Starting phenix.real_space_refine on Fri Jul 3 11:11:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ux7_64575/07_2026/9ux7_64575.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ux7_64575/07_2026/9ux7_64575.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ux7_64575/07_2026/9ux7_64575.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ux7_64575/07_2026/9ux7_64575.map" model { file = "/net/cci-nas-00/data/ceres_data/9ux7_64575/07_2026/9ux7_64575.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ux7_64575/07_2026/9ux7_64575.cif" } resolution = 3.73 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= 0.000 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 80 5.49 5 S 38 5.16 5 C 8375 2.51 5 N 2241 2.21 5 O 2761 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13495 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4682 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 555} Chain: "B" Number of atoms: 4682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4682 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 555} Chain: "C" Number of atoms: 2456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2456 Classifications: {'peptide': 304} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 294} Chain: "D" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 836 Classifications: {'DNA': 41} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 40} Chain: "E" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 839 Classifications: {'DNA': 41} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 40} Time building chain proxies: 2.69, per 1000 atoms: 0.20 Number of scatterers: 13495 At special positions: 0 Unit cell: (148.42, 124.64, 160.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 P 80 15.00 O 2761 8.00 N 2241 7.00 C 8375 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: 0.90 Conformation dependent library (CDL) restraints added in 401.6 milliseconds 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2790 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 8 sheets defined 61.2% alpha, 9.5% beta 37 base pairs and 72 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 36 through 49 Processing helix chain 'A' and resid 96 through 108 Processing helix chain 'A' and resid 126 through 132 Processing helix chain 'A' and resid 133 through 135 No H-bonds generated for 'chain 'A' and resid 133 through 135' Processing helix chain 'A' and resid 161 through 169 Processing helix chain 'A' and resid 173 through 211 Processing helix chain 'A' and resid 222 through 276 removed outlier: 3.536A pdb=" N ASN A 226 " --> pdb=" O LYS A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 removed outlier: 4.796A pdb=" N ARG A 300 " --> pdb=" O GLN A 296 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N LEU A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LEU A 303 " --> pdb=" O THR A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 351 Processing helix chain 'A' and resid 357 through 429 removed outlier: 3.606A pdb=" N ALA A 364 " --> pdb=" O ASP A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 480 removed outlier: 3.594A pdb=" N LYS A 478 " --> pdb=" O SER A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 512 Processing helix chain 'A' and resid 525 through 530 removed outlier: 4.267A pdb=" N LYS A 528 " --> pdb=" O GLU A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 536 removed outlier: 3.795A pdb=" N SER A 535 " --> pdb=" O PHE A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 555 Processing helix chain 'A' and resid 556 through 558 No H-bonds generated for 'chain 'A' and resid 556 through 558' Processing helix chain 'B' and resid 36 through 48 Processing helix chain 'B' and resid 97 through 108 Processing helix chain 'B' and resid 126 through 132 Processing helix chain 'B' and resid 133 through 135 No H-bonds generated for 'chain 'B' and resid 133 through 135' Processing helix chain 'B' and resid 151 through 155 Processing helix chain 'B' and resid 161 through 169 Processing helix chain 'B' and resid 176 through 211 Processing helix chain 'B' and resid 223 through 281 removed outlier: 4.255A pdb=" N LYS B 227 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ASP B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 299 removed outlier: 3.720A pdb=" N SER B 297 " --> pdb=" O THR B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 351 Processing helix chain 'B' and resid 353 through 429 removed outlier: 3.838A pdb=" N THR B 357 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ASP B 359 " --> pdb=" O LEU B 355 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASP B 360 " --> pdb=" O LEU B 356 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN B 387 " --> pdb=" O LEU B 383 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU B 398 " --> pdb=" O VAL B 394 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LYS B 426 " --> pdb=" O PHE B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 434 removed outlier: 3.768A pdb=" N THR B 434 " --> pdb=" O ASP B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 480 Processing helix chain 'B' and resid 498 through 512 Processing helix chain 'B' and resid 525 through 530 removed outlier: 4.073A pdb=" N LYS B 528 " --> pdb=" O GLU B 525 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 530 " --> pdb=" O LEU B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 536 Processing helix chain 'B' and resid 550 through 556 removed outlier: 3.855A pdb=" N LEU B 556 " --> pdb=" O ASP B 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 