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 560 ASN Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 44 HIS Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 214 LYS Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 472 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 21 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 74 optimal weight: 0.0970 chunk 71 optimal weight: 0.9990 chunk 88 optimal weight: 0.0870 chunk 26 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 23 optimal weight: 8.9990 chunk 1 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 372 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.158611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.139510 restraints weight = 16002.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.143919 restraints weight = 8769.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.146923 restraints weight = 5561.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.148904 restraints weight = 3896.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.150406 restraints weight = 2947.096| |-----------------------------------------------------------------------------| r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6584 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8079 Z= 0.148 Angle : 0.717 13.476 10972 Z= 0.350 Chirality : 0.045 0.172 1245 Planarity : 0.004 0.048 1324 Dihedral : 6.361 57.566 1021 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 5.84 % Allowed : 31.35 % Favored : 62.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.28), residues: 919 helix: 1.35 (0.20), residues: 678 sheet: -1.20 (0.73), residues: 38 loop : -1.21 (0.46), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 359 TYR 0.027 0.002 TYR A 569 PHE 0.023 0.001 PHE A 232 TRP 0.011 0.001 TRP B 285 HIS 0.004 0.001 HIS B 56 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 8079) covalent geometry : angle 0.71744 (10972) hydrogen bonds : bond 0.04194 ( 540) hydrogen bonds : angle 5.06371 ( 1605) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 235 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 ASP cc_start: 0.7587 (t0) cc_final: 0.7030 (t70) REVERT: B 54 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7740 (tpt170) REVERT: B 117 ASN cc_start: 0.7924 (t0) cc_final: 0.7676 (t0) REVERT: B 132 LYS cc_start: 0.7491 (ttpt) cc_final: 0.7228 (mtpp) REVERT: B 133 TRP cc_start: 0.7747 (m100) cc_final: 0.6809 (m-10) REVERT: B 212 MET cc_start: 0.6621 (mmm) cc_final: 0.6168 (tmm) REVERT: B 229 LEU cc_start: 0.8753 (tt) cc_final: 0.8385 (tp) REVERT: B 233 GLN cc_start: 0.8286 (mm-40) cc_final: 0.8075 (mm-40) REVERT: B 240 GLU cc_start: 0.7331 (tp30) cc_final: 0.7105 (tp30) REVERT: B 275 ASN cc_start: 0.5725 (m110) cc_final: 0.4766 (t0) REVERT: B 276 LYS cc_start: 0.7127 (mmtt) cc_final: 0.6732 (mmtt) REVERT: B 293 ASN cc_start: 0.7785 (m-40) cc_final: 0.7387 (m-40) REVERT: B 296 LYS cc_start: 0.8447 (ptmt) cc_final: 0.7956 (ptmt) REVERT: B 297 SER cc_start: 0.8262 (p) cc_final: 0.7818 (p) REVERT: B 400 PHE cc_start: 0.6303 (m-80) cc_final: 0.5847 (m-80) REVERT: B 417 MET cc_start: 0.7464 (mtp) cc_final: 0.7233 (mtp) REVERT: B 513 SER cc_start: 0.7565 (t) cc_final: 0.7308 (p) REVERT: B 565 ASN cc_start: 0.7205 (m-40) cc_final: 0.6829 (m110) REVERT: B 566 ILE cc_start: 0.6941 (OUTLIER) cc_final: 0.6657 (mm) REVERT: B 574 GLU cc_start: 0.7542 (tm-30) cc_final: 0.7273 (tm-30) REVERT: A 40 ILE cc_start: 0.8209 (OUTLIER) cc_final: 0.7919 (tp) REVERT: A 59 ASN cc_start: 0.8261 (t0) cc_final: 0.8007 (t0) REVERT: A 89 HIS cc_start: 0.7029 (m-70) cc_final: 0.6681 (m-70) REVERT: A 178 GLU cc_start: 0.6895 (tm-30) cc_final: 0.6643 (tm-30) REVERT: A 275 ASN cc_start: 0.7553 (m-40) cc_final: 0.7062 (t0) REVERT: A 282 MET cc_start: 0.6749 (mtt) cc_final: 0.6417 (mtt) REVERT: A 286 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8175 (mt-10) REVERT: A 