Starting phenix.real_space_refine on Sun Apr 5 21:59:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ux7_64575/04_2026/9ux7_64575.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ux7_64575/04_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 { model { file = "/net/cci-nas-00/data/ceres_data/9ux7_64575/04_2026/9ux7_64575.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ux7_64575/04_2026/9ux7_64575.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ux7_64575/04_2026/9ux7_64575.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ux7_64575/04_2026/9ux7_64575.map" } 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-2.1rc1-6017/lib/python3.9/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: 2.81, per 1000 atoms: 0.21 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: 0.95 Conformation dependent library (CDL) restraints added in 417.0 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: 1.80 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: 1.27 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=" CG LEU C 251 " pdb=" CD1 LEU C 251 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.75e+00 bond pdb=" C SER C 85 " pdb=" N PRO C 86 " ideal model delta sigma weight residual 1.328 1.350 -0.022 1.26e-02 6.30e+03 3.01e+00 bond pdb=" C ILE A 484 " pdb=" N PRO A 485 " ideal model delta sigma weight residual 1.330 1.346 -0.015 1.19e-02 7.06e+03 1.65e+00 bond pdb=" CG GLU B 102 " pdb=" CD GLU B 102 " ideal model delta sigma weight residual 1.516 1.484 0.032 2.50e-02 1.60e+03 1.59e+00 bond pdb=" CB GLU C 249 " pdb=" CG GLU C 249 " ideal model delta sigma weight residual 1.520 1.485 0.035 3.00e-02 1.11e+03 1.37e+00 ... (remaining 13878 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 18406 1.77 - 3.55: 526 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=" C LEU B 298 " pdb=" N THR B 299 " pdb=" CA THR B 299 " ideal model delta sigma weight residual 122.46 115.38 7.08 1.80e+00 3.09e-01 1.55e+01 angle pdb=" N GLU B 102 " pdb=" CA GLU B 102 " pdb=" CB GLU B 102 " ideal model delta sigma weight residual 110.12 115.43 -5.31 1.47e+00 4.63e-01 1.31e+01 angle pdb=" N VAL C 176 " pdb=" CA VAL C 176 " pdb=" C VAL C 176 " ideal model delta sigma weight residual 111.62 108.81 2.81 7.90e-01 1.60e+00 1.26e+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: 1680 0.045 - 0.089: 366 0.089 - 0.134: 94 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: 2.870 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: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.970 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 13883 Z= 0.171 Angle : 0.689 8.864 19032 Z= 0.406 Chirality : 0.041 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 covalent geometry : bond 0.00346 (13883) covalent geometry : angle 0.68871 (19032) hydrogen bonds : bond 0.17043 ( 819) hydrogen bonds : angle 6.30856 ( 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 : 0.533 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: 0.1168 time to fit residues: 34.9417 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 : 0.538 ------------------------------------------------------------------------------- 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: 10.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 ASN 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 462 ASN ** B 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 529 HIS ** 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 = 0.4348 r_free = 0.4348 target = 0.165294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.109615 restraints weight = 29830.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.112229 restraints weight = 17091.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.112319 restraints weight = 10410.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.113119 restraints weight = 10709.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.112857 restraints weight = 9774.683| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 13883 Z= 0.237 Angle : 0.669 9.025 19032 Z= 0.365 Chirality : 0.044 0.243 2151 Planarity : 0.004 0.044 2125 Dihedral : 19.676 59.913 2436 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.36 % Favored : 95.29 % Rotamer: Outliers : 1.33 % Allowed : 9.97 % Favored : 88.70 % 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: 1.23 (0.22), residues: 1422 helix: 1.96 (0.18), residues: 804 sheet: 0.35 (0.39), residues: 166 loop : -1.13 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 277 TYR 0.036 0.002 TYR B 45 PHE 0.019 0.002 PHE A 169 TRP 0.015 0.002 TRP A 142 HIS 0.007 0.001 HIS B 346 Details of bonding