30 removed outlier: 4.249A pdb=" N ILE C 22 " --> pdb=" O GLN C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 70 Processing helix chain 'C' and resid 72 through 76 Processing helix chain 'C' and resid 78 through 85 Processing helix chain 'C' and resid 101 through 106 Processing helix chain 'C' and resid 123 through 135 Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 157 through 172 Processing helix chain 'C' and resid 177 through 198 removed outlier: 3.564A pdb=" N ALA C 181 " --> pdb=" O SER C 177 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE C 198 " --> pdb=" O ARG C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 210 Processing helix chain 'C' and resid 213 through 236 removed outlier: 4.704A pdb=" N ASP C 230 " --> pdb=" O LYS C 226 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU C 231 " --> pdb=" O GLU C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 257 removed outlier: 3.799A pdb=" N LYS C 245 " --> pdb=" O ILE C 241 " (cutoff:3.500A) Proline residue: C 254 - end of helix Processing helix chain 'C' and resid 258 through 268 Processing helix chain 'C' and resid 269 through 276 removed outlier: 3.565A pdb=" N LEU C 273 " --> pdb=" O ASP C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 293 Processing helix chain 'C' and resid 300 through 315 removed outlier: 3.705A pdb=" N GLU C 315 " --> pdb=" O CYS C 311 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 20 removed outlier: 6.648A pdb=" N GLU A 69 " --> pdb=" O ILE A 4 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N PHE A 6 " --> pdb=" O GLN A 67 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N GLN A 67 " --> pdb=" O PHE A 6 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ILE A 8 " --> pdb=" O TYR A 65 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N TYR A 65 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 70 " --> pdb=" O TYR A 77 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 486 through 488 removed outlier: 6.485A pdb=" N PHE A 486 " --> pdb=" O PHE A 519 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N SER A 521 " --> pdb=" O PHE A 486 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N MET A 488 " --> pdb=" O SER A 521 " (cutoff:3.500A) removed outlier: 9.579A pdb=" N VAL A 523 " --> pdb=" O MET A 488 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N THR A 25 " --> pdb=" O ASN A 537 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ILE A 539 " --> pdb=" O THR A 25 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU A 27 " --> pdb=" O ILE A 539 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N VAL A 541 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL A 29 " --> pdb=" O VAL A 541 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 113 through 115 Processing sheet with id=AA4, first strand: chain 'B' and resid 15 through 20 removed outlier: 5.638A pdb=" N ILE B 3 " --> pdb=" O LEU B 71 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU B 71 " --> pdb=" O ILE B 3 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA B 5 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 486 through 488 removed outlier: 6.281A pdb=" N PHE B 486 " --> pdb=" O PHE B 519 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N SER B 521 " --> pdb=" O PHE B 486 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N MET B 488 " --> pdb=" O SER B 521 " (cutoff:3.500A) removed outlier: 9.415A pdb=" N VAL B 523 " --> pdb=" O MET B 488 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N GLY B 24 " --> pdb=" O SER B 518 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N PHE B 520 " --> pdb=" O GLY B 24 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ASN B 26 " --> pdb=" O PHE B 520 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ILE B 522 " --> pdb=" O ASN B 26 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ILE B 28 " --> pdb=" O ILE B 522 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR B 25 " --> pdb=" O ASN B 537 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ILE B 539 " --> pdb=" O THR B 25 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU B 27 " --> pdb=" O ILE B 539 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 113 through 115 Processing sheet with id=AA7, first strand: chain 'C' and resid 147 through 151 removed outlier: 5.899A pdb=" N THR C 53 " --> pdb=" O ILE C 92 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N LYS C 94 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N PHE C 55 " --> pdb=" O LYS C 94 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N PHE C 96 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLN C 57 " --> pdb=" O PHE C 96 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 109 through 112 729 hydrogen bonds defined for protein. 