287 ASN cc_start: 0.8152 (t0) cc_final: 0.7852 (t0) REVERT: A 295 LYS cc_start: 0.6523 (mtmm) cc_final: 0.5829 (mtmm) REVERT: A 324 MET cc_start: 0.7011 (tmm) cc_final: 0.6803 (tpt) REVERT: A 363 GLN cc_start: 0.8050 (tp40) cc_final: 0.7488 (tm-30) REVERT: A 367 PHE cc_start: 0.6371 (m-80) cc_final: 0.6087 (m-80) REVERT: A 441 PHE cc_start: 0.8379 (OUTLIER) cc_final: 0.7654 (m-80) REVERT: A 453 MET cc_start: 0.7416 (mtt) cc_final: 0.7008 (mtp) REVERT: A 529 LEU cc_start: 0.8188 (mm) cc_final: 0.7892 (mt) REVERT: A 584 PHE cc_start: 0.7773 (m-80) cc_final: 0.7205 (m-80) outliers start: 52 outliers final: 41 residues processed: 266 average time/residue: 0.0690 time to fit residues: 25.6998 Evaluate side-chains 277 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 232 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 431 TRP Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 560 ASN Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 44 HIS Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 472 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 53 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 77 optimal weight: 0.0670 chunk 31 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.157131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.138019 restraints weight = 15966.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.142369 restraints weight = 8782.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.145344 restraints weight = 5572.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.147420 restraints weight = 3910.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.148781 restraints weight = 2945.848| |-----------------------------------------------------------------------------| r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8079 Z= 0.188 Angle : 0.753 13.205 10972 Z= 0.374 Chirality : 0.046 0.183 1245 Planarity : 0.004 0.048 1324 Dihedral : 6.449 58.150 1021 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 5.84 % Allowed : 31.57 % Favored : 62.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.28), residues: 919 helix: 1.22 (0.20), residues: 678 sheet: -1.33 (0.72), residues: 38 loop : -1.22 (0.46), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 359 TYR 0.028 0.002 TYR A 426 PHE 0.023 0.001 PHE A 232 TRP 0.025 0.002 TRP A 165 HIS 0.004 0.001 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 8079) covalent geometry : angle 0.75342 (10972) hydrogen bonds : bond 0.04468 ( 540) hydrogen bonds : angle 5.19961 ( 1605) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 233 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7990 (mt) REVERT: B 9 ASP cc_start: 0.7644 (t0) cc_final: 0.6985 (t70) REVERT: B 11 ASN cc_start: 0.7245 (m110) cc_final: 0.6963 (m-40) REVERT: B 31 PHE cc_start: 0.7433 (m-10) cc_final: 0.7204 (m-10) REVERT: B 41 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7005 (mm-30) REVERT: B 54 ARG cc_start: 0.8254 (tmt-80) cc_final: 0.7710 (tpt170) REVERT: B 117 ASN cc_start: 0.7944 (t0) cc_final: 0.7681 (t0) REVERT: B 132 LYS cc_start: 0.7442 (ttpt) cc_final: 0.7168 (mtpp) REVERT: B 133 TRP cc_start: 0.7846 (m100) cc_final: 0.6894 (m-10) REVERT: B 212 MET cc_start: 0.6657 (mmm) cc_final: 0.6194 (tmm) REVERT: B 229 LEU cc_start: 0.8736 (tt) cc_final: 0.8408 (tp) REVERT: B 240 GLU cc_start: 0.7325 (tp30) cc_final: 0.7102 (tp30) REVERT: B 275 ASN cc_start: 0.5712 (m110) cc_final: 0.4762 (t0) REVERT: B 293 ASN cc_start: 0.7791 (m-40) cc_final: 0.7390 (m-40) REVERT: B 296 LYS cc_start: 0.8462 (ptmt) cc_final: 0.7966 (ptmt) REVERT: B 400 PHE cc_start: 0.6864 (m-80) cc_final: 0.6421 (m-80) REVERT: B 417 MET cc_start: 0.7499 (mtp) cc_final: 0.7259 (mtp) REVERT: B 513 SER cc_start: 0.7633 (t) cc_final: 0.7392 (p) REVERT: B 566 ILE cc_start: 0.6961 (OUTLIER) cc_final: 0.6658 (mm) REVERT: B 574 GLU cc_start: 0.7558 (tm-30) cc_final: 0.7290 (tm-30) REVERT: A 40 