type rmsd covalent geometry : bond 0.00543 (13883) covalent geometry : angle 0.66883 (19032) hydrogen bonds : bond 0.04875 ( 819) hydrogen bonds : angle 4.55818 ( 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 174 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 165 PHE cc_start: 0.8580 (m-80) cc_final: 0.8224 (m-80) REVERT: B 80 THR cc_start: 0.9277 (m) cc_final: 0.8986 (p) REVERT: B 82 GLN cc_start: 0.8903 (tm-30) cc_final: 0.8274 (tm-30) REVERT: B 331 PHE cc_start: 0.8520 (OUTLIER) cc_final: 0.6928 (t80) REVERT: B 347 ARG cc_start: 0.8872 (ttp80) cc_final: 0.8283 (tpm170) REVERT: B 463 LYS cc_start: 0.8832 (mppt) cc_final: 0.8546 (ptmt) REVERT: C 218 GLN cc_start: 0.8842 (mm-40) cc_final: 0.8607 (mm-40) outliers start: 18 outliers final: 10 residues processed: 168 average time/residue: 0.1078 time to fit residues: 27.4594 Evaluate side-chains 141 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 PHE 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 398 GLU Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 251 LEU 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 47 optimal weight: 20.0000 chunk 55 optimal weight: 30.0000 chunk 146 optimal weight: 40.0000 chunk 10 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 83 optimal weight: 0.6980 chunk 105 optimal weight: 0.5980 chunk 131 optimal weight: 0.9990 chunk 132 optimal weight: 0.9980 chunk 145 optimal weight: 30.0000 chunk 81 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN 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 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 GLN ** 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 = 0.4349 r_free = 0.4349 target = 0.165380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.112607 restraints weight = 29951.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.112970 restraints weight = 18418.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.113300 restraints weight = 11995.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.113860 restraints weight = 11063.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.113886 restraints weight = 11069.118| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 13883 Z= 0.161 Angle : 0.583 9.596 19032 Z= 0.319 Chirality : 0.041 0.305 2151 Planarity : 0.003 0.041 2125 Dihedral : 19.809 59.905 2436 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.01 % Favored : 95.64 % Rotamer: Outliers : 1.70 % Allowed : 11.96 % Favored : 86.34 % 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: 1.40 (0.23), residues: 1422 helix: 2.13 (0.18), residues: 794 sheet: 0.59 (0.42), residues: 149 loop : -1.05 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 415 TYR 0.031 0.001 TYR B 45 PHE 0.015 0.001 PHE B 513 TRP 0.013 0.001 TRP A 103 HIS 0.007 0.001 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00360 (13883) covalent geometry : angle 0.58276 (19032) hydrogen bonds : bond 0.04361 ( 819) hydrogen bonds : angle 4.28428 ( 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 184 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 PHE cc_start: 0.8406 (m-80) cc_final: 0.8079 (m-80) REVERT: A 251 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.7580 (mt) REVERT: B 35 LYS cc_start: 0.8335 (tttt) cc_final: 0.8008 (tttm) REVERT: B 64 MET cc_start: 0.8325 (mmm) cc_final: 0.7770 (mmm) REVERT: B 80 THR cc_start: 0.9075 (m) cc_final: 0.8799 (p) REVERT: B 82 GLN cc_start: 0.8752 (tm-30) cc_final: 0.8550 (tm-30) REVERT: B 331 PHE cc_start: 0.8502 (OUTLIER) cc_final: 0.6990 (t80) REVERT: B 347 ARG cc_start: 0.8864 (ttp80) cc_final: 0.8239 (tpm170) REVERT: B 395 LEU cc_start: 0.9174 (mm) cc_final: 0.8663 (tp) REVERT: B 407 GLU cc_start: 0.9078 (tp30) cc_final: 0.8612 (tp30) REVERT: B 459 MET cc_start: 0.8412 (tpt) cc_final: 0.7870 (tpp) outliers start: 23 outliers final: 13 residues processed: 177 average time/residue: 0.1113 time to fit residues: 29.5768 Evaluate side-chains 151 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.486 ------------------------------------------------------------------------------- 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 236 GLN Chi-restraints excluded: chain B residue 331 PHE Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 293 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 22 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 47 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 135 optimal weight: 0.8980 chunk 3 optimal weight: 30.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 236 GLN ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 351 ASN ** 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 = 0.165321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.113988 restraints weight = 29759.