2124 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 90 hydrogen bonds 180 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 72 stacking parallelities Total time for adding SS restraints: 2.48 Time building geometry restraints manager: 1.29 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: 3832 1.34 - 1.46: 2511 1.46 - 1.57: 7312 1.57 - 1.69: 160 1.69 - 1.81: 68 Bond restraints: 13883 Sorted by residual: bond pdb=" C3' DG D 18 " pdb=" C2' DG D 18 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.89e+00 bond pdb=" C3' DT D 8 " pdb=" C2' DT D 8 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.85e+00 bond pdb=" C3' DT E 39 " pdb=" C2' DT E 39 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.47e+00 bond pdb=" C3' DT E 43 " pdb=" C2' DT E 43 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.99e+00 bond pdb=" C3' DA E 38 " pdb=" C2' DA E 38 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.91e+00 ... (remaining 13878 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 18306 1.77 - 3.55: 626 3.55 - 5.32: 81 5.32 - 7.09: 16 7.09 - 8.86: 3 Bond angle restraints: 19032 Sorted by residual: angle pdb=" N LEU C 115 " pdb=" CA LEU C 115 " pdb=" C LEU C 115 " ideal model delta sigma weight residual 113.97 107.61 6.36 1.28e+00 6.10e-01 2.47e+01 angle pdb=" C SER A 304 " pdb=" CA SER A 304 " pdb=" CB SER A 304 " ideal model delta sigma weight residual 115.79 110.44 5.35 1.19e+00 7.06e-01 2.02e+01 angle pdb=" N3 DT D 22 " pdb=" C4 DT D 22 " pdb=" O4 DT D 22 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT E 36 " pdb=" C4 DT E 36 " pdb=" O4 DT E 36 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT E 53 " pdb=" C4 DT E 53 " pdb=" O4 DT E 53 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.70e+01 ... (remaining 19027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 7074 17.88 - 35.77: 827 35.77 - 53.65: 351 53.65 - 71.54: 68 71.54 - 89.42: 25 Dihedral angle restraints: 8345 sinusoidal: 4065 harmonic: 4280 Sorted by residual: dihedral pdb=" CA THR B 357 " pdb=" C THR B 357 " pdb=" N ILE B 358 " pdb=" CA ILE B 358 " ideal model delta harmonic sigma weight residual -180.00 -157.66 -22.34 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA GLU C 300 " pdb=" C GLU C 300 " pdb=" N LEU C 301 " pdb=" CA LEU C 301 " ideal model delta harmonic sigma weight residual 180.00 160.45 19.55 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA VAL A 533 " pdb=" C VAL A 533 " pdb=" N ASP A 534 " pdb=" CA ASP A 534 " ideal model delta harmonic sigma weight residual -180.00 -160.54 -19.46 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 8342 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1586 0.045 - 0.089: 423 0.089 - 0.134: 131 0.134 - 0.179: 10 0.179 - 0.223: 1 Chirality restraints: 2151 Sorted by residual: chirality pdb=" CB ILE C 253 " pdb=" CA ILE C 253 " pdb=" CG1 ILE C 253 " pdb=" CG2 ILE C 253 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA ILE B 484 " pdb=" N ILE B 484 " pdb=" C ILE B 484 " pdb=" CB ILE B 484 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.71e-01 chirality pdb=" CA ASN B 170 " pdb=" N ASN B 170 " pdb=" C ASN B 170 " pdb=" CB ASN B 170 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.26e-01 ... (remaining 2148 not shown) Planarity restraints: 2125 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 362 " -0.014 2.00e-02 2.50e+03 2.75e-02 7.55e+00 pdb=" C VAL B 362 " 0.048 2.00e-02 2.50e+03 pdb=" O VAL B 362 " -0.018 2.00e-02 2.50e+03 pdb=" N LYS B 363 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 363 " 0.012 2.00e-02 2.50e+03 2.41e-02 5.81e+00 pdb=" C LYS B 363 " -0.042 2.00e-02 2.50e+03 pdb=" O LYS B 363 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA B 364 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 484 " -0.036 5.00e-02 4.00e+02 5.47e-02 4.78e+00 pdb=" N PRO B 485 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 485 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 485 " -0.030 5.00e-02 4.00e+02 ... (remaining 2122 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 261 2.67 - 3.23: 13181 3.23 - 3.78: 22646 3.78 - 4.34: 29813 4.34 - 4.90: 46704 Nonbonded interactions: 112605 Sorted by model distance: nonbonded pdb=" OH TYR B 45 " pdb=" O PRO B 485 " model vdw 2.110 3.040 nonbonded pdb=" O LYS B 98 " pdb=" OG SER B 101 " model vdw 2.127 3.040 nonbonded pdb=" NZ LYS B 98 " pdb=" OE2 GLU B 102 " model vdw 2.136 3.120 nonbonded pdb=" O ALA C 101 " pdb=" OG1 THR C 104 " model vdw 2.189 3.040 nonbonded pdb=" OD1 ASN B 305 " pdb=" NH1 ARG C 180 " model vdw 2.192 3.120 ... (remaining 112600 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 3.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.090 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 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 : 0.004 0.064 13883 Z= 0.308 Angle : 0.727 8.864 19032 Z= 0.491 Chirality : 0.045 0.223 2151 Planarity : 0.004 0.055 2125 Dihedral : 18.586 89.424 5555 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.01 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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 (0.23), residues: 1422 helix: 1.86 (0.19), residues: 776 sheet: 0.75 (0.41), residues: 160 loop : -1.23 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 477 TYR 0.024 0.001 TYR B 479 PHE 0.024 0.002 PHE A 532 TRP 0.020 0.002 TRP C 98 HIS 0.008 0.001 HIS B 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.31 (13883) covalent geometry : angle 0.72677 / 0.49 (19032) hydrogen bonds : bond 0.17043 / 11.38 ( 819) hydrogen bonds : angle 6.30856 / 4.45 ( 2304) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 LEU cc_start: 0.8518 (mp) cc_final: 0.7939 (mp) REVERT: B 80 THR cc_start: 0.9346 (m) cc_final: 0.9085 (p) REVERT: B 82 GLN cc_start: 0.8989 (tm-30) cc_final: 0.8733 (tm-30) REVERT: B 83 LYS cc_start: 0.8132 (mttt) cc_final: 0.7842 (mttp) REVERT: B 347 ARG cc_start: 0.8515 (ttp80) cc_final: 0.8253 (tpm170) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.1004 time to fit residues: 30.2766 Evaluate side-chains 130 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 30.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 33 ASN B 105 GLN B 236 GLN B 237 ASN ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.169037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.116047 restraints weight = 28466.