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7960 (tp) REVERT: A 53 ILE cc_start: 0.7282 (OUTLIER) cc_final: 0.6749 (tp) REVERT: A 89 HIS cc_start: 0.7130 (m-70) cc_final: 0.6784 (m-70) REVERT: A 178 GLU cc_start: 0.6962 (tm-30) cc_final: 0.6745 (tm-30) REVERT: A 282 MET cc_start: 0.6718 (mtt) cc_final: 0.6393 (mtt) REVERT: A 295 LYS cc_start: 0.6201 (mtmm) cc_final: 0.5723 (ptpp) REVERT: A 296 LYS cc_start: 0.7725 (ttpt) cc_final: 0.7463 (tppt) REVERT: A 324 MET cc_start: 0.7067 (tmm) cc_final: 0.6866 (tpt) REVERT: A 363 GLN cc_start: 0.8051 (tp40) cc_final: 0.7822 (tm-30) REVERT: A 367 PHE cc_start: 0.6375 (m-80) cc_final: 0.6140 (m-80) REVERT: A 441 PHE cc_start: 0.8433 (OUTLIER) cc_final: 0.7717 (m-80) REVERT: A 453 MET cc_start: 0.7484 (mtt) cc_final: 0.7104 (mtp) REVERT: A 485 LYS cc_start: 0.7832 (ttmt) cc_final: 0.7261 (ptpt) REVERT: A 584 PHE cc_start: 0.7759 (m-80) cc_final: 0.7187 (m-80) outliers start: 52 outliers final: 42 residues processed: 264 average time/residue: 0.0671 time to fit residues: 24.9146 Evaluate side-chains 278 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 231 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 431 TRP Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 560 ASN Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 44 HIS Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 358 LYS Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 472 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 0.9980 chunk 9 optimal weight: 0.0870 chunk 19 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 0.0470 chunk 80 optimal weight: 0.8980 chunk 56 optimal weight: 0.4980 chunk 68 optimal weight: 2.9990 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 372 GLN A 302 ASN A 363 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.159133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.139800 restraints weight = 16059.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.144277 restraints weight = 8753.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.147146 restraints weight = 5531.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.149338 restraints weight = 3920.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.150872 restraints weight = 2957.457| |-----------------------------------------------------------------------------| r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8079 Z= 0.157 Angle : 0.762 13.187 10972 Z= 0.376 Chirality : 0.046 0.177 1245 Planarity : 0.004 0.048 1324 Dihedral : 6.456 58.275 1021 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 5.73 % Allowed : 32.47 % Favored : 61.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.28), residues: 919 helix: 1.30 (0.20), residues: 676 sheet: -1.24 (0.75), residues: 38 loop : -1.27 (0.45), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 359 TYR 0.043 0.002 TYR B 247 PHE 0.024 0.001 PHE A 232 TRP 0.035 0.002 TRP A 165 HIS 0.004 0.001 HIS B 56 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 8079) covalent geometry : angle 0.76215 (10972) hydrogen bonds : bond 0.04308 ( 540) hydrogen bonds : angle 5.11557 ( 1605) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 231 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.8017 (mt) REVERT: B 9 ASP cc_start: 0.7583 (t0) cc_final: 0.6930 (t70) REVERT: B 11 ASN cc_start: 0.7211 (m110) cc_final: 0.6920 (m-40) REVERT: B 41 GLU cc_start: 0.7488 (mm-30) cc_final: 0.6996 (mm-30) REVERT: B 54 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7692 (tpt170) REVERT: B 117 ASN cc_start: 0.7938 (t0) cc_final: 0.7686 (t0) REVERT: B 132 LYS cc_start: 0.7418 (ttpt) cc_final: 0.7145 (mtpp) REVERT: B 133 TRP cc_start: 0.7798 (m100) cc_final: 0.6810 (m-10) REVERT: B 212 MET cc_start: 0.6682 (mmm) cc_final: 0.6219 (tmm) REVERT: B 229 LEU cc_start: 0.8520 (tt) cc_final: 0.8311 (tp) REVERT: B 275 ASN cc_start: 0.5744 (m110) cc_final: 0.4775 (t0) REVERT: B 276 LYS cc_start: 0.7183 (mmtt) cc_final: 0.6784 (mmtt) REVERT: B 293 ASN cc_start: 0.7787 (m-40) cc_final: 0.7399 (m-40) REVERT: B 296 LYS cc_start: 0.8464 (ptmt) cc_final: 0.7965 (ptmt) REVERT: B 400 PHE cc_start: 0.6973 (m-80) cc_final: 0.6435 (m-80) REVERT: B 417 MET cc_start: 0.7475 (mtp) cc_final: 0.7189 (mtp) REVERT: B 513 SER cc_start: 0.7595 (t) cc_final: 0.7348 (p) REVERT: B 565 ASN cc_start: 0.7228 (m-40) cc_final: 0.6844 (m110) REVERT: B 566 ILE cc_start: 0.6953 (OUTLIER) cc_final: 0.6678 (mm) REVERT: B 574 GLU cc_start: 0.7561 (tm-30) cc_final: 0.7284 (tm-30) REVERT: A 40 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7967 (tp) REVERT: A 53 ILE cc_start: 0.7279 (OUTLIER) cc_final: 0.6725 (tp) REVERT: A 59 ASN cc_start: 0.7612 (t0) cc_final: 0.7400 (t0) REVERT: A 89 HIS cc_start: 0.7150 (m-70) cc_final: 0.6800 (m-70) REVERT: A 144 ILE cc_start: 0.6915 (pt) cc_final: 0.6606 (tp) REVERT: A 178 GLU cc_start: 0.6911 (tm-30) cc_final: 0.6670 (tm-30) REVERT: A 282 MET cc_start: 0.6910 (mtt) cc_final: 0.6622 (mtt) REVERT: A 295 LYS cc_start: 0.6156 (mtmm) cc_final: 0.5352 (mtmm) REVERT: A 363 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7826 (tm-30) REVERT: A 367 PHE cc_start: 0.6356 (m-80) cc_final: 0.6118 (m-80) REVERT: A 441 PHE cc_start: 0.8407 (OUTLIER) cc_final: 0.7738 (m-80) REVERT: A 453 MET cc_start: 0.7401 (mtt) cc_final: 0.6998 (mtp) REVERT: A 485 LYS cc_start: 0.7710 (ttmt) cc_final: 0.7116 (ptpt) REVERT: A 491 PHE cc_start: 0.7271 (p90) cc_final: 0.6974 (p90) REVERT: A 529 LEU cc_start: 0.8125 (mm) cc_final: 0.7882 (mt) REVERT: A 584 PHE cc_start: 0.7770 (m-80) cc_final: 0.7189 (m-80) outliers start: 51 outliers final: 39 residues processed: 259 average time/residue: 0.0658 time to fit residues: 24.0410 Evaluate side-chains 278 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 232 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 431 TRP Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 560 ASN Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 44 HIS Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 358 LYS Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 363 GLN Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 472 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 9 optimal weight: 0.0670 chunk 86 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 83 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN A 363 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.158828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.139921 restraints weight = 15879.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.144288 restraints weight = 8716.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.147293 restraints weight = 5533.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.149358 restraints weight = 3864.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.150661 restraints weight = 2890.337| |-----------------------------------------------------------------------------| r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8079 Z= 0.164 Angle : 0.767 12.970 10972 Z= 0.382 Chirality : 0.046 0.198 1245 Planarity : 0.004 0.048 1324 Dihedral : 5.926 58.682 1016 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 5.62 % Allowed : 32.70 % Favored : 61.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.28), residues: 919 helix: 1.28 (0.20), residues: 677 sheet: -1.21 (0.76), residues: 38 loop : -1.30 (0.45), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 359 TYR 0.045 0.002 TYR A 569 PHE 0.023 0.001 PHE A 232 TRP 0.038 0.002 TRP B 165 HIS 0.004 0.001 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 8079) covalent geometry : angle 0.76726 (10972) hydrogen bonds : bond 0.04339 ( 540) hydrogen bonds : angle 5.13206 ( 1605) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1202.71 seconds wall clock time: 21 minutes 35.23 seconds (1295.23 seconds total)