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.112938 restraints weight = 18116.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.112973 restraints weight = 13580.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.113653 restraints weight = 12647.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.113859 restraints weight = 10820.766| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 13883 Z= 0.160 Angle : 0.578 10.406 19032 Z= 0.315 Chirality : 0.041 0.319 2151 Planarity : 0.003 0.050 2125 Dihedral : 19.790 59.844 2436 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.94 % Favored : 95.71 % Rotamer: Outliers : 2.14 % Allowed : 13.96 % 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: 1.42 (0.23), residues: 1422 helix: 2.20 (0.18), residues: 787 sheet: 0.43 (0.43), residues: 148 loop : -1.05 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 415 TYR 0.030 0.001 TYR B 45 PHE 0.023 0.001 PHE A 532 TRP 0.010 0.001 TRP A 103 HIS 0.005 0.001 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00358 (13883) covalent geometry : angle 0.57757 (19032) hydrogen bonds : bond 0.04209 ( 819) hydrogen bonds : angle 4.25663 ( 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 176 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 147 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 PHE cc_start: 0.8225 (m-80) cc_final: 0.7962 (m-80) REVERT: A 251 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8023 (tp) REVERT: B 35 LYS cc_start: 0.8205 (tttt) cc_final: 0.7977 (tttm) REVERT: B 331 PHE cc_start: 0.8501 (OUTLIER) cc_final: 0.7178 (t80) REVERT: B 347 ARG cc_start: 0.8766 (ttp80) cc_final: 0.8238 (tpm170) REVERT: B 368 LYS cc_start: 0.8770 (tttt) cc_final: 0.8378 (mmmt) REVERT: B 395 LEU cc_start: 0.9109 (mm) cc_final: 0.8637 (tp) REVERT: B 407 GLU cc_start: 0.8972 (tp30) cc_final: 0.8666 (tp30) REVERT: B 415 ARG cc_start: 0.8222 (ttp-110) cc_final: 0.7928 (ttm110) outliers start: 29 outliers final: 15 residues processed: 167 average time/residue: 0.1050 time to fit residues: 26.7058 Evaluate side-chains 149 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 236 GLN Chi-restraints excluded: chain B residue 331 PHE Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 309 CYS 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: 3.9990 chunk 116 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 149 optimal weight: 10.0000 chunk 136 optimal weight: 0.0980 chunk 101 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 141 optimal weight: 0.5980 chunk 9 optimal weight: 9.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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 = 0.4359 r_free = 0.4359 target = 0.165917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.113907 restraints weight = 29566.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.113879 restraints weight = 18003.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.113810 restraints weight = 12172.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.114277 restraints weight = 12208.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.114602 restraints weight = 10697.749| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13883 Z= 0.133 Angle : 0.574 12.820 19032 Z= 0.309 Chirality : 0.041 0.312 2151 Planarity : 0.003 0.040 2125 Dihedral : 19.755 59.626 2436 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.08 % Favored : 95.57 % Rotamer: Outliers : 2.22 % Allowed : 14.33 % Favored : 83.46 % 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: 1.52 (0.23), residues: 1422 helix: 2.30 (0.18), residues: 783 sheet: 0.56 (0.44), residues: 150 loop : -1.04 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 415 TYR 0.032 0.001 TYR B 479 PHE 0.033 0.001 PHE B 448 TRP 0.006 0.001 TRP C 98 HIS 0.008 0.001 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00286 (13883) covalent geometry : angle 0.57419 (19032) hydrogen bonds : bond 0.04033 ( 819) hydrogen bonds : angle 4.17590 ( 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 188 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 158 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 PHE cc_start: 0.8489 (m-80) cc_final: 0.8166 (m-80) REVERT: A 251 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.7492 (mt) REVERT: A 356 LEU cc_start: 0.8896 (tp) cc_final: 0.8650 (tt) REVERT: B 64 MET cc_start: 0.7748 (mmm) cc_final: 0.7509 (mmm) REVERT: B 83 LYS cc_start: 0.8439 (mttt) cc_final: 0.8131 (mttp) REVERT: B 237 ASN cc_start: 0.9066 (OUTLIER) cc_final: 0.8650 (m-40) REVERT: B 331 PHE cc_start: 0.8479 (OUTLIER) cc_final: 0.7432 (t80) REVERT: B 347 ARG cc_start: 0.8832 (ttp80) cc_final: 0.8297 (tpm170) REVERT: B 368 LYS cc_start: 0.8839 (tttt) cc_final: 0.8395 (mmmt) REVERT: B 395 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8671 (tp) REVERT: B 407 GLU cc_start: 0.9093 (tp30) cc_final: 0.8698 (tp30) REVERT: B 459 MET cc_start: 0.8484 (tpt) cc_final: 0.7837 (tpp) REVERT: C 205 ASP cc_start: 0.8108 (m-30) cc_final: 0.7451 (m-30) outliers start: 30 outliers final: 16 residues processed: 178 average time/residue: 0.1073 time to fit residues: 29.0731 Evaluate side-chains 152 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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 236 GLN Chi-restraints excluded: chain B residue 237 ASN 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 449 LEU Chi-restraints excluded: chain B residue 518 SER 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 251 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 293 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 3 optimal weight: 10.0000 chunk 142 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 127 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 136 optimal weight: 0.1980 chunk 35 optimal weight: 6.9990 chunk 83 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 236 GLN ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.165945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.116111 restraints weight = 29947.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.116183 restraints weight = 17756.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.116421 restraints weight = 12619.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.117031 restraints weight = 11469.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.117162 restraints weight = 10108.079| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13883 Z= 0.143 Angle : 0.573 13.453 19032 Z= 0.308 Chirality : 0.041 0.335 2151 Planarity : 0.003 0.041 2125 Dihedral : 19.754 59.984 2436 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.15 % Favored : 95.57 % Rotamer: Outliers : 2.44 % Allowed : 14.77 % Favored : 82.79 % 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: 1.53 (0.23), residues: 1422 helix: 2.29 (0.18), residues: 788 sheet: 0.57 (0.45), residues: 142 loop : -1.00 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 415 TYR 0.027 0.001 TYR B 45 PHE 0.033 0.001 PHE A 532 TRP 0.015 0.001 TRP A 103 HIS 0.006 0.001 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00315 (13883) covalent geometry : angle 0.57341 (19032) hydrogen bonds : bond 0.03982 ( 819) hydrogen bonds : angle 4.12844 ( 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 174 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 141 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.7451 (mt) REVERT: A 356 LEU cc_start: 0.8814 (tp) cc_final: 0.8546 (tt) REVERT: B 83 LYS cc_start: 0.8389 (mttt) cc_final: 0.8115 (mttp) REVERT: B 237 ASN cc_start: 0.8996 (OUTLIER) cc_final: 0.8560 (m-40) REVERT: B 320 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7754 (tt0) REVERT: B 331 PHE cc_start: 0.8451 (OUTLIER) cc_final: 0.7481 (t80) REVERT: B 347 ARG cc_start: 0.8726 (ttp80) cc_final: 0.8271 (tpm170) REVERT: B 368 LYS cc_start: 0.8831 (tttt) cc_final: 0.8409 (mmmt) REVERT: B 395 LEU cc_start: 0.9103 (mm) cc_final: 0.8642 (tp) REVERT: B 407 GLU cc_start: 0.8957 (tp30) cc_final: 0.8577 (tp30) REVERT: B 459 MET cc_start: 0.8391 (tpt) cc_final: 0.7746 (tpp) REVERT: C 144 MET cc_start: 0.8619 (mmm) cc_final: 0.8373 (mmm) REVERT: C 205 ASP cc_start: 0.8099 (m-30) cc_final: 0.7495 (m-30) REVERT: C 228 MET cc_start: 0.8917 (ttp) cc_final: 0.8589 (tmm) outliers start: 33 outliers final: 19 residues processed: 165 average time/residue: 0.1103 time to fit residues: 27.9097 Evaluate side-chains 159 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 0.514 ------------------------------------------------------------------------------- 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 236 GLN Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 320 GLU 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 449 LEU Chi-restraints excluded: chain B residue 484 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 151 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 293 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 127 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 42 optimal weight: 20.0000 chunk 82 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN B 236 GLN B 240 ASN ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 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 147 GLN ** 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 = 0.4328 r_free = 0.4328 target = 0.163879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.110218 restraints weight = 29884.