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.115005 restraints weight = 17959.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.116704 restraints weight = 13886.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.117284 restraints weight = 10436.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.117474 restraints weight = 10030.569| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 13883 Z= 0.236 Angle : 0.693 9.527 19032 Z= 0.383 Chirality : 0.046 0.220 2151 Planarity : 0.004 0.042 2125 Dihedral : 19.583 59.874 2436 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.22 % Favored : 95.50 % Rotamer: Outliers : 1.11 % Allowed : 9.75 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 1.18 (0.22), residues: 1422 helix: 1.91 (0.18), residues: 808 sheet: 0.31 (0.39), residues: 166 loop : -1.15 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 180 TYR 0.033 0.002 TYR B 45 PHE 0.022 0.002 PHE B 448 TRP 0.016 0.002 TRP A 142 HIS 0.004 0.001 HIS C 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.24 (13883) covalent geometry : angle 0.69290 / 0.38 (19032) hydrogen bonds : bond 0.05351 / 3.46 ( 819) hydrogen bonds : angle 4.70403 / 3.33 ( 2304) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: A 165 PHE cc_start: 0.8169 (m-80) cc_final: 0.7874 (m-80) REVERT: B 82 GLN cc_start: 0.8948 (tm-30) cc_final: 0.8718 (tm-30) REVERT: B 347 ARG cc_start: 0.8659 (ttp80) cc_final: 0.8204 (tpm170) REVERT: C 43 GLU cc_start: 0.5758 (OUTLIER) cc_final: 0.5499 (mt-10) outliers start: 15 outliers final: 7 residues processed: 164 average time/residue: 0.0937 time to fit residues: 23.0991 Evaluate side-chains 134 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 331 PHE Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 289 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 47 optimal weight: 30.0000 chunk 55 optimal weight: 10.0000 chunk 146 optimal weight: 50.0000 chunk 10 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 105 optimal weight: 7.9990 chunk 131 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 chunk 145 optimal weight: 50.0000 chunk 81 optimal weight: 2.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 73 ASN A 274 ASN B 236 GLN ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 462 ASN ** B 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 529 HIS C 126 GLN C 147 GLN ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.164736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.111616 restraints weight = 29516.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.110712 restraints weight = 18780.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.111522 restraints weight = 13202.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.112308 restraints weight = 11791.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.112352 restraints weight = 10392.660| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 13883 Z= 0.254 Angle : 0.684 10.831 19032 Z= 0.372 Chirality : 0.045 0.336 2151 Planarity : 0.004 0.045 2125 Dihedral : 20.089 59.868 2436 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.50 % Favored : 95.22 % Rotamer: Outliers : 2.22 % Allowed : 11.96 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 1.11 (0.22), residues: 1422 helix: 1.92 (0.18), residues: 804 sheet: 0.02 (0.40), residues: 158 loop : -1.15 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 277 TYR 0.044 0.002 TYR B 287 PHE 0.020 0.002 PHE B 560 TRP 0.013 0.002 TRP A 103 HIS 0.007 0.001 HIS B 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.25 (13883) covalent geometry : angle 0.68403 / 0.37 (19032) hydrogen bonds : bond 0.05169 / 3.35 ( 819) hydrogen bonds : angle 4.58270 / 3.26 ( 2304) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 165 PHE cc_start: 0.8249 (m-80) cc_final: 0.7958 (m-80) REVERT: A 251 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.7621 (mt) REVERT: B 64 MET cc_start: 0.8321 (mmm) cc_final: 0.7948 (mmm) REVERT: B 82 GLN cc_start: 0.8996 (tm-30) cc_final: 0.8300 (tm-30) REVERT: B 331 PHE cc_start: 0.8622 (OUTLIER) cc_final: 0.6995 (t80) REVERT: B 347 ARG cc_start: 0.8759 (ttp80) cc_final: 0.8209 (tpm170) REVERT: B 407 GLU cc_start: 0.9008 (tp30) cc_final: 0.8730 (tp30) REVERT: B 459 MET cc_start: 0.8554 (tpt) cc_final: 0.8269 (tpt) outliers start: 30 outliers final: 15 residues processed: 163 average time/residue: 0.0937 time to fit residues: 23.1131 Evaluate side-chains 137 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 331 PHE Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 309 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 22 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 47 optimal weight: 30.0000 chunk 95 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 135 optimal weight: 0.9980 chunk 3 optimal weight: 30.0000 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 236 GLN ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.165373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.111398 restraints weight = 29575.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.111694 restraints weight = 18276.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.112731 restraints weight = 12272.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.113462 restraints weight = 10982.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.113500 restraints weight = 9216.608| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13883 Z= 0.158 Angle : 0.607 12.857 19032 Z= 0.333 Chirality : 0.043 0.335 2151 Planarity : 0.003 0.038 2125 Dihedral : 20.249 59.967 2436 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.01 % Favored : 95.71 % Rotamer: Outliers : 1.92 % Allowed : 13.00 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 1.24 (0.23), residues: 1422 helix: 2.01 (0.18), residues: 795 sheet: 0.17 (0.42), residues: 149 loop : -1.04 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 415 TYR 0.032 0.002 TYR B 45 PHE 0.016 0.001 PHE B 513 TRP 0.008 0.001 TRP A 103 HIS 0.005 0.001 HIS B 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 (13883) covalent geometry : angle 0.60693 / 0.33 (19032) hydrogen bonds : bond 0.04566 / 2.95 ( 819) hydrogen bonds : angle 4.41301 / 3.14 ( 2304) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 PHE cc_start: 0.8437 (m-80) cc_final: 0.8089 (m-80) REVERT: A 251 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.7504 (mt) REVERT: B 64 MET cc_start: 0.8216 (mmm) cc_final: 0.7402 (mmm) REVERT: B 82 GLN cc_start: 0.8869 (tm-30) cc_final: 0.8359 (tm-30) REVERT: B 331 PHE cc_start: 0.8477 (OUTLIER) cc_final: 0.6937 (t80) REVERT: B 347 ARG cc_start: 0.8812 (ttp80) cc_final: 0.8215 (tpm170) REVERT: B 407 GLU cc_start: 0.9066 (tp30) cc_final: 0.8694 (tp30) REVERT: B 459 MET cc_start: 0.8587 (tpt) cc_final: 0.8371 (tpt) outliers start: 26 outliers final: 14 residues processed: 163 average time/residue: 0.0856 time to fit residues: 21.5510 Evaluate side-chains 141 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 331 PHE Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 289 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 149 optimal weight: 40.0000 chunk 136 optimal weight: 0.1980 chunk 101 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 141 optimal weight: 0.7980 chunk 9 optimal weight: 7.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 73 ASN B 236 GLN ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 351 ASN ** B 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.165064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.113254 restraints weight = 29913.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.112828 restraints weight = 19226.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.113319 restraints weight = 12637.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.113917 restraints weight = 11351.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.114107 restraints weight = 10747.912| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 13883 Z= 0.166 Angle : 0.597 11.744 19032 Z= 0.325 Chirality : 0.042 0.312 2151 Planarity : 0.003 0.040 2125 Dihedral : 20.295 59.693 2436 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.94 % Favored : 95.71 % Rotamer: Outliers : 1.85 % Allowed : 14.25 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 1.31 (0.23), residues: 1422 helix: 2.04 (0.18), residues: 795 sheet: 0.23 (0.44), residues: 141 loop : -0.94 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 277 TYR 0.030 0.001 TYR B 45 PHE 0.020 0.001 PHE B 513 TRP 0.007 0.001 TRP A 103 HIS 0.009 0.001 HIS B 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 (13883) covalent geometry : angle 0.59655 / 0.32 (19032) hydrogen bonds : bond 0.04470 / 2.87 ( 819) hydrogen bonds : angle 4.37487 / 3.11 ( 2304) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 PHE cc_start: 0.8242 (m-80) cc_final: 0.8004 (m-80) REVERT: A 251 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.7443 (mt) REVERT: B 82 GLN cc_start: 0.8786 (tm-30) cc_final: 0.8112 (tm-30) REVERT: B 83 LYS cc_start: 0.8276 (mttt) cc_final: 0.7979 (mttp) REVERT: B 331 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.7035 (t80) REVERT: B 347 ARG cc_start: 0.8783 (ttp80) cc_final: 0.8219 (tpm170) REVERT: B 395 LEU cc_start: 0.9115 (mm) cc_final: 0.8639 (tp) REVERT: B 407 GLU cc_start: 0.9029 (tp30) cc_final: 0.8715 (tp30) REVERT: B 459 MET cc_start: 0.8563 (tpt) cc_final: 0.8198 (tpt) REVERT: C 144 MET cc_start: 0.8644 (mmm) cc_final: 0.8366 (mmm) outliers start: 25 outliers final: 12 residues processed: 161 average time/residue: 0.0919 time to fit residues: 22.5940 Evaluate side-chains 144 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 331 PHE Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 289 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 3 optimal weight: 9.9990 chunk 142 optimal weight: 30.0000 chunk 56 optimal weight: 0.9980 chunk 10 optimal weight: 10.0000 chunk 127 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 chunk 136 optimal weight: 0.4980 chunk 35 optimal weight: 6.9990 chunk 83 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 236 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.165586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.114418 restraints weight = 29808.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.113880 restraints weight = 17259.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.114026 restraints weight = 12162.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.114736 restraints weight = 10954.