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.109945 restraints weight = 14714.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.110761 restraints weight = 11315.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.110998 restraints weight = 10759.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.111006 restraints weight = 9735.954| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 13883 Z= 0.192 Angle : 0.611 11.924 19032 Z= 0.325 Chirality : 0.042 0.315 2151 Planarity : 0.004 0.052 2125 Dihedral : 19.815 59.747 2436 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.29 % Favored : 95.43 % Rotamer: Outliers : 2.36 % Allowed : 15.51 % 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: 1.42 (0.23), residues: 1422 helix: 2.17 (0.18), residues: 788 sheet: 0.42 (0.45), residues: 142 loop : -0.96 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 415 TYR 0.033 0.002 TYR B 45 PHE 0.029 0.002 PHE A 165 TRP 0.020 0.002 TRP C 98 HIS 0.005 0.001 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00439 (13883) covalent geometry : angle 0.61085 (19032) hydrogen bonds : bond 0.04185 ( 819) hydrogen bonds : angle 4.23256 ( 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 173 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 141 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.7936 (tp) REVERT: B 35 LYS cc_start: 0.8168 (tttt) cc_final: 0.7888 (tttm) REVERT: B 331 PHE cc_start: 0.8522 (OUTLIER) cc_final: 0.7374 (t80) REVERT: B 347 ARG cc_start: 0.8807 (ttp80) cc_final: 0.8279 (tpm170) REVERT: B 368 LYS cc_start: 0.8915 (tttt) cc_final: 0.8397 (mmmt) REVERT: B 395 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8654 (tp) REVERT: B 407 GLU cc_start: 0.9035 (tp30) cc_final: 0.8636 (tp30) REVERT: B 459 MET cc_start: 0.8532 (tpt) cc_final: 0.7901 (tpp) REVERT: C 82 LYS cc_start: 0.8881 (pttm) cc_final: 0.8673 (pttm) REVERT: C 207 GLU cc_start: 0.8507 (mm-30) cc_final: 0.7962 (mm-30) outliers start: 32 outliers final: 20 residues processed: 165 average time/residue: 0.1114 time to fit residues: 27.6780 Evaluate side-chains 156 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.495 ------------------------------------------------------------------------------- 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 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 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 405 GLU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 449 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 147 GLN Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 293 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 83 optimal weight: 0.9980 chunk 120 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 144 optimal weight: 10.0000 chunk 66 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 138 optimal weight: 0.9980 chunk 118 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 236 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.165437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.112299 restraints weight = 29933.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.112111 restraints weight = 16289.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.112914 restraints weight = 11455.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.113756 restraints weight = 10279.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.113747 restraints weight = 8586.429| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13883 Z= 0.152 Angle : 0.600 12.398 19032 Z= 0.316 Chirality : 0.042 0.321 2151 Planarity : 0.004 0.051 2125 Dihedral : 19.827 59.926 2436 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.29 % Favored : 95.43 % Rotamer: Outliers : 2.29 % Allowed : 15.73 % Favored : 81.98 % 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: 1.38 (0.23), residues: 1422 helix: 2.16 (0.18), residues: 794 sheet: 0.18 (0.45), residues: 141 loop : -1.00 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 415 TYR 0.027 0.001 TYR B 45 PHE 0.014 0.001 PHE B 448 TRP 0.018 0.002 TRP C 98 HIS 0.005 0.001 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00344 (13883) covalent geometry : angle 0.59974 (19032) hydrogen bonds : bond 0.03997 ( 819) hydrogen bonds : angle 4.19701 ( 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 175 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 144 