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.114909 restraints weight = 10052.112| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13883 Z= 0.142 Angle : 0.599 12.246 19032 Z= 0.324 Chirality : 0.042 0.320 2151 Planarity : 0.003 0.039 2125 Dihedral : 20.303 59.809 2436 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.66 % Favored : 95.99 % Rotamer: Outliers : 2.36 % Allowed : 14.48 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 1.36 (0.23), residues: 1422 helix: 2.09 (0.18), residues: 793 sheet: 0.21 (0.45), residues: 141 loop : -0.88 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 415 TYR 0.030 0.001 TYR B 45 PHE 0.012 0.001 PHE B 11 TRP 0.016 0.001 TRP C 98 HIS 0.005 0.001 HIS B 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (13883) covalent geometry : angle 0.59928 / 0.32 (19032) hydrogen bonds : bond 0.04324 / 2.79 ( 819) hydrogen bonds : angle 4.30907 / 3.06 ( 2304) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 VAL cc_start: 0.3668 (OUTLIER) cc_final: 0.3410 (t) REVERT: A 165 PHE cc_start: 0.8261 (m-80) cc_final: 0.8009 (m-80) REVERT: A 251 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.7411 (mt) REVERT: B 35 LYS cc_start: 0.8278 (tttt) cc_final: 0.7977 (tttm) REVERT: B 82 GLN cc_start: 0.8735 (tm-30) cc_final: 0.8517 (tp40) REVERT: B 83 LYS cc_start: 0.8305 (mttt) cc_final: 0.8077 (mttp) REVERT: B 237 ASN cc_start: 0.9216 (OUTLIER) cc_final: 0.8987 (m-40) REVERT: B 331 PHE cc_start: 0.8506 (OUTLIER) cc_final: 0.7056 (t80) REVERT: B 347 ARG cc_start: 0.8807 (ttp80) cc_final: 0.8255 (tpm170) REVERT: B 360 ASP cc_start: 0.8636 (m-30) cc_final: 0.8425 (m-30) REVERT: B 395 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8634 (tp) REVERT: B 407 GLU cc_start: 0.9018 (tp30) cc_final: 0.8690 (tp30) REVERT: B 459 MET cc_start: 0.8557 (tpt) cc_final: 0.8312 (tpt) outliers start: 32 outliers final: 15 residues processed: 170 average time/residue: 0.0985 time to fit residues: 26.1067 Evaluate side-chains 150 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 331 PHE Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 289 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 127 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 82 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 106 HIS B 236 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.164278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.111792 restraints weight = 30151.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.111785 restraints weight = 18997.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.112120 restraints weight = 12415.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.112714 restraints weight = 11374.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.112866 restraints weight = 10864.472| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 13883 Z= 0.205 Angle : 0.636 11.736 19032 Z= 0.340 Chirality : 0.043 0.337 2151 Planarity : 0.003 0.039 2125 Dihedral : 20.323 59.324 2436 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.22 % Favored : 95.50 % Rotamer: Outliers : 2.58 % Allowed : 15.14 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 1.30 (0.23), residues: 1422 helix: 2.10 (0.18), residues: 793 sheet: 0.02 (0.44), residues: 149 loop : -1.00 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 194 TYR 0.028 0.002 TYR B 45 PHE 0.012 0.001 PHE C 154 TRP 0.013 0.001 TRP C 98 HIS 0.008 0.001 HIS B 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.21 (13883) covalent geometry : angle 0.63558 / 0.34 (19032) hydrogen bonds : bond 0.04481 / 2.88 ( 819) hydrogen bonds : angle 4.38138 / 3.11 ( 2304) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 VAL cc_start: 0.3687 (OUTLIER) cc_final: 0.3406 (t) REVERT: A 165 PHE cc_start: 0.8275 (m-80) cc_final: 0.7997 (m-80) REVERT: A 177 LEU cc_start: 0.9097 (mt) cc_final: 0.8873 (pp) REVERT: A 251 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.7462 (mt) REVERT: A 356 LEU cc_start: 0.8783 (tp) cc_final: 0.8546 (tt) REVERT: B 35 LYS cc_start: 0.8300 (tttt) cc_final: 0.7987 (tttm) REVERT: B 82 GLN cc_start: 0.8833 (tm-30) cc_final: 0.8626 (tm-30) REVERT: B 83 LYS cc_start: 0.8271 (mttt) cc_final: 0.8022 (mttp) REVERT: B 237 ASN cc_start: 0.9222 (OUTLIER) cc_final: 0.8924 (m-40) REVERT: B 331 PHE cc_start: 0.8546 (OUTLIER) cc_final: 0.7190 (t80) REVERT: B 332 GLU cc_start: 0.8186 (tt0) cc_final: 0.7942 (tm-30) REVERT: B 347 ARG cc_start: 0.8835 (ttp80) cc_final: 0.8268 (tpm170) REVERT: B 360 ASP cc_start: 0.8693 (m-30) cc_final: 0.8478 (m-30) REVERT: B 395 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8639 (tp) REVERT: B 407 GLU cc_start: 0.9111 (tp30) cc_final: 0.8754 (tp30) REVERT: B 459 MET cc_start: 0.8624 (tpt) cc_final: 0.8044 (tpp) REVERT: C 205 ASP cc_start: 0.8154 (m-30) cc_final: 0.7625 (m-30) outliers start: 35 outliers final: 19 residues processed: 170 average time/residue: 0.0941 time to fit residues: 24.3560 Evaluate side-chains 161 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 331 PHE Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 309 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 83 optimal weight: 0.5980 chunk 120 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 chunk 144 optimal weight: 50.0000 chunk 66 optimal weight: 0.0980 chunk 7 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 chunk 138 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 236 GLN B 240 ASN ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.165290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.114851 restraints weight = 29805.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.114733 restraints weight = 17763.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.114974 restraints weight = 12350.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.115582 restraints weight = 11145.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.115743 restraints weight = 9971.310| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13883 Z= 0.138 Angle : 0.619 11.233 19032 Z= 0.328 Chirality : 0.043 0.339 2151 Planarity : 0.003 0.044 2125 Dihedral : 20.304 59.452 2436 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.80 % Favored : 95.92 % Rotamer: Outliers : 2.22 % Allowed : 15.73 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 1.36 (0.23), residues: 1422 helix: 2.10 (0.18), residues: 787 sheet: 0.23 (0.46), residues: 143 loop : -0.90 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 415 TYR 0.030 0.001 TYR B 45 PHE 0.014 0.001 PHE B 11 TRP 0.016 0.002 TRP C 98 HIS 0.003 0.000 HIS B 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 (13883) covalent geometry : angle 0.61909 / 0.33 (19032) hydrogen bonds : bond 0.04233 / 2.72 ( 819) hydrogen bonds : angle 4.28924 / 3.06 ( 2304) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 149 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 VAL cc_start: 0.3707 (OUTLIER) cc_final: 0.3460 (t) REVERT: A 165 PHE cc_start: 0.8222 (m-80) cc_final: 0.7996 (m-80) REVERT: A 177 LEU cc_start: 0.9072 (mt) cc_final: 0.8843 (pp) REVERT: A 178 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8150 (pm20) REVERT: A 251 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.7375 (mt) REVERT: A 356 LEU cc_start: 0.8740 (tp) cc_final: 0.8467 (tt) REVERT: B 35 LYS cc_start: 0.8265 (tttt) cc_final: 0.7968 (tttm) REVERT: B 82 GLN cc_start: 0.8798 (tm-30) cc_final: 0.8571 (tp40) REVERT: B 83 LYS cc_start: 0.8278 (mttt) cc_final: 0.8037 (mttp) REVERT: B 137 ASP cc_start: 0.7843 (t0) cc_final: 0.7525 (t70) REVERT: B 331 PHE cc_start: 0.8503 (OUTLIER) cc_final: 0.7165 (t80) REVERT: B 347 ARG cc_start: 0.8781 (ttp80) cc_final: 0.8250 (tpm170) REVERT: B 360 ASP cc_start: 0.8612 (m-30) cc_final: 0.8411 (m-30) REVERT: B 395 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8630 (tp) REVERT: B 407 GLU cc_start: 0.9083 (tp30) cc_final: 0.8705 (tp30) REVERT: B 459 MET cc_start: 0.8560 (tpt) cc_final: 0.8003 (tpp) REVERT: C 82 LYS cc_start: 0.8886 (pttm) cc_final: 0.8620 (pttm) REVERT: C 144 MET cc_start: 0.8663 (mmm) cc_final: 0.8238 (mmp) outliers start: 30 outliers final: 18 residues processed: 171 average time/residue: 0.0890 time to fit residues: 23.3569 Evaluate side-chains 165 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 331 PHE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 289 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 50 optimal weight: 40.0000 chunk 35 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 15 optimal weight: 0.0370 chunk 122 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.9860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 274 ASN B 236 GLN B 240 ASN ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.164984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.112484 restraints weight = 30249.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.112214 restraints weight = 14124.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.113245 restraints weight = 10984.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.113539 restraints weight = 9499.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.113624 restraints weight = 8778.934| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 13883 Z= 0.159 Angle : 0.621 12.899 19032 Z= 0.330 Chirality : 0.043 0.344 2151 Planarity : 0.003 0.040 2125 Dihedral : 20.308 59.984 2436 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.94 % Favored : 95.78 % Rotamer: Outliers : 2.29 % Allowed : 15.58 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 1.34 (0.23), residues: 1422 helix: 2.08 (0.18), residues: 793 sheet: 0.21 (0.46), residues: 143 loop : -0.92 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 194 TYR 0.028 0.001 TYR B 45 PHE 0.022 0.001 PHE B 50 TRP 0.025 0.002 TRP C 98 HIS 0.003 0.000 HIS B 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (13883) covalent geometry : angle 0.62117 / 0.33 (19032) hydrogen bonds : bond 0.04251 / 2.73 ( 819) hydrogen bonds : angle 4.30732 / 3.07 ( 2304) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 VAL cc_start: 0.3506 (OUTLIER) cc_final: 0.3256 (t) REVERT: A 165 PHE cc_start: 0.8299 (m-80) cc_final: 0.8061 (m-80) REVERT: A 178 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8302 (pm20) REVERT: A 248 MET cc_start: 0.7937 (mmm) cc_final: 0.7225 (ttp) REVERT: A 251 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.7461 (mt) REVERT: A 356 LEU cc_start: 0.8797 (tp) cc_final: 0.8566 (tt) REVERT: B 35 LYS cc_start: 0.8250 (tttt) cc_final: 0.7961 (tttm) REVERT: B 82 GLN cc_start: 0.8842 (tm-30) cc_final: 0.8180 (tm-30) REVERT: B 83 LYS cc_start: 0.8283 (mttt) cc_final: 0.7926 (mttp) REVERT: B 331 PHE cc_start: 0.8503 (OUTLIER) cc_final: 0.7176 (t80) REVERT: B 332 GLU cc_start: 0.8159 (tt0) cc_final: 0.7929 (tm-30) REVERT: B 347 ARG cc_start: 0.8794 (ttp80) cc_final: 0.8265 (tpm170) REVERT: B 360 ASP cc_start: 0.8676 (m-30) cc_final: 0.8456 (m-30) REVERT: B 368 LYS cc_start: 0.8832 (tttt) cc_final: 0.8390 (mmmt) REVERT: B 395 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8649 (tp) REVERT: B 407 GLU cc_start: 0.9064 (tp30) cc_final: 0.8685 (tp30) REVERT: B 459 MET cc_start: 0.8583 (tpt) cc_final: 0.8324 (tpt) REVERT: C 55 PHE cc_start: 0.8217 (m-80) cc_final: 0.7984 (m-80) REVERT: C 82 LYS cc_start: 0.8877 (pttm) cc_final: 0.8600 (pttm) REVERT: C 144 MET cc_start: 0.8690 (mmm) cc_final: 0.8275 (mmp) REVERT: C 205 ASP cc_start: 0.8160 (m-30) cc_final: 0.7603 (m-30) REVERT: C 207 GLU cc_start: 0.8383 (mm-30) cc_final: 0.7923 (mm-30) REVERT: C 256 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8412 (mp) outliers start: 31 outliers final: 19 residues processed: 171 average time/residue: 0.1009 time to fit residues: 26.1907 Evaluate side-chains 166 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 331 PHE Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 289 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 58 optimal weight: 3.9990 chunk 126 optimal weight: 0.0970 chunk 142 optimal weight: 30.0000 chunk 93 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 0 optimal weight: 60.0000 chunk 102 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 53 optimal weight: 0.0270 overall best weight: 1.0038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 ASN ** 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 = 0.4342 r_free = 0.4342 target = 0.164838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.112318 restraints weight = 29812.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.112619 restraints weight = 16453.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.113043 restraints weight = 10964.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.113752 restraints weight = 10743.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.113704 restraints weight = 9383.349| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 13883 Z= 0.161 Angle : 0.641 13.176 19032 Z= 0.339 Chirality : 0.043 0.337 2151 Planarity : 0.003 0.040 2125 Dihedral : 20.310 59.547 2436 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.87 % Favored : 95.85 % Rotamer: Outliers : 1.77 % Allowed : 16.03 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 1.29 (0.23), residues: 1422 helix: 2.05 (0.18), residues: 793 sheet: 0.18 (0.46), residues: 143 loop : -0.97 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 194 TYR 0.028 0.001 TYR B 45 PHE 0.015 0.001 PHE A 169 TRP 0.021 0.002 TRP C 98 HIS 0.002 0.000 HIS B 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (13883) covalent geometry : angle 0.64081 / 0.34 (19032) hydrogen bonds : bond 0.04258 / 2.74 ( 819) hydrogen bonds : angle 4.32285 / 3.09 ( 2304) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 VAL cc_start: 0.3495 (OUTLIER) cc_final: 0.3248 (t) REVERT: A 165 PHE cc_start: 0.8281 (m-80) cc_final: 0.8034 (m-80) REVERT: A 177 LEU cc_start: 0.9101 (mt) cc_final: 0.8852 (pp) REVERT: A 178 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8178 (pm20) REVERT: A 251 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.7417 (mt) REVERT: A 356 LEU cc_start: 0.8812 (tp) cc_final: 0.8590 (tt) REVERT: B 35 LYS cc_start: 0.8184 (tttt) cc_final: 0.7905 (tttm) REVERT: B 82 GLN cc_start: 0.8822 (tm-30) cc_final: 0.8072 (tm-30) REVERT: B 83 LYS cc_start: 0.8303 (mttt) cc_final: 0.7916 (mttp) REVERT: B 331 PHE cc_start: 0.8521 (OUTLIER) cc_final: 0.7122 (t80) REVERT: B 332 GLU cc_start: 0.8200 (tt0) cc_final: 0.7938 (tm-30) REVERT: B 347 ARG cc_start: 0.8812 (ttp80) cc_final: 0.8271 (tpm170) REVERT: B 360 ASP cc_start: 0.8694 (m-30) cc_final: 0.8467 (m-30) REVERT: B 368 LYS cc_start: 0.8863 (tttt) cc_final: 0.8407 (mmmt) REVERT: B 395 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8653 (tp) REVERT: B 407 GLU cc_start: 0.9076 (tp30) cc_final: 0.8686 (tp30) REVERT: B 459 MET cc_start: 0.8547 (tpt) cc_final: 0.8278 (tpt) REVERT: C 55 PHE cc_start: 0.8166 (m-80) cc_final: 0.7943 (m-80) REVERT: C 82 LYS cc_start: 0.8888 (pttm) cc_final: 0.8626 (pttm) REVERT: C 144 MET cc_start: 0.8661 (mmm) cc_final: 0.8296 (mmp) REVERT: C 205 ASP cc_start: 0.8130 (m-30) cc_final: 0.7590 (m-30) REVERT: C 207 GLU cc_start: 0.8400 (mm-30) cc_final: 0.7906 (mm-30) REVERT: C 228 MET cc_start: 0.9006 (ttp) cc_final: 0.8733 (tmm) outliers start: 24 outliers final: 17 residues processed: 164 average time/residue: 0.1008 time to fit residues: 25.0389 Evaluate side-chains 165 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 331 PHE Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 289 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 9 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 127 optimal weight: 2.9990 chunk 51 optimal weight: 30.0000 chunk 74 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 305 ASN B 106 HIS B 236 GLN ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.163521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.108620 restraints weight = 30213.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.108298 restraints weight = 17641.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.108923 restraints weight = 12664.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.109818 restraints weight = 10891.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.110154 restraints weight = 9542.071| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 13883 Z= 0.244 Angle : 0.697 13.475 19032 Z= 0.368 Chirality : 0.045 0.284 2151 Planarity : 0.004 0.039 2125 Dihedral : 20.392 59.887 2436 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.57 % Favored : 95.15 % Rotamer: Outliers : 1.92 % Allowed : 16.25 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 1.03 (0.23), residues: 1422 helix: 1.86 (0.18), residues: 795 sheet: -0.23 (0.43), residues: 155 loop : -1.05 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 194 TYR 0.030 0.002 TYR B 45 PHE 0.017 0.002 PHE B 513 TRP 0.022 0.002 TRP C 98 HIS 0.009 0.001 HIS B 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00564 / 0.24 (13883) covalent geometry : angle 0.69667 / 0.37 (19032) hydrogen bonds : bond 0.04650 / 2.98 ( 819) hydrogen bonds : angle 4.47155 / 3.20 ( 2304) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2210.97 seconds wall clock time: 39 minutes 6.88 seconds (2346.88 seconds total)