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.7448 (mt) REVERT: B 35 LYS cc_start: 0.8142 (tttt) cc_final: 0.7890 (tttm) REVERT: B 331 PHE cc_start: 0.8455 (OUTLIER) cc_final: 0.7286 (t80) REVERT: B 347 ARG cc_start: 0.8806 (ttp80) cc_final: 0.8286 (tpm170) REVERT: B 368 LYS cc_start: 0.8925 (tttt) cc_final: 0.8391 (mmmt) REVERT: B 395 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.7691 (tp) REVERT: B 407 GLU cc_start: 0.9072 (tp30) cc_final: 0.8655 (tp30) REVERT: B 459 MET cc_start: 0.8500 (tpt) cc_final: 0.7880 (tpp) REVERT: C 144 MET cc_start: 0.8713 (mmm) cc_final: 0.8311 (mmp) REVERT: C 207 GLU cc_start: 0.8499 (mm-30) cc_final: 0.7938 (mm-30) outliers start: 31 outliers final: 20 residues processed: 167 average time/residue: 0.1068 time to fit residues: 27.1204 Evaluate side-chains 156 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 197 ILE 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 405 GLU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 309 CYS 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: 2.9990 chunk 79 optimal weight: 4.9990 chunk 50 optimal weight: 40.0000 chunk 35 optimal weight: 6.9990 chunk 140 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 15 optimal weight: 20.0000 chunk 122 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 HIS B 236 GLN ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 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 = 0.4346 r_free = 0.4346 target = 0.165442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.109991 restraints weight = 30082.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.111417 restraints weight = 17219.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.113041 restraints weight = 11609.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.113785 restraints weight = 9226.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.113699 restraints weight = 8769.208| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13883 Z= 0.139 Angle : 0.602 12.399 19032 Z= 0.316 Chirality : 0.042 0.325 2151 Planarity : 0.003 0.050 2125 Dihedral : 19.828 59.864 2436 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.36 % Favored : 95.36 % Rotamer: Outliers : 1.77 % Allowed : 16.99 % Favored : 81.24 % 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: 1.50 (0.23), residues: 1422 helix: 2.21 (0.18), residues: 799 sheet: 0.49 (0.47), residues: 127 loop : -0.93 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 415 TYR 0.025 0.001 TYR B 45 PHE 0.013 0.001 PHE A 169 TRP 0.023 0.002 TRP C 98 HIS 0.009 0.001 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00308 (13883) covalent geometry : angle 0.60157 (19032) hydrogen bonds : bond 0.03916 ( 819) hydrogen bonds : angle 4.15575 ( 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 176 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 MET cc_start: 0.7804 (mmm) cc_final: 0.7202 (ttp) REVERT: A 251 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.7460 (mt) REVERT: A 459 MET cc_start: 0.1356 (tmm) cc_final: 0.1128 (tmm) REVERT: B 35 LYS cc_start: 0.8109 (tttt) cc_final: 0.7873 (tttm) REVERT: B 331 PHE cc_start: 0.8435 (OUTLIER) cc_final: 0.7341 (t80) REVERT: B 347 ARG cc_start: 0.8799 (ttp80) cc_final: 0.8272 (tpm170) REVERT: B 368 LYS cc_start: 0.8903 (tttt) cc_final: 0.8395 (mmmt) REVERT: B 407 GLU cc_start: 0.8962 (tp30) cc_final: 0.8565 (tp30) REVERT: B 459 MET cc_start: 0.8439 (tpt) cc_final: 0.7807 (tpp) REVERT: C 207 GLU cc_start: 0.8404 (mm-30) cc_final: 0.7891 (mm-30) outliers start: 24 outliers final: 16 residues processed: 171 average time/residue: 0.1100 time to fit residues: 28.6598 Evaluate side-chains 155 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.538 ------------------------------------------------------------------------------- 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 236 GLN Chi-restraints excluded: chain B residue 331 PHE Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 309 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 58 optimal weight: 4.9990 chunk 126 optimal weight: 0.8980 chunk 142 optimal weight: 10.0000 chunk 93 optimal weight: 0.8980 chunk 127 optimal weight: 1.9990 chunk 0 optimal weight: 80.0000 chunk 102 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 8 optimal weight: 20.0000 chunk 40 optimal weight: 4.9990 chunk 53 optimal weight: 30.0000 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 HIS B 236 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 GLN ** 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 = 0.4308 r_free = 0.4308 target = 0.162199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.107632 restraints weight = 29949.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.107543 restraints weight = 21455.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.108004 restraints weight = 13653.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.108688 restraints weight = 12156.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.108900 restraints weight = 11161.983| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 13883 Z= 0.296 Angle : 0.734 12.696 19032 Z= 0.383 Chirality : 0.046 0.318 2151 Planarity : 0.005 0.107 2125 Dihedral : 20.023 59.573 2436 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.71 % Favored : 94.94 % Rotamer: Outliers : 1.77 % Allowed : 17.50 % Favored : 80.72 % 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: 1.09 (0.23), residues: 1422 helix: 1.88 (0.18), residues: 801 sheet: -0.30 (0.43), residues: 141 loop : -0.95 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 415 TYR 0.040 0.002 TYR B 45 PHE 0.025 0.002 PHE B 63 TRP 0.028 0.002 TRP C 98 HIS 0.008 0.001 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00688 (13883) covalent geometry : angle 0.73390 (19032) hydrogen bonds : bond 0.04681 ( 819) hydrogen bonds : angle 4.46008 ( 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 162 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 0.471 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.2049 (mmt) cc_final: 0.1309 (mmt) REVERT: A 251 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.7615 (mt) REVERT: A 410 ARG cc_start: 0.7861 (tmm160) cc_final: 0.7617 (ttp80) REVERT: A 459 MET cc_start: 0.1577 (tmm) cc_final: 0.1320 (tmm) REVERT: B 331 PHE cc_start: 0.8616 (OUTLIER) cc_final: 0.7555 (t80) REVERT: B 347 ARG cc_start: 0.8864 (ttp80) cc_final: 0.8375 (tpm170) REVERT: B 368 LYS cc_start: 0.8966 (tttt) cc_final: 0.8474 (mmmt) REVERT: B 395 LEU cc_start: 0.9163 (mm) cc_final: 0.8738 (tp) REVERT: B 407 GLU cc_start: 0.9136 (tp30) cc_final: 0.8753 (tp30) REVERT: B 459 MET cc_start: 0.8594 (tpt) cc_final: 0.7975 (tpp) REVERT: C 82 LYS cc_start: 0.8906 (pttm) cc_final: 0.8677 (pttm) REVERT: C 144 MET cc_start: 0.8614 (mmm) cc_final: 0.8084 (mmp) REVERT: C 207 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8135 (mm-30) outliers start: 24 outliers final: 19 residues processed: 155 average time/residue: 0.1124 time to fit residues: 26.1540 Evaluate side-chains 154 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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 68 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 236 GLN Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 331 PHE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 309 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 9 optimal weight: 8.9990 chunk 67 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 54 optimal weight: 40.0000 chunk 128 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 chunk 14 optimal weight: 20.0000 chunk 127 optimal weight: 0.9980 chunk 51 optimal weight: 20.0000 chunk 74 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 ASN B 106 HIS B 236 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 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 = 0.4345 r_free = 0.4345 target = 0.165228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.113948 restraints weight = 30061.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.114249 restraints weight = 16910.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.114531 restraints weight = 11668.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.115131 restraints weight = 10810.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.115267 restraints weight = 9502.310| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13883 Z= 0.154 Angle : 0.647 13.164 19032 Z= 0.339 Chirality : 0.043 0.323 2151 Planarity : 0.004 0.080 2125 Dihedral : 19.967 60.000 2436 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.29 % Favored : 95.43 % Rotamer: Outliers : 1.26 % Allowed : 18.83 % Favored : 79.91 % 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: 2.04 (0.18), residues: 800 sheet: -0.10 (0.44), residues: 139 loop : -1.00 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 415 TYR 0.026 0.002 TYR B 45 PHE 0.017 0.002 PHE B 63 TRP 0.022 0.002 TRP C 98 HIS 0.010 0.001 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00344 (13883) covalent geometry : angle 0.64662 (19032) hydrogen bonds : bond 0.04131 ( 819) hydrogen bonds : angle 4.28842 ( 2304) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2565.20 seconds wall clock time: 45 minutes 10.31 seconds (